From 6462b87e2e2bf691f04c89190c4ba1e72dac0f90 Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Thu, 6 Dec 2018 14:37:14 +0100 Subject: [PATCH 001/507] Refactor the AD drivers classes. This commit significantly reworks the implementation of the AD driver classes. Firstly, all class methods are moved to the associated source file. The (logically) static class methods have been removed, so all methods must be called through an instance of a driver class. The previously implemented logic for existant ADOL-C tapes has been superceeded by low-level calls to the library itself. The ADHelper classes are updated to accommodate the changes to the driver classes. Fixes #7335 Fixes #7372 --- .../deal.II/differentiation/ad/ad_drivers.h | 1577 +++--------- .../deal.II/differentiation/ad/ad_helpers.h | 3 + source/differentiation/ad/CMakeLists.txt | 5 +- source/differentiation/ad/ad_drivers.cc | 2258 +++++++++++++++++ source/differentiation/ad/ad_drivers.inst1.in | 73 + source/differentiation/ad/ad_drivers.inst2.in | 83 + source/differentiation/ad/ad_helpers.cc | 61 +- 7 files changed, 2808 insertions(+), 1252 deletions(-) create mode 100644 source/differentiation/ad/ad_drivers.cc create mode 100644 source/differentiation/ad/ad_drivers.inst1.in create mode 100644 source/differentiation/ad/ad_drivers.inst2.in diff --git a/include/deal.II/differentiation/ad/ad_drivers.h b/include/deal.II/differentiation/ad/ad_drivers.h index 05ec55840673..5af046665bf6 100644 --- a/include/deal.II/differentiation/ad/ad_drivers.h +++ b/include/deal.II/differentiation/ad/ad_drivers.h @@ -20,12 +20,9 @@ #include #include -#include #include #include -#include -#include #include #include @@ -33,10 +30,7 @@ #ifdef DEAL_II_WITH_ADOLC DEAL_II_DISABLE_EXTRA_DIAGNOSTICS -# include -# include # include -# include DEAL_II_ENABLE_EXTRA_DIAGNOSTICS #endif // DEAL_II_WITH_ADOLC @@ -136,7 +130,7 @@ namespace Differentiation /** - * A driver class for taped auto-differentiable numbers. + * A prototype driver class for taped auto-differentiable numbers. * * It is intended that this class be specialized for the valid * combinations of auto-differentiable numbers and output scalar @@ -258,6 +252,12 @@ namespace Differentiation const typename Types::tape_index active_tape_index, const bool write_tapes_to_file); + /** + * Return a list of registered tape indices. + */ + std::vector::tape_index> + get_registered_tape_indices() const; + /** * Select a tape to record to or read from. * @@ -275,6 +275,39 @@ namespace Differentiation void activate_tape(const typename Types::tape_index tape_index); + /** + * Return a flag that, when true, indicates that the retaping + * of the dependent function for the chosen @p tape_index is necessary for + * a reliable computation to be performed. + * This may be necessary a sign comparison within branched operations + * yields different results to those computed at the original tape + * evaluation point. + * + * @note The chosen tape index must be greater than + * Numbers::invalid_tape_index and less than + * Numbers::max_tape_index. + */ + bool + requires_retaping( + const typename Types::tape_index tape_index) const; + + /** + * Return a flag that, when true, indicates that the retaping + * of the dependent function is necessary for a reliable computation to be + * performed on the active tape. + * This may be necessary a sign comparison within branched operations + * yields different results to those computed at the original tape + * evaluation point. + */ + bool + last_action_requires_retaping() const; + + /** + * Completely erases the tape with the given @p tape_index. + */ + void + remove_tape(const typename Types::tape_index tape_index); + /** * Reset the state of the class. * @@ -302,10 +335,10 @@ namespace Differentiation * @param[out] stream The output stream to which the values are to be * written. */ - static void + void print_tape_stats( const typename Types::tape_index tape_index, - std::ostream & stream); + std::ostream & stream) const; //@} @@ -324,9 +357,9 @@ namespace Differentiation * * @return The scalar value of the function. */ - static ScalarType + ScalarType value(const typename Types::tape_index active_tape_index, - const std::vector &independent_variables); + const std::vector &independent_variables) const; /** * Compute the gradient of the scalar field with respect to all @@ -341,10 +374,10 @@ namespace Differentiation * correct size (with length * n_independent_variables). */ - static void + void gradient(const typename Types::tape_index active_tape_index, const std::vector &independent_variables, - Vector & gradient); + Vector & gradient) const; /** * Compute the Hessian of the scalar field with respect to all @@ -359,10 +392,10 @@ namespace Differentiation * size (with dimensions * n_independent_variables$\times$n_independent_variables). */ - static void + void hessian(const typename Types::tape_index active_tape_index, const std::vector &independent_variables, - FullMatrix & hessian); + FullMatrix & hessian) const; //@} @@ -383,11 +416,11 @@ namespace Differentiation * It is expected that this vector be of the correct size * (with length n_dependent_variables). */ - static void + void values(const typename Types::tape_index active_tape_index, const unsigned int n_dependent_variables, const std::vector &independent_variables, - Vector & values); + Vector & values) const; /** * Compute the Jacobian of the vector field. @@ -407,11 +440,11 @@ namespace Differentiation * size (with dimensions * n_dependent_variables$\times$n_independent_variables). */ - static void + void jacobian(const typename Types::tape_index active_tape_index, const unsigned int n_dependent_variables, const std::vector &independent_variables, - FullMatrix & jacobian); + FullMatrix & jacobian) const; //@} }; @@ -510,8 +543,8 @@ namespace Differentiation * * @return The scalar value of the function. */ - static ScalarType - value(const std::vector &dependent_variables); + ScalarType + value(const std::vector &dependent_variables) const; /** * Compute the gradient of the scalar field with respect to all @@ -526,10 +559,10 @@ namespace Differentiation * correct size (with length * n_independent_variables). */ - static void + void gradient(const std::vector &independent_variables, const std::vector &dependent_variables, - Vector & gradient); + Vector & gradient) const; /** * Compute the Hessian of the scalar field with respect to all @@ -544,10 +577,10 @@ namespace Differentiation * size (with dimensions * n_independent_variables$\times$n_independent_variables). */ - static void + void hessian(const std::vector &independent_variables, const std::vector &dependent_variables, - FullMatrix & hessian); + FullMatrix & hessian) const; //@} @@ -565,9 +598,9 @@ namespace Differentiation * It is expected that this vector be of the correct size * (with length n_dependent_variables). */ - static void + void values(const std::vector &dependent_variables, - Vector & values); + Vector & values) const; /** * Compute the Jacobian of the vector field. @@ -586,10 +619,10 @@ namespace Differentiation * size (with dimensions * n_dependent_variables$\times$n_independent_variables). */ - static void + void jacobian(const std::vector &independent_variables, const std::vector &dependent_variables, - FullMatrix & jacobian); + FullMatrix & jacobian) const; //@} }; @@ -608,170 +641,6 @@ namespace Differentiation { namespace AD { - // ------------- TapedDrivers ------------- - - - template - bool - TapedDrivers::is_recording() const - { - AssertThrow(false, ExcRequiresADNumberSpecialization()); - return false; - } - - - template - typename Types::tape_index - TapedDrivers::active_tape_index() const - { - AssertThrow(false, ExcRequiresADNumberSpecialization()); - return Numbers::invalid_tape_index; - } - - - template - bool - TapedDrivers::is_registered_tape( - const typename Types::tape_index) const - { - AssertThrow(false, ExcRequiresADNumberSpecialization()); - return false; - } - - - template - bool - TapedDrivers::keep_independent_values() const - { - AssertThrow(false, ExcRequiresADNumberSpecialization()); - return false; - } - - - template - void - TapedDrivers::set_tape_buffer_sizes( - const typename Types::tape_buffer_sizes, - const typename Types::tape_buffer_sizes, - const typename Types::tape_buffer_sizes, - const typename Types::tape_buffer_sizes) - { - AssertThrow(false, ExcRequiresADNumberSpecialization()); - } - - - template - void - TapedDrivers::start_taping( - const typename Types::tape_index, - const bool) - { - AssertThrow(false, ExcRequiresADNumberSpecialization()); - } - - - template - void - TapedDrivers::stop_taping( - const typename Types::tape_index, - const bool) - { - AssertThrow(false, ExcRequiresADNumberSpecialization()); - } - - - template - void - TapedDrivers::activate_tape( - const typename Types::tape_index) - { - AssertThrow(false, ExcRequiresADNumberSpecialization()); - } - - - template - void - TapedDrivers::reset(const bool) - { - AssertThrow(false, ExcRequiresADNumberSpecialization()); - } - - - template - void - TapedDrivers::print(std::ostream &) const - { - AssertThrow(false, ExcRequiresADNumberSpecialization()); - } - - - template - void - TapedDrivers::print_tape_stats( - const typename Types::tape_index, - std::ostream &) - { - AssertThrow(false, ExcRequiresADNumberSpecialization()); - } - - - template - ScalarType - TapedDrivers::value( - const typename Types::tape_index, - const std::vector &) - { - AssertThrow(false, ExcRequiresADNumberSpecialization()); - return ScalarType(0.0); - } - - - template - void - TapedDrivers::gradient( - const typename Types::tape_index, - const std::vector &, - Vector &) - { - AssertThrow(false, ExcRequiresADNumberSpecialization()); - } - - - template - void - TapedDrivers::hessian( - const typename Types::tape_index, - const std::vector &, - FullMatrix &) - { - AssertThrow(false, ExcRequiresADNumberSpecialization()); - } - - - template - void - TapedDrivers::values( - const typename Types::tape_index, - const unsigned int, - const std::vector &, - Vector &) - { - AssertThrow(false, ExcRequiresADNumberSpecialization()); - } - - - template - void - TapedDrivers::jacobian( - const typename Types::tape_index, - const unsigned int, - const std::vector &, - FullMatrix &) - { - AssertThrow(false, ExcRequiresADNumberSpecialization()); - } - - # ifdef DEAL_II_WITH_ADOLC /** @@ -846,309 +715,114 @@ namespace Differentiation { using scalar_type = double; - TapedDrivers() - : active_tape(Numbers::invalid_tape_index) - , keep_values(true) - , is_recording_flag(false) - , use_stored_taped_buffer_sizes(false) - , obufsize(0u) - , lbufsize(0u) - , vbufsize(0u) - , tbufsize(0u) - {} + /** + * Constructor + */ + TapedDrivers(); + - // === Taping === + /** + * @name Taping + */ + //@{ bool - is_recording() const - { - return is_recording_flag; - } + is_recording() const; typename Types::tape_index - active_tape_index() const - { - return active_tape; - } + active_tape_index() const; bool - keep_independent_values() const - { - return keep_values; - } + keep_independent_values() const; bool is_registered_tape( - const typename Types::tape_index tape_index) const - { - // See https://gitlab.com/adol-c/adol-c/issues/11#note_108341333 - try - { - std::vector counts(STAT_SIZE); - ::tapestats(tape_index, counts.data()); - return true; - } - catch (const ::FatalError &exc) - { - return false; - } - } + const typename Types::tape_index tape_index) const; void set_tape_buffer_sizes( const typename Types::tape_buffer_sizes in_obufsize, const typename Types::tape_buffer_sizes in_lbufsize, const typename Types::tape_buffer_sizes in_vbufsize, - const typename Types::tape_buffer_sizes in_tbufsize) - { - // When valid for the chosen AD number type, these values will be used - // the next time start_recording_operations() is called. - obufsize = in_obufsize; - lbufsize = in_lbufsize; - vbufsize = in_vbufsize; - tbufsize = in_tbufsize; - use_stored_taped_buffer_sizes = true; - } + const typename Types::tape_buffer_sizes in_tbufsize); void start_taping(const typename Types::tape_index tape_index, - const bool keep_independent_values) - { - if (use_stored_taped_buffer_sizes) - trace_on(tape_index, - keep_independent_values, - obufsize, - lbufsize, - vbufsize, - tbufsize); - else - trace_on(tape_index, keep_independent_values); - - // Set some other flags to their indicated / required values - keep_values = keep_independent_values; - is_recording_flag = true; - } + const bool keep_independent_values); void stop_taping( const typename Types::tape_index active_tape_index, - const bool write_tapes_to_file) - { - if (write_tapes_to_file) - trace_off(active_tape_index); // Slow - else - trace_off(); // Fast(er) - - // Now that we've turned tracing off, we've definitely - // stopped all tape recording. - is_recording_flag = false; - - // If the keep_values flag is set, then we expect the user to use this - // tape immediately after recording it. There is therefore no need to - // invalidate it. However, there is now also no way to double-check - // that the newly recorded tape is indeed the active tape. - if (keep_independent_values() == false) - active_tape = Numbers::invalid_tape_index; - } - - void - activate_tape(const typename Types::tape_index tape_index) - { - active_tape = tape_index; - } - - void - reset(const bool clear_registered_tapes) - { - active_tape = Numbers::invalid_tape_index; - is_recording_flag = false; - if (clear_registered_tapes) - { - const std::vector::tape_index> - registered_tape_indices = get_registered_tape_indices(); - for (const auto &tape_index : registered_tape_indices) - removeTape(tape_index, TapeRemovalType::ADOLC_REMOVE_COMPLETELY); - } - } - - void - print(std::ostream &stream) const - { - const std::vector::tape_index> - registered_tape_indices = get_registered_tape_indices(); - stream << "Registered tapes: "; - auto it_registered_tape = registered_tape_indices.begin(); - for (unsigned int i = 0; i < registered_tape_indices.size(); - ++i, ++it_registered_tape) - stream << *it_registered_tape - << (i < (registered_tape_indices.size() - 1) ? "," : ""); - stream << "\n"; - - stream << "Keep values? " << keep_independent_values() << "\n"; - stream << "Use stored tape buffer sizes? " - << use_stored_taped_buffer_sizes << "\n"; - } + const bool write_tapes_to_file); - static void + std::vector::tape_index> + get_registered_tape_indices() const; + + void + activate_tape(const typename Types::tape_index tape_index); + + bool + requires_retaping( + const typename Types::tape_index tape_index) const; + + bool + last_action_requires_retaping() const; + + void + remove_tape(const typename Types::tape_index tape_index); + + void + reset(const bool clear_registered_tapes); + + void + print(std::ostream &stream) const; + + void print_tape_stats( const typename Types::tape_index tape_index, - std::ostream & stream) - { - // See ADOL-C manual section 2.1 - // and adolc/taping.h - std::vector counts(STAT_SIZE); - ::tapestats(tape_index, counts.data()); - Assert(counts.size() >= 18, ExcInternalError()); - stream - << "Tape index: " << tape_index << "\n" - << "Number of independent variables: " << counts[0] << "\n" - << "Number of dependent variables: " << counts[1] << "\n" - << "Max number of live, active variables: " << counts[2] << "\n" - << "Size of taylor stack (number of overwrites): " << counts[3] - << "\n" - << "Operations buffer size: " << counts[4] << "\n" - << "Total number of recorded operations: " << counts[5] << "\n" - << "Operations file written or not: " << counts[6] << "\n" - << "Overall number of locations: " << counts[7] << "\n" - << "Locations file written or not: " << counts[8] << "\n" - << "Overall number of values: " << counts[9] << "\n" - << "Values file written or not: " << counts[10] << "\n" - << "Locations buffer size: " << counts[11] << "\n" - << "Values buffer size: " << counts[12] << "\n" - << "Taylor buffer size: " << counts[13] << "\n" - << "Number of eq_*_prod for sparsity pattern: " << counts[14] << "\n" - << "Use of 'min_op', deferred to 'abs_op' for piecewise calculations: " - << counts[15] << "\n" - << "Number of 'abs' calls that can switch branch: " << counts[16] - << "\n" - << "Number of parameters (doubles) interchangeable without retaping: " - << counts[17] << "\n" - << std::flush; - } - - - // === Scalar drivers === - - static scalar_type - value(const typename Types::tape_index active_tape_index, - const std::vector &independent_variables) - { - scalar_type value = 0.0; + std::ostream & stream) const; + + //@} - ::function(active_tape_index, - 1, // Only one dependent variable - independent_variables.size(), - const_cast(independent_variables.data()), - &value); + /** + * @name Drivers for scalar functions (one dependent variable) + */ + //@{ - return value; - } + scalar_type + value(const typename Types::tape_index active_tape_index, + const std::vector &independent_variables) const; - static void + void gradient(const typename Types::tape_index active_tape_index, const std::vector &independent_variables, - Vector & gradient) - { - Assert( - AD::ADNumberTraits::n_supported_derivative_levels >= 1, - ExcSupportedDerivativeLevels( - AD::ADNumberTraits::n_supported_derivative_levels, - 1)); - Assert(gradient.size() == independent_variables.size(), - ExcDimensionMismatch(gradient.size(), - independent_variables.size())); - - // Note: ADOL-C's ::gradient function expects a *double as the last - // parameter. Here we take advantage of the fact that the data in the - // Vector class is aligned (e.g. stored as an Array) - ::gradient(active_tape_index, - independent_variables.size(), - const_cast(independent_variables.data()), - gradient.data()); - } + Vector & gradient) const; - static void + void hessian(const typename Types::tape_index active_tape_index, const std::vector &independent_variables, - FullMatrix & hessian) - { - Assert( - AD::ADNumberTraits::n_supported_derivative_levels >= 2, - ExcSupportedDerivativeLevels( - AD::ADNumberTraits::n_supported_derivative_levels, - 2)); - Assert(hessian.m() == independent_variables.size(), - ExcDimensionMismatch(hessian.m(), independent_variables.size())); - Assert(hessian.n() == independent_variables.size(), - ExcDimensionMismatch(hessian.n(), independent_variables.size())); - - const unsigned int n_independent_variables = - independent_variables.size(); - std::vector H(n_independent_variables); - for (unsigned int i = 0; i < n_independent_variables; ++i) - H[i] = &hessian[i][0]; - - ::hessian(active_tape_index, - n_independent_variables, - const_cast(independent_variables.data()), - H.data()); - - // ADOL-C builds only the lower-triangular part of the - // symmetric Hessian, so we should copy the relevant - // entries into the upper triangular part. - for (unsigned int i = 0; i < n_independent_variables; i++) - for (unsigned int j = 0; j < i; j++) - hessian[j][i] = hessian[i][j]; // Symmetry - } - - // === Vector drivers === + FullMatrix & hessian) const; - static void + //@} + + /** + * @name Drivers for vector functions (multiple dependent variables) + */ + //@{ + + void values(const typename Types::tape_index active_tape_index, const unsigned int n_dependent_variables, const std::vector &independent_variables, - Vector & values) - { - Assert(values.size() == n_dependent_variables, - ExcDimensionMismatch(values.size(), n_dependent_variables)); - - // Note: ADOL-C's ::function function expects a *double as the last - // parameter. Here we take advantage of the fact that the data in the - // Vector class is aligned (e.g. stored as an Array) - ::function(active_tape_index, - n_dependent_variables, - independent_variables.size(), - const_cast(independent_variables.data()), - values.data()); - } + Vector & values) const; - static void + void jacobian(const typename Types::tape_index active_tape_index, const unsigned int n_dependent_variables, const std::vector &independent_variables, - FullMatrix & jacobian) - { - Assert( - AD::ADNumberTraits::n_supported_derivative_levels >= 1, - ExcSupportedDerivativeLevels( - AD::ADNumberTraits::n_supported_derivative_levels, - 1)); - Assert(jacobian.m() == n_dependent_variables, - ExcDimensionMismatch(jacobian.m(), n_dependent_variables)); - Assert(jacobian.n() == independent_variables.size(), - ExcDimensionMismatch(jacobian.n(), - independent_variables.size())); - - std::vector J(n_dependent_variables); - for (unsigned int i = 0; i < n_dependent_variables; ++i) - J[i] = &jacobian[i][0]; - - ::jacobian(active_tape_index, - n_dependent_variables, - independent_variables.size(), - independent_variables.data(), - J.data()); - } + FullMatrix & jacobian) const; + + //@} protected: /** @@ -1171,6 +845,33 @@ namespace Differentiation */ bool is_recording_flag; + /** + * The status of the last function or derivative evaluation performed on + * the selected tape. As quoted from the ADOL-C manual, this can take + * on one of six different values with the following interpretation: + * + * - +3: The function is locally analytic. + * - +2: The function is locally analytic but the sparsity + * structure (compared to the situation at the taping point) may have + * changed, e.g. while at taping arguments fmax(a,b) + * returned a, we get b at the argument + * currently used. + * - +1: At least one of the functions fmin, + * fmax or fabs is evaluated at a tie or + * zero, respectively. Hence, the function to be differentiated is + * Lipschitz-continuous but possibly non-differentiable. + * - 0: Some arithmetic comparison involving adoubles yields a + * tie. Hence, the function to be differentiated may be discontinuous. + * - -1: An adouble comparison yields different + * results from the evaluation point at which the tape was generated. + * - -2: The argument of a user-defined quadrature has changed from + * the evaluation point at which the tape was generated. + * + * When the @p status variable takes a negative value, retaping of the dependent + * function is necessary for a reliable computation to be performed. + */ + mutable std::map::tape_index, int> status; + /** * A flag indicating that we should preferentially use the user-defined * taped buffer sizes as opposed to either the default values selected @@ -1198,30 +899,9 @@ namespace Differentiation * ADOL-C Taylor buffer size. */ typename Types::tape_buffer_sizes tbufsize; - - /** - * Return a list of registered tape indices - */ - std::vector::tape_index> - get_registered_tape_indices() const - { - // We've chosen to use unsigned shorts for the tape - // index type (a safety precaution) so we need to - // perform a conversion betwwen ADOL-C's native tape - // index type and that chosen by us. - std::vector registered_tape_indices_s; - cachedTraceTags(registered_tape_indices_s); - - std::vector::tape_index> - registered_tape_indices(registered_tape_indices_s.size()); - std::copy(registered_tape_indices_s.begin(), - registered_tape_indices_s.end(), - registered_tape_indices.begin()); - return registered_tape_indices; - } }; -# else // DEAL_II_WITH_ADOLC +# else /** * Specialization for taped ADOL-C auto-differentiable numbers. @@ -1229,7 +909,7 @@ namespace Differentiation * Although we could revert to the default definition for the * unspecialized TapedDrivers class, we add this specialization * to provide a more descriptive error message if any of its - * static member functions are called. + * member functions are called. */ template struct TapedDrivers< @@ -1240,134 +920,107 @@ namespace Differentiation { using scalar_type = double; - // === Taping === + /** + * @name Taping + */ + //@{ bool - is_recording() const - { - AssertThrow(false, ExcRequiresADOLC()); - return false; - } + is_recording() const; typename Types::tape_index - active_tape_index() const - { - AssertThrow(false, ExcRequiresADOLC()); - return Numbers::invalid_tape_index; - } + active_tape_index() const; bool - keep_independent_values() const - { - AssertThrow(false, ExcRequiresADOLC()); - return false; - } + keep_independent_values() const; bool - is_registered_tape(const typename Types::tape_index) const - { - AssertThrow(false, ExcRequiresADOLC()); - return false; - } + is_registered_tape( + const typename Types::tape_index tape_index) const; void set_tape_buffer_sizes( const typename Types::tape_buffer_sizes, const typename Types::tape_buffer_sizes, const typename Types::tape_buffer_sizes, - const typename Types::tape_buffer_sizes) - { - AssertThrow(false, ExcRequiresADOLC()); - } + const typename Types::tape_buffer_sizes); void - start_taping(const typename Types::tape_index, const bool) - { - AssertThrow(false, ExcRequiresADOLC()); - } + start_taping(const typename Types::tape_index, const bool); void - stop_taping(const typename Types::tape_index, const bool) - { - AssertThrow(false, ExcRequiresADOLC()); - } + stop_taping(const typename Types::tape_index, const bool); + + std::vector::tape_index> + get_registered_tape_indices() const; void - activate_tape(const typename Types::tape_index) - { - AssertThrow(false, ExcRequiresADOLC()); - } + activate_tape(const typename Types::tape_index); + + bool + requires_retaping(const typename Types::tape_index) const; + + bool + last_action_requires_retaping() const; void - reset(const bool) - { - AssertThrow(false, ExcRequiresADOLC()); - } + remove_tape(const typename Types::tape_index); void - print(std::ostream &) const - { - AssertThrow(false, ExcRequiresADOLC()); - } + reset(const bool); - static void + void + print(std::ostream &stream) const; + + void print_tape_stats(const typename Types::tape_index, - std::ostream &) - { - AssertThrow(false, ExcRequiresADOLC()); - } + std::ostream &) const; + //@} - // === Scalar drivers === + /** + * @name Drivers for scalar functions (one dependent variable) + */ + //@{ - static scalar_type + scalar_type value(const typename Types::tape_index, - const std::vector &) - { - AssertThrow(false, ExcRequiresADOLC()); - return 0.0; - } + const std::vector &) const; - static void + void gradient(const typename Types::tape_index, const std::vector &, - Vector &) - { - AssertThrow(false, ExcRequiresADOLC()); - } + Vector &) const; - static void + void hessian(const typename Types::tape_index, const std::vector &, - FullMatrix &) - { - AssertThrow(false, ExcRequiresADOLC()); - } + FullMatrix &) const; - // === Vector drivers === + //@} - static void + /** + * @name Drivers for vector functions (multiple dependent variables) + */ + //@{ + + void values(const typename Types::tape_index, const unsigned int, const std::vector &, - Vector &) - { - AssertThrow(false, ExcRequiresADOLC()); - } + Vector &) const; - static void + void jacobian(const typename Types::tape_index, const unsigned int, const std::vector &, - FullMatrix &) - { - AssertThrow(false, ExcRequiresADOLC()); - } + FullMatrix &) const; + + //@} }; # endif // DEAL_II_WITH_ADOLC - /** * Specialization for ADOL-C taped numbers. It is expected that the * scalar return type for this class is a float. @@ -1385,191 +1038,115 @@ namespace Differentiation { using scalar_type = float; - // === Taping === + /** + * @name Taping + */ + //@{ bool - is_recording() const - { - // ADOL-C only supports 'double', not 'float', so we can forward to - // the 'double' implementation of this function - return taped_driver.is_recording(); - } + is_recording() const; typename Types::tape_index - active_tape_index() const - { - // ADOL-C only supports 'double', not 'float', so we can forward to - // the 'double' implementation of this function - return taped_driver.active_tape_index(); - } + active_tape_index() const; bool - keep_independent_values() const - { - return taped_driver.keep_independent_values(); - } + keep_independent_values() const; bool is_registered_tape( - const typename Types::tape_index tape_index) const - { - // ADOL-C only supports 'double', not 'float', so we can forward to - // the 'double' implementation of this function - return taped_driver.is_registered_tape(tape_index); - } + const typename Types::tape_index tape_index) const; void set_tape_buffer_sizes( const typename Types::tape_buffer_sizes obufsize, const typename Types::tape_buffer_sizes lbufsize, const typename Types::tape_buffer_sizes vbufsize, - const typename Types::tape_buffer_sizes tbufsize) - { - // ADOL-C only supports 'double', not 'float', so we can forward to - // the 'double' implementation of this function - taped_driver.set_tape_buffer_sizes(obufsize, - lbufsize, - vbufsize, - tbufsize); - } + const typename Types::tape_buffer_sizes tbufsize); void start_taping(const typename Types::tape_index tape_index, - const bool keep_independent_values) - { - // ADOL-C only supports 'double', not 'float', so we can forward to - // the 'double' implementation of this function - taped_driver.start_taping(tape_index, keep_independent_values); - } + const bool keep_independent_values); void stop_taping( const typename Types::tape_index active_tape_index, - const bool write_tapes_to_file) - { - // ADOL-C only supports 'double', not 'float', so we can forward to - // the 'double' implementation of this function - taped_driver.stop_taping(active_tape_index, write_tapes_to_file); - } + const bool write_tapes_to_file); + + std::vector::tape_index> + get_registered_tape_indices() const; + + void + activate_tape(const typename Types::tape_index tape_index); + + bool + requires_retaping( + const typename Types::tape_index tape_index) const; + + bool + last_action_requires_retaping() const; void - activate_tape(const typename Types::tape_index tape_index) - { - taped_driver.activate_tape(tape_index); - } + remove_tape(const typename Types::tape_index tape_index); void - reset(const bool clear_registered_tapes) - { - taped_driver.reset(clear_registered_tapes); - } + reset(const bool clear_registered_tapes); void - print(std::ostream &stream) const - { - taped_driver.print(stream); - } + print(std::ostream &stream) const; - static void + void print_tape_stats( const typename Types::tape_index tape_index, - std::ostream & stream) - { - // ADOL-C only supports 'double', not 'float', so we can forward to - // the 'double' implementation of this function - TapedDrivers::print_tape_stats(tape_index, - stream); - } + std::ostream & stream) const; + + //@} - // === Scalar drivers === + /** + * @name Drivers for scalar functions (one dependent variable) + */ + //@{ - static scalar_type + scalar_type value(const typename Types::tape_index active_tape_index, - const std::vector &independent_variables) - { - // ADOL-C only supports 'double', not 'float', so we can forward to - // the 'double' implementation of this function - return TapedDrivers::value( - active_tape_index, vector_float_to_double(independent_variables)); - } + const std::vector &independent_variables) const; - static void + void gradient(const typename Types::tape_index active_tape_index, const std::vector &independent_variables, - Vector & gradient) - { - Vector gradient_double(gradient.size()); - // ADOL-C only supports 'double', not 'float', so we can forward to - // the 'double' implementation of this function - TapedDrivers::gradient(active_tape_index, - vector_float_to_double( - independent_variables), - gradient_double); - gradient = gradient_double; - } + Vector & gradient) const; - static void + void hessian(const typename Types::tape_index active_tape_index, const std::vector &independent_variables, - FullMatrix & hessian) - { - FullMatrix hessian_double(hessian.m(), hessian.n()); - // ADOL-C only supports 'double', not 'float', so we can forward to - // the 'double' implementation of this function - TapedDrivers::hessian(active_tape_index, - vector_float_to_double( - independent_variables), - hessian_double); - hessian = hessian_double; - } - - // === Vector drivers === + FullMatrix & hessian) const; - static void + //@} + + /** + * @name Drivers for vector functions (multiple dependent variables) + */ + //@{ + + void values(const typename Types::tape_index active_tape_index, const unsigned int n_dependent_variables, const std::vector &independent_variables, - Vector & values) - { - Vector values_double(values.size()); - // ADOL-C only supports 'double', not 'float', so we can forward to - // the 'double' implementation of this function - TapedDrivers::values(active_tape_index, - n_dependent_variables, - vector_float_to_double( - independent_variables), - values_double); - values = values_double; - } + Vector & values) const; - static void + void jacobian(const typename Types::tape_index active_tape_index, const unsigned int n_dependent_variables, const std::vector &independent_variables, - FullMatrix & jacobian) - { - FullMatrix jacobian_double(jacobian.m(), jacobian.n()); - // ADOL-C only supports 'double', not 'float', so we can forward to - // the 'double' implementation of this function - TapedDrivers::jacobian(active_tape_index, - n_dependent_variables, - vector_float_to_double( - independent_variables), - jacobian_double); - jacobian = jacobian_double; - } + FullMatrix & jacobian) const; + + //@} private: /** * Copy a vector of floats into a vector of doubles */ - static std::vector - vector_float_to_double(const std::vector &in) - { - std::vector out(in.size()); - std::copy(in.begin(), in.end(), out.begin()); - return out; - } + std::vector + vector_float_to_double(const std::vector &in) const; /** * The object that actually takes care of the taping @@ -1581,235 +1158,6 @@ namespace Differentiation // ------------- TapelessDrivers ------------- - template - void - TapelessDrivers::initialize_global_environment( - const unsigned int) - { - AssertThrow(false, ExcRequiresADNumberSpecialization()); - } - - template - void - TapelessDrivers:: - allow_dependent_variable_marking() - { - AssertThrow(false, ExcRequiresADNumberSpecialization()); - } - - template - void - TapelessDrivers:: - prevent_dependent_variable_marking() - { - AssertThrow(false, ExcRequiresADNumberSpecialization()); - } - - template - bool - TapelessDrivers:: - is_dependent_variable_marking_allowed() const - { - AssertThrow(false, ExcRequiresADNumberSpecialization()); - return false; - } - - - template - ScalarType - TapelessDrivers::value( - const std::vector &) - { - AssertThrow(false, ExcRequiresADNumberSpecialization()); - return ScalarType(0.0); - } - - - template - void - TapelessDrivers::gradient( - const std::vector &, - const std::vector &, - Vector &) - { - AssertThrow(false, ExcRequiresADNumberSpecialization()); - } - - - template - void - TapelessDrivers::hessian( - const std::vector &, - const std::vector &, - FullMatrix &) - { - AssertThrow(false, ExcRequiresADNumberSpecialization()); - } - - - template - void - TapelessDrivers::values( - const std::vector &, - Vector &) - { - AssertThrow(false, ExcRequiresADNumberSpecialization()); - } - - - template - void - TapelessDrivers::jacobian( - const std::vector &, - const std::vector &, - FullMatrix &) - { - AssertThrow(false, ExcRequiresADNumberSpecialization()); - } - - - namespace internal - { - /** - * A dummy function to define the active dependent variable when using - * reverse-mode AD. - */ - template - typename std::enable_if::type_code == - NumberTypes::sacado_rad || - ADNumberTraits::type_code == - NumberTypes::sacado_rad_dfad)>::type - reverse_mode_dependent_variable_activation(ADNumberType &) - {} - -# ifdef DEAL_II_TRILINOS_WITH_SACADO - - - /** - * Define the active dependent variable when using reverse-mode AD. - * - * If there are multiple dependent variables then it is necessary to - * inform the independent variables, from which the adjoints are computed, - * which dependent variable they are computing the gradients with respect - * to. This function broadcasts this information. - */ - template - typename std::enable_if::type_code == - NumberTypes::sacado_rad || - ADNumberTraits::type_code == - NumberTypes::sacado_rad_dfad>::type - reverse_mode_dependent_variable_activation( - ADNumberType &dependent_variable) - { - // Compute all gradients (adjoints) for this - // reverse-mode Sacado dependent variable. - // For reverse-mode Sacado numbers it is necessary to broadcast to - // all independent variables that it is time to compute gradients. - // For one dependent variable one would just need to call - // ADNumberType::Gradcomp(), but since we have a more - // generic implementation for vectors of dependent variables - // (vector mode) we default to the complex case. - ADNumberType::Outvar_Gradcomp(dependent_variable); - } - -# endif - - - /** - * A dummy function to enable vector mode for tapeless - * auto-differentiable numbers. - */ - template - typename std::enable_if::type_code == - NumberTypes::adolc_tapeless)>::type - configure_tapeless_mode(const unsigned int) - {} - - -# ifdef DEAL_II_WITH_ADOLC - - - /** - * Enable vector mode for ADOL-C tapeless numbers. - * - * This function checks to see if its legal to increase the maximum - * number of directional derivatives to be considered during calculations. - * If not then it throws an error. - */ - template - typename std::enable_if::type_code == - NumberTypes::adolc_tapeless>::type - configure_tapeless_mode(const unsigned int n_directional_derivatives) - { -# ifdef DEAL_II_ADOLC_WITH_TAPELESS_REFCOUNTING - // See ADOL-C manual section 7.1 - // - // NOTE: It is critical that this is done for tapeless mode BEFORE - // any adtl::adouble are created. If this is not done, then we see - // this scary warning: - // - // " - // ADOL-C Warning: Tapeless: Setting numDir could change memory - // allocation of derivatives in existing adoubles and may lead to - // erroneous results or memory corruption - // " - // - // So we use this dummy function to configure this setting before - // we create and initialize our class data - const std::size_t n_live_variables = adtl::refcounter::getNumLiveVar(); - if (n_live_variables == 0) - { - adtl::setNumDir(n_directional_derivatives); - } - else - { - // So there are some live active variables floating around. Here we - // check if we ask to increase the number of computable - // directional derivatives. If this really is necessary then it's - // absolutely vital that there exist no live variables before doing - // so. - const std::size_t n_set_directional_derivatives = adtl::getNumDir(); - if (n_directional_derivatives > n_set_directional_derivatives) - AssertThrow( - n_live_variables == 0, - ExcMessage( - "There are currently " + - Utilities::to_string(n_live_variables) + - " live " - "adtl::adouble variables in existence. They currently " - "assume " + - Utilities::to_string(n_set_directional_derivatives) + - " directional derivatives " - "but you wish to increase this to " + - Utilities::to_string(n_directional_derivatives) + - ". \n" - "To safely change (or more specifically in this case, " - "increase) the number of directional derivatives, there " - "must be no tapeless doubles in local/global scope.")); - } -# else - // If ADOL-C is not configured with tapeless number reference counting - // then there is no way that we can guarantee that the following call - // is safe. No comment... :-/ - adtl::setNumDir(n_directional_derivatives); -# endif - } - -# else // DEAL_II_WITH_ADOLC - - template - typename std::enable_if::type_code == - NumberTypes::adolc_tapeless>::type - configure_tapeless_mode(const unsigned int /*n_directional_derivatives*/) - { - AssertThrow(false, ExcRequiresADOLC()); - } - -# endif - - } // namespace internal - - /** * Specialization for auto-differentiable numbers that use * reverse mode to compute the first derivatives (and, if supported, @@ -1824,192 +1172,72 @@ namespace Differentiation ADNumberTraits::type_code == NumberTypes::sacado_rad_dfad>::type> { - TapelessDrivers() - : dependent_variable_marking_safe(false) - {} + /** + * Constructor + */ + TapelessDrivers(); - // === Configuration === + /** + * @name Configuration + */ + //@{ static void - initialize_global_environment(const unsigned int n_independent_variables) - { - internal::configure_tapeless_mode( - n_independent_variables); - } + initialize_global_environment(const unsigned int n_independent_variables); + + //@} + + /** + * Operation status + */ + //@{ - // === Operation status === void - allow_dependent_variable_marking() - { - dependent_variable_marking_safe = true; - } + allow_dependent_variable_marking(); void - prevent_dependent_variable_marking() - { - dependent_variable_marking_safe = false; - } + prevent_dependent_variable_marking(); bool - is_dependent_variable_marking_allowed() const - { - return dependent_variable_marking_safe; - } - - // === Scalar drivers === - - static ScalarType - value(const std::vector &dependent_variables) - { - Assert(dependent_variables.size() == 1, - ExcDimensionMismatch(dependent_variables.size(), 1)); - return ADNumberTraits::get_scalar_value( - dependent_variables[0]); - } + is_dependent_variable_marking_allowed() const; - static void + //@} + + /** + * @name Drivers for scalar functions + */ + //@{ + + ScalarType + value(const std::vector &dependent_variables) const; + + void gradient(const std::vector &independent_variables, const std::vector &dependent_variables, - Vector & gradient) - { - Assert( - AD::ADNumberTraits::n_supported_derivative_levels >= 1, - ExcSupportedDerivativeLevels( - AD::ADNumberTraits::n_supported_derivative_levels, - 1)); - Assert(dependent_variables.size() == 1, - ExcDimensionMismatch(dependent_variables.size(), 1)); - Assert(gradient.size() == independent_variables.size(), - ExcDimensionMismatch(gradient.size(), - independent_variables.size())); - - // In reverse mode, the gradients are computed from the - // independent variables (i.e. the adjoint) - internal::reverse_mode_dependent_variable_activation( - const_cast(dependent_variables[0])); - const std::size_t n_independent_variables = - independent_variables.size(); - for (unsigned int i = 0; i < n_independent_variables; i++) - gradient[i] = internal::NumberType::value( - ADNumberTraits::get_directional_derivative( - independent_variables[i], - 0 /*This number doesn't really matter*/)); - } + Vector & gradient) const; - static void + void hessian(const std::vector &independent_variables, const std::vector &dependent_variables, - FullMatrix & hessian) - { - Assert( - AD::ADNumberTraits::n_supported_derivative_levels >= 2, - ExcSupportedDerivativeLevels( - AD::ADNumberTraits::n_supported_derivative_levels, - 2)); - Assert(dependent_variables.size() == 1, - ExcDimensionMismatch(dependent_variables.size(), 1)); - Assert(hessian.m() == independent_variables.size(), - ExcDimensionMismatch(hessian.m(), independent_variables.size())); - Assert(hessian.n() == independent_variables.size(), - ExcDimensionMismatch(hessian.n(), independent_variables.size())); - - // In reverse mode, the gradients are computed from the - // independent variables (i.e. the adjoint) - internal::reverse_mode_dependent_variable_activation( - const_cast(dependent_variables[0])); - const std::size_t n_independent_variables = - independent_variables.size(); - for (unsigned int i = 0; i < n_independent_variables; i++) - { - using derivative_type = - typename ADNumberTraits::derivative_type; - const derivative_type gradient_i = - ADNumberTraits::get_directional_derivative( - independent_variables[i], i); - - for (unsigned int j = 0; j <= i; ++j) // Symmetry - { - // Extract higher-order directional derivatives. Depending on - // the AD number type, the result may be another AD number or a - // floating point value. - const ScalarType hessian_ij = - internal::NumberType::value( - ADNumberTraits::get_directional_derivative( - gradient_i, j)); - hessian[i][j] = hessian_ij; - if (i != j) - hessian[j][i] = hessian_ij; // Symmetry - } - } - } - - // === Vector drivers === + FullMatrix & hessian) const; - static void - values(const std::vector &dependent_variables, - Vector & values) - { - Assert(values.size() == dependent_variables.size(), - ExcDimensionMismatch(values.size(), dependent_variables.size())); + //@} - const std::size_t n_dependent_variables = dependent_variables.size(); - for (unsigned int i = 0; i < n_dependent_variables; i++) - values[i] = ADNumberTraits::get_scalar_value( - dependent_variables[i]); - } + /** + * @name Drivers for vector functions + */ + //@{ - static void + void + values(const std::vector &dependent_variables, + Vector & values) const; + + void jacobian(const std::vector &independent_variables, const std::vector &dependent_variables, - FullMatrix & jacobian) - { - Assert( - AD::ADNumberTraits::n_supported_derivative_levels >= 1, - ExcSupportedDerivativeLevels( - AD::ADNumberTraits::n_supported_derivative_levels, - 1)); - Assert(jacobian.m() == dependent_variables.size(), - ExcDimensionMismatch(jacobian.m(), dependent_variables.size())); - Assert(jacobian.n() == independent_variables.size(), - ExcDimensionMismatch(jacobian.n(), - independent_variables.size())); - - const std::size_t n_independent_variables = - independent_variables.size(); - const std::size_t n_dependent_variables = dependent_variables.size(); - - // In reverse mode, the gradients are computed from the - // independent variables (i.e. the adjoint). - // For a demonstration of why this accumulation process is - // required, see the unit tests - // sacado/basic_01b.cc and sacado/basic_02b.cc - // Here we also take into consideration the derivative type: - // The Sacado number may be of the nested variety, in which - // case the effect of the accumulation process on the - // sensitivities of the nested number need to be accounted for. - using accumulation_type = - typename ADNumberTraits::derivative_type; - std::vector rad_accumulation( - n_independent_variables, - dealii::internal::NumberType::value(0.0)); - - for (unsigned int i = 0; i < n_dependent_variables; i++) - { - internal::reverse_mode_dependent_variable_activation( - const_cast(dependent_variables[i])); - for (unsigned int j = 0; j < n_independent_variables; j++) - { - const accumulation_type df_i_dx_j = - ADNumberTraits::get_directional_derivative( - independent_variables[j], - i /*This number doesn't really matter*/) - - rad_accumulation[j]; - jacobian[i][j] = - internal::NumberType::value(df_i_dx_j); - rad_accumulation[j] += df_i_dx_j; - } - } - } + FullMatrix & jacobian) const; + + //@} private: /** @@ -2036,163 +1264,72 @@ namespace Differentiation ADNumberTraits::type_code == NumberTypes::sacado_dfad_dfad>::type> { - TapelessDrivers() - : dependent_variable_marking_safe(false) - {} + /** + * Constructor + */ + TapelessDrivers(); - // === Configuration === + /** + * @name Configuration + */ + //@{ static void - initialize_global_environment(const unsigned int n_independent_variables) - { - internal::configure_tapeless_mode( - n_independent_variables); - } + initialize_global_environment(const unsigned int n_independent_variables); + + //@} + + /** + * Operation status + */ + //@{ - // === Operation status === void - allow_dependent_variable_marking() - { - dependent_variable_marking_safe = true; - } + allow_dependent_variable_marking(); void - prevent_dependent_variable_marking() - { - dependent_variable_marking_safe = false; - } + prevent_dependent_variable_marking(); bool - is_dependent_variable_marking_allowed() const - { - return dependent_variable_marking_safe; - } - - // === Scalar drivers === - - static ScalarType - value(const std::vector &dependent_variables) - { - Assert(dependent_variables.size() == 1, - ExcDimensionMismatch(dependent_variables.size(), 1)); - return ADNumberTraits::get_scalar_value( - dependent_variables[0]); - } + is_dependent_variable_marking_allowed() const; - static void + //@} + + /** + * @name Drivers for scalar functions + */ + //@{ + + ScalarType + value(const std::vector &dependent_variables) const; + + void gradient(const std::vector &independent_variables, const std::vector &dependent_variables, - Vector & gradient) - { - Assert( - AD::ADNumberTraits::n_supported_derivative_levels >= 1, - ExcSupportedDerivativeLevels( - AD::ADNumberTraits::n_supported_derivative_levels, - 1)); - Assert(dependent_variables.size() == 1, - ExcDimensionMismatch(dependent_variables.size(), 1)); - Assert(gradient.size() == independent_variables.size(), - ExcDimensionMismatch(gradient.size(), - independent_variables.size())); - - // In forward mode, the gradients are computed from the - // dependent variables - const std::size_t n_independent_variables = - independent_variables.size(); - for (unsigned int i = 0; i < n_independent_variables; i++) - gradient[i] = internal::NumberType::value( - ADNumberTraits::get_directional_derivative( - dependent_variables[0], i)); - } + Vector & gradient) const; - static void + void hessian(const std::vector &independent_variables, const std::vector &dependent_variables, - FullMatrix & hessian) - { - Assert( - AD::ADNumberTraits::n_supported_derivative_levels >= 2, - ExcSupportedDerivativeLevels( - AD::ADNumberTraits::n_supported_derivative_levels, - 2)); - Assert(dependent_variables.size() == 1, - ExcDimensionMismatch(dependent_variables.size(), 1)); - Assert(hessian.m() == independent_variables.size(), - ExcDimensionMismatch(hessian.m(), independent_variables.size())); - Assert(hessian.n() == independent_variables.size(), - ExcDimensionMismatch(hessian.n(), independent_variables.size())); - - // In forward mode, the gradients are computed from the - // dependent variables - const std::size_t n_independent_variables = - independent_variables.size(); - for (unsigned int i = 0; i < n_independent_variables; i++) - { - using derivative_type = - typename ADNumberTraits::derivative_type; - const derivative_type gradient_i = - ADNumberTraits::get_directional_derivative( - dependent_variables[0], i); - - for (unsigned int j = 0; j <= i; ++j) // Symmetry - { - // Extract higher-order directional derivatives. Depending on - // the AD number type, the result may be another AD number or a - // floating point value. - const ScalarType hessian_ij = - internal::NumberType::value( - ADNumberTraits::get_directional_derivative( - gradient_i, j)); - hessian[i][j] = hessian_ij; - if (i != j) - hessian[j][i] = hessian_ij; // Symmetry - } - } - } - - // === Vector drivers === + FullMatrix & hessian) const; - static void - values(const std::vector &dependent_variables, - Vector & values) - { - Assert(values.size() == dependent_variables.size(), - ExcDimensionMismatch(values.size(), dependent_variables.size())); + //@} - const std::size_t n_dependent_variables = dependent_variables.size(); - for (unsigned int i = 0; i < n_dependent_variables; i++) - values[i] = ADNumberTraits::get_scalar_value( - dependent_variables[i]); - } + /** + * @name Drivers for vector functions + */ + //@{ - static void + void + values(const std::vector &dependent_variables, + Vector & values) const; + + void jacobian(const std::vector &independent_variables, const std::vector &dependent_variables, - FullMatrix & jacobian) - { - Assert( - AD::ADNumberTraits::n_supported_derivative_levels >= 1, - ExcSupportedDerivativeLevels( - AD::ADNumberTraits::n_supported_derivative_levels, - 1)); - Assert(jacobian.m() == dependent_variables.size(), - ExcDimensionMismatch(jacobian.m(), dependent_variables.size())); - Assert(jacobian.n() == independent_variables.size(), - ExcDimensionMismatch(jacobian.n(), - independent_variables.size())); - - const std::size_t n_independent_variables = - independent_variables.size(); - const std::size_t n_dependent_variables = dependent_variables.size(); - - // In forward mode, the gradients are computed from the - // dependent variables - for (unsigned int i = 0; i < n_dependent_variables; i++) - for (unsigned int j = 0; j < n_independent_variables; j++) - jacobian[i][j] = internal::NumberType::value( - ADNumberTraits::get_directional_derivative( - dependent_variables[i], j)); - } + FullMatrix & jacobian) const; + + //@} private: /** diff --git a/include/deal.II/differentiation/ad/ad_helpers.h b/include/deal.II/differentiation/ad/ad_helpers.h index 83e8a899c571..7aad5de7edab 100644 --- a/include/deal.II/differentiation/ad/ad_helpers.h +++ b/include/deal.II/differentiation/ad/ad_helpers.h @@ -328,6 +328,9 @@ namespace Differentiation * image space. * @param[in] clear_registered_tapes A flag that indicates the that * list of @p registered_tapes must be cleared. + * If set to true then the data structure that tracks which + * tapes have been recorded is cleared as well. It is then expected that + * any preexisting tapes be re-recorded. * * @note This also resets the active tape number to an invalid number, and * deactivates the recording mode for taped variables. diff --git a/source/differentiation/ad/CMakeLists.txt b/source/differentiation/ad/CMakeLists.txt index 81e83bb6339c..9a2f31e4dc67 100644 --- a/source/differentiation/ad/CMakeLists.txt +++ b/source/differentiation/ad/CMakeLists.txt @@ -1,6 +1,6 @@ ## --------------------------------------------------------------------- ## -## Copyright (C) 2017 by the deal.II authors +## Copyright (C) 2017 - 2018 by the deal.II authors ## ## This file is part of the deal.II library. ## @@ -16,12 +16,15 @@ INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_BINARY_DIR}) SET(_src + ad_drivers.cc ad_helpers.cc adolc_number_types.cc sacado_number_types.cc ) SET(_inst + ad_drivers.inst1.in + ad_drivers.inst2.in ad_helpers.inst1.in ad_helpers.inst2.in adolc_number_types.inst.in diff --git a/source/differentiation/ad/ad_drivers.cc b/source/differentiation/ad/ad_drivers.cc new file mode 100644 index 000000000000..a0447c8d7702 --- /dev/null +++ b/source/differentiation/ad/ad_drivers.cc @@ -0,0 +1,2258 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2018 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + +#include + +#if defined(DEAL_II_WITH_ADOLC) || defined(DEAL_II_TRILINOS_WITH_SACADO) + +# include +# include +# include + +# include +# include +# include +# include +# include + +# include +# include + +# ifdef DEAL_II_WITH_ADOLC + +DEAL_II_DISABLE_EXTRA_DIAGNOSTICS +# include +# include +# include +DEAL_II_ENABLE_EXTRA_DIAGNOSTICS + +# endif // DEAL_II_WITH_ADOLC + +# include + + +DEAL_II_NAMESPACE_OPEN + + +namespace Differentiation +{ + namespace AD + { + // ------------- TapedDrivers ------------- + + + template + bool + TapedDrivers::is_recording() const + { + AssertThrow(false, ExcRequiresADNumberSpecialization()); + return false; + } + + + template + typename Types::tape_index + TapedDrivers::active_tape_index() const + { + AssertThrow(false, ExcRequiresADNumberSpecialization()); + return Numbers::invalid_tape_index; + } + + + template + bool + TapedDrivers::is_registered_tape( + const typename Types::tape_index) const + { + AssertThrow(false, ExcRequiresADNumberSpecialization()); + return false; + } + + + template + bool + TapedDrivers::keep_independent_values() const + { + AssertThrow(false, ExcRequiresADNumberSpecialization()); + return false; + } + + + template + void + TapedDrivers::set_tape_buffer_sizes( + const typename Types::tape_buffer_sizes, + const typename Types::tape_buffer_sizes, + const typename Types::tape_buffer_sizes, + const typename Types::tape_buffer_sizes) + { + AssertThrow(false, ExcRequiresADNumberSpecialization()); + } + + + template + void + TapedDrivers::start_taping( + const typename Types::tape_index, + const bool) + { + AssertThrow(false, ExcRequiresADNumberSpecialization()); + } + + + template + void + TapedDrivers::stop_taping( + const typename Types::tape_index, + const bool) + { + AssertThrow(false, ExcRequiresADNumberSpecialization()); + } + + + template + std::vector::tape_index> + TapedDrivers::get_registered_tape_indices() + const + { + AssertThrow(false, ExcRequiresADNumberSpecialization()); + return std::vector::tape_index>(); + } + + + template + void + TapedDrivers::activate_tape( + const typename Types::tape_index) + { + AssertThrow(false, ExcRequiresADNumberSpecialization()); + } + + + template + bool + TapedDrivers::requires_retaping( + const typename Types::tape_index) const + { + AssertThrow(false, ExcRequiresADNumberSpecialization()); + return false; + } + + + template + bool + TapedDrivers::last_action_requires_retaping() + const + { + AssertThrow(false, ExcRequiresADNumberSpecialization()); + return false; + } + + + template + void + TapedDrivers::remove_tape( + const typename Types::tape_index) + { + AssertThrow(false, ExcRequiresADNumberSpecialization()); + } + + + template + void + TapedDrivers::reset(const bool) + { + AssertThrow(false, ExcRequiresADNumberSpecialization()); + } + + + template + void + TapedDrivers::print(std::ostream &) const + { + AssertThrow(false, ExcRequiresADNumberSpecialization()); + } + + + template + void + TapedDrivers::print_tape_stats( + const typename Types::tape_index, + std::ostream &) const + { + AssertThrow(false, ExcRequiresADNumberSpecialization()); + } + + + template + ScalarType + TapedDrivers::value( + const typename Types::tape_index, + const std::vector &) const + { + AssertThrow(false, ExcRequiresADNumberSpecialization()); + return ScalarType(0.0); + } + + + template + void + TapedDrivers::gradient( + const typename Types::tape_index, + const std::vector &, + Vector &) const + { + AssertThrow(false, ExcRequiresADNumberSpecialization()); + } + + + template + void + TapedDrivers::hessian( + const typename Types::tape_index, + const std::vector &, + FullMatrix &) const + { + AssertThrow(false, ExcRequiresADNumberSpecialization()); + } + + + template + void + TapedDrivers::values( + const typename Types::tape_index, + const unsigned int, + const std::vector &, + Vector &) const + { + AssertThrow(false, ExcRequiresADNumberSpecialization()); + } + + + template + void + TapedDrivers::jacobian( + const typename Types::tape_index, + const unsigned int, + const std::vector &, + FullMatrix &) const + { + AssertThrow(false, ExcRequiresADNumberSpecialization()); + } + + + +# ifdef DEAL_II_WITH_ADOLC + + // Specialization for taped ADOL-C auto-differentiable numbers. + + template + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>::TapedDrivers() + : active_tape(Numbers::invalid_tape_index) + , keep_values(true) + , is_recording_flag(false) + , use_stored_taped_buffer_sizes(false) + , obufsize(0u) + , lbufsize(0u) + , vbufsize(0u) + , tbufsize(0u) + {} + + + template + bool + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>::is_recording() + const + { + return is_recording_flag; + } + + + template + typename Types::tape_index + TapedDrivers::type_code == + NumberTypes::adolc_taped>::type>::active_tape_index() const + { + return active_tape; + } + + + template + bool + TapedDrivers::type_code == + NumberTypes::adolc_taped>::type>::keep_independent_values() + const + { + return keep_values; + } + + + template + bool + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + is_registered_tape( + const typename Types::tape_index tape_index) const + { + // Sigh... This is a mess :-/ + // The most succinct way to get this piece of information, would be to + // use the getTapeInfos() function, but would come at the expense of + // creating an inactive tape data within ADOL-C's global store. For + // hints as to why this is the way it is, see the getTapeInfos() + // function in + // https://gitlab.com/adol-c/adol-c/blob/master/ADOL-C/src/tape_handling.cpp + // An alternative solution would be to manually access the tape data; + // see the removeTape() function in + // https://gitlab.com/adol-c/adol-c/blob/master/ADOL-C/src/tape_handling.cpp + // with the consideration of the #defines in + // https://gitlab.com/adol-c/adol-c/blob/master/ADOL-C/src/taping_p.h + // as to how this would be performed. + // Doing things "manually" (the second way) without creating the + // additional data object would be a lot more work... + // + // Both of the above solutions would be possible IF ADOL-C exposed + // this data object or a method to access it to the outside world. + // But they don't :-( + // Instead, what we'll have to do is get the statistics for this tape + // and make our own determination as to whether or not this tape exists. + // This effectively executes the first solution, with even more + // overhead! If the tape is in existence, we can assume that it should a + // non-zero number of dependent and independent variables. Those are + // stored in the zeroth and first entries of the statistics vector. + // + // But, oh wait... Surprise! This will trigger an error if the tape + // doesn't exist at all! So lets first check their tape info cache to + // see if the tape REALLY exists (i.e. has been touched, even if nothing + // has been written to it) before trying to access it. It'll only take + // an O(n) search, but at this point who really cares about efficiency? + // + // It has been suggested in + // https://gitlab.com/adol-c/adol-c/issues/11 + // that a simply try-catch block around ::tapestats is the solution that + // we want here. Unfortunately this results in unwanted pollution of + // the terminal, of the form + // ADOL-C error: reading integer tape number 4! + // >>> File or directory not found! <<< + // , every time a query is made about a non-existant tape. + // So either way we have to guard that check with something more + // conervative so that we don't output useless messages for our users. + const std::vector::tape_index> + registered_tape_indices = get_registered_tape_indices(); + const auto it = std::find(registered_tape_indices.begin(), + registered_tape_indices.end(), + tape_index); + if (it == registered_tape_indices.end()) + return false; + + // See https://gitlab.com/adol-c/adol-c/issues/11#note_108341333 + try + { + std::vector counts(STAT_SIZE); + ::tapestats(tape_index, counts.data()); + return true; + } + catch (const ::FatalError &exc) + { + return false; + } + } + + + template + void + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + set_tape_buffer_sizes( + const typename Types::tape_buffer_sizes in_obufsize, + const typename Types::tape_buffer_sizes in_lbufsize, + const typename Types::tape_buffer_sizes in_vbufsize, + const typename Types::tape_buffer_sizes in_tbufsize) + { + // When valid for the chosen AD number type, these values will be used + // the next time start_recording_operations() is called. + obufsize = in_obufsize; + lbufsize = in_lbufsize; + vbufsize = in_vbufsize; + tbufsize = in_tbufsize; + use_stored_taped_buffer_sizes = true; + } + + + template + void + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + start_taping(const typename Types::tape_index tape_index, + const bool keep_independent_values) + { + if (use_stored_taped_buffer_sizes) + trace_on(tape_index, + keep_independent_values, + obufsize, + lbufsize, + vbufsize, + tbufsize); + else + trace_on(tape_index, keep_independent_values); + + // Set some other flags to their indicated / required values + keep_values = keep_independent_values; + is_recording_flag = true; + } + + + template + void + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + stop_taping( + const typename Types::tape_index active_tape_index, + const bool write_tapes_to_file) + { + if (write_tapes_to_file) + trace_off(active_tape_index); // Slow + else + trace_off(); // Fast(er) + + // Now that we've turned tracing off, we've definitely + // stopped all tape recording. + is_recording_flag = false; + + // If the keep_values flag is set, then we expect the user to use this + // tape immediately after recording it. There is therefore no need to + // invalidate it. However, there is now also no way to double-check + // that the newly recorded tape is indeed the active tape. + if (keep_independent_values() == false) + active_tape = Numbers::invalid_tape_index; + } + + + template + std::vector::tape_index> + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + get_registered_tape_indices() const + { + // We've chosen to use unsigned shorts for the tape + // index type (a safety precaution) so we need to + // perform a conversion betwwen ADOL-C's native tape + // index type and that chosen by us. + std::vector registered_tape_indices_s; + cachedTraceTags(registered_tape_indices_s); + + std::vector::tape_index> + registered_tape_indices(registered_tape_indices_s.size()); + std::copy(registered_tape_indices_s.begin(), + registered_tape_indices_s.end(), + registered_tape_indices.begin()); + return registered_tape_indices; + } + + + template + void + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + activate_tape(const typename Types::tape_index tape_index) + { + active_tape = tape_index; + } + + + template + bool + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + requires_retaping( + const typename Types::tape_index tape_index) const + { + Assert( + is_registered_tape(tape_index) == true, + ExcMessage( + "Cannot ask for the status of a tape that has not yet been recorded and used.")); + + const auto it_status_tape = status.find(tape_index); + + // This tape's status has not been found in the map. This could be + // because a non-existant tape_index has been used as an argument, or + // because the tape exists but has not been used (in a way that + // initiated a status update). For example, on can create a tape in one + // section of code and then query the status of all existing tapes in a + // completely different section of code that knows nothing about the + // first tape. There is no prerequisite that the first tape is ever + // used, and it can therefore not have a status. So, in this case + // there's not much we can do other than to report that the tape does + // not require retaping. + if (it_status_tape == status.end()) + return false; + + const auto status_tape = it_status_tape->second; + + // See ADOL-C manual section 1.7 and comments in last paragraph of + // section 3.1 + Assert(status_tape < 4 && status_tape >= -2, + ExcIndexRange(status_tape, -2, 4)); + return (status_tape < 0); + } + + + template + bool + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + last_action_requires_retaping() const + { + return requires_retaping(active_tape); + } + + + template + void + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + remove_tape(const typename Types::tape_index tape_index) + { + Assert(is_registered_tape(tape_index), + ExcMessage( + "This tape does not exist, and therefore cannot be cleared.")); + removeTape(tape_index, TapeRemovalType::ADOLC_REMOVE_COMPLETELY); + } + + + template + void + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + reset(const bool clear_registered_tapes) + { + active_tape = Numbers::invalid_tape_index; + is_recording_flag = false; + status.clear(); + if (clear_registered_tapes) + { + const std::vector::tape_index> + registered_tape_indices = get_registered_tape_indices(); + for (const auto &tape_index : registered_tape_indices) + remove_tape(tape_index); + } + } + + + template + void + TapedDrivers::type_code == + NumberTypes::adolc_taped>::type>::print(std::ostream &stream) + const + { + const std::vector::tape_index> + registered_tape_indices = get_registered_tape_indices(); + stream << "Registered tapes and their status: "; + auto it_registered_tape = registered_tape_indices.begin(); + for (unsigned int i = 0; i < registered_tape_indices.size(); + ++i, ++it_registered_tape) + { + const auto tape_index = *it_registered_tape; + const auto it_status_tape = status.find(tape_index); + Assert(it_status_tape != status.end(), + ExcMessage( + "This tape's status has not been found in the map.")); + const auto status_tape = it_status_tape->second; + + stream << tape_index << "->" << status_tape + << (i < (registered_tape_indices.size() - 1) ? "," : ""); + } + stream << "\n"; + + stream << "Keep values? " << keep_independent_values() << "\n"; + stream << "Use stored tape buffer sizes? " + << use_stored_taped_buffer_sizes << "\n"; + } + + + template + void + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + print_tape_stats( + const typename Types::tape_index tape_index, + std::ostream & stream) const + { + // See ADOL-C manual section 2.1 + // and adolc/taping.h + std::vector counts(STAT_SIZE); + ::tapestats(tape_index, counts.data()); + Assert(counts.size() >= 18, ExcInternalError()); + stream + << "Tape index: " << tape_index << "\n" + << "Number of independent variables: " << counts[0] << "\n" + << "Number of dependent variables: " << counts[1] << "\n" + << "Max number of live, active variables: " << counts[2] << "\n" + << "Size of taylor stack (number of overwrites): " << counts[3] << "\n" + << "Operations buffer size: " << counts[4] << "\n" + << "Total number of recorded operations: " << counts[5] << "\n" + << "Operations file written or not: " << counts[6] << "\n" + << "Overall number of locations: " << counts[7] << "\n" + << "Locations file written or not: " << counts[8] << "\n" + << "Overall number of values: " << counts[9] << "\n" + << "Values file written or not: " << counts[10] << "\n" + << "Locations buffer size: " << counts[11] << "\n" + << "Values buffer size: " << counts[12] << "\n" + << "Taylor buffer size: " << counts[13] << "\n" + << "Number of eq_*_prod for sparsity pattern: " << counts[14] << "\n" + << "Use of 'min_op', deferred to 'abs_op' for piecewise calculations: " + << counts[15] << "\n" + << "Number of 'abs' calls that can switch branch: " << counts[16] + << "\n" + << "Number of parameters (doubles) interchangeable without retaping: " + << counts[17] << "\n" + << std::flush; + } + + + template + typename TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>::scalar_type + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + value(const typename Types::tape_index active_tape_index, + const std::vector &independent_variables) const + { + Assert(is_registered_tape(active_tape_index), + ExcMessage("This tape has not yet been recorded.")); + + scalar_type value = 0.0; + + status[active_tape_index] = + ::function(active_tape_index, + 1, // Only one dependent variable + independent_variables.size(), + const_cast(independent_variables.data()), + &value); + + return value; + } + + + template + void + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + gradient(const typename Types::tape_index active_tape_index, + const std::vector &independent_variables, + Vector & gradient) const + { + Assert(AD::ADNumberTraits::n_supported_derivative_levels >= + 1, + ExcSupportedDerivativeLevels( + AD::ADNumberTraits::n_supported_derivative_levels, + 1)); + Assert(gradient.size() == independent_variables.size(), + ExcDimensionMismatch(gradient.size(), + independent_variables.size())); + Assert(is_registered_tape(active_tape_index), + ExcMessage("This tape has not yet been recorded.")); + + // Note: ADOL-C's ::gradient function expects a *double as the last + // parameter. Here we take advantage of the fact that the data in the + // Vector class is aligned (e.g. stored as an Array) + status[active_tape_index] = + ::gradient(active_tape_index, + independent_variables.size(), + const_cast(independent_variables.data()), + gradient.data()); + } + + + template + void + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + hessian(const typename Types::tape_index active_tape_index, + const std::vector &independent_variables, + FullMatrix & hessian) const + { + Assert(AD::ADNumberTraits::n_supported_derivative_levels >= + 2, + ExcSupportedDerivativeLevels( + AD::ADNumberTraits::n_supported_derivative_levels, + 2)); + Assert(hessian.m() == independent_variables.size(), + ExcDimensionMismatch(hessian.m(), independent_variables.size())); + Assert(hessian.n() == independent_variables.size(), + ExcDimensionMismatch(hessian.n(), independent_variables.size())); + Assert(is_registered_tape(active_tape_index), + ExcMessage("This tape has not yet been recorded.")); + + const unsigned int n_independent_variables = independent_variables.size(); + std::vector H(n_independent_variables); + for (unsigned int i = 0; i < n_independent_variables; ++i) + H[i] = &hessian[i][0]; + + status[active_tape_index] = + ::hessian(active_tape_index, + n_independent_variables, + const_cast(independent_variables.data()), + H.data()); + + // ADOL-C builds only the lower-triangular part of the + // symmetric Hessian, so we should copy the relevant + // entries into the upper triangular part. + for (unsigned int i = 0; i < n_independent_variables; i++) + for (unsigned int j = 0; j < i; j++) + hessian[j][i] = hessian[i][j]; // Symmetry + } + + + template + void + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + values(const typename Types::tape_index active_tape_index, + const unsigned int n_dependent_variables, + const std::vector &independent_variables, + Vector & values) const + { + Assert(values.size() == n_dependent_variables, + ExcDimensionMismatch(values.size(), n_dependent_variables)); + Assert(is_registered_tape(active_tape_index), + ExcMessage("This tape has not yet been recorded.")); + + // Note: ADOL-C's ::function function expects a *double as the last + // parameter. Here we take advantage of the fact that the data in the + // Vector class is aligned (e.g. stored as an Array) + status[active_tape_index] = + ::function(active_tape_index, + n_dependent_variables, + independent_variables.size(), + const_cast(independent_variables.data()), + values.data()); + } + + + template + void + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + jacobian(const typename Types::tape_index active_tape_index, + const unsigned int n_dependent_variables, + const std::vector &independent_variables, + FullMatrix & jacobian) const + { + Assert(AD::ADNumberTraits::n_supported_derivative_levels >= + 1, + ExcSupportedDerivativeLevels( + AD::ADNumberTraits::n_supported_derivative_levels, + 1)); + Assert(jacobian.m() == n_dependent_variables, + ExcDimensionMismatch(jacobian.m(), n_dependent_variables)); + Assert(jacobian.n() == independent_variables.size(), + ExcDimensionMismatch(jacobian.n(), independent_variables.size())); + Assert(is_registered_tape(active_tape_index), + ExcMessage("This tape has not yet been recorded.")); + + std::vector J(n_dependent_variables); + for (unsigned int i = 0; i < n_dependent_variables; ++i) + J[i] = &jacobian[i][0]; + + status[active_tape_index] = ::jacobian(active_tape_index, + n_dependent_variables, + independent_variables.size(), + independent_variables.data(), + J.data()); + } + +# else + + // Specialization for taped ADOL-C auto-differentiable numbers. + + template + bool + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>::is_recording() + const + { + AssertThrow(false, ExcRequiresADOLC()); + return false; + } + + + template + typename Types::tape_index + TapedDrivers::type_code == + NumberTypes::adolc_taped>::type>::active_tape_index() const + { + AssertThrow(false, ExcRequiresADOLC()); + return Numbers::invalid_tape_index; + } + + + template + bool + TapedDrivers::type_code == + NumberTypes::adolc_taped>::type>::keep_independent_values() + const + { + AssertThrow(false, ExcRequiresADOLC()); + return false; + } + + + template + bool + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + is_registered_tape( + const typename Types::tape_index tape_index) const + { + AssertThrow(false, ExcRequiresADOLC()); + return false; + } + + + template + void + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + set_tape_buffer_sizes( + const typename Types::tape_buffer_sizes, + const typename Types::tape_buffer_sizes, + const typename Types::tape_buffer_sizes, + const typename Types::tape_buffer_sizes) + { + AssertThrow(false, ExcRequiresADOLC()); + } + + + template + void + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + start_taping(const typename Types::tape_index, const bool) + { + AssertThrow(false, ExcRequiresADOLC()); + } + + + template + void + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + stop_taping(const typename Types::tape_index, const bool) + { + AssertThrow(false, ExcRequiresADOLC()); + } + + std::vector::tape_index> + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + get_registered_tape_indices() const + { + AssertThrow(false, ExcRequiresADOLC()); + return std::vector::tape_index>(); + } + + + template + void + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + activate_tape(const typename Types::tape_index) + { + AssertThrow(false, ExcRequiresADOLC()); + } + + + template + bool + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + requires_retaping(const typename Types::tape_index) const + { + AssertThrow(false, ExcRequiresADOLC()); + return false; + } + + + template + bool + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + last_action_requires_retaping() const + { + AssertThrow(false, ExcRequiresADOLC()); + return false; + } + + + template + void + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + remove_tape(const typename Types::tape_index) + { + AssertThrow(false, ExcRequiresADOLC()); + } + + + template + void + TapedDrivers::type_code == + NumberTypes::adolc_taped>::type>::reset(const bool) + { + AssertThrow(false, ExcRequiresADOLC()); + } + + + template + void + TapedDrivers::type_code == + NumberTypes::adolc_taped>::type>::print(std::ostream &stream) + const + { + AssertThrow(false, ExcRequiresADOLC()); + } + + + template + void + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + print_tape_stats(const typename Types::tape_index, + std::ostream &) const + { + AssertThrow(false, ExcRequiresADOLC()); + } + + + template + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>::scalar_type + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + value(const typename Types::tape_index, + const std::vector &) const + { + AssertThrow(false, ExcRequiresADOLC()); + return 0.0; + } + + + template + void + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + gradient(const typename Types::tape_index, + const std::vector &, + Vector &) const + { + AssertThrow(false, ExcRequiresADOLC()); + } + + void + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + hessian(const typename Types::tape_index, + const std::vector &, + FullMatrix &) const + { + AssertThrow(false, ExcRequiresADOLC()); + } + + + template + void + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + values(const typename Types::tape_index, + const unsigned int, + const std::vector &, + Vector &) const + { + AssertThrow(false, ExcRequiresADOLC()); + } + + + template + void + TapedDrivers< + ADNumberType, + double, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + jacobian(const typename Types::tape_index, + const unsigned int, + const std::vector &, + FullMatrix &) const + { + AssertThrow(false, ExcRequiresADOLC()); + } + +# endif // DEAL_II_WITH_ADOLC + + + // Specialization for ADOL-C taped numbers. It is expected that the + // scalar return type for this class is a float. + + template + bool + TapedDrivers< + ADNumberType, + float, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>::is_recording() + const + { + // ADOL-C only supports 'double', not 'float', so we can forward to + // the 'double' implementation of this function + return taped_driver.is_recording(); + } + + + template + typename Types::tape_index + TapedDrivers::type_code == + NumberTypes::adolc_taped>::type>::active_tape_index() const + { + // ADOL-C only supports 'double', not 'float', so we can forward to + // the 'double' implementation of this function + return taped_driver.active_tape_index(); + } + + + template + bool + TapedDrivers::type_code == + NumberTypes::adolc_taped>::type>::keep_independent_values() + const + { + return taped_driver.keep_independent_values(); + } + + + template + bool + TapedDrivers< + ADNumberType, + float, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + is_registered_tape( + const typename Types::tape_index tape_index) const + { + // ADOL-C only supports 'double', not 'float', so we can forward to + // the 'double' implementation of this function + return taped_driver.is_registered_tape(tape_index); + } + + + template + void + TapedDrivers< + ADNumberType, + float, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + set_tape_buffer_sizes( + const typename Types::tape_buffer_sizes obufsize, + const typename Types::tape_buffer_sizes lbufsize, + const typename Types::tape_buffer_sizes vbufsize, + const typename Types::tape_buffer_sizes tbufsize) + { + // ADOL-C only supports 'double', not 'float', so we can forward to + // the 'double' implementation of this function + taped_driver.set_tape_buffer_sizes(obufsize, + lbufsize, + vbufsize, + tbufsize); + } + + + template + void + TapedDrivers< + ADNumberType, + float, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + start_taping(const typename Types::tape_index tape_index, + const bool keep_independent_values) + { + // ADOL-C only supports 'double', not 'float', so we can forward to + // the 'double' implementation of this function + taped_driver.start_taping(tape_index, keep_independent_values); + } + + + template + void + TapedDrivers< + ADNumberType, + float, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + stop_taping( + const typename Types::tape_index active_tape_index, + const bool write_tapes_to_file) + { + // ADOL-C only supports 'double', not 'float', so we can forward to + // the 'double' implementation of this function + taped_driver.stop_taping(active_tape_index, write_tapes_to_file); + } + + + template + std::vector::tape_index> + TapedDrivers< + ADNumberType, + float, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + get_registered_tape_indices() const + { + return taped_driver.get_registered_tape_indices(); + } + + + template + void + TapedDrivers< + ADNumberType, + float, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + activate_tape(const typename Types::tape_index tape_index) + { + taped_driver.activate_tape(tape_index); + } + + + template + bool + TapedDrivers< + ADNumberType, + float, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + requires_retaping( + const typename Types::tape_index tape_index) const + { + return taped_driver.requires_retaping(tape_index); + } + + + template + bool + TapedDrivers< + ADNumberType, + float, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + last_action_requires_retaping() const + { + return taped_driver.last_action_requires_retaping(); + } + + + template + void + TapedDrivers< + ADNumberType, + float, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + remove_tape(const typename Types::tape_index tape_index) + { + taped_driver.remove_tape(tape_index); + } + + + template + void + TapedDrivers< + ADNumberType, + float, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + reset(const bool clear_registered_tapes) + { + taped_driver.reset(clear_registered_tapes); + } + + + template + void + TapedDrivers::type_code == + NumberTypes::adolc_taped>::type>::print(std::ostream &stream) + const + { + taped_driver.print(stream); + } + + + template + void + TapedDrivers< + ADNumberType, + float, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + print_tape_stats( + const typename Types::tape_index tape_index, + std::ostream & stream) const + { + // ADOL-C only supports 'double', not 'float', so we can forward to + // the 'double' implementation of this function + taped_driver.print_tape_stats(tape_index, stream); + } + + + template + typename TapedDrivers< + ADNumberType, + float, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>::scalar_type + TapedDrivers< + ADNumberType, + float, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + value(const typename Types::tape_index active_tape_index, + const std::vector &independent_variables) const + { + // ADOL-C only supports 'double', not 'float', so we can forward to + // the 'double' implementation of this function + return taped_driver.value(active_tape_index, + vector_float_to_double(independent_variables)); + } + + + template + void + TapedDrivers< + ADNumberType, + float, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + gradient(const typename Types::tape_index active_tape_index, + const std::vector &independent_variables, + Vector & gradient) const + { + Vector gradient_double(gradient.size()); + // ADOL-C only supports 'double', not 'float', so we can forward to + // the 'double' implementation of this function + taped_driver.gradient(active_tape_index, + vector_float_to_double(independent_variables), + gradient_double); + gradient = gradient_double; + } + + + template + void + TapedDrivers< + ADNumberType, + float, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + hessian(const typename Types::tape_index active_tape_index, + const std::vector &independent_variables, + FullMatrix & hessian) const + { + FullMatrix hessian_double(hessian.m(), hessian.n()); + // ADOL-C only supports 'double', not 'float', so we can forward to + // the 'double' implementation of this function + taped_driver.hessian(active_tape_index, + vector_float_to_double(independent_variables), + hessian_double); + hessian = hessian_double; + } + + + template + void + TapedDrivers< + ADNumberType, + float, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + values(const typename Types::tape_index active_tape_index, + const unsigned int n_dependent_variables, + const std::vector &independent_variables, + Vector & values) const + { + Vector values_double(values.size()); + // ADOL-C only supports 'double', not 'float', so we can forward to + // the 'double' implementation of this function + taped_driver.values(active_tape_index, + n_dependent_variables, + vector_float_to_double(independent_variables), + values_double); + values = values_double; + } + + + template + void + TapedDrivers< + ADNumberType, + float, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + jacobian(const typename Types::tape_index active_tape_index, + const unsigned int n_dependent_variables, + const std::vector &independent_variables, + FullMatrix & jacobian) const + { + FullMatrix jacobian_double(jacobian.m(), jacobian.n()); + // ADOL-C only supports 'double', not 'float', so we can forward to + // the 'double' implementation of this function + taped_driver.jacobian(active_tape_index, + n_dependent_variables, + vector_float_to_double(independent_variables), + jacobian_double); + jacobian = jacobian_double; + } + + + template + std::vector + TapedDrivers< + ADNumberType, + float, + typename std::enable_if::type_code == + NumberTypes::adolc_taped>::type>:: + vector_float_to_double(const std::vector &in) const + { + std::vector out(in.size()); + std::copy(in.begin(), in.end(), out.begin()); + return out; + } + + + // ------------- TapelessDrivers ------------- + + + template + void + TapelessDrivers::initialize_global_environment( + const unsigned int) + { + AssertThrow(false, ExcRequiresADNumberSpecialization()); + } + + template + void + TapelessDrivers:: + allow_dependent_variable_marking() + { + AssertThrow(false, ExcRequiresADNumberSpecialization()); + } + + template + void + TapelessDrivers:: + prevent_dependent_variable_marking() + { + AssertThrow(false, ExcRequiresADNumberSpecialization()); + } + + template + bool + TapelessDrivers:: + is_dependent_variable_marking_allowed() const + { + AssertThrow(false, ExcRequiresADNumberSpecialization()); + return false; + } + + + template + ScalarType + TapelessDrivers::value( + const std::vector &) const + { + AssertThrow(false, ExcRequiresADNumberSpecialization()); + return ScalarType(0.0); + } + + + template + void + TapelessDrivers::gradient( + const std::vector &, + const std::vector &, + Vector &) const + { + AssertThrow(false, ExcRequiresADNumberSpecialization()); + } + + + template + void + TapelessDrivers::hessian( + const std::vector &, + const std::vector &, + FullMatrix &) const + { + AssertThrow(false, ExcRequiresADNumberSpecialization()); + } + + + template + void + TapelessDrivers::values( + const std::vector &, + Vector &) const + { + AssertThrow(false, ExcRequiresADNumberSpecialization()); + } + + + template + void + TapelessDrivers::jacobian( + const std::vector &, + const std::vector &, + FullMatrix &) const + { + AssertThrow(false, ExcRequiresADNumberSpecialization()); + } + + + namespace internal + { + /** + * A dummy function to define the active dependent variable when using + * reverse-mode AD. + */ + template + typename std::enable_if::type_code == + NumberTypes::sacado_rad || + ADNumberTraits::type_code == + NumberTypes::sacado_rad_dfad)>::type + reverse_mode_dependent_variable_activation(ADNumberType &) + {} + +# ifdef DEAL_II_TRILINOS_WITH_SACADO + + + /** + * Define the active dependent variable when using reverse-mode AD. + * + * If there are multiple dependent variables then it is necessary to + * inform the independent variables, from which the adjoints are computed, + * which dependent variable they are computing the gradients with respect + * to. This function broadcasts this information. + */ + template + typename std::enable_if::type_code == + NumberTypes::sacado_rad || + ADNumberTraits::type_code == + NumberTypes::sacado_rad_dfad>::type + reverse_mode_dependent_variable_activation( + ADNumberType &dependent_variable) + { + // Compute all gradients (adjoints) for this + // reverse-mode Sacado dependent variable. + // For reverse-mode Sacado numbers it is necessary to broadcast to + // all independent variables that it is time to compute gradients. + // For one dependent variable one would just need to call + // ADNumberType::Gradcomp(), but since we have a more + // generic implementation for vectors of dependent variables + // (vector mode) we default to the complex case. + ADNumberType::Outvar_Gradcomp(dependent_variable); + } + +# endif + + + /** + * A dummy function to enable vector mode for tapeless + * auto-differentiable numbers. + */ + template + typename std::enable_if::type_code == + NumberTypes::adolc_tapeless)>::type + configure_tapeless_mode(const unsigned int) + {} + + +# ifdef DEAL_II_WITH_ADOLC + + + /** + * Enable vector mode for ADOL-C tapeless numbers. + * + * This function checks to see if its legal to increase the maximum + * number of directional derivatives to be considered during calculations. + * If not then it throws an error. + */ + template + typename std::enable_if::type_code == + NumberTypes::adolc_tapeless>::type + configure_tapeless_mode(const unsigned int n_directional_derivatives) + { +# ifdef DEAL_II_ADOLC_WITH_TAPELESS_REFCOUNTING + // See ADOL-C manual section 7.1 + // + // NOTE: It is critical that this is done for tapeless mode BEFORE + // any adtl::adouble are created. If this is not done, then we see + // this scary warning: + // + // " + // ADOL-C Warning: Tapeless: Setting numDir could change memory + // allocation of derivatives in existing adoubles and may lead to + // erroneous results or memory corruption + // " + // + // So we use this dummy function to configure this setting before + // we create and initialize our class data + const std::size_t n_live_variables = adtl::refcounter::getNumLiveVar(); + if (n_live_variables == 0) + { + adtl::setNumDir(n_directional_derivatives); + } + else + { + // So there are some live active variables floating around. Here we + // check if we ask to increase the number of computable + // directional derivatives. If this really is necessary then it's + // absolutely vital that there exist no live variables before doing + // so. + const std::size_t n_set_directional_derivatives = adtl::getNumDir(); + if (n_directional_derivatives > n_set_directional_derivatives) + AssertThrow( + n_live_variables == 0, + ExcMessage( + "There are currently " + + Utilities::to_string(n_live_variables) + + " live " + "adtl::adouble variables in existence. They currently " + "assume " + + Utilities::to_string(n_set_directional_derivatives) + + " directional derivatives " + "but you wish to increase this to " + + Utilities::to_string(n_directional_derivatives) + + ". \n" + "To safely change (or more specifically in this case, " + "increase) the number of directional derivatives, there " + "must be no tapeless doubles in local/global scope.")); + } +# else + // If ADOL-C is not configured with tapeless number reference counting + // then there is no way that we can guarantee that the following call + // is safe. No comment... :-/ + adtl::setNumDir(n_directional_derivatives); +# endif + } + +# else // DEAL_II_WITH_ADOLC + + template + typename std::enable_if::type_code == + NumberTypes::adolc_tapeless>::type + configure_tapeless_mode(const unsigned int /*n_directional_derivatives*/) + { + AssertThrow(false, ExcRequiresADOLC()); + } + +# endif + + } // namespace internal + + + + // Specialization for auto-differentiable numbers that use + // reverse mode to compute the first derivatives (and, if supported, + // forward mode for the second). + + template + TapelessDrivers< + ADNumberType, + ScalarType, + typename std::enable_if< + ADNumberTraits::type_code == NumberTypes::sacado_rad || + ADNumberTraits::type_code == + NumberTypes::sacado_rad_dfad>::type>::TapelessDrivers() + : dependent_variable_marking_safe(false) + {} + + + template + void + TapelessDrivers< + ADNumberType, + ScalarType, + typename std::enable_if::type_code == + NumberTypes::sacado_rad || + ADNumberTraits::type_code == + NumberTypes::sacado_rad_dfad>::type>:: + initialize_global_environment(const unsigned int n_independent_variables) + { + internal::configure_tapeless_mode(n_independent_variables); + } + + + template + void + TapelessDrivers< + ADNumberType, + ScalarType, + typename std::enable_if::type_code == + NumberTypes::sacado_rad || + ADNumberTraits::type_code == + NumberTypes::sacado_rad_dfad>::type>:: + allow_dependent_variable_marking() + { + dependent_variable_marking_safe = true; + } + + + template + void + TapelessDrivers< + ADNumberType, + ScalarType, + typename std::enable_if::type_code == + NumberTypes::sacado_rad || + ADNumberTraits::type_code == + NumberTypes::sacado_rad_dfad>::type>:: + prevent_dependent_variable_marking() + { + dependent_variable_marking_safe = false; + } + + + template + bool + TapelessDrivers< + ADNumberType, + ScalarType, + typename std::enable_if::type_code == + NumberTypes::sacado_rad || + ADNumberTraits::type_code == + NumberTypes::sacado_rad_dfad>::type>:: + is_dependent_variable_marking_allowed() const + { + return dependent_variable_marking_safe; + } + + + template + ScalarType + TapelessDrivers< + ADNumberType, + ScalarType, + typename std::enable_if::type_code == + NumberTypes::sacado_rad || + ADNumberTraits::type_code == + NumberTypes::sacado_rad_dfad>::type>:: + value(const std::vector &dependent_variables) const + { + Assert(dependent_variables.size() == 1, + ExcDimensionMismatch(dependent_variables.size(), 1)); + return ADNumberTraits::get_scalar_value( + dependent_variables[0]); + } + + + template + void + TapelessDrivers< + ADNumberType, + ScalarType, + typename std::enable_if::type_code == + NumberTypes::sacado_rad || + ADNumberTraits::type_code == + NumberTypes::sacado_rad_dfad>::type>:: + gradient(const std::vector &independent_variables, + const std::vector &dependent_variables, + Vector & gradient) const + { + Assert(AD::ADNumberTraits::n_supported_derivative_levels >= + 1, + ExcSupportedDerivativeLevels( + AD::ADNumberTraits::n_supported_derivative_levels, + 1)); + Assert(dependent_variables.size() == 1, + ExcDimensionMismatch(dependent_variables.size(), 1)); + Assert(gradient.size() == independent_variables.size(), + ExcDimensionMismatch(gradient.size(), + independent_variables.size())); + + // In reverse mode, the gradients are computed from the + // independent variables (i.e. the adjoint) + internal::reverse_mode_dependent_variable_activation( + const_cast(dependent_variables[0])); + const std::size_t n_independent_variables = independent_variables.size(); + for (unsigned int i = 0; i < n_independent_variables; i++) + gradient[i] = internal::NumberType::value( + ADNumberTraits::get_directional_derivative( + independent_variables[i], 0 /*This number doesn't really matter*/)); + } + + + template + void + TapelessDrivers< + ADNumberType, + ScalarType, + typename std::enable_if::type_code == + NumberTypes::sacado_rad || + ADNumberTraits::type_code == + NumberTypes::sacado_rad_dfad>::type>:: + hessian(const std::vector &independent_variables, + const std::vector &dependent_variables, + FullMatrix & hessian) const + { + Assert(AD::ADNumberTraits::n_supported_derivative_levels >= + 2, + ExcSupportedDerivativeLevels( + AD::ADNumberTraits::n_supported_derivative_levels, + 2)); + Assert(dependent_variables.size() == 1, + ExcDimensionMismatch(dependent_variables.size(), 1)); + Assert(hessian.m() == independent_variables.size(), + ExcDimensionMismatch(hessian.m(), independent_variables.size())); + Assert(hessian.n() == independent_variables.size(), + ExcDimensionMismatch(hessian.n(), independent_variables.size())); + + // In reverse mode, the gradients are computed from the + // independent variables (i.e. the adjoint) + internal::reverse_mode_dependent_variable_activation( + const_cast(dependent_variables[0])); + const std::size_t n_independent_variables = independent_variables.size(); + for (unsigned int i = 0; i < n_independent_variables; i++) + { + using derivative_type = + typename ADNumberTraits::derivative_type; + const derivative_type gradient_i = + ADNumberTraits::get_directional_derivative( + independent_variables[i], i); + + for (unsigned int j = 0; j <= i; ++j) // Symmetry + { + // Extract higher-order directional derivatives. Depending on + // the AD number type, the result may be another AD number or a + // floating point value. + const ScalarType hessian_ij = + internal::NumberType::value( + ADNumberTraits::get_directional_derivative( + gradient_i, j)); + hessian[i][j] = hessian_ij; + if (i != j) + hessian[j][i] = hessian_ij; // Symmetry + } + } + } + + + template + void + TapelessDrivers< + ADNumberType, + ScalarType, + typename std::enable_if::type_code == + NumberTypes::sacado_rad || + ADNumberTraits::type_code == + NumberTypes::sacado_rad_dfad>::type>:: + values(const std::vector &dependent_variables, + Vector & values) const + { + Assert(values.size() == dependent_variables.size(), + ExcDimensionMismatch(values.size(), dependent_variables.size())); + + const std::size_t n_dependent_variables = dependent_variables.size(); + for (unsigned int i = 0; i < n_dependent_variables; i++) + values[i] = ADNumberTraits::get_scalar_value( + dependent_variables[i]); + } + + + template + void + TapelessDrivers< + ADNumberType, + ScalarType, + typename std::enable_if::type_code == + NumberTypes::sacado_rad || + ADNumberTraits::type_code == + NumberTypes::sacado_rad_dfad>::type>:: + jacobian(const std::vector &independent_variables, + const std::vector &dependent_variables, + FullMatrix & jacobian) const + { + Assert(AD::ADNumberTraits::n_supported_derivative_levels >= + 1, + ExcSupportedDerivativeLevels( + AD::ADNumberTraits::n_supported_derivative_levels, + 1)); + Assert(jacobian.m() == dependent_variables.size(), + ExcDimensionMismatch(jacobian.m(), dependent_variables.size())); + Assert(jacobian.n() == independent_variables.size(), + ExcDimensionMismatch(jacobian.n(), independent_variables.size())); + + const std::size_t n_independent_variables = independent_variables.size(); + const std::size_t n_dependent_variables = dependent_variables.size(); + + // In reverse mode, the gradients are computed from the + // independent variables (i.e. the adjoint). + // For a demonstration of why this accumulation process is + // required, see the unit tests + // sacado/basic_01b.cc and sacado/basic_02b.cc + // Here we also take into consideration the derivative type: + // The Sacado number may be of the nested variety, in which + // case the effect of the accumulation process on the + // sensitivities of the nested number need to be accounted for. + using accumulation_type = + typename ADNumberTraits::derivative_type; + std::vector rad_accumulation( + n_independent_variables, + dealii::internal::NumberType::value(0.0)); + + for (unsigned int i = 0; i < n_dependent_variables; i++) + { + internal::reverse_mode_dependent_variable_activation( + const_cast(dependent_variables[i])); + for (unsigned int j = 0; j < n_independent_variables; j++) + { + const accumulation_type df_i_dx_j = + ADNumberTraits::get_directional_derivative( + independent_variables[j], + i /*This number doesn't really matter*/) - + rad_accumulation[j]; + jacobian[i][j] = + internal::NumberType::value(df_i_dx_j); + rad_accumulation[j] += df_i_dx_j; + } + } + } + + + + // Specialization for auto-differentiable numbers that use + // forward mode to compute the first (and, if supported, second) + // derivatives. + + template + TapelessDrivers< + ADNumberType, + ScalarType, + typename std::enable_if< + ADNumberTraits::type_code == + NumberTypes::adolc_tapeless || + ADNumberTraits::type_code == NumberTypes::sacado_dfad || + ADNumberTraits::type_code == + NumberTypes::sacado_dfad_dfad>::type>::TapelessDrivers() + : dependent_variable_marking_safe(false) + {} + + + template + void + TapelessDrivers< + ADNumberType, + ScalarType, + typename std::enable_if::type_code == + NumberTypes::adolc_tapeless || + ADNumberTraits::type_code == + NumberTypes::sacado_dfad || + ADNumberTraits::type_code == + NumberTypes::sacado_dfad_dfad>::type>:: + initialize_global_environment(const unsigned int n_independent_variables) + { + internal::configure_tapeless_mode(n_independent_variables); + } + + + template + void + TapelessDrivers< + ADNumberType, + ScalarType, + typename std::enable_if::type_code == + NumberTypes::adolc_tapeless || + ADNumberTraits::type_code == + NumberTypes::sacado_dfad || + ADNumberTraits::type_code == + NumberTypes::sacado_dfad_dfad>::type>:: + allow_dependent_variable_marking() + { + dependent_variable_marking_safe = true; + } + + + template + void + TapelessDrivers< + ADNumberType, + ScalarType, + typename std::enable_if::type_code == + NumberTypes::adolc_tapeless || + ADNumberTraits::type_code == + NumberTypes::sacado_dfad || + ADNumberTraits::type_code == + NumberTypes::sacado_dfad_dfad>::type>:: + prevent_dependent_variable_marking() + { + dependent_variable_marking_safe = false; + } + + + template + bool + TapelessDrivers< + ADNumberType, + ScalarType, + typename std::enable_if::type_code == + NumberTypes::adolc_tapeless || + ADNumberTraits::type_code == + NumberTypes::sacado_dfad || + ADNumberTraits::type_code == + NumberTypes::sacado_dfad_dfad>::type>:: + is_dependent_variable_marking_allowed() const + { + return dependent_variable_marking_safe; + } + + + template + ScalarType + TapelessDrivers< + ADNumberType, + ScalarType, + typename std::enable_if::type_code == + NumberTypes::adolc_tapeless || + ADNumberTraits::type_code == + NumberTypes::sacado_dfad || + ADNumberTraits::type_code == + NumberTypes::sacado_dfad_dfad>::type>:: + value(const std::vector &dependent_variables) const + { + Assert(dependent_variables.size() == 1, + ExcDimensionMismatch(dependent_variables.size(), 1)); + return ADNumberTraits::get_scalar_value( + dependent_variables[0]); + } + + + template + void + TapelessDrivers< + ADNumberType, + ScalarType, + typename std::enable_if::type_code == + NumberTypes::adolc_tapeless || + ADNumberTraits::type_code == + NumberTypes::sacado_dfad || + ADNumberTraits::type_code == + NumberTypes::sacado_dfad_dfad>::type>:: + gradient(const std::vector &independent_variables, + const std::vector &dependent_variables, + Vector & gradient) const + { + Assert(AD::ADNumberTraits::n_supported_derivative_levels >= + 1, + ExcSupportedDerivativeLevels( + AD::ADNumberTraits::n_supported_derivative_levels, + 1)); + Assert(dependent_variables.size() == 1, + ExcDimensionMismatch(dependent_variables.size(), 1)); + Assert(gradient.size() == independent_variables.size(), + ExcDimensionMismatch(gradient.size(), + independent_variables.size())); + + // In forward mode, the gradients are computed from the + // dependent variables + const std::size_t n_independent_variables = independent_variables.size(); + for (unsigned int i = 0; i < n_independent_variables; i++) + gradient[i] = internal::NumberType::value( + ADNumberTraits::get_directional_derivative( + dependent_variables[0], i)); + } + + + template + void + TapelessDrivers< + ADNumberType, + ScalarType, + typename std::enable_if::type_code == + NumberTypes::adolc_tapeless || + ADNumberTraits::type_code == + NumberTypes::sacado_dfad || + ADNumberTraits::type_code == + NumberTypes::sacado_dfad_dfad>::type>:: + hessian(const std::vector &independent_variables, + const std::vector &dependent_variables, + FullMatrix & hessian) const + { + Assert(AD::ADNumberTraits::n_supported_derivative_levels >= + 2, + ExcSupportedDerivativeLevels( + AD::ADNumberTraits::n_supported_derivative_levels, + 2)); + Assert(dependent_variables.size() == 1, + ExcDimensionMismatch(dependent_variables.size(), 1)); + Assert(hessian.m() == independent_variables.size(), + ExcDimensionMismatch(hessian.m(), independent_variables.size())); + Assert(hessian.n() == independent_variables.size(), + ExcDimensionMismatch(hessian.n(), independent_variables.size())); + + // In forward mode, the gradients are computed from the + // dependent variables + const std::size_t n_independent_variables = independent_variables.size(); + for (unsigned int i = 0; i < n_independent_variables; i++) + { + using derivative_type = + typename ADNumberTraits::derivative_type; + const derivative_type gradient_i = + ADNumberTraits::get_directional_derivative( + dependent_variables[0], i); + + for (unsigned int j = 0; j <= i; ++j) // Symmetry + { + // Extract higher-order directional derivatives. Depending on + // the AD number type, the result may be another AD number or a + // floating point value. + const ScalarType hessian_ij = + internal::NumberType::value( + ADNumberTraits::get_directional_derivative( + gradient_i, j)); + hessian[i][j] = hessian_ij; + if (i != j) + hessian[j][i] = hessian_ij; // Symmetry + } + } + } + + + template + void + TapelessDrivers< + ADNumberType, + ScalarType, + typename std::enable_if::type_code == + NumberTypes::adolc_tapeless || + ADNumberTraits::type_code == + NumberTypes::sacado_dfad || + ADNumberTraits::type_code == + NumberTypes::sacado_dfad_dfad>::type>:: + values(const std::vector &dependent_variables, + Vector & values) const + { + Assert(values.size() == dependent_variables.size(), + ExcDimensionMismatch(values.size(), dependent_variables.size())); + + const std::size_t n_dependent_variables = dependent_variables.size(); + for (unsigned int i = 0; i < n_dependent_variables; i++) + values[i] = ADNumberTraits::get_scalar_value( + dependent_variables[i]); + } + + + template + void + TapelessDrivers< + ADNumberType, + ScalarType, + typename std::enable_if::type_code == + NumberTypes::adolc_tapeless || + ADNumberTraits::type_code == + NumberTypes::sacado_dfad || + ADNumberTraits::type_code == + NumberTypes::sacado_dfad_dfad>::type>:: + jacobian(const std::vector &independent_variables, + const std::vector &dependent_variables, + FullMatrix & jacobian) const + { + Assert(AD::ADNumberTraits::n_supported_derivative_levels >= + 1, + ExcSupportedDerivativeLevels( + AD::ADNumberTraits::n_supported_derivative_levels, + 1)); + Assert(jacobian.m() == dependent_variables.size(), + ExcDimensionMismatch(jacobian.m(), dependent_variables.size())); + Assert(jacobian.n() == independent_variables.size(), + ExcDimensionMismatch(jacobian.n(), independent_variables.size())); + + const std::size_t n_independent_variables = independent_variables.size(); + const std::size_t n_dependent_variables = dependent_variables.size(); + + // In forward mode, the gradients are computed from the + // dependent variables + for (unsigned int i = 0; i < n_dependent_variables; i++) + for (unsigned int j = 0; j < n_independent_variables; j++) + jacobian[i][j] = internal::NumberType::value( + ADNumberTraits::get_directional_derivative( + dependent_variables[i], j)); + } + + + } // namespace AD +} // namespace Differentiation + + +/* --- Explicit instantiations --- */ +# ifdef DEAL_II_WITH_ADOLC +# include "ad_drivers.inst1" +# endif +# ifdef DEAL_II_TRILINOS_WITH_SACADO +# include "ad_drivers.inst2" +# endif + + +DEAL_II_NAMESPACE_CLOSE + + +#endif // defined(DEAL_II_WITH_ADOLC) || defined(DEAL_II_TRILINOS_WITH_SACADO) diff --git a/source/differentiation/ad/ad_drivers.inst1.in b/source/differentiation/ad/ad_drivers.inst1.in new file mode 100644 index 000000000000..f0829398fb98 --- /dev/null +++ b/source/differentiation/ad/ad_drivers.inst1.in @@ -0,0 +1,73 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2018 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + +// TODO: Include complex types + +for (number : REAL_SCALARS) +{ + namespace Differentiation + \{ + namespace AD + \{ + + // -------------------------- TapedDrivers ---------------------- + + template + struct TapedDrivers::ad_type,number>; + + template + struct TapedDrivers::ad_type,number>; + + // -------------------------- TapelessDrivers ---------------------- + + template + struct TapelessDrivers::ad_type,number>; + + template + struct TapelessDrivers::ad_type,number>; + + \} + \} +} + +// Instantiations for ADHelpers for which the underlying number type is fixed +for () +{ + namespace Differentiation + \{ + namespace AD + \{ + + + + // -------------------------- Types ---------------------- + + template + struct Types::ad_type>; + + template + struct Types::ad_type>; + + // -------------------------- Numbers ---------------------- + + template + struct Numbers::ad_type>; + + template + struct Numbers::ad_type>; + + \} + \} +} \ No newline at end of file diff --git a/source/differentiation/ad/ad_drivers.inst2.in b/source/differentiation/ad/ad_drivers.inst2.in new file mode 100644 index 000000000000..f8aa39e134b7 --- /dev/null +++ b/source/differentiation/ad/ad_drivers.inst2.in @@ -0,0 +1,83 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2016 - 2017 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + +// TODO: Include complex types + +for (number : REAL_SCALARS) +{ + namespace Differentiation + \{ + namespace AD + \{ + + // -------------------------- Types ---------------------- + + template + struct Types::ad_type>; + + template + struct Types::ad_type>; + + template + struct Types::ad_type>; + + template + struct Types::ad_type>; + + // -------------------------- Numbers ---------------------- + + template + struct Numbers::ad_type>; + + template + struct Numbers::ad_type>; + + template + struct Numbers::ad_type>; + + template + struct Numbers::ad_type>; + + // -------------------------- TapedDrivers ---------------------- + + template + struct TapedDrivers::ad_type,number>; + + template + struct TapedDrivers::ad_type,number>; + + template + struct TapedDrivers::ad_type,number>; + + template + struct TapedDrivers::ad_type,number>; + + // -------------------------- TapelessDrivers ---------------------- + + template + struct TapelessDrivers::ad_type,number>; + + template + struct TapelessDrivers::ad_type,number>; + + template + struct TapelessDrivers::ad_type,number>; + + template + struct TapelessDrivers::ad_type,number>; + + \} + \} +} diff --git a/source/differentiation/ad/ad_helpers.cc b/source/differentiation/ad/ad_helpers.cc index 941f6c830fc2..c1a29cb1f389 100644 --- a/source/differentiation/ad/ad_helpers.cc +++ b/source/differentiation/ad/ad_helpers.cc @@ -377,7 +377,7 @@ namespace Differentiation Assert(is_registered_tape(tape_index), ExcMessage("Tape number not registered")); - TapedDrivers::print_tape_stats(tape_index, stream); + this->taped_driver.print_tape_stats(tape_index, stream); } @@ -829,8 +829,8 @@ namespace Differentiation ExcDimensionMismatch(this->independent_variable_values.size(), this->n_independent_variables())); - return TapedDrivers::value( - this->active_tape_index(), this->independent_variable_values); + return this->taped_driver.value(this->active_tape_index(), + this->independent_variable_values); } else { @@ -840,8 +840,7 @@ namespace Differentiation this->n_independent_variables(), ExcInternalError()); - return TapelessDrivers::value( - this->dependent_variables); + return this->tapeless_driver.value(this->dependent_variables); } } @@ -891,10 +890,9 @@ namespace Differentiation ExcDimensionMismatch(this->independent_variable_values.size(), this->n_independent_variables())); - TapedDrivers::gradient( - this->active_tape_index(), - this->independent_variable_values, - gradient); + this->taped_driver.gradient(this->active_tape_index(), + this->independent_variable_values, + gradient); } else { @@ -904,8 +902,9 @@ namespace Differentiation this->n_independent_variables(), ExcInternalError()); - TapelessDrivers::gradient( - this->independent_variables, this->dependent_variables, gradient); + this->tapeless_driver.gradient(this->independent_variables, + this->dependent_variables, + gradient); } } @@ -961,10 +960,9 @@ namespace Differentiation ExcDimensionMismatch(this->independent_variable_values.size(), this->n_independent_variables())); - TapedDrivers::hessian( - this->active_tape_index(), - this->independent_variable_values, - hessian); + this->taped_driver.hessian(this->active_tape_index(), + this->independent_variable_values, + hessian); } else { @@ -973,8 +971,10 @@ namespace Differentiation Assert(this->independent_variables.size() == this->n_independent_variables(), ExcInternalError()); - TapelessDrivers::hessian( - this->independent_variables, this->dependent_variables, hessian); + + this->tapeless_driver.hessian(this->independent_variables, + this->dependent_variables, + hessian); } } @@ -1048,18 +1048,16 @@ namespace Differentiation ExcDimensionMismatch(this->independent_variable_values.size(), this->n_independent_variables())); - TapedDrivers::values( - this->active_tape_index(), - this->n_dependent_variables(), - this->independent_variable_values, - values); + this->taped_driver.values(this->active_tape_index(), + this->n_dependent_variables(), + this->independent_variable_values, + values); } else { Assert(ADNumberTraits::is_tapeless == true, ExcInternalError()); - TapelessDrivers::values( - this->dependent_variables, values); + this->tapeless_driver.values(this->dependent_variables, values); } } @@ -1106,11 +1104,10 @@ namespace Differentiation ExcDimensionMismatch(this->independent_variable_values.size(), this->n_independent_variables())); - TapedDrivers::jacobian( - this->active_tape_index(), - this->n_dependent_variables(), - this->independent_variable_values, - jacobian); + this->taped_driver.jacobian(this->active_tape_index(), + this->n_dependent_variables(), + this->independent_variable_values, + jacobian); } else { @@ -1119,8 +1116,10 @@ namespace Differentiation Assert(this->independent_variables.size() == this->n_independent_variables(), ExcInternalError()); - TapelessDrivers::jacobian( - this->independent_variables, this->dependent_variables, jacobian); + + this->tapeless_driver.jacobian(this->independent_variables, + this->dependent_variables, + jacobian); } } From b8b6915b2504ecf5b2166c36d47cb0069fb33e60 Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Thu, 6 Dec 2018 14:40:50 +0100 Subject: [PATCH 002/507] Expose AD driver methods via ADHelper bass class. Further features provided by the drivers are exposed through the base helper class. --- .../deal.II/differentiation/ad/ad_helpers.h | 44 +++++++++++++++++++ source/differentiation/ad/ad_helpers.cc | 38 ++++++++++++++++ 2 files changed, 82 insertions(+) diff --git a/include/deal.II/differentiation/ad/ad_helpers.h b/include/deal.II/differentiation/ad/ad_helpers.h index 7aad5de7edab..4d8bcc78a325 100644 --- a/include/deal.II/differentiation/ad/ad_helpers.h +++ b/include/deal.II/differentiation/ad/ad_helpers.h @@ -478,6 +478,50 @@ namespace Differentiation activate_recorded_tape( const typename Types::tape_index tape_index); + /** + * Return a flag that, when true, indicates that the + * retaping of the dependent function is necessary for a reliable + * computation to be performed on a tape with the given @p tape_index. + * This may be necessary a sign comparison within branched operations + * yields different results to those computed at the original tape + * evaluation point. + * + * For the output of this function to be meaningful, it must be called + * after the activate_recorded_tape() is called and the new evaluation + * point for the tape (i.e. values of the independent variables) have + * been set and subsequently used (i.e. in the determination of the values + * or derivatives of the dependent variables). + */ + bool + recorded_tape_requires_retaping( + const typename Types::tape_index tape_index) const; + + /** + * Return a flag that, when true, indicates that the + * retaping of the dependent function is necessary for a reliable + * computation to be performed on the avtive tape. This may be necessary a + * sign comparison within branched operations yields different results to + * those computed at the original tape evaluation point. + * + * For the output of this function to be meaningful, it must be called + * after the activate_recorded_tape() is called and the new evaluation + * point for the tape (i.e. values of the independent variables) have + * been set and subsequently used (i.e. in the determination of the values + * or derivatives of the dependent variables). + */ + bool + active_tape_requires_retaping() const; + + /** + * Clears and removes the currently active tape. + * + * This is typically only necessary when branch switching is detected on + * the original tape at evaluation point. This state can be checked using + * the active_tape_requires_retaping() function. + */ + void + clear_active_tape(); + //@} protected: diff --git a/source/differentiation/ad/ad_helpers.cc b/source/differentiation/ad/ad_helpers.cc index c1a29cb1f389..d8a7866ba377 100644 --- a/source/differentiation/ad/ad_helpers.cc +++ b/source/differentiation/ad/ad_helpers.cc @@ -475,6 +475,44 @@ namespace Differentiation + template + bool + ADHelperBase::recorded_tape_requires_retaping( + const typename Types::tape_index tape_index) const + { + if (ADNumberTraits::is_tapeless == true) + return false; + + return taped_driver.requires_retaping(tape_index); + } + + + + template + bool + ADHelperBase::active_tape_requires_retaping() + const + { + if (ADNumberTraits::is_tapeless == true) + return false; + + return taped_driver.last_action_requires_retaping(); + } + + + + template + void + ADHelperBase::clear_active_tape() + { + if (ADNumberTraits::is_tapeless == true) + return; + + taped_driver.remove_tape(taped_driver.active_tape_index()); + } + + + template void ADHelperBase::activate_tape( From c7c946aac00869577af146fa79516f8bbcd565b0 Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Thu, 6 Dec 2018 14:41:28 +0100 Subject: [PATCH 003/507] Improve some error messages in ADHelper classes. --- source/differentiation/ad/ad_helpers.cc | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/source/differentiation/ad/ad_helpers.cc b/source/differentiation/ad/ad_helpers.cc index d8a7866ba377..e259ab6019c6 100644 --- a/source/differentiation/ad/ad_helpers.cc +++ b/source/differentiation/ad/ad_helpers.cc @@ -752,7 +752,8 @@ namespace Differentiation this->finalize_sensitive_independent_variables(); Assert(this->independent_variables.size() == this->n_independent_variables(), - ExcInternalError()); + ExcDimensionMismatch(this->independent_variables.size(), + this->n_independent_variables())); return this->independent_variables; } @@ -876,7 +877,8 @@ namespace Differentiation ExcInternalError()); Assert(this->independent_variables.size() == this->n_independent_variables(), - ExcInternalError()); + ExcDimensionMismatch(this->independent_variables.size(), + this->n_independent_variables())); return this->tapeless_driver.value(this->dependent_variables); } @@ -938,7 +940,8 @@ namespace Differentiation ExcInternalError()); Assert(this->independent_variables.size() == this->n_independent_variables(), - ExcInternalError()); + ExcDimensionMismatch(this->independent_variables.size(), + this->n_independent_variables())); this->tapeless_driver.gradient(this->independent_variables, this->dependent_variables, @@ -1008,7 +1011,8 @@ namespace Differentiation ExcInternalError()); Assert(this->independent_variables.size() == this->n_independent_variables(), - ExcInternalError()); + ExcDimensionMismatch(this->independent_variables.size(), + this->n_independent_variables())); this->tapeless_driver.hessian(this->independent_variables, this->dependent_variables, @@ -1153,7 +1157,8 @@ namespace Differentiation ExcInternalError()); Assert(this->independent_variables.size() == this->n_independent_variables(), - ExcInternalError()); + ExcDimensionMismatch(this->independent_variables.size(), + this->n_independent_variables())); this->tapeless_driver.jacobian(this->independent_variables, this->dependent_variables, From aa2b68ee540a3d8ab8223e901590601eca7e409e Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Thu, 6 Dec 2018 14:41:52 +0100 Subject: [PATCH 004/507] Improve some documentation in ADHelper classes. --- include/deal.II/differentiation/ad/ad_helpers.h | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/include/deal.II/differentiation/ad/ad_helpers.h b/include/deal.II/differentiation/ad/ad_helpers.h index 4d8bcc78a325..c8bd16a31b7d 100644 --- a/include/deal.II/differentiation/ad/ad_helpers.h +++ b/include/deal.II/differentiation/ad/ad_helpers.h @@ -949,7 +949,7 @@ namespace Differentiation * Depending on the selected @p ADNumberTypeCode, this may or may not * correspond with the @p ScalarType prescribed as a template argument. * - * @note If the keep flag has been set when + * @note If the @p keep_independent_values flag has been set when * ADHelperBase::start_recording_operations() is called then the tape is * immediately usable after creation, and the values of the independent * variables set by register_dof_values() are those at which the function @@ -969,7 +969,7 @@ namespace Differentiation * which to extract the local degree of freedom values. This would * typically obtained by calling cell->get_dof_indices(). * - * @note If the keep flag has been set when + * @note If the @p keep_independent_values flag has been set when * ADHelperBase::start_recording_operations() is called then the tape is * immediately usable after creation, and the values of the independent * variables set by register_dof_values() are those at which the function From 9387ce1dca1bd41683b1f7d89cc7e096fa6a4b39 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Sat, 8 Dec 2018 12:11:03 +0100 Subject: [PATCH 005/507] Fix compiling and avoid warnings in tests --- source/differentiation/ad/ad_drivers.cc | 12 +++++++----- 1 file changed, 7 insertions(+), 5 deletions(-) diff --git a/source/differentiation/ad/ad_drivers.cc b/source/differentiation/ad/ad_drivers.cc index a0447c8d7702..3d29e40a5bdd 100644 --- a/source/differentiation/ad/ad_drivers.cc +++ b/source/differentiation/ad/ad_drivers.cc @@ -893,8 +893,7 @@ namespace Differentiation double, typename std::enable_if::type_code == NumberTypes::adolc_taped>::type>:: - is_registered_tape( - const typename Types::tape_index tape_index) const + is_registered_tape(const typename Types::tape_index) const { AssertThrow(false, ExcRequiresADOLC()); return false; @@ -943,6 +942,8 @@ namespace Differentiation AssertThrow(false, ExcRequiresADOLC()); } + + template std::vector::tape_index> TapedDrivers< ADNumberType, @@ -1028,8 +1029,7 @@ namespace Differentiation double, typename std::enable_if< ADNumberTraits::type_code == - NumberTypes::adolc_taped>::type>::print(std::ostream &stream) - const + NumberTypes::adolc_taped>::type>::print(std::ostream &) const { AssertThrow(false, ExcRequiresADOLC()); } @@ -1050,7 +1050,7 @@ namespace Differentiation template - TapedDrivers< + typename TapedDrivers< ADNumberType, double, typename std::enable_if::type_code == @@ -1082,6 +1082,8 @@ namespace Differentiation AssertThrow(false, ExcRequiresADOLC()); } + + template void TapedDrivers< ADNumberType, From e2ae49cbf79e256343543906b09a2d6c1a8890a2 Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Tue, 22 Jan 2019 16:17:45 +0100 Subject: [PATCH 006/507] Improve documentation in AD drivers header --- .../deal.II/differentiation/ad/ad_drivers.h | 48 ++++++++++++++++++- 1 file changed, 46 insertions(+), 2 deletions(-) diff --git a/include/deal.II/differentiation/ad/ad_drivers.h b/include/deal.II/differentiation/ad/ad_drivers.h index 5af046665bf6..7f76fe846134 100644 --- a/include/deal.II/differentiation/ad/ad_drivers.h +++ b/include/deal.II/differentiation/ad/ad_drivers.h @@ -279,10 +279,31 @@ namespace Differentiation * Return a flag that, when true, indicates that the retaping * of the dependent function for the chosen @p tape_index is necessary for * a reliable computation to be performed. - * This may be necessary a sign comparison within branched operations + * This may be necessary if a sign comparison within branched operations * yields different results to those computed at the original tape * evaluation point. * + * This issue, known as "branch switching", can be clarified by means of + * a trivial example: + * @code + * ADNumberType func (ADNumberType x, ADNumberType y, ADNumberType z) + * { + * if (x < y) + * return y; + * else + * return x*z; + * } + * @endcode + * During taping, the conditional statement may be either true or + * false, and the result (with its sensitivities) returned by + * this function. For some other evaluation of the tape (i.e. for some + * different + * inputs @p x and @p y, the other branch of the conditional check may be + * chosen. The result of following this code path has not been recorded on + * the tape, and therefore cannot be evaluated. In such a case, it is + * therefore necessary to re-record the tape at the new evaluation point + * in order to resolve the new code branch. + * * @note The chosen tape index must be greater than * Numbers::invalid_tape_index and less than * Numbers::max_tape_index. @@ -295,9 +316,30 @@ namespace Differentiation * Return a flag that, when true, indicates that the retaping * of the dependent function is necessary for a reliable computation to be * performed on the active tape. - * This may be necessary a sign comparison within branched operations + * This may be necessary if a sign comparison within branched operations * yields different results to those computed at the original tape * evaluation point. + * + * This issue, known as "branch switching", can be clarified by means of + * a trivial example: + * @code + * ADNumberType func (ADNumberType x, ADNumberType y, ADNumberType z) + * { + * if (x < y) + * return y; + * else + * return x*z; + * } + * @endcode + * During taping, the conditional statement may be either true or + * false, and the result (with its sensitivities) returned by + * this function. For some other evaluation of the tape (i.e. for some + * different + * inputs @p x and @p y, the other branch of the conditional check may be + * chosen. The result of following this code path has not been recorded on + * the tape, and therefore cannot be evaluated. In such a case, it is + * therefore necessary to re-record the tape at the new evaluation point + * in order to resolve the new code branch. */ bool last_action_requires_retaping() const; @@ -869,6 +911,8 @@ namespace Differentiation * * When the @p status variable takes a negative value, retaping of the dependent * function is necessary for a reliable computation to be performed. + * This status can be queried through the requires_retaping() and + * last_action_requires_retaping() functions. */ mutable std::map::tape_index, int> status; From 79c6959019e0978510b49f8ef7aa6a90bbbf3ee2 Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Tue, 22 Jan 2019 16:18:57 +0100 Subject: [PATCH 007/507] Remove unnecessary temporary object when copying a vector --- source/differentiation/ad/ad_drivers.cc | 16 +++++++--------- 1 file changed, 7 insertions(+), 9 deletions(-) diff --git a/source/differentiation/ad/ad_drivers.cc b/source/differentiation/ad/ad_drivers.cc index 3d29e40a5bdd..ff0a9637cf40 100644 --- a/source/differentiation/ad/ad_drivers.cc +++ b/source/differentiation/ad/ad_drivers.cc @@ -476,17 +476,13 @@ namespace Differentiation { // We've chosen to use unsigned shorts for the tape // index type (a safety precaution) so we need to - // perform a conversion betwwen ADOL-C's native tape + // perform a conversion between ADOL-C's native tape // index type and that chosen by us. std::vector registered_tape_indices_s; cachedTraceTags(registered_tape_indices_s); - std::vector::tape_index> - registered_tape_indices(registered_tape_indices_s.size()); - std::copy(registered_tape_indices_s.begin(), - registered_tape_indices_s.end(), - registered_tape_indices.begin()); - return registered_tape_indices; + return std::vector::tape_index>( + registered_tape_indices_s.begin(), registered_tape_indices_s.end()); } @@ -537,8 +533,10 @@ namespace Differentiation // See ADOL-C manual section 1.7 and comments in last paragraph of // section 3.1 - Assert(status_tape < 4 && status_tape >= -2, - ExcIndexRange(status_tape, -2, 4)); + Assert( + status_tape < 4 && status_tape >= -2, + ExcMessage( + "The tape status is not within the range specified within the ADOL-C documentation.")); return (status_tape < 0); } From 7aceecd2706833c12f194bd2332ee9595f76a415 Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Tue, 22 Jan 2019 16:19:15 +0100 Subject: [PATCH 008/507] Improve documentation to AD helpers header. --- .../deal.II/differentiation/ad/ad_helpers.h | 55 +++++++++++++++++-- 1 file changed, 49 insertions(+), 6 deletions(-) diff --git a/include/deal.II/differentiation/ad/ad_helpers.h b/include/deal.II/differentiation/ad/ad_helpers.h index c8bd16a31b7d..ac716dfd94c2 100644 --- a/include/deal.II/differentiation/ad/ad_helpers.h +++ b/include/deal.II/differentiation/ad/ad_helpers.h @@ -482,12 +482,33 @@ namespace Differentiation * Return a flag that, when true, indicates that the * retaping of the dependent function is necessary for a reliable * computation to be performed on a tape with the given @p tape_index. - * This may be necessary a sign comparison within branched operations + * This may be necessary if a sign comparison within branched operations * yields different results to those computed at the original tape * evaluation point. * + * This issue, known as "branch switching", can be clarified by means of + * a trivial example: + * @code + * ADNumberType func (ADNumberType x, ADNumberType y, ADNumberType z) + * { + * if (x < y) + * return y; + * else + * return x*z; + * } + * @endcode + * During taping, the conditional statement may be either true or + * false, and the result (with its sensitivities) returned by + * this function. For some other evaluation of the tape (i.e. for some + * different + * inputs @p x and @p y, the other branch of the conditional check may be + * chosen. The result of following this code path has not been recorded on + * the tape, and therefore cannot be evaluated. In such a case, it is + * therefore necessary to re-record the tape at the new evaluation point + * in order to resolve the new code branch. + * * For the output of this function to be meaningful, it must be called - * after the activate_recorded_tape() is called and the new evaluation + * after activate_recorded_tape() is called and the new evaluation * point for the tape (i.e. values of the independent variables) have * been set and subsequently used (i.e. in the determination of the values * or derivatives of the dependent variables). @@ -499,12 +520,34 @@ namespace Differentiation /** * Return a flag that, when true, indicates that the * retaping of the dependent function is necessary for a reliable - * computation to be performed on the avtive tape. This may be necessary a - * sign comparison within branched operations yields different results to - * those computed at the original tape evaluation point. + * computation to be performed on the active tape. + * This may be necessary if a sign comparison within branched operations + * yields different results to those computed at the original tape + * evaluation point. + * + * This issue, known as "branch switching", can be clarified by means of + * a trivial example: + * @code + * ADNumberType func (ADNumberType x, ADNumberType y, ADNumberType z) + * { + * if (x < y) + * return y; + * else + * return x*z; + * } + * @endcode + * During taping, the conditional statement may be either true or + * false, and the result (with its sensitivities) returned by + * this function. For some other evaluation of the tape (i.e. for some + * different + * inputs @p x and @p y, the other branch of the conditional check may be + * chosen. The result of following this code path has not been recorded on + * the tape, and therefore cannot be evaluated. In such a case, it is + * therefore necessary to re-record the tape at the new evaluation point + * in order to resolve the new code branch. * * For the output of this function to be meaningful, it must be called - * after the activate_recorded_tape() is called and the new evaluation + * after activate_recorded_tape() is called and the new evaluation * point for the tape (i.e. values of the independent variables) have * been set and subsequently used (i.e. in the determination of the values * or derivatives of the dependent variables). From 1caf7e71b5f353520772936eeb9fe4ec3bdea2e8 Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Tue, 22 Jan 2019 16:20:03 +0100 Subject: [PATCH 009/507] Fix a typo in documentation for ADHelperResidualLinearization class --- include/deal.II/differentiation/ad/ad_helpers.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/include/deal.II/differentiation/ad/ad_helpers.h b/include/deal.II/differentiation/ad/ad_helpers.h index ac716dfd94c2..f5cb753260e4 100644 --- a/include/deal.II/differentiation/ad/ad_helpers.h +++ b/include/deal.II/differentiation/ad/ad_helpers.h @@ -1417,7 +1417,7 @@ namespace Differentiation * // must refer to one of these types. See the example for the * // ADHelperEnergyFunctional for details on how to extend * // support to taped AD numbers. - * using ADHelper = AD::ADHelperEnergyFunctional<...>; + * using ADHelper = AD::ADHelperResidualLinearization<...>; * using ADNumberType = typename ADHelper::ad_type; * * // Create and initialize an instance of the helper class. From 877fb0179735fe7c2258a3c0dbd970d9115f1fc3 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Thu, 24 Jan 2019 23:41:35 +0100 Subject: [PATCH 010/507] Parse boundary_ids in GMSH-4 format --- source/grid/grid_in.cc | 94 ++++++++++++++++++++++++++++++++++-------- 1 file changed, 77 insertions(+), 17 deletions(-) diff --git a/source/grid/grid_in.cc b/source/grid/grid_in.cc index c00da148814e..87fe841d9c03 100644 --- a/source/grid/grid_in.cc +++ b/source/grid/grid_in.cc @@ -1404,10 +1404,11 @@ GridIn::read_msh(std::istream &in) Assert(tria != nullptr, ExcNoTriangulationSelected()); AssertThrow(in, ExcIO()); - unsigned int n_vertices; - unsigned int n_cells; - unsigned int dummy; - std::string line; + unsigned int n_vertices; + unsigned int n_cells; + unsigned int dummy; + std::string line; + std::array, 4> tag_maps; in >> line; @@ -1451,14 +1452,73 @@ GridIn::read_msh(std::istream &in) in >> line; } - // if the next block is of kind $Entities, ignore it + // if the next block is of kind $Entities, parse it if (line == "$Entities") { - do + unsigned long numPoints, numCurves, numSurfaces, numVolumes, + numPhysicals; + int tag, physicalTag; + double boxMinX, boxMinY, boxMinZ, boxMaxX, boxMaxY, boxMaxZ; + + in >> numPoints >> numCurves >> numSurfaces >> numVolumes; + for (unsigned int i = 0; i < numPoints; ++i) { - in >> line; + // parse point ids + in >> tag >> boxMinX >> boxMinY >> boxMinZ >> boxMaxX >> + boxMaxY >> boxMaxZ >> numPhysicals; + AssertThrow(numPhysicals < 2, + ExcMessage("More than one tag is not supported!")); + for (unsigned int j = 0; j < numPhysicals; ++j) + in >> physicalTag; + tag_maps[0][tag] = (numPhysicals == 0) ? 0 : physicalTag; + } + for (unsigned int i = 0; i < numCurves; ++i) + { + // parse curve ids + in >> tag >> boxMinX >> boxMinY >> boxMinZ >> boxMaxX >> + boxMaxY >> boxMaxZ >> numPhysicals; + AssertThrow(numPhysicals < 2, + ExcMessage("More than one tag is not supported!")); + for (unsigned int j = 0; j < numPhysicals; ++j) + in >> physicalTag; + tag_maps[1][tag] = (numPhysicals == 0) ? 0 : physicalTag; + in >> numPoints; + for (unsigned int j = 0; j < numPoints; ++j) + in >> tag; + } + + for (unsigned int i = 0; i < numSurfaces; ++i) + { + // parse surface ids + in >> tag >> boxMinX >> boxMinY >> boxMinZ >> boxMaxX >> + boxMaxY >> boxMaxZ >> numPhysicals; + AssertThrow(numPhysicals < 2, + ExcMessage("More than one tag is not supported!")); + for (unsigned int j = 0; j < numPhysicals; ++j) + in >> physicalTag; + tag_maps[2][tag] = (numPhysicals == 0) ? 0 : physicalTag; + in >> numCurves; + for (unsigned int j = 0; j < numCurves; ++j) + in >> tag; + } + for (unsigned int i = 0; i < numVolumes; ++i) + { + // parse volume ids + in >> tag >> boxMinX >> boxMinY >> boxMinZ >> boxMaxX >> + boxMaxY >> boxMaxZ >> numPhysicals; + AssertThrow(numPhysicals < 2, + ExcMessage("More than one tag is not supported!")); + for (unsigned int j = 0; j < numPhysicals; ++j) + in >> physicalTag; + tag_maps[3][tag] = (numPhysicals == 0) ? 0 : physicalTag; + in >> numSurfaces; + for (unsigned int j = 0; j < numSurfaces; ++j) + in >> tag; } - while (line != "$EndEntities"); + std::cout << line << std::endl; + in >> line; + std::cout << line << std::endl; + AssertThrow(line == "$EndEntities", ExcInvalidGMSHInput(line)); in >> line; } @@ -1497,20 +1557,19 @@ GridIn::read_msh(std::istream &in) unsigned int global_vertex = 0; for (int entity_block = 0; entity_block < n_entity_blocks; ++entity_block) { - int tagEntity; - int dimEntity; int parametric; unsigned long numNodes; if (gmsh_file_format < 4) { - tagEntity = 0; - dimEntity = 0; numNodes = n_vertices; parametric = 0; } else - in >> tagEntity >> dimEntity >> parametric >> numNodes; + { + int tagEntity, dimEntity; + in >> tagEntity >> dimEntity >> parametric >> numNodes; + } for (unsigned long vertex_per_entity = 0; vertex_per_entity < numNodes; ++vertex_per_entity, ++global_vertex) { @@ -1574,20 +1633,21 @@ GridIn::read_msh(std::istream &in) for (int entity_block = 0; entity_block < n_entity_blocks; ++entity_block) { unsigned int material_id; - int dimEntity; unsigned long numElements; int cell_type; if (gmsh_file_format < 4) { material_id = 0; - dimEntity = 0; cell_type = 0; numElements = n_cells; } else - in >> material_id >> dimEntity >> cell_type >> numElements; - + { + int tagEntity, dimEntity; + in >> tagEntity >> dimEntity >> cell_type >> numElements; + material_id = tag_maps[dimEntity][tagEntity]; + } for (unsigned int cell_per_entity = 0; cell_per_entity < numElements; ++cell_per_entity, ++global_cell) { From 5d4ae1a463fef3661961903702d3a71f9f44c5cd Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Fri, 25 Jan 2019 15:20:49 +0100 Subject: [PATCH 011/507] Add GMSH-4 tests --- tests/grid/grid_in_gmsh_01_v4.cc | 136 + tests/grid/grid_in_gmsh_01_v4.output | 16 + tests/grid/grid_in_msh_02_13_v4.cc | 75 + tests/grid/grid_in_msh_02_13_v4.output | 3 + tests/grid/grid_in_msh_02_v4.cc | 70 + tests/grid/grid_in_msh_02_v4.output | 3 + tests/grid/grid_in_msh_03_v4.cc | 69 + tests/grid/grid_in_msh_03_v4.output | 569 + tests/grid/grid_in_msh_03_v4/mesh.msh | 213 + tests/grid/grid_in_msh_v4.cc | 63 + tests/grid/grid_in_msh_v4.output | 1262 ++ tests/grid/grid_in_msh_v4/mesh.msh | 501 + tests/grid/grid_in_msh_version_4.cc | 159 + tests/grid/grid_in_msh_version_4.output | 7 + tests/grid/grid_in_msh_version_4/hole81.msh | 205 + tests/grid/grid_in_msh_version_4/hole8170.msh | 16634 ++++++++++++++++ tests/grid/grids/grid_in_msh_01.2d.v4.msh | 36 + tests/grid/grids/grid_in_msh_01.2da.v4.msh | 904 + tests/grid/grids/grid_in_msh_01.3d.v4.msh | 48 + tests/grid/grids/grid_in_msh_01.3d_neg.v4.msh | 48 + tests/grid/grids/grid_in_msh_01.3da.v4.msh | 1218 ++ tests/grid/grids/grid_in_msh_02_v4.msh | 44 + 22 files changed, 22283 insertions(+) create mode 100644 tests/grid/grid_in_gmsh_01_v4.cc create mode 100644 tests/grid/grid_in_gmsh_01_v4.output create mode 100644 tests/grid/grid_in_msh_02_13_v4.cc create mode 100644 tests/grid/grid_in_msh_02_13_v4.output create mode 100644 tests/grid/grid_in_msh_02_v4.cc create mode 100644 tests/grid/grid_in_msh_02_v4.output create mode 100644 tests/grid/grid_in_msh_03_v4.cc create mode 100644 tests/grid/grid_in_msh_03_v4.output create mode 100644 tests/grid/grid_in_msh_03_v4/mesh.msh create mode 100644 tests/grid/grid_in_msh_v4.cc create mode 100644 tests/grid/grid_in_msh_v4.output create mode 100644 tests/grid/grid_in_msh_v4/mesh.msh create mode 100644 tests/grid/grid_in_msh_version_4.cc create mode 100644 tests/grid/grid_in_msh_version_4.output create mode 100644 tests/grid/grid_in_msh_version_4/hole81.msh create mode 100644 tests/grid/grid_in_msh_version_4/hole8170.msh create mode 100644 tests/grid/grids/grid_in_msh_01.2d.v4.msh create mode 100644 tests/grid/grids/grid_in_msh_01.2da.v4.msh create mode 100644 tests/grid/grids/grid_in_msh_01.3d.v4.msh create mode 100644 tests/grid/grids/grid_in_msh_01.3d_neg.v4.msh create mode 100644 tests/grid/grids/grid_in_msh_01.3da.v4.msh create mode 100644 tests/grid/grids/grid_in_msh_02_v4.msh diff --git a/tests/grid/grid_in_gmsh_01_v4.cc b/tests/grid/grid_in_gmsh_01_v4.cc new file mode 100644 index 000000000000..1caeb40fa525 --- /dev/null +++ b/tests/grid/grid_in_gmsh_01_v4.cc @@ -0,0 +1,136 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2004 - 2017 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + + +// check whether we can read in with the gmsh format and obtain the same results +// for the GMSH-2 format and the GMSH-4 format + +#include +#include +#include +#include +#include + +#include "../tests.h" + + + +template +void +gmsh_grid(const char *name_v2, const char *name_v4) +{ + Triangulation tria_v2; + { + GridIn grid_in; + grid_in.attach_triangulation(tria_v2); + std::ifstream input_file(name_v2); + grid_in.read_msh(input_file); + } + + Triangulation tria_v4; + { + GridIn grid_in; + grid_in.attach_triangulation(tria_v4); + std::ifstream input_file(name_v4); + grid_in.read_msh(input_file); + } + + // The vertex index is different between the meshes parsed from the GMSH-2 and + // the GMSH-4 fil but all other information should match. + AssertThrow(tria_v2.n_active_cells() == tria_v4.n_active_cells(), + ExcInternalError()); + deallog << " " << tria_v2.n_active_cells() << " active cells" << std::endl; + + auto cell_v2 = tria_v2.begin_active(); + auto cell_v4 = tria_v4.begin_active(); + const auto end_v2 = tria_v2.end(); + for (; cell_v2 != end_v2; ++cell_v2, ++cell_v4) + { + AssertThrow(cell_v2->material_id() == cell_v4->material_id(), + ExcInternalError()); + for (unsigned int i = 0; i < GeometryInfo::vertices_per_cell; ++i) + { + AssertThrow((cell_v2->vertex(i) - cell_v4->vertex(i)).norm() < 1.e-10, + ExcInternalError()); + } + for (unsigned int i = 0; i < GeometryInfo::faces_per_cell; ++i) + { + AssertThrow(cell_v2->face(i)->boundary_id() == + cell_v4->face(i)->boundary_id(), + ExcInternalError()); + } + for (unsigned int i = 0; i < GeometryInfo::lines_per_cell; ++i) + { + AssertThrow(cell_v2->line(i)->boundary_id() == + cell_v4->line(i)->boundary_id(), + ExcInternalError()); + } + } + deallog << " OK" << std::endl; +} + + +int +main() +{ + initlog(); + + try + { + deallog << "/grid_in_msh_01.2d.v4.msh" << std::endl; + gmsh_grid<2>(SOURCE_DIR "/grids/grid_in_msh_01.2d.msh", + SOURCE_DIR "/grids/grid_in_msh_01.2d.v4.msh"); + deallog << "/grid_in_msh_01.2da.v4.msh" << std::endl; + gmsh_grid<2>(SOURCE_DIR "/grids/grid_in_msh_01.2da.msh", + SOURCE_DIR "/grids/grid_in_msh_01.2da.v4.msh"); + deallog << "/grid_in_msh_01.3d.v4.msh" << std::endl; + gmsh_grid<3>(SOURCE_DIR "/grids/grid_in_msh_01.3d.msh", + SOURCE_DIR "/grids/grid_in_msh_01.3d.v4.msh"); + deallog << "/grid_in_msh_01.3da.v4.msh" << std::endl; + gmsh_grid<3>(SOURCE_DIR "/grids/grid_in_msh_01.3da.msh", + SOURCE_DIR "/grids/grid_in_msh_01.3da.v4.msh"); + deallog << "/grid_in_msh_01.3d_neg.v4.msh" << std::endl; + gmsh_grid<3>(SOURCE_DIR "/grids/grid_in_msh_01.3d_neg.msh", + SOURCE_DIR "/grids/grid_in_msh_01.3d_neg.v4.msh"); + } + catch (std::exception &exc) + { + deallog << std::endl + << std::endl + << "----------------------------------------------------" + << std::endl; + deallog << "Exception on processing: " << std::endl + << exc.what() << std::endl + << "Aborting!" << std::endl + << "----------------------------------------------------" + << std::endl; + return 1; + } + catch (...) + { + deallog << std::endl + << std::endl + << "----------------------------------------------------" + << std::endl; + deallog << "Unknown exception!" << std::endl + << "Aborting!" << std::endl + << "----------------------------------------------------" + << std::endl; + return 1; + }; + + return 0; +} diff --git a/tests/grid/grid_in_gmsh_01_v4.output b/tests/grid/grid_in_gmsh_01_v4.output new file mode 100644 index 000000000000..861a472dcdf5 --- /dev/null +++ b/tests/grid/grid_in_gmsh_01_v4.output @@ -0,0 +1,16 @@ + +DEAL::/grid_in_msh_01.2d.v4.msh +DEAL:: 1 active cells +DEAL:: OK +DEAL::/grid_in_msh_01.2da.v4.msh +DEAL:: 360 active cells +DEAL:: OK +DEAL::/grid_in_msh_01.3d.v4.msh +DEAL:: 1 active cells +DEAL:: OK +DEAL::/grid_in_msh_01.3da.v4.msh +DEAL:: 200 active cells +DEAL:: OK +DEAL::/grid_in_msh_01.3d_neg.v4.msh +DEAL:: 1 active cells +DEAL:: OK diff --git a/tests/grid/grid_in_msh_02_13_v4.cc b/tests/grid/grid_in_msh_02_13_v4.cc new file mode 100644 index 000000000000..3c5c5c12e112 --- /dev/null +++ b/tests/grid/grid_in_msh_02_13_v4.cc @@ -0,0 +1,75 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2002 - 2018 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + +// in 1d, we have to read vertex information to set boundary +// indicators +// +// test case by Jan Strebel +// +// this is a variation of the grid_in_msh_02 testcase, but as in Jan's +// original code snippet, it uses GridIn<1,3> (which wasn't +// instantiated at the time) +// +// This is the same as grid_in_msh_02_13 but uses an input file in GMSH-4 +// format + + +#include + +#include +#include +#include +#include +#include +#include +#include + +#include + +#include "../tests.h" + +void +check_file() +{ + Triangulation<1, 3> tria; + GridIn<1, 3> gi; + gi.attach_triangulation(tria); + std::ifstream in(SOURCE_DIR "/../grid/grids/grid_in_msh_02_v4.msh"); + gi.read_msh(in); + + for (Triangulation<1, 3>::active_cell_iterator cell = tria.begin_active(); + cell != tria.end(); + ++cell) + { + for (unsigned int face = 0; face < 2; ++face) + { + if (cell->at_boundary(face)) + deallog << "vertex " << cell->face_index(face) + << " has boundary indicator " + << (int)cell->face(face)->boundary_id() << std::endl; + } + } +} + + +int +main() +{ + initlog(); + deallog << std::setprecision(2); + + check_file(); +} diff --git a/tests/grid/grid_in_msh_02_13_v4.output b/tests/grid/grid_in_msh_02_13_v4.output new file mode 100644 index 000000000000..2ebba38d85c8 --- /dev/null +++ b/tests/grid/grid_in_msh_02_13_v4.output @@ -0,0 +1,3 @@ + +DEAL::vertex 0 has boundary indicator 10 +DEAL::vertex 1 has boundary indicator 20 diff --git a/tests/grid/grid_in_msh_02_v4.cc b/tests/grid/grid_in_msh_02_v4.cc new file mode 100644 index 000000000000..4b75eec21fae --- /dev/null +++ b/tests/grid/grid_in_msh_02_v4.cc @@ -0,0 +1,70 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2002 - 2018 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + +// in 1d, we have to read vertex information to set boundary +// indicators +// +// test case by Jan Strebel +// +// This is the same as grid_in_msh_02 but uses an input file in GMSH-4 format + + +#include + +#include +#include +#include +#include +#include +#include +#include + +#include + +#include "../tests.h" + +void +check_file() +{ + Triangulation<1> tria; + GridIn<1> gi; + gi.attach_triangulation(tria); + std::ifstream in(SOURCE_DIR "/../grid/grids/grid_in_msh_02_v4.msh"); + gi.read_msh(in); + + for (Triangulation<1>::active_cell_iterator cell = tria.begin_active(); + cell != tria.end(); + ++cell) + { + for (unsigned int face = 0; face < 2; ++face) + { + if (cell->at_boundary(face)) + deallog << "vertex " << cell->face_index(face) + << " has boundary indicator " + << (int)cell->face(face)->boundary_id() << std::endl; + } + } +} + + +int +main() +{ + initlog(); + deallog << std::setprecision(2); + + check_file(); +} diff --git a/tests/grid/grid_in_msh_02_v4.output b/tests/grid/grid_in_msh_02_v4.output new file mode 100644 index 000000000000..2ebba38d85c8 --- /dev/null +++ b/tests/grid/grid_in_msh_02_v4.output @@ -0,0 +1,3 @@ + +DEAL::vertex 0 has boundary indicator 10 +DEAL::vertex 1 has boundary indicator 20 diff --git a/tests/grid/grid_in_msh_03_v4.cc b/tests/grid/grid_in_msh_03_v4.cc new file mode 100644 index 000000000000..b978ada7a9b7 --- /dev/null +++ b/tests/grid/grid_in_msh_03_v4.cc @@ -0,0 +1,69 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2002 - 2018 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + +// read a file in the MSH format used by the GMSH program. this +// particular mesh has type-15 cells (nodes) with more than one +// associated vertex. we failed to read the vertices +// +// This is the same as grid_in_msh_03 but uses an input file in GMSH-4 format + +#include + +#include +#include +#include +#include +#include +#include +#include + +#include + +#include "../tests.h" + +template +void +check_file(const std::string name, typename GridIn::Format format) +{ + Triangulation tria; + GridIn gi; + gi.attach_triangulation(tria); + gi.read(name, format); + std::string source_dir(SOURCE_DIR "/"); + std::string relative_name(name.begin() + source_dir.size(), name.end()); + deallog << relative_name << '\t' << tria.n_vertices() << '\t' + << tria.n_cells() << std::endl; + + GridOut grid_out; + grid_out.write_gnuplot(tria, deallog.get_file_stream()); +} + +void +filename_resolution() +{ + check_file<2>(std::string(SOURCE_DIR "/grid_in_msh_03_v4/mesh"), + GridIn<2>::msh); +} + + +int +main() +{ + initlog(false, std::ios_base::fmtflags()); + deallog.get_file_stream() << std::setprecision(2); + + filename_resolution(); +} diff --git a/tests/grid/grid_in_msh_03_v4.output b/tests/grid/grid_in_msh_03_v4.output new file mode 100644 index 000000000000..0915ff09d954 --- /dev/null +++ b/tests/grid/grid_in_msh_03_v4.output @@ -0,0 +1,569 @@ + +DEAL::grid_in_msh_03_v4/mesh 100 81 +0 0 0 2 +2.2 0 0 2 +2.2 1.1 0 2 +0 1.1 0 2 +0 0 0 2 + + +0 1.1 0 2 +2.2 1.1 0 2 +2.2 2.2 0 2 +0 2.2 0 2 +0 1.1 0 2 + + +0 2.2 0 2 +2.2 2.2 0 2 +2.2 3.3 0 2 +0 3.3 0 2 +0 2.2 0 2 + + +0 3.3 0 2 +2.2 3.3 0 2 +2.2 4.4 0 2 +0 4.4 0 2 +0 3.3 0 2 + + +0 4.4 0 2 +2.2 4.4 0 2 +2.2 5.6 0 2 +0 5.6 0 2 +0 4.4 0 2 + + +0 5.6 0 2 +2.2 5.6 0 2 +2.2 6.7 0 2 +0 6.7 0 2 +0 5.6 0 2 + + +0 6.7 0 2 +2.2 6.7 0 2 +2.2 7.8 0 2 +0 7.8 0 2 +0 6.7 0 2 + + +0 7.8 0 2 +2.2 7.8 0 2 +2.2 8.9 0 2 +0 8.9 0 2 +0 7.8 0 2 + + +0 8.9 0 2 +2.2 8.9 0 2 +2.2 10 0 2 +0 10 0 2 +0 8.9 0 2 + + +2.2 0 0 2 +4.4 0 0 2 +4.4 1.1 0 2 +2.2 1.1 0 2 +2.2 0 0 2 + + +2.2 1.1 0 2 +4.4 1.1 0 2 +4.4 2.2 0 2 +2.2 2.2 0 2 +2.2 1.1 0 2 + + +2.2 2.2 0 2 +4.4 2.2 0 2 +4.4 3.3 0 2 +2.2 3.3 0 2 +2.2 2.2 0 2 + + +2.2 3.3 0 2 +4.4 3.3 0 2 +4.4 4.4 0 2 +2.2 4.4 0 2 +2.2 3.3 0 2 + + +2.2 4.4 0 2 +4.4 4.4 0 2 +4.4 5.6 0 2 +2.2 5.6 0 2 +2.2 4.4 0 2 + + +2.2 5.6 0 2 +4.4 5.6 0 2 +4.4 6.7 0 2 +2.2 6.7 0 2 +2.2 5.6 0 2 + + +2.2 6.7 0 2 +4.4 6.7 0 2 +4.4 7.8 0 2 +2.2 7.8 0 2 +2.2 6.7 0 2 + + +2.2 7.8 0 2 +4.4 7.8 0 2 +4.4 8.9 0 2 +2.2 8.9 0 2 +2.2 7.8 0 2 + + +2.2 8.9 0 2 +4.4 8.9 0 2 +4.4 10 0 2 +2.2 10 0 2 +2.2 8.9 0 2 + + +4.4 0 0 2 +6.7 0 0 2 +6.7 1.1 0 2 +4.4 1.1 0 2 +4.4 0 0 2 + + +4.4 1.1 0 2 +6.7 1.1 0 2 +6.7 2.2 0 2 +4.4 2.2 0 2 +4.4 1.1 0 2 + + +4.4 2.2 0 2 +6.7 2.2 0 2 +6.7 3.3 0 2 +4.4 3.3 0 2 +4.4 2.2 0 2 + + +4.4 3.3 0 2 +6.7 3.3 0 2 +6.7 4.4 0 2 +4.4 4.4 0 2 +4.4 3.3 0 2 + + +4.4 4.4 0 2 +6.7 4.4 0 2 +6.7 5.6 0 2 +4.4 5.6 0 2 +4.4 4.4 0 2 + + +4.4 5.6 0 2 +6.7 5.6 0 2 +6.7 6.7 0 2 +4.4 6.7 0 2 +4.4 5.6 0 2 + + +4.4 6.7 0 2 +6.7 6.7 0 2 +6.7 7.8 0 2 +4.4 7.8 0 2 +4.4 6.7 0 2 + + +4.4 7.8 0 2 +6.7 7.8 0 2 +6.7 8.9 0 2 +4.4 8.9 0 2 +4.4 7.8 0 2 + + +4.4 8.9 0 2 +6.7 8.9 0 2 +6.7 10 0 2 +4.4 10 0 2 +4.4 8.9 0 2 + + +6.7 0 0 2 +8.9 0 0 2 +8.9 1.1 0 2 +6.7 1.1 0 2 +6.7 0 0 2 + + +6.7 1.1 0 2 +8.9 1.1 0 2 +8.9 2.2 0 2 +6.7 2.2 0 2 +6.7 1.1 0 2 + + +6.7 2.2 0 2 +8.9 2.2 0 2 +8.9 3.3 0 2 +6.7 3.3 0 2 +6.7 2.2 0 2 + + +6.7 3.3 0 2 +8.9 3.3 0 2 +8.9 4.4 0 2 +6.7 4.4 0 2 +6.7 3.3 0 2 + + +6.7 4.4 0 2 +8.9 4.4 0 2 +8.9 5.6 0 2 +6.7 5.6 0 2 +6.7 4.4 0 2 + + +6.7 5.6 0 2 +8.9 5.6 0 2 +8.9 6.7 0 2 +6.7 6.7 0 2 +6.7 5.6 0 2 + + +6.7 6.7 0 2 +8.9 6.7 0 2 +8.9 7.8 0 2 +6.7 7.8 0 2 +6.7 6.7 0 2 + + +6.7 7.8 0 2 +8.9 7.8 0 2 +8.9 8.9 0 2 +6.7 8.9 0 2 +6.7 7.8 0 2 + + +6.7 8.9 0 2 +8.9 8.9 0 2 +8.9 10 0 2 +6.7 10 0 2 +6.7 8.9 0 2 + + +8.9 0 0 2 +11 0 0 2 +11 1.1 0 2 +8.9 1.1 0 2 +8.9 0 0 2 + + +8.9 1.1 0 2 +11 1.1 0 2 +11 2.2 0 2 +8.9 2.2 0 2 +8.9 1.1 0 2 + + +8.9 2.2 0 2 +11 2.2 0 2 +11 3.3 0 2 +8.9 3.3 0 2 +8.9 2.2 0 2 + + +8.9 3.3 0 2 +11 3.3 0 2 +11 4.4 0 2 +8.9 4.4 0 2 +8.9 3.3 0 2 + + +8.9 4.4 0 2 +11 4.4 0 2 +11 5.6 0 2 +8.9 5.6 0 2 +8.9 4.4 0 2 + + +8.9 5.6 0 2 +11 5.6 0 2 +11 6.7 0 2 +8.9 6.7 0 2 +8.9 5.6 0 2 + + +8.9 6.7 0 2 +11 6.7 0 2 +11 7.8 0 2 +8.9 7.8 0 2 +8.9 6.7 0 2 + + +8.9 7.8 0 2 +11 7.8 0 2 +11 8.9 0 2 +8.9 8.9 0 2 +8.9 7.8 0 2 + + +8.9 8.9 0 2 +11 8.9 0 2 +11 10 0 2 +8.9 10 0 2 +8.9 8.9 0 2 + + +11 0 0 2 +13 0 0 2 +13 1.1 0 2 +11 1.1 0 2 +11 0 0 2 + + +11 1.1 0 2 +13 1.1 0 2 +13 2.2 0 2 +11 2.2 0 2 +11 1.1 0 2 + + +11 2.2 0 2 +13 2.2 0 2 +13 3.3 0 2 +11 3.3 0 2 +11 2.2 0 2 + + +11 3.3 0 2 +13 3.3 0 2 +13 4.4 0 2 +11 4.4 0 2 +11 3.3 0 2 + + +11 4.4 0 2 +13 4.4 0 2 +13 5.6 0 2 +11 5.6 0 2 +11 4.4 0 2 + + +11 5.6 0 2 +13 5.6 0 2 +13 6.7 0 2 +11 6.7 0 2 +11 5.6 0 2 + + +11 6.7 0 2 +13 6.7 0 2 +13 7.8 0 2 +11 7.8 0 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found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + +// read a file in the MSH format used by the GMSH program +// +// This is the same as grid_in_msh but uses an input file in GMSH-4 format + +#include + +#include +#include +#include +#include +#include +#include +#include + +#include + +#include "../tests.h" + +template +void +check_file(const std::string name, typename GridIn::Format format) +{ + Triangulation tria; + GridIn gi; + gi.attach_triangulation(tria); + gi.read(name, format); + deallog << '\t' << tria.n_vertices() << '\t' << tria.n_cells() << std::endl; + + GridOut grid_out; + grid_out.write_gnuplot(tria, deallog.get_file_stream()); +} + +void +filename_resolution() +{ + check_file<2>(std::string(SOURCE_DIR "/grid_in_msh_v4/mesh"), GridIn<2>::msh); +} + + +int +main() +{ + initlog(); + deallog.get_file_stream() << std::setprecision(2); + + filename_resolution(); +} diff 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General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + +// read a file in the MSH format used by the GMSH program. +// and test that files in GMSH-2 format and in GMSH-4 format produce the same +// result. + +#include + +#include +#include +#include +#include +#include +#include +#include + +#include + +#include "../tests.h" + +template +struct PointComparator +{ + bool + operator()(const Point &lhs, const Point &rhs) const + { + double downstream_size = 0; + double weight = 1.; + for (unsigned int d = 0; d < dim; ++d) + { + downstream_size += (rhs[d] - lhs[d]) * weight; + weight *= 1e-5; + } + if (downstream_size < 0) + return false; + else if (downstream_size > 0) + return true; + else + { + for (unsigned int d = 0; d < dim; ++d) + { + if (lhs[d] == rhs[d]) + continue; + return lhs[d] < rhs[d]; + } + return false; + } + } +}; + + +template +void +gmsh_grid(const char *name_v2, const char *name_v4) +{ + Triangulation tria_v2; + { + GridIn grid_in; + grid_in.attach_triangulation(tria_v2); + std::ifstream input_file(name_v2); + grid_in.read_msh(input_file); + } + + Triangulation tria_v4; + { + GridIn grid_in; + grid_in.attach_triangulation(tria_v4); + std::ifstream input_file(name_v4); + grid_in.read_msh(input_file); + } + + AssertThrow(tria_v2.n_active_cells() == tria_v4.n_active_cells(), + ExcInternalError()); + deallog << " " << tria_v2.n_active_cells() << " active cells" << std::endl; + + // The cells and faces in the two files are in reversed order + // but the vertex index is the same. + auto cell_v2 = tria_v2.begin_active(); + auto cell_v4 = + std::next(tria_v4.begin_active(), tria_v4.n_active_cells() - 1); + const auto end_v2 = tria_v2.end(); + for (; cell_v2 != end_v2; ++cell_v2, --cell_v4) + { + AssertThrow(cell_v2->material_id() == cell_v4->material_id(), + ExcInternalError()); + std::set vertices_v2; + std::set vertices_v4; + for (unsigned int i = 0; i < GeometryInfo::vertices_per_cell; ++i) + { + AssertThrow((tria_v2.get_vertices()[cell_v2->vertex_index(i)] - + tria_v4.get_vertices()[cell_v2->vertex_index(i)]) + .norm() < 1.e-10, + ExcInternalError()); + AssertThrow((tria_v2.get_vertices()[cell_v4->vertex_index(i)] - + tria_v4.get_vertices()[cell_v4->vertex_index(i)]) + .norm() < 1.e-10, + ExcInternalError()); + vertices_v2.insert(cell_v2->vertex_index(i)); + vertices_v4.insert(cell_v4->vertex_index(i)); + } + AssertThrow(vertices_v2 == vertices_v4, ExcInternalError()); + std::map, types::boundary_id, PointComparator> faces_v2; + std::map, types::boundary_id, PointComparator> faces_v4; + for (unsigned int i = 0; i < GeometryInfo::faces_per_cell; ++i) + { + faces_v2[cell_v2->face(i)->center()] = + cell_v2->face(i)->boundary_id(); + faces_v4[cell_v4->face(i)->center()] = + cell_v4->face(i)->boundary_id(); + } + AssertThrow(faces_v2 == faces_v4, ExcInternalError()); + std::map, types::boundary_id, PointComparator> lines_v2; + std::map, types::boundary_id, PointComparator> lines_v4; + for (unsigned int i = 0; i < GeometryInfo::lines_per_cell; ++i) + { + lines_v2[cell_v2->line(i)->center()] = + cell_v2->line(i)->boundary_id(); + lines_v4[cell_v4->line(i)->center()] = + cell_v4->line(i)->boundary_id(); + } + AssertThrow(lines_v2 == lines_v4, ExcInternalError()); + } + deallog << " OK" << std::endl; +} + +void +filename_resolution() +{ + deallog << "grid_in_msh_version_2/hole81" << std::endl; + gmsh_grid<2>(SOURCE_DIR "/grid_in_msh_version_2/hole81.msh", + SOURCE_DIR "/grid_in_msh_version_4/hole81.msh"); + deallog << "grid_in_msh_version_2/hole8170" << std::endl; + gmsh_grid<2>(SOURCE_DIR "/grid_in_msh_version_2/hole8170.msh", + SOURCE_DIR "/grid_in_msh_version_4/hole8170.msh"); +} + + +int +main() +{ + initlog(); + deallog.get_file_stream() << std::setprecision(5); + + filename_resolution(); +} diff --git a/tests/grid/grid_in_msh_version_4.output b/tests/grid/grid_in_msh_version_4.output new file mode 100644 index 000000000000..3dd5e3673860 --- /dev/null +++ b/tests/grid/grid_in_msh_version_4.output @@ -0,0 +1,7 @@ + +DEAL::grid_in_msh_version_2/hole81 +DEAL:: 81 active cells +DEAL:: OK +DEAL::grid_in_msh_version_2/hole8170 +DEAL:: 8170 active cells +DEAL:: OK diff --git a/tests/grid/grid_in_msh_version_4/hole81.msh b/tests/grid/grid_in_msh_version_4/hole81.msh new file mode 100644 index 000000000000..c10687073913 --- /dev/null +++ b/tests/grid/grid_in_msh_version_4/hole81.msh @@ -0,0 +1,205 @@ +$MeshFormat +4 0 8 +$EndMeshFormat +$Entities +0 0 1 0 +0 0 0 0 1 1 0 1 1 0 +$EndEntities +$Nodes +1 109 +0 2 0 109 +1 0.323223 0.323223 0 +2 0.26903 0.404329 0 +3 0.205471 0.335785 0 +4 0.261688 0.253588 0 +5 0.25 0.5 0 +6 0.168897 0.421825 0 +7 0.351915 0.201897 0 +8 0.404329 0.26903 0 +9 0.151061 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416 1393 1448 +200 430 416 1393 1448 381 377 677 684 +$EndElements diff --git a/tests/grid/grids/grid_in_msh_02_v4.msh b/tests/grid/grids/grid_in_msh_02_v4.msh new file mode 100644 index 000000000000..a2676871b9a2 --- /dev/null +++ b/tests/grid/grids/grid_in_msh_02_v4.msh @@ -0,0 +1,44 @@ +$MeshFormat +4 0 8 +$EndMeshFormat +$Entities +2 1 0 0 +1 0 0 0 0 0 0 1 10 +2 1 0 0 1 0 0 1 20 +1 0 0 0 1 0 0 1 100 0 +$EndEntities +$Nodes +3 11 +1 0 0 1 +1 0 0 0 +2 0 0 1 +2 1 0 0 +1 1 0 9 +3 0.1 0 0 +4 0.2 0 0 +5 0.3 0 0 +6 0.4 0 0 +7 0.5 0 0 +8 0.6 0 0 +9 0.7 0 0 +10 0.8 0 0 +11 0.9 0 0 +$EndNodes +$Elements +3 12 +1 0 15 1 +1 1 +2 0 15 1 +2 2 +1 1 1 10 +3 1 3 +4 3 4 +5 4 5 +6 5 6 +7 6 7 +8 7 8 +9 8 9 +10 9 10 +11 10 11 +12 11 2 +$EndElements From ef7fa1d3469fd98cba6925fdd7029237612b12f6 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Sat, 26 Jan 2019 15:34:33 +0100 Subject: [PATCH 012/507] Fix TrilinosWrappers::PreconditionMueLu --- source/lac/trilinos_precondition_muelu.cc | 12 ++---------- 1 file changed, 2 insertions(+), 10 deletions(-) diff --git a/source/lac/trilinos_precondition_muelu.cc b/source/lac/trilinos_precondition_muelu.cc index f36f7cbd6746..cbaa3124a40a 100644 --- a/source/lac/trilinos_precondition_muelu.cc +++ b/source/lac/trilinos_precondition_muelu.cc @@ -18,21 +18,11 @@ #ifdef DEAL_II_WITH_TRILINOS # if DEAL_II_TRILINOS_VERSION_GTE(11, 14, 0) - # include -# include # include -# include -# include -# include # include -# include -# include -# include -# include # include -# include DEAL_II_NAMESPACE_OPEN @@ -98,6 +88,8 @@ namespace TrilinosWrappers // Build the AMG preconditioner. Teuchos::ParameterList parameter_list; + parameter_list.set("parameterlist: syntax", "ml"); + if (additional_data.elliptic == true) ML_Epetra::SetDefaults("SA", parameter_list); else From d10fed17a8ab6fc7b7634a8727e2944dbc74f2aa Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Sat, 26 Jan 2019 16:13:16 +0100 Subject: [PATCH 013/507] Don't use __builtin_expect in Utilities::pow --- include/deal.II/base/utilities.h | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/include/deal.II/base/utilities.h b/include/deal.II/base/utilities.h index f2a1cb6b6e1b..f49c3021321b 100644 --- a/include/deal.II/base/utilities.h +++ b/include/deal.II/base/utilities.h @@ -404,9 +404,10 @@ namespace Utilities constexpr unsigned int pow(const unsigned int base, const int iexp) { -#ifdef DEAL_II_WITH_CXX14 -# ifdef DEAL_II_HAVE_CXX14_CONSTEXPR_CAN_CALL_NONCONSTEXPR -# if defined(DEAL_II_HAVE_BUILTIN_EXPECT) && defined(__INTEL_COMPILER) +#if defined(DEBUG) && defined(DEAL_II_WITH_CXX14) && \ + defined(DEAL_II_HAVE_CXX14_CONSTEXPR_CAN_CALL_NONCONSTEXPR) + // Up to __builtin_expect this is the same code as in the 'Assert' macro. + // The call to __builtin_expect turns out to be problematic. if (!(iexp >= 0)) ::dealii::deal_II_exceptions::internals::issue_error_noreturn( ::dealii::deal_II_exceptions::internals::abort_or_throw_on_exception, @@ -416,10 +417,6 @@ namespace Utilities "iexp>=0", "ExcMessage(\"The exponent must not be negative!\")", ExcMessage("The exponent must not be negative!")); -# else - Assert(iexp >= 0, ExcMessage("The exponent must not be negative!")); -# endif -# endif #endif // The "exponentiation by squaring" algorithm used below has to be // compressed to one statement due to C++11's restrictions on constexpr From 033699e59ff20c5cdb86e069259eba3e715f5cf4 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Sat, 26 Jan 2019 16:54:16 +0100 Subject: [PATCH 014/507] Rename variables using snake_case style --- source/grid/grid_in.cc | 83 +++++++++++++++++++++--------------------- 1 file changed, 41 insertions(+), 42 deletions(-) diff --git a/source/grid/grid_in.cc b/source/grid/grid_in.cc index 87fe841d9c03..2aac678cadd5 100644 --- a/source/grid/grid_in.cc +++ b/source/grid/grid_in.cc @@ -1455,69 +1455,68 @@ GridIn::read_msh(std::istream &in) // if the next block is of kind $Entities, parse it if (line == "$Entities") { - unsigned long numPoints, numCurves, numSurfaces, numVolumes, - numPhysicals; - int tag, physicalTag; - double boxMinX, boxMinY, boxMinZ, boxMaxX, boxMaxY, boxMaxZ; - - in >> numPoints >> numCurves >> numSurfaces >> numVolumes; - for (unsigned int i = 0; i < numPoints; ++i) + unsigned long n_points, n_curves, n_surfaces, n_volumes, n_physicals; + int tag, physical_tag; + double box_min_x, box_min_y, box_min_z, box_max_x, box_max_y, + box_max_z; + + // we only care for physical_tag to fill tag_maps + in >> n_points >> n_curves >> n_surfaces >> n_volumes; + for (unsigned int i = 0; i < n_points; ++i) { // parse point ids - in >> tag >> boxMinX >> boxMinY >> boxMinZ >> boxMaxX >> - boxMaxY >> boxMaxZ >> numPhysicals; - AssertThrow(numPhysicals < 2, + in >> tag >> box_min_x >> box_min_y >> box_min_z >> box_max_x >> + box_max_y >> box_max_z >> n_physicals; + AssertThrow(n_physicals < 2, ExcMessage("More than one tag is not supported!")); - for (unsigned int j = 0; j < numPhysicals; ++j) - in >> physicalTag; - tag_maps[0][tag] = (numPhysicals == 0) ? 0 : physicalTag; + for (unsigned int j = 0; j < n_physicals; ++j) + in >> physical_tag; + tag_maps[0][tag] = (n_physicals == 0) ? 0 : physical_tag; } - for (unsigned int i = 0; i < numCurves; ++i) + for (unsigned int i = 0; i < n_curves; ++i) { // parse curve ids - in >> tag >> boxMinX >> boxMinY >> boxMinZ >> boxMaxX >> - boxMaxY >> boxMaxZ >> numPhysicals; - AssertThrow(numPhysicals < 2, + in >> tag >> box_min_x >> box_min_y >> box_min_z >> box_max_x >> + box_max_y >> box_max_z >> n_physicals; + AssertThrow(n_physicals < 2, ExcMessage("More than one tag is not supported!")); - for (unsigned int j = 0; j < numPhysicals; ++j) - in >> physicalTag; - tag_maps[1][tag] = (numPhysicals == 0) ? 0 : physicalTag; - in >> numPoints; - for (unsigned int j = 0; j < numPoints; ++j) + for (unsigned int j = 0; j < n_physicals; ++j) + in >> physical_tag; + tag_maps[1][tag] = (n_physicals == 0) ? 0 : physical_tag; + in >> n_points; + for (unsigned int j = 0; j < n_points; ++j) in >> tag; } - for (unsigned int i = 0; i < numSurfaces; ++i) + for (unsigned int i = 0; i < n_surfaces; ++i) { // parse surface ids - in >> tag >> boxMinX >> boxMinY >> boxMinZ >> boxMaxX >> - boxMaxY >> boxMaxZ >> numPhysicals; - AssertThrow(numPhysicals < 2, + in >> tag >> box_min_x >> box_min_y >> box_min_z >> box_max_x >> + box_max_y >> box_max_z >> n_physicals; + AssertThrow(n_physicals < 2, ExcMessage("More than one tag is not supported!")); - for (unsigned int j = 0; j < numPhysicals; ++j) - in >> physicalTag; - tag_maps[2][tag] = (numPhysicals == 0) ? 0 : physicalTag; - in >> numCurves; - for (unsigned int j = 0; j < numCurves; ++j) + for (unsigned int j = 0; j < n_physicals; ++j) + in >> physical_tag; + tag_maps[2][tag] = (n_physicals == 0) ? 0 : physical_tag; + in >> n_curves; + for (unsigned int j = 0; j < n_curves; ++j) in >> tag; } - for (unsigned int i = 0; i < numVolumes; ++i) + for (unsigned int i = 0; i < n_volumes; ++i) { // parse volume ids - in >> tag >> boxMinX >> boxMinY >> boxMinZ >> boxMaxX >> - boxMaxY >> boxMaxZ >> numPhysicals; - AssertThrow(numPhysicals < 2, + in >> tag >> box_min_x >> box_min_y >> box_min_z >> box_max_x >> + box_max_y >> box_max_z >> n_physicals; + AssertThrow(n_physicals < 2, ExcMessage("More than one tag is not supported!")); - for (unsigned int j = 0; j < numPhysicals; ++j) - in >> physicalTag; - tag_maps[3][tag] = (numPhysicals == 0) ? 0 : physicalTag; - in >> numSurfaces; - for (unsigned int j = 0; j < numSurfaces; ++j) + for (unsigned int j = 0; j < n_physicals; ++j) + in >> physical_tag; + tag_maps[3][tag] = (n_physicals == 0) ? 0 : physical_tag; + in >> n_surfaces; + for (unsigned int j = 0; j < n_surfaces; ++j) in >> tag; } - std::cout << line << std::endl; in >> line; - std::cout << line << std::endl; AssertThrow(line == "$EndEntities", ExcInvalidGMSHInput(line)); in >> line; } From e3578030656392270b92be80198fea5859fb8a2f Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Sat, 26 Jan 2019 17:35:22 +0100 Subject: [PATCH 015/507] Use default destructor and avoid constructor to be defaulted --- include/deal.II/lac/trilinos_precondition.h | 2 +- source/lac/trilinos_precondition_muelu.cc | 17 +++++++---------- 2 files changed, 8 insertions(+), 11 deletions(-) diff --git a/include/deal.II/lac/trilinos_precondition.h b/include/deal.II/lac/trilinos_precondition.h index 0b75cd92a8b3..cb6d2ee11b62 100644 --- a/include/deal.II/lac/trilinos_precondition.h +++ b/include/deal.II/lac/trilinos_precondition.h @@ -1783,7 +1783,7 @@ namespace TrilinosWrappers /** * Destructor. */ - ~PreconditionAMGMueLu() override; + virtual ~PreconditionAMGMueLu() override = default; /** * Let Trilinos compute a multilevel hierarchy for the solution of a diff --git a/source/lac/trilinos_precondition_muelu.cc b/source/lac/trilinos_precondition_muelu.cc index cbaa3124a40a..3a26b73462e1 100644 --- a/source/lac/trilinos_precondition_muelu.cc +++ b/source/lac/trilinos_precondition_muelu.cc @@ -55,19 +55,16 @@ namespace TrilinosWrappers PreconditionAMGMueLu::PreconditionAMGMueLu() { + // clang-tidy wants to default the constructor if we disable the check + // in case we compile without 64-bit indices # ifdef DEAL_II_WITH_64BIT_INDICES - AssertThrow(false, + constexpr bool enabled = false; +# else + constexpr bool enabled = true; +# endif + AssertThrow(enabled, ExcMessage( "PreconditionAMGMueLu does not support 64bit-indices!")); -# endif - } - - - - PreconditionAMGMueLu::~PreconditionAMGMueLu() - { - preconditioner.reset(); - trilinos_matrix.reset(); } From c7dc2af1af5fe17420262d1607df1a5bee749646 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Sun, 27 Jan 2019 11:15:31 +0100 Subject: [PATCH 016/507] Add more comments --- source/grid/grid_in.cc | 20 +++++++++++++++++++- 1 file changed, 19 insertions(+), 1 deletion(-) diff --git a/source/grid/grid_in.cc b/source/grid/grid_in.cc index 2aac678cadd5..c063e1794e2e 100644 --- a/source/grid/grid_in.cc +++ b/source/grid/grid_in.cc @@ -1460,29 +1460,37 @@ GridIn::read_msh(std::istream &in) double box_min_x, box_min_y, box_min_z, box_max_x, box_max_y, box_max_z; - // we only care for physical_tag to fill tag_maps + // we only care for 'physical_tag' to fill tag_maps in >> n_points >> n_curves >> n_surfaces >> n_volumes; for (unsigned int i = 0; i < n_points; ++i) { // parse point ids + // we only care for 'tag' as key for tag_maps[0] in >> tag >> box_min_x >> box_min_y >> box_min_z >> box_max_x >> box_max_y >> box_max_z >> n_physicals; + // if there is a physical tag, we will use it as boundary id below AssertThrow(n_physicals < 2, ExcMessage("More than one tag is not supported!")); for (unsigned int j = 0; j < n_physicals; ++j) in >> physical_tag; + // if there is no physical tag, use 0 as default tag_maps[0][tag] = (n_physicals == 0) ? 0 : physical_tag; } for (unsigned int i = 0; i < n_curves; ++i) { // parse curve ids + // we only care for 'tag' as key for tag_maps[1] in >> tag >> box_min_x >> box_min_y >> box_min_z >> box_max_x >> box_max_y >> box_max_z >> n_physicals; + // if there is a physical tag, we will use it as boundary id below AssertThrow(n_physicals < 2, ExcMessage("More than one tag is not supported!")); for (unsigned int j = 0; j < n_physicals; ++j) in >> physical_tag; + // if there is no physical tag, use 0 as default tag_maps[1][tag] = (n_physicals == 0) ? 0 : physical_tag; + // we don't care about the points associated to a curve, but have + // to parse them anyway because their format is unstructured in >> n_points; for (unsigned int j = 0; j < n_points; ++j) in >> tag; @@ -1491,13 +1499,18 @@ GridIn::read_msh(std::istream &in) for (unsigned int i = 0; i < n_surfaces; ++i) { // parse surface ids + // we only care for 'tag' as key for tag_maps[2] in >> tag >> box_min_x >> box_min_y >> box_min_z >> box_max_x >> box_max_y >> box_max_z >> n_physicals; + // if there is a physical tag, we will use it as boundary id below AssertThrow(n_physicals < 2, ExcMessage("More than one tag is not supported!")); for (unsigned int j = 0; j < n_physicals; ++j) in >> physical_tag; + // if there is no physical tag, use 0 as default tag_maps[2][tag] = (n_physicals == 0) ? 0 : physical_tag; + // we don't care about the curves associated to a surface, but + // have to parse them anyway because their format is unstructured in >> n_curves; for (unsigned int j = 0; j < n_curves; ++j) in >> tag; @@ -1505,13 +1518,18 @@ GridIn::read_msh(std::istream &in) for (unsigned int i = 0; i < n_volumes; ++i) { // parse volume ids + // we only care for 'tag' as key for tag_maps[3] in >> tag >> box_min_x >> box_min_y >> box_min_z >> box_max_x >> box_max_y >> box_max_z >> n_physicals; + // if there is a physical tag, we will use it as boundary id below AssertThrow(n_physicals < 2, ExcMessage("More than one tag is not supported!")); for (unsigned int j = 0; j < n_physicals; ++j) in >> physical_tag; + // if there is no physical tag, use 0 as default tag_maps[3][tag] = (n_physicals == 0) ? 0 : physical_tag; + // we don't care about the surfaces associated to a volume, but + // have to parse them anyway because their format is unstructured in >> n_surfaces; for (unsigned int j = 0; j < n_surfaces; ++j) in >> tag; From ab38b0beb03be3e58bcf369abca609beb1d8fa15 Mon Sep 17 00:00:00 2001 From: David Wells Date: Sun, 27 Jan 2019 16:48:17 -0500 Subject: [PATCH 017/507] Explicitly use Zoltan in two tests. This doesn't matter in 05 (since that test only uses one processor) but the output file states that we use Zoltan, so we should be consistent. This is needed in 07 since the default third argument to partition_triangulation is metis, but the output file states that we use Zoltan. --- tests/fe/fe_enriched_color_05.cc | 6 ++++-- tests/fe/fe_enriched_color_07.cc | 4 +++- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/tests/fe/fe_enriched_color_05.cc b/tests/fe/fe_enriched_color_05.cc index 650462f4cb46..0f4d5c629f54 100644 --- a/tests/fe/fe_enriched_color_05.cc +++ b/tests/fe/fe_enriched_color_05.cc @@ -254,8 +254,10 @@ main(int argc, char **argv) } #ifdef DATA_OUT_FE_ENRICHED - GridTools::partition_triangulation( - Utilities::MPI::n_mpi_processes(MPI_COMM_WORLD), triangulation); + GridTools::partition_triangulation(Utilities::MPI::n_mpi_processes( + MPI_COMM_WORLD), + triangulation, + SparsityTools::Partitioner::zoltan); dof_handler.distribute_dofs(*fe_collection); plot_shape_function(dof_handler, 5); diff --git a/tests/fe/fe_enriched_color_07.cc b/tests/fe/fe_enriched_color_07.cc index cb542663952a..1ff3fa834e05 100644 --- a/tests/fe/fe_enriched_color_07.cc +++ b/tests/fe/fe_enriched_color_07.cc @@ -1424,7 +1424,9 @@ LaplaceProblem::setup_system() { pcout << "...start setup system" << std::endl; - GridTools::partition_triangulation(n_mpi_processes, triangulation); + GridTools::partition_triangulation(n_mpi_processes, + triangulation, + SparsityTools::Partitioner::zoltan); dof_handler.distribute_dofs(*fe_collection); From 34e105d67b4de6411073e30eabb8324352fa0181 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Mon, 28 Jan 2019 14:15:57 +0100 Subject: [PATCH 018/507] Declare VectorizedArray::n_array_elemnts outside the class in the general case --- include/deal.II/base/vectorization.h | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/include/deal.II/base/vectorization.h b/include/deal.II/base/vectorization.h index 1a6d223e62a7..3f82e165c52e 100644 --- a/include/deal.II/base/vectorization.h +++ b/include/deal.II/base/vectorization.h @@ -174,9 +174,11 @@ class VectorizedArray { public: /** - * This gives the number of vectors collected in this class. + * This gives the number of elements collected in this class. In the general + * case, there is only one element. Specializations use SIMD intrinsics and + * can work on multiple elements at the same time. */ - static const unsigned int n_array_elements = 1; + static const unsigned int n_array_elements; // POD means that there should be no user-defined constructors, destructors // and copy functions (the standard is somewhat relaxed in C++2011, though). @@ -449,6 +451,10 @@ class VectorizedArray std::min(const VectorizedArray &, const VectorizedArray &); }; +// We need to have a separate declaration for static const members +template +const unsigned int VectorizedArray::n_array_elements = 1; + /** From 1dfa511f2ea11dcfb7129baad827298b91ed9563 Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Wed, 16 Jan 2019 17:43:46 -0700 Subject: [PATCH 019/507] [CI] test on OSX - add a separate Jenkinsfile for OSX - compile deal.II using clang on OSX --- contrib/ci/Jenkinsfile.osx | 88 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 88 insertions(+) create mode 100644 contrib/ci/Jenkinsfile.osx diff --git a/contrib/ci/Jenkinsfile.osx b/contrib/ci/Jenkinsfile.osx new file mode 100644 index 000000000000..fbee05a7686f --- /dev/null +++ b/contrib/ci/Jenkinsfile.osx @@ -0,0 +1,88 @@ +#!groovy + +/* +Settings to apply inside Jenkins: + - discover pull requests (remove branches/master) + - Strategy: merged PR + - enable "Disable GitHub Multibranch Status Plugin" + - trigger build on pull request comment: .* /rebuild.* (without space) + - Jenkinsfile: choose contrib/ci/Jenkinsfile.osx + - scan: every 4 hours + - discard: 5+ items +*/ + +pipeline +{ + agent { + node { + label 'osx' + } + } + + stages + { + stage("check") + { + when { + allOf { + not {branch 'master'} + } + } + + steps + { + githubNotify context: 'OSX', description: 'pending...', status: 'PENDING' + sh ''' + wget -q -O - https://api.github.com/repos/dealii/dealii/issues/${CHANGE_ID}/labels | grep 'ready to test' || \ + { echo "This commit will only be tested when it has the label 'ready to test'. Trigger a rebuild by adding a comment that contains '/rebuild'..."; exit 1; } + ''' + } + post + { + failure + { + githubNotify context: 'OSX', description: 'need ready to test label and /rebuild', status: 'PENDING' + script + { + currentBuild.result='NOT_BUILT' + } + } + } + } + + stage('build') + { + steps + { + timeout(time: 1, unit: 'HOURS') + { + sh "echo \"building on node ${env.NODE_NAME}\"" + sh '''#!/bin/bash + mkdir build && cd build + cmake \ + -D DEAL_II_WITH_MPI=OFF \ + -D DEAL_II_CXX_FLAGS='-Werror' \ + -D CMAKE_BUILD_TYPE=Debug \ + $WORKSPACE/ && make -j 4 + ''' + } + } + + post + { + failure + { + githubNotify context: 'OSX', description: 'build failed', status: 'FAILURE' + } + } + } + + stage("finalize") + { + steps + { + githubNotify context: 'OSX', description: 'OK', status: 'SUCCESS' + } + } + } +} From be7654056ae98f3841220236484ff053be05afc3 Mon Sep 17 00:00:00 2001 From: David Wells Date: Mon, 28 Jan 2019 16:51:31 -0500 Subject: [PATCH 020/507] Mark a few Subscriptor functions as inline. These are simple enough that they should live in the header. This will allow classes inheriting from Subscriptor to potentially inline some more constructors too. --- include/deal.II/base/subscriptor.h | 31 +++++++++++++++++++++++++++ source/base/subscriptor.cc | 34 ------------------------------ 2 files changed, 31 insertions(+), 34 deletions(-) diff --git a/include/deal.II/base/subscriptor.h b/include/deal.II/base/subscriptor.h index f59d18283973..431f8c03e412 100644 --- a/include/deal.II/base/subscriptor.h +++ b/include/deal.II/base/subscriptor.h @@ -290,6 +290,37 @@ class Subscriptor //--------------------------------------------------------------------------- +inline Subscriptor::Subscriptor() + : counter(0) + , object_info(nullptr) +{} + + + +inline Subscriptor::Subscriptor(const Subscriptor &) + : counter(0) + , object_info(nullptr) +{} + + + +inline Subscriptor & +Subscriptor::operator=(const Subscriptor &s) +{ + object_info = s.object_info; + return *this; +} + + + +inline unsigned int +Subscriptor::n_subscriptions() const +{ + return counter; +} + + + template inline void Subscriptor::serialize(Archive &, const unsigned int) diff --git a/source/base/subscriptor.cc b/source/base/subscriptor.cc index aeac2c0807dd..669f71b9092b 100644 --- a/source/base/subscriptor.cc +++ b/source/base/subscriptor.cc @@ -31,23 +31,6 @@ static const char *unknown_subscriber = "unknown subscriber"; std::mutex Subscriptor::mutex; -Subscriptor::Subscriptor() - : counter(0) - , object_info(nullptr) -{ - // this has to go somewhere to avoid an extra warning. - (void)unknown_subscriber; -} - - - -Subscriptor::Subscriptor(const Subscriptor &) - : counter(0) - , object_info(nullptr) -{} - - - Subscriptor::Subscriptor(Subscriptor &&subscriptor) noexcept : counter(0) , object_info(subscriptor.object_info) @@ -132,15 +115,6 @@ Subscriptor::check_no_subscribers() const noexcept -Subscriptor & -Subscriptor::operator=(const Subscriptor &s) -{ - object_info = s.object_info; - return *this; -} - - - Subscriptor & Subscriptor::operator=(Subscriptor &&s) noexcept { @@ -224,14 +198,6 @@ Subscriptor::unsubscribe(std::atomic *const validity, -unsigned int -Subscriptor::n_subscriptions() const -{ - return counter; -} - - - void Subscriptor::list_subscribers() const { From b7195c403286301321129fad732fb81f9a657ce8 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Tue, 29 Jan 2019 02:01:52 +0100 Subject: [PATCH 021/507] Move some declarations around and document tag_maps --- source/grid/grid_in.cc | 41 ++++++++++++++++++++++++++++++++--------- 1 file changed, 32 insertions(+), 9 deletions(-) diff --git a/source/grid/grid_in.cc b/source/grid/grid_in.cc index c063e1794e2e..f1adce9915e5 100644 --- a/source/grid/grid_in.cc +++ b/source/grid/grid_in.cc @@ -1404,10 +1404,13 @@ GridIn::read_msh(std::istream &in) Assert(tria != nullptr, ExcNoTriangulationSelected()); AssertThrow(in, ExcIO()); - unsigned int n_vertices; - unsigned int n_cells; - unsigned int dummy; - std::string line; + unsigned int n_vertices; + unsigned int n_cells; + unsigned int dummy; + std::string line; + // This array stores maps from the 'entities' to the 'physical tags' for + // points, curves, surfaces and volumes. We use this information later to + // assign boundary ids. std::array, 4> tag_maps; in >> line; @@ -1455,22 +1458,24 @@ GridIn::read_msh(std::istream &in) // if the next block is of kind $Entities, parse it if (line == "$Entities") { - unsigned long n_points, n_curves, n_surfaces, n_volumes, n_physicals; - int tag, physical_tag; - double box_min_x, box_min_y, box_min_z, box_max_x, box_max_y, - box_max_z; + unsigned long n_points, n_curves, n_surfaces, n_volumes; - // we only care for 'physical_tag' to fill tag_maps in >> n_points >> n_curves >> n_surfaces >> n_volumes; for (unsigned int i = 0; i < n_points; ++i) { // parse point ids + int tag; + unsigned int n_physicals; + double box_min_x, box_min_y, box_min_z, box_max_x, box_max_y, + box_max_z; + // we only care for 'tag' as key for tag_maps[0] in >> tag >> box_min_x >> box_min_y >> box_min_z >> box_max_x >> box_max_y >> box_max_z >> n_physicals; // if there is a physical tag, we will use it as boundary id below AssertThrow(n_physicals < 2, ExcMessage("More than one tag is not supported!")); + int physical_tag; for (unsigned int j = 0; j < n_physicals; ++j) in >> physical_tag; // if there is no physical tag, use 0 as default @@ -1479,12 +1484,18 @@ GridIn::read_msh(std::istream &in) for (unsigned int i = 0; i < n_curves; ++i) { // parse curve ids + int tag; + unsigned int n_physicals; + double box_min_x, box_min_y, box_min_z, box_max_x, box_max_y, + box_max_z; + // we only care for 'tag' as key for tag_maps[1] in >> tag >> box_min_x >> box_min_y >> box_min_z >> box_max_x >> box_max_y >> box_max_z >> n_physicals; // if there is a physical tag, we will use it as boundary id below AssertThrow(n_physicals < 2, ExcMessage("More than one tag is not supported!")); + int physical_tag; for (unsigned int j = 0; j < n_physicals; ++j) in >> physical_tag; // if there is no physical tag, use 0 as default @@ -1499,12 +1510,18 @@ GridIn::read_msh(std::istream &in) for (unsigned int i = 0; i < n_surfaces; ++i) { // parse surface ids + int tag; + unsigned int n_physicals; + double box_min_x, box_min_y, box_min_z, box_max_x, box_max_y, + box_max_z; + // we only care for 'tag' as key for tag_maps[2] in >> tag >> box_min_x >> box_min_y >> box_min_z >> box_max_x >> box_max_y >> box_max_z >> n_physicals; // if there is a physical tag, we will use it as boundary id below AssertThrow(n_physicals < 2, ExcMessage("More than one tag is not supported!")); + int physical_tag; for (unsigned int j = 0; j < n_physicals; ++j) in >> physical_tag; // if there is no physical tag, use 0 as default @@ -1518,12 +1535,18 @@ GridIn::read_msh(std::istream &in) for (unsigned int i = 0; i < n_volumes; ++i) { // parse volume ids + int tag; + unsigned int n_physicals; + double box_min_x, box_min_y, box_min_z, box_max_x, box_max_y, + box_max_z; + // we only care for 'tag' as key for tag_maps[3] in >> tag >> box_min_x >> box_min_y >> box_min_z >> box_max_x >> box_max_y >> box_max_z >> n_physicals; // if there is a physical tag, we will use it as boundary id below AssertThrow(n_physicals < 2, ExcMessage("More than one tag is not supported!")); + int physical_tag; for (unsigned int j = 0; j < n_physicals; ++j) in >> physical_tag; // if there is no physical tag, use 0 as default From d54882b789fef2396453d2c571dee4930d7038de Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Tue, 29 Jan 2019 10:52:18 +0100 Subject: [PATCH 022/507] modernize-return-braced-init-list --- examples/step-33/step-33.cc | 8 ++-- examples/step-42/step-42.cc | 2 +- examples/step-49/step-49.cc | 2 +- examples/step-53/step-53.cc | 7 ++- include/deal.II/base/geometry_info.h | 6 ++- include/deal.II/base/index_set.h | 14 ++---- include/deal.II/base/symmetric_tensor.h | 46 +++++++++---------- include/deal.II/fe/fe_values.h | 22 ++++----- .../deal.II/grid/tria_accessor.templates.h | 4 +- include/deal.II/lac/block_indices.h | 2 +- include/deal.II/lac/chunk_sparsity_pattern.h | 10 ++-- .../deal.II/lac/dynamic_sparsity_pattern.h | 12 ++--- include/deal.II/lac/linear_operator.h | 4 +- include/deal.II/lac/sparsity_pattern.h | 10 ++-- include/deal.II/lac/trilinos_sparse_matrix.h | 2 +- include/deal.II/matrix_free/matrix_free.h | 5 +- source/base/data_out_base.cc | 2 +- source/base/function_lib.cc | 2 +- source/base/hdf5.cc | 8 ++-- source/dofs/dof_handler_policy.cc | 2 +- source/fe/fe.cc | 20 ++++---- source/fe/mapping_q_generic.cc | 10 ++-- source/grid/grid_tools.cc | 22 ++++----- source/grid/manifold.cc | 20 ++++---- source/grid/manifold_lib.cc | 12 ++--- source/grid/tria_accessor.cc | 6 +-- source/opencascade/manifold_lib.cc | 2 +- 27 files changed, 124 insertions(+), 138 deletions(-) diff --git a/examples/step-33/step-33.cc b/examples/step-33/step-33.cc index a3ce08eb58b4..917b51fcd30d 100644 --- a/examples/step-33/step-33.cc +++ b/examples/step-33/step-33.cc @@ -2152,8 +2152,7 @@ namespace Step33 direct.solve(system_matrix, newton_update, right_hand_side); - return std::pair(solver_control.last_step(), - solver_control.last_value()); + return {solver_control.last_step(), solver_control.last_value()}; } // Likewise, if we are to use an iterative solver, we use Aztec's GMRES @@ -2215,13 +2214,12 @@ namespace Step33 solver.Iterate(parameters.max_iterations, parameters.linear_residual); - return std::pair(solver.NumIters(), - solver.TrueResidual()); + return {solver.NumIters(), solver.TrueResidual()}; } } Assert(false, ExcNotImplemented()); - return std::pair(0, 0); + return {0, 0}; } diff --git a/examples/step-42/step-42.cc b/examples/step-42/step-42.cc index 2006200602e5..94cc9e445aa9 100644 --- a/examples/step-42/step-42.cc +++ b/examples/step-42/step-42.cc @@ -897,7 +897,7 @@ namespace Step42 // indicator one. Point<3> rotate_half_sphere(const Point<3> &in) { - return Point<3>(in(2), in(1), -in(0)); + return {in(2), in(1), -in(0)}; } template diff --git a/examples/step-49/step-49.cc b/examples/step-49/step-49.cc index a40312e76b40..c99e66a0e32a 100644 --- a/examples/step-49/step-49.cc +++ b/examples/step-49/step-49.cc @@ -278,7 +278,7 @@ struct Grid6Func Point<2> operator()(const Point<2> &in) const { - return Point<2>(in(0), trans(in(1))); + return {in(0), trans(in(1))}; } }; diff --git a/examples/step-53/step-53.cc b/examples/step-53/step-53.cc index f60c0755e1ee..3e4eb436a5c9 100644 --- a/examples/step-53/step-53.cc +++ b/examples/step-53/step-53.cc @@ -277,10 +277,9 @@ namespace Step53 const double R_bar = R / std::sqrt(1 - (ellipticity * ellipticity * std::sin(theta) * std::sin(theta))); - return Point<3>((R_bar + d) * std::cos(phi) * std::cos(theta), - (R_bar + d) * std::sin(phi) * std::cos(theta), - ((1 - ellipticity * ellipticity) * R_bar + d) * - std::sin(theta)); + return {(R_bar + d) * std::cos(phi) * std::cos(theta), + (R_bar + d) * std::sin(phi) * std::cos(theta), + ((1 - ellipticity * ellipticity) * R_bar + d) * std::sin(theta)}; } Point<3> AfricaGeometry::pull_back_wgs84(const Point<3> &x) const diff --git a/include/deal.II/base/geometry_info.h b/include/deal.II/base/geometry_info.h index 31e75d1f0e0e..f5b35f8fddc8 100644 --- a/include/deal.II/base/geometry_info.h +++ b/include/deal.II/base/geometry_info.h @@ -2519,7 +2519,7 @@ GeometryInfo<2>::unit_cell_vertex(const unsigned int vertex) Assert(vertex < vertices_per_cell, ExcIndexRange(vertex, 0, vertices_per_cell)); - return Point<2>(vertex % 2, vertex / 2); + return {static_cast(vertex % 2), static_cast(vertex / 2)}; } @@ -2531,7 +2531,9 @@ GeometryInfo<3>::unit_cell_vertex(const unsigned int vertex) Assert(vertex < vertices_per_cell, ExcIndexRange(vertex, 0, vertices_per_cell)); - return Point<3>(vertex % 2, vertex / 2 % 2, vertex / 4); + return {static_cast(vertex % 2), + static_cast(vertex / 2 % 2), + static_cast(vertex / 4)}; } diff --git a/include/deal.II/base/index_set.h b/include/deal.II/base/index_set.h index 439775a1309f..fec38b883f22 100644 --- a/include/deal.II/base/index_set.h +++ b/include/deal.II/base/index_set.h @@ -1030,9 +1030,7 @@ inline IndexSet::ElementIterator IndexSet::IntervalAccessor::begin() const { Assert(is_valid(), ExcMessage("invalid iterator")); - return IndexSet::ElementIterator(index_set, - range_idx, - index_set->ranges[range_idx].begin); + return {index_set, range_idx, index_set->ranges[range_idx].begin}; } @@ -1044,9 +1042,7 @@ IndexSet::IntervalAccessor::end() const // point to first index in next interval unless we are the last interval. if (range_idx < index_set->ranges.size() - 1) - return IndexSet::ElementIterator(index_set, - range_idx + 1, - index_set->ranges[range_idx + 1].begin); + return {index_set, range_idx + 1, index_set->ranges[range_idx + 1].begin}; else return index_set->end(); } @@ -1479,7 +1475,7 @@ IndexSet::begin() const { compress(); if (ranges.size() > 0) - return IndexSet::ElementIterator(this, 0, ranges[0].begin); + return {this, 0, ranges[0].begin}; else return end(); } @@ -1530,9 +1526,9 @@ IndexSet::at(const size_type global_index) const // [a,b[ and we will return an iterator pointing directly at global_index // (else branch). if (global_index < p->begin) - return IndexSet::ElementIterator(this, p - ranges.begin(), p->begin); + return {this, static_cast(p - ranges.begin()), p->begin}; else - return IndexSet::ElementIterator(this, p - ranges.begin(), global_index); + return {this, static_cast(p - ranges.begin()), global_index}; } diff --git a/include/deal.II/base/symmetric_tensor.h b/include/deal.II/base/symmetric_tensor.h index f903c4078da6..f16414247234 100644 --- a/include/deal.II/base/symmetric_tensor.h +++ b/include/deal.II/base/symmetric_tensor.h @@ -101,9 +101,9 @@ namespace internal Assert(position < 2, ExcIndexRange(position, 0, 2)); if (position == 0) - return TableIndices<2>(new_index, numbers::invalid_unsigned_int); + return {new_index, numbers::invalid_unsigned_int}; else - return TableIndices<2>(previous_indices[0], new_index); + return {previous_indices[0], new_index}; } @@ -124,28 +124,28 @@ namespace internal switch (position) { case 0: - return TableIndices<4>(new_index, - numbers::invalid_unsigned_int, - numbers::invalid_unsigned_int, - numbers::invalid_unsigned_int); + return {new_index, + numbers::invalid_unsigned_int, + numbers::invalid_unsigned_int, + numbers::invalid_unsigned_int}; case 1: - return TableIndices<4>(previous_indices[0], - new_index, - numbers::invalid_unsigned_int, - numbers::invalid_unsigned_int); + return {previous_indices[0], + new_index, + numbers::invalid_unsigned_int, + numbers::invalid_unsigned_int}; case 2: - return TableIndices<4>(previous_indices[0], - previous_indices[1], - new_index, - numbers::invalid_unsigned_int); + return {previous_indices[0], + previous_indices[1], + new_index, + numbers::invalid_unsigned_int}; case 3: - return TableIndices<4>(previous_indices[0], - previous_indices[1], - previous_indices[2], - new_index); + return {previous_indices[0], + previous_indices[1], + previous_indices[2], + new_index}; } Assert(false, ExcInternalError()); - return TableIndices<4>(); + return {}; } @@ -2463,7 +2463,7 @@ namespace internal { case 1: { - return TableIndices<2>(0, 0); + return {0, 0}; } case 2: @@ -2487,16 +2487,16 @@ namespace internal default: if (i < dim) - return TableIndices<2>(i, i); + return {i, i}; for (unsigned int d = 0, c = 0; d < dim; ++d) for (unsigned int e = d + 1; e < dim; ++e, ++c) if (c == i) - return TableIndices<2>(d, e); + return {d, e}; // should never get here: Assert(false, ExcInternalError()); - return TableIndices<2>(0, 0); + return {0, 0}; } } diff --git a/include/deal.II/fe/fe_values.h b/include/deal.II/fe/fe_values.h index 311cbbd64e12..3e03139485d1 100644 --- a/include/deal.II/fe/fe_values.h +++ b/include/deal.II/fe/fe_values.h @@ -4363,8 +4363,7 @@ namespace FEValuesViews Assert(n < 1, ExcIndexRange(n, 0, 1)); (void)n; - const double array[1] = {t[0]}; - return dealii::SymmetricTensor<2, 1>(array); + return {{t[0]}}; } @@ -4376,18 +4375,16 @@ namespace FEValuesViews { case 0: { - const double array[3] = {t[0], 0, t[1] / 2}; - return dealii::SymmetricTensor<2, 2>(array); + return {{t[0], 0, t[1] / 2}}; } case 1: { - const double array[3] = {0, t[1], t[0] / 2}; - return dealii::SymmetricTensor<2, 2>(array); + return {{0, t[1], t[0] / 2}}; } default: { Assert(false, ExcIndexRange(n, 0, 2)); - return dealii::SymmetricTensor<2, 2>(); + return {}; } } } @@ -4401,23 +4398,20 @@ namespace FEValuesViews { case 0: { - const double array[6] = {t[0], 0, 0, t[1] / 2, t[2] / 2, 0}; - return dealii::SymmetricTensor<2, 3>(array); + return {{t[0], 0, 0, t[1] / 2, t[2] / 2, 0}}; } case 1: { - const double array[6] = {0, t[1], 0, t[0] / 2, 0, t[2] / 2}; - return dealii::SymmetricTensor<2, 3>(array); + return {{0, t[1], 0, t[0] / 2, 0, t[2] / 2}}; } case 2: { - const double array[6] = {0, 0, t[2], 0, t[0] / 2, t[1] / 2}; - return dealii::SymmetricTensor<2, 3>(array); + return {{0, 0, t[2], 0, t[0] / 2, t[1] / 2}}; } default: { Assert(false, ExcIndexRange(n, 0, 3)); - return dealii::SymmetricTensor<2, 3>(); + return {}; } } } diff --git a/include/deal.II/grid/tria_accessor.templates.h b/include/deal.II/grid/tria_accessor.templates.h index 03fa332247bc..bd9bc7b43cd2 100644 --- a/include/deal.II/grid/tria_accessor.templates.h +++ b/include/deal.II/grid/tria_accessor.templates.h @@ -2586,7 +2586,7 @@ template inline RefinementCase<0> TriaAccessor<0, dim, spacedim>::refinement_case() { - return RefinementCase<0>(RefinementPossibilities<0>::no_refinement); + return {RefinementPossibilities<0>::no_refinement}; } @@ -2998,7 +2998,7 @@ template inline RefinementCase<0> TriaAccessor<0, 1, spacedim>::refinement_case() { - return RefinementCase<0>(RefinementPossibilities<0>::no_refinement); + return {RefinementPossibilities<0>::no_refinement}; } template diff --git a/include/deal.II/lac/block_indices.h b/include/deal.II/lac/block_indices.h index 4860a039b9fd..6ada38375a72 100644 --- a/include/deal.II/lac/block_indices.h +++ b/include/deal.II/lac/block_indices.h @@ -337,7 +337,7 @@ BlockIndices::global_to_local(const size_type i) const while (i < start_indices[block]) --block; - return std::pair(block, i - start_indices[block]); + return {block, i - start_indices[block]}; } diff --git a/include/deal.II/lac/chunk_sparsity_pattern.h b/include/deal.II/lac/chunk_sparsity_pattern.h index 261786b52663..4a458f598213 100644 --- a/include/deal.II/lac/chunk_sparsity_pattern.h +++ b/include/deal.II/lac/chunk_sparsity_pattern.h @@ -1105,14 +1105,14 @@ namespace ChunkSparsityPatternIterators inline ChunkSparsityPattern::iterator ChunkSparsityPattern::begin() const { - return iterator(this, 0); + return {this, 0}; } inline ChunkSparsityPattern::iterator ChunkSparsityPattern::end() const { - return iterator(this, n_rows()); + return {this, n_rows()}; } @@ -1121,7 +1121,7 @@ inline ChunkSparsityPattern::iterator ChunkSparsityPattern::begin(const unsigned int r) const { Assert(r < n_rows(), ExcIndexRange(r, 0, n_rows())); - return iterator(this, r); + return {this, r}; } @@ -1129,8 +1129,8 @@ ChunkSparsityPattern::begin(const unsigned int r) const inline ChunkSparsityPattern::iterator ChunkSparsityPattern::end(const unsigned int r) const { - Assert(r < n_rows(), ExcIndexRange(r, 0, n_rows())) return iterator(this, - r + 1); + Assert(r < n_rows(), ExcIndexRange(r, 0, n_rows())); + return {this, r + 1}; } diff --git a/include/deal.II/lac/dynamic_sparsity_pattern.h b/include/deal.II/lac/dynamic_sparsity_pattern.h index 2feb05a52d16..b5f1dd36a1d5 100644 --- a/include/deal.II/lac/dynamic_sparsity_pattern.h +++ b/include/deal.II/lac/dynamic_sparsity_pattern.h @@ -1089,7 +1089,7 @@ DynamicSparsityPattern::begin() const inline DynamicSparsityPattern::iterator DynamicSparsityPattern::end() const { - return iterator(this); + return {this}; } @@ -1100,7 +1100,7 @@ DynamicSparsityPattern::begin(const size_type r) const Assert(r < n_rows(), ExcIndexRangeType(r, 0, n_rows())); if (!have_entries) - return iterator(this); + return {this}; if (rowset.size() > 0) { @@ -1131,7 +1131,7 @@ DynamicSparsityPattern::begin(const size_type r) const if (it == rowset.end()) return end(); else - return iterator(this, *it, 0); + return {this, *it, 0}; } // Without an index set we have to do a linear search starting at @@ -1145,9 +1145,9 @@ DynamicSparsityPattern::begin(const size_type r) const } if (row == n_rows()) - return iterator(this); + return {this}; else - return iterator(this, row, 0); + return {this, row, 0}; } @@ -1159,7 +1159,7 @@ DynamicSparsityPattern::end(const size_type r) const unsigned int row = r + 1; if (row == n_rows()) - return iterator(this); + return {this}; else return begin(row); } diff --git a/include/deal.II/lac/linear_operator.h b/include/deal.II/lac/linear_operator.h index 5278b34ee65b..e066190781cd 100644 --- a/include/deal.II/lac/linear_operator.h +++ b/include/deal.II/lac/linear_operator.h @@ -1022,7 +1022,7 @@ namespace internal inline EmptyPayload operator+(const EmptyPayload &, const EmptyPayload &) { - return EmptyPayload(); + return {}; } /** @@ -1031,7 +1031,7 @@ namespace internal */ inline EmptyPayload operator*(const EmptyPayload &, const EmptyPayload &) { - return EmptyPayload(); + return {}; } diff --git a/include/deal.II/lac/sparsity_pattern.h b/include/deal.II/lac/sparsity_pattern.h index 3f58fe141358..4182a1fd7349 100644 --- a/include/deal.II/lac/sparsity_pattern.h +++ b/include/deal.II/lac/sparsity_pattern.h @@ -1254,7 +1254,7 @@ inline SparsityPattern::iterator SparsityPattern::begin() const { if (n_rows() > 0) - return iterator(this, rowstart[0]); + return {this, rowstart[0]}; else return end(); } @@ -1265,9 +1265,9 @@ inline SparsityPattern::iterator SparsityPattern::end() const { if (n_rows() > 0) - return iterator(this, rowstart[rows]); + return {this, rowstart[rows]}; else - return iterator(nullptr, 0); + return {nullptr, 0}; } @@ -1277,7 +1277,7 @@ SparsityPattern::begin(const size_type r) const { Assert(r < n_rows(), ExcIndexRangeType(r, 0, n_rows())); - return iterator(this, rowstart[r]); + return {this, rowstart[r]}; } @@ -1287,7 +1287,7 @@ SparsityPattern::end(const size_type r) const { Assert(r < n_rows(), ExcIndexRangeType(r, 0, n_rows())); - return iterator(this, rowstart[r + 1]); + return {this, rowstart[r + 1]}; } diff --git a/include/deal.II/lac/trilinos_sparse_matrix.h b/include/deal.II/lac/trilinos_sparse_matrix.h index ed9f193523f5..25478951f673 100644 --- a/include/deal.II/lac/trilinos_sparse_matrix.h +++ b/include/deal.II/lac/trilinos_sparse_matrix.h @@ -2745,7 +2745,7 @@ namespace TrilinosWrappers Accessor::value() const { Assert(a_row < matrix->m(), ExcBeyondEndOfMatrix()); - return Reference(*this); + return {*this}; } diff --git a/include/deal.II/matrix_free/matrix_free.h b/include/deal.II/matrix_free/matrix_free.h index d38ed5055f00..15a1e5e32dc7 100644 --- a/include/deal.II/matrix_free/matrix_free.h +++ b/include/deal.II/matrix_free/matrix_free.h @@ -2032,14 +2032,13 @@ MatrixFree::create_cell_subrange_hp( if (dof_info[dof_handler_component].fe_index_conversion[0][0] == degree) return range; else - return std::pair(range.second, - range.second); + return {range.second, range.second}; } const unsigned int fe_index = dof_info[dof_handler_component].fe_index_from_degree(0, degree); if (fe_index >= dof_info[dof_handler_component].max_fe_index) - return std::pair(range.second, range.second); + return {range.second, range.second}; else return create_cell_subrange_hp_by_index(range, fe_index, diff --git a/source/base/data_out_base.cc b/source/base/data_out_base.cc index 998382526004..65336ef19154 100644 --- a/source/base/data_out_base.cc +++ b/source/base/data_out_base.cc @@ -7630,7 +7630,7 @@ DataOutInterface::create_xdmf_entry( } else { - return XDMFEntry(); + return {}; } } diff --git a/source/base/function_lib.cc b/source/base/function_lib.cc index 891cf67524d3..5ec40c443112 100644 --- a/source/base/function_lib.cc +++ b/source/base/function_lib.cc @@ -1435,7 +1435,7 @@ namespace Functions const unsigned int /*component*/) const { Assert(false, ExcNotImplemented()); - return Tensor<1, 2>(); + return {}; } diff --git a/source/base/hdf5.cc b/source/base/hdf5.cc index 2e4f3c02de5f..d8fe0dca80c1 100644 --- a/source/base/hdf5.cc +++ b/source/base/hdf5.cc @@ -1313,7 +1313,7 @@ namespace HDF5 Group Group::open_group(const std::string &name) const { - return Group(name, *this, mpi, GroupAccessMode::open); + return {name, *this, mpi, GroupAccessMode::open}; } @@ -1321,7 +1321,7 @@ namespace HDF5 Group Group::create_group(const std::string &name) const { - return Group(name, *this, mpi, GroupAccessMode::create); + return {name, *this, mpi, GroupAccessMode::create}; } @@ -1329,7 +1329,7 @@ namespace HDF5 DataSet Group::open_dataset(const std::string &name) const { - return DataSet(name, *hdf5_reference, mpi); + return {name, *hdf5_reference, mpi}; } @@ -1340,7 +1340,7 @@ namespace HDF5 const std::vector &dimensions) const { std::shared_ptr t_type = internal::get_hdf5_datatype(); - return DataSet(name, *hdf5_reference, dimensions, t_type, mpi); + return {name, *hdf5_reference, dimensions, t_type, mpi}; } diff --git a/source/dofs/dof_handler_policy.cc b/source/dofs/dof_handler_policy.cc index bdb9b68d537b..aa9b53c70372 100644 --- a/source/dofs/dof_handler_policy.cc +++ b/source/dofs/dof_handler_policy.cc @@ -4206,7 +4206,7 @@ namespace internal // multigrid is not currently implemented for shared triangulations Assert(false, ExcNotImplemented()); - return NumberCache(); + return {}; } diff --git a/source/fe/fe.cc b/source/fe/fe.cc index a45d0b0fd377..861777b58402 100644 --- a/source/fe/fe.cc +++ b/source/fe/fe.cc @@ -446,7 +446,7 @@ FiniteElement::component_mask(const BlockMask &block_mask) const // if we get a block mask that represents all blocks, then // do the same for the returned component mask if (block_mask.represents_the_all_selected_mask()) - return ComponentMask(); + return {}; AssertDimension(block_mask.size(), this->n_blocks()); @@ -502,7 +502,7 @@ FiniteElement::block_mask( // if we get a component mask that represents all component, then // do the same for the returned block mask if (component_mask.represents_the_all_selected_mask()) - return BlockMask(); + return {}; AssertDimension(component_mask.size(), this->n_components()); @@ -859,20 +859,18 @@ FiniteElement::interface_constraints_size() const switch (dim) { case 1: - return TableIndices<2>(0U, 0U); + return {0U, 0U}; case 2: - return TableIndices<2>(this->dofs_per_vertex + 2 * this->dofs_per_line, - this->dofs_per_face); + return {this->dofs_per_vertex + 2 * this->dofs_per_line, + this->dofs_per_face}; case 3: - return TableIndices<2>(5 * this->dofs_per_vertex + - 12 * this->dofs_per_line + - 4 * this->dofs_per_quad, - this->dofs_per_face); + return {5 * this->dofs_per_vertex + 12 * this->dofs_per_line + + 4 * this->dofs_per_quad, + this->dofs_per_face}; default: Assert(false, ExcNotImplemented()); } - return TableIndices<2>(numbers::invalid_unsigned_int, - numbers::invalid_unsigned_int); + return {numbers::invalid_unsigned_int, numbers::invalid_unsigned_int}; } diff --git a/source/fe/mapping_q_generic.cc b/source/fe/mapping_q_generic.cc index 44400569ddce..4dfaf968dc6c 100644 --- a/source/fe/mapping_q_generic.cc +++ b/source/fe/mapping_q_generic.cc @@ -174,7 +174,7 @@ namespace internal if (std::abs(xi_denominator0) > 1e-10 * max_x) { const double xi = (x + subexpr0) / xi_denominator0; - return Point<2>(xi, eta); + return {xi, static_cast(eta)}; } else { @@ -187,7 +187,7 @@ namespace internal if (std::abs(xi_denominator1) > 1e-10 * max_y) { const double xi = (subexpr1 + y) / xi_denominator1; - return Point<2>(xi, eta); + return {xi, static_cast(eta)}; } else // give up and try Newton iteration { @@ -200,8 +200,8 @@ namespace internal // bogus return to placate compiler. It should not be possible to get // here. Assert(false, ExcInternalError()); - return Point<2>(std::numeric_limits::quiet_NaN(), - std::numeric_limits::quiet_NaN()); + return {std::numeric_limits::quiet_NaN(), + std::numeric_limits::quiet_NaN()}; } @@ -2517,7 +2517,7 @@ MappingQGeneric<1, 3>::transform_real_to_unit_cell_internal( const Point<1> &) const { Assert(false, ExcNotImplemented()); - return Point<1>(); + return {}; } diff --git a/source/grid/grid_tools.cc b/source/grid/grid_tools.cc index 2b50ee5f4056..201dfe03f9ee 100644 --- a/source/grid/grid_tools.cc +++ b/source/grid/grid_tools.cc @@ -815,8 +815,8 @@ namespace GridTools Point<2> operator()(const Point<2> &p) const { - return Point<2>(std::cos(angle) * p(0) - std::sin(angle) * p(1), - std::sin(angle) * p(0) + std::cos(angle) * p(1)); + return {std::cos(angle) * p(0) - std::sin(angle) * p(1), + std::sin(angle) * p(0) + std::cos(angle) * p(1)}; } private: @@ -836,17 +836,17 @@ namespace GridTools operator()(const Point<3> &p) const { if (axis == 0) - return Point<3>(p(0), - std::cos(angle) * p(1) - std::sin(angle) * p(2), - std::sin(angle) * p(1) + std::cos(angle) * p(2)); + return {p(0), + std::cos(angle) * p(1) - std::sin(angle) * p(2), + std::sin(angle) * p(1) + std::cos(angle) * p(2)}; else if (axis == 1) - return Point<3>(std::cos(angle) * p(0) + std::sin(angle) * p(2), - p(1), - -std::sin(angle) * p(0) + std::cos(angle) * p(2)); + return {std::cos(angle) * p(0) + std::sin(angle) * p(2), + p(1), + -std::sin(angle) * p(0) + std::cos(angle) * p(2)}; else - return Point<3>(std::cos(angle) * p(0) - std::sin(angle) * p(1), - std::sin(angle) * p(0) + std::cos(angle) * p(1), - p(2)); + return {std::cos(angle) * p(0) - std::sin(angle) * p(1), + std::sin(angle) * p(0) + std::cos(angle) * p(1), + p(2)}; } private: diff --git a/source/grid/manifold.cc b/source/grid/manifold.cc index 35d213df01a3..e668286c4a2e 100644 --- a/source/grid/manifold.cc +++ b/source/grid/manifold.cc @@ -379,7 +379,7 @@ Manifold<1, 1>::get_new_point_on_face( const Triangulation<1, 1>::face_iterator &) const { Assert(false, ExcImpossibleInDim(1)); - return Point<1>(); + return {}; } @@ -390,7 +390,7 @@ Manifold<1, 2>::get_new_point_on_face( const Triangulation<1, 2>::face_iterator &) const { Assert(false, ExcImpossibleInDim(1)); - return Point<2>(); + return {}; } @@ -401,7 +401,7 @@ Manifold<1, 3>::get_new_point_on_face( const Triangulation<1, 3>::face_iterator &) const { Assert(false, ExcImpossibleInDim(1)); - return Point<3>(); + return {}; } @@ -412,7 +412,7 @@ Manifold<1, 1>::get_new_point_on_quad( const Triangulation<1, 1>::quad_iterator &) const { Assert(false, ExcImpossibleInDim(1)); - return Point<1>(); + return {}; } @@ -423,7 +423,7 @@ Manifold<1, 2>::get_new_point_on_quad( const Triangulation<1, 2>::quad_iterator &) const { Assert(false, ExcImpossibleInDim(1)); - return Point<2>(); + return {}; } @@ -434,7 +434,7 @@ Manifold<1, 3>::get_new_point_on_quad( const Triangulation<1, 3>::quad_iterator &) const { Assert(false, ExcImpossibleInDim(1)); - return Point<3>(); + return {}; } @@ -492,7 +492,7 @@ namespace internal // the implementation below is bogus for this case anyway // (see the assert at the beginning of that function). Assert(false, ExcNotImplemented()); - return Tensor<1, 3>(); + return {}; } @@ -808,7 +808,7 @@ FlatManifold<1, 1>::normal_vector(const Triangulation<1, 1>::face_iterator &, const Point<1> &) const { Assert(false, ExcNotImplemented()); - return Tensor<1, 1>(); + return {}; } @@ -819,7 +819,7 @@ FlatManifold<1, 2>::normal_vector(const Triangulation<1, 2>::face_iterator &, const Point<2> &) const { Assert(false, ExcNotImplemented()); - return Tensor<1, 2>(); + return {}; } @@ -830,7 +830,7 @@ FlatManifold<1, 3>::normal_vector(const Triangulation<1, 3>::face_iterator &, const Point<3> &) const { Assert(false, ExcNotImplemented()); - return Tensor<1, 3>(); + return {}; } diff --git a/source/grid/manifold_lib.cc b/source/grid/manifold_lib.cc index c13d73f40537..4dd1c9a31d05 100644 --- a/source/grid/manifold_lib.cc +++ b/source/grid/manifold_lib.cc @@ -1268,7 +1268,7 @@ EllipticalManifold<2, 2>::pull_back(const Point<2> &space_point) const } const double eta = std::acos(cos_eta); const double pt1 = (std::signbit(y) ? 2.0 * numbers::PI - eta : eta); - return Point<2>(pt0, pt1); + return {pt0, pt1}; } @@ -1279,7 +1279,7 @@ EllipticalManifold::push_forward_gradient( const Point &) const { Assert(false, ExcNotImplemented()); - return DerivativeForm<1, spacedim, spacedim>(); + return {}; } @@ -1481,7 +1481,7 @@ TorusManifold::pull_back(const Point<3> &p) const double w = std::sqrt(std::pow(y - std::sin(phi) * R, 2.0) + std::pow(x - std::cos(phi) * R, 2.0) + z * z) / r; - return Point<3>(phi, theta, w); + return {phi, theta, w}; } @@ -1494,9 +1494,9 @@ TorusManifold::push_forward(const Point<3> &chart_point) const double theta = chart_point(1); double w = chart_point(2); - return Point<3>(std::cos(phi) * R + r * w * std::cos(theta) * std::cos(phi), - r * w * std::sin(theta), - std::sin(phi) * R + r * w * std::cos(theta) * std::sin(phi)); + return {std::cos(phi) * R + r * w * std::cos(theta) * std::cos(phi), + r * w * std::sin(theta), + std::sin(phi) * R + r * w * std::cos(theta) * std::sin(phi)}; } diff --git a/source/grid/tria_accessor.cc b/source/grid/tria_accessor.cc index 4e62fde8deb4..c7a1bfdee33c 100644 --- a/source/grid/tria_accessor.cc +++ b/source/grid/tria_accessor.cc @@ -210,7 +210,7 @@ namespace t9 * y[1] - t11 * y[0] + x[0] * t53 - t59 * x[2] + t59 * x[1] - t39 * x[0]; - return Point<2>(t27 * t37 / 3, t63 * t37 / 3); + return {t27 * t37 / 3, t63 * t37 / 3}; } @@ -1233,7 +1233,7 @@ namespace s2 = s3 * s4; const double unknown2 = s1 * s2; - return Point<3>(unknown0, unknown1, unknown2); + return {unknown0, unknown1, unknown2}; } @@ -2218,7 +2218,7 @@ CellAccessor::id() const Assert(ptr.level() == 0, ExcInternalError()); const unsigned int coarse_index = ptr.index(); - return CellId(coarse_index, n_child_indices, id.data()); + return {coarse_index, n_child_indices, id.data()}; } diff --git a/source/opencascade/manifold_lib.cc b/source/opencascade/manifold_lib.cc index c872b0d2fcbe..209043ef6b8a 100644 --- a/source/opencascade/manifold_lib.cc +++ b/source/opencascade/manifold_lib.cc @@ -404,7 +404,7 @@ namespace OpenCASCADE double u = proj_params.X(); double v = proj_params.Y(); - return Point<2>(u, v); + return {u, v}; } template From 24f226f508f08d459e4c9946d97f9f2cb87df7f9 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Tue, 29 Jan 2019 10:57:27 +0100 Subject: [PATCH 023/507] modernize-use-equals-default --- include/deal.II/grid/filtered_iterator.h | 13 ------------- include/deal.II/lac/dynamic_sparsity_pattern.h | 8 +------- include/deal.II/matrix_free/matrix_free.h | 2 +- 3 files changed, 2 insertions(+), 21 deletions(-) diff --git a/include/deal.II/grid/filtered_iterator.h b/include/deal.II/grid/filtered_iterator.h index c7b6b8e771e4..88f47c7a3bfb 100644 --- a/include/deal.II/grid/filtered_iterator.h +++ b/include/deal.II/grid/filtered_iterator.h @@ -567,11 +567,6 @@ class FilteredIterator : public BaseIterator */ FilteredIterator(const FilteredIterator &fi); - /** - * Destructor. - */ - ~FilteredIterator(); - /** * Assignment operator. Copy the iterator value of the argument, but as * discussed in the class documentation, the predicate of the argument is @@ -966,14 +961,6 @@ inline FilteredIterator::FilteredIterator( -template -inline FilteredIterator::~FilteredIterator() -{ - predicate.reset(); -} - - - template inline FilteredIterator & FilteredIterator::operator=(const FilteredIterator &fi) diff --git a/include/deal.II/lac/dynamic_sparsity_pattern.h b/include/deal.II/lac/dynamic_sparsity_pattern.h index b5f1dd36a1d5..ed2a200179cc 100644 --- a/include/deal.II/lac/dynamic_sparsity_pattern.h +++ b/include/deal.II/lac/dynamic_sparsity_pattern.h @@ -210,7 +210,7 @@ namespace DynamicSparsityPatternIterators * here only to be able to store iterators in STL containers such as * `std::vector`. */ - Iterator(); + Iterator() = default; /** * Prefix increment. @@ -886,12 +886,6 @@ namespace DynamicSparsityPatternIterators - inline Iterator::Iterator() - : accessor() - {} - - - inline Iterator & Iterator::operator++() { diff --git a/include/deal.II/matrix_free/matrix_free.h b/include/deal.II/matrix_free/matrix_free.h index 15a1e5e32dc7..a0134ebfe76d 100644 --- a/include/deal.II/matrix_free/matrix_free.h +++ b/include/deal.II/matrix_free/matrix_free.h @@ -2666,7 +2666,7 @@ namespace internal 3); } - ~VectorDataExchange() + ~VectorDataExchange() // NOLINT { # ifdef DEAL_II_WITH_MPI for (unsigned int i = 0; i < tmp_data.size(); ++i) From 551145b514900669ab799dc17a4f9ae23e31d377 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Tue, 29 Jan 2019 10:58:02 +0100 Subject: [PATCH 024/507] modernize-use-nullptr --- include/deal.II/numerics/error_estimator.h | 20 ++++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/include/deal.II/numerics/error_estimator.h b/include/deal.II/numerics/error_estimator.h index ecb9786ffef4..a9b3fa4a6087 100644 --- a/include/deal.II/numerics/error_estimator.h +++ b/include/deal.II/numerics/error_estimator.h @@ -398,7 +398,7 @@ class KellyErrorEstimator const std::vector &solutions, std::vector *> & errors, const ComponentMask & component_mask = ComponentMask(), - const Function * coefficients = 0, + const Function * coefficients = nullptr, const unsigned int n_threads = numbers::invalid_unsigned_int, const types::subdomain_id subdomain_id = numbers::invalid_subdomain_id, const types::material_id material_id = numbers::invalid_material_id, @@ -419,7 +419,7 @@ class KellyErrorEstimator const std::vector &solutions, std::vector *> & errors, const ComponentMask & component_mask = ComponentMask(), - const Function * coefficients = 0, + const Function * coefficients = nullptr, const unsigned int n_threads = numbers::invalid_unsigned_int, const types::subdomain_id subdomain_id = numbers::invalid_subdomain_id, const types::material_id material_id = numbers::invalid_material_id, @@ -442,7 +442,7 @@ class KellyErrorEstimator const InputVector & solution, Vector & error, const ComponentMask & component_mask = ComponentMask(), - const Function *coefficients = 0, + const Function *coefficients = nullptr, const unsigned int n_threads = numbers::invalid_unsigned_int, const types::subdomain_id subdomain_id = numbers::invalid_subdomain_id, const types::material_id material_id = numbers::invalid_material_id, @@ -487,7 +487,7 @@ class KellyErrorEstimator const std::vector &solutions, std::vector *> & errors, const ComponentMask & component_mask = ComponentMask(), - const Function * coefficients = 0, + const Function * coefficients = nullptr, const unsigned int n_threads = numbers::invalid_unsigned_int, const types::subdomain_id subdomain_id = numbers::invalid_subdomain_id, const types::material_id material_id = numbers::invalid_material_id, @@ -686,7 +686,7 @@ class KellyErrorEstimator<1, spacedim> const std::vector &solutions, std::vector *> & errors, const ComponentMask & component_mask = ComponentMask(), - const Function * coefficients = 0, + const Function * coefficients = nullptr, const unsigned int n_threads = numbers::invalid_unsigned_int, const types::subdomain_id subdomain_id = numbers::invalid_subdomain_id, const types::material_id material_id = numbers::invalid_material_id, @@ -707,7 +707,7 @@ class KellyErrorEstimator<1, spacedim> const std::vector &solutions, std::vector *> & errors, const ComponentMask & component_mask = ComponentMask(), - const Function * coefficients = 0, + const Function * coefficients = nullptr, const unsigned int n_threads = numbers::invalid_unsigned_int, const types::subdomain_id subdomain_id = numbers::invalid_subdomain_id, const types::material_id material_id = numbers::invalid_material_id, @@ -730,7 +730,7 @@ class KellyErrorEstimator<1, spacedim> const InputVector & solution, Vector & error, const ComponentMask & component_mask = ComponentMask(), - const Function *coefficients = 0, + const Function *coefficients = nullptr, const unsigned int n_threads = numbers::invalid_unsigned_int, const types::subdomain_id subdomain_id = numbers::invalid_subdomain_id, const types::material_id material_id = numbers::invalid_material_id, @@ -752,7 +752,7 @@ class KellyErrorEstimator<1, spacedim> const InputVector & solution, Vector & error, const ComponentMask & component_mask = ComponentMask(), - const Function *coefficients = 0, + const Function *coefficients = nullptr, const unsigned int n_threads = numbers::invalid_unsigned_int, const types::subdomain_id subdomain_id = numbers::invalid_subdomain_id, const types::material_id material_id = numbers::invalid_material_id, @@ -775,7 +775,7 @@ class KellyErrorEstimator<1, spacedim> const std::vector &solutions, std::vector *> & errors, const ComponentMask & component_mask = ComponentMask(), - const Function * coefficients = 0, + const Function * coefficients = nullptr, const unsigned int n_threads = numbers::invalid_unsigned_int, const types::subdomain_id subdomain_id = numbers::invalid_subdomain_id, const types::material_id material_id = numbers::invalid_material_id, @@ -797,7 +797,7 @@ class KellyErrorEstimator<1, spacedim> const std::vector &solutions, std::vector *> & errors, const ComponentMask & component_mask = ComponentMask(), - const Function * coefficients = 0, + const Function * coefficients = nullptr, const unsigned int n_threads = numbers::invalid_unsigned_int, const types::subdomain_id subdomain_id = numbers::invalid_subdomain_id, const types::material_id material_id = numbers::invalid_material_id, From 723f41aa2dd617dad4529463225c400cd2075bce Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Tue, 29 Jan 2019 10:59:11 +0100 Subject: [PATCH 025/507] performance-unnecessary-value-param --- source/base/hdf5.cc | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/source/base/hdf5.cc b/source/base/hdf5.cc index d8fe0dca80c1..b8c958679012 100644 --- a/source/base/hdf5.cc +++ b/source/base/hdf5.cc @@ -518,16 +518,12 @@ namespace HDF5 template <> void HDF5Object::set_attribute(const std::string &attr_name, - const std::string value) + const std::string value) // NOLINT { // Writes a UTF8 variable string // // code inspired from // https://support.hdfgroup.org/ftp/HDF5/examples/misc-examples/vlstratt.c - // - // In the case of a variable length string, H5Awrite needs the address of a - // (char *). For this reason the std::string value has been copied to a C - // string. hid_t attr; hid_t aid; From 4975f4b31816fcd423d714df84f83977fb7a2015 Mon Sep 17 00:00:00 2001 From: Giovanni Alzetta Date: Wed, 9 Jan 2019 22:13:56 +0100 Subject: [PATCH 026/507] Added covering rtree and flag to GridTools::Cache --- .../changes/minor/20190111GiovanniAlzetta | 5 + include/deal.II/grid/grid_tools_cache.h | 33 + .../grid/grid_tools_cache_update_flags.h | 12 + source/grid/grid_tools_cache.cc | 41 + tests/grid/grid_tools_cache_04.cc | 120 ++ ...h_mpi=true.with_p4est=true.mpirun=1.output | 238 ++++ ...h_mpi=true.with_p4est=true.mpirun=4.output | 1007 +++++++++++++++++ 7 files changed, 1456 insertions(+) create mode 100644 doc/news/changes/minor/20190111GiovanniAlzetta create mode 100644 tests/grid/grid_tools_cache_04.cc create mode 100644 tests/grid/grid_tools_cache_04.with_mpi=true.with_p4est=true.mpirun=1.output create mode 100644 tests/grid/grid_tools_cache_04.with_mpi=true.with_p4est=true.mpirun=4.output diff --git a/doc/news/changes/minor/20190111GiovanniAlzetta b/doc/news/changes/minor/20190111GiovanniAlzetta new file mode 100644 index 000000000000..868aee927f14 --- /dev/null +++ b/doc/news/changes/minor/20190111GiovanniAlzetta @@ -0,0 +1,5 @@ +New: GridTools::Cache::get_covering_rtree() automatically stores and generates +a rtree of bounding boxes covering the whole triangulation. In a distributed setting +it can identify which processes have locally owned cells in any part of the mesh. +
+(Giovanni Alzetta, 2019/01/11) diff --git a/include/deal.II/grid/grid_tools_cache.h b/include/deal.II/grid/grid_tools_cache.h index ddbfc8444d1e..e348103f6dbd 100644 --- a/include/deal.II/grid/grid_tools_cache.h +++ b/include/deal.II/grid/grid_tools_cache.h @@ -150,6 +150,33 @@ namespace GridTools const Mapping & get_mapping() const; + + /** + * This function returns an object that allows identifying + * which process(es) in a parallel computation may own the + * cell that surrounds a given point. The elements of this + * object -- an Rtree -- are pairs of bounding boxes denoting + * areas that cover all or parts of the local portion of a + * parallel triangulation, and an unsigned int representing + * the process or subdomain that owns these cells. + * Given a point on a parallel::Triangulation, this tree + * allows to identify one, or few candidate processes, for + * which the point lies on a locally owned cell. + * + * Constructing or updating the rtree requires a call to + * GridTools::build_global_description_tree(), which exchanges + * bounding boxes between all processes using + * Utilities::MPI::all_gather(), a collective operation. + * Therefore this function must be called by all processes + * at the same time. + * + * While each box may only cover part of a process's locally + * owned part of the triangulation, the boxes associated with + * each process jointly cover the entire local portion. + */ + const RTree, unsigned int>> & + get_covering_rtree() const; + #ifdef DEAL_II_WITH_NANOFLANN /** * Return the cached vertex_kdtree object, constructed with the vertices of @@ -191,6 +218,12 @@ namespace GridTools mutable std::vector>> vertex_to_cell_centers; + /** + * An rtree object covering the whole mesh. + */ + mutable RTree, unsigned int>> + covering_rtree; + #ifdef DEAL_II_WITH_NANOFLANN /** * A KDTree object constructed with the vertices of the triangulation. diff --git a/include/deal.II/grid/grid_tools_cache_update_flags.h b/include/deal.II/grid/grid_tools_cache_update_flags.h index a119af38ab97..9ae073b7d17f 100644 --- a/include/deal.II/grid/grid_tools_cache_update_flags.h +++ b/include/deal.II/grid/grid_tools_cache_update_flags.h @@ -73,6 +73,16 @@ namespace GridTools */ update_cell_bounding_boxes_rtree = 0x020, + /** + * Update the covering rtree object, initialized with pairs + * of a bounding box and an unsigned int. The bounding + * boxes are used to describe approximately which portion + * of the mesh contains locally owned cells by the + * process of rank the second element of the pair. + * + */ + update_covering_rtree = 0x040, + /** * Update all objects. */ @@ -94,6 +104,8 @@ namespace GridTools s << "|vertex_to_cell_map"; if (u & update_vertex_to_cell_centers_directions) s << "|vertex_to_cells_centers_directions"; + if (u & update_covering_rtree) + s << "|covering_rtree"; #ifdef DEAL_II_WITH_NANOFLANN if (u & update_vertex_kdtree) s << "|vertex_kdtree"; diff --git a/source/grid/grid_tools_cache.cc b/source/grid/grid_tools_cache.cc index 96219c99966f..6c8b6af8a195 100644 --- a/source/grid/grid_tools_cache.cc +++ b/source/grid/grid_tools_cache.cc @@ -13,9 +13,15 @@ // // --------------------------------------------------------------------- +#include +#include + +#include #include #include +#include + DEAL_II_NAMESPACE_OPEN namespace GridTools @@ -146,6 +152,41 @@ namespace GridTools } return vertex_kdtree; } + + + + template + const RTree, unsigned int>> & + Cache::get_covering_rtree() const + { + if (update_flags & update_covering_rtree) + { + // TO DO: the locally owned portion of the domain + // might consists of more separate pieces: a single + // bounding box might not always be the best choice. + IteratorFilters::LocallyOwnedCell locally_owned_cell_predicate; + const BoundingBox bbox = + GridTools::compute_bounding_box(*tria, locally_owned_cell_predicate); + + + std::vector> bbox_v(1, bbox); + if (const auto tria_mpi = + dynamic_cast *>( + &(*tria))) + { + covering_rtree = GridTools::build_global_description_tree( + bbox_v, tria_mpi->get_communicator()); + } + else + { + covering_rtree = + GridTools::build_global_description_tree(bbox_v, MPI_COMM_SELF); + } + update_flags = update_flags & ~update_covering_rtree; + } + + return covering_rtree; + } #endif #include "grid_tools_cache.inst" diff --git a/tests/grid/grid_tools_cache_04.cc b/tests/grid/grid_tools_cache_04.cc new file mode 100644 index 000000000000..42116eca171f --- /dev/null +++ b/tests/grid/grid_tools_cache_04.cc @@ -0,0 +1,120 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2001 - 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + +// Validate grid_tools_cache for the creation of build global rtree + + +#include +#include +#include + +#include +#include +#include +#include +#include + +#include +#include +#include + +#include "../tests.h" + +using namespace dealii; + +namespace bg = boost::geometry; +namespace bgi = boost::geometry::index; + + +template +void +test(unsigned int n_points) +{ + deallog << "Testing for dim = " << dim << std::endl; + + // Creating a grid in the square [0,1]x[0,1] + parallel::shared::Triangulation tria(MPI_COMM_WORLD); + GridGenerator::hyper_cube(tria); + tria.refine_global(std::max(8 - dim, 3)); + + + GridTools::Cache cache(tria); + + const auto &global_description = cache.get_covering_rtree(); + + // Creating the random points + std::vector> points; + + for (size_t i = 0; i < n_points; ++i) + points.push_back(random_point()); + + + + const auto cell_qpoint_map = + GridTools::compute_point_locations(cache, points); + const auto & cells = std::get<0>(cell_qpoint_map); + const auto & maps = std::get<2>(cell_qpoint_map); + unsigned int n_cells = cells.size(); + + for (unsigned int c = 0; c < n_cells; ++c) + { + // We know the owner as we're working on a shared triangulation + unsigned int cell_owner = cells[c]->subdomain_id(); + for (unsigned int idx : maps[c]) + { + std::vector, unsigned int>> test_results; + global_description.query(bgi::intersects(points[idx]), + std::back_inserter(test_results)); + bool found = false; + + // Printing and checking function output + for (const auto &ans : test_results) + { + const auto &bd_points = ans.first.get_boundary_points(); + deallog << "Bounding box: p1 " << bd_points.first << " p2 " + << bd_points.second << " rank owner: " << ans.second + << std::endl; + // Check if the guess made from the tree contains the answer + if (ans.second == cell_owner) + found = true; + } + + if (!found) + deallog << "Error point " << points[idx] << " was not found." + << std::endl; + } + } + deallog << "Test for dim " << dim << " finished." << std::endl; +} + + + +int +main(int argc, char **argv) +{ + Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1); +#ifdef DEAL_II_WITH_MPI + MPILogInitAll log; +#else + initlog(); + deallog.push("0"); +#endif + + test<1>(50); + test<2>(80); + test<3>(101); + + return 0; +} diff --git a/tests/grid/grid_tools_cache_04.with_mpi=true.with_p4est=true.mpirun=1.output b/tests/grid/grid_tools_cache_04.with_mpi=true.with_p4est=true.mpirun=1.output new file mode 100644 index 000000000000..2c5df042b4d6 --- /dev/null +++ b/tests/grid/grid_tools_cache_04.with_mpi=true.with_p4est=true.mpirun=1.output @@ -0,0 +1,238 @@ + +DEAL:0::Testing for dim = 1 +DEAL:0::Bounding box: p1 0.00000 p2 1.00000 rank owner: 0 +DEAL:0::Bounding box: p1 0.00000 p2 1.00000 rank owner: 0 +DEAL:0::Bounding box: p1 0.00000 p2 1.00000 rank owner: 0 +DEAL:0::Bounding box: p1 0.00000 p2 1.00000 rank owner: 0 +DEAL:0::Bounding box: p1 0.00000 p2 1.00000 rank owner: 0 +DEAL:0::Bounding box: p1 0.00000 p2 1.00000 rank owner: 0 +DEAL:0::Bounding box: p1 0.00000 p2 1.00000 rank owner: 0 +DEAL:0::Bounding box: p1 0.00000 p2 1.00000 rank owner: 0 +DEAL:0::Bounding box: p1 0.00000 p2 1.00000 rank owner: 0 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0.562500 1.00000 1.00000 rank owner: 0 +DEAL:3::Bounding box: p1 0.531250 0.531250 0.00000 p2 1.00000 1.00000 1.00000 rank owner: 2 +DEAL:3::Bounding box: p1 0.00000 0.468750 0.00000 p2 0.562500 1.00000 1.00000 rank owner: 0 +DEAL:3::Test for dim 3 finished. + From d716983f2a91177d5a2364ec6ba5d8c1c8b25175 Mon Sep 17 00:00:00 2001 From: David Wells Date: Sun, 20 Jan 2019 22:32:32 -0500 Subject: [PATCH 027/507] Use AlignedVector to manage Vector's memory. Vector already requires that the underlying buffer be aligned and uses exactly the same function (posix_memalign) as AlignedVector to do it: we can simplify the implementation of Vector a lot by just using an AlignedVector to manage the data instead. --- include/deal.II/lac/vector.h | 102 ++----- include/deal.II/lac/vector.templates.h | 383 +++++++++---------------- tests/serialization/vector.output | 4 +- 3 files changed, 165 insertions(+), 324 deletions(-) diff --git a/include/deal.II/lac/vector.h b/include/deal.II/lac/vector.h index d44d28ee3b27..2dadf1da5e10 100644 --- a/include/deal.II/lac/vector.h +++ b/include/deal.II/lac/vector.h @@ -19,6 +19,7 @@ #include +#include #include #include #include @@ -29,14 +30,6 @@ #include #include -// boost::serialization::make_array used to be in array.hpp, but was -// moved to a different file in BOOST 1.64 -#include -#if BOOST_VERSION >= 106400 -# include -#else -# include -#endif #include #include @@ -152,6 +145,8 @@ class Vector : public Subscriptor * * We would like to make this constructor explicit, but standard containers * insist on using it implicitly. + * + * @dealiiOperationIsMultithreaded */ Vector(const Vector &v); @@ -159,19 +154,13 @@ class Vector : public Subscriptor * Move constructor. Creates a new vector by stealing the internal data of * the vector @p v. */ - Vector(Vector &&v) noexcept; + Vector(Vector &&v) noexcept = default; /** * Copy constructor taking a vector of another data type. This will fail if * there is no conversion path from @p OtherNumber to @p Number. Note that * you may lose accuracy when copying to a vector with data elements with * less accuracy. - * - * Older versions of gcc did not honor the @p explicit keyword on template - * constructors. In such cases, it is easy to accidentally write code that - * can be very inefficient, since the compiler starts performing hidden - * conversions. To avoid this, this function is disabled if we have detected - * a broken compiler during configuration. */ template explicit Vector(const Vector &v); @@ -365,7 +354,7 @@ class Vector : public Subscriptor * have after being newly default-constructed. */ Vector & - operator=(Vector &&v) noexcept; + operator=(Vector &&v) noexcept = default; /** * Copy the given vector. Resize the present vector if necessary. @@ -993,27 +982,9 @@ class Vector : public Subscriptor private: /** - * Dimension. Actual number of components contained in the vector. Get this - * number by calling size(). - */ - size_type vec_size; - - /** - * Amount of memory actually reserved for this vector. This number may be - * greater than @p vec_size if a @p reinit was called with less memory - * requirements than the vector needed last time. At present @p reinit does - * not free memory when the number of needed elements is reduced. - */ - size_type max_vec_size; - - /** - * Pointer to the array of elements of this vector. - * - * Because we allocate these arrays via Utilities::System::posix_memalign, - * we need to use a custom deleter for this object that does not call - * delete[], but instead calls @p free(). + * Array of elements owned by this vector. */ - std::unique_ptr values; + AlignedVector values; /** * For parallel loops with TBB, this member variable stores the affinity @@ -1022,25 +993,11 @@ class Vector : public Subscriptor mutable std::shared_ptr thread_loop_partitioner; - /** - * Allocate and align @p values along 64-byte boundaries. The size of the - * allocated memory is determined by @p max_vec_size . Copy first - * @p copy_n_el from the old values. - */ - void - allocate(const size_type copy_n_el = 0); - /** * Make all other vector types friends. */ template friend class Vector; - - /** - * LAPACK matrices need access to the data. - */ - template - friend class LAPACKFullMatrix; }; /*@}*/ @@ -1060,9 +1017,6 @@ Vector::lp_norm(const real_type) const; template inline Vector::Vector() - : vec_size(0) - , max_vec_size(0) - , values(nullptr, &free) { // virtual functions called in constructors and destructors never use the // override in a derived class @@ -1075,9 +1029,6 @@ inline Vector::Vector() template template Vector::Vector(const InputIterator first, const InputIterator last) - : vec_size(0) - , max_vec_size(0) - , values(nullptr, &free) { // allocate memory. do not initialize it, as we will copy over to it in a // second @@ -1089,9 +1040,6 @@ Vector::Vector(const InputIterator first, const InputIterator last) template inline Vector::Vector(const size_type n) - : vec_size(0) - , max_vec_size(0) - , values(nullptr, &free) { // virtual functions called in constructors and destructors never use the // override in a derived class @@ -1105,7 +1053,7 @@ template inline typename Vector::size_type Vector::size() const { - return vec_size; + return values.size(); } @@ -1122,7 +1070,7 @@ template inline typename Vector::pointer Vector::data() { - return values.get(); + return values.data(); } @@ -1131,7 +1079,7 @@ template inline typename Vector::const_pointer Vector::data() const { - return values.get(); + return values.data(); } @@ -1140,7 +1088,7 @@ template inline typename Vector::iterator Vector::begin() { - return values.get(); + return values.begin(); } @@ -1149,7 +1097,7 @@ template inline typename Vector::const_iterator Vector::begin() const { - return values.get(); + return values.begin(); } @@ -1158,7 +1106,7 @@ template inline typename Vector::iterator Vector::end() { - return values.get() + vec_size; + return values.end(); } @@ -1167,7 +1115,7 @@ template inline typename Vector::const_iterator Vector::end() const { - return values.get() + vec_size; + return values.end(); } @@ -1176,7 +1124,7 @@ template inline Number Vector::operator()(const size_type i) const { - Assert(i < vec_size, ExcIndexRange(i, 0, vec_size)); + Assert(i < size(), ExcIndexRange(i, 0, size())); return values[i]; } @@ -1186,7 +1134,7 @@ template inline Number & Vector::operator()(const size_type i) { - Assert(i < vec_size, ExcIndexRangeType(i, 0, vec_size)); + Assert(i < size(), ExcIndexRangeType(i, 0, size())); return values[i]; } @@ -1271,7 +1219,7 @@ Vector::add(const std::vector &indices, { Assert(indices.size() == values.size(), ExcDimensionMismatch(indices.size(), values.size())); - add(indices.size(), indices.data(), values.values.get()); + add(indices.size(), indices.data(), values.values.begin()); } @@ -1285,7 +1233,7 @@ Vector::add(const size_type n_indices, { for (size_type i = 0; i < n_indices; ++i) { - Assert(indices[i] < vec_size, ExcIndexRange(indices[i], 0, vec_size)); + Assert(indices[i] < size(), ExcIndexRange(indices[i], 0, size())); Assert( numbers::is_finite(values[i]), ExcMessage( @@ -1327,8 +1275,6 @@ template inline void Vector::swap(Vector &v) { - std::swap(vec_size, v.vec_size); - std::swap(max_vec_size, v.max_vec_size); std::swap(values, v.values); } @@ -1341,9 +1287,7 @@ Vector::save(Archive &ar, const unsigned int) const { // forward to serialization function in the base class. ar &static_cast(*this); - - ar &vec_size &max_vec_size; - ar & boost::serialization::make_array(values.get(), max_vec_size); + ar &values; } @@ -1353,15 +1297,9 @@ template inline void Vector::load(Archive &ar, const unsigned int) { - // get rid of previous content - values.reset(); - // the load stuff again from the archive ar &static_cast(*this); - ar &vec_size &max_vec_size; - - allocate(); - ar &boost::serialization::make_array(values.get(), max_vec_size); + ar &values; } #endif diff --git a/include/deal.II/lac/vector.templates.h b/include/deal.II/lac/vector.templates.h index e67ffd71ae18..87c126c8b8b4 100644 --- a/include/deal.II/lac/vector.templates.h +++ b/include/deal.II/lac/vector.templates.h @@ -46,15 +46,8 @@ DEAL_II_NAMESPACE_OPEN template Vector::Vector(const Vector &v) : Subscriptor() - , vec_size(v.size()) - , max_vec_size(v.size()) - , values(nullptr, &free) { - if (vec_size != 0) - { - allocate(); - *this = v; - } + *this = v; } @@ -73,34 +66,11 @@ Vector::apply_givens_rotation(const std::array &csr, -template -Vector::Vector(Vector &&v) noexcept - : Subscriptor(std::move(v)) - , vec_size(v.vec_size) - , max_vec_size(v.max_vec_size) - , values(std::move(v.values)) - , thread_loop_partitioner(std::move(v.thread_loop_partitioner)) -{ - v.vec_size = 0; - v.max_vec_size = 0; - v.values = nullptr; -} - - - template template Vector::Vector(const Vector &v) - : Subscriptor() - , vec_size(v.size()) - , max_vec_size(v.size()) - , values(nullptr, &free) { - if (vec_size != 0) - { - allocate(); - *this = v; - } + *this = v; } @@ -154,10 +124,6 @@ namespace internal template Vector::Vector(const PETScWrappers::VectorBase &v) - : Subscriptor() - , vec_size(0) - , max_vec_size(0) - , values(nullptr, &free) { if (v.size() != 0) { @@ -171,15 +137,10 @@ Vector::Vector(const PETScWrappers::VectorBase &v) template Vector::Vector(const TrilinosWrappers::MPI::Vector &v) - : Subscriptor() - , vec_size(v.size()) - , max_vec_size(v.size()) - , values(nullptr, &free) + : values(v.size()) { - if (vec_size != 0) + if (size() != 0) { - allocate(); - // Copy the distributed vector to // a local one at all processors // that know about the original vector. @@ -188,12 +149,12 @@ Vector::Vector(const TrilinosWrappers::MPI::Vector &v) // this, but it has not yet been // found. TrilinosWrappers::MPI::Vector localized_vector; - localized_vector.reinit(complete_index_set(vec_size), + localized_vector.reinit(complete_index_set(size()), v.get_mpi_communicator()); localized_vector.reinit(v, false, true); - Assert(localized_vector.size() == vec_size, - ExcDimensionMismatch(localized_vector.size(), vec_size)); + Assert(localized_vector.size() == size(), + ExcDimensionMismatch(localized_vector.size(), size())); // get a representation of the vector // and copy it @@ -202,7 +163,7 @@ Vector::Vector(const TrilinosWrappers::MPI::Vector &v) int ierr = localized_vector.trilinos_vector().ExtractView(&start_ptr); AssertThrow(ierr == 0, ExcTrilinosError(ierr)); - std::copy(start_ptr[0], start_ptr[0] + vec_size, begin()); + std::copy(start_ptr[0], start_ptr[0] + size(), begin()); } } @@ -217,16 +178,16 @@ Vector::operator=(const Vector &v) return *this; thread_loop_partitioner = v.thread_loop_partitioner; - if (vec_size != v.vec_size) + if (size() != v.size()) reinit(v, true); - if (vec_size > 0) + if (0 < size()) { dealii::internal::VectorOperations::Vector_copy copier( - v.values.get(), values.get()); + v.begin(), begin()); internal::VectorOperations::parallel_for(copier, 0, - vec_size, + size(), thread_loop_partitioner); } @@ -235,39 +196,20 @@ Vector::operator=(const Vector &v) -template -inline Vector & -Vector::operator=(Vector &&v) noexcept -{ - Subscriptor::operator=(std::move(v)); - - vec_size = v.vec_size; - max_vec_size = v.max_vec_size; - values = std::move(v.values); - thread_loop_partitioner = std::move(v.thread_loop_partitioner); - - v.vec_size = 0; - v.max_vec_size = 0; - - return *this; -} - - - template template inline Vector & Vector::operator=(const Vector &v) { thread_loop_partitioner = v.thread_loop_partitioner; - if (vec_size != v.vec_size) + if (size() != v.size()) reinit(v, true); dealii::internal::VectorOperations::Vector_copy copier( - v.values.get(), values.get()); + v.begin(), begin()); internal::VectorOperations::parallel_for(copier, 0, - vec_size, + size(), thread_loop_partitioner); return *this; @@ -279,35 +221,41 @@ template inline void Vector::reinit(const size_type n, const bool omit_zeroing_entries) { - if (n == 0) + const std::size_t old_size = size(); + + // avoid allocating if the new size is not larger than the old size + if (n <= size()) { - values.reset(); - max_vec_size = vec_size = 0; thread_loop_partitioner = std::make_shared(); + if (n == 0) + { + values.clear(); + } + else if (n != size()) + values.resize_fast(n); + + if (!omit_zeroing_entries) + values.fill(); return; } - if (n > max_vec_size) - { - max_vec_size = n; - allocate(); - } + // otherwise size() < n and we must allocate + AlignedVector new_values; + new_values.resize_fast(n); + if (!omit_zeroing_entries) + new_values.fill(); + new_values.swap(values); - if (vec_size != n) + if (old_size != size()) { - vec_size = n; - // only reset the partitioner if we actually expect a significant vector // size - if (vec_size >= + if (size() >= 4 * internal::VectorImplementation::minimum_parallel_grain_size) thread_loop_partitioner = std::make_shared(); } - - if (omit_zeroing_entries == false) - *this = Number(); } @@ -316,37 +264,26 @@ template inline void Vector::grow_or_shrink(const size_type n) { + const std::size_t old_size = size(); if (n == 0) { - values.reset(); - max_vec_size = vec_size = 0; + values.clear(); thread_loop_partitioner = std::make_shared(); return; } - const size_type s = std::min(vec_size, n); - if (n > max_vec_size) - { - max_vec_size = n; - allocate(s); - } + values.resize(n); - if (vec_size != n) + if (old_size != n) { - vec_size = n; - // only reset the partitioner if we actually expect a significant vector // size - if (vec_size >= + if (size() >= 4 * internal::VectorImplementation::minimum_parallel_grain_size) thread_loop_partitioner = std::make_shared(); } - - // pad with zeroes - for (size_type i = s; i < vec_size; ++i) - values[i] = Number(); } @@ -359,21 +296,7 @@ Vector::reinit(const Vector &v, { thread_loop_partitioner = v.thread_loop_partitioner; - if (v.vec_size == 0) - { - values.reset(); - max_vec_size = vec_size = 0; - return; - } - - if (v.vec_size > max_vec_size) - { - max_vec_size = v.vec_size; - allocate(); - } - vec_size = v.vec_size; - if (omit_zeroing_entries == false) - *this = Number(); + reinit(v.size(), omit_zeroing_entries); } @@ -382,9 +305,9 @@ template bool Vector::all_zero() const { - Assert(vec_size != 0, ExcEmptyObject()); + Assert(size() != 0, ExcEmptyObject()); - for (size_type i = 0; i < vec_size; ++i) + for (size_type i = 0; i < size(); ++i) if (values[i] != Number()) return false; return true; @@ -396,9 +319,9 @@ template bool Vector::is_non_negative() const { - Assert(vec_size != 0, ExcEmptyObject()); + Assert(size() != 0, ExcEmptyObject()); - for (size_type i = 0; i < vec_size; ++i) + for (size_type i = 0; i < size(); ++i) if (!internal::VectorOperations::is_non_negative(values[i])) return false; @@ -413,14 +336,14 @@ Vector::operator=(const Number s) { AssertIsFinite(s); if (s != Number()) - Assert(vec_size != 0, ExcEmptyObject()); + Assert(size() != 0, ExcEmptyObject()); - if (vec_size > 0) + if (size() > 0) { - internal::VectorOperations::Vector_set setter(s, values.get()); + internal::VectorOperations::Vector_set setter(s, values.begin()); internal::VectorOperations::parallel_for(setter, 0, - vec_size, + size(), thread_loop_partitioner); } @@ -435,14 +358,14 @@ Vector::operator*=(const Number factor) { AssertIsFinite(factor); - Assert(vec_size != 0, ExcEmptyObject()); + Assert(size() != 0, ExcEmptyObject()); internal::VectorOperations::Vectorization_multiply_factor - vector_multiply(values.get(), factor); + vector_multiply(values.begin(), factor); internal::VectorOperations::parallel_for(vector_multiply, 0, - vec_size, + size(), thread_loop_partitioner); return *this; @@ -456,14 +379,14 @@ Vector::add(const Number a, const Vector &v) { AssertIsFinite(a); - Assert(vec_size != 0, ExcEmptyObject()); - Assert(vec_size == v.vec_size, ExcDimensionMismatch(vec_size, v.vec_size)); + Assert(size() != 0, ExcEmptyObject()); + Assert(size() == v.size(), ExcDimensionMismatch(size(), v.size())); internal::VectorOperations::Vectorization_add_av vector_add_av( - values.get(), v.values.get(), a); + values.begin(), v.values.begin(), a); internal::VectorOperations::parallel_for(vector_add_av, 0, - vec_size, + size(), thread_loop_partitioner); } @@ -476,14 +399,14 @@ Vector::sadd(const Number x, const Number a, const Vector &v) AssertIsFinite(x); AssertIsFinite(a); - Assert(vec_size != 0, ExcEmptyObject()); - Assert(vec_size == v.vec_size, ExcDimensionMismatch(vec_size, v.vec_size)); + Assert(size() != 0, ExcEmptyObject()); + Assert(size() == v.size(), ExcDimensionMismatch(size(), v.size())); internal::VectorOperations::Vectorization_sadd_xav vector_sadd_xav( - values.get(), v.values.get(), a, x); + values.begin(), v.values.begin(), a, x); internal::VectorOperations::parallel_for(vector_sadd_xav, 0, - vec_size, + size(), thread_loop_partitioner); } @@ -493,18 +416,18 @@ template template Number Vector::operator*(const Vector &v) const { - Assert(vec_size != 0, ExcEmptyObject()); + Assert(size() != 0, ExcEmptyObject()); if (PointerComparison::equal(this, &v)) return norm_sqr(); - Assert(vec_size == v.size(), ExcDimensionMismatch(vec_size, v.size())); + Assert(size() == v.size(), ExcDimensionMismatch(size(), v.size())); Number sum; - internal::VectorOperations::Dot dot(values.get(), - v.values.get()); + internal::VectorOperations::Dot dot(values.begin(), + v.values.begin()); internal::VectorOperations::parallel_reduce( - dot, 0, vec_size, sum, thread_loop_partitioner); + dot, 0, size(), sum, thread_loop_partitioner); AssertIsFinite(sum); return sum; @@ -516,12 +439,12 @@ template typename Vector::real_type Vector::norm_sqr() const { - Assert(vec_size != 0, ExcEmptyObject()); + Assert(size() != 0, ExcEmptyObject()); real_type sum; - internal::VectorOperations::Norm2 norm2(values.get()); + internal::VectorOperations::Norm2 norm2(values.begin()); internal::VectorOperations::parallel_reduce( - norm2, 0, vec_size, sum, thread_loop_partitioner); + norm2, 0, size(), sum, thread_loop_partitioner); AssertIsFinite(sum); @@ -534,12 +457,12 @@ template Number Vector::mean_value() const { - Assert(vec_size != 0, ExcEmptyObject()); + Assert(size() != 0, ExcEmptyObject()); Number sum; - internal::VectorOperations::MeanValue mean(values.get()); + internal::VectorOperations::MeanValue mean(values.begin()); internal::VectorOperations::parallel_reduce( - mean, 0, vec_size, sum, thread_loop_partitioner); + mean, 0, size(), sum, thread_loop_partitioner); return sum / real_type(size()); } @@ -550,12 +473,12 @@ template typename Vector::real_type Vector::l1_norm() const { - Assert(vec_size != 0, ExcEmptyObject()); + Assert(size() != 0, ExcEmptyObject()); real_type sum; - internal::VectorOperations::Norm1 norm1(values.get()); + internal::VectorOperations::Norm1 norm1(values.begin()); internal::VectorOperations::parallel_reduce( - norm1, 0, vec_size, sum, thread_loop_partitioner); + norm1, 0, size(), sum, thread_loop_partitioner); return sum; } @@ -571,12 +494,12 @@ Vector::l2_norm() const // might still be finite. In that case, recompute it (this is a rare case, // so working on the vector twice is uncritical and paid off by the extended // precision) using the BLAS approach with a weight, see e.g. dnrm2.f. - Assert(vec_size != 0, ExcEmptyObject()); + Assert(size() != 0, ExcEmptyObject()); real_type norm_square; - internal::VectorOperations::Norm2 norm2(values.get()); + internal::VectorOperations::Norm2 norm2(values.begin()); internal::VectorOperations::parallel_reduce( - norm2, 0, vec_size, norm_square, thread_loop_partitioner); + norm2, 0, size(), norm_square, thread_loop_partitioner); if (numbers::is_finite(norm_square) && norm_square >= std::numeric_limits::min()) return static_cast::real_type>( @@ -585,7 +508,7 @@ Vector::l2_norm() const { real_type scale = 0.; real_type sum = 1.; - for (size_type i = 0; i < vec_size; ++i) + for (size_type i = 0; i < size(); ++i) { if (values[i] != Number()) { @@ -612,7 +535,7 @@ template typename Vector::real_type Vector::lp_norm(const real_type p) const { - Assert(vec_size != 0, ExcEmptyObject()); + Assert(size() != 0, ExcEmptyObject()); if (p == 1.) return l1_norm(); @@ -620,9 +543,9 @@ Vector::lp_norm(const real_type p) const return l2_norm(); real_type sum; - internal::VectorOperations::NormP normp(values.get(), p); + internal::VectorOperations::NormP normp(values.begin(), p); internal::VectorOperations::parallel_reduce( - normp, 0, vec_size, sum, thread_loop_partitioner); + normp, 0, size(), sum, thread_loop_partitioner); if (numbers::is_finite(sum) && sum >= std::numeric_limits::min()) return std::pow(sum, static_cast(1. / p)); @@ -630,7 +553,7 @@ Vector::lp_norm(const real_type p) const { real_type scale = 0.; real_type sum = 1.; - for (size_type i = 0; i < vec_size; ++i) + for (size_type i = 0; i < size(); ++i) { if (values[i] != Number()) { @@ -655,11 +578,11 @@ template typename Vector::real_type Vector::linfty_norm() const { - Assert(vec_size != 0, ExcEmptyObject()); + Assert(size() != 0, ExcEmptyObject()); real_type max = 0.; - for (size_type i = 0; i < vec_size; ++i) + for (size_type i = 0; i < size(); ++i) max = std::max(numbers::NumberTraits::abs(values[i]), max); return max; @@ -673,17 +596,17 @@ Vector::add_and_dot(const Number a, const Vector &V, const Vector &W) { - Assert(vec_size != 0, ExcEmptyObject()); - AssertDimension(vec_size, V.size()); - AssertDimension(vec_size, W.size()); + Assert(size() != 0, ExcEmptyObject()); + AssertDimension(size(), V.size()); + AssertDimension(size(), W.size()); Number sum; - internal::VectorOperations::AddAndDot adder(this->values.get(), - V.values.get(), - W.values.get(), + internal::VectorOperations::AddAndDot adder(values.begin(), + V.values.begin(), + W.values.begin(), a); internal::VectorOperations::parallel_reduce( - adder, 0, vec_size, sum, thread_loop_partitioner); + adder, 0, size(), sum, thread_loop_partitioner); AssertIsFinite(sum); return sum; @@ -695,14 +618,14 @@ template Vector & Vector::operator+=(const Vector &v) { - Assert(vec_size != 0, ExcEmptyObject()); - Assert(vec_size == v.vec_size, ExcDimensionMismatch(vec_size, v.vec_size)); + Assert(size() != 0, ExcEmptyObject()); + Assert(size() == v.size(), ExcDimensionMismatch(size(), v.size())); internal::VectorOperations::Vectorization_add_v vector_add( - values.get(), v.values.get()); + values.begin(), v.values.begin()); internal::VectorOperations::parallel_for(vector_add, 0, - vec_size, + size(), thread_loop_partitioner); return *this; } @@ -713,14 +636,14 @@ template Vector & Vector::operator-=(const Vector &v) { - Assert(vec_size != 0, ExcEmptyObject()); - Assert(vec_size == v.vec_size, ExcDimensionMismatch(vec_size, v.vec_size)); + Assert(size() != 0, ExcEmptyObject()); + Assert(size() == v.size(), ExcDimensionMismatch(size(), v.size())); internal::VectorOperations::Vectorization_subtract_v vector_subtract( - values.get(), v.values.get()); + values.begin(), v.values.begin()); internal::VectorOperations::parallel_for(vector_subtract, 0, - vec_size, + size(), thread_loop_partitioner); return *this; @@ -732,13 +655,13 @@ template void Vector::add(const Number v) { - Assert(vec_size != 0, ExcEmptyObject()); + Assert(size() != 0, ExcEmptyObject()); internal::VectorOperations::Vectorization_add_factor vector_add( - values.get(), v); + values.begin(), v); internal::VectorOperations::parallel_for(vector_add, 0, - vec_size, + size(), thread_loop_partitioner); } @@ -754,15 +677,15 @@ Vector::add(const Number a, AssertIsFinite(a); AssertIsFinite(b); - Assert(vec_size != 0, ExcEmptyObject()); - Assert(vec_size == v.vec_size, ExcDimensionMismatch(vec_size, v.vec_size)); - Assert(vec_size == w.vec_size, ExcDimensionMismatch(vec_size, w.vec_size)); + Assert(size() != 0, ExcEmptyObject()); + Assert(size() == v.size(), ExcDimensionMismatch(size(), v.size())); + Assert(size() == w.size(), ExcDimensionMismatch(size(), w.size())); internal::VectorOperations::Vectorization_add_avpbw vector_add( - values.get(), v.values.get(), w.values.get(), a, b); + values.begin(), v.values.begin(), w.values.begin(), a, b); internal::VectorOperations::parallel_for(vector_add, 0, - vec_size, + size(), thread_loop_partitioner); } @@ -774,14 +697,14 @@ Vector::sadd(const Number x, const Vector &v) { AssertIsFinite(x); - Assert(vec_size != 0, ExcEmptyObject()); - Assert(vec_size == v.vec_size, ExcDimensionMismatch(vec_size, v.vec_size)); + Assert(size() != 0, ExcEmptyObject()); + Assert(size() == v.size(), ExcDimensionMismatch(size(), v.size())); internal::VectorOperations::Vectorization_sadd_xv vector_sadd( - values.get(), v.values.get(), x); + values.begin(), v.values.begin(), x); internal::VectorOperations::parallel_for(vector_sadd, 0, - vec_size, + size(), thread_loop_partitioner); } @@ -791,14 +714,14 @@ template void Vector::scale(const Vector &s) { - Assert(vec_size != 0, ExcEmptyObject()); - Assert(vec_size == s.vec_size, ExcDimensionMismatch(vec_size, s.vec_size)); + Assert(size() != 0, ExcEmptyObject()); + Assert(size() == s.size(), ExcDimensionMismatch(size(), s.size())); internal::VectorOperations::Vectorization_scale vector_scale( - values.get(), s.values.get()); + values.begin(), s.values.begin()); internal::VectorOperations::parallel_for(vector_scale, 0, - vec_size, + size(), thread_loop_partitioner); } @@ -809,10 +732,10 @@ template void Vector::scale(const Vector &s) { - Assert(vec_size != 0, ExcEmptyObject()); - Assert(vec_size == s.vec_size, ExcDimensionMismatch(vec_size, s.vec_size)); + Assert(size() != 0, ExcEmptyObject()); + Assert(size() == s.size(), ExcDimensionMismatch(size(), s.size())); - for (size_type i = 0; i < vec_size; ++i) + for (size_type i = 0; i < size(); ++i) values[i] *= Number(s.values[i]); } @@ -824,14 +747,14 @@ Vector::equ(const Number a, const Vector &u) { AssertIsFinite(a); - Assert(vec_size != 0, ExcEmptyObject()); - Assert(vec_size == u.vec_size, ExcDimensionMismatch(vec_size, u.vec_size)); + Assert(size() != 0, ExcEmptyObject()); + Assert(size() == u.size(), ExcDimensionMismatch(size(), u.size())); internal::VectorOperations::Vectorization_equ_au vector_equ( - values.get(), u.values.get(), a); + values.begin(), u.values.begin(), a); internal::VectorOperations::parallel_for(vector_equ, 0, - vec_size, + size(), thread_loop_partitioner); } @@ -844,8 +767,8 @@ Vector::equ(const Number a, const Vector &u) { AssertIsFinite(a); - Assert(vec_size != 0, ExcEmptyObject()); - Assert(vec_size == u.vec_size, ExcDimensionMismatch(vec_size, u.vec_size)); + Assert(size() != 0, ExcEmptyObject()); + Assert(size() == u.size(), ExcDimensionMismatch(size(), u.size())); // set the result vector to a*u. we have to // convert the elements of u to the type of @@ -853,7 +776,7 @@ Vector::equ(const Number a, const Vector &u) // because // operator*(complex,complex) // is not defined by default - for (size_type i = 0; i < vec_size; ++i) + for (size_type i = 0; i < size(); ++i) values[i] = a * Number(u.values[i]); } @@ -863,19 +786,18 @@ template void Vector::ratio(const Vector &a, const Vector &b) { - Assert(vec_size != 0, ExcEmptyObject()); - Assert(a.vec_size == b.vec_size, - ExcDimensionMismatch(a.vec_size, b.vec_size)); + Assert(size() != 0, ExcEmptyObject()); + Assert(a.size() == b.size(), ExcDimensionMismatch(a.size(), b.size())); // no need to reinit with zeros, since // we overwrite them anyway reinit(a.size(), true); internal::VectorOperations::Vectorization_ratio vector_ratio( - values.get(), a.values.get(), b.values.get()); + values.begin(), a.begin(), b.begin()); internal::VectorOperations::parallel_for(vector_ratio, 0, - vec_size, + size(), thread_loop_partitioner); } @@ -885,7 +807,7 @@ template Vector & Vector::operator=(const BlockVector &v) { - if (v.size() != vec_size) + if (v.size() != size()) reinit(v.size(), true); size_type this_index = 0; @@ -915,9 +837,9 @@ template Vector & Vector::operator=(const TrilinosWrappers::MPI::Vector &v) { - if (v.size() != vec_size) + if (v.size() != size()) reinit(v.size(), true); - if (vec_size != 0) + if (size() != 0) { // Copy the distributed vector to // a local one at all processors @@ -927,12 +849,12 @@ Vector::operator=(const TrilinosWrappers::MPI::Vector &v) // this, but it has not yet been // found. TrilinosWrappers::MPI::Vector localized_vector; - localized_vector.reinit(complete_index_set(vec_size), + localized_vector.reinit(complete_index_set(size()), v.get_mpi_communicator()); localized_vector.reinit(v, false, true); - Assert(localized_vector.size() == vec_size, - ExcDimensionMismatch(localized_vector.size(), vec_size)); + Assert(localized_vector.size() == size(), + ExcDimensionMismatch(localized_vector.size(), size())); // get a representation of the vector // and copy it @@ -941,7 +863,7 @@ Vector::operator=(const TrilinosWrappers::MPI::Vector &v) int ierr = localized_vector.trilinos_vector().ExtractView(&start_ptr); AssertThrow(ierr == 0, ExcTrilinosError(ierr)); - std::copy(start_ptr[0], start_ptr[0] + vec_size, begin()); + std::copy(start_ptr[0], start_ptr[0] + size(), begin()); } return *this; @@ -954,8 +876,7 @@ template bool Vector::operator==(const Vector &v) const { - Assert(vec_size != 0, ExcEmptyObject()); - Assert(vec_size == v.size(), ExcDimensionMismatch(vec_size, v.size())); + Assert(size() == v.size(), ExcDimensionMismatch(size(), v.size())); // compare the two vector. we have to // convert the elements of v to the type of @@ -963,7 +884,7 @@ Vector::operator==(const Vector &v) const // because // operator==(complex,complex) // is not defined by default - for (size_type i = 0; i < vec_size; ++i) + for (size_type i = 0; i < size(); ++i) if (values[i] != Number(v.values[i])) return false; @@ -976,7 +897,7 @@ template void Vector::print(const char *format) const { - Assert(vec_size != 0, ExcEmptyObject()); + Assert(size() != 0, ExcEmptyObject()); for (size_type j = 0; j < size(); ++j) internal::VectorOperations::print(values[j], format); @@ -992,7 +913,7 @@ Vector::print(std::ostream & out, const bool scientific, const bool across) const { - Assert(vec_size != 0, ExcEmptyObject()); + Assert(size() != 0, ExcEmptyObject()); AssertThrow(out, ExcIO()); std::ios::fmtflags old_flags = out.flags(); @@ -1026,7 +947,7 @@ Vector::print(LogStream & out, const unsigned int width, const bool across) const { - Assert(vec_size != 0, ExcEmptyObject()); + Assert(size() != 0, ExcEmptyObject()); if (across) for (size_type i = 0; i < size(); ++i) @@ -1121,28 +1042,10 @@ template std::size_t Vector::memory_consumption() const { - return sizeof(*this) + (max_vec_size * sizeof(Number)); + return sizeof(*this) + values.memory_consumption() - sizeof(values); } - -template -void -Vector::allocate(const size_type copy_n_el) -{ - // allocate memory with the proper alignment requirements of 64 bytes - Number *new_values; - Utilities::System::posix_memalign(reinterpret_cast(&new_values), - 64, - sizeof(Number) * max_vec_size); - // copy: - for (size_type i = 0; i < copy_n_el; ++i) - new_values[i] = values[i]; - values.reset(new_values); -} - - - DEAL_II_NAMESPACE_CLOSE #endif diff --git a/tests/serialization/vector.output b/tests/serialization/vector.output index 2fc4d411cf08..d51d6c2c0222 100644 --- a/tests/serialization/vector.output +++ b/tests/serialization/vector.output @@ -1,6 +1,6 @@ -DEAL::0 0 0 0 5 5 0 1 2 3 4 +DEAL::0 0 0 0 0 0 5 0 1 2 3 4 -DEAL::0 0 0 0 5 5 0 1 2 3 4 +DEAL::0 0 0 0 0 0 5 0 1 2 3 4 DEAL::OK From 80f73b5ecc2d658a3bbc5eb372105ac058428906 Mon Sep 17 00:00:00 2001 From: David Wells Date: Sat, 26 Jan 2019 19:23:24 -0500 Subject: [PATCH 028/507] Update the .gdbinit script. --- contrib/utilities/dotgdbinit.py | 50 +++++++++++++++++++++++---------- 1 file changed, 35 insertions(+), 15 deletions(-) diff --git a/contrib/utilities/dotgdbinit.py b/contrib/utilities/dotgdbinit.py index a4fb32598441..57d6ae956921 100644 --- a/contrib/utilities/dotgdbinit.py +++ b/contrib/utilities/dotgdbinit.py @@ -1,6 +1,6 @@ # --------------------------------------------------------------------- # -# Copyright (C) 2015 - 2017 by the deal.II authors +# Copyright (C) 2015 - 2018 by the deal.II authors # # This file is part of the deal.II library. # @@ -25,7 +25,7 @@ # slightly older versions of GDB (the Python interface was added in 7.0, # released in 2009). # -# Authors: Wolfgang Bangerth, 2015, David Wells, 2015 - 2017 +# Authors: Wolfgang Bangerth, 2015, David Wells, 2015 - 2018 # set print pretty 1 @@ -52,6 +52,31 @@ def build_output_string(keys, accessor): "\n}") +class AlignedVectorPrinter(object): + """Print a deal.II AlignedVector instance.""" + def __init__(self, typename, val): + self.typename = typename + self.val = val + self.length = int(self.val['data_end'] - self.val['data_begin']) + + def children(self): + # The first entry (see the "Pretty Printing API" documentation of GDB) + # in the tuple should be a name for the child, which should be nothing + # (the array elements don't have individual names) here. + return (("", (self.val['data_begin'] + count).dereference()) + for count in range(self.length)) + + def to_string(self): + return "AlignedVector<{}>({})".format(self.val.type.template_argument(0), + self.length) + + @staticmethod + def display_hint(): + """Provide a hint to GDB that this is an array-like container + (so print values in sequence).""" + return "array" + + class PointPrinter(object): """Print a deal.II Point instance.""" def __init__(self, typename, val): @@ -94,23 +119,17 @@ class VectorPrinter(object): def __init__(self, typename, val): self.typename = typename self.val = val + a_vec = self.val['values'] + self.length = int(a_vec['data_end'] - a_vec['data_begin']) def children(self): - # The first entry (see the "Pretty Printing API" documentation of GDB) - # in the tuple should be a name for the child, which should be nothing - # (an empty string) here. - return (("", (self.val['values'] + count).dereference()) - for count in range(int(self.val['vec_size']))) + return (("values", self.val['values']), + ("thread_loop_partitioner", + self.val['thread_loop_partitioner'])) def to_string(self): - return "{}[{}]".format(self.val.type.template_argument(0), - self.val['vec_size']) - - @staticmethod - def display_hint(): - """Provide a hint to GDB that this is an array-like container - (so print values in sequence).""" - return "array" + return "Vector<{}>({})".format(self.val.type.template_argument(0), + self.length) class QuadraturePrinter(object): @@ -184,6 +203,7 @@ def __call__(self, val): def register_dealii_printers(): """Register deal.II pretty-printers with gdb.""" printers = { + AlignedVectorPrinter: ['AlignedVector'], PointPrinter: ['Point'], TensorPrinter: ['Tensor'], VectorPrinter: ['Vector'], From 174fe8cce2d9ec68185227ea190274695160a3f4 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Tue, 29 Jan 2019 23:23:50 +0100 Subject: [PATCH 029/507] Disable SIMD vectorization in CUDA device code --- include/deal.II/base/config.h.in | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/include/deal.II/base/config.h.in b/include/deal.II/base/config.h.in index 7801a2397f44..9da0d4818f2e 100644 --- a/include/deal.II/base/config.h.in +++ b/include/deal.II/base/config.h.in @@ -114,7 +114,14 @@ */ #cmakedefine DEAL_II_WORDS_BIGENDIAN -#define DEAL_II_COMPILER_VECTORIZATION_LEVEL @DEAL_II_COMPILER_VECTORIZATION_LEVEL@ +// We need to disable SIMD vectorization for CUDA device code. +// Otherwise, nvcc compilers from version 9 on will emit an error message like: +// "[...] contains a vector, which is not supported in device code" +#ifdef __CUDA_ARCH__ +# define DEAL_II_COMPILER_VECTORIZATION_LEVEL 0 +#else +# define DEAL_II_COMPILER_VECTORIZATION_LEVEL @DEAL_II_COMPILER_VECTORIZATION_LEVEL@ +#endif #define DEAL_II_OPENMP_SIMD_PRAGMA @DEAL_II_OPENMP_SIMD_PRAGMA@ From aa56d092232c384222aff86578ee4b6f1a359bb9 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Tue, 29 Jan 2019 23:48:08 +0100 Subject: [PATCH 030/507] Add missing headers in CUDA header file --- include/deal.II/matrix_free/cuda_tensor_product_kernels.h | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/include/deal.II/matrix_free/cuda_tensor_product_kernels.h b/include/deal.II/matrix_free/cuda_tensor_product_kernels.h index 81c8fff6ab22..c27561646e1e 100644 --- a/include/deal.II/matrix_free/cuda_tensor_product_kernels.h +++ b/include/deal.II/matrix_free/cuda_tensor_product_kernels.h @@ -19,6 +19,10 @@ #include +#include + +#include + #ifdef DEAL_II_COMPILER_CUDA_AWARE DEAL_II_NAMESPACE_OPEN From bfd22d07ce53528ad4bdc36069d29cf165169458 Mon Sep 17 00:00:00 2001 From: Giovanni Alzetta Date: Tue, 29 Jan 2019 16:29:15 +0100 Subject: [PATCH 031/507] Generalizing GridGenerator::general_cell to tria --- .../changes/minor/20190130GiovanniAlzetta | 5 + include/deal.II/grid/grid_generator.h | 24 +++-- source/grid/grid_generator.cc | 10 +- source/grid/grid_generator.inst.in | 9 +- ...l.cc => grid_generator_general_cell_01.cc} | 0 ... => grid_generator_general_cell_01.output} | 0 tests/grid/grid_generator_general_cell_02.cc | 95 +++++++++++++++++++ .../grid_generator_general_cell_02.output | 87 +++++++++++++++++ 8 files changed, 211 insertions(+), 19 deletions(-) create mode 100644 doc/news/changes/minor/20190130GiovanniAlzetta rename tests/grid/{grid_generator_general_cell.cc => grid_generator_general_cell_01.cc} (100%) rename tests/grid/{grid_generator_general_cell.output => grid_generator_general_cell_01.output} (100%) create mode 100644 tests/grid/grid_generator_general_cell_02.cc create mode 100644 tests/grid/grid_generator_general_cell_02.output diff --git a/doc/news/changes/minor/20190130GiovanniAlzetta b/doc/news/changes/minor/20190130GiovanniAlzetta new file mode 100644 index 000000000000..a9b64415e3ee --- /dev/null +++ b/doc/news/changes/minor/20190130GiovanniAlzetta @@ -0,0 +1,5 @@ +Changed: Function GridGenerator::general_cell() can now generate +a cell of dimension `dim` inside a space of dimension `spacedim` +with `dim <= spacedim` +
+(Giovanni Alzetta, 2019/01/30) diff --git a/include/deal.II/grid/grid_generator.h b/include/deal.II/grid/grid_generator.h index 354037d6f20a..0a4d52818f7d 100644 --- a/include/deal.II/grid/grid_generator.h +++ b/include/deal.II/grid/grid_generator.h @@ -462,11 +462,13 @@ namespace GridGenerator const bool colorize = false); /** - * A general quadrilateral in 2d or a general hexahedron in 3d. It is the - * responsibility of the user to provide the vertices in the right order (see - * the documentation of the GeometryInfo class) because the vertices are - * stored in the same order as they are given. It is also important to make - * sure that the volume of the cell is positive. + * A general @p dim -dimensional cell (a segment if dim is 1, a quadrilateral + * if @p dim is 2, or a hexahedron if @p dim is 3) immersed in a + * @p spacedim -dimensional space. It is the responsibility of the user to + * provide the vertices in the right order (see the documentation of the + * GeometryInfo class) because the vertices are stored in the same order as + * they are given. It is also important to make sure that the volume of the + * cell is positive. * * If the argument @p colorize is false, then all boundary indicators are * set to zero for 2d and 3d. If it is true, the boundary is colorized as in @@ -474,13 +476,17 @@ namespace GridGenerator * @ref GlossColorization "the glossary entry on colorization"). In 1d the * indicators are always colorized, see hyper_rectangle(). * + * @param tria The triangulation that will be created + * @param vertices The 2^dim vertices of the cell + * @param colorize If true, set different boundary ids. + * * @author Bruno Turcksin */ - template + template void - general_cell(Triangulation & tria, - const std::vector> &vertices, - const bool colorize = false); + general_cell(Triangulation & tria, + const std::vector> &vertices, + const bool colorize = false); /** * A parallelogram. The first corner point is the origin. The @p dim diff --git a/source/grid/grid_generator.cc b/source/grid/grid_generator.cc index a51cbe29a312..9738d7937287 100644 --- a/source/grid/grid_generator.cc +++ b/source/grid/grid_generator.cc @@ -749,11 +749,11 @@ namespace GridGenerator - template + template void - general_cell(Triangulation & tria, - const std::vector> &vertices, - const bool colorize) + general_cell(Triangulation & tria, + const std::vector> &vertices, + const bool colorize) { Assert(vertices.size() == dealii::GeometryInfo::vertices_per_cell, ExcMessage("Wrong number of vertices.")); @@ -761,7 +761,7 @@ namespace GridGenerator // First create a hyper_rectangle and then deform it. hyper_cube(tria, 0, 1, colorize); - typename Triangulation::active_cell_iterator cell = + typename Triangulation::active_cell_iterator cell = tria.begin_active(); for (unsigned int i = 0; i < GeometryInfo::vertices_per_cell; ++i) cell->vertex(i) = vertices[i]; diff --git a/source/grid/grid_generator.inst.in b/source/grid/grid_generator.inst.in index 0084a2851210..2253edee987a 100644 --- a/source/grid/grid_generator.inst.in +++ b/source/grid/grid_generator.inst.in @@ -106,6 +106,10 @@ for (deal_II_dimension : DIMENSIONS; deal_II_space_dimension : SPACE_DIMENSIONS) &cells_to_remove, Triangulation &result); + template void + general_cell(Triangulation &, + const std::vector> &, + const bool); #endif \} } @@ -153,11 +157,6 @@ for (deal_II_dimension : DIMENSIONS) const Point &, const bool); - template void - general_cell(Triangulation &, - const std::vector> &, - const bool); - template void simplex( Triangulation &, diff --git a/tests/grid/grid_generator_general_cell.cc b/tests/grid/grid_generator_general_cell_01.cc similarity index 100% rename from tests/grid/grid_generator_general_cell.cc rename to tests/grid/grid_generator_general_cell_01.cc diff --git a/tests/grid/grid_generator_general_cell.output b/tests/grid/grid_generator_general_cell_01.output similarity index 100% rename from tests/grid/grid_generator_general_cell.output rename to tests/grid/grid_generator_general_cell_01.output diff --git a/tests/grid/grid_generator_general_cell_02.cc b/tests/grid/grid_generator_general_cell_02.cc new file mode 100644 index 000000000000..cd60e7aec13d --- /dev/null +++ b/tests/grid/grid_generator_general_cell_02.cc @@ -0,0 +1,95 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2016 - 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + +// Test output for GridGenerator::general_cell() for dim != spacedim + +#include +#include +#include + +#include "../tests.h" + +void +dim_2_3(std::ostream &os) +{ + std::vector> vertices(4); + vertices[0](0) = -1.; + vertices[0](1) = -1.; + vertices[0](0) = 0.; + + vertices[1](0) = 1.; + vertices[1](1) = -1.5; + vertices[1](2) = 0.; + + vertices[2](0) = 1.5; + vertices[2](1) = 1.5; + vertices[2](2) = 0.; + + vertices[3](0) = 2.; + vertices[3](1) = 0.5; + vertices[3](2) = 0.; + + Triangulation<2, 3> tria; + GridGenerator::general_cell<2, 3>(tria, vertices); + + GridOut gout; + gout.write_vtk(tria, os); +} + +void +dim_1_3(std::ostream &os) +{ + std::vector> vertices(2); + vertices[0](0) = -1.; + vertices[0](1) = -1.; + vertices[0](2) = -1.; + vertices[1](0) = 1.; + vertices[1](1) = -1.5; + vertices[1](2) = -1.5; + + Triangulation<1, 3> tria; + GridGenerator::general_cell<1, 3>(tria, vertices); + + GridOut gout; + gout.write_vtk(tria, os); +} + +void +dim_1_2(std::ostream &os) +{ + std::vector> vertices(2); + vertices[0](0) = -1.; + vertices[0](1) = -1.; + + vertices[1](0) = 1.; + vertices[1](1) = -1.5; + + Triangulation<1, 2> tria; + GridGenerator::general_cell<1, 2>(tria, vertices); + + GridOut gout; + gout.write_vtk(tria, os); +} + + +int +main() +{ + initlog(true); + std::ostream &logfile = deallog.get_file_stream(); + dim_2_3(logfile); + dim_1_3(logfile); + dim_1_2(logfile); +} diff --git a/tests/grid/grid_generator_general_cell_02.output b/tests/grid/grid_generator_general_cell_02.output new file mode 100644 index 000000000000..8a44d1386273 --- /dev/null +++ b/tests/grid/grid_generator_general_cell_02.output @@ -0,0 +1,87 @@ + +# vtk DataFile Version 3.0 +Triangulation generated with deal.II +ASCII +DATASET UNSTRUCTURED_GRID +POINTS 4 double +0.00000 -1.00000 0.00000 +1.00000 -1.50000 0.00000 +1.50000 1.50000 0.00000 +2.00000 0.500000 0.00000 + +CELLS 1 5 +4 0 1 3 2 + +CELL_TYPES 1 +9 + + + +CELL_DATA 1 +SCALARS MaterialID int 1 +LOOKUP_TABLE default +0 + + + +SCALARS ManifoldID int 1 +LOOKUP_TABLE default +-1 + + +# vtk DataFile Version 3.0 +Triangulation generated with deal.II +ASCII +DATASET UNSTRUCTURED_GRID +POINTS 2 double +-1.00000 -1.00000 -1.00000 +1.00000 -1.50000 -1.50000 + +CELLS 1 3 +2 0 1 + +CELL_TYPES 1 +3 + + + +CELL_DATA 1 +SCALARS MaterialID int 1 +LOOKUP_TABLE default +0 + + + +SCALARS ManifoldID int 1 +LOOKUP_TABLE default +-1 + + +# vtk DataFile Version 3.0 +Triangulation generated with deal.II +ASCII +DATASET UNSTRUCTURED_GRID +POINTS 2 double +-1.00000 -1.00000 0 +1.00000 -1.50000 0 + +CELLS 1 3 +2 0 1 + +CELL_TYPES 1 +3 + + + +CELL_DATA 1 +SCALARS MaterialID int 1 +LOOKUP_TABLE default +0 + + + +SCALARS ManifoldID int 1 +LOOKUP_TABLE default +-1 + + From 2f90725fe6839f1f3d636c4463c90ec0a51f41dc Mon Sep 17 00:00:00 2001 From: Pratik Nayak Date: Wed, 30 Jan 2019 12:47:50 +0100 Subject: [PATCH 032/507] Detect Ginkgo and compile the ginkgo files: CMake. --- cmake/configure/configure_2_ginkgo.cmake | 39 +++++++++++++ cmake/modules/FindGINKGO.cmake | 72 ++++++++++++++++++++++++ include/deal.II/base/config.h.in | 3 +- source/lac/CMakeLists.txt | 7 +++ tests/run_testsuite.cmake | 4 +- 5 files changed, 122 insertions(+), 3 deletions(-) create mode 100644 cmake/configure/configure_2_ginkgo.cmake create mode 100644 cmake/modules/FindGINKGO.cmake diff --git a/cmake/configure/configure_2_ginkgo.cmake b/cmake/configure/configure_2_ginkgo.cmake new file mode 100644 index 000000000000..5b778ae75a11 --- /dev/null +++ b/cmake/configure/configure_2_ginkgo.cmake @@ -0,0 +1,39 @@ +## --------------------------------------------------------------------- +## +## Copyright (C) 2018 by the deal.II authors +## +## This file is part of the deal.II library. +## +## The deal.II library is free software; you can use it, redistribute +## it, and/or modify it under the terms of the GNU Lesser General +## Public License as published by the Free Software Foundation; either +## version 2.1 of the License, or (at your option) any later version. +## The full text of the license can be found in the file LICENSE.md at +## the top level directory of deal.II. +## +## --------------------------------------------------------------------- + +# +# Configuration for the Ginkgo library: +# + +MACRO(FEATURE_GINKGO_ERROR_MESSAGE) + MESSAGE(FATAL_ERROR "\n" + "Could not find Ginkgo and supporting libraries!\n" + "Please ensure that the libraries are installed on your computer.\n" + "If the libraries are not at a default location, either provide some hints\n" + "for the autodetection:\n" + " $ GINKGO_DIR=\"...\" cmake <...>\n" + " $ cmake -DGINKGO_DIR=\"...\" <...>\n" + "or set the relevant variables by hand in ccmake.\n" + "Relevant hints for GINKGO are GINKGO_DIR.\n" + ) +ENDMACRO() + +MACRO(FEATURE_GINKGO_CONFIGURE_EXTERNAL) + SET(DEAL_II_GINKGO_BUILT_REFERENCE ${GINKGO_BUILT_REFERENCE}) + SET(DEAL_II_GINKGO_BUILT_OPENMP ${GINKGO_BUILT_OMP}) + SET(DEAL_II_GINKGO_BUILT_CUDA ${GINKGO_BUILT_CUDA}) +ENDMACRO() + +CONFIGURE_FEATURE(GINKGO) diff --git a/cmake/modules/FindGINKGO.cmake b/cmake/modules/FindGINKGO.cmake new file mode 100644 index 000000000000..d05c2528bf15 --- /dev/null +++ b/cmake/modules/FindGINKGO.cmake @@ -0,0 +1,72 @@ +## --------------------------------------------------------------------- +## +## Copyright (C) 2018 by the deal.II authors +## +## This file is part of the deal.II library. +## +## The deal.II library is free software; you can use it, redistribute +## it, and/or modify it under the terms of the GNU Lesser General +## Public License as published by the Free Software Foundation; either +## version 2.1 of the License, or (at your option) any later version. +## The full text of the license can be found in the file LICENSE.md at +## the top level directory of deal.II. +## +## --------------------------------------------------------------------- + +# +# Try to find the GINKGO library +# +# This module exports +# +# GINKGO_INCLUDE_DIRS +# + +SET(GINKGO_DIR "" CACHE PATH "An optional hint to a GINKGO installation") +SET_IF_EMPTY(GINKGO_DIR "$ENV{GINKGO_DIR}") + +DEAL_II_FIND_LIBRARY(GINKGO_LIBRARY + NAMES ginkgo + HINTS ${GINKGO_DIR} + PATH_SUFFIXES + lib${LIB_SUFFIX} lib64 lib + # This is a hint, isn't it? + build/${CMAKE_CXX_PLATFORM_ID}-${CMAKE_SYSTEM_PROCESSOR}/libginkgo + ) +DEAL_II_FIND_LIBRARY(GINKGO_REFERENCE_LIBRARY + NAMES ginkgo_reference + HINTS ${GINKGO_DIR} + PATH_SUFFIXES + lib${LIB_SUFFIX} lib64 lib + # This is a hint, isn't it? + build/${CMAKE_CXX_PLATFORM_ID}-${CMAKE_SYSTEM_PROCESSOR}/libginkgo_reference + ) +DEAL_II_FIND_LIBRARY(GINKGO_OMP_LIBRARY + NAMES ginkgo_omp + HINTS ${GINKGO_DIR} + PATH_SUFFIXES + lib${LIB_SUFFIX} lib64 lib + # This is a hint, isn't it? + build/${CMAKE_CXX_PLATFORM_ID}-${CMAKE_SYSTEM_PROCESSOR}/libginkgo_omp + ) +DEAL_II_FIND_LIBRARY(GINKGO_CUDA_LIBRARY + NAMES ginkgo_cuda + HINTS ${GINKGO_DIR} + PATH_SUFFIXES + lib${LIB_SUFFIX} lib64 lib + # This is a hint, isn't it? + build/${CMAKE_CXX_PLATFORM_ID}-${CMAKE_SYSTEM_PROCESSOR}/libginkgo_cuda + ) + +DEAL_II_FIND_PATH(GINKGO_INCLUDE_DIR ginkgo/ginkgo.hpp + HINTS ${GINKGO_DIR} + PATH_SUFFIXES include + ) + +DEAL_II_PACKAGE_HANDLE(GINKGO + LIBRARIES + REQUIRED GINKGO_LIBRARY GINKGO_REFERENCE_LIBRARY GINKGO_OMP_LIBRARY GINKGO_CUDA_LIBRARY + INCLUDE_DIRS REQUIRED GINKGO_INCLUDE_DIR + USER_INCLUDE_DIRS REQUIRED GINKGO_INCLUDE_DIR + CLEAR + GINKGO_INCLUDE_DIR + ) diff --git a/include/deal.II/base/config.h.in b/include/deal.II/base/config.h.in index 7801a2397f44..84e17b338438 100644 --- a/include/deal.II/base/config.h.in +++ b/include/deal.II/base/config.h.in @@ -1,6 +1,6 @@ // --------------------------------------------------------------------- // -// Copyright (C) 2012 - 2016 by the deal.II authors +// Copyright (C) 2012 - 2018 by the deal.II authors // // This file is part of the deal.II library. // @@ -43,6 +43,7 @@ #cmakedefine DEAL_II_WITH_CUDA_AWARE_MPI #cmakedefine DEAL_II_WITH_CXX14 #cmakedefine DEAL_II_WITH_CXX17 +#cmakedefine DEAL_II_WITH_GINKGO #cmakedefine DEAL_II_WITH_GSL #cmakedefine DEAL_II_WITH_GMSH #cmakedefine DEAL_II_WITH_HDF5 diff --git a/source/lac/CMakeLists.txt b/source/lac/CMakeLists.txt index 2cecfbc24f36..a6ce60360fe8 100644 --- a/source/lac/CMakeLists.txt +++ b/source/lac/CMakeLists.txt @@ -112,6 +112,13 @@ IF(DEAL_II_WITH_SLEPC) ) ENDIF() +IF(DEAL_II_WITH_GINKGO) + SET(_unity_include_src + ${_unity_include_src} + ginkgo_solver.cc + ) +ENDIF() + # Also add Trilinos wrapper files IF(DEAL_II_WITH_TRILINOS) SET(_unity_include_src diff --git a/tests/run_testsuite.cmake b/tests/run_testsuite.cmake index 713c31b614c0..688ae9da6500 100644 --- a/tests/run_testsuite.cmake +++ b/tests/run_testsuite.cmake @@ -1,6 +1,6 @@ ## --------------------------------------------------------------------- ## -## Copyright (C) 2013 - 2016 by the deal.II authors +## Copyright (C) 2013 - 2018 by the deal.II authors ## ## This file is part of the deal.II library. ## @@ -273,7 +273,7 @@ FOREACH(_var ${_variables}) IF( _var MATCHES "^(TEST|DEAL_II|ALLOW|WITH|FORCE|COMPONENT)_" OR _var MATCHES "^(DOCUMENTATION|EXAMPLES)" OR _var MATCHES "^(ADOLC|ARPACK|BOOST|OPENCASCADE|MUPARSER|HDF5|METIS|MPI)_" OR - _var MATCHES "^(NETCDF|P4EST|PETSC|SCALAPACK|SLEPC|THREADS|TBB|TRILINOS)_" OR + _var MATCHES "^(GINKGO|NETCDF|P4EST|PETSC|SCALAPACK|SLEPC|THREADS|TBB|TRILINOS)_" OR _var MATCHES "^(UMFPACK|ZLIB|LAPACK|MUPARSER|CUDA)_" OR _var MATCHES "^(CMAKE|DEAL_II)_(C|CXX|Fortran|BUILD)_(COMPILER|FLAGS)" OR _var MATCHES "^CMAKE_BUILD_TYPE$" OR From b4957baf7539f67123fa3b19e1c9a0f5e0e72380 Mon Sep 17 00:00:00 2001 From: Pratik Nayak Date: Wed, 30 Jan 2019 12:49:04 +0100 Subject: [PATCH 033/507] Add documentation to readme.html and ginkgo.html files --- doc/external-libs/ginkgo.html | 96 +++++++++++++++++++++++++++++++++++ doc/readme.html | 16 ++++++ 2 files changed, 112 insertions(+) create mode 100644 doc/external-libs/ginkgo.html diff --git a/doc/external-libs/ginkgo.html b/doc/external-libs/ginkgo.html new file mode 100644 index 000000000000..d918e17f7357 --- /dev/null +++ b/doc/external-libs/ginkgo.html @@ -0,0 +1,96 @@ + + + + The deal.II Readme on interfacing to Ginkgo + + + + + + + +

Interfacing deal.II to Ginkgo

+ +

+ Ginkgo is + A numerical linear algebra software package that provides its users with + highly optimized fine grid level linear algebra operations. It currently has + the capability to solve on the CPU with the support of OpenMP and on the GPU + with NVIDIA's CUDA libraries. For some operations it uses NVIDIA's own libraries, CuSparse + and CuBLAS, but some routines also have self implemented CUDA functions.See the Ginkgo documentation + for more details. +

+ +

+ deal.II has wrapper classes to the linear algebra + parts of Ginkgo that provide almost the + same interfaces as the built-in deal.II linear algebra operations. +

+ +

Installing deal.II with Ginkgo

+ +

+ During the CMake configuration, the following flags should be specified: +

    +
  • -DDEAL_II_WITH_GINKGO=ON, to enable the Ginkgo library. +
  • -DGINKGO_DIR=, to specify the path where Ginkgo has been installed. +
+

+ +

Installing Ginkgo

+ +

+ Installing Ginkgo is quite simple. Ginkgo currently uses CMake and hence one can use + the following commands to easily install Ginkgo. For different dependencies and compatible + libraries, please refer to Ginkgo. + The different flags that can be added are: +

    +
  • -DBUILD_REFERENCE={ON,OFF}: Builds the reference single thread implementation + used to check the more sophisticated implementations of the GPU/CPU. +
  • -DBUILD_CUDA={ON,OFF}: Builds the GPU implementation, specifically the NVIDIA + CUDA implementations. This needs CUDA to be installed on the machine. +
  • -DBUILD_OMP={ON,OFF}: Builds the multithreaded OpenMP implementations. +
+ To install Ginkgo, you would need to: + 
+	git clone https://github.com/ginkgo-project/ginkgo.git
+  mkdir build; cd build 
+  cmake -DBUILD_REFERENCE=on/off -DBUILD_CUDA=on/off -DBUILD_OMP=on/off -DCMAKE_INSTALL_PREFIX=/path/to/install/ -DCMAKE_BUILD_TYPE=Debug
+	make install
+
+

+ +

Running the Ginkgo tests

+ +

+ Ginkgo uses gtests to run unit tests. The reference implementations are + non-optimized versions to which the OpenMP and CUDA versions are compared with for + correctness. + + The following command, executed in Ginkgo's build directory, launches its test suite. + 

+	make test
+
+ The output should contain several lines of the form: + 
+     Start  1: path/to/test
+ 1/13 Test  #1: path/to/test .............................   Passed    0.01 sec
+
+ To run only a specific test for more details, from the build directory, run + 
+	./path/to/test
+
+

+ +
+
+ + Valid HTML 4.01! + + Valid CSS! +
+ + diff --git a/doc/readme.html b/doc/readme.html index 2294bfbfa659..406981e5f710 100644 --- a/doc/readme.html +++ b/doc/readme.html @@ -423,6 +423,22 @@

Optional interfaces to other software packages

about compatibility and configuration can be found here.

+
+ Ginkgo
+
+

+ Ginkgo + is a numerical linear algebra library with highly optimized kernels + for many core architectures with a focus on fine level parallelism. + It allows for easy switching of the executing paradigm (CUDA, OpenMP, .etc) + while providing a multitude of linear solvers and preconditioners + and extension to other linear operators with minimal changes required in the code. + To enable Ginkgo, pass -DGINKGO_DIR=/path/to/ginkgo to CMake when + configuring deal.II. For more detailed instructions, one can refer to + this page. +

+
+
Gmsh
From 7dc7cbab1214364fac2cfd5466099cd3f8bd6908 Mon Sep 17 00:00:00 2001 From: Pratik Nayak Date: Wed, 30 Jan 2019 12:49:36 +0100 Subject: [PATCH 034/507] Add initial tests for ginkgo --- tests/ginkgo/CMakeLists.txt | 6 ++++ tests/ginkgo/solver.cc | 67 +++++++++++++++++++++++++++++++++++++ tests/ginkgo/solver.output | 3 ++ 3 files changed, 76 insertions(+) create mode 100644 tests/ginkgo/CMakeLists.txt create mode 100644 tests/ginkgo/solver.cc create mode 100644 tests/ginkgo/solver.output diff --git a/tests/ginkgo/CMakeLists.txt b/tests/ginkgo/CMakeLists.txt new file mode 100644 index 000000000000..f549331a0595 --- /dev/null +++ b/tests/ginkgo/CMakeLists.txt @@ -0,0 +1,6 @@ +CMAKE_MINIMUM_REQUIRED(VERSION 2.8.12) +INCLUDE(../setup_testsubproject.cmake) +PROJECT(testsuite CXX) +IF(DEAL_II_WITH_GINKGO) + DEAL_II_PICKUP_TESTS() +ENDIF() diff --git a/tests/ginkgo/solver.cc b/tests/ginkgo/solver.cc new file mode 100644 index 000000000000..560d9117c411 --- /dev/null +++ b/tests/ginkgo/solver.cc @@ -0,0 +1,67 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2018 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + +// test the Ginkgo CG solver + +#include +#include +#include +#include + +#include +#include + +#include "../testmatrix.h" +#include "../tests.h" + +int +main(int argc, char **argv) +{ + initlog(); + deallog << std::setprecision(4); + + { + SolverControl control(100, 1e-3); + + const unsigned int size = 32; + unsigned int dim = (size - 1) * (size - 1); + + deallog << "Size " << size << " Unknowns " << dim << std::endl; + + // Make matrix + FDMatrix testproblem(size, size); + SparsityPattern structure(dim, dim, 5); + testproblem.five_point_structure(structure); + structure.compress(); + SparseMatrix A(structure); + testproblem.five_point(A); + + Vector f(dim); + f = 1.; + Vector u(dim); + u = 0.; + + // std::shared_ptr exec = gko::CudaExecutor::create(0, + // gko::OmpExecutor::create()); + // std::shared_ptr exec = gko::OmpExecutor::create(); + std::shared_ptr exec = gko::ReferenceExecutor::create(); + GinkgoWrappers::SolverCG<> solver(control, exec); + + check_solver_within_range(solver.solve(A, u, f), + control.last_step(), + 35, + 39); + } +} diff --git a/tests/ginkgo/solver.output b/tests/ginkgo/solver.output new file mode 100644 index 000000000000..4ce62b0ef7c1 --- /dev/null +++ b/tests/ginkgo/solver.output @@ -0,0 +1,3 @@ + +DEAL::Size 32 Unknowns 961 +DEAL::Solver stopped within 35 - 39 iterations From 57381dfaaeb088cda88e1628a7336c56dfc6ba18 Mon Sep 17 00:00:00 2001 From: Pratik Nayak Date: Wed, 30 Jan 2019 12:50:06 +0100 Subject: [PATCH 035/507] Add the ginkgo source and include files. --- include/deal.II/lac/ginkgo_solver.h | 243 +++++++++++++++++++++ source/lac/ginkgo_solver.cc | 313 ++++++++++++++++++++++++++++ 2 files changed, 556 insertions(+) create mode 100644 include/deal.II/lac/ginkgo_solver.h create mode 100644 source/lac/ginkgo_solver.cc diff --git a/include/deal.II/lac/ginkgo_solver.h b/include/deal.II/lac/ginkgo_solver.h new file mode 100644 index 000000000000..3ac50c912836 --- /dev/null +++ b/include/deal.II/lac/ginkgo_solver.h @@ -0,0 +1,243 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2018 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + +#ifndef dealii_ginkgo_solver_h +# define dealii_ginkgo_solver_h + + +# include + +# ifdef DEAL_II_WITH_GINKGO + +# include +# include +# include +# include +# include + +# include + +# include + +DEAL_II_NAMESPACE_OPEN + +namespace GinkgoWrappers +{ + /** + * This class forms the base class for all of Ginkgo's iterative solvers. + * The various derived classes only take + * the additional data that is specific to them and solve the given linear + * system. The entire collection of solvers that Ginkgo implements is + * available at documentation + * and manual pages. + * + * @ingroup GinkgoWrappers + */ + template + class SolverBase + { + public: + /** + * Constructor. + * + * The @p executor defines the paradigm where the solution is computed. + * Ginkgo currently supports three different executor types: + * + * + OmpExecutor specifies that the data should be stored and the + * associated operations executed on an OpenMP-supporting device (e.g. host + * CPU); + * ``` + * auto omp = gko::create(); + * ``` + * + CudaExecutor specifies that the data should be stored and the + * operations executed on the NVIDIA GPU accelerator; + * ``` + * if(gko::CudaExecutor::get_num_devices() > 0 ) { + * auto cuda = gko::create(); + * } + * ``` + * + ReferenceExecutor executes a non-optimized reference implementation, + * which can be used to debug the library. + * ``` + * auto ref = gko::create(); + * ``` + * + * The following code snippet demonstrates the using of the OpenMP executor + * to create a solver which would use the OpenMP paradigm to the solve the + * system on the CPU. + * + * ``` + * auto omp = gko::create(); + * using cg = gko::solver::Cg<>; + * auto solver_gen = + * cg::build() + * .with_criteria( + * gko::stop::Iteration::build().with_max_iters(20u).on(omp), + * gko::stop::ResidualNormReduction<>::build() + * .with_reduction_factor(1e-6) + * .on(omp)) + * .on(omp); + * auto solver = solver_gen->generate(system_matrix); + * + * solver->apply(lend(rhs), lend(solution)); + * ``` + * + * + * The @p solver_control object is the same as for other + * deal.II iterative solvers. + */ + SolverBase(SolverControl & solver_control, + std::shared_ptr executor); + + /** + * Destructor. + */ + virtual ~SolverBase() = default; + + /** + * Initialize the matrix and copy over its data to Ginkgo's data structures. + */ + void + initialize(const SparseMatrix &matrix); + + /** + * Solve the linear system Ax=b. Dependent on the information + * provided by derived classes one of Ginkgo's linear solvers is + * chosen. + */ + void + apply(Vector &solution, const Vector &rhs); + + /** + * Solve the linear system Ax=b. Dependent on the information + * provided by derived classes one of Ginkgo's linear solvers is + * chosen. + */ + void + solve(const SparseMatrix &matrix, + Vector & solution, + const Vector & rhs); + + /** + * Access to the object that controls convergence. + */ + SolverControl & + control() const; + + + protected: + /** + * Reference to the object that controls convergence of the iterative + * solvers. + */ + SolverControl &solver_control; + + /** + * The Ginkgo generated solver factory object. + */ + std::shared_ptr solver_gen; + + /** + * The residual criterion object that controls the reduction of the residual + * based on the tolerance set in the solver_control member. + */ + std::shared_ptr::Factory> + residual_criterion; + + /** + * The Ginkgo convergence logger used to check for convergence and other + * solver data if needed. + */ + std::shared_ptr> convergence_logger; + + /** + * The Ginkgo combined factory object is used to create a combined stopping + * criterion to be passed to the solver. + */ + std::shared_ptr combined_factory; + + /** + * The execution paradigm in Ginkgo. The choices are between + * `gko::OmpExecutor`, `gko::CudaExecutor` and `gko::ReferenceExecutor` + * and more details can be found in Ginkgo's documentation. + */ + std::shared_ptr executor; + + private: + /** + * Initialize the Ginkgo logger object with event masks. Refer to + * Ginkgo's + * logging event masks. + */ + void + initialize_ginkgo_log(); + + /** + * Ginkgo matrix data structure. First template parameter is for storing the + * array of the non-zeros of the matrix. The second is for the row pointers + * and the column indices. + * + * @todo Templatize based on Matrix type. + */ + std::shared_ptr> system_matrix; + }; + + + /** + * An implementation of the solver interface using the Ginkgo CG solver. + * + * @ingroup GinkgoWrappers + */ + template + class SolverCG : public SolverBase + { + public: + /** + * A standardized data struct to pipe additional data to the solver. + */ + struct AdditionalData + {}; + + /** + * Constructor. + * + * @p solver_control The solver control object is then used to set the + * parameters and setup the CG solver from the CG factory which solves the + * linear system. + * + * @p executor The execution paradigm for the CG solver. + */ + SolverCG(SolverControl & solver_control, + std::shared_ptr executor, + const AdditionalData & data = AdditionalData()); + + protected: + /** + * Store a copy of the settings for this particular solver. + */ + const AdditionalData additional_data; + }; + + +} // namespace GinkgoWrappers + +DEAL_II_NAMESPACE_CLOSE + +# endif // DEAL_II_WITH_GINKGO + +#endif +/*---------------------------- ginkgo_solver.h ---------------------------*/ diff --git a/source/lac/ginkgo_solver.cc b/source/lac/ginkgo_solver.cc new file mode 100644 index 000000000000..b1e08892ee7d --- /dev/null +++ b/source/lac/ginkgo_solver.cc @@ -0,0 +1,313 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2018 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + +#include +#include + +#include + +#ifdef DEAL_II_WITH_GINKGO + +# include + +# include + + +DEAL_II_NAMESPACE_OPEN + +namespace GinkgoWrappers +{ + template + SolverBase::SolverBase( + SolverControl & solver_control, + std::shared_ptr executor) + : solver_control(solver_control) + , executor(executor) + { + using ResidualCriterionFactory = gko::stop::ResidualNormReduction<>; + residual_criterion = ResidualCriterionFactory::build() + .with_reduction_factor(solver_control.tolerance()) + .on(executor); + + combined_factory = + gko::stop::Combined::build() + .with_criteria(residual_criterion, + gko::stop::Iteration::build() + .with_max_iters(solver_control.max_steps()) + .on(executor)) + .on(executor); + } + + template + void + SolverBase::initialize_ginkgo_log() + { + // Add the logger object. See the different masks available in Ginkgo's + // documentation + convergence_logger = gko::log::Convergence<>::create( + executor, gko::log::Logger::criterion_check_completed_mask); + } + + template + void + SolverBase::apply(Vector & solution, + const Vector &rhs) + { + // some shortcuts. + using val_array = gko::Array; + using vec = gko::matrix::Dense; + + Assert(system_matrix, ExcNotInitialized()); + Assert(executor, ExcNotInitialized()); + Assert(rhs.size() == solution.size(), + ExcDimensionMismatch(rhs.size(), solution.size())); + + // Generate the solver from the solver using the system matrix. + auto solver = solver_gen->generate(system_matrix); + + // Create the rhs vector in Ginkgo's format. + std::vector f(rhs.size()); + std::copy(rhs.begin(), rhs.begin() + rhs.size(), f.begin()); + auto b = + vec::create(executor, + gko::dim<2>(rhs.size(), 1), + val_array::view(executor->get_master(), rhs.size(), f.data()), + 1); + + // Create the solution vector in Ginkgo's format. + std::vector u(solution.size()); + std::copy(solution.begin(), solution.begin() + solution.size(), u.begin()); + auto x = vec::create(executor, + gko::dim<2>(solution.size(), 1), + val_array::view(executor->get_master(), + solution.size(), + u.data()), + 1); + + // Create the logger object to log some data from the solvers to confirm + // convergence. + initialize_ginkgo_log(); + + Assert(convergence_logger, ExcNotInitialized()); + // Add the convergence logger object to the combined factory to retrieve the + // solver and other data + combined_factory->add_logger(convergence_logger); + + // Finally, apply the solver to b and get the solution in x. + solver->apply(gko::lend(b), gko::lend(x)); + + // The convergence_logger object contains the residual vector after the + // solver has returned. use this vector to compute the residual norm of the + // solution. Get the residual norm from the logger. As the convergence + // logger returns a `linop`, it is necessary to convert it to a Dense + // matrix. Additionally, if the logger is logging on the gpu, it is + // necessary to copy the data to the host and hence the + // `residual_norm_d_master` + auto residual_norm = convergence_logger->get_residual_norm(); + auto residual_norm_d = + gko::as>(residual_norm); + auto residual_norm_d_master = + gko::matrix::Dense::create(executor->get_master(), + gko::dim<2>{1, 1}); + residual_norm_d_master->copy_from(residual_norm_d); + + // Get the number of iterations taken to converge to the solution. + auto num_iteration = convergence_logger->get_num_iterations(); + + // Ginkgo works with a relative residual norm through its + // ResidualNormReduction criterion. Therefore, to get the normalized + // residual, we divide by the norm of the rhs. + auto b_norm = gko::matrix::Dense::create(executor->get_master(), + gko::dim<2>{1, 1}); + if (executor != executor->get_master()) + { + auto b_master = vec::create(executor->get_master(), + gko::dim<2>(rhs.size(), 1), + val_array::view(executor->get_master(), + rhs.size(), + f.data()), + 1); + b_master->compute_norm2(b_norm.get()); + } + else + { + b->compute_norm2(b_norm.get()); + } + + Assert(b_norm.get()->at(0, 0) != 0.0, ExcDivideByZero()); + // Pass the number of iterations and residual norm to the solver_control + // object. As both `residual_norm_d_master` and `b_norm` are seen as Dense + // matrices, we use the `at` function to get the first value here. In case + // of multiple right hand sides, this will need to be modified. + const SolverControl::State state = + solver_control.check(num_iteration, + residual_norm_d_master->at(0, 0) / b_norm->at(0, 0)); + + // in case of failure: throw exception + if (state != SolverControl::success) + AssertThrow(false, + SolverControl::NoConvergence(solver_control.last_step(), + solver_control.last_value())); + + // Check if the solution is on a CUDA device, if so, copy it over to the + // host. + if (executor != executor->get_master()) + { + auto x_master = vec::create(executor->get_master(), + gko::dim<2>(solution.size(), 1), + val_array::view(executor, + solution.size(), + x->get_values()), + 1); + x.reset(x_master.release()); + } + // Finally copy over the solution vector to deal.II's solution vector. + std::copy(x->get_values(), + x->get_values() + solution.size(), + solution.begin()); + } + + + template + SolverControl & + SolverBase::control() const + { + return solver_control; + } + + + template + void + SolverBase::initialize( + const SparseMatrix &matrix) + { + // Needs to be a square matrix + Assert(matrix.m() == matrix.n(), ExcNotQuadratic()); + + using size_type = dealii::types::global_dof_index; + const size_type N = matrix.m(); + + using mtx = gko::matrix::Csr; + std::shared_ptr system_matrix_compute; + system_matrix_compute = mtx::create(executor->get_master(), + gko::dim<2>(N), + matrix.n_nonzero_elements()); + ValueType *mat_values = system_matrix_compute->get_values(); + IndexType *mat_row_ptrs = system_matrix_compute->get_row_ptrs(); + IndexType *mat_col_idxs = system_matrix_compute->get_col_idxs(); + + // Copy over the data from the matrix to the data structures Ginkgo needs. + // + // Final note: if the matrix has entries in the sparsity pattern that are + // actually occupied by entries that have a zero numerical value, then we + // keep them anyway. people are supposed to provide accurate sparsity + // patterns. + + // first fill row lengths array + mat_row_ptrs[0] = 0; + for (size_type row = 1; row <= N; ++row) + mat_row_ptrs[row] = + mat_row_ptrs[row - 1] + matrix.get_row_length(row - 1); + + // Copy over matrix elements. note that for sparse matrices, + // iterators are sorted so that they traverse each row from start to end + // before moving on to the next row. however, this isn't true for block + // matrices, so we have to do a bit of book keeping + { + // Have an array that for each row points to the first entry not yet + // written to + std::vector row_pointers(N + 1); + std::copy(system_matrix_compute->get_row_ptrs(), + system_matrix_compute->get_row_ptrs() + N + 1, + row_pointers.begin()); + + // Loop over the elements of the matrix row by row, as suggested in the + // documentation of the sparse matrix iterator class + for (size_type row = 0; row < N; ++row) + { + for (typename SparseMatrix::const_iterator p = + matrix.begin(row); + p != matrix.end(row); + ++p) + { + // Write entry into the first free one for this row + mat_col_idxs[row_pointers[row]] = p->column(); + mat_values[row_pointers[row]] = p->value(); + + // Then move pointer ahead + ++row_pointers[row]; + } + } + + // At the end, we should have written all rows completely + for (size_type i = 0; i < N - 1; ++i) + Assert(row_pointers[i] == mat_row_ptrs[i + 1], ExcInternalError()); + } + system_matrix = + mtx::create(executor, gko::dim<2>(N), matrix.n_nonzero_elements()); + system_matrix->copy_from(system_matrix_compute.get()); + } + + + template + void + SolverBase::solve(const SparseMatrix &matrix, + Vector & solution, + const Vector &rhs) + { + initialize(matrix); + apply(solution, rhs); + } + + + /* ---------------------- SolverCG ------------------------ */ + + template + SolverCG::SolverCG( + SolverControl & solver_control, + std::shared_ptr executor, + const AdditionalData & data) + : SolverBase(solver_control, executor) + , additional_data(data) + { + using cg = gko::solver::Cg; + this->solver_gen = + cg::build().with_criteria(this->combined_factory).on(executor); + } + + // Explicit instantiations in GinkgoWrappers +# define GKO_DEALII_INSTANTIATE_FOR_EACH_VALUE_AND_INDEX_TYPE(_macro) \ + template _macro(float, int32_t); \ + template _macro(double, int32_t); \ + template _macro(float, int64_t); \ + template _macro(double, int64_t); + +# define DECLARE_SOLVER_BASE(ValueType, IndexType) \ + class SolverBase + GKO_DEALII_INSTANTIATE_FOR_EACH_VALUE_AND_INDEX_TYPE(DECLARE_SOLVER_BASE); +# undef DECLARE_SOLVER_BASE + +# define DECLARE_SOLVER_CG(ValueType, IndexType) \ + class SolverCG + GKO_DEALII_INSTANTIATE_FOR_EACH_VALUE_AND_INDEX_TYPE(DECLARE_SOLVER_CG); +# undef DECLARE_SOLVER_CG + +} // namespace GinkgoWrappers + + +DEAL_II_NAMESPACE_CLOSE + +#endif // DEAL_II_WITH_GINKGO From 145821cc0e91951c52f5e3c0f1536f633ebbc8c6 Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Wed, 30 Jan 2019 14:20:29 +0100 Subject: [PATCH 036/507] Improve documentation of some functions --- .../deal.II/differentiation/ad/ad_drivers.h | 42 +++++++++++-------- .../deal.II/differentiation/ad/ad_helpers.h | 42 +++++++++++-------- 2 files changed, 50 insertions(+), 34 deletions(-) diff --git a/include/deal.II/differentiation/ad/ad_drivers.h b/include/deal.II/differentiation/ad/ad_drivers.h index 7f76fe846134..cdde7694598e 100644 --- a/include/deal.II/differentiation/ad/ad_drivers.h +++ b/include/deal.II/differentiation/ad/ad_drivers.h @@ -284,7 +284,7 @@ namespace Differentiation * evaluation point. * * This issue, known as "branch switching", can be clarified by means of - * a trivial example: + * a trivial, contrived example: * @code * ADNumberType func (ADNumberType x, ADNumberType y, ADNumberType z) * { @@ -296,13 +296,17 @@ namespace Differentiation * @endcode * During taping, the conditional statement may be either true or * false, and the result (with its sensitivities) returned by - * this function. For some other evaluation of the tape (i.e. for some - * different - * inputs @p x and @p y, the other branch of the conditional check may be - * chosen. The result of following this code path has not been recorded on - * the tape, and therefore cannot be evaluated. In such a case, it is - * therefore necessary to re-record the tape at the new evaluation point - * in order to resolve the new code branch. + * this function. + * The AD library doesn't just record the parse tree of the operations + * applied on the branch chosen at the time to taping, but also checks + * that the condition continues to be satisfied. For some other evaluation + * of the tape (i.e. for some different inputs @p x and @p y), the other + * branch of the conditional check may be chosen. The result of following + * this code path has not been recorded on the tape, and therefore cannot + * be evaluated. In such a case, the underlying AD library will be able to + * tell you that it is necessary to re-record the tape at the new + * evaluation point in order to resolve the new code branch. This function + * can be used to find out whether this is so. * * @note The chosen tape index must be greater than * Numbers::invalid_tape_index and less than @@ -315,13 +319,13 @@ namespace Differentiation /** * Return a flag that, when true, indicates that the retaping * of the dependent function is necessary for a reliable computation to be - * performed on the active tape. + * performed on the currently active tape. * This may be necessary if a sign comparison within branched operations * yields different results to those computed at the original tape * evaluation point. * * This issue, known as "branch switching", can be clarified by means of - * a trivial example: + * a trivial, contrived example: * @code * ADNumberType func (ADNumberType x, ADNumberType y, ADNumberType z) * { @@ -333,13 +337,17 @@ namespace Differentiation * @endcode * During taping, the conditional statement may be either true or * false, and the result (with its sensitivities) returned by - * this function. For some other evaluation of the tape (i.e. for some - * different - * inputs @p x and @p y, the other branch of the conditional check may be - * chosen. The result of following this code path has not been recorded on - * the tape, and therefore cannot be evaluated. In such a case, it is - * therefore necessary to re-record the tape at the new evaluation point - * in order to resolve the new code branch. + * this function. + * The AD library doesn't just record the parse tree of the operations + * applied on the branch chosen at the time to taping, but also checks + * that the condition continues to be satisfied. For some other evaluation + * of the tape (i.e. for some different inputs @p x and @p y), the other + * branch of the conditional check may be chosen. The result of following + * this code path has not been recorded on the tape, and therefore cannot + * be evaluated. In such a case, the underlying AD library will be able to + * tell you that it is necessary to re-record the tape at the new + * evaluation point in order to resolve the new code branch. This function + * can be used to find out whether this is so. */ bool last_action_requires_retaping() const; diff --git a/include/deal.II/differentiation/ad/ad_helpers.h b/include/deal.II/differentiation/ad/ad_helpers.h index f5cb753260e4..ff94ee962f1b 100644 --- a/include/deal.II/differentiation/ad/ad_helpers.h +++ b/include/deal.II/differentiation/ad/ad_helpers.h @@ -487,7 +487,7 @@ namespace Differentiation * evaluation point. * * This issue, known as "branch switching", can be clarified by means of - * a trivial example: + * a trivial, contrived example: * @code * ADNumberType func (ADNumberType x, ADNumberType y, ADNumberType z) * { @@ -499,13 +499,17 @@ namespace Differentiation * @endcode * During taping, the conditional statement may be either true or * false, and the result (with its sensitivities) returned by - * this function. For some other evaluation of the tape (i.e. for some - * different - * inputs @p x and @p y, the other branch of the conditional check may be - * chosen. The result of following this code path has not been recorded on - * the tape, and therefore cannot be evaluated. In such a case, it is - * therefore necessary to re-record the tape at the new evaluation point - * in order to resolve the new code branch. + * this function. + * The AD library doesn't just record the parse tree of the operations + * applied on the branch chosen at the time to taping, but also checks + * that the condition continues to be satisfied. For some other evaluation + * of the tape (i.e. for some different inputs @p x and @p y), the other + * branch of the conditional check may be chosen. The result of following + * this code path has not been recorded on the tape, and therefore cannot + * be evaluated. In such a case, the underlying AD library will be able to + * tell you that it is necessary to re-record the tape at the new + * evaluation point in order to resolve the new code branch. This function + * can be used to find out whether this is so. * * For the output of this function to be meaningful, it must be called * after activate_recorded_tape() is called and the new evaluation @@ -520,13 +524,13 @@ namespace Differentiation /** * Return a flag that, when true, indicates that the * retaping of the dependent function is necessary for a reliable - * computation to be performed on the active tape. + * computation to be performed on the currently active tape. * This may be necessary if a sign comparison within branched operations * yields different results to those computed at the original tape * evaluation point. * * This issue, known as "branch switching", can be clarified by means of - * a trivial example: + * a trivial, contrived example: * @code * ADNumberType func (ADNumberType x, ADNumberType y, ADNumberType z) * { @@ -538,13 +542,17 @@ namespace Differentiation * @endcode * During taping, the conditional statement may be either true or * false, and the result (with its sensitivities) returned by - * this function. For some other evaluation of the tape (i.e. for some - * different - * inputs @p x and @p y, the other branch of the conditional check may be - * chosen. The result of following this code path has not been recorded on - * the tape, and therefore cannot be evaluated. In such a case, it is - * therefore necessary to re-record the tape at the new evaluation point - * in order to resolve the new code branch. + * this function. + * The AD library doesn't just record the parse tree of the operations + * applied on the branch chosen at the time to taping, but also checks + * that the condition continues to be satisfied. For some other evaluation + * of the tape (i.e. for some different inputs @p x and @p y), the other + * branch of the conditional check may be chosen. The result of following + * this code path has not been recorded on the tape, and therefore cannot + * be evaluated. In such a case, the underlying AD library will be able to + * tell you that it is necessary to re-record the tape at the new + * evaluation point in order to resolve the new code branch. This function + * can be used to find out whether this is so. * * For the output of this function to be meaningful, it must be called * after activate_recorded_tape() is called and the new evaluation From a7cbf3c0ade5dee64c5849b450e37e2235bc281f Mon Sep 17 00:00:00 2001 From: Pratik Nayak Date: Wed, 30 Jan 2019 16:20:39 +0100 Subject: [PATCH 037/507] Add changelog entry and fix a typo. --- doc/news/changes/major/20190130ginkgo-developers | 7 +++++++ doc/readme.html | 2 +- 2 files changed, 8 insertions(+), 1 deletion(-) create mode 100644 doc/news/changes/major/20190130ginkgo-developers diff --git a/doc/news/changes/major/20190130ginkgo-developers b/doc/news/changes/major/20190130ginkgo-developers new file mode 100644 index 000000000000..646f6b3d140d --- /dev/null +++ b/doc/news/changes/major/20190130ginkgo-developers @@ -0,0 +1,7 @@ +New: Support for Ginkgo, a high-performance numerical linear algebra library +has been added. Ginkgo provides advanced highly optimized linear solvers, +matrix formats and an abstraction to easily create linear operators on both +the cpu and the gpu. The deal.II's Ginkgo interface can currently be used to +solve linear systems using Krylov solvers with the cuda and OpenMP paradigms. +
+(Ginkgo developers, 2019/01/30) diff --git a/doc/readme.html b/doc/readme.html index 406981e5f710..9d7cf59ead41 100644 --- a/doc/readme.html +++ b/doc/readme.html @@ -430,7 +430,7 @@

Optional interfaces to other software packages

Ginkgo is a numerical linear algebra library with highly optimized kernels for many core architectures with a focus on fine level parallelism. - It allows for easy switching of the executing paradigm (CUDA, OpenMP, .etc) + It allows for easy switching of the executing paradigm (CUDA, OpenMP, etc.) while providing a multitude of linear solvers and preconditioners and extension to other linear operators with minimal changes required in the code. To enable Ginkgo, pass -DGINKGO_DIR=/path/to/ginkgo to CMake when From ad3df66bb2f18e4582bfe07eaba4a459e39d3999 Mon Sep 17 00:00:00 2001 From: Zhuoran Wang Date: Fri, 27 Apr 2018 16:31:49 +0000 Subject: [PATCH 038/507] Add step-61. This tutorial program adds a code that solves the Poisson equation using the weak Galerkin formulation. --- examples/step-61/CMakeLists.txt | 39 + examples/step-61/doc/builds-on | 1 + examples/step-61/doc/intro.dox | 279 ++++++ examples/step-61/doc/kind | 1 + examples/step-61/doc/results.dox | 88 ++ examples/step-61/doc/step-61.wg000_2d_2.png | Bin 0 -> 7590 bytes examples/step-61/doc/step-61.wg000_2d_4.png | Bin 0 -> 21571 bytes examples/step-61/doc/step-61.wg000_3d_2.png | Bin 0 -> 9996 bytes examples/step-61/doc/step-61.wg000_3d_4.png | Bin 0 -> 40641 bytes examples/step-61/doc/step-61.wg111_2d_4.png | Bin 0 -> 114303 bytes examples/step-61/doc/step-61.wg111_3d_4.png | Bin 0 -> 118587 bytes examples/step-61/doc/step-61.wg222_2d_5.png | Bin 0 -> 136893 bytes examples/step-61/doc/step-61.wg222_3d_5.png | Bin 0 -> 220122 bytes examples/step-61/doc/tooltip | 1 + examples/step-61/step-61.cc | 915 ++++++++++++++++++++ 15 files changed, 1324 insertions(+) create mode 100644 examples/step-61/CMakeLists.txt create mode 100644 examples/step-61/doc/builds-on create mode 100644 examples/step-61/doc/intro.dox create mode 100644 examples/step-61/doc/kind create mode 100644 examples/step-61/doc/results.dox create mode 100644 examples/step-61/doc/step-61.wg000_2d_2.png create mode 100644 examples/step-61/doc/step-61.wg000_2d_4.png create mode 100644 examples/step-61/doc/step-61.wg000_3d_2.png create mode 100644 examples/step-61/doc/step-61.wg000_3d_4.png create mode 100644 examples/step-61/doc/step-61.wg111_2d_4.png create mode 100644 examples/step-61/doc/step-61.wg111_3d_4.png create mode 100644 examples/step-61/doc/step-61.wg222_2d_5.png create mode 100644 examples/step-61/doc/step-61.wg222_3d_5.png create mode 100644 examples/step-61/doc/tooltip create mode 100644 examples/step-61/step-61.cc diff --git a/examples/step-61/CMakeLists.txt b/examples/step-61/CMakeLists.txt new file mode 100644 index 000000000000..83a33d091ac2 --- /dev/null +++ b/examples/step-61/CMakeLists.txt @@ -0,0 +1,39 @@ +## +# CMake script for the step-61 tutorial program: +## + +# Set the name of the project and target: +SET(TARGET "step-61") + +# Declare all source files the target consists of. Here, this is only +# the one step-X.cc file, but as you expand your project you may wish +# to add other source files as well. If your project becomes much larger, +# you may want to either replace the following statement by something like +# FILE(GLOB_RECURSE TARGET_SRC "source/*.cc") +# FILE(GLOB_RECURSE TARGET_INC "include/*.h") +# SET(TARGET_SRC ${TARGET_SRC} ${TARGET_INC}) +# or switch altogether to the large project CMakeLists.txt file discussed +# in the "CMake in user projects" page accessible from the "User info" +# page of the documentation. +SET(TARGET_SRC + ${TARGET}.cc + ) + +# Usually, you will not need to modify anything beyond this point... + +CMAKE_MINIMUM_REQUIRED(VERSION 2.8.12) + +FIND_PACKAGE(deal.II 9.0.0 QUIET + HINTS ${deal.II_DIR} ${DEAL_II_DIR} ../ ../../ $ENV{DEAL_II_DIR} + ) +IF(NOT ${deal.II_FOUND}) + MESSAGE(FATAL_ERROR "\n" + "*** Could not locate a (sufficiently recent) version of deal.II. ***\n\n" + "You may want to either pass a flag -DDEAL_II_DIR=/path/to/deal.II to cmake\n" + "or set an environment variable \"DEAL_II_DIR\" that contains this path." + ) +ENDIF() + +DEAL_II_INITIALIZE_CACHED_VARIABLES() +PROJECT(${TARGET}) +DEAL_II_INVOKE_AUTOPILOT() diff --git a/examples/step-61/doc/builds-on b/examples/step-61/doc/builds-on new file mode 100644 index 000000000000..2bb1b6e1daea --- /dev/null +++ b/examples/step-61/doc/builds-on @@ -0,0 +1 @@ +step-51 step-7 step-20 diff --git a/examples/step-61/doc/intro.dox b/examples/step-61/doc/intro.dox new file mode 100644 index 000000000000..f5ca096683c0 --- /dev/null +++ b/examples/step-61/doc/intro.dox @@ -0,0 +1,279 @@ +
+ + +This program was contributed by Zhuoran Wang. + + + +

Introduction

+ +This tutorial program presents an implementation of the "weak Galerkin" +finite element method for the Poisson equation. In some sense, the motivation for +considering this method starts from the same point as in step-51: We would like to +consider discontinuous shape functions, but then need to address the fact that +the resulting problem has a large number of degrees of freedom (because, for +example, each vertex carries as many degrees of freedom as there are adjacent cells). +We also have to address the fact that, in general, every degree of freedom +on one cell couples with all of the degrees of freedom on each of its face neighbor +cells. Consequently, the matrix one gets from the "traditional" discontinuous +Galerkin methods are both large and relatively dense. + +Both the hybridized discontinuous Galerkin method (HDG) in step-51 and the weak +Galerkin (WG) method in this tutorial address the issue of coupling by introducing +additional degrees of freedom whose shape functions only live on a face between +cells (i.e., on the "skeleton" of the mesh), and which therefore "insulate" the +degrees of freedom on the adjacent cells from each other: cell degrees of freedom +only couple with other cell degrees of freedom on the same cell, as well as face +degrees of freedom, but not with cell degrees of freedom on neighboring cells. +Consequently, the shape functions for these cell degrees of freedom are +discontinuous and only "live" on exactly one cell. + +For a given equation, say the second order Poisson equation, +the difference between the HDG and the WG method is how exactly one formulates +the problem that connects all of these different shape functions. The HDG does +things by reformulating second order problems in terms of a system of first +order equations and then conceptually considers the face degrees of freedom +to be "fluxes" of this first order system. In contrast, the WG method keeps things +in second order form and considers the face degrees of freedom as of the same +type as the primary solution variable, just restricted to the lower-dimensional +faces. For the purposes of the equation, one then needs to somehow "extend" +these shape functions into the interior of the cell when defining what it means +to apply a differential operator to them. Compared to the HDG, the method +has the advantage that it does not lead to a proliferation of unknowns due +to rewriting the equation as a first-order system, but it is also not quite +as easy to implement. However, as we will see in the following, this +additional effort is not prohibitive. + + +

Weak Galerkin finite element methods

+ +Weak Galerkin Finite Element Methods (WGFEMs) use discrete weak functions +to approximate scalar unknowns and discrete weak gradients to +approximate classical gradients. +It was introduced by Junping Wang and Xiu Ye +in the paper: A weak Galerkin finite element method for second order elliptic problems, +J. Comput. Appl. Math., 2013, 103-115. +Compared to the continuous Galerkin method, +the weak Galerkin method satisfies important physical properties, namely +local mass conservation and bulk normal flux continuity. +It results in a SPD linear system, and expected convergence rates can +be obtained with mesh refinement. + + +

WGFEM applied to the Poisson equation

+This program solves the Poisson equation +using the weak Galerkin finite element method: +@f{eqnarray*} + \nabla \cdot \left( -\mathbf{K} \nabla p \right) + = f, + \quad \mathbf{x} \in \Omega, \\ + p = p_D,\quad \mathbf{x} \in \Gamma^D, \\ + \mathbf{u} \cdot \mathbf{n} = u_N, + \quad \mathbf{x} \in \Gamma^N, +@f} +where $\Omega \subset \mathbb{R}^n (n=2,3)$ is a bounded domain. +In the context of the flow of a fluid through a porous medium, +$p$ is the pressure, $\mathbf{K}$ is a permeability tensor, +$ f $ is the source term, and +$ p_D, u_N $ represent Dirichlet and Neumann boundary conditions. +We can introduce a flux, $\mathbf{u} = -\mathbf{K} \nabla p$, that corresponds +to the Darcy velocity (in the way we did in step-20) and this variable will +be important in the considerations below. + +In this program, we will consider a test case where the exact pressure +is $p = \sin \left( \pi x)\sin(\pi y \right)$ on the unit square domain, +with homogenous Dirichelet boundary conditions and identity matrix $\mathbf{K}$. +Then we will calculate $L_2$ errors of pressure, velocity and flux. + + +

Weak Galerkin scheme

+ +Via integration by parts, the weak Galerkin scheme for the Poisson equation is +@f{equation*} +\mathcal{A}_h\left(p_h,q \right) = \mathcal{F} \left(q \right), +@f} +where +@f{equation*} +\mathcal{A}_h\left(p_h,q\right) + := \sum_{T \in \mathcal{T}_h} + \int_T \mathbf{K} \nabla_{w,d} p_h \cdot \nabla_{w,d} q \mathrm{d}x, +@f} +and +@f{equation*} +\mathcal{F}\left(q\right) + := \sum_{T \in \mathcal{T}_h} \int_T f \, q^\circ \mathrm{d}x + - \sum_{\gamma \in \Gamma_h^N} \int_\gamma u_N q^\partial \mathrm{d}x, +@f} +$q^\circ$ is the shape function of the polynomial space in the interior, +$q^\partial$ is the shape function of the polynomial space on faces, $ \nabla_{w,d} $ means the discrete weak gradient used to approximate the classical gradient. +We use FE_DGQ as the interior polynomial space, +FE_FaceQ as the face polynomial space, and Raviart-Thomas elements for the velocity +$\mathbf{u} = -{\mathbf{K}} \nabla_{w,d} p$. + +

Assembling the linear system

+ +First, we solve for the pressure. +We collect two local spaces together in one FESystem, +the first component in this finite element system denotes +the space for interior pressure, and the second denotes +the space for face pressure. +For the interior component, we use the polynomial space FE_DGQ. +For the face component, we use FE_FaceQ. + +We use shape functions defined on spaces FE_DGQ and FE_FaceQ to +approximate pressures, i.e., $p_h = \sum a_i \phi_i,$ +where $\phi_i$ are shape functions of FESystem. +We construct the local system by using discrete weak gradients of +shape functions of FE_DGQ and FE_FaceQ. +The discrete weak gradients of shape functions $\nabla_{w,d} \phi$ are defined as +$\nabla_{w,d} \phi = \sum_{i=1}^m c_i \mathbf{w}_i,$ +where $\mathbf{w}_i$ is the basis function of $RT(k)$. + +Using integration by parts, we have a small linear system +on each element $T$, +@f{equation*} +\int_{T} \left(\nabla_{w,d} \phi \right) \cdot \mathbf{w} \mathrm{d}x= +\int_{T^\partial} \phi^{\partial} \left(\mathbf{w} \cdot \mathbf{n}\right) \mathrm{d}x- +\int_{T^\circ} \phi^{\circ} \left(\nabla \cdot \mathbf{w}\right) \mathrm{d}x, +\quad \forall \mathbf{w} \in RT_{[k]}(E), +@f} + +@f{equation*} +\sum_{i=1}^m c_i \int_T \mathbf{w}_i \cdot \mathbf{w}_j \mathrm{d}x = +\int_{T^{\partial}} \phi_i^{\partial} +\left(\mathbf{w}_j \cdot \mathbf{n} \right) \mathrm{d}x - +\int_{T^{\circ}} \phi_i^{\circ} \left (\nabla \cdot \mathbf{w}_j \right)\mathrm{d}x, +@f} +which can be simplified to be +@f{equation*} +\mathbf{C}_{E}\mathbf{M}_{E} = \mathbf{F}_{E}, +@f} +where $\mathbf{C}_E$ is the matrix with unknown coefficients $c$, +$\mathbf{M}_E$ is the Gram matrix +$\left[ \int_T \mathbf{w}_i \cdot \mathbf{w}_j \right] \mathrm{d}x$, +$\mathbf{F}_E$ is the matrix of right hand side, +$\mathbf{w}$ and $\phi_i^{\circ}$ are in FEValues, +$\phi_i^{\partial}$ is in FEFaceValues. +Then we solve for $\mathbf{C}_E = \mathbf{F}_E \mathbf{M}_E^{-1}$. +Now, discrete weak gradients of shape functions are written as +linear combinations of basis functions of the $RT$ space. +In our code, we name $\mathbf{C}_E$ as cell_matrix_C, +$\mathbf{M}_E$ as cell_matrix_rt, +$\mathbf{F}_E$ as cell_matrix_F. + +The components of the local cell matrices $\mathbf{A}$ are +@f{equation*} +\mathbf{A}_{ij} = +\int_{T} \mathbf{K} \nabla_{w,d} \phi_i \cdot \nabla_{w,d} \phi_j \mathrm{d}x. +@f} +From previous steps, we know $\nabla_{w,d} \phi_i = \sum_{k=1}^m c_{ik} \mathbf{w}_k,$ +and $\nabla_{w,d} \phi_j = \sum_{l=1}^m c_{jl} \mathbf{w}_l.$ +Then combining the coefficients we have calculated, components of $\mathbf{A}$ are calculated as +@f{equation*} +\int_T \sum_{k,l = 1}^{m}c_{ik} c_{jl} \left(\mathbf{K} \mathbf{w}_i \cdot \mathbf{w}_j\right) \mathrm{d}x += \sum_{k,l = 1}^{m}c_{ik} c_{jl} \int_{T} \mathbf{K} \mathbf{w}_i \cdot \mathbf{w}_j \mathrm{d}x. +@f} + +Next, we use ConstraintMatrix::distribute_local_to_global to +distribute contributions from local matrices $\mathbf{A}$ to the system matrix. + +In the scheme +$\mathcal{A}_h\left(p_h,q \right) = \mathcal{F} \left( q \right),$ +we have system matrix and system right hand side, +we can solve for the coefficients of the system matrix. +The solution vector of the scheme represents the pressure values in interiors and on faces. + +

Post-processing and $L_2$-errors

+ +After we have calculated the numerical pressure $p$, +we use discrete weak gradients of $p$ to calculate the velocity on each element. + +On each element the gradient of the numerical pressure $\nabla p$ can be +approximated by discrete weak gradients $ \nabla_{w,d}\phi_i$, so +@f{equation*} +\nabla_{w,d} p_h = \sum_{i} a_i \nabla_{w,d}\phi_i. +@f} + +The numerical velocity $ \mathbf{u}_h = -\mathbf{K} \nabla_{w,d}p_h$ can be written as +@f{equation*} +\mathbf{u}_h = -\mathbf{K} \nabla_{w,d} p = +-\sum_{i} \sum_{j} a_ic_{ij}\mathbf{K}\mathbf{w}_j, +@f} +where $c_{ij}$ is the coefficient of Gram matrix, +$\mathbf{w}_j$ is the basis function of the $RT$ space. +$\mathbf{K} \mathbf{w}_j$ may not be in the $RT$ space. +So we need $L_2$-projection to project it back to the $RT$ space. + +We define the projection as +$ \mathbf{Q}_h \left( \mathbf{K}\mathbf{w}_j \right) = +\sum_{k} d_{jk}\mathbf{w}_k$. +For any $j$, +$\left( \mathbf{Q}_h \left( \mathbf{Kw}_j \right),\mathbf{w}_k \right)_E = +\left( \mathbf{Kw}_j,\mathbf{w}_k \right)_E.$ +So the numerical velocity becomes +@f{equation*} +\mathbf{u}_h = \mathbf{Q}_h \left( -\mathbf{K}\nabla_{w,d}p_h \right) = +-\sum_{i=0}^{4} \sum_{j=1}^{4}a_ib_{ij}\mathbf{Q}_h \left( \mathbf{K}\mathbf{w}_j \right), +@f} +and we have the following system to solve for the coefficients $d_{jk}$, +@f{equation*} + \left[ + \begin{matrix} + \left(\mathbf{w}_i,\mathbf{w}_j \right) + \end{matrix} + \right] + \left[ + \begin{matrix} + d_{jk} + \end{matrix} + \right] + = + \left[ + \begin{matrix} + \left( \mathbf{Kw}_j,\mathbf{w}_k \right) + \end{matrix} + \right]. +@f} +$ + \left[ + \begin{matrix} + d_{jk} + \end{matrix} + \right] +$ +is named cell_matrix_D, +$ +\left[ + \begin{matrix} + \left( \mathbf{Kw}_j,\mathbf{w}_k \right) + \end{matrix} + \right] +$ +is named cell_matrix_E. + +Then the elementwise velocity is +@f{equation*} +\mathbf{u}_h = -\sum_{i} \sum_{j}a_ic_{ij}\sum_{k}d_{jk}\mathbf{w}_k = +\sum_{k}- \left(\sum_{j} \sum_{i} a_ic_{ij}d_{jk} \right)\mathbf{w}_k, +@f} +where $-\sum_{j} \sum_{i} a_ic_{ij}d_{jk}$ is named +beta in the code. + +We calculate the $L_2$-errors of pressure, velocity and flux +by the following formulas, +@f{eqnarray*} +\|p-p_h^\circ\|^2 + = \sum_{T \in \mathcal{T}_h} \|p-p_h^\circ\|_{L^2(E)}^2, \\ + \|\mathbf{u}-\mathbf{u}_h\|^2 + = \sum_{T \in \mathcal{T}_h} \|\mathbf{u}-\mathbf{u}_h\|_{L^2(E)^2}^2,\\ +\|(\mathbf{u}-\mathbf{u}_h) \cdot \mathbf{n}\|^2 + = \sum_{T \in \mathcal{T}_h} \sum_{\gamma \subset T^\partial} + \frac{|T|}{|\gamma|} \|\mathbf{u} \cdot \mathbf{n} - \mathbf{u}_h \cdot \mathbf{n}\|_{L^2(\gamma)}^2, +@f} +where $| T |$ is the area of the element, +$\gamma$ are faces of the element, +$\mathbf{n}$ are unit normal vectors of each face. + +We will extract interior pressure solutions of each cell +from the global solution and calculate the $L_2$ error +by using function VectorTools::integrate_difference. diff --git a/examples/step-61/doc/kind b/examples/step-61/doc/kind new file mode 100644 index 000000000000..c1d9154931a7 --- /dev/null +++ b/examples/step-61/doc/kind @@ -0,0 +1 @@ +techniques diff --git a/examples/step-61/doc/results.dox b/examples/step-61/doc/results.dox new file mode 100644 index 000000000000..b71c57abb177 --- /dev/null +++ b/examples/step-61/doc/results.dox @@ -0,0 +1,88 @@ +

Results

+ +We run the test example $p = \sin(\pi x) \sin(\pi y)$ with homogenous Dirichelet boundary conditions in the domain $\Omega = (0,1)^2$. And $\mathbf{K}$ is the identity matrix. We test it on $\mbox{WG}(Q_0,Q_0;RT_{[0]})$, $\mbox{WG}(Q_1,Q_1;RT_{[1]})$ and $\mbox{WG}(Q_2,Q_2;RT_{[2]})$. We will visualize pressure values in interiors and on faces. We want to see the pressure maximum is around 1 and the minimum is around 0. With the mesh refinement, the convergence rates of pressure, velocity and flux should be around 1 on $\mbox{WG}(Q_0,Q_0;RT_{[0]})$ , 2 on $\mbox{WG}(Q_1,Q_1;RT_{[1]})$, and 3 on $\mbox{WG}(Q_2,Q_2;RT_{[2]})$. + +

Test results on $\mbox{WG}(Q_0,Q_0;RT_{[0]})$

+The following figures are interior pressures and face pressures implemented on $\mbox{WG}(Q_0,Q_0;RT_{[0]})$. The mesh is refined 2 times and 4 times separately. + + + + + + + + + + +
+ +From the figures, we can see that with the mesh refinement, the maximum and minimum are approaching to what we expect. +Since the mesh is a rectangular mesh and numbers of refinement are even, we have symmetric solutions. From the 3d figures, we can see that on $\mbox{WG}(Q_0,Q_0;RT_{[0]})$, pressure is a constant in the interior of the cell. + +

Convergence table

+ +We run the code with finer meshes and get the following convergence rates of pressure, +velocity and flux. + +@code +number of refinements $\|p-p_h^\circ\|$ $\|\mathbf{u}-\mathbf{u}_h\|$ $\|(\mathbf{u}-\mathbf{u}_h) \cdot \mathbf{n}\|$ + 2 1.587e-01 5.113e-01 7.062e-01 + 3 8.000e-02 2.529e-01 3.554e-01 + 4 4.006e-02 1.260e-01 1.780e-01 + 5 2.004e-02 6.297e-02 8.902e-02 +Conv.rate 1.00 1.00 1.00 +@endcode +We can see that the convergence rates of $\mbox{WG}(Q_0,Q_0;RT_{[0]})$ are around 1. + + +

Test results on $\mbox{WG}(Q_1,Q_1;RT_{[1]})$

+ +The following figures are interior pressures and face pressures implemented on $\mbox{WG}(Q_1,Q_1;RT_{[1]})$. The mesh is refined 4 times. Compared to the previous figures on +$\mbox{WG}(Q_0,Q_0;RT_{[0]})$, on each cell, the result is not a constant. Because we use higher order polynomials to do approximation. So there are 4 pressure values in one interior, 2 pressure values on each face. We use data_out_face.build_patches (fe.degree) +to divide each cell interior into 4 subcells. + + + + + + +
+ +

Convergence table

+ +These are the convergence rates of pressure, velocity and flux on $\mbox{WG}(Q_1,Q_1;RT_{[1]})$ + +@code +number of refinements $\|p-p_h^\circ\|$ $\|\mathbf{u}-\mathbf{u}_h\|$ $\|(\mathbf{u}-\mathbf{u}_h) \cdot \mathbf{n}\|$ + 2 1.613e-02 5.093e-02 7.167e-02 + 3 4.056e-03 1.276e-02 1.802e-02 + 4 1.015e-03 3.191e-03 4.512e-03 + 5 2.540e-04 7.979e-04 1.128e-03 +Conv.rate 2.00 2.00 2.00 +@endcode +The convergence rates of $WG(Q_1,Q_1;RT_{[1]})$ are around 2. + +

Test results on $WG(Q_2,Q_2;RT_{[2]})$

+ +These are interior pressures and face pressures implemented on $WG(Q_2,Q_2;RT_{[2]})$, with mesh size $h = 1/32$. + + + + + + +
+ +

Convergence table

+ +This is the convergence table of $L_2$ errors of pressure, velocity and flux on $\mbox{WG}(Q_2,Q_2;RT_{[2]})$ + +@code +number of refinements $\|p-p_h^\circ\|$ $\|\mathbf{u}-\mathbf{u}_h\|$ $\|(\mathbf{u}-\mathbf{u}_h) \cdot \mathbf{n}\|$ + 2 1.072e-03 3.375e-03 4.762e-03 + 3 1.347e-04 4.233e-04 5.982e-04 + 4 1.685e-05 5.295e-05 7.487e-05 + 5 2.107e-06 6.620e-06 9.362e-06 +Conv.rate 3.00 3.00 3.00 +@endcode +The convergence rates of $\mbox{WG}(Q_2,Q_2;RT_{[2]})$ are around 3. diff --git a/examples/step-61/doc/step-61.wg000_2d_2.png b/examples/step-61/doc/step-61.wg000_2d_2.png new file mode 100644 index 0000000000000000000000000000000000000000..bf3be238e6caf7398be7df1c0ef2d9ebe5d0edbd GIT binary patch literal 7590 zcmeHMYfzI{8a`ZQxJQ@579VBuh-{;F#40 zaUr{;S8d1|(M4-#|13}oM!G6ZdZzNhwRpu3qdL`TZ3P&9#GX!hqKkTePAOoTjbf{D z{MW{7bn9rhb*hnPMLq=ZjFn>U6aB!>1No}V?;qAFG%m((_YbuRN_~B4Zf^a0<-@oKVe&ooqGBdWSE2 zyS?-l`0+#LvOpT>*|>jfISr(qiyK}CPV8ZByV?`DE-nJzgh1nZK977#(}uZ3KJwjp 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In the post-processing step, we will +// calculate $L_2$-errors of velocity and flux. +template +class WGDarcyEquation +{ +public: + WGDarcyEquation(); + void run(); + +private: + void make_grid(); + void setup_system(); + void assemble_system(); + void solve(); + void postprocess(); + void process_solution(); + void output_results() const; + + Triangulation triangulation; + + AffineConstraints constraints; + + FE_RaviartThomas fe_rt; + DoFHandler dof_handler_rt; + + // The finite element system is used for interior and face solutions. + FESystem fe; + DoFHandler dof_handler; + + SparsityPattern sparsity_pattern; + SparseMatrix system_matrix; + + Vector solution; + Vector system_rhs; +}; + +// @sect3{Right hand side, boundary values, and exact solution} + +// Next, we define the coefficient matrix $\mathbf{K}$, +// Dirichlet boundary conditions, the right-hand side $f = 2\pi^2 \sin(\pi x) +// \sin(\pi y)$, and the reference solutions $p = \sin(\pi x) \sin(\pi y) $. +// +// The coefficient matrix $\mathbf{K}$ is the identity matrix as a test example. +template +class Coefficient : public TensorFunction<2, dim> +{ +public: + Coefficient() + : TensorFunction<2, dim>() + {} + virtual void value_list(const std::vector> &points, + std::vector> & values) const override; +}; + +template +void Coefficient::value_list(const std::vector> &points, + std::vector> & values) const +{ + Assert(points.size() == values.size(), + ExcDimensionMismatch(points.size(), values.size())); + for (unsigned int p = 0; p < points.size(); ++p) + { + values[p].clear(); + for (unsigned int d = 0; d < dim; ++d) + values[p][d][d] = 1; + } +} + +template +class BoundaryValues : public Function +{ +public: + BoundaryValues() + : Function(2) + {} + virtual double value(const Point & p, + const unsigned int component = 0) const override; +}; + +template +double BoundaryValues::value(const Point & /*p*/, + const unsigned int /*component*/) const +{ + return 0; +} + +template +class RightHandSide : public Function +{ +public: + RightHandSide() + : Function() + {} + virtual double value(const Point & p, + const unsigned int component = 0) const; +}; + +template +double RightHandSide::value(const Point &p, + const unsigned int /*component*/) const +{ + double return_value = 0.0; + return_value = 2 * M_PI * M_PI * sin(M_PI * p[0]) * sin(M_PI * p[1]); + return return_value; +} + +template +class Solution : public Function +{ +public: + Solution() + : Function(1) + {} + virtual double value(const Point &p, const unsigned int) const; +}; + +template +double Solution::value(const Point &p, const unsigned int) const +{ + double return_value = 0; + return_value = sin(M_PI * p[0]) * sin(M_PI * p[1]); + return return_value; +} + +template +class Velocity : public TensorFunction<1, dim> +{ +public: + Velocity() + : TensorFunction<1, dim>() + {} + virtual Tensor<1, dim> value(const Point &p) const override; +}; + +template +Tensor<1, dim> Velocity::value(const Point &p) const +{ + Tensor<1, dim> return_value; + return_value[0] = -M_PI * cos(M_PI * p[0]) * sin(M_PI * p[1]); + return_value[1] = -M_PI * sin(M_PI * p[0]) * cos(M_PI * p[1]); + return return_value; +} + +// @sect3{WGDarcyEquation class implementation} + +// @sect4{WGDarcyEquation::WGDarcyEquation} + +// In this constructor, we create a finite element space for vector valued +// functions, FE_RaviartThomas. We will need shape functions in +// this space to approximate discrete weak gradients. + +// FESystem defines finite element spaces in the interior and on +// edges of elements. Each of them gets an individual component. Others are the +// same as previous tutorial programs. +template +WGDarcyEquation::WGDarcyEquation() + : fe_rt(0) + , dof_handler_rt(triangulation) + , + + fe(FE_DGQ(0), 1, FE_FaceQ(0), 1) + , dof_handler(triangulation) + +{} + +// @sect4{WGDarcyEquation::make_grid} + +// We generate a mesh on the unit square domain and refine it. + +template +void WGDarcyEquation::make_grid() +{ + GridGenerator::hyper_cube(triangulation, 0, 1); + triangulation.refine_global(1); + + std::cout << " Number of active cells: " << triangulation.n_active_cells() + << std::endl + << " Total number of cells: " << triangulation.n_cells() + << std::endl; +} + +// @sect4{WGDarcyEquation::setup_system} + +// After we create the mesh, we distribute degrees of freedom for the two +// DoFHandler objects. + +template +void WGDarcyEquation::setup_system() +{ + dof_handler_rt.distribute_dofs(fe_rt); + dof_handler.distribute_dofs(fe); + + std::cout << " Number of flux degrees of freedom: " + << dof_handler_rt.n_dofs() << std::endl; + + std::cout << " Number of pressure degrees of freedom: " + << dof_handler.n_dofs() << std::endl; + + solution.reinit(dof_handler.n_dofs()); + system_rhs.reinit(dof_handler.n_dofs()); + + { + constraints.clear(); + FEValuesExtractors::Scalar face(1); + ComponentMask face_pressure_mask = fe.component_mask(face); + VectorTools::interpolate_boundary_values( + dof_handler, 0, BoundaryValues(), constraints, face_pressure_mask); + constraints.close(); + } + + + // In the bilinear form, there is no integration term over faces + // between two neighboring cells, so we can just use + // DoFTools::make_sparsity_pattern to calculate the sparse + // matrix. + DynamicSparsityPattern dsp(dof_handler.n_dofs()); + DoFTools::make_sparsity_pattern(dof_handler, dsp, constraints); + sparsity_pattern.copy_from(dsp); + + system_matrix.reinit(sparsity_pattern); + + // solution.reinit(dof_handler.n_dofs()); + // system_rhs.reinit(dof_handler.n_dofs()); +} + +// @sect4{WGDarcyEquation::assemble_system} + +// First, we create quadrature points and FEValue objects for cells +// and faces. Then we allocate space for all cell matrices and the right-hand +// side vector. The following definitions have been explained in previous +// tutorials. +template +void WGDarcyEquation::assemble_system() +{ + QGauss quadrature_formula(fe_rt.degree + 1); + QGauss face_quadrature_formula(fe_rt.degree + 1); + const RightHandSide right_hand_side; + + // We define objects to evaluate values and + // gradients of shape functions at the quadrature points. + // Since we need shape functions and normal vectors on faces, we need + // FEFaceValues. + FEValues fe_values_rt(fe_rt, + quadrature_formula, + update_values | update_gradients | + update_quadrature_points | update_JxW_values); + + FEValues fe_values(fe, + quadrature_formula, + update_values | update_quadrature_points | + update_JxW_values); + + FEFaceValues fe_face_values(fe, + face_quadrature_formula, + update_values | update_normal_vectors | + update_quadrature_points | + update_JxW_values); + + FEFaceValues fe_face_values_rt(fe_rt, + face_quadrature_formula, + update_values | update_normal_vectors | + update_quadrature_points | + update_JxW_values); + + + const unsigned int dofs_per_cell_rt = fe_rt.dofs_per_cell; + const unsigned int dofs_per_cell = fe.dofs_per_cell; + + const unsigned int n_q_points = fe_values.get_quadrature().size(); + const unsigned int n_q_points_rt = fe_values_rt.get_quadrature().size(); + const unsigned int n_face_q_points = fe_face_values.get_quadrature().size(); + + std::vector local_dof_indices(dofs_per_cell); + + // We will construct these cell matrices to solve for the pressure. + FullMatrix cell_matrix_rt(dofs_per_cell_rt, dofs_per_cell_rt); + FullMatrix cell_matrix_F(dofs_per_cell, dofs_per_cell_rt); + FullMatrix cell_matrix_C(dofs_per_cell, dofs_per_cell_rt); + FullMatrix local_matrix(dofs_per_cell, dofs_per_cell); + Vector cell_rhs(dofs_per_cell); + Vector cell_solution(dofs_per_cell); + + const Coefficient coefficient; + std::vector> coefficient_values(n_q_points_rt); + + // We need FEValuesExtractors to access the @p interior and + // @p face component of the FESystem shape functions. + const FEValuesExtractors::Vector velocities(0); + const FEValuesExtractors::Scalar interior(0); + const FEValuesExtractors::Scalar face(1); + + typename DoFHandler::active_cell_iterator cell = + dof_handler.begin_active(), + endc = dof_handler.end(); + typename DoFHandler::active_cell_iterator cell_rt = + dof_handler_rt.begin_active(); + + // Here, we will calculate cell matrices used to construct the local matrix on + // each cell. We need shape functions for the Raviart-Thomas space as well, so + // we also loop over the corresponding velocity cell iterators. + for (; cell != endc; ++cell, ++cell_rt) + { + // On each cell, cell matrices are different, so in every loop, they need + // to be re-computed. + fe_values_rt.reinit(cell_rt); + fe_values.reinit(cell); + coefficient.value_list(fe_values_rt.get_quadrature_points(), + coefficient_values); + + // This cell matrix is the mass matrix for the Raviart-Thomas space. + // Hence, we need to loop over all the quadrature points + // for the velocity FEValues object. + cell_matrix_rt = 0; + for (unsigned int q = 0; q < n_q_points_rt; ++q) + { + for (unsigned int i = 0; i < dofs_per_cell_rt; ++i) + { + const Tensor<1, dim> phi_i_u = + fe_values_rt[velocities].value(i, q); + for (unsigned int j = 0; j < dofs_per_cell_rt; ++j) + { + const Tensor<1, dim> phi_j_u = + fe_values_rt[velocities].value(j, q); + cell_matrix_rt(i, j) += + (phi_i_u * phi_j_u * fe_values_rt.JxW(q)); + } + } + } + // Next we take the inverse of this matrix by using + // gauss_jordan(). It will be used to calculate the + // coefficient matrix later. + cell_matrix_rt.gauss_jordan(); + + // From the introduction, we know that the right hand side + // is the difference between a face integral and a cell integral. + // Here, we approximate the negative of the contribution in the interior. + // Each component of this matrix is the integral of a product between a + // basis function of the polynomial space and the divergence of a basis + // function of the Raviart-Thomas space. These basis functions are defined + // in the interior. + cell_matrix_F = 0; + for (unsigned int q = 0; q < n_q_points; ++q) + { + for (unsigned int i = 0; i < dofs_per_cell; ++i) + { + for (unsigned int k = 0; k < dofs_per_cell_rt; ++k) + { + const double phi_k_u_div = + fe_values_rt[velocities].divergence(k, q); + cell_matrix_F(i, k) -= (fe_values[interior].value(i, q) * + phi_k_u_div * fe_values.JxW(q)); + } + } + } + + // Now, we approximate the integral on faces. + // Each component is the integral of a product between a basis function of + // the polynomial space and the dot product of a basis function of the + // Raviart-Thomas space and the normal vector. So we loop over all the + // faces of the element and obtain the normal vector. + for (unsigned int face_n = 0; face_n < GeometryInfo::faces_per_cell; + ++face_n) + { + fe_face_values.reinit(cell, face_n); + fe_face_values_rt.reinit(cell_rt, face_n); + for (unsigned int q = 0; q < n_face_q_points; ++q) + { + const Tensor<1, dim> normal = fe_face_values.normal_vector(q); + for (unsigned int i = 0; i < dofs_per_cell; ++i) + { + for (unsigned int k = 0; k < dofs_per_cell_rt; ++k) + { + const Tensor<1, dim> phi_k_u = + fe_face_values_rt[velocities].value(k, q); + cell_matrix_F(i, k) += + (fe_face_values[face].value(i, q) * (phi_k_u * normal) * + fe_face_values.JxW(q)); + } + } + } + } + + // @p cell_matrix_C is matrix product between the inverse of mass matrix @p cell_matrix_rt and @p cell_matrix_F. + cell_matrix_C = 0; + cell_matrix_F.mmult(cell_matrix_C, cell_matrix_rt); + + // Element $a_{ij}$ of the local cell matrix $A$ is given by + // $\int_{E} \sum_{k,l} c_{ik} c_{jl} (\mathbf{K} \mathbf{w}_k) \cdot + // \mathbf{w}_l \mathrm{d}x.$ We have calculated coefficients $c$ in the + // previous step. + local_matrix = 0; + for (unsigned int q = 0; q < n_q_points_rt; ++q) + { + for (unsigned int i = 0; i < dofs_per_cell; ++i) + { + for (unsigned int j = 0; j < dofs_per_cell; ++j) + { + for (unsigned int k = 0; k < dofs_per_cell_rt; ++k) + { + const Tensor<1, dim> phi_k_u = + fe_values_rt[velocities].value(k, q); + for (unsigned int l = 0; l < dofs_per_cell_rt; ++l) + { + const Tensor<1, dim> phi_l_u = + fe_values_rt[velocities].value(l, q); + local_matrix(i, j) += coefficient_values[q] * + cell_matrix_C[i][k] * phi_k_u * + cell_matrix_C[j][l] * phi_l_u * + fe_values_rt.JxW(q); + } + } + } + } + } + + // Next, we calculate the right hand side, $\int_{E} f q \mathrm{d}x$. + cell_rhs = 0; + for (unsigned int q = 0; q < n_q_points; ++q) + { + for (unsigned int i = 0; i < dofs_per_cell; ++i) + { + cell_rhs(i) += + (fe_values[interior].value(i, q) * + right_hand_side.value(fe_values.quadrature_point(q)) * + fe_values.JxW(q)); + } + } + + // In this part, we distribute components of this local matrix into the + // system matrix and transfer components of the cell right-hand side into + // the system right hand side. + cell->get_dof_indices(local_dof_indices); + constraints.distribute_local_to_global( + local_matrix, cell_rhs, local_dof_indices, system_matrix, system_rhs); + } +} + +// @sect4{WGDarcyEquation::solve} + +// Solving the system of the Darcy equation. Now, we have pressures in the +// interior and on the faces of all the cells. +template +void WGDarcyEquation::solve() +{ + SolverControl solver_control(1000, 1e-8 * system_rhs.l2_norm()); + SolverCG<> solver(solver_control); + solver.solve(system_matrix, solution, system_rhs, PreconditionIdentity()); + constraints.distribute(solution); +} + +// @sect4{WGDarcyEquation::process_solution} + +// This part is to calculate the $L_2$ error of the pressure. +template +void WGDarcyEquation::process_solution() +{ + // Since we have two different spaces for finite elements in interior and on + // faces, if we want to calculate $L_2$ errors in interior, we need degrees of + // freedom only defined in cells. In FESystem, we have two + // components, the first one is for interior, the second one is for skeletons. + // fe.base_element(0) shows we only need degrees of freedom + // defined in cells. + DoFHandler interior_dof_handler(triangulation); + interior_dof_handler.distribute_dofs(fe.base_element(0)); + // We define a vector to extract pressures in cells. + // The size of the vector is the collective number of all degrees of freedom + // in the interior of all the elements. + Vector interior_solution(interior_dof_handler.n_dofs()); + { + // types::global_dof_index is used to know the global indices + // of degrees of freedom. So here, we get the global indices of local + // degrees of freedom and the global indices of interior degrees of freedom. + std::vector local_dof_indices(fe.dofs_per_cell); + std::vector interior_local_dof_indices( + fe.base_element(0).dofs_per_cell); + typename DoFHandler::active_cell_iterator + cell = dof_handler.begin_active(), + endc = dof_handler.end(), + interior_cell = interior_dof_handler.begin_active(); + + // In the loop of all cells and interior of the cell, + // we extract interior solutions from the global solution. + for (; cell != endc; ++cell, ++interior_cell) + { + cell->get_dof_indices(local_dof_indices); + interior_cell->get_dof_indices(interior_local_dof_indices); + + for (unsigned int i = 0; i < fe.base_element(0).dofs_per_cell; ++i) + interior_solution(interior_local_dof_indices[i]) = + solution(local_dof_indices[fe.component_to_system_index(0, i)]); + } + } + + // We define a vector that holds the norm of the error on each cell. + // Next, we use VectorTool::integrate_difference + // to compute the error in the $L_2$ norm on each cell. + // Finally, we get the global $L_2$ norm. + Vector difference_per_cell(triangulation.n_active_cells()); + VectorTools::integrate_difference(interior_dof_handler, + interior_solution, + Solution(), + difference_per_cell, + QGauss(fe.degree + 2), + VectorTools::L2_norm); + + const double L2_error = difference_per_cell.l2_norm(); + std::cout << "L2_error_pressure " << L2_error << std::endl; +} + +// @sect4{WGDarcyEquation::postprocess} + +// After we calculated the numerical pressure, we evaluate $L_2$ errors for the +// velocity on each cell and $L_2$ errors for the flux on faces. + +// We are going to evaluate velocities on each cell and calculate the difference +// between numerical and exact velocities. To calculate velocities, we need +// interior and face pressure values of each element, and some other cell +// matrices. + +template +void WGDarcyEquation::postprocess() +{ + QGauss quadrature_formula(fe_rt.degree + 1); + QGauss face_quadrature_formula(fe_rt.degree + 1); + + FEValues fe_values_rt(fe_rt, + quadrature_formula, + update_values | update_gradients | + update_quadrature_points | update_JxW_values); + + FEValues fe_values(fe, + quadrature_formula, + update_values | update_quadrature_points | + update_JxW_values); + + FEFaceValues fe_face_values(fe, + face_quadrature_formula, + update_values | update_normal_vectors | + update_quadrature_points | + update_JxW_values); + + FEFaceValues fe_face_values_rt(fe_rt, + face_quadrature_formula, + update_values | update_normal_vectors | + update_quadrature_points | + update_JxW_values); + + const unsigned int dofs_per_cell_rt = fe_rt.dofs_per_cell; + const unsigned int dofs_per_cell = fe.dofs_per_cell; + + const unsigned int n_q_points_rt = fe_values_rt.get_quadrature().size(); + const unsigned int n_q_points = fe_values.get_quadrature().size(); + const unsigned int n_face_q_points = fe_face_values.get_quadrature().size(); + const unsigned int n_face_q_points_rt = + fe_face_values_rt.get_quadrature().size(); + + + std::vector local_dof_indices(dofs_per_cell); + FullMatrix cell_matrix_rt(dofs_per_cell_rt, dofs_per_cell_rt); + FullMatrix cell_matrix_F(dofs_per_cell, dofs_per_cell_rt); + FullMatrix cell_matrix_C(dofs_per_cell, dofs_per_cell_rt); + FullMatrix local_matrix(dofs_per_cell, dofs_per_cell); + FullMatrix cell_matrix_D(dofs_per_cell_rt, dofs_per_cell_rt); + FullMatrix cell_matrix_E(dofs_per_cell_rt, dofs_per_cell_rt); + Vector cell_rhs(dofs_per_cell); + Vector cell_solution(dofs_per_cell); + Tensor<1, dim> velocity_cell; + Tensor<1, dim> velocity_face; + Tensor<1, dim> exact_velocity_face; + double L2_err_velocity_cell_sqr_global; + L2_err_velocity_cell_sqr_global = 0; + double L2_err_flux_sqr; + L2_err_flux_sqr = 0; + + typename DoFHandler::active_cell_iterator cell = + dof_handler.begin_active(), + endc = dof_handler.end(); + + typename DoFHandler::active_cell_iterator cell_rt = + dof_handler_rt.begin_active(); + + const Coefficient coefficient; + std::vector> coefficient_values(n_q_points_rt); + const FEValuesExtractors::Vector velocities(0); + const FEValuesExtractors::Scalar pressure(dim); + const FEValuesExtractors::Scalar interior(0); + const FEValuesExtractors::Scalar face(1); + + Velocity exact_velocity; + + // In the loop over all cells, we will calculate $L_2$ errors of velocity and + // flux. + + // First, we calculate the $L_2$ velocity error. + // In the introduction, we explained how to calculate the numerical velocity + // on the cell. We need the pressure solution values on each cell, + // coefficients of the Gram matrix and coefficients of the $L_2$ projection. + // We have already calculated the global solution, so we will extract the cell + // solution from the global solution. The coefficients of the Gram matrix have + // been calculated when we assembled the system matrix for the pressures. We + // will do the same way here. For the coefficients of the projection, we do + // matrix multiplication, i.e., the inverse of the Gram matrix times the + // matrix with $(\mathbf{K} \mathbf{w}, \mathbf{w})$ as components. Then, we + // multiply all these coefficients and call them beta. The numerical velocity + // is the product of beta and the basis functions of the Raviart-Thomas space. + for (; cell != endc; ++cell, ++cell_rt) + { + fe_values_rt.reinit(cell_rt); + fe_values.reinit(cell); + coefficient.value_list(fe_values_rt.get_quadrature_points(), + coefficient_values); + + // The component of this cell_matrix_E is the integral of + // $(\mathbf{K} \mathbf{w}, \mathbf{w})$. cell_matrix_rt is + // the Gram matrix. + cell_matrix_E = 0; + cell_matrix_rt = 0; + for (unsigned int q = 0; q < n_q_points_rt; ++q) + { + for (unsigned int i = 0; i < dofs_per_cell_rt; ++i) + { + const Tensor<1, dim> phi_i_u = + fe_values_rt[velocities].value(i, q); + + for (unsigned int j = 0; j < dofs_per_cell_rt; ++j) + { + const Tensor<1, dim> phi_j_u = + fe_values_rt[velocities].value(j, q); + + cell_matrix_E(i, j) += (coefficient_values[q] * phi_j_u * + phi_i_u * fe_values_rt.JxW(q)); + cell_matrix_rt(i, j) += + (phi_i_u * phi_j_u * fe_values_rt.JxW(q)); + } + } + } + + // We take the inverse of the Gram matrix, take matrix multiplication and + // get the matrix with coefficients of projection. + cell_matrix_D = 0; + cell_matrix_rt.gauss_jordan(); + cell_matrix_rt.mmult(cell_matrix_D, cell_matrix_E); + + // This cell matrix will be used to calculate the coefficients of the Gram + // matrix. This part is the same as the part in evaluating pressure. + cell_matrix_F = 0; + for (unsigned int q = 0; q < n_q_points; ++q) + { + for (unsigned int i = 0; i < dofs_per_cell; ++i) + { + for (unsigned int k = 0; k < dofs_per_cell_rt; ++k) + { + const double phi_k_u_div = + fe_values_rt[velocities].divergence(k, q); + cell_matrix_F(i, k) -= (fe_values[interior].value(i, q) * + phi_k_u_div * fe_values.JxW(q)); + } + } + } + + for (unsigned int face_n = 0; face_n < GeometryInfo::faces_per_cell; + ++face_n) + { + fe_face_values.reinit(cell, face_n); + fe_face_values_rt.reinit(cell_rt, face_n); + for (unsigned int q = 0; q < n_face_q_points; ++q) + { + const Tensor<1, dim> normal = fe_face_values.normal_vector(q); + for (unsigned int i = 0; i < dofs_per_cell; ++i) + { + for (unsigned int k = 0; k < dofs_per_cell_rt; ++k) + { + const Tensor<1, dim> phi_k_u = + fe_face_values_rt[velocities].value(k, q); + cell_matrix_F(i, k) += + (fe_face_values[face].value(i, q) * (phi_k_u * normal) * + fe_face_values.JxW(q)); + } + } + } + } + cell_matrix_C = 0; + cell_matrix_F.mmult(cell_matrix_C, cell_matrix_rt); + + // This is to extract pressure values of the element. + cell->get_dof_indices(local_dof_indices); + cell_solution = 0; + for (unsigned int i = 0; i < dofs_per_cell; ++i) + { + cell_solution(i) = solution(local_dof_indices[i]); + } + + // From previous calculations we obtained all the coefficients needed to + // calculate beta. + Vector beta(dofs_per_cell_rt); + beta = 0; + for (unsigned int k = 0; k < dofs_per_cell_rt; ++k) + { + for (unsigned int j = 0; j < dofs_per_cell_rt; ++j) + { + for (unsigned int i = 0; i < dofs_per_cell; ++i) + { + beta(k) += -(cell_solution(i) * cell_matrix_C(i, j) * + cell_matrix_D(k, j)); + } + } + } + + // Now, we can calculate the numerical velocity at each quadrature point + // and compute the $L_2$ error on each cell. + double L2_err_velocity_cell_sqr_local; + double difference_velocity_cell_sqr; + L2_err_velocity_cell_sqr_local = 0; + velocity_cell = 0; + for (unsigned int q = 0; q < n_q_points_rt; ++q) + { + difference_velocity_cell_sqr = 0; + velocity_cell = 0; + for (unsigned int k = 0; k < dofs_per_cell_rt; ++k) + { + const Tensor<1, dim> phi_k_u = + fe_values_rt[velocities].value(k, q); + velocity_cell += beta(k) * phi_k_u; + } + difference_velocity_cell_sqr = + (velocity_cell - + exact_velocity.value(fe_values_rt.quadrature_point(q))) * + (velocity_cell - + exact_velocity.value(fe_values_rt.quadrature_point(q))); + L2_err_velocity_cell_sqr_local += + difference_velocity_cell_sqr * fe_values_rt.JxW(q); + } + + L2_err_velocity_cell_sqr_global += L2_err_velocity_cell_sqr_local; + + // For reconstructing the flux we need the size of cells and faces. Since + // fluxes are calculated on faces, we have the loop over all four faces of + // each cell. To calculate face velocity, we use the coefficient beta we + // have calculated previously. Then, we calculate the squared velocity + // error in normal direction. Finally, we calculate $L_2$ flux error on + // the cell and add it to the global error. + double difference_velocity_face_sqr; + double L2_err_flux_face_sqr_local; + double err_flux_each_face; + double err_flux_face; + L2_err_flux_face_sqr_local = 0; + err_flux_face = 0; + const double cell_area = cell->measure(); + for (unsigned int face_n = 0; face_n < GeometryInfo::faces_per_cell; + ++face_n) + { + const double face_length = cell->face(face_n)->measure(); + fe_face_values.reinit(cell, face_n); + fe_face_values_rt.reinit(cell_rt, face_n); + L2_err_flux_face_sqr_local = 0; + err_flux_each_face = 0; + for (unsigned int q = 0; q < n_face_q_points_rt; ++q) + { + difference_velocity_face_sqr = 0; + velocity_face = 0; + const Tensor<1, dim> normal = fe_face_values.normal_vector(q); + for (unsigned int k = 0; k < dofs_per_cell_rt; ++k) + { + const Tensor<1, dim> phi_k_u = + fe_face_values_rt[velocities].value(k, q); + velocity_face += beta(k) * phi_k_u; + } + exact_velocity_face = + exact_velocity.value(fe_face_values_rt.quadrature_point(q)); + difference_velocity_face_sqr = + (velocity_face * normal - exact_velocity_face * normal) * + (velocity_face * normal - exact_velocity_face * normal); + L2_err_flux_face_sqr_local += + difference_velocity_face_sqr * fe_face_values_rt.JxW(q); + } + err_flux_each_face = + L2_err_flux_face_sqr_local / (face_length) * (cell_area); + err_flux_face += err_flux_each_face; + } + L2_err_flux_sqr += err_flux_face; + } + + // After adding up errors over all cells, we take square root and get the + // $L_2$ errors of velocity and flux. + const double L2_err_velocity_cell = + std::sqrt(L2_err_velocity_cell_sqr_global); + std::cout << "L2_error_vel " << L2_err_velocity_cell << std::endl; + const double L2_err_flux_face = std::sqrt(L2_err_flux_sqr); + std::cout << "L2_error_flux " << L2_err_flux_face << std::endl; +} + + +// @sect4{WGDarcyEquation::output_results} + +// We have 2 sets of results to output: the interior solution +// and the skeleton solution. We use DataOut to visualize interior +// results. The graphical output for the skeleton results is done by using the +// DataOutFaces class. +template +void WGDarcyEquation::output_results() const +{ + DataOut data_out; + data_out.attach_dof_handler(dof_handler); + data_out.add_data_vector(solution, "Pressure_Interior"); + data_out.build_patches(fe.degree); + std::ofstream output("Pressure_Interior.vtk"); + data_out.write_vtk(output); + + DataOutFaces data_out_face(false); + std::vector + face_component_type(2, DataComponentInterpretation::component_is_scalar); + data_out_face.add_data_vector(dof_handler, + solution, + "Pressure_Edge", + face_component_type); + data_out_face.build_patches(fe.degree); + std::ofstream face_output("Pressure_Edge.vtk"); + data_out_face.write_vtk(face_output); +} + + +// @sect4{WGDarcyEquation::run} + +// This is the final function of the main class. It calls the other functions of +// our class. +template +void WGDarcyEquation::run() +{ + std::cout << "Solving problem in " << dim << " space dimensions." + << std::endl; + make_grid(); + setup_system(); + assemble_system(); + solve(); + process_solution(); + postprocess(); + output_results(); +} + +// @sect3{The main function} + +// This is the main function. We can change the dimension here to run in 3d. +int main() +{ + deallog.depth_console(2); + WGDarcyEquation<2> WGDarcyEquationTest; + WGDarcyEquationTest.run(); + + return 0; +} From fc4d48b4ca8a7bd66098c0ef8c589dbb4c4eb5b8 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Fri, 25 Jan 2019 22:18:17 +0100 Subject: [PATCH 039/507] Add internal::MatrixFreeFunctions::DoFInfo::get_dof_indices_on_cell_batch() --- .../images/dofinfo_get_dof_indices.png | Bin 0 -> 6257 bytes doc/news/changes/minor/20190130DenisDavydov | 4 + include/deal.II/matrix_free/dof_info.h | 24 ++ .../deal.II/matrix_free/dof_info.templates.h | 67 ++++++ tests/matrix_free/dof_info_01.cc | 203 +++++++++++++++++ ...h_mpi=true.with_p4est=true.mpirun=1.output | 34 +++ tests/matrix_free/dof_info_02.cc | 205 ++++++++++++++++++ ...h_mpi=true.with_p4est=true.mpirun=1.output | 34 +++ 8 files changed, 571 insertions(+) create mode 100644 doc/doxygen/images/dofinfo_get_dof_indices.png create mode 100644 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z{TCl}-~)N-$;W`$lz++11mK_(kDmZ+y%4DpL%2A?fX;x9(k-Ed*PDeThf|qH!)Z0n zJpLgAwezwdlz}j$fc=NR#xn`%mf|@ z^SFWMDyguAv$A!JN_Xm+l(xwo#IkQ;WMO#G>3(qN`F*O*k_=WKXr&lz+Kim0hQ-F_ z;h+xlzwDL@@|fTcbT(#C<)>RHm$Z|kc&6Uk@+M^cST=Z4mk~i9pk+q>?D=*vu@*CZ z)VbQ`_tCpd6OAX2V_{KLAX_VNDRRB0pN%*G{O@TwwFgTC$OX=SAKIv?#J#Qnb!8o; Ja)qY>{{fV@wLbs= literal 0 HcmV?d00001 diff --git a/doc/news/changes/minor/20190130DenisDavydov b/doc/news/changes/minor/20190130DenisDavydov new file mode 100644 index 000000000000..4cf4ec962c56 --- /dev/null +++ b/doc/news/changes/minor/20190130DenisDavydov @@ -0,0 +1,4 @@ +New: Add internal::MatrixFreeFunctions::DoFInfo::get_dof_indices_on_cell_batch() to +return locally owned DoFs used by matrix-free framework on a given cell. +
+(Denis Davydov, 2019/01/30) diff --git a/include/deal.II/matrix_free/dof_info.h b/include/deal.II/matrix_free/dof_info.h index 6839cd1d353d..8f80cf23342c 100644 --- a/include/deal.II/matrix_free/dof_info.h +++ b/include/deal.II/matrix_free/dof_info.h @@ -102,6 +102,30 @@ namespace internal fe_index_from_degree(const unsigned int first_selected_component, const unsigned int fe_degree) const; + /** + * Populate the vector @p locall_indices with locally owned degrees of freedom + * stored on the cell block @p cell. + * If @p with_constraints is `true`, then the returned vector will contain indices + * required to resolve constraints. + * + * The image below illustrates the output of this function for cell blocks + * zero and one with zero Dirichlet boundary conditions at the bottom of + * the domain. Note that due to the presence of constraints, the DoFs + * returned by this function for the case `with_constraints = true` are + * not a simple union + * of per cell DoFs on the cell block @p cell. + * + * @image html dofinfo_get_dof_indices.png + * + * @note The returned indices may contain duplicates. The unique set can be + * obtain using `std::sort()` followed by `std::unique()` and + * `std::vector::erase()`. + */ + void + get_dof_indices_on_cell_batch(std::vector &locall_indices, + const unsigned int cell, + const bool with_constraints = true) const; + /** * This internal method takes the local indices on a cell and fills them * into this class. It resolves the constraints and distributes the diff --git a/include/deal.II/matrix_free/dof_info.templates.h b/include/deal.II/matrix_free/dof_info.templates.h index 153e6a8236fc..a2a7c6ae68f9 100644 --- a/include/deal.II/matrix_free/dof_info.templates.h +++ b/include/deal.II/matrix_free/dof_info.templates.h @@ -183,6 +183,73 @@ namespace internal + void + DoFInfo::get_dof_indices_on_cell_batch(std::vector &my_rows, + const unsigned int cell, + const bool apply_constraints) const + { + const unsigned int n_fe_components = start_components.back(); + const unsigned int fe_index = + dofs_per_cell.size() == 1 ? 0 : cell_active_fe_index[cell]; + const unsigned int dofs_this_cell = dofs_per_cell[fe_index]; + + const unsigned int n_vectorization = vectorization_length; + constexpr auto dof_access_index = dof_access_cell; + AssertIndexRange(cell, + n_vectorization_lanes_filled[dof_access_index].size()); + const unsigned int n_vectorization_actual = + n_vectorization_lanes_filled[dof_access_index][cell]; + + // we might have constraints, so the final number + // of indices is not known a priori. + // conservatively reserve the maximum without constraints + my_rows.reserve(n_vectorization * dofs_this_cell); + my_rows.resize(0); + unsigned int total_size = 0; + for (unsigned int v = 0; v < n_vectorization_actual; ++v) + { + const unsigned int ib = + (cell * n_vectorization + v) * n_fe_components; + const unsigned int ie = + (cell * n_vectorization + v + 1) * n_fe_components; + + // figure out constraints by comparing constraint_indicator row + // shift for this cell within the block as compared to the next + // one + const bool has_constraints = + row_starts[ib].second != row_starts[ib + n_fe_components].second; + + auto do_copy = [&](const unsigned int *begin, + const unsigned int *end) { + const unsigned int shift = total_size; + total_size += (end - begin); + my_rows.resize(total_size); + std::copy(begin, end, my_rows.begin() + shift); + }; + + if (!has_constraints || apply_constraints) + { + const unsigned int *begin = + dof_indices.data() + row_starts[ib].first; + const unsigned int *end = + dof_indices.data() + row_starts[ie].first; + do_copy(begin, end); + } + else + { + Assert(row_starts_plain_indices[cell * n_vectorization + v] != + numbers::invalid_unsigned_int, + ExcNotInitialized()); + const unsigned int *begin = + plain_dof_indices.data() + + row_starts_plain_indices[cell * n_vectorization + v]; + const unsigned int *end = begin + dofs_this_cell; + do_copy(begin, end); + } + } + } + + template void DoFInfo ::read_dof_indices( diff --git a/tests/matrix_free/dof_info_01.cc b/tests/matrix_free/dof_info_01.cc new file mode 100644 index 000000000000..462abcac7880 --- /dev/null +++ b/tests/matrix_free/dof_info_01.cc @@ -0,0 +1,203 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + + +// Tests DoFInfo::get_dof_indices() + +#include + +#include +#include + +#include + +#include +#include + +#include + +#include + +#include + +#include + +#include "../tests.h" + + + +template +void +test(const bool adaptive_ref = true) +{ + MPI_Comm mpi_communicator(MPI_COMM_WORLD); + const unsigned int this_mpi_core = + dealii::Utilities::MPI::this_mpi_process(mpi_communicator); + + parallel::distributed::Triangulation tria(mpi_communicator); + GridGenerator::hyper_cube(tria, 0, 1, true); + tria.refine_global(1); + if (adaptive_ref) + { + for (auto cell : tria.active_cell_iterators()) + if (cell->is_locally_owned()) + if (cell->center().norm() < 0.5) + cell->set_refine_flag(); + tria.execute_coarsening_and_refinement(); + for (auto cell : tria.active_cell_iterators()) + if (cell->is_locally_owned()) + if (cell->center()[0] < 0.2) + cell->set_refine_flag(); + tria.execute_coarsening_and_refinement(); + } + else + { + tria.refine_global(1); + } + + FE_Q fe(fe_degree); + DoFHandler dof(tria); + dof.distribute_dofs(fe); + + IndexSet owned_set = dof.locally_owned_dofs(); + IndexSet relevant_set; + DoFTools::extract_locally_relevant_dofs(dof, relevant_set); + + AffineConstraints constraints(relevant_set); + DoFTools::make_hanging_node_constraints(dof, constraints); + // constrain bottom part of the boundary (lower in y direction) + VectorTools::interpolate_boundary_values(dof, + 2, + Functions::ZeroFunction(), + constraints); + constraints.close(); + + deallog << "Testing " << dof.get_fe().get_name() << std::endl; + + std::shared_ptr> mf_data( + new MatrixFree()); + { + const QGauss<1> quad(fe_degree + 1); + typename MatrixFree::AdditionalData data; + data.tasks_parallel_scheme = MatrixFree::AdditionalData::none; + data.tasks_block_size = 7; + mf_data->reinit(dof, constraints, quad, data); + } + + const unsigned int n_cells = mf_data->n_macro_cells(); + const auto & dof_info = mf_data->get_dof_info(); + constexpr unsigned int n_vectorization = + VectorizedArray::n_array_elements; + + std::vector my_rows; + my_rows.reserve(fe.dofs_per_cell * n_vectorization); + + constexpr auto dof_access_index = + internal::MatrixFreeFunctions::DoFInfo::dof_access_cell; + + bool checked_interleaved = false; + for (unsigned int cell = 0; cell < n_cells; ++cell) + { + deallog << "Cell: " << cell << std::endl; + checked_interleaved |= + (dof_info.index_storage_variants[dof_access_index][cell] == + internal::MatrixFreeFunctions::DoFInfo::IndexStorageVariants:: + interleaved); + auto get_and_log = [&](const bool apply_constraints) { + dof_info.get_dof_indices_on_cell_batch(my_rows, + cell, + apply_constraints); + // sort and make unique to make visual inspection easier: + std::sort(my_rows.begin(), my_rows.end()); + my_rows.erase(std::unique(my_rows.begin(), my_rows.end()), + my_rows.end()); + for (auto el : my_rows) + deallog << " " << el; + deallog << std::endl; + }; + get_and_log(true); + get_and_log(false); + } + + // if we don't have adaptive refinement, we should have + // some cells interleaved (at least that is the intention of this + // part of the test) + Assert(checked_interleaved || adaptive_ref, ExcInternalError()); + + // output in Gnuplot + if (dim == 2) + { + std::map> support_points; + MappingQ1 mapping; + DoFTools::map_dofs_to_support_points(mapping, dof, support_points); + + const std::string prefix = + std::is_same::value ? "float_" : "double_"; + const std::string href = (adaptive_ref ? "" : "global_"); + const std::string base_filename = + prefix + href + "grid" + dealii::Utilities::int_to_string(dim) + "_" + + dealii::Utilities::int_to_string(fe_degree) + "_p" + + dealii::Utilities::int_to_string(this_mpi_core); + + const std::string filename = base_filename + ".gp"; + std::ofstream f(filename.c_str()); + + f << "set terminal png size 400,410 enhanced font \"Helvetica,8\"" + << std::endl + << "set output \"" << base_filename << ".png\"" << std::endl + << "set size square" << std::endl + << "set view equal xy" << std::endl + << "unset xtics" << std::endl + << "unset ytics" << std::endl + << "unset grid" << std::endl + << "unset border" << std::endl + << "plot '-' using 1:2 with lines notitle, '-' with labels tc rgb 'red' nopoint notitle, '-' with labels point pt 4 offset 1,1 notitle" + << std::endl; + GridOut().write_gnuplot(tria, f); + f << "e" << std::endl; + + // output cell blocks: + for (unsigned int cell = 0; cell < n_cells; ++cell) + for (unsigned int c = 0; c < mf_data->n_components_filled(cell); ++c) + { + const auto dof_cell = mf_data->get_cell_iterator(cell, c); + f << dof_cell->center() << " \"" << cell << "\"\n"; + } + + f << std::flush; + f << "e" << std::endl << std::endl; + + DoFTools::write_gnuplot_dof_support_point_info(f, support_points); + + f << "e" << std::endl; + } +} + + +int +main(int argc, char **argv) +{ + Utilities::MPI::MPI_InitFinalize mpi_initialization( + argc, argv, testing_max_num_threads()); + + MPILogInitAll mpi_init_log; + + deallog.push("2d"); + test<2, 1>(); + test<2, 1, float>(); + test<2, 1>(false); + deallog.pop(); +} diff --git a/tests/matrix_free/dof_info_01.with_mpi=true.with_p4est=true.mpirun=1.output b/tests/matrix_free/dof_info_01.with_mpi=true.with_p4est=true.mpirun=1.output new file mode 100644 index 000000000000..226a54f49664 --- /dev/null +++ b/tests/matrix_free/dof_info_01.with_mpi=true.with_p4est=true.mpirun=1.output @@ -0,0 +1,34 @@ + +DEAL:0:2d::Testing FE_Q<2>(1) +DEAL:0:2d::Cell: 0 +DEAL:0:2d:: 7 18 19 21 22 +DEAL:0:2d:: 6 7 16 17 18 19 20 21 22 +DEAL:0:2d::Cell: 1 +DEAL:0:2d:: 2 7 9 10 21 22 23 24 +DEAL:0:2d:: 0 6 7 8 10 21 22 23 24 25 26 +DEAL:0:2d::Cell: 2 +DEAL:0:2d:: 2 3 7 9 10 11 12 24 +DEAL:0:2d:: 0 1 2 3 7 8 9 10 11 12 24 25 26 +DEAL:0:2d::Cell: 3 +DEAL:0:2d:: 2 3 4 5 9 11 12 14 15 +DEAL:0:2d:: 2 3 4 5 9 11 12 13 14 15 +DEAL:0:2d::Testing FE_Q<2>(1) +DEAL:0:2d::Cell: 0 +DEAL:0:2d:: 2 7 9 10 18 19 21 22 23 24 +DEAL:0:2d:: 0 6 7 8 10 16 17 18 19 20 21 22 23 24 25 26 +DEAL:0:2d::Cell: 1 +DEAL:0:2d:: 2 3 4 5 7 9 10 11 12 14 15 24 +DEAL:0:2d:: 0 1 2 3 4 5 7 8 9 10 11 12 13 14 15 24 25 26 +DEAL:0:2d::Testing FE_Q<2>(1) +DEAL:0:2d::Cell: 0 +DEAL:0:2d:: 2 3 5 6 7 8 +DEAL:0:2d:: 0 1 2 3 4 5 6 7 8 +DEAL:0:2d::Cell: 1 +DEAL:0:2d:: 5 8 10 12 13 14 +DEAL:0:2d:: 4 5 8 9 10 11 12 13 14 +DEAL:0:2d::Cell: 2 +DEAL:0:2d:: 6 7 8 15 16 17 18 19 20 +DEAL:0:2d:: 6 7 8 15 16 17 18 19 20 +DEAL:0:2d::Cell: 3 +DEAL:0:2d:: 8 13 14 17 20 21 22 23 24 +DEAL:0:2d:: 8 13 14 17 20 21 22 23 24 diff --git a/tests/matrix_free/dof_info_02.cc b/tests/matrix_free/dof_info_02.cc new file mode 100644 index 000000000000..a980641a68d4 --- /dev/null +++ b/tests/matrix_free/dof_info_02.cc @@ -0,0 +1,205 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + + +// Tests DoFInfo::get_dof_indices() for multi-component system + +#include + +#include +#include + +#include +#include + +#include +#include + +#include + +#include + +#include + +#include + +#include "../tests.h" + + + +template +void +test(const bool adaptive_ref = true) +{ + MPI_Comm mpi_communicator(MPI_COMM_WORLD); + const unsigned int this_mpi_core = + dealii::Utilities::MPI::this_mpi_process(mpi_communicator); + + parallel::distributed::Triangulation tria(mpi_communicator); + GridGenerator::hyper_cube(tria, 0, 1, true); + tria.refine_global(1); + if (adaptive_ref) + { + for (auto cell : tria.active_cell_iterators()) + if (cell->is_locally_owned()) + if (cell->center().norm() < 0.5) + cell->set_refine_flag(); + tria.execute_coarsening_and_refinement(); + for (auto cell : tria.active_cell_iterators()) + if (cell->is_locally_owned()) + if (cell->center()[0] < 0.2) + cell->set_refine_flag(); + tria.execute_coarsening_and_refinement(); + } + else + { + tria.refine_global(1); + } + + FE_Q feq(fe_degree); + FESystem fe(feq, dim); + DoFHandler dof(tria); + dof.distribute_dofs(fe); + + IndexSet owned_set = dof.locally_owned_dofs(); + IndexSet relevant_set; + DoFTools::extract_locally_relevant_dofs(dof, relevant_set); + + AffineConstraints constraints(relevant_set); + DoFTools::make_hanging_node_constraints(dof, constraints); + // constrain bottom part of the boundary (lower in y direction) + VectorTools::interpolate_boundary_values(dof, + 2, + Functions::ZeroFunction(2), + constraints); + constraints.close(); + + deallog << "Testing " << dof.get_fe().get_name() << std::endl; + + std::shared_ptr> mf_data( + new MatrixFree()); + { + const QGauss<1> quad(fe_degree + 1); + typename MatrixFree::AdditionalData data; + data.tasks_parallel_scheme = MatrixFree::AdditionalData::none; + data.tasks_block_size = 7; + mf_data->reinit(dof, constraints, quad, data); + } + + const unsigned int n_cells = mf_data->n_macro_cells(); + const auto & dof_info = mf_data->get_dof_info(); + constexpr unsigned int n_vectorization = + VectorizedArray::n_array_elements; + + std::vector my_rows; + my_rows.reserve(fe.dofs_per_cell * n_vectorization); + + constexpr auto dof_access_index = + internal::MatrixFreeFunctions::DoFInfo::dof_access_cell; + + bool checked_interleaved = false; + for (unsigned int cell = 0; cell < n_cells; ++cell) + { + deallog << "Cell: " << cell << std::endl; + checked_interleaved |= + (dof_info.index_storage_variants[dof_access_index][cell] == + internal::MatrixFreeFunctions::DoFInfo::IndexStorageVariants:: + interleaved); + auto get_and_log = [&](const bool apply_constraints) { + dof_info.get_dof_indices_on_cell_batch(my_rows, + cell, + apply_constraints); + // sort and make unique to make visual inspection easier: + std::sort(my_rows.begin(), my_rows.end()); + my_rows.erase(std::unique(my_rows.begin(), my_rows.end()), + my_rows.end()); + for (auto el : my_rows) + deallog << " " << el; + deallog << std::endl; + }; + get_and_log(true); + get_and_log(false); + } + + // if we don't have adaptive refinement, we should have + // some cells interleaved (at least that is the intention of this + // part of the test) + Assert(checked_interleaved || adaptive_ref, ExcInternalError()); + + // output in Gnuplot + if (dim == 2) + { + std::map> support_points; + MappingQ1 mapping; + DoFTools::map_dofs_to_support_points(mapping, dof, support_points); + + const std::string prefix = + std::is_same::value ? "float_" : "double_"; + const std::string href = (adaptive_ref ? "" : "global_"); + const std::string base_filename = + prefix + href + "grid" + dealii::Utilities::int_to_string(dim) + "_" + + dealii::Utilities::int_to_string(fe_degree) + "_p" + + dealii::Utilities::int_to_string(this_mpi_core); + + const std::string filename = base_filename + ".gp"; + std::ofstream f(filename.c_str()); + + f << "set terminal png size 400,410 enhanced font \"Helvetica,8\"" + << std::endl + << "set output \"" << base_filename << ".png\"" << std::endl + << "set size square" << std::endl + << "set view equal xy" << std::endl + << "unset xtics" << std::endl + << "unset ytics" << std::endl + << "unset grid" << std::endl + << "unset border" << std::endl + << "plot '-' using 1:2 with lines notitle, '-' with labels tc rgb 'red' nopoint notitle, '-' with labels point pt 4 offset 1,1 notitle" + << std::endl; + GridOut().write_gnuplot(tria, f); + f << "e" << std::endl; + + // output cell blocks: + for (unsigned int cell = 0; cell < n_cells; ++cell) + for (unsigned int c = 0; c < mf_data->n_components_filled(cell); ++c) + { + const auto dof_cell = mf_data->get_cell_iterator(cell, c); + f << dof_cell->center() << " \"" << cell << "\"\n"; + } + + f << std::flush; + f << "e" << std::endl << std::endl; + + DoFTools::write_gnuplot_dof_support_point_info(f, support_points); + + f << "e" << std::endl; + } +} + + +int +main(int argc, char **argv) +{ + Utilities::MPI::MPI_InitFinalize mpi_initialization( + argc, argv, testing_max_num_threads()); + + MPILogInitAll mpi_init_log; + + deallog.push("2d"); + test<2, 1>(); + test<2, 1, float>(); + test<2, 1>(false); + deallog.pop(); +} diff --git a/tests/matrix_free/dof_info_02.with_mpi=true.with_p4est=true.mpirun=1.output b/tests/matrix_free/dof_info_02.with_mpi=true.with_p4est=true.mpirun=1.output new file mode 100644 index 000000000000..1da9dc63eaed --- /dev/null +++ b/tests/matrix_free/dof_info_02.with_mpi=true.with_p4est=true.mpirun=1.output @@ -0,0 +1,34 @@ + +DEAL:0:2d::Testing FESystem<2>[FE_Q<2>(1)^2] +DEAL:0:2d::Cell: 0 +DEAL:0:2d:: 14 15 36 37 38 39 42 43 44 45 +DEAL:0:2d:: 12 13 14 15 32 33 34 35 36 37 38 39 40 41 42 43 44 45 +DEAL:0:2d::Cell: 1 +DEAL:0:2d:: 4 5 14 15 18 19 20 21 42 43 44 45 46 47 48 49 +DEAL:0:2d:: 0 1 12 13 14 15 16 17 20 21 42 43 44 45 46 47 48 49 50 51 52 53 +DEAL:0:2d::Cell: 2 +DEAL:0:2d:: 4 5 6 7 14 15 18 19 20 21 22 23 24 25 48 49 +DEAL:0:2d:: 0 1 2 3 4 5 6 7 14 15 16 17 18 19 20 21 22 23 24 25 48 49 50 51 52 53 +DEAL:0:2d::Cell: 3 +DEAL:0:2d:: 4 5 6 7 8 9 10 11 18 19 22 23 24 25 28 29 30 31 +DEAL:0:2d:: 4 5 6 7 8 9 10 11 18 19 22 23 24 25 26 27 28 29 30 31 +DEAL:0:2d::Testing FESystem<2>[FE_Q<2>(1)^2] +DEAL:0:2d::Cell: 0 +DEAL:0:2d:: 4 5 14 15 18 19 20 21 36 37 38 39 42 43 44 45 46 47 48 49 +DEAL:0:2d:: 0 1 12 13 14 15 16 17 20 21 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 +DEAL:0:2d::Cell: 1 +DEAL:0:2d:: 4 5 6 7 8 9 10 11 14 15 18 19 20 21 22 23 24 25 28 29 30 31 48 49 +DEAL:0:2d:: 0 1 2 3 4 5 6 7 8 9 10 11 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 48 49 50 51 52 53 +DEAL:0:2d::Testing FESystem<2>[FE_Q<2>(1)^2] +DEAL:0:2d::Cell: 0 +DEAL:0:2d:: 4 5 6 7 10 11 12 13 14 15 16 17 +DEAL:0:2d:: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 +DEAL:0:2d::Cell: 1 +DEAL:0:2d:: 10 11 16 17 20 21 24 25 26 27 28 29 +DEAL:0:2d:: 8 9 10 11 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +DEAL:0:2d::Cell: 2 +DEAL:0:2d:: 12 13 14 15 16 17 30 31 32 33 34 35 36 37 38 39 40 41 +DEAL:0:2d:: 12 13 14 15 16 17 30 31 32 33 34 35 36 37 38 39 40 41 +DEAL:0:2d::Cell: 3 +DEAL:0:2d:: 16 17 26 27 28 29 34 35 40 41 42 43 44 45 46 47 48 49 +DEAL:0:2d:: 16 17 26 27 28 29 34 35 40 41 42 43 44 45 46 47 48 49 From 7d99efb93bb43ea9927ec1efeae9f0362ae2ad0a Mon Sep 17 00:00:00 2001 From: Rene Gassmoeller Date: Wed, 30 Jan 2019 16:42:20 -0800 Subject: [PATCH 040/507] Fix invalid memory access in particle properties after transfer --- include/deal.II/particles/particle.h | 10 +- source/particles/particle.cc | 7 +- source/particles/particle_handler.cc | 6 + tests/particles/particle_handler_08.cc | 183 ++++++++++++++++++ ...particle_handler_08.with_p4est=true.output | 139 +++++++++++++ 5 files changed, 342 insertions(+), 3 deletions(-) create mode 100644 tests/particles/particle_handler_08.cc create mode 100644 tests/particles/particle_handler_08.with_p4est=true.output diff --git a/include/deal.II/particles/particle.h b/include/deal.II/particles/particle.h index b4d3de0581b3..df6ebd17418e 100644 --- a/include/deal.II/particles/particle.h +++ b/include/deal.II/particles/particle.h @@ -256,7 +256,12 @@ namespace Particles set_properties(const ArrayView &new_properties); /** - * Get write-access to properties of this particle. + * Get write-access to properties of this particle. If the + * particle has no properties yet, but has access to a + * PropertyPool object it will allocate properties to + * allow writing into them. If it has no properties and + * has no access to a PropertyPool this function will + * throw an exception. * * @return An ArrayView of the properties of this particle. */ @@ -264,7 +269,8 @@ namespace Particles get_properties(); /** - * Get read-access to properties of this particle. + * Get read-access to properties of this particle. If the particle + * has no properties this function throws an exception. * * @return An ArrayView of the properties of this particle. */ diff --git a/source/particles/particle.cc b/source/particles/particle.cc index b5dea11fa8d0..03f90811b333 100644 --- a/source/particles/particle.cc +++ b/source/particles/particle.cc @@ -284,6 +284,8 @@ namespace Particles Particle::set_properties( const ArrayView &new_properties) { + Assert(property_pool != nullptr, ExcInternalError()); + if (properties == PropertyPool::invalid_handle) properties = property_pool->allocate_properties_array(); @@ -313,7 +315,7 @@ namespace Particles const ArrayView Particle::get_properties() const { - Assert(property_pool != nullptr, ExcInternalError()); + Assert(has_properties(), ExcInternalError()); return property_pool->get_properties(properties); } @@ -326,6 +328,9 @@ namespace Particles { Assert(property_pool != nullptr, ExcInternalError()); + if (properties == PropertyPool::invalid_handle) + properties = property_pool->allocate_properties_array(); + return property_pool->get_properties(properties); } diff --git a/source/particles/particle_handler.cc b/source/particles/particle_handler.cc index 84f61ff4da79..af3b69a03160 100644 --- a/source/particles/particle_handler.cc +++ b/source/particles/particle_handler.cc @@ -1200,6 +1200,12 @@ namespace Particles data_range.end(), /*allow_compression=*/true); + // Update the reference to the current property pool for all particles. + // This was not stored, because they might be transported across process + // domains. + for (auto &particle : loaded_particles_on_cell) + particle.set_property_pool(*property_pool); + switch (status) { case parallel::distributed::Triangulation::CELL_PERSIST: diff --git a/tests/particles/particle_handler_08.cc b/tests/particles/particle_handler_08.cc new file mode 100644 index 000000000000..d5cd3be2b643 --- /dev/null +++ b/tests/particles/particle_handler_08.cc @@ -0,0 +1,183 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2017 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + + +// like particle_handler_05, but check that the properties of particles are +// correctly transferred during grid +// refinement/coarsening. Note that this in particular tests for a bug, where +// references to the property pool where lost during particle transfer. + +#include + +#include + +#include +#include + +#include + +#include "../tests.h" + +template +void +create_regular_particle_distribution( + Particles::ParticleHandler & particle_handler, + const parallel::distributed::Triangulation &tr, + const unsigned int particles_per_direction = 3) +{ + for (unsigned int i = 0; i < particles_per_direction; ++i) + for (unsigned int j = 0; j < particles_per_direction; ++j) + { + Point position; + Point reference_position; + unsigned int id = i * particles_per_direction + j; + + position[0] = static_cast(i) / + static_cast(particles_per_direction - 1); + position[1] = static_cast(j) / + static_cast(particles_per_direction - 1); + + if (dim > 2) + for (unsigned int k = 0; k < particles_per_direction; ++k) + { + position[2] = static_cast(j) / + static_cast(particles_per_direction - 1); + id = i * particles_per_direction * particles_per_direction + + j * particles_per_direction + k; + Particles::Particle particle(position, + reference_position, + id); + + typename parallel::distributed::Triangulation:: + active_cell_iterator cell = + GridTools::find_active_cell_around_point( + tr, particle.get_location()); + + Particles::ParticleIterator pit = + particle_handler.insert_particle(particle, cell); + + for (unsigned int i = 0; i < spacedim; ++i) + pit->get_properties()[i] = pit->get_location()[i]; + } + else + { + Particles::Particle particle(position, + reference_position, + id); + + typename parallel::distributed::Triangulation:: + active_cell_iterator cell = + GridTools::find_active_cell_around_point( + tr, particle.get_location()); + + Particles::ParticleIterator pit = + particle_handler.insert_particle(particle, cell); + + for (unsigned int i = 0; i < spacedim; ++i) + pit->get_properties()[i] = pit->get_location()[i]; + } + } +} + +template +void +test() +{ + { + parallel::distributed::Triangulation tr(MPI_COMM_WORLD); + + GridGenerator::hyper_cube(tr); + MappingQ mapping(1); + + const unsigned int n_properties = spacedim; + Particles::ParticleHandler particle_handler(tr, + mapping, + n_properties); + + // TODO: Move this into the Particle handler class. Unfortunately, there are + // some interactions with the SolutionTransfer class that prevent us from + // doing this at the moment. When doing this, check that transferring a + // solution and particles during the same refinement is possible (in + // particular that the order of serialization/deserialization is preserved). + tr.signals.pre_distributed_refinement.connect(std::bind( + &Particles::ParticleHandler::register_store_callback_function, + &particle_handler)); + + tr.signals.post_distributed_refinement.connect(std::bind( + &Particles::ParticleHandler::register_load_callback_function, + &particle_handler, + false)); + + create_regular_particle_distribution(particle_handler, tr); + + for (auto particle = particle_handler.begin(); + particle != particle_handler.end(); + ++particle) + deallog << "Before refinement particle id " << particle->get_id() + << " has first property " << particle->get_properties()[0] + << " and second property " << particle->get_properties()[1] + << std::endl; + + // Check that all particles are moved to children + tr.refine_global(1); + + for (auto particle = particle_handler.begin(); + particle != particle_handler.end(); + ++particle) + deallog << "After refinement particle id " << particle->get_id() + << " has first property " << particle->get_properties()[0] + << " and second property " << particle->get_properties()[1] + << std::endl; + + // Reverse the refinement and check again + for (auto cell = tr.begin_active(); cell != tr.end(); ++cell) + cell->set_coarsen_flag(); + + tr.execute_coarsening_and_refinement(); + + for (auto particle = particle_handler.begin(); + particle != particle_handler.end(); + ++particle) + deallog << "After coarsening particle id " << particle->get_id() + << " has first property " << particle->get_properties()[0] + << " and second property " << particle->get_properties()[1] + << std::endl; + } + + deallog << "OK" << std::endl; +} + + + +int +main(int argc, char *argv[]) +{ + Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1); + + MPILogInitAll all; + + deallog.push("2d/2d"); + test<2, 2>(); + deallog.pop(); + deallog.push("2d/3d"); + test<2, 3>(); + deallog.pop(); + deallog.push("3d/3d"); + test<3, 3>(); + deallog.pop(); +} diff --git a/tests/particles/particle_handler_08.with_p4est=true.output b/tests/particles/particle_handler_08.with_p4est=true.output new file mode 100644 index 000000000000..f54a16d67e73 --- /dev/null +++ b/tests/particles/particle_handler_08.with_p4est=true.output @@ -0,0 +1,139 @@ + +DEAL:0:2d/2d::Before refinement particle id 0 has first property 0.00000 and second property 0.00000 +DEAL:0:2d/2d::Before refinement particle id 1 has first property 0.00000 and second property 0.500000 +DEAL:0:2d/2d::Before refinement particle id 2 has first property 0.00000 and second property 1.00000 +DEAL:0:2d/2d::Before refinement particle id 3 has first property 0.500000 and second property 0.00000 +DEAL:0:2d/2d::Before refinement particle id 4 has first property 0.500000 and second property 0.500000 +DEAL:0:2d/2d::Before refinement particle id 5 has first property 0.500000 and second property 1.00000 +DEAL:0:2d/2d::Before refinement particle id 6 has first property 1.00000 and second property 0.00000 +DEAL:0:2d/2d::Before refinement particle id 7 has first property 1.00000 and second property 0.500000 +DEAL:0:2d/2d::Before refinement particle id 8 has first property 1.00000 and second property 1.00000 +DEAL:0:2d/2d::After refinement particle id 0 has first property 0.00000 and second property 0.00000 +DEAL:0:2d/2d::After refinement particle id 1 has first property 0.00000 and second property 0.500000 +DEAL:0:2d/2d::After refinement particle id 3 has first property 0.500000 and second property 0.00000 +DEAL:0:2d/2d::After refinement particle id 4 has first property 0.500000 and second property 0.500000 +DEAL:0:2d/2d::After refinement particle id 6 has first property 1.00000 and second property 0.00000 +DEAL:0:2d/2d::After refinement particle id 7 has first property 1.00000 and second property 0.500000 +DEAL:0:2d/2d::After refinement particle id 2 has first property 0.00000 and second property 1.00000 +DEAL:0:2d/2d::After refinement particle id 5 has first property 0.500000 and second property 1.00000 +DEAL:0:2d/2d::After refinement particle id 8 has first property 1.00000 and second property 1.00000 +DEAL:0:2d/2d::After coarsening particle id 0 has first property 0.00000 and second property 0.00000 +DEAL:0:2d/2d::After coarsening particle id 1 has first property 0.00000 and second property 0.500000 +DEAL:0:2d/2d::After coarsening particle id 3 has first property 0.500000 and second property 0.00000 +DEAL:0:2d/2d::After coarsening particle id 4 has first property 0.500000 and second property 0.500000 +DEAL:0:2d/2d::After coarsening particle id 6 has first property 1.00000 and second property 0.00000 +DEAL:0:2d/2d::After coarsening particle id 7 has first property 1.00000 and second property 0.500000 +DEAL:0:2d/2d::After coarsening particle id 2 has first property 0.00000 and second property 1.00000 +DEAL:0:2d/2d::After coarsening particle id 5 has first property 0.500000 and second property 1.00000 +DEAL:0:2d/2d::After coarsening particle id 8 has first property 1.00000 and second property 1.00000 +DEAL:0:2d/2d::OK +DEAL:0:2d/3d::Before refinement particle id 0 has first property 0.00000 and second property 0.00000 +DEAL:0:2d/3d::Before refinement particle id 1 has first property 0.00000 and second property 0.500000 +DEAL:0:2d/3d::Before refinement particle id 2 has first property 0.00000 and second property 1.00000 +DEAL:0:2d/3d::Before refinement particle id 3 has first property 0.500000 and second property 0.00000 +DEAL:0:2d/3d::Before refinement particle id 4 has first property 0.500000 and second property 0.500000 +DEAL:0:2d/3d::Before refinement particle id 5 has first property 0.500000 and second property 1.00000 +DEAL:0:2d/3d::Before refinement particle id 6 has first property 1.00000 and second property 0.00000 +DEAL:0:2d/3d::Before refinement particle id 7 has first property 1.00000 and second property 0.500000 +DEAL:0:2d/3d::Before refinement particle id 8 has first property 1.00000 and second property 1.00000 +DEAL:0:2d/3d::After refinement particle id 0 has first property 0.00000 and second property 0.00000 +DEAL:0:2d/3d::After refinement particle id 1 has first property 0.00000 and second property 0.500000 +DEAL:0:2d/3d::After refinement particle id 3 has first property 0.500000 and second property 0.00000 +DEAL:0:2d/3d::After refinement particle id 4 has first property 0.500000 and second property 0.500000 +DEAL:0:2d/3d::After refinement particle id 6 has first property 1.00000 and second property 0.00000 +DEAL:0:2d/3d::After refinement particle id 7 has first property 1.00000 and second property 0.500000 +DEAL:0:2d/3d::After refinement particle id 2 has first property 0.00000 and second property 1.00000 +DEAL:0:2d/3d::After refinement particle id 5 has first property 0.500000 and second property 1.00000 +DEAL:0:2d/3d::After refinement particle id 8 has first property 1.00000 and second property 1.00000 +DEAL:0:2d/3d::After coarsening particle id 0 has first property 0.00000 and second property 0.00000 +DEAL:0:2d/3d::After coarsening particle id 1 has first property 0.00000 and second property 0.500000 +DEAL:0:2d/3d::After coarsening particle id 3 has first property 0.500000 and second property 0.00000 +DEAL:0:2d/3d::After coarsening particle id 4 has first property 0.500000 and second property 0.500000 +DEAL:0:2d/3d::After coarsening particle id 6 has first property 1.00000 and second property 0.00000 +DEAL:0:2d/3d::After coarsening particle id 7 has first property 1.00000 and second property 0.500000 +DEAL:0:2d/3d::After coarsening particle id 2 has first property 0.00000 and second property 1.00000 +DEAL:0:2d/3d::After coarsening particle id 5 has first property 0.500000 and second property 1.00000 +DEAL:0:2d/3d::After coarsening particle id 8 has first property 1.00000 and second property 1.00000 +DEAL:0:2d/3d::OK +DEAL:0:3d/3d::Before refinement particle id 0 has first property 0.00000 and second property 0.00000 +DEAL:0:3d/3d::Before refinement particle id 1 has first property 0.00000 and second property 0.00000 +DEAL:0:3d/3d::Before refinement particle id 2 has first property 0.00000 and second property 0.00000 +DEAL:0:3d/3d::Before refinement particle id 3 has first property 0.00000 and second property 0.500000 +DEAL:0:3d/3d::Before refinement particle id 4 has first property 0.00000 and second property 0.500000 +DEAL:0:3d/3d::Before refinement particle id 5 has first property 0.00000 and second property 0.500000 +DEAL:0:3d/3d::Before refinement particle id 6 has first property 0.00000 and second property 1.00000 +DEAL:0:3d/3d::Before refinement particle id 7 has first property 0.00000 and second property 1.00000 +DEAL:0:3d/3d::Before refinement particle id 8 has first property 0.00000 and second property 1.00000 +DEAL:0:3d/3d::Before refinement particle id 9 has first property 0.500000 and second property 0.00000 +DEAL:0:3d/3d::Before refinement particle id 10 has first property 0.500000 and second property 0.00000 +DEAL:0:3d/3d::Before refinement particle id 11 has first property 0.500000 and second property 0.00000 +DEAL:0:3d/3d::Before refinement particle id 12 has first property 0.500000 and second property 0.500000 +DEAL:0:3d/3d::Before refinement particle id 13 has first property 0.500000 and second property 0.500000 +DEAL:0:3d/3d::Before refinement particle id 14 has first property 0.500000 and second property 0.500000 +DEAL:0:3d/3d::Before refinement particle id 15 has first property 0.500000 and second property 1.00000 +DEAL:0:3d/3d::Before refinement particle id 16 has first property 0.500000 and second property 1.00000 +DEAL:0:3d/3d::Before refinement particle id 17 has first property 0.500000 and second property 1.00000 +DEAL:0:3d/3d::Before refinement particle id 18 has first property 1.00000 and second property 0.00000 +DEAL:0:3d/3d::Before refinement particle id 19 has first property 1.00000 and second property 0.00000 +DEAL:0:3d/3d::Before refinement particle id 20 has first property 1.00000 and second property 0.00000 +DEAL:0:3d/3d::Before refinement particle id 21 has first property 1.00000 and second property 0.500000 +DEAL:0:3d/3d::Before refinement particle id 22 has first property 1.00000 and second property 0.500000 +DEAL:0:3d/3d::Before refinement particle id 23 has first property 1.00000 and second property 0.500000 +DEAL:0:3d/3d::Before refinement particle id 24 has first property 1.00000 and second property 1.00000 +DEAL:0:3d/3d::Before refinement particle id 25 has first property 1.00000 and second property 1.00000 +DEAL:0:3d/3d::Before refinement particle id 26 has first property 1.00000 and second property 1.00000 +DEAL:0:3d/3d::After refinement particle id 0 has first property 0.00000 and second property 0.00000 +DEAL:0:3d/3d::After refinement particle id 1 has first property 0.00000 and second property 0.00000 +DEAL:0:3d/3d::After refinement particle id 2 has first property 0.00000 and second property 0.00000 +DEAL:0:3d/3d::After refinement particle id 3 has first property 0.00000 and second property 0.500000 +DEAL:0:3d/3d::After refinement particle id 4 has first property 0.00000 and second property 0.500000 +DEAL:0:3d/3d::After refinement particle id 5 has first property 0.00000 and second property 0.500000 +DEAL:0:3d/3d::After refinement particle id 9 has first property 0.500000 and second property 0.00000 +DEAL:0:3d/3d::After refinement particle id 10 has first property 0.500000 and second property 0.00000 +DEAL:0:3d/3d::After refinement particle id 11 has first property 0.500000 and second property 0.00000 +DEAL:0:3d/3d::After refinement particle id 12 has first property 0.500000 and second property 0.500000 +DEAL:0:3d/3d::After refinement particle id 13 has first property 0.500000 and second property 0.500000 +DEAL:0:3d/3d::After refinement particle id 14 has first property 0.500000 and second property 0.500000 +DEAL:0:3d/3d::After refinement particle id 18 has first property 1.00000 and second property 0.00000 +DEAL:0:3d/3d::After refinement particle id 19 has first property 1.00000 and second property 0.00000 +DEAL:0:3d/3d::After refinement particle id 20 has first property 1.00000 and second property 0.00000 +DEAL:0:3d/3d::After refinement particle id 21 has first property 1.00000 and second property 0.500000 +DEAL:0:3d/3d::After refinement particle id 22 has first property 1.00000 and second property 0.500000 +DEAL:0:3d/3d::After refinement particle id 23 has first property 1.00000 and second property 0.500000 +DEAL:0:3d/3d::After refinement particle id 6 has first property 0.00000 and second property 1.00000 +DEAL:0:3d/3d::After refinement particle id 7 has first property 0.00000 and second property 1.00000 +DEAL:0:3d/3d::After refinement particle id 8 has first property 0.00000 and second property 1.00000 +DEAL:0:3d/3d::After refinement particle id 15 has first property 0.500000 and second property 1.00000 +DEAL:0:3d/3d::After refinement particle id 16 has first property 0.500000 and second property 1.00000 +DEAL:0:3d/3d::After refinement particle id 17 has first property 0.500000 and second property 1.00000 +DEAL:0:3d/3d::After refinement particle id 24 has first property 1.00000 and second property 1.00000 +DEAL:0:3d/3d::After refinement particle id 25 has first property 1.00000 and second property 1.00000 +DEAL:0:3d/3d::After refinement particle id 26 has first property 1.00000 and second property 1.00000 +DEAL:0:3d/3d::After coarsening particle id 0 has first property 0.00000 and second property 0.00000 +DEAL:0:3d/3d::After coarsening particle id 1 has first property 0.00000 and second property 0.00000 +DEAL:0:3d/3d::After coarsening particle id 2 has first property 0.00000 and second property 0.00000 +DEAL:0:3d/3d::After coarsening particle id 3 has first property 0.00000 and second property 0.500000 +DEAL:0:3d/3d::After coarsening particle id 4 has first property 0.00000 and second property 0.500000 +DEAL:0:3d/3d::After coarsening particle id 5 has first property 0.00000 and second property 0.500000 +DEAL:0:3d/3d::After coarsening particle id 9 has first property 0.500000 and second property 0.00000 +DEAL:0:3d/3d::After coarsening particle id 10 has first property 0.500000 and second property 0.00000 +DEAL:0:3d/3d::After coarsening particle id 11 has first property 0.500000 and second property 0.00000 +DEAL:0:3d/3d::After coarsening particle id 12 has first property 0.500000 and second property 0.500000 +DEAL:0:3d/3d::After coarsening particle id 13 has first property 0.500000 and second property 0.500000 +DEAL:0:3d/3d::After coarsening particle id 14 has first property 0.500000 and second property 0.500000 +DEAL:0:3d/3d::After coarsening particle id 18 has first property 1.00000 and second property 0.00000 +DEAL:0:3d/3d::After coarsening particle id 19 has first property 1.00000 and second property 0.00000 +DEAL:0:3d/3d::After coarsening particle id 20 has first property 1.00000 and second property 0.00000 +DEAL:0:3d/3d::After coarsening particle id 21 has first property 1.00000 and second property 0.500000 +DEAL:0:3d/3d::After coarsening particle id 22 has first property 1.00000 and second property 0.500000 +DEAL:0:3d/3d::After coarsening particle id 23 has first property 1.00000 and second property 0.500000 +DEAL:0:3d/3d::After coarsening particle id 6 has first property 0.00000 and second property 1.00000 +DEAL:0:3d/3d::After coarsening particle id 7 has first property 0.00000 and second property 1.00000 +DEAL:0:3d/3d::After coarsening particle id 8 has first property 0.00000 and second property 1.00000 +DEAL:0:3d/3d::After coarsening particle id 15 has first property 0.500000 and second property 1.00000 +DEAL:0:3d/3d::After coarsening particle id 16 has first property 0.500000 and second property 1.00000 +DEAL:0:3d/3d::After coarsening particle id 17 has first property 0.500000 and second property 1.00000 +DEAL:0:3d/3d::After coarsening particle id 24 has first property 1.00000 and second property 1.00000 +DEAL:0:3d/3d::After coarsening particle id 25 has first property 1.00000 and second property 1.00000 +DEAL:0:3d/3d::After coarsening particle id 26 has first property 1.00000 and second property 1.00000 +DEAL:0:3d/3d::OK From c811784bddae1708ba9a5481787c95120e5e3e2b Mon Sep 17 00:00:00 2001 From: Giovanni Alzetta Date: Thu, 10 Jan 2019 16:29:40 +0100 Subject: [PATCH 041/507] Added point constructor from boost point and test --- include/deal.II/base/point.h | 33 +++++++++++++++++++ tests/base/point_04.cc | 62 ++++++++++++++++++++++++++++++++++++ tests/base/point_04.output | 0 3 files changed, 95 insertions(+) create mode 100644 tests/base/point_04.cc create mode 100644 tests/base/point_04.output diff --git a/include/deal.II/base/point.h b/include/deal.II/base/point.h index 8bae4ecb0344..38a87c6f24f4 100644 --- a/include/deal.II/base/point.h +++ b/include/deal.II/base/point.h @@ -22,6 +22,8 @@ #include #include +#include + #include DEAL_II_NAMESPACE_OPEN @@ -143,6 +145,15 @@ class Point : public Tensor<1, dim, Number> */ Point(const Number x, const Number y, const Number z); + /** + * Convert a boost::geometry::point to a dealii::Point. + */ + template + Point(const boost::geometry::model:: + point &boost_pt, + typename std::enable_if<(dim == dummy_dim) && (dummy_dim != 0), + int>::type = 0); + /** * Return a unit vector in coordinate direction i, i.e., a vector * that is zero in all coordinates except for a single 1 in the ith @@ -358,6 +369,28 @@ inline Point::Point(const Number x, const Number y, const Number z) } + +template +template +inline Point::Point( + const boost::geometry::model:: + point &boost_pt, + typename std::enable_if<(dim == dummy_dim) && (dummy_dim != 0), int>::type) +{ + Assert(dim <= 3, ExcNotImplemented()); + this->values[0] = boost::geometry::get<0>(boost_pt); + constexpr unsigned int y_index = (dim < 2) ? 0 : 1; + constexpr unsigned int z_index = (dim < 3) ? 0 : 2; + + if (dim >= 2) + this->values[y_index] = boost::geometry::get(boost_pt); + + if (dim >= 3) + this->values[z_index] = boost::geometry::get(boost_pt); +} + + + template inline Point Point::unit_vector(unsigned int i) diff --git a/tests/base/point_04.cc b/tests/base/point_04.cc new file mode 100644 index 000000000000..7dbb62241b5f --- /dev/null +++ b/tests/base/point_04.cc @@ -0,0 +1,62 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2010 - 2017 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + +// test for Point::operator() + +#include + +#include + +#include + +#include "../tests.h" + +namespace bg = boost::geometry; + +template +void +check() +{ + bg::model::point bg_point; + + constexpr unsigned int y_index = (spacedim < 2) ? 0 : 1; + constexpr unsigned int z_index = (spacedim < 3) ? 0 : 2; + + bg_point.set<0>(42.0); + + if (dim >= 2) + bg_point.set(42.0 + dim); + + if (dim >= 3) + bg_point.set(42.0 + dim + 1); + + Point p(bg_point); + + for (unsigned int i = 0; i < dim; ++i) + deallog << p(i) << ' '; + deallog << std::endl; +} + +int +main() +{ + initlog(); + deallog << std::setprecision(3); + + check<1>(); + check<2>(); + check<3>(); +} diff --git a/tests/base/point_04.output b/tests/base/point_04.output new file mode 100644 index 000000000000..e69de29bb2d1 From 4100f1edfdd6332dfc8f13fe32805f83275d6857 Mon Sep 17 00:00:00 2001 From: Wolfgang Bangerth Date: Tue, 29 Jan 2019 09:25:31 -0700 Subject: [PATCH 042/507] Change the way the constructor template argument works. --- include/deal.II/base/point.h | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/include/deal.II/base/point.h b/include/deal.II/base/point.h index 38a87c6f24f4..d486ae36c858 100644 --- a/include/deal.II/base/point.h +++ b/include/deal.II/base/point.h @@ -148,9 +148,9 @@ class Point : public Tensor<1, dim, Number> /** * Convert a boost::geometry::point to a dealii::Point. */ - template + template Point(const boost::geometry::model:: - point &boost_pt, + point &boost_pt, typename std::enable_if<(dim == dummy_dim) && (dummy_dim != 0), int>::type = 0); @@ -374,7 +374,7 @@ template template inline Point::Point( const boost::geometry::model:: - point &boost_pt, + point &boost_pt, typename std::enable_if<(dim == dummy_dim) && (dummy_dim != 0), int>::type) { Assert(dim <= 3, ExcNotImplemented()); From 6c89f3783f74db28e1127a351494514a84463199 Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Mon, 28 Jan 2019 14:17:53 -0700 Subject: [PATCH 043/507] [CI] introduce clang-tidy check - remove -fix - allow bundled/ by including two .clang-tidy files - add jenkins script --- .clang-tidy | 9 +++ bundled/.clang-tidy | 6 ++ contrib/ci/Jenkinsfile.tidy | 90 +++++++++++++++++++++++++++++ contrib/utilities/run_clang_tidy.sh | 43 +++++++------- 4 files changed, 125 insertions(+), 23 deletions(-) create mode 100644 .clang-tidy create mode 100644 bundled/.clang-tidy create mode 100644 contrib/ci/Jenkinsfile.tidy diff --git a/.clang-tidy b/.clang-tidy new file mode 100644 index 000000000000..5b4e0fd7781a --- /dev/null +++ b/.clang-tidy @@ -0,0 +1,9 @@ +# Settings file automatically used by clang-tidy +# +# See ./contrib/utilities/run_clang_tidy.sh for details + +# We disable performance-inefficient-string-concatenation because we don't care about "a"+to_string(5)+... + +Checks: "-*,cppcoreguidelines-pro-type-static-cast-downcast,google-readability-casting,modernize-*,-modernize-pass-by-value,-modernize-raw-string-literal,-modernize-use-auto,-modernize-use-override,-modernize-use-default-member-init,-modernize-use-transparent-functors,use-emplace,mpi-*,performance-*,-performance-inefficient-string-concatenation" + +WarningsAsErrors: '*' diff --git a/bundled/.clang-tidy b/bundled/.clang-tidy new file mode 100644 index 000000000000..eb40a98a77a0 --- /dev/null +++ b/bundled/.clang-tidy @@ -0,0 +1,6 @@ +# Disable all checks because we don't want to fix things inside +# bundled/. Clang-tidy fails if nothing is chosen, so we just enable a single +# harmless warning: + +Checks: "-*,misc-sizeof-container" + diff --git a/contrib/ci/Jenkinsfile.tidy b/contrib/ci/Jenkinsfile.tidy new file mode 100644 index 000000000000..05c013482631 --- /dev/null +++ b/contrib/ci/Jenkinsfile.tidy @@ -0,0 +1,90 @@ +#!groovy + +/* +Settings to apply inside Jenkins: + - discover pull requests (remove branches/master) + - Strategy: merged PR + - enable "Disable GitHub Multibranch Status Plugin" + - trigger build on pull request comment: .* /rebuild.* (without space!) + - Jenkinsfile: choose contrib/ci/Jenkinsfile.tidy + - scan: every 4 hours + - discard: 5+ items +*/ + +pipeline +{ + agent none + + stages + { + stage("check") + { + when { + allOf { + not {branch 'master'} + } + } + + agent + { + docker + { + image 'dealii/indent' + } + } + + steps + { + githubNotify context: 'tidy', description: 'pending...', status: 'PENDING' + sh ''' + wget -q -O - https://api.github.com/repos/dealii/dealii/issues/${CHANGE_ID}/labels | grep 'ready to test' || \ + { echo "This commit will only be tested when it has the label 'ready to test'. Trigger a rebuild by adding a comment that contains '/rebuild'..."; exit 1; } + ''' + } + post + { + failure + { + githubNotify context: 'tidy', description: 'need ready to test label and /rebuild', status: 'PENDING' + script + { + currentBuild.result='NOT_BUILT' + } + } + } + } + + stage('build') + { + agent + { + docker + { + image 'tjhei/candi-base-clang' + } + } + steps + { + timeout(time: 2, unit: 'HOURS') + { + sh "echo \"building on node ${env.NODE_NAME}\"" + + sh '''#!/bin/bash + mkdir build && cd build + $WORKSPACE/contrib/utilities/run_clang_tidy.sh $WORKSPACE + ''' + githubNotify context: 'tidy', description: 'OK', status: 'SUCCESS' + } + } + + post + { + failure + { + githubNotify context: 'tidy', description: 'build failed', status: 'FAILURE' + } + } + } + + } +} diff --git a/contrib/utilities/run_clang_tidy.sh b/contrib/utilities/run_clang_tidy.sh index d292ef84a084..d013f5663947 100755 --- a/contrib/utilities/run_clang_tidy.sh +++ b/contrib/utilities/run_clang_tidy.sh @@ -21,7 +21,7 @@ # Usage: # /contrib/utilities/run_clang_tidy.sh SRC_DIR OPTIONAL_CMAKE_ARGS # with: -# SRC_DIR is an absolute path to a deal.II source directory +# SRC_DIR points to a deal.II source directory # OPTIONAL_CMAKE_ARGS are optional arguments to pass to CMake # make sure to run this script in an empty build directory # @@ -29,8 +29,9 @@ # Clang 5.0.1+ and have clang, clang++, and run-clang-tidy.py in # your path. -# grab first argument: +# grab first argument and make relative path an absolute one: SRC=$1 +SRC=$(cd "$SRC";pwd) shift if test ! -d "$SRC/source" -o ! -d "$SRC/include" -o ! -d "$SRC/examples" -o ! -f "$SRC/CMakeLists.txt" ; then @@ -40,36 +41,32 @@ if test ! -d "$SRC/source" -o ! -d "$SRC/include" -o ! -d "$SRC/examples" -o ! - fi echo "SRC-DIR=$SRC" -# do not allow bundled packages, otherwise we get too many warnings from TBB/UMFPACK/etc. # enable MPI (to get MPI warnings) # export compile commands (so that run-clang-tidy.py works) -ARGS="-D DEAL_II_ALLOW_BUNDLED=OFF -D DEAL_II_WITH_MPI=ON -D CMAKE_EXPORT_COMPILE_COMMANDS=ON $@" +ARGS=("-D" "DEAL_II_WITH_MPI=ON" "-D" "CMAKE_EXPORT_COMPILE_COMMANDS=ON" "$@") -# disable performance-inefficient-string-concatenation because we don't care about "a"+to_string(5)+... -CHECKS="-*, - cppcoreguidelines-pro-type-static-cast-downcast, - google-readability-casting, - modernize-*, - -modernize-pass-by-value, - -modernize-raw-string-literal, - -modernize-use-auto, - -modernize-use-override, - -modernize-use-default-member-init, - -modernize-use-transparent-functors, - mpi-*, - performance-*, - -performance-inefficient-string-concatenation" - -CHECKS="$(echo "${CHECKS}" | tr -d '[:space:]')" -echo "$CHECKS" +# for a list of checks, see /.clang-tidy +cat "$SRC/.clang-tidy" if ! [ -x "$(command -v run-clang-tidy.py)" ] || ! [ -x "$(command -v clang++)" ]; then echo "make sure clang, clang++, and run-clang-tidy.py (part of clang) are in the path" exit 2 fi -CC=clang CXX=clang++ cmake $ARGS "$SRC" || (echo "cmake failed!"; false) || exit 2 +CC=clang CXX=clang++ cmake "${ARGS[@]}" "$SRC" || (echo "cmake failed!"; false) || exit 2 cmake --build . --target expand_all_instantiations || (echo "make expand_all_instantiations failed!"; false) || exit 3 -run-clang-tidy.py -p . -checks="$CHECKS" -quiet -header-filter="$SRC/include/*" -fix +# finally run it: +# pipe away stderr (just contains nonsensical "x warnings generated") +# pipe output to output.txt +run-clang-tidy.py -p . -quiet -header-filter="$SRC/include/*" 2>error.txt >output.txt + +if grep -E -q '(warning|error): ' output.txt; then + grep -E '(warning|error): ' output.txt + exit 4 +fi + +echo "OK" +exit 0 + From 274448a0012602f53d9029daf3480d79c5639f86 Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Tue, 29 Jan 2019 12:44:47 -0700 Subject: [PATCH 044/507] convert for loops --- source/grid/grid_in.cc | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/source/grid/grid_in.cc b/source/grid/grid_in.cc index c00da148814e..6a9a6fba5324 100644 --- a/source/grid/grid_in.cc +++ b/source/grid/grid_in.cc @@ -2075,8 +2075,8 @@ GridIn<2>::read_netcdf(const std::string &filename) n_bquads, vertices_per_quad); - for (unsigned int i = 0; i < vertex_indices.size(); ++i) - AssertThrow(vertex_indices[i] >= 0, ExcIO()); + for (const int idx : vertex_indices) + AssertThrow(idx >= 0, ExcIO()); // next we read // double points_xc(no_of_points) @@ -2237,8 +2237,8 @@ GridIn<3>::read_netcdf(const std::string &filename) // vector::iterator to int * vertex_indices_var->get(&*vertex_indices.begin(), n_cells, vertices_per_hex); - for (unsigned int i = 0; i < vertex_indices.size(); ++i) - AssertThrow(vertex_indices[i] >= 0, ExcIO()); + for (const int idx : vertex_indices) + AssertThrow(idx >= 0, ExcIO()); // next we read // double points_xc(no_of_points) @@ -2335,9 +2335,9 @@ GridIn<3>::read_netcdf(const std::string &filename) // types::boundary_id. Also, we don't // take numbers::internal_face_boundary_id // as it denotes an internal face - for (unsigned int i = 0; i < bmarker.size(); ++i) - Assert(0 <= bmarker[i] && static_cast(bmarker[i]) != - numbers::internal_face_boundary_id, + for (const int id : bmarker) + Assert(0 <= id && static_cast(id) != + numbers::internal_face_boundary_id, ExcIO()); // finally we setup the boundary From 1e94813d078896e77e318f8ec92977073e40580e Mon Sep 17 00:00:00 2001 From: Rene Gassmoeller Date: Thu, 31 Jan 2019 11:45:03 -0800 Subject: [PATCH 045/507] Fix serialization of variable data attachements --- source/distributed/tria.cc | 1 + tests/mpi/p4est_save_07.cc | 205 ++++++++++++++++++ ...st_save_07.with_p4est=true.mpirun=5.output | 122 +++++++++++ ...st_save_07.with_petsc=true.mpirun=4.output | 10 + 4 files changed, 338 insertions(+) create mode 100644 tests/mpi/p4est_save_07.cc create mode 100644 tests/mpi/p4est_save_07.with_p4est=true.mpirun=5.output create mode 100644 tests/mpi/p4est_save_07.with_petsc=true.mpirun=4.output diff --git a/source/distributed/tria.cc b/source/distributed/tria.cc index 99068c23dac9..5fe3afb1c834 100644 --- a/source/distributed/tria.cc +++ b/source/distributed/tria.cc @@ -2751,6 +2751,7 @@ namespace parallel tria->cell_attached_data.n_attached_data_sets = 0; tria->cell_attached_data.pack_callbacks_fixed.clear(); + tria->cell_attached_data.pack_callbacks_variable.clear(); } } diff --git a/tests/mpi/p4est_save_07.cc b/tests/mpi/p4est_save_07.cc new file mode 100644 index 000000000000..e409ce4fecb5 --- /dev/null +++ b/tests/mpi/p4est_save_07.cc @@ -0,0 +1,205 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2009 - 2017 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + + +// save and load a triangulation with a different number of cpus +// with variable size data attach +// this is a variation of p4est_save_05, but it saves the triangulation +// multiple times before loading to catch a bug that was not properly +// clearing variables upon save (i.e. multiple saves before a load would +// cause corrupted checkpoints for variable data size attachments). + +#include +#include + +#include + +#include +#include +#include +#include +#include + +#include "../tests.h" + + + +template +std::vector +pack_function( + const typename parallel::distributed::Triangulation::cell_iterator + &cell, + const typename parallel::distributed::Triangulation::CellStatus + status) +{ + static unsigned int some_number = 1; + std::vector some_vector(some_number); + for (unsigned int i = 0; i < some_number; ++i) + some_vector[i] = i; + + std::vector buffer; + buffer.reserve(some_number * sizeof(unsigned int)); + for (auto vector_it = some_vector.cbegin(); vector_it != some_vector.cend(); + ++vector_it) + { + Utilities::pack(*vector_it, buffer, /*allow_compression=*/false); + } + + deallog << "packing cell " << cell->id() + << " with data size=" << buffer.size() << " accumulated data=" + << std::accumulate(some_vector.begin(), some_vector.end(), 0) + << std::endl; + + Assert((status == + parallel::distributed::Triangulation::CELL_PERSIST), + ExcInternalError()); + + ++some_number; + return buffer; +} + + + +template +void +unpack_function( + const typename parallel::distributed::Triangulation::cell_iterator + &cell, + const typename parallel::distributed::Triangulation::CellStatus + status, + const boost::iterator_range::const_iterator> &data_range) +{ + const unsigned int data_in_bytes = + std::distance(data_range.begin(), data_range.end()); + + std::vector intdatavector(data_in_bytes / sizeof(unsigned int)); + + auto vector_it = intdatavector.begin(); + auto data_it = data_range.begin(); + for (; data_it != data_range.end(); + ++vector_it, data_it += sizeof(unsigned int)) + { + *vector_it = + Utilities::unpack(data_it, + data_it + sizeof(unsigned int), + /*allow_compression=*/false); + } + + deallog << "unpacking cell " << cell->id() << " with data size=" + << std::distance(data_range.begin(), data_range.end()) + << " accumulated data=" + << std::accumulate(intdatavector.begin(), intdatavector.end(), 0) + << std::endl; + + Assert((status == + parallel::distributed::Triangulation::CELL_PERSIST), + ExcInternalError()); +} + + + +template +void +save(MPI_Comm com_small, parallel::distributed::Triangulation &tr) +{ + deallog << "writing with " << Utilities::MPI::n_mpi_processes(com_small) + << std::endl; + + unsigned int handle = + tr.register_data_attach(pack_function, + /*returns_variable_size_data=*/true); + + tr.save("file"); + deallog << "#cells = " << tr.n_global_active_cells() << std::endl; + deallog << "Checksum: " << tr.get_checksum() << std::endl; +} + + + +template +void +test() +{ + unsigned int myid = Utilities::MPI::this_mpi_process(MPI_COMM_WORLD); + MPI_Comm com_all = MPI_COMM_WORLD; + MPI_Comm com_small; + + // split the communicator in proc 0,1,2 and 3,4 + MPI_Comm_split(com_all, (myid < 3) ? 0 : 1, myid, &com_small); + + // write with small com + if (myid < 3) + { + parallel::distributed::Triangulation tr(com_small); + GridGenerator::subdivided_hyper_cube(tr, 2); + tr.refine_global(1); + + typename Triangulation::active_cell_iterator cell; + for (cell = tr.begin_active(); cell != tr.end(); ++cell) + { + if (cell->is_locally_owned()) + { + if (cell->id().to_string() == "0_1:0") + cell->set_refine_flag(); + else if (cell->parent()->id().to_string() == "3_0:") + cell->set_coarsen_flag(); + } + } + tr.execute_coarsening_and_refinement(); + + // save two times into the same file, overwrite it the second time + save(com_small, tr); + save(com_small, tr); + } + + MPI_Barrier(MPI_COMM_WORLD); + + deallog << "reading with " << Utilities::MPI::n_mpi_processes(com_all) + << std::endl; + + { + parallel::distributed::Triangulation tr(com_all); + + GridGenerator::subdivided_hyper_cube(tr, 2); + tr.load("file"); + + unsigned int handle = + tr.register_data_attach(pack_function, + /*returns_variable_size_data=*/true); + + tr.notify_ready_to_unpack(handle, unpack_function); + + deallog << "#cells = " << tr.n_global_active_cells() << std::endl; + deallog << "Checksum: " << tr.get_checksum() << std::endl; + + // now check if saving again succeeds. This checks for the correct number of + // attached data packs in tr and caught the bug. + save(com_all, tr); + } + + if (Utilities::MPI::this_mpi_process(MPI_COMM_WORLD) == 0) + deallog << "OK" << std::endl; +} + + +int +main(int argc, char *argv[]) +{ + Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1); + MPILogInitAll log; + + test<2>(); +} diff --git a/tests/mpi/p4est_save_07.with_p4est=true.mpirun=5.output b/tests/mpi/p4est_save_07.with_p4est=true.mpirun=5.output new file mode 100644 index 000000000000..06bf11bda4e5 --- /dev/null +++ b/tests/mpi/p4est_save_07.with_p4est=true.mpirun=5.output @@ -0,0 +1,122 @@ + +DEAL:0::writing with 3 +DEAL:0::packing cell 0_2:00 with data size=4 accumulated data=0 +DEAL:0::packing cell 0_2:01 with data size=8 accumulated data=1 +DEAL:0::packing cell 0_2:02 with data size=12 accumulated data=3 +DEAL:0::packing cell 0_2:03 with data size=16 accumulated data=6 +DEAL:0::packing cell 0_1:1 with data size=20 accumulated data=10 +DEAL:0::#cells = 16 +DEAL:0::Checksum: 2822439380 +DEAL:0::writing with 3 +DEAL:0::packing cell 0_2:00 with data size=24 accumulated data=15 +DEAL:0::packing cell 0_2:01 with data size=28 accumulated data=21 +DEAL:0::packing cell 0_2:02 with data size=32 accumulated data=28 +DEAL:0::packing cell 0_2:03 with data size=36 accumulated data=36 +DEAL:0::packing cell 0_1:1 with data size=40 accumulated data=45 +DEAL:0::#cells = 16 +DEAL:0::Checksum: 2822439380 +DEAL:0::reading with 5 +DEAL:0::unpacking cell 0_2:00 with data size=24 accumulated data=15 +DEAL:0::unpacking cell 0_2:01 with data size=28 accumulated data=21 +DEAL:0::unpacking cell 0_2:02 with data size=32 accumulated data=28 +DEAL:0::unpacking cell 0_2:03 with data size=36 accumulated data=36 +DEAL:0::#cells = 16 +DEAL:0::Checksum: 2822439380 +DEAL:0::writing with 5 +DEAL:0::packing cell 0_2:00 with data size=44 accumulated data=55 +DEAL:0::packing cell 0_2:01 with data size=48 accumulated data=66 +DEAL:0::packing cell 0_2:02 with data size=52 accumulated data=78 +DEAL:0::packing cell 0_2:03 with data size=56 accumulated data=91 +DEAL:0::#cells = 16 +DEAL:0::Checksum: 2822439380 +DEAL:0::OK + +DEAL:1::writing with 3 +DEAL:1::packing cell 0_1:2 with data size=4 accumulated data=0 +DEAL:1::packing cell 0_1:3 with data size=8 accumulated data=1 +DEAL:1::packing cell 1_1:0 with data size=12 accumulated data=3 +DEAL:1::packing cell 1_1:1 with data size=16 accumulated data=6 +DEAL:1::packing cell 1_1:2 with data size=20 accumulated data=10 +DEAL:1::packing cell 1_1:3 with data size=24 accumulated data=15 +DEAL:1::#cells = 16 +DEAL:1::Checksum: 0 +DEAL:1::writing with 3 +DEAL:1::packing cell 0_1:2 with data size=28 accumulated data=21 +DEAL:1::packing cell 0_1:3 with data size=32 accumulated data=28 +DEAL:1::packing cell 1_1:0 with data size=36 accumulated data=36 +DEAL:1::packing cell 1_1:1 with data size=40 accumulated data=45 +DEAL:1::packing cell 1_1:2 with data size=44 accumulated data=55 +DEAL:1::packing cell 1_1:3 with data size=48 accumulated data=66 +DEAL:1::#cells = 16 +DEAL:1::Checksum: 0 +DEAL:1::reading with 5 +DEAL:1::unpacking cell 0_1:1 with data size=40 accumulated data=45 +DEAL:1::unpacking cell 0_1:2 with data size=28 accumulated data=21 +DEAL:1::#cells = 16 +DEAL:1::Checksum: 0 +DEAL:1::writing with 5 +DEAL:1::packing cell 0_1:1 with data size=52 accumulated data=78 +DEAL:1::packing cell 0_1:2 with data size=56 accumulated data=91 +DEAL:1::#cells = 16 +DEAL:1::Checksum: 0 + + +DEAL:2::writing with 3 +DEAL:2::packing cell 2_1:0 with data size=4 accumulated data=0 +DEAL:2::packing cell 2_1:1 with data size=8 accumulated data=1 +DEAL:2::packing cell 2_1:2 with data size=12 accumulated data=3 +DEAL:2::packing cell 2_1:3 with data size=16 accumulated data=6 +DEAL:2::packing cell 3_0: with data size=20 accumulated data=10 +DEAL:2::#cells = 16 +DEAL:2::Checksum: 0 +DEAL:2::writing with 3 +DEAL:2::packing cell 2_1:0 with data size=24 accumulated data=15 +DEAL:2::packing cell 2_1:1 with data size=28 accumulated data=21 +DEAL:2::packing cell 2_1:2 with data size=32 accumulated data=28 +DEAL:2::packing cell 2_1:3 with data size=36 accumulated data=36 +DEAL:2::packing cell 3_0: with data size=40 accumulated data=45 +DEAL:2::#cells = 16 +DEAL:2::Checksum: 0 +DEAL:2::reading with 5 +DEAL:2::unpacking cell 0_1:3 with data size=32 accumulated data=28 +DEAL:2::unpacking cell 1_1:0 with data size=36 accumulated data=36 +DEAL:2::unpacking cell 1_1:1 with data size=40 accumulated data=45 +DEAL:2::unpacking cell 1_1:2 with data size=44 accumulated data=55 +DEAL:2::unpacking cell 1_1:3 with data size=48 accumulated data=66 +DEAL:2::#cells = 16 +DEAL:2::Checksum: 0 +DEAL:2::writing with 5 +DEAL:2::packing cell 0_1:3 with data size=44 accumulated data=55 +DEAL:2::packing cell 1_1:0 with data size=48 accumulated data=66 +DEAL:2::packing cell 1_1:1 with data size=52 accumulated data=78 +DEAL:2::packing cell 1_1:2 with data size=56 accumulated data=91 +DEAL:2::packing cell 1_1:3 with data size=60 accumulated data=105 +DEAL:2::#cells = 16 +DEAL:2::Checksum: 0 + + +DEAL:3::reading with 5 +DEAL:3::#cells = 16 +DEAL:3::Checksum: 0 +DEAL:3::writing with 5 +DEAL:3::#cells = 16 +DEAL:3::Checksum: 0 + + +DEAL:4::reading with 5 +DEAL:4::unpacking cell 2_1:0 with data size=24 accumulated data=15 +DEAL:4::unpacking cell 2_1:1 with data size=28 accumulated data=21 +DEAL:4::unpacking cell 2_1:2 with data size=32 accumulated data=28 +DEAL:4::unpacking cell 2_1:3 with data size=36 accumulated data=36 +DEAL:4::unpacking cell 3_0: with data size=40 accumulated data=45 +DEAL:4::#cells = 16 +DEAL:4::Checksum: 0 +DEAL:4::writing with 5 +DEAL:4::packing cell 2_1:0 with data size=4 accumulated data=0 +DEAL:4::packing cell 2_1:1 with data size=8 accumulated data=1 +DEAL:4::packing cell 2_1:2 with data size=12 accumulated data=3 +DEAL:4::packing cell 2_1:3 with data size=16 accumulated data=6 +DEAL:4::packing cell 3_0: with data size=20 accumulated data=10 +DEAL:4::#cells = 16 +DEAL:4::Checksum: 0 + diff --git a/tests/mpi/p4est_save_07.with_petsc=true.mpirun=4.output b/tests/mpi/p4est_save_07.with_petsc=true.mpirun=4.output new file mode 100644 index 000000000000..bf97dfd8ef1a --- /dev/null +++ b/tests/mpi/p4est_save_07.with_petsc=true.mpirun=4.output @@ -0,0 +1,10 @@ + +DEAL:0:2d::hyper_cube +DEAL:0:2d::#cells = 19 +DEAL:0:2d::cells(0) = 10 +DEAL:0:2d::Checksum: 136119115 +DEAL:0:2d::#cells = 19 +DEAL:0:2d::cells(0) = 10 +DEAL:0:2d::Checksum: 136119115 +DEAL:0:2d::sum: 435.000 870.000 +DEAL:0:2d::OK From 197cb40c92db95ebf2c3a657b783ca543899ac4c Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Thu, 31 Jan 2019 23:47:38 +0100 Subject: [PATCH 046/507] Be explicit about initialization of static const Tensor variables --- include/deal.II/base/patterns.h | 2 +- include/deal.II/base/tensor_function.templates.h | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/include/deal.II/base/patterns.h b/include/deal.II/base/patterns.h index 2789bf843407..d4ea6babc0b2 100644 --- a/include/deal.II/base/patterns.h +++ b/include/deal.II/base/patterns.h @@ -1521,7 +1521,7 @@ namespace Patterns std::is_same::value || std::is_same::value) str << static_cast(value); else if (std::is_same::value) - str << (value ? "true" : "false"); + str << (static_cast(value) ? "true" : "false"); else str << value; AssertThrow(p->match(str.str()), ExcNoMatch(str.str(), p.get())); diff --git a/include/deal.II/base/tensor_function.templates.h b/include/deal.II/base/tensor_function.templates.h index cb53e448c14d..d760d22070bf 100644 --- a/include/deal.II/base/tensor_function.templates.h +++ b/include/deal.II/base/tensor_function.templates.h @@ -123,7 +123,7 @@ template typename TensorFunction::gradient_type ConstantTensorFunction::gradient(const Point &) const { - static const Tensor zero; + static const Tensor zero{}; return zero; } @@ -140,7 +140,7 @@ ConstantTensorFunction::gradient_list( Assert(gradients.size() == points.size(), ExcDimensionMismatch(gradients.size(), points.size())); - static const Tensor zero; + static const Tensor zero{}; for (unsigned int i = 0; i < gradients.size(); ++i) gradients[i] = zero; From c2c8f2bd282863ed710fc5a0c504cdfc554d143c Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Fri, 1 Feb 2019 14:12:29 +0100 Subject: [PATCH 047/507] Fix compiling with MSVC --- include/deal.II/base/subscriptor.h | 5 +++++ include/deal.II/base/vectorization.h | 4 ++-- source/base/vectorization.cc | 2 +- 3 files changed, 8 insertions(+), 3 deletions(-) diff --git a/include/deal.II/base/subscriptor.h b/include/deal.II/base/subscriptor.h index 431f8c03e412..aae53ff17d17 100644 --- a/include/deal.II/base/subscriptor.h +++ b/include/deal.II/base/subscriptor.h @@ -340,6 +340,11 @@ Subscriptor::list_subscribers(StreamType &stream) const << it.first << '\"' << std::endl; } +// forward declare template specialization +template <> +void +Subscriptor::subscribe(std::atomic *const validity, + const char * id) const; DEAL_II_NAMESPACE_CLOSE #endif diff --git a/include/deal.II/base/vectorization.h b/include/deal.II/base/vectorization.h index 3f82e165c52e..1b8c47005c3c 100644 --- a/include/deal.II/base/vectorization.h +++ b/include/deal.II/base/vectorization.h @@ -178,7 +178,7 @@ class VectorizedArray * case, there is only one element. Specializations use SIMD intrinsics and * can work on multiple elements at the same time. */ - static const unsigned int n_array_elements; + static const unsigned int n_array_elements = 1; // POD means that there should be no user-defined constructors, destructors // and copy functions (the standard is somewhat relaxed in C++2011, though). @@ -453,7 +453,7 @@ class VectorizedArray // We need to have a separate declaration for static const members template -const unsigned int VectorizedArray::n_array_elements = 1; +const unsigned int VectorizedArray::n_array_elements; diff --git a/source/base/vectorization.cc b/source/base/vectorization.cc index 1cc3fe6de667..88ffb1f6bce9 100644 --- a/source/base/vectorization.cc +++ b/source/base/vectorization.cc @@ -17,7 +17,7 @@ DEAL_II_NAMESPACE_OPEN -#if DEAL_II_COMPILER_VECTORIZATION_LEVEL >= 1 +#if DEAL_II_COMPILER_VECTORIZATION_LEVEL >= 1 && !defined(DEAL_II_MSVC) const unsigned int VectorizedArray::n_array_elements; const unsigned int VectorizedArray::n_array_elements; #endif From 7bb7d7bbe8af22f094e70fc01b9f4c4c4fb86963 Mon Sep 17 00:00:00 2001 From: Rene Gassmoeller Date: Thu, 31 Jan 2019 10:24:06 -0800 Subject: [PATCH 048/507] Ensure particle property initialization --- source/particles/particle.cc | 10 ++++- tests/particles/particle_07.cc | 64 ++++++++++++++++++++++++++++++ tests/particles/particle_07.output | 2 + 3 files changed, 75 insertions(+), 1 deletion(-) create mode 100644 tests/particles/particle_07.cc create mode 100644 tests/particles/particle_07.output diff --git a/source/particles/particle.cc b/source/particles/particle.cc index 03f90811b333..b426aac4ccdb 100644 --- a/source/particles/particle.cc +++ b/source/particles/particle.cc @@ -328,8 +328,16 @@ namespace Particles { Assert(property_pool != nullptr, ExcInternalError()); + // If this particle has no properties yet, allocate and initialize them. if (properties == PropertyPool::invalid_handle) - properties = property_pool->allocate_properties_array(); + { + properties = property_pool->allocate_properties_array(); + + ArrayView my_properties = + property_pool->get_properties(properties); + + std::fill(my_properties.begin(), my_properties.end(), 0.0); + } return property_pool->get_properties(properties); } diff --git a/tests/particles/particle_07.cc b/tests/particles/particle_07.cc new file mode 100644 index 000000000000..0df754f23fdf --- /dev/null +++ b/tests/particles/particle_07.cc @@ -0,0 +1,64 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2017 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + + +// Like particle_03, but test property initialization. + +#include + +#include + +#include "../tests.h" + + +template +void +test() +{ + { + const unsigned int n_properties_per_particle = 3; + Particles::PropertyPool pool(n_properties_per_particle); + + Point<2> position; + position(0) = 0.3; + position(1) = 0.5; + + Point<2> reference_position; + reference_position(0) = 0.2; + reference_position(1) = 0.4; + + const types::particle_index index(7); + + std::vector properties = {0.15, 0.45, 0.75}; + + Particles::Particle<2> particle(position, reference_position, index); + particle.set_property_pool(pool); + + for (unsigned int i = 0; i < n_properties_per_particle; ++i) + AssertThrow(particle.get_properties()[i] == 0.0, ExcInternalError()); + } + + deallog << "OK" << std::endl; +} + + + +int +main() +{ + initlog(); + test<2>(); +} diff --git a/tests/particles/particle_07.output b/tests/particles/particle_07.output new file mode 100644 index 000000000000..0fd8fc12f0b4 --- /dev/null +++ b/tests/particles/particle_07.output @@ -0,0 +1,2 @@ + +DEAL::OK From a5e1a72930e4b8f7b791125dbb1ea35f9a480092 Mon Sep 17 00:00:00 2001 From: Daniel Garcia-Sanchez Date: Sat, 2 Feb 2019 14:26:44 +0100 Subject: [PATCH 049/507] Remove unused variable warning --- source/grid/grid_in.cc | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/source/grid/grid_in.cc b/source/grid/grid_in.cc index aaa1b79d945c..ad18740f2849 100644 --- a/source/grid/grid_in.cc +++ b/source/grid/grid_in.cc @@ -2436,9 +2436,12 @@ GridIn<3>::read_netcdf(const std::string &filename) // take numbers::internal_face_boundary_id // as it denotes an internal face for (const int id : bmarker) - Assert(0 <= id && static_cast(id) != - numbers::internal_face_boundary_id, - ExcIO()); + { + Assert(0 <= id && static_cast(id) != + numbers::internal_face_boundary_id, + ExcIO()); + (void)id; + } // finally we setup the boundary // information From 40538ad31a71495649d174b0f7be5f7135d0a905 Mon Sep 17 00:00:00 2001 From: David Wells Date: Sat, 2 Feb 2019 10:00:38 -0500 Subject: [PATCH 050/507] Avoid calling a deprecated MPI function. This was deprecated a long time ago (1996) and is not present in the latest version of openMPI (4.0): see https://www.open-mpi.org/faq/?category=mpi-removed Credit goes to Pratik Nayak for finding this issue. --- source/base/mpi.cc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/source/base/mpi.cc b/source/base/mpi.cc index bd1f7f9846a2..b8cd45e7c26a 100644 --- a/source/base/mpi.cc +++ b/source/base/mpi.cc @@ -448,7 +448,7 @@ namespace Utilities MPI_Aint displacements[] = {0, offsetof(MinMaxAvg, min_index)}; MPI_Datatype types[] = {MPI_DOUBLE, MPI_INT}; - ierr = MPI_Type_struct(2, lengths, displacements, types, &type); + ierr = MPI_Type_create_struct(2, lengths, displacements, types, &type); AssertThrowMPI(ierr); ierr = MPI_Type_commit(&type); From c08769422a8c0775fde64452a9ef57d345fc3892 Mon Sep 17 00:00:00 2001 From: Wolfgang Bangerth Date: Fri, 1 Feb 2019 08:04:58 -0700 Subject: [PATCH 051/507] Simplify some code. --- include/deal.II/base/tensor_function.templates.h | 13 ++++++------- 1 file changed, 6 insertions(+), 7 deletions(-) diff --git a/include/deal.II/base/tensor_function.templates.h b/include/deal.II/base/tensor_function.templates.h index d760d22070bf..11c2f54cb73a 100644 --- a/include/deal.II/base/tensor_function.templates.h +++ b/include/deal.II/base/tensor_function.templates.h @@ -123,9 +123,8 @@ template typename TensorFunction::gradient_type ConstantTensorFunction::gradient(const Point &) const { - static const Tensor zero{}; - - return zero; + // Return a zero (=default initialized) tensor + return {}; } @@ -140,10 +139,10 @@ ConstantTensorFunction::gradient_list( Assert(gradients.size() == points.size(), ExcDimensionMismatch(gradients.size(), points.size())); - static const Tensor zero{}; - - for (unsigned int i = 0; i < gradients.size(); ++i) - gradients[i] = zero; + // Return an array of zero tensors. + std::fill(gradients.begin(), + gradients.end(), + typename TensorFunction::gradient_type()); } From 7d5993168d1ce1d8e12b743f924faa16827f6842 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Sat, 2 Feb 2019 13:05:31 +0100 Subject: [PATCH 052/507] Fix p4est test --- ...5.output => p4est_save_05.mpirun=5.output} | 0 tests/mpi/p4est_save_07.mpirun=4.output | 114 ++++++++++++++++++ ...5.output => p4est_save_07.mpirun=5.output} | 0 ...st_save_07.with_petsc=true.mpirun=4.output | 10 -- 4 files changed, 114 insertions(+), 10 deletions(-) rename tests/mpi/{p4est_save_05.with_p4est=true.mpirun=5.output => p4est_save_05.mpirun=5.output} (100%) create mode 100644 tests/mpi/p4est_save_07.mpirun=4.output rename tests/mpi/{p4est_save_07.with_p4est=true.mpirun=5.output => p4est_save_07.mpirun=5.output} (100%) delete mode 100644 tests/mpi/p4est_save_07.with_petsc=true.mpirun=4.output diff --git a/tests/mpi/p4est_save_05.with_p4est=true.mpirun=5.output b/tests/mpi/p4est_save_05.mpirun=5.output similarity index 100% rename from tests/mpi/p4est_save_05.with_p4est=true.mpirun=5.output rename to tests/mpi/p4est_save_05.mpirun=5.output diff --git a/tests/mpi/p4est_save_07.mpirun=4.output b/tests/mpi/p4est_save_07.mpirun=4.output new file mode 100644 index 000000000000..92b527f8aa94 --- /dev/null +++ b/tests/mpi/p4est_save_07.mpirun=4.output @@ -0,0 +1,114 @@ + +DEAL:0::writing with 3 +DEAL:0::packing cell 0_2:00 with data size=4 accumulated data=0 +DEAL:0::packing cell 0_2:01 with data size=8 accumulated data=1 +DEAL:0::packing cell 0_2:02 with data size=12 accumulated data=3 +DEAL:0::packing cell 0_2:03 with data size=16 accumulated data=6 +DEAL:0::packing cell 0_1:1 with data size=20 accumulated data=10 +DEAL:0::#cells = 16 +DEAL:0::Checksum: 2822439380 +DEAL:0::writing with 3 +DEAL:0::packing cell 0_2:00 with data size=24 accumulated data=15 +DEAL:0::packing cell 0_2:01 with data size=28 accumulated data=21 +DEAL:0::packing cell 0_2:02 with data size=32 accumulated data=28 +DEAL:0::packing cell 0_2:03 with data size=36 accumulated data=36 +DEAL:0::packing cell 0_1:1 with data size=40 accumulated data=45 +DEAL:0::#cells = 16 +DEAL:0::Checksum: 2822439380 +DEAL:0::reading with 4 +DEAL:0::unpacking cell 0_2:00 with data size=24 accumulated data=15 +DEAL:0::unpacking cell 0_2:01 with data size=28 accumulated data=21 +DEAL:0::unpacking cell 0_2:02 with data size=32 accumulated data=28 +DEAL:0::unpacking cell 0_2:03 with data size=36 accumulated data=36 +DEAL:0::#cells = 16 +DEAL:0::Checksum: 2822439380 +DEAL:0::writing with 4 +DEAL:0::packing cell 0_2:00 with data size=44 accumulated data=55 +DEAL:0::packing cell 0_2:01 with data size=48 accumulated data=66 +DEAL:0::packing cell 0_2:02 with data size=52 accumulated data=78 +DEAL:0::packing cell 0_2:03 with data size=56 accumulated data=91 +DEAL:0::#cells = 16 +DEAL:0::Checksum: 2822439380 +DEAL:0::OK + +DEAL:1::writing with 3 +DEAL:1::packing cell 0_1:2 with data size=4 accumulated data=0 +DEAL:1::packing cell 0_1:3 with data size=8 accumulated data=1 +DEAL:1::packing cell 1_1:0 with data size=12 accumulated data=3 +DEAL:1::packing cell 1_1:1 with data size=16 accumulated data=6 +DEAL:1::packing cell 1_1:2 with data size=20 accumulated data=10 +DEAL:1::packing cell 1_1:3 with data size=24 accumulated data=15 +DEAL:1::#cells = 16 +DEAL:1::Checksum: 0 +DEAL:1::writing with 3 +DEAL:1::packing cell 0_1:2 with data size=28 accumulated data=21 +DEAL:1::packing cell 0_1:3 with data size=32 accumulated data=28 +DEAL:1::packing cell 1_1:0 with data size=36 accumulated data=36 +DEAL:1::packing cell 1_1:1 with data size=40 accumulated data=45 +DEAL:1::packing cell 1_1:2 with data size=44 accumulated data=55 +DEAL:1::packing cell 1_1:3 with data size=48 accumulated data=66 +DEAL:1::#cells = 16 +DEAL:1::Checksum: 0 +DEAL:1::reading with 4 +DEAL:1::unpacking cell 0_1:1 with data size=40 accumulated data=45 +DEAL:1::unpacking cell 0_1:2 with data size=28 accumulated data=21 +DEAL:1::unpacking cell 0_1:3 with data size=32 accumulated data=28 +DEAL:1::#cells = 16 +DEAL:1::Checksum: 0 +DEAL:1::writing with 4 +DEAL:1::packing cell 0_1:1 with data size=52 accumulated data=78 +DEAL:1::packing cell 0_1:2 with data size=56 accumulated data=91 +DEAL:1::packing cell 0_1:3 with data size=60 accumulated data=105 +DEAL:1::#cells = 16 +DEAL:1::Checksum: 0 + + +DEAL:2::writing with 3 +DEAL:2::packing cell 2_1:0 with data size=4 accumulated data=0 +DEAL:2::packing cell 2_1:1 with data size=8 accumulated data=1 +DEAL:2::packing cell 2_1:2 with data size=12 accumulated data=3 +DEAL:2::packing cell 2_1:3 with data size=16 accumulated data=6 +DEAL:2::packing cell 3_0: with data size=20 accumulated data=10 +DEAL:2::#cells = 16 +DEAL:2::Checksum: 0 +DEAL:2::writing with 3 +DEAL:2::packing cell 2_1:0 with data size=24 accumulated data=15 +DEAL:2::packing cell 2_1:1 with data size=28 accumulated data=21 +DEAL:2::packing cell 2_1:2 with data size=32 accumulated data=28 +DEAL:2::packing cell 2_1:3 with data size=36 accumulated data=36 +DEAL:2::packing cell 3_0: with data size=40 accumulated data=45 +DEAL:2::#cells = 16 +DEAL:2::Checksum: 0 +DEAL:2::reading with 4 +DEAL:2::unpacking cell 1_1:0 with data size=36 accumulated data=36 +DEAL:2::unpacking cell 1_1:1 with data size=40 accumulated data=45 +DEAL:2::unpacking cell 1_1:2 with data size=44 accumulated data=55 +DEAL:2::unpacking cell 1_1:3 with data size=48 accumulated data=66 +DEAL:2::#cells = 16 +DEAL:2::Checksum: 0 +DEAL:2::writing with 4 +DEAL:2::packing cell 1_1:0 with data size=44 accumulated data=55 +DEAL:2::packing cell 1_1:1 with data size=48 accumulated data=66 +DEAL:2::packing cell 1_1:2 with data size=52 accumulated data=78 +DEAL:2::packing cell 1_1:3 with data size=56 accumulated data=91 +DEAL:2::#cells = 16 +DEAL:2::Checksum: 0 + + +DEAL:3::reading with 4 +DEAL:3::unpacking cell 2_1:0 with data size=24 accumulated data=15 +DEAL:3::unpacking cell 2_1:1 with data size=28 accumulated data=21 +DEAL:3::unpacking cell 2_1:2 with data size=32 accumulated data=28 +DEAL:3::unpacking cell 2_1:3 with data size=36 accumulated data=36 +DEAL:3::unpacking cell 3_0: with data size=40 accumulated data=45 +DEAL:3::#cells = 16 +DEAL:3::Checksum: 0 +DEAL:3::writing with 4 +DEAL:3::packing cell 2_1:0 with data size=4 accumulated data=0 +DEAL:3::packing cell 2_1:1 with data size=8 accumulated data=1 +DEAL:3::packing cell 2_1:2 with data size=12 accumulated data=3 +DEAL:3::packing cell 2_1:3 with data size=16 accumulated data=6 +DEAL:3::packing cell 3_0: with data size=20 accumulated data=10 +DEAL:3::#cells = 16 +DEAL:3::Checksum: 0 + diff --git a/tests/mpi/p4est_save_07.with_p4est=true.mpirun=5.output b/tests/mpi/p4est_save_07.mpirun=5.output similarity index 100% rename from tests/mpi/p4est_save_07.with_p4est=true.mpirun=5.output rename to tests/mpi/p4est_save_07.mpirun=5.output diff --git a/tests/mpi/p4est_save_07.with_petsc=true.mpirun=4.output b/tests/mpi/p4est_save_07.with_petsc=true.mpirun=4.output deleted file mode 100644 index bf97dfd8ef1a..000000000000 --- a/tests/mpi/p4est_save_07.with_petsc=true.mpirun=4.output +++ /dev/null @@ -1,10 +0,0 @@ - -DEAL:0:2d::hyper_cube -DEAL:0:2d::#cells = 19 -DEAL:0:2d::cells(0) = 10 -DEAL:0:2d::Checksum: 136119115 -DEAL:0:2d::#cells = 19 -DEAL:0:2d::cells(0) = 10 -DEAL:0:2d::Checksum: 136119115 -DEAL:0:2d::sum: 435.000 870.000 -DEAL:0:2d::OK From 78b5898a7afc8417e5696d239373372a6de57069 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Sat, 2 Feb 2019 18:45:12 +0100 Subject: [PATCH 053/507] Document the minimal supported MPI version --- doc/news/changes/minor/20190202Arndt | 3 +++ doc/readme.html | 1 + 2 files changed, 4 insertions(+) create mode 100644 doc/news/changes/minor/20190202Arndt diff --git a/doc/news/changes/minor/20190202Arndt b/doc/news/changes/minor/20190202Arndt new file mode 100644 index 000000000000..a3357d6bf42c --- /dev/null +++ b/doc/news/changes/minor/20190202Arndt @@ -0,0 +1,3 @@ +Documented: The minimal supported MPI version is MPI-2.0. +
+(Daniel Arndt, 2019/02/02) diff --git a/doc/readme.html b/doc/readme.html index 9d7cf59ead41..f938801714e6 100644 --- a/doc/readme.html +++ b/doc/readme.html @@ -312,6 +312,7 @@

Selecting optional library features

MPI: To enable parallel computations beyond a single node using the Message Passing Interface (MPI), pass the -DDEAL_II_WITH_MPI=ON argument to cmake. If cmake found MPI but you specifically do not want to use it, then pass -DDEAL_II_WITH_MPI=OFF. + The minimal supported version is MPI-2.0.

From 9df0fcfeb3477ca73a718eafdc1b661150ce4372 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Sun, 3 Feb 2019 12:06:36 +0100 Subject: [PATCH 054/507] Fix building TBB with nvcc_wrapper --- include/deal.II/base/function_parser.h | 8 ------ include/deal.II/base/thread_management.h | 9 ------ source/matrix_free/task_info.cc | 36 +++++++++++------------- 3 files changed, 17 insertions(+), 36 deletions(-) diff --git a/include/deal.II/base/function_parser.h b/include/deal.II/base/function_parser.h index fc03c246d249..d8f07a35481b 100644 --- a/include/deal.II/base/function_parser.h +++ b/include/deal.II/base/function_parser.h @@ -379,16 +379,8 @@ class FunctionParser : public AutoDerivativeFunction * storing a unique_ptr so that we don't need to include the definition of * mu::Parser in this header. */ -# if TBB_VERSION_MAJOR >= 4 mutable Threads::ThreadLocalStorage>> fp; -# else - // older TBBs have a bug in which they want to return thread-local - // objects by value. this doesn't work for std::unique_ptr, so use a - // std::shared_ptr - mutable Threads::ThreadLocalStorage>> - fp; -# endif /** * An array to keep track of all the constants, required to initialize fp in diff --git a/include/deal.II/base/thread_management.h b/include/deal.II/base/thread_management.h index b3993b51b790..931e7f30d705 100644 --- a/include/deal.II/base/thread_management.h +++ b/include/deal.II/base/thread_management.h @@ -1353,16 +1353,7 @@ namespace Threads tbb::task *worker = new (task->allocate_child()) TaskEntryPoint(*this); - // in earlier versions of the TBB, task::spawn was a regular - // member function; however, in later versions, it was converted - // into a static function. we could always call it as a regular member - // function of *task, but that appears to confuse the NVidia nvcc - // compiler. consequently, the following work-around: -# if TBB_VERSION_MAJOR >= 4 tbb::task::spawn(*worker); -# else - task->spawn(*worker); -# endif } diff --git a/source/matrix_free/task_info.cc b/source/matrix_free/task_info.cc index a1617d4c3dc0..33bee62a3cc6 100644 --- a/source/matrix_free/task_info.cc +++ b/source/matrix_free/task_info.cc @@ -118,7 +118,7 @@ namespace internal work(); if (is_blocked == true) - dummy->spawn(*dummy); + tbb::empty_task::spawn(*dummy); return nullptr; } @@ -172,7 +172,7 @@ namespace internal worker[j]->set_ref_count(2); blocked_worker[j - 1]->dummy = new (worker[j]->allocate_child()) tbb::empty_task; - worker[j - 1]->spawn(*blocked_worker[j - 1]); + tbb::task::spawn(*blocked_worker[j - 1]); } else worker[j]->set_ref_count(1); @@ -195,13 +195,13 @@ namespace internal 2 * j + 1, task_info, false); - worker[j]->spawn(*worker[evens]); + tbb::task::spawn(*worker[evens]); } else { tbb::empty_task *child = new (worker[j]->allocate_child()) tbb::empty_task(); - worker[j]->spawn(*child); + tbb::task::spawn(*child); } } } @@ -209,7 +209,7 @@ namespace internal root->wait_for_all(); root->destroy(*root); if (is_blocked == true) - dummy->spawn(*dummy); + tbb::empty_task::spawn(*dummy); return nullptr; } @@ -289,7 +289,7 @@ namespace internal parallel_for(tbb::blocked_range(0, n_chunks, 1), CellWork(worker, task_info, partition)); if (is_blocked == true) - dummy->spawn(*dummy); + tbb::empty_task::spawn(*dummy); return nullptr; } @@ -364,9 +364,9 @@ namespace internal blocked_worker[j - 1]->dummy = new (worker[j]->allocate_child()) tbb::empty_task; if (j > 1) - worker[j - 1]->spawn(*blocked_worker[j - 1]); + tbb::task::spawn(*blocked_worker[j - 1]); else - worker_compr->spawn(*blocked_worker[j - 1]); + tbb::task::spawn(*blocked_worker[j - 1]); } else { @@ -376,7 +376,7 @@ namespace internal MPICommunication *worker_dist = new (worker[j]->allocate_child()) MPICommunication(funct, false); - worker_dist->spawn(*worker_dist); + tbb::task::spawn(*worker_dist); } if (j < evens - 1) { @@ -392,13 +392,13 @@ namespace internal 2 * j + 1, *this, false); - worker[j]->spawn(*worker[evens]); + tbb::task::spawn(*worker[evens]); } else { tbb::empty_task *child = new (worker[j]->allocate_child()) tbb::empty_task(); - worker[j]->spawn(*child); + tbb::task::spawn(*child); } } } @@ -467,14 +467,12 @@ namespace internal tbb::empty_task; worker_index++; if (spawn_index_child == -1) - worker[spawn_index]->spawn( - *blocked_worker[(part - 1) / 2]); + tbb::task::spawn(*blocked_worker[(part - 1) / 2]); else { Assert(spawn_index_child >= 0, ExcInternalError()); - worker[spawn_index]->spawn( - *worker[spawn_index_child]); + tbb::task::spawn(*worker[spawn_index_child]); } spawn_index = spawn_index_new; spawn_index_child = -2; @@ -484,7 +482,7 @@ namespace internal MPICommunication *worker_dist = new (worker[worker_index]->allocate_child()) MPICommunication(funct, false); - worker_dist->spawn(*worker_dist); + tbb::task::spawn(*worker_dist); worker_index++; } part += 1; @@ -539,14 +537,14 @@ namespace internal tbb::empty_task *final = new (worker[worker_index - 1]->allocate_child()) tbb::empty_task; - worker[spawn_index]->spawn(*final); + tbb::task::spawn(*final); spawn_index_child = worker_index - 1; } } if (evens == odds) { Assert(spawn_index_child >= 0, ExcInternalError()); - worker[spawn_index]->spawn(*worker[spawn_index_child]); + tbb::task::spawn(*worker[spawn_index_child]); } root->wait_for_all(); root->destroy(*root); @@ -568,7 +566,7 @@ namespace internal color::PartitionWork *worker = new (root->allocate_child()) color::PartitionWork(funct, color, *this, false); - root->spawn(*worker); + tbb::empty_task::spawn(*worker); root->wait_for_all(); root->destroy(*root); } From 6261c20ca19fa3f9ba370bf8c84a963e9bfc4578 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Sun, 3 Feb 2019 14:04:33 +0100 Subject: [PATCH 055/507] Remove unused variables --- source/matrix_free/task_info.cc | 3 --- 1 file changed, 3 deletions(-) diff --git a/source/matrix_free/task_info.cc b/source/matrix_free/task_info.cc index 33bee62a3cc6..1fd323d2cfa6 100644 --- a/source/matrix_free/task_info.cc +++ b/source/matrix_free/task_info.cc @@ -423,7 +423,6 @@ namespace internal std::vector blocked_worker( n_blocked_workers); unsigned int worker_index = 0, slice_index = 0; - unsigned int spawn_index = 0; int spawn_index_child = -2; MPICommunication *worker_compr = new (root->allocate_child()) MPICommunication(funct, true); @@ -432,7 +431,6 @@ namespace internal part < partition_row_index.size() - 1; part++) { - const unsigned int spawn_index_new = worker_index; if (part == 0) worker[worker_index] = new (worker_compr->allocate_child()) @@ -474,7 +472,6 @@ namespace internal ExcInternalError()); tbb::task::spawn(*worker[spawn_index_child]); } - spawn_index = spawn_index_new; spawn_index_child = -2; } else From 0f9ec68aaf5b9b3d750b90b5817a3cd689bba555 Mon Sep 17 00:00:00 2001 From: Matthias Maier Date: Sun, 3 Feb 2019 12:06:59 -0600 Subject: [PATCH 056/507] CMake: Bugfix: Guard DEAL_II_HAVE_OPENMP_SIMD test We also have to guard the DEAL_II_HAVE_OPENMP_SIMD test with DEAL_II_ALLOW_PLATFORM_INTROSPECTION. If the latter is set to false our cmake configuration does not attempt to determine any specifics of the unerlying CPU or architecture (and instead relies on the user specifying everything by hand). This is necessary for scenarios where deal.II gets compiled on a different machine than the one it will be run on eventually. In reference to #7663. --- cmake/checks/check_01_cpu_features.cmake | 54 +++++++++++++++--------- 1 file changed, 33 insertions(+), 21 deletions(-) diff --git a/cmake/checks/check_01_cpu_features.cmake b/cmake/checks/check_01_cpu_features.cmake index f69c1ee268f5..c86145d6feff 100644 --- a/cmake/checks/check_01_cpu_features.cmake +++ b/cmake/checks/check_01_cpu_features.cmake @@ -28,8 +28,8 @@ # DEAL_II_HAVE_AVX *) # DEAL_II_HAVE_AVX512 *) # DEAL_II_HAVE_ALTIVEC *) -# DEAL_II_COMPILER_VECTORIZATION_LEVEL # DEAL_II_HAVE_OPENMP_SIMD *) +# DEAL_II_COMPILER_VECTORIZATION_LEVEL # DEAL_II_OPENMP_SIMD_PRAGMA # # *) @@ -245,7 +245,36 @@ IF(DEAL_II_ALLOW_PLATFORM_INTROSPECTION) } " DEAL_II_HAVE_ALTIVEC) -ENDIF() + + # + # OpenMP 4.0 can be used for vectorization. Only the vectorization + # instructions are allowed, the threading must be done through TBB. + # + + # + # Choosing the right compiler flag is a bit of a mess: + # + IF(CMAKE_CXX_COMPILER_ID MATCHES "Intel") + IF("${CMAKE_CXX_COMPILER_VERSION}" VERSION_GREATER "15" ) + SET(_keyword "qopenmp") + ELSEIF("${CMAKE_CXX_COMPILER_VERSION}" VERSION_GREATER "14" ) + SET(_keyword "openmp") + ENDIF() + ELSEIF(CMAKE_CXX_COMPILER_ID MATCHES "Clang") + SET(_keyword "openmp") + ELSE() + SET(_keyword "fopenmp") + ENDIF() + + CHECK_CXX_COMPILER_FLAG("-${_keyword}-simd" DEAL_II_HAVE_OPENMP_SIMD) + +ENDIF() # IF DEAL_II_ALLOW_PLATFORM_INTROSPECTION + + +# +# Choose DEAL_II_COMPILER_VECTORIZATION level depending on AVX support +# (that was autodetected or manually specified). +# IF(DEAL_II_HAVE_AVX512) SET(DEAL_II_COMPILER_VECTORIZATION_LEVEL 3) @@ -263,26 +292,9 @@ ENDIF() # -# OpenMP 4.0 can be used for vectorization. Only the vectorization -# instructions are allowed, the threading must be done through TBB. -# - +# If we have OpenMP SIMD support (i.e. DEAL_II_HAVE_OPENMP_SIMD is true) +# populate DEAL_II_OPENMP_SIMD_PRAGMA. # -# Choosing the right compiler flag is a bit of a mess: -# -IF(CMAKE_CXX_COMPILER_ID MATCHES "Intel") - IF("${CMAKE_CXX_COMPILER_VERSION}" VERSION_GREATER "15" ) - SET(_keyword "qopenmp") - ELSEIF("${CMAKE_CXX_COMPILER_VERSION}" VERSION_GREATER "14" ) - SET(_keyword "openmp") - ENDIF() -ELSEIF(CMAKE_CXX_COMPILER_ID MATCHES "Clang") - SET(_keyword "openmp") -ELSE() - SET(_keyword "fopenmp") -ENDIF() - -CHECK_CXX_COMPILER_FLAG("-${_keyword}-simd" DEAL_II_HAVE_OPENMP_SIMD) SET(DEAL_II_OPENMP_SIMD_PRAGMA " ") IF(DEAL_II_HAVE_OPENMP_SIMD) From 7c3223347d55c131c4daf797b3ba579007e56dca Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Mon, 4 Feb 2019 02:08:20 +0100 Subject: [PATCH 057/507] Fix MPI support for older versions --- include/deal.II/lac/scalapack.h | 3 +++ source/lac/scalapack.cc | 20 ++++++++++++++++---- source/lac/sparsity_tools.cc | 30 ++++++++++++++++-------------- 3 files changed, 35 insertions(+), 18 deletions(-) diff --git a/include/deal.II/lac/scalapack.h b/include/deal.II/lac/scalapack.h index e44ef1ffe48c..ebc212f622fd 100644 --- a/include/deal.II/lac/scalapack.h +++ b/include/deal.II/lac/scalapack.h @@ -203,6 +203,8 @@ class ScaLAPACKMatrix : protected TransposeTable * The user has to ensure that all processes call this with identical @p rank. * The @p rank refers to a process of the MPI communicator used to create the process grid * of the distributed matrix. + * + * @note This function requires MPI-3.0 support */ void copy_from(const LAPACKFullMatrix &matrix, @@ -213,6 +215,7 @@ class ScaLAPACKMatrix : protected TransposeTable * * @note This function should only be used for relatively small matrix * dimensions. It is primarily intended for debugging purposes. + * This function requires MPI-3.0 support */ void copy_to(FullMatrix &matrix) const; diff --git a/source/lac/scalapack.cc b/source/lac/scalapack.cc index 9a5f1bb15735..8651557833d8 100644 --- a/source/lac/scalapack.cc +++ b/source/lac/scalapack.cc @@ -361,18 +361,19 @@ void ScaLAPACKMatrix::copy_from(const LAPACKFullMatrix &B, const unsigned int rank) { +# if DEAL_II_MPI_VERSION_GTE(3, 0) if (n_rows * n_columns == 0) return; const unsigned int this_mpi_process( Utilities::MPI::this_mpi_process(this->grid->mpi_communicator)); -# ifdef DEBUG +# ifdef DEBUG Assert(Utilities::MPI::max(rank, this->grid->mpi_communicator) == rank, ExcMessage("All processes have to call routine with identical rank")); Assert(Utilities::MPI::min(rank, this->grid->mpi_communicator) == rank, ExcMessage("All processes have to call routine with identical rank")); -# endif +# endif // root process has to be active in the grid of A if (this_mpi_process == rank) @@ -484,6 +485,11 @@ ScaLAPACKMatrix::copy_from(const LAPACKFullMatrix &B, MPI_Comm_free(&communicator_B); state = LAPACKSupport::matrix; +# else + (void)B; + (void)rank; + AssertThrow(false, ExcNotImplemented()); +# endif } @@ -528,18 +534,19 @@ void ScaLAPACKMatrix::copy_to(LAPACKFullMatrix &B, const unsigned int rank) const { +# if DEAL_II_MPI_VERSION_GTE(3, 0) if (n_rows * n_columns == 0) return; const unsigned int this_mpi_process( Utilities::MPI::this_mpi_process(this->grid->mpi_communicator)); -# ifdef DEBUG +# ifdef DEBUG Assert(Utilities::MPI::max(rank, this->grid->mpi_communicator) == rank, ExcMessage("All processes have to call routine with identical rank")); Assert(Utilities::MPI::min(rank, this->grid->mpi_communicator) == rank, ExcMessage("All processes have to call routine with identical rank")); -# endif +# endif if (this_mpi_process == rank) { @@ -650,6 +657,11 @@ ScaLAPACKMatrix::copy_to(LAPACKFullMatrix &B, MPI_Group_free(&group_B); if (MPI_COMM_NULL != communicator_B) MPI_Comm_free(&communicator_B); +# else + (void)B; + (void)rank; + AssertThrow(false, ExcNotImplemented()); +# endif } diff --git a/source/lac/sparsity_tools.cc b/source/lac/sparsity_tools.cc index e6698f28aa2c..e04c9e54f4fa 100644 --- a/source/lac/sparsity_tools.cc +++ b/source/lac/sparsity_tools.cc @@ -994,13 +994,14 @@ namespace SparsityTools unsigned int idx = 0; for (const auto &sparsity_line : send_data) { - const int ierr = MPI_Isend(sparsity_line.second.data(), - sparsity_line.second.size(), - DEAL_II_DOF_INDEX_MPI_TYPE, - sparsity_line.first, - 124, - mpi_comm, - &requests[idx++]); + const int ierr = + MPI_Isend(DEAL_II_MPI_CONST_CAST(sparsity_line.second.data()), + sparsity_line.second.size(), + DEAL_II_DOF_INDEX_MPI_TYPE, + sparsity_line.first, + 124, + mpi_comm, + &requests[idx++]); AssertThrowMPI(ierr); } } @@ -1138,13 +1139,14 @@ namespace SparsityTools unsigned int idx = 0; for (const auto &sparsity_line : send_data) { - const int ierr = MPI_Isend(sparsity_line.second.data(), - sparsity_line.second.size(), - DEAL_II_DOF_INDEX_MPI_TYPE, - sparsity_line.first, - 124, - mpi_comm, - &requests[idx++]); + const int ierr = + MPI_Isend(DEAL_II_MPI_CONST_CAST(sparsity_line.second.data()), + sparsity_line.second.size(), + DEAL_II_DOF_INDEX_MPI_TYPE, + sparsity_line.first, + 124, + mpi_comm, + &requests[idx++]); AssertThrowMPI(ierr); } } From ddbb09b90e85afb1f0e1f039500036fec4681e24 Mon Sep 17 00:00:00 2001 From: Stefan Meggendorfer Date: Mon, 4 Feb 2019 14:56:57 +0100 Subject: [PATCH 058/507] MappingQGeneric: use of MatrixFree only for higher order elements --- source/fe/mapping_q_generic.cc | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/source/fe/mapping_q_generic.cc b/source/fe/mapping_q_generic.cc index 4dfaf968dc6c..d7d8e96d88f2 100644 --- a/source/fe/mapping_q_generic.cc +++ b/source/fe/mapping_q_generic.cc @@ -730,6 +730,10 @@ MappingQGeneric::InternalData::initialize( tensor_product_quadrature = q.is_tensor_product(); + // use of MatrixFree only for higher order elements + if (polynomial_degree < 2) + tensor_product_quadrature = false; + if (dim > 1) { // find out if the one-dimensional formula is the same From 4112d6b0a296ce9bdaa8c4639faa15c41a41ef82 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Mon, 4 Feb 2019 17:12:06 +0100 Subject: [PATCH 059/507] More output files for matrix_free/dof_info_01/2 --- ...=true.with_p4est=true.mpirun=1.output.vec0 | 148 ++++++++++++++++++ ...=true.with_p4est=true.mpirun=1.output.vec1 | 64 ++++++++ ...=true.with_p4est=true.mpirun=1.output.vec3 | 19 +++ ...=true.with_p4est=true.mpirun=1.output.vec0 | 148 ++++++++++++++++++ ...=true.with_p4est=true.mpirun=1.output.vec1 | 64 ++++++++ ...=true.with_p4est=true.mpirun=1.output.vec3 | 19 +++ 6 files changed, 462 insertions(+) create mode 100644 tests/matrix_free/dof_info_01.with_mpi=true.with_p4est=true.mpirun=1.output.vec0 create mode 100644 tests/matrix_free/dof_info_01.with_mpi=true.with_p4est=true.mpirun=1.output.vec1 create mode 100644 tests/matrix_free/dof_info_01.with_mpi=true.with_p4est=true.mpirun=1.output.vec3 create mode 100644 tests/matrix_free/dof_info_02.with_mpi=true.with_p4est=true.mpirun=1.output.vec0 create mode 100644 tests/matrix_free/dof_info_02.with_mpi=true.with_p4est=true.mpirun=1.output.vec1 create mode 100644 tests/matrix_free/dof_info_02.with_mpi=true.with_p4est=true.mpirun=1.output.vec3 diff --git a/tests/matrix_free/dof_info_01.with_mpi=true.with_p4est=true.mpirun=1.output.vec0 b/tests/matrix_free/dof_info_01.with_mpi=true.with_p4est=true.mpirun=1.output.vec0 new file mode 100644 index 000000000000..f2547ea76df9 --- /dev/null +++ b/tests/matrix_free/dof_info_01.with_mpi=true.with_p4est=true.mpirun=1.output.vec0 @@ -0,0 +1,148 @@ + +DEAL:0:2d::Testing FE_Q<2>(1) +DEAL:0:2d::Cell: 0 +DEAL:0:2d:: 18 19 +DEAL:0:2d:: 16 17 18 19 +DEAL:0:2d::Cell: 1 +DEAL:0:2d:: 7 19 +DEAL:0:2d:: 6 17 19 20 +DEAL:0:2d::Cell: 2 +DEAL:0:2d:: 18 19 21 22 +DEAL:0:2d:: 18 19 21 22 +DEAL:0:2d::Cell: 3 +DEAL:0:2d:: 7 19 22 +DEAL:0:2d:: 7 19 20 22 +DEAL:0:2d::Cell: 4 +DEAL:0:2d:: 2 7 +DEAL:0:2d:: 0 6 7 8 +DEAL:0:2d::Cell: 5 +DEAL:0:2d:: 21 22 23 24 +DEAL:0:2d:: 21 22 23 24 +DEAL:0:2d::Cell: 6 +DEAL:0:2d:: 7 9 22 24 +DEAL:0:2d:: 7 22 24 25 +DEAL:0:2d::Cell: 7 +DEAL:0:2d:: 9 10 23 24 +DEAL:0:2d:: 10 23 24 26 +DEAL:0:2d::Cell: 8 +DEAL:0:2d:: 7 9 10 24 +DEAL:0:2d:: 9 24 25 26 +DEAL:0:2d::Cell: 9 +DEAL:0:2d:: 2 7 9 +DEAL:0:2d:: 2 7 8 9 +DEAL:0:2d::Cell: 10 +DEAL:0:2d:: 2 3 +DEAL:0:2d:: 0 1 2 3 +DEAL:0:2d::Cell: 11 +DEAL:0:2d:: 9 10 11 12 +DEAL:0:2d:: 9 10 11 12 +DEAL:0:2d::Cell: 12 +DEAL:0:2d:: 2 4 9 12 +DEAL:0:2d:: 2 9 12 13 +DEAL:0:2d::Cell: 13 +DEAL:0:2d:: 11 12 14 15 +DEAL:0:2d:: 11 12 14 15 +DEAL:0:2d::Cell: 14 +DEAL:0:2d:: 2 4 12 15 +DEAL:0:2d:: 4 12 13 15 +DEAL:0:2d::Cell: 15 +DEAL:0:2d:: 2 3 4 5 +DEAL:0:2d:: 2 3 4 5 +DEAL:0:2d::Testing FE_Q<2>(1) +DEAL:0:2d::Cell: 0 +DEAL:0:2d:: 18 19 +DEAL:0:2d:: 16 17 18 19 +DEAL:0:2d::Cell: 1 +DEAL:0:2d:: 7 19 +DEAL:0:2d:: 6 17 19 20 +DEAL:0:2d::Cell: 2 +DEAL:0:2d:: 18 19 21 22 +DEAL:0:2d:: 18 19 21 22 +DEAL:0:2d::Cell: 3 +DEAL:0:2d:: 7 19 22 +DEAL:0:2d:: 7 19 20 22 +DEAL:0:2d::Cell: 4 +DEAL:0:2d:: 2 7 +DEAL:0:2d:: 0 6 7 8 +DEAL:0:2d::Cell: 5 +DEAL:0:2d:: 21 22 23 24 +DEAL:0:2d:: 21 22 23 24 +DEAL:0:2d::Cell: 6 +DEAL:0:2d:: 7 9 22 24 +DEAL:0:2d:: 7 22 24 25 +DEAL:0:2d::Cell: 7 +DEAL:0:2d:: 9 10 23 24 +DEAL:0:2d:: 10 23 24 26 +DEAL:0:2d::Cell: 8 +DEAL:0:2d:: 7 9 10 24 +DEAL:0:2d:: 9 24 25 26 +DEAL:0:2d::Cell: 9 +DEAL:0:2d:: 2 7 9 +DEAL:0:2d:: 2 7 8 9 +DEAL:0:2d::Cell: 10 +DEAL:0:2d:: 2 3 +DEAL:0:2d:: 0 1 2 3 +DEAL:0:2d::Cell: 11 +DEAL:0:2d:: 9 10 11 12 +DEAL:0:2d:: 9 10 11 12 +DEAL:0:2d::Cell: 12 +DEAL:0:2d:: 2 4 9 12 +DEAL:0:2d:: 2 9 12 13 +DEAL:0:2d::Cell: 13 +DEAL:0:2d:: 11 12 14 15 +DEAL:0:2d:: 11 12 14 15 +DEAL:0:2d::Cell: 14 +DEAL:0:2d:: 2 4 12 15 +DEAL:0:2d:: 4 12 13 15 +DEAL:0:2d::Cell: 15 +DEAL:0:2d:: 2 3 4 5 +DEAL:0:2d:: 2 3 4 5 +DEAL:0:2d::Testing FE_Q<2>(1) +DEAL:0:2d::Cell: 0 +DEAL:0:2d:: 2 3 +DEAL:0:2d:: 0 1 2 3 +DEAL:0:2d::Cell: 1 +DEAL:0:2d:: 3 5 +DEAL:0:2d:: 1 3 4 5 +DEAL:0:2d::Cell: 2 +DEAL:0:2d:: 2 3 6 7 +DEAL:0:2d:: 2 3 6 7 +DEAL:0:2d::Cell: 3 +DEAL:0:2d:: 3 5 7 8 +DEAL:0:2d:: 3 5 7 8 +DEAL:0:2d::Cell: 4 +DEAL:0:2d:: 5 10 +DEAL:0:2d:: 4 5 9 10 +DEAL:0:2d::Cell: 5 +DEAL:0:2d:: 10 12 +DEAL:0:2d:: 9 10 11 12 +DEAL:0:2d::Cell: 6 +DEAL:0:2d:: 5 8 10 13 +DEAL:0:2d:: 5 8 10 13 +DEAL:0:2d::Cell: 7 +DEAL:0:2d:: 10 12 13 14 +DEAL:0:2d:: 10 12 13 14 +DEAL:0:2d::Cell: 8 +DEAL:0:2d:: 6 7 15 16 +DEAL:0:2d:: 6 7 15 16 +DEAL:0:2d::Cell: 9 +DEAL:0:2d:: 7 8 16 17 +DEAL:0:2d:: 7 8 16 17 +DEAL:0:2d::Cell: 10 +DEAL:0:2d:: 15 16 18 19 +DEAL:0:2d:: 15 16 18 19 +DEAL:0:2d::Cell: 11 +DEAL:0:2d:: 16 17 19 20 +DEAL:0:2d:: 16 17 19 20 +DEAL:0:2d::Cell: 12 +DEAL:0:2d:: 8 13 17 21 +DEAL:0:2d:: 8 13 17 21 +DEAL:0:2d::Cell: 13 +DEAL:0:2d:: 13 14 21 22 +DEAL:0:2d:: 13 14 21 22 +DEAL:0:2d::Cell: 14 +DEAL:0:2d:: 17 20 21 23 +DEAL:0:2d:: 17 20 21 23 +DEAL:0:2d::Cell: 15 +DEAL:0:2d:: 21 22 23 24 +DEAL:0:2d:: 21 22 23 24 diff --git a/tests/matrix_free/dof_info_01.with_mpi=true.with_p4est=true.mpirun=1.output.vec1 b/tests/matrix_free/dof_info_01.with_mpi=true.with_p4est=true.mpirun=1.output.vec1 new file mode 100644 index 000000000000..96b8f2351b79 --- /dev/null +++ b/tests/matrix_free/dof_info_01.with_mpi=true.with_p4est=true.mpirun=1.output.vec1 @@ -0,0 +1,64 @@ + +DEAL:0:2d::Testing FE_Q<2>(1) +DEAL:0:2d::Cell: 0 +DEAL:0:2d:: 7 18 19 +DEAL:0:2d:: 6 16 17 18 19 20 +DEAL:0:2d::Cell: 1 +DEAL:0:2d:: 7 18 19 21 22 +DEAL:0:2d:: 7 18 19 20 21 22 +DEAL:0:2d::Cell: 2 +DEAL:0:2d:: 2 7 21 22 23 24 +DEAL:0:2d:: 0 6 7 8 21 22 23 24 +DEAL:0:2d::Cell: 3 +DEAL:0:2d:: 7 9 10 22 23 24 +DEAL:0:2d:: 7 10 22 23 24 25 26 +DEAL:0:2d::Cell: 4 +DEAL:0:2d:: 2 7 9 10 24 +DEAL:0:2d:: 2 7 8 9 24 25 26 +DEAL:0:2d::Cell: 5 +DEAL:0:2d:: 2 3 9 10 11 12 +DEAL:0:2d:: 0 1 2 3 9 10 11 12 +DEAL:0:2d::Cell: 6 +DEAL:0:2d:: 2 4 9 11 12 14 15 +DEAL:0:2d:: 2 9 11 12 13 14 15 +DEAL:0:2d::Cell: 7 +DEAL:0:2d:: 2 3 4 5 12 15 +DEAL:0:2d:: 2 3 4 5 12 13 15 +DEAL:0:2d::Testing FE_Q<2>(1) +DEAL:0:2d::Cell: 0 +DEAL:0:2d:: 7 18 19 21 22 +DEAL:0:2d:: 6 7 16 17 18 19 20 21 22 +DEAL:0:2d::Cell: 1 +DEAL:0:2d:: 2 7 9 10 21 22 23 24 +DEAL:0:2d:: 0 6 7 8 10 21 22 23 24 25 26 +DEAL:0:2d::Cell: 2 +DEAL:0:2d:: 2 3 7 9 10 11 12 24 +DEAL:0:2d:: 0 1 2 3 7 8 9 10 11 12 24 25 26 +DEAL:0:2d::Cell: 3 +DEAL:0:2d:: 2 3 4 5 9 11 12 14 15 +DEAL:0:2d:: 2 3 4 5 9 11 12 13 14 15 +DEAL:0:2d::Testing FE_Q<2>(1) +DEAL:0:2d::Cell: 0 +DEAL:0:2d:: 2 3 5 +DEAL:0:2d:: 0 1 2 3 4 5 +DEAL:0:2d::Cell: 1 +DEAL:0:2d:: 2 3 5 6 7 8 +DEAL:0:2d:: 2 3 5 6 7 8 +DEAL:0:2d::Cell: 2 +DEAL:0:2d:: 5 10 12 +DEAL:0:2d:: 4 5 9 10 11 12 +DEAL:0:2d::Cell: 3 +DEAL:0:2d:: 5 8 10 12 13 14 +DEAL:0:2d:: 5 8 10 12 13 14 +DEAL:0:2d::Cell: 4 +DEAL:0:2d:: 6 7 8 15 16 17 +DEAL:0:2d:: 6 7 8 15 16 17 +DEAL:0:2d::Cell: 5 +DEAL:0:2d:: 15 16 17 18 19 20 +DEAL:0:2d:: 15 16 17 18 19 20 +DEAL:0:2d::Cell: 6 +DEAL:0:2d:: 8 13 14 17 21 22 +DEAL:0:2d:: 8 13 14 17 21 22 +DEAL:0:2d::Cell: 7 +DEAL:0:2d:: 17 20 21 22 23 24 +DEAL:0:2d:: 17 20 21 22 23 24 diff --git a/tests/matrix_free/dof_info_01.with_mpi=true.with_p4est=true.mpirun=1.output.vec3 b/tests/matrix_free/dof_info_01.with_mpi=true.with_p4est=true.mpirun=1.output.vec3 new file mode 100644 index 000000000000..2d2edc3e8920 --- /dev/null +++ b/tests/matrix_free/dof_info_01.with_mpi=true.with_p4est=true.mpirun=1.output.vec3 @@ -0,0 +1,19 @@ + +DEAL:0:2d::Testing FE_Q<2>(1) +DEAL:0:2d::Cell: 0 +DEAL:0:2d:: 2 7 9 10 18 19 21 22 23 24 +DEAL:0:2d:: 0 6 7 8 10 16 17 18 19 20 21 22 23 24 25 26 +DEAL:0:2d::Cell: 1 +DEAL:0:2d:: 2 3 4 5 7 9 10 11 12 14 15 24 +DEAL:0:2d:: 0 1 2 3 4 5 7 8 9 10 11 12 13 14 15 24 25 26 +DEAL:0:2d::Testing FE_Q<2>(1) +DEAL:0:2d::Cell: 0 +DEAL:0:2d:: 2 3 4 5 7 9 10 11 12 14 15 18 19 21 22 23 24 +DEAL:0:2d:: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 +DEAL:0:2d::Testing FE_Q<2>(1) +DEAL:0:2d::Cell: 0 +DEAL:0:2d:: 2 3 5 6 7 8 10 12 13 14 +DEAL:0:2d:: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 +DEAL:0:2d::Cell: 1 +DEAL:0:2d:: 6 7 8 13 14 15 16 17 18 19 20 21 22 23 24 +DEAL:0:2d:: 6 7 8 13 14 15 16 17 18 19 20 21 22 23 24 diff --git a/tests/matrix_free/dof_info_02.with_mpi=true.with_p4est=true.mpirun=1.output.vec0 b/tests/matrix_free/dof_info_02.with_mpi=true.with_p4est=true.mpirun=1.output.vec0 new file mode 100644 index 000000000000..f4dfc08d467d --- /dev/null +++ b/tests/matrix_free/dof_info_02.with_mpi=true.with_p4est=true.mpirun=1.output.vec0 @@ -0,0 +1,148 @@ + +DEAL:0:2d::Testing FESystem<2>[FE_Q<2>(1)^2] +DEAL:0:2d::Cell: 0 +DEAL:0:2d:: 36 37 38 39 +DEAL:0:2d:: 32 33 34 35 36 37 38 39 +DEAL:0:2d::Cell: 1 +DEAL:0:2d:: 14 15 38 39 +DEAL:0:2d:: 12 13 34 35 38 39 40 41 +DEAL:0:2d::Cell: 2 +DEAL:0:2d:: 36 37 38 39 42 43 44 45 +DEAL:0:2d:: 36 37 38 39 42 43 44 45 +DEAL:0:2d::Cell: 3 +DEAL:0:2d:: 14 15 38 39 44 45 +DEAL:0:2d:: 14 15 38 39 40 41 44 45 +DEAL:0:2d::Cell: 4 +DEAL:0:2d:: 4 5 14 15 +DEAL:0:2d:: 0 1 12 13 14 15 16 17 +DEAL:0:2d::Cell: 5 +DEAL:0:2d:: 42 43 44 45 46 47 48 49 +DEAL:0:2d:: 42 43 44 45 46 47 48 49 +DEAL:0:2d::Cell: 6 +DEAL:0:2d:: 14 15 18 19 44 45 48 49 +DEAL:0:2d:: 14 15 44 45 48 49 50 51 +DEAL:0:2d::Cell: 7 +DEAL:0:2d:: 18 19 20 21 46 47 48 49 +DEAL:0:2d:: 20 21 46 47 48 49 52 53 +DEAL:0:2d::Cell: 8 +DEAL:0:2d:: 14 15 18 19 20 21 48 49 +DEAL:0:2d:: 18 19 48 49 50 51 52 53 +DEAL:0:2d::Cell: 9 +DEAL:0:2d:: 4 5 14 15 18 19 +DEAL:0:2d:: 4 5 14 15 16 17 18 19 +DEAL:0:2d::Cell: 10 +DEAL:0:2d:: 4 5 6 7 +DEAL:0:2d:: 0 1 2 3 4 5 6 7 +DEAL:0:2d::Cell: 11 +DEAL:0:2d:: 18 19 20 21 22 23 24 25 +DEAL:0:2d:: 18 19 20 21 22 23 24 25 +DEAL:0:2d::Cell: 12 +DEAL:0:2d:: 4 5 8 9 18 19 24 25 +DEAL:0:2d:: 4 5 18 19 24 25 26 27 +DEAL:0:2d::Cell: 13 +DEAL:0:2d:: 22 23 24 25 28 29 30 31 +DEAL:0:2d:: 22 23 24 25 28 29 30 31 +DEAL:0:2d::Cell: 14 +DEAL:0:2d:: 4 5 8 9 24 25 30 31 +DEAL:0:2d:: 8 9 24 25 26 27 30 31 +DEAL:0:2d::Cell: 15 +DEAL:0:2d:: 4 5 6 7 8 9 10 11 +DEAL:0:2d:: 4 5 6 7 8 9 10 11 +DEAL:0:2d::Testing FESystem<2>[FE_Q<2>(1)^2] +DEAL:0:2d::Cell: 0 +DEAL:0:2d:: 36 37 38 39 +DEAL:0:2d:: 32 33 34 35 36 37 38 39 +DEAL:0:2d::Cell: 1 +DEAL:0:2d:: 14 15 38 39 +DEAL:0:2d:: 12 13 34 35 38 39 40 41 +DEAL:0:2d::Cell: 2 +DEAL:0:2d:: 36 37 38 39 42 43 44 45 +DEAL:0:2d:: 36 37 38 39 42 43 44 45 +DEAL:0:2d::Cell: 3 +DEAL:0:2d:: 14 15 38 39 44 45 +DEAL:0:2d:: 14 15 38 39 40 41 44 45 +DEAL:0:2d::Cell: 4 +DEAL:0:2d:: 4 5 14 15 +DEAL:0:2d:: 0 1 12 13 14 15 16 17 +DEAL:0:2d::Cell: 5 +DEAL:0:2d:: 42 43 44 45 46 47 48 49 +DEAL:0:2d:: 42 43 44 45 46 47 48 49 +DEAL:0:2d::Cell: 6 +DEAL:0:2d:: 14 15 18 19 44 45 48 49 +DEAL:0:2d:: 14 15 44 45 48 49 50 51 +DEAL:0:2d::Cell: 7 +DEAL:0:2d:: 18 19 20 21 46 47 48 49 +DEAL:0:2d:: 20 21 46 47 48 49 52 53 +DEAL:0:2d::Cell: 8 +DEAL:0:2d:: 14 15 18 19 20 21 48 49 +DEAL:0:2d:: 18 19 48 49 50 51 52 53 +DEAL:0:2d::Cell: 9 +DEAL:0:2d:: 4 5 14 15 18 19 +DEAL:0:2d:: 4 5 14 15 16 17 18 19 +DEAL:0:2d::Cell: 10 +DEAL:0:2d:: 4 5 6 7 +DEAL:0:2d:: 0 1 2 3 4 5 6 7 +DEAL:0:2d::Cell: 11 +DEAL:0:2d:: 18 19 20 21 22 23 24 25 +DEAL:0:2d:: 18 19 20 21 22 23 24 25 +DEAL:0:2d::Cell: 12 +DEAL:0:2d:: 4 5 8 9 18 19 24 25 +DEAL:0:2d:: 4 5 18 19 24 25 26 27 +DEAL:0:2d::Cell: 13 +DEAL:0:2d:: 22 23 24 25 28 29 30 31 +DEAL:0:2d:: 22 23 24 25 28 29 30 31 +DEAL:0:2d::Cell: 14 +DEAL:0:2d:: 4 5 8 9 24 25 30 31 +DEAL:0:2d:: 8 9 24 25 26 27 30 31 +DEAL:0:2d::Cell: 15 +DEAL:0:2d:: 4 5 6 7 8 9 10 11 +DEAL:0:2d:: 4 5 6 7 8 9 10 11 +DEAL:0:2d::Testing FESystem<2>[FE_Q<2>(1)^2] +DEAL:0:2d::Cell: 0 +DEAL:0:2d:: 4 5 6 7 +DEAL:0:2d:: 0 1 2 3 4 5 6 7 +DEAL:0:2d::Cell: 1 +DEAL:0:2d:: 6 7 10 11 +DEAL:0:2d:: 2 3 6 7 8 9 10 11 +DEAL:0:2d::Cell: 2 +DEAL:0:2d:: 4 5 6 7 12 13 14 15 +DEAL:0:2d:: 4 5 6 7 12 13 14 15 +DEAL:0:2d::Cell: 3 +DEAL:0:2d:: 6 7 10 11 14 15 16 17 +DEAL:0:2d:: 6 7 10 11 14 15 16 17 +DEAL:0:2d::Cell: 4 +DEAL:0:2d:: 10 11 20 21 +DEAL:0:2d:: 8 9 10 11 18 19 20 21 +DEAL:0:2d::Cell: 5 +DEAL:0:2d:: 20 21 24 25 +DEAL:0:2d:: 18 19 20 21 22 23 24 25 +DEAL:0:2d::Cell: 6 +DEAL:0:2d:: 10 11 16 17 20 21 26 27 +DEAL:0:2d:: 10 11 16 17 20 21 26 27 +DEAL:0:2d::Cell: 7 +DEAL:0:2d:: 20 21 24 25 26 27 28 29 +DEAL:0:2d:: 20 21 24 25 26 27 28 29 +DEAL:0:2d::Cell: 8 +DEAL:0:2d:: 12 13 14 15 30 31 32 33 +DEAL:0:2d:: 12 13 14 15 30 31 32 33 +DEAL:0:2d::Cell: 9 +DEAL:0:2d:: 14 15 16 17 32 33 34 35 +DEAL:0:2d:: 14 15 16 17 32 33 34 35 +DEAL:0:2d::Cell: 10 +DEAL:0:2d:: 30 31 32 33 36 37 38 39 +DEAL:0:2d:: 30 31 32 33 36 37 38 39 +DEAL:0:2d::Cell: 11 +DEAL:0:2d:: 32 33 34 35 38 39 40 41 +DEAL:0:2d:: 32 33 34 35 38 39 40 41 +DEAL:0:2d::Cell: 12 +DEAL:0:2d:: 16 17 26 27 34 35 42 43 +DEAL:0:2d:: 16 17 26 27 34 35 42 43 +DEAL:0:2d::Cell: 13 +DEAL:0:2d:: 26 27 28 29 42 43 44 45 +DEAL:0:2d:: 26 27 28 29 42 43 44 45 +DEAL:0:2d::Cell: 14 +DEAL:0:2d:: 34 35 40 41 42 43 46 47 +DEAL:0:2d:: 34 35 40 41 42 43 46 47 +DEAL:0:2d::Cell: 15 +DEAL:0:2d:: 42 43 44 45 46 47 48 49 +DEAL:0:2d:: 42 43 44 45 46 47 48 49 diff --git a/tests/matrix_free/dof_info_02.with_mpi=true.with_p4est=true.mpirun=1.output.vec1 b/tests/matrix_free/dof_info_02.with_mpi=true.with_p4est=true.mpirun=1.output.vec1 new file mode 100644 index 000000000000..3dc9c8420fbb --- /dev/null +++ b/tests/matrix_free/dof_info_02.with_mpi=true.with_p4est=true.mpirun=1.output.vec1 @@ -0,0 +1,64 @@ + +DEAL:0:2d::Testing FESystem<2>[FE_Q<2>(1)^2] +DEAL:0:2d::Cell: 0 +DEAL:0:2d:: 14 15 36 37 38 39 +DEAL:0:2d:: 12 13 32 33 34 35 36 37 38 39 40 41 +DEAL:0:2d::Cell: 1 +DEAL:0:2d:: 14 15 36 37 38 39 42 43 44 45 +DEAL:0:2d:: 14 15 36 37 38 39 40 41 42 43 44 45 +DEAL:0:2d::Cell: 2 +DEAL:0:2d:: 4 5 14 15 42 43 44 45 46 47 48 49 +DEAL:0:2d:: 0 1 12 13 14 15 16 17 42 43 44 45 46 47 48 49 +DEAL:0:2d::Cell: 3 +DEAL:0:2d:: 14 15 18 19 20 21 44 45 46 47 48 49 +DEAL:0:2d:: 14 15 20 21 44 45 46 47 48 49 50 51 52 53 +DEAL:0:2d::Cell: 4 +DEAL:0:2d:: 4 5 14 15 18 19 20 21 48 49 +DEAL:0:2d:: 4 5 14 15 16 17 18 19 48 49 50 51 52 53 +DEAL:0:2d::Cell: 5 +DEAL:0:2d:: 4 5 6 7 18 19 20 21 22 23 24 25 +DEAL:0:2d:: 0 1 2 3 4 5 6 7 18 19 20 21 22 23 24 25 +DEAL:0:2d::Cell: 6 +DEAL:0:2d:: 4 5 8 9 18 19 22 23 24 25 28 29 30 31 +DEAL:0:2d:: 4 5 18 19 22 23 24 25 26 27 28 29 30 31 +DEAL:0:2d::Cell: 7 +DEAL:0:2d:: 4 5 6 7 8 9 10 11 24 25 30 31 +DEAL:0:2d:: 4 5 6 7 8 9 10 11 24 25 26 27 30 31 +DEAL:0:2d::Testing FESystem<2>[FE_Q<2>(1)^2] +DEAL:0:2d::Cell: 0 +DEAL:0:2d:: 14 15 36 37 38 39 42 43 44 45 +DEAL:0:2d:: 12 13 14 15 32 33 34 35 36 37 38 39 40 41 42 43 44 45 +DEAL:0:2d::Cell: 1 +DEAL:0:2d:: 4 5 14 15 18 19 20 21 42 43 44 45 46 47 48 49 +DEAL:0:2d:: 0 1 12 13 14 15 16 17 20 21 42 43 44 45 46 47 48 49 50 51 52 53 +DEAL:0:2d::Cell: 2 +DEAL:0:2d:: 4 5 6 7 14 15 18 19 20 21 22 23 24 25 48 49 +DEAL:0:2d:: 0 1 2 3 4 5 6 7 14 15 16 17 18 19 20 21 22 23 24 25 48 49 50 51 52 53 +DEAL:0:2d::Cell: 3 +DEAL:0:2d:: 4 5 6 7 8 9 10 11 18 19 22 23 24 25 28 29 30 31 +DEAL:0:2d:: 4 5 6 7 8 9 10 11 18 19 22 23 24 25 26 27 28 29 30 31 +DEAL:0:2d::Testing FESystem<2>[FE_Q<2>(1)^2] +DEAL:0:2d::Cell: 0 +DEAL:0:2d:: 4 5 6 7 10 11 +DEAL:0:2d:: 0 1 2 3 4 5 6 7 8 9 10 11 +DEAL:0:2d::Cell: 1 +DEAL:0:2d:: 4 5 6 7 10 11 12 13 14 15 16 17 +DEAL:0:2d:: 4 5 6 7 10 11 12 13 14 15 16 17 +DEAL:0:2d::Cell: 2 +DEAL:0:2d:: 10 11 20 21 24 25 +DEAL:0:2d:: 8 9 10 11 18 19 20 21 22 23 24 25 +DEAL:0:2d::Cell: 3 +DEAL:0:2d:: 10 11 16 17 20 21 24 25 26 27 28 29 +DEAL:0:2d:: 10 11 16 17 20 21 24 25 26 27 28 29 +DEAL:0:2d::Cell: 4 +DEAL:0:2d:: 12 13 14 15 16 17 30 31 32 33 34 35 +DEAL:0:2d:: 12 13 14 15 16 17 30 31 32 33 34 35 +DEAL:0:2d::Cell: 5 +DEAL:0:2d:: 30 31 32 33 34 35 36 37 38 39 40 41 +DEAL:0:2d:: 30 31 32 33 34 35 36 37 38 39 40 41 +DEAL:0:2d::Cell: 6 +DEAL:0:2d:: 16 17 26 27 28 29 34 35 42 43 44 45 +DEAL:0:2d:: 16 17 26 27 28 29 34 35 42 43 44 45 +DEAL:0:2d::Cell: 7 +DEAL:0:2d:: 34 35 40 41 42 43 44 45 46 47 48 49 +DEAL:0:2d:: 34 35 40 41 42 43 44 45 46 47 48 49 diff --git a/tests/matrix_free/dof_info_02.with_mpi=true.with_p4est=true.mpirun=1.output.vec3 b/tests/matrix_free/dof_info_02.with_mpi=true.with_p4est=true.mpirun=1.output.vec3 new file mode 100644 index 000000000000..f8507beb6ea3 --- /dev/null +++ b/tests/matrix_free/dof_info_02.with_mpi=true.with_p4est=true.mpirun=1.output.vec3 @@ -0,0 +1,19 @@ + +DEAL:0:2d::Testing FESystem<2>[FE_Q<2>(1)^2] +DEAL:0:2d::Cell: 0 +DEAL:0:2d:: 4 5 14 15 18 19 20 21 36 37 38 39 42 43 44 45 46 47 48 49 +DEAL:0:2d:: 0 1 12 13 14 15 16 17 20 21 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 +DEAL:0:2d::Cell: 1 +DEAL:0:2d:: 4 5 6 7 8 9 10 11 14 15 18 19 20 21 22 23 24 25 28 29 30 31 48 49 +DEAL:0:2d:: 0 1 2 3 4 5 6 7 8 9 10 11 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 48 49 50 51 52 53 +DEAL:0:2d::Testing FESystem<2>[FE_Q<2>(1)^2] +DEAL:0:2d::Cell: 0 +DEAL:0:2d:: 4 5 6 7 8 9 10 11 14 15 18 19 20 21 22 23 24 25 28 29 30 31 36 37 38 39 42 43 44 45 46 47 48 49 +DEAL:0:2d:: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 +DEAL:0:2d::Testing FESystem<2>[FE_Q<2>(1)^2] +DEAL:0:2d::Cell: 0 +DEAL:0:2d:: 4 5 6 7 10 11 12 13 14 15 16 17 20 21 24 25 26 27 28 29 +DEAL:0:2d:: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 +DEAL:0:2d::Cell: 1 +DEAL:0:2d:: 12 13 14 15 16 17 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 +DEAL:0:2d:: 12 13 14 15 16 17 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 From f7f359106346926819a4102f25b2223ef8b21ba2 Mon Sep 17 00:00:00 2001 From: Matthias Maier Date: Mon, 4 Feb 2019 10:55:39 -0600 Subject: [PATCH 060/507] example/step-4: Return the correct return value This commit reverts a stray change that should have probably never made it into 0e12f6f87a0b84fadd8df629f55da42a8494ce8f --- examples/step-4/step-4.cc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/examples/step-4/step-4.cc b/examples/step-4/step-4.cc index a63c86d40e5a..a4b0aa53907b 100644 --- a/examples/step-4/step-4.cc +++ b/examples/step-4/step-4.cc @@ -186,7 +186,7 @@ double RightHandSide::value(const Point &p, for (unsigned int i = 0; i < dim; ++i) return_value += 4.0 * std::pow(p(i), 4.0); - return 1.; // return_value; + return return_value; } From bb5fb7de671a7700ecef591d597acb696c5b31d4 Mon Sep 17 00:00:00 2001 From: Rene Gassmoeller Date: Mon, 4 Feb 2019 13:12:12 -0800 Subject: [PATCH 061/507] Fix serialization of XDMFEntry class --- include/deal.II/base/data_out_base.h | 5 +- tests/serialization/xdmf_entry.cc | 74 +++++++++++++++++++++++++++ tests/serialization/xdmf_entry.output | 36 +++++++++++++ 3 files changed, 114 insertions(+), 1 deletion(-) create mode 100644 tests/serialization/xdmf_entry.cc create mode 100644 tests/serialization/xdmf_entry.output diff --git a/include/deal.II/base/data_out_base.h b/include/deal.II/base/data_out_base.h index 8e05a6aacbdd..2a6da9fd79e1 100644 --- a/include/deal.II/base/data_out_base.h +++ b/include/deal.II/base/data_out_base.h @@ -26,6 +26,9 @@ #include +// To be able to serialize XDMFEntry +#include + #include #include #include @@ -3599,7 +3602,7 @@ class XDMFEntry serialize(Archive &ar, const unsigned int /*version*/) { ar &valid &h5_sol_filename &h5_mesh_filename &entry_time &num_nodes - &num_cells &dimension &attribute_dims; + &num_cells &dimension &space_dimension &attribute_dims; } /** diff --git a/tests/serialization/xdmf_entry.cc b/tests/serialization/xdmf_entry.cc new file mode 100644 index 000000000000..2a3c3b5948e6 --- /dev/null +++ b/tests/serialization/xdmf_entry.cc @@ -0,0 +1,74 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + +// check serialization for XDMFEntry + +#include + +#include "serialization.h" + +void +test() +{ + const std::string mesh_filename = "mesh.h5"; + const std::string solution_filename = "solution.h5"; + + const double time = 0.5; + const unsigned int nodes = 128; + const unsigned int cells = 16; + const unsigned int dim = 2; + const unsigned int spacedim = 3; + + XDMFEntry entry1( + mesh_filename, solution_filename, time, nodes, cells, dim, spacedim); + XDMFEntry entry2; + + // save data to archive + std::ostringstream oss; + { + boost::archive::text_oarchive oa(oss, boost::archive::no_header); + oa << entry1; + // archive and stream closed when destructors are called + } + deallog << oss.str() << std::endl; + + // verify correctness of the serialization + { + std::istringstream iss(oss.str()); + boost::archive::text_iarchive ia(iss, boost::archive::no_header); + ia >> entry2; + } + + deallog << "XDMFEntry before serialization: " << std::endl + << std::endl + << entry1.get_xdmf_content(0) << std::endl; + + deallog << "XDMFEntry after de-serialization: " << std::endl + << std::endl + << entry2.get_xdmf_content(0) << std::endl; +} + + +int +main() +{ + initlog(); + deallog << std::setprecision(3); + + test(); + + deallog << "OK" << std::endl; +} diff --git a/tests/serialization/xdmf_entry.output b/tests/serialization/xdmf_entry.output new file mode 100644 index 000000000000..fdeaefeca94a --- /dev/null +++ b/tests/serialization/xdmf_entry.output @@ -0,0 +1,36 @@ + +DEAL::0 0 1 11 solution.h5 7 mesh.h5 5.00000000000000000e-01 128 16 2 3 0 0 0 0 + +DEAL::XDMFEntry before serialization: +DEAL:: +DEAL:: + + +DEAL::XDMFEntry after de-serialization: +DEAL:: +DEAL:: + + +DEAL::OK From 461fb7721cfdd7a2989bbacd71a7076d727e5eeb Mon Sep 17 00:00:00 2001 From: David Wells Date: Sun, 3 Feb 2019 22:35:36 -0500 Subject: [PATCH 062/507] Cleanup the Vector::thread_loop_partitioner logic. It was previously possible to, in one function call, either set up the partitioner multiple times or for inappropriately small vectors. This commit cleans up the way we handle the partitioner in multiple places so that, when possible, vectors share partitioners and do not set up partitioners if they are too small. --- include/deal.II/lac/vector.h | 20 +++- include/deal.II/lac/vector.templates.h | 123 +++++++++++++------------ 2 files changed, 81 insertions(+), 62 deletions(-) diff --git a/include/deal.II/lac/vector.h b/include/deal.II/lac/vector.h index 2dadf1da5e10..b413f686b129 100644 --- a/include/deal.II/lac/vector.h +++ b/include/deal.II/lac/vector.h @@ -986,6 +986,22 @@ class Vector : public Subscriptor */ AlignedVector values; + /** + * Convenience function used at the end of initialization or + * reinitialization. Resets (if necessary) the loop partitioner to the + * correct state, based on its current state and the length of the vector. + */ + void + maybe_reset_thread_partitioner(); + + /** + * Actual implementation of the reinit functions. + */ + void + do_reinit(const size_type new_size, + const bool omit_zeroing_entries, + const bool reset_partitioner); + /** * For parallel loops with TBB, this member variable stores the affinity * information of loops. @@ -1275,7 +1291,8 @@ template inline void Vector::swap(Vector &v) { - std::swap(values, v.values); + values.swap(v.values); + std::swap(thread_loop_partitioner, v.thread_loop_partitioner); } @@ -1300,6 +1317,7 @@ Vector::load(Archive &ar, const unsigned int) // the load stuff again from the archive ar &static_cast(*this); ar &values; + maybe_reset_thread_partitioner(); } #endif diff --git a/include/deal.II/lac/vector.templates.h b/include/deal.II/lac/vector.templates.h index 87c126c8b8b4..bc98f73050e5 100644 --- a/include/deal.II/lac/vector.templates.h +++ b/include/deal.II/lac/vector.templates.h @@ -83,6 +83,11 @@ namespace internal copy_petsc_vector(const PETScWrappers::VectorBase &v, ::dealii::Vector & out) { + if (v.size() == 0) + { + out.reinit(0); + return; + } // Create a sequential PETSc vector and then copy over the entries into // the deal.II vector. Vec sequential_vector; @@ -125,10 +130,7 @@ namespace internal template Vector::Vector(const PETScWrappers::VectorBase &v) { - if (v.size() != 0) - { - internal::copy_petsc_vector(v, *this); - } + internal::copy_petsc_vector(v, *this); } #endif @@ -164,6 +166,8 @@ Vector::Vector(const TrilinosWrappers::MPI::Vector &v) AssertThrow(ierr == 0, ExcTrilinosError(ierr)); std::copy(start_ptr[0], start_ptr[0] + size(), begin()); + + maybe_reset_thread_partitioner(); } } @@ -177,7 +181,6 @@ Vector::operator=(const Vector &v) if (PointerComparison::equal(this, &v)) return *this; - thread_loop_partitioner = v.thread_loop_partitioner; if (size() != v.size()) reinit(v, true); @@ -201,7 +204,6 @@ template inline Vector & Vector::operator=(const Vector &v) { - thread_loop_partitioner = v.thread_loop_partitioner; if (size() != v.size()) reinit(v, true); @@ -221,41 +223,7 @@ template inline void Vector::reinit(const size_type n, const bool omit_zeroing_entries) { - const std::size_t old_size = size(); - - // avoid allocating if the new size is not larger than the old size - if (n <= size()) - { - thread_loop_partitioner = - std::make_shared(); - if (n == 0) - { - values.clear(); - } - else if (n != size()) - values.resize_fast(n); - - if (!omit_zeroing_entries) - values.fill(); - return; - } - - // otherwise size() < n and we must allocate - AlignedVector new_values; - new_values.resize_fast(n); - if (!omit_zeroing_entries) - new_values.fill(); - new_values.swap(values); - - if (old_size != size()) - { - // only reset the partitioner if we actually expect a significant vector - // size - if (size() >= - 4 * internal::VectorImplementation::minimum_parallel_grain_size) - thread_loop_partitioner = - std::make_shared(); - } + do_reinit(n, omit_zeroing_entries, true); } @@ -264,26 +232,9 @@ template inline void Vector::grow_or_shrink(const size_type n) { - const std::size_t old_size = size(); - if (n == 0) - { - values.clear(); - thread_loop_partitioner = - std::make_shared(); - return; - } - values.resize(n); - if (old_size != n) - { - // only reset the partitioner if we actually expect a significant vector - // size - if (size() >= - 4 * internal::VectorImplementation::minimum_parallel_grain_size) - thread_loop_partitioner = - std::make_shared(); - } + maybe_reset_thread_partitioner(); } @@ -294,9 +245,8 @@ void Vector::reinit(const Vector &v, const bool omit_zeroing_entries) { + do_reinit(v.size(), omit_zeroing_entries, false); thread_loop_partitioner = v.thread_loop_partitioner; - - reinit(v.size(), omit_zeroing_entries); } @@ -1046,6 +996,57 @@ Vector::memory_consumption() const } + +template +void +Vector::maybe_reset_thread_partitioner() +{ + if (size() >= 4 * internal::VectorImplementation::minimum_parallel_grain_size) + { + if (thread_loop_partitioner == nullptr) + thread_loop_partitioner = + std::make_shared(); + } + else + thread_loop_partitioner.reset(); +} + + + +template +void +Vector::do_reinit(const size_type new_size, + const bool omit_zeroing_entries, + const bool reset_partitioner) +{ + if (new_size <= size()) + { + if (new_size == 0) + { + values.clear(); + } + else + { + values.resize_fast(new_size); + if (!omit_zeroing_entries) + values.fill(); + } + } + else + { + // otherwise size() < new_size and we must allocate + AlignedVector new_values; + new_values.resize_fast(new_size); + if (!omit_zeroing_entries) + new_values.fill(); + new_values.swap(values); + } + + if (reset_partitioner) + maybe_reset_thread_partitioner(); +} + + DEAL_II_NAMESPACE_CLOSE #endif From a0ad3a186d4507726fd2b36650999b623d4cd97c Mon Sep 17 00:00:00 2001 From: Wolfgang Bangerth Date: Mon, 4 Feb 2019 07:51:52 -0700 Subject: [PATCH 063/507] Update documentation of some VectorTools functions. --- include/deal.II/numerics/vector_tools.h | 147 +++++++++++++++++++++--- 1 file changed, 134 insertions(+), 13 deletions(-) diff --git a/include/deal.II/numerics/vector_tools.h b/include/deal.II/numerics/vector_tools.h index 20b2d9b74d6b..ec060968c17b 100644 --- a/include/deal.II/numerics/vector_tools.h +++ b/include/deal.II/numerics/vector_tools.h @@ -2163,17 +2163,50 @@ namespace VectorTools * vector is deleted. This function is for the case of a scalar finite * element. * - * It is worth noting that delta functions do not exist in reality, and - * consequently, using this function does not model any real situation. This - * is, because no real object is able to focus an infinite force density - * at an infinitesimally small part of the domain. Rather, all real - * devices will spread out the force over a finite area. Only if this - * area is so small that it cannot be resolved by any mesh does it make - * sense to model the situation in a way that uses a delta function with - * the same overall force. On the other hand, a situation that is probably - * more fruitfully simulated with a delta function is the electric potential - * of a point source; in this case, the solution is known to have a - * logarithmic singularity (in 2d) or a $\frac{1}{r}$ singularity (in 3d), + * This function is typically used in one of these two contexts: + * - Let's say you want to solve the same kind of problems many times + * over, with different values for right hand sides or coefficients, + * and then evaluate the solution at the same point every time. You + * could do this by calling VectorTools::point_value() after each + * solve, or you could realize that to evaluate the solution $u_h$ + * at a point $p$, you could rearrange operations like this: + * @f{align*}{ + * u_h(p) &= \sum_j U_j \varphi_j(p) = \sum_j U_j F_j + * \\ &= U \cdot F + * @f} + * with the vector as defined above. In other words, point evaluation + * can be achieved with just a single vector-vector product, and the + * vector $F$ can be computed once and for all and reused + * for each solve, without having to go through the mesh every time + * to find out which cell (and where in the cell) the point $p$ is + * located. + * - This function is also useful if you wanted to compute the Green's + * function for the problem you are solving. This is because the + * Green's function $G(x,p)$ is defined by + * @f{align*}{ + * L G(x,p) &= \delta(x-p)$ + * @f} + * where $L$ is the differential operator of your problem. The discrete + * version then requires computing the right hand side vector + * $F_i = \int_\Omega \varphi_i(x) \delta(x-p)$, which is exactly + * the vector computed by the current function. + * + * While maybe not relevant for documenting what this + * function does, it may be interesting to note that delta functions + * do not exist in reality, and consequently, using this function + * does not model any real situation. This is, because no real + * object is able to focus an infinite force density at an + * infinitesimally small part of the domain (rather, all real + * devices will spread out the force over a finite area); nor is it + * possible to measure values at individual points (but all + * measurements will somehow be averaged over small areas). Only if + * this area is so small that it cannot be resolved by any mesh does + * it make sense to model the situation in a way that uses a delta + * function with the same overall force or sensitivity. On the other + * hand, a situation that is probably more fruitfully simulated with + * a delta function is the electric potential of a point source; in + * this case, the solution is known to have a logarithmic + * singularity (in 2d) or a $\frac{1}{r}$ singularity (in 3d), * neither of which is bounded. * * Mathematically, the use of delta functions typically leads to exact @@ -2610,13 +2643,24 @@ namespace VectorTools * point, and return the (vector) value of this function through the last * argument. * - * This function uses a Q1-mapping for the cell the point is evaluated + * This function uses a $Q_1$-mapping for the cell the point is evaluated * in. If you need to evaluate using a different mapping (for example when * using curved boundaries), use the point_difference() function that takes * a mapping. * + * This function is not particularly cheap. This is because it first + * needs to find which cell a given point is in, then find the point + * on the reference cell that matches the given evaluation point, + * and then evaluate the shape functions there. You probably do not + * want to use this function to evaluate the solution at many + * points. For this kind of application, the FEFieldFunction class + * offers at least some optimizations. On the other hand, if you + * want to evaluate many solutions at the same point, you may + * want to look at the VectorTools::create_point_source_vector() + * function. + * * @note If the cell in which the point is found is not locally owned, an - * exception of type VectorTools::ExcPointNotAvailableHere is thrown. + * exception of type VectorTools::ExcPointNotAvailableHere is thrown. * * @note This function needs to find the cell within which a point lies, * and this can only be done up to a certain numerical tolerance of course. @@ -2670,6 +2714,17 @@ namespace VectorTools * using curved boundaries), use the point_difference() function that takes * a mapping. * + * This function is not particularly cheap. This is because it first + * needs to find which cell a given point is in, then find the point + * on the reference cell that matches the given evaluation point, + * and then evaluate the shape functions there. You probably do not + * want to use this function to evaluate the solution at many + * points. For this kind of application, the FEFieldFunction class + * offers at least some optimizations. On the other hand, if you + * want to evaluate many solutions at the same point, you may + * want to look at the VectorTools::create_point_source_vector() + * function. + * * This function is used in the "Possibilities for extensions" part of the * results section of * @ref step_3 "step-3". @@ -2726,6 +2781,17 @@ namespace VectorTools * Compared with the other function of the same name, this function uses an * arbitrary mapping to evaluate the point value. * + * This function is not particularly cheap. This is because it first + * needs to find which cell a given point is in, then find the point + * on the reference cell that matches the given evaluation point, + * and then evaluate the shape functions there. You probably do not + * want to use this function to evaluate the solution at many + * points. For this kind of application, the FEFieldFunction class + * offers at least some optimizations. On the other hand, if you + * want to evaluate many solutions at the same point, you may + * want to look at the VectorTools::create_point_source_vector() + * function. + * * @note If the cell in which the point is found is not locally owned, an * exception of type VectorTools::ExcPointNotAvailableHere is thrown. * @@ -2781,6 +2847,17 @@ namespace VectorTools * Compared with the other function of the same name, this function uses an * arbitrary mapping to evaluate the difference. * + * This function is not particularly cheap. This is because it first + * needs to find which cell a given point is in, then find the point + * on the reference cell that matches the given evaluation point, + * and then evaluate the shape functions there. You probably do not + * want to use this function to evaluate the solution at many + * points. For this kind of application, the FEFieldFunction class + * offers at least some optimizations. On the other hand, if you + * want to evaluate many solutions at the same point, you may + * want to look at the VectorTools::create_point_source_vector() + * function. + * * @note If the cell in which the point is found is not locally owned, an * exception of type VectorTools::ExcPointNotAvailableHere is thrown. * @@ -2834,6 +2911,17 @@ namespace VectorTools * This is a wrapper function using a Q1-mapping for cell boundaries to call * the other point_gradient() function. * + * This function is not particularly cheap. This is because it first + * needs to find which cell a given point is in, then find the point + * on the reference cell that matches the given evaluation point, + * and then evaluate the shape functions there. You probably do not + * want to use this function to evaluate the solution at many + * points. For this kind of application, the FEFieldFunction class + * offers at least some optimizations. On the other hand, if you + * want to evaluate many solutions at the same point, you may + * want to look at the VectorTools::create_point_source_vector() + * function. + * * @note If the cell in which the point is found is not locally owned, an * exception of type VectorTools::ExcPointNotAvailableHere is thrown. * @@ -2887,6 +2975,17 @@ namespace VectorTools * Compared with the other function of the same name, this is a wrapper * function using a Q1-mapping for cells. * + * This function is not particularly cheap. This is because it first + * needs to find which cell a given point is in, then find the point + * on the reference cell that matches the given evaluation point, + * and then evaluate the shape functions there. You probably do not + * want to use this function to evaluate the solution at many + * points. For this kind of application, the FEFieldFunction class + * offers at least some optimizations. On the other hand, if you + * want to evaluate many solutions at the same point, you may + * want to look at the VectorTools::create_point_source_vector() + * function. + * * @note If the cell in which the point is found is not locally owned, an * exception of type VectorTools::ExcPointNotAvailableHere is thrown. * @@ -2936,6 +3035,17 @@ namespace VectorTools * Compared with the other function of the same name, this function uses an * arbitrary mapping for evaluation. * + * This function is not particularly cheap. This is because it first + * needs to find which cell a given point is in, then find the point + * on the reference cell that matches the given evaluation point, + * and then evaluate the shape functions there. You probably do not + * want to use this function to evaluate the solution at many + * points. For this kind of application, the FEFieldFunction class + * offers at least some optimizations. On the other hand, if you + * want to evaluate many solutions at the same point, you may + * want to look at the VectorTools::create_point_source_vector() + * function. + * * @note If the cell in which the point is found is not locally owned, an * exception of type VectorTools::ExcPointNotAvailableHere is thrown. * @@ -2991,6 +3101,17 @@ namespace VectorTools * Compared with the other function of the same name, this function uses an * arbitrary mapping for evaluation. * + * This function is not particularly cheap. This is because it first + * needs to find which cell a given point is in, then find the point + * on the reference cell that matches the given evaluation point, + * and then evaluate the shape functions there. You probably do not + * want to use this function to evaluate the solution at many + * points. For this kind of application, the FEFieldFunction class + * offers at least some optimizations. On the other hand, if you + * want to evaluate many solutions at the same point, you may + * want to look at the VectorTools::create_point_source_vector() + * function. + * * @note If the cell in which the point is found is not locally owned, an * exception of type VectorTools::ExcPointNotAvailableHere is thrown. * From f809d49183e94d267d5ec0a71ffd6c4ff328adfb Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Tue, 5 Feb 2019 16:02:13 -0700 Subject: [PATCH 064/507] [CI]: add Jenkins.mark Add a separate Jenkins pipeline that runs in a few seconds to set the commit status to pending. This is needed as Jenkins only starts setting a commit status when the normal jobs start running and not when they are in the queue. This can lead to a) accidental merges before we test things and b) repeated /rebuild triggers. --- Jenkinsfile | 3 +++ contrib/ci/Jenkinsfile.mark | 51 +++++++++++++++++++++++++++++++++++++ 2 files changed, 54 insertions(+) create mode 100644 contrib/ci/Jenkinsfile.mark diff --git a/Jenkinsfile b/Jenkinsfile index 09370d793b2a..9e3e48848fc8 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -42,6 +42,9 @@ pipeline { steps { + // we are finally running, so we can mark the 'ready' context from Jenkinsfile.mark as success: + githubNotify context: 'ready', description: ':-)', status: 'SUCCESS' + // We can not use 'indent' because we are missing the master branch: // "fatal: ambiguous argument 'master': unknown revision or path" sh ''' diff --git a/contrib/ci/Jenkinsfile.mark b/contrib/ci/Jenkinsfile.mark new file mode 100644 index 000000000000..c10638a5133d --- /dev/null +++ b/contrib/ci/Jenkinsfile.mark @@ -0,0 +1,51 @@ +#!groovy + +// This Jenkinsfile is used to mark jobs as "pending" as quickly as +// possible. The other longer running jobs only set the status to pending once +// they start running. +// +// See https://jenkins.tjhei.info/job/dealii-mark/ for details. + +/* +Settings to apply inside Jenkins: + - discover pull requests (remove branches/master) + - Strategy: merged PR + - enable "Disable GitHub Multibranch Status Plugin" + - trigger build on pull request comment: .* /rebuild.* (without space) + - Jenkinsfile: choose contrib/ci/Jenkinsfile.mark + - scan: every 4 hours + - discard: 5+ items + - docker label: small +*/ + +pipeline +{ + agent none + + stages + { + stage("check") + { + steps + { + githubNotify context: 'ready', description: 'please be patient, testers are spinning up...', status: 'PENDING' + sh ''' + wget -q -O - https://api.github.com/repos/dealii/dealii/issues/${CHANGE_ID}/labels | grep 'ready to test' || \ + { echo "This commit will only be tested when it has the label 'ready to test'. Trigger a rebuild by adding a comment that contains '/rebuild'..."; exit 1; } + ''' + } + post + { + failure + { + githubNotify context: 'ready', description: 'need ready to test label and /rebuild', status: 'PENDING' + script + { + currentBuild.result='NOT_BUILT' + } + } + } + } + + } +} From a1e4ce9bbe4a92b71b09add8df2efd75626c44ed Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Tue, 5 Feb 2019 16:08:43 -0700 Subject: [PATCH 065/507] set agent --- contrib/ci/Jenkinsfile.mark | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/contrib/ci/Jenkinsfile.mark b/contrib/ci/Jenkinsfile.mark index c10638a5133d..37aa15478cd7 100644 --- a/contrib/ci/Jenkinsfile.mark +++ b/contrib/ci/Jenkinsfile.mark @@ -20,7 +20,13 @@ Settings to apply inside Jenkins: pipeline { - agent none + agent + { + docker + { + image 'dealii/indent' + } + } stages { From 881e97e1a440ca834a4c0d7cfa86dba4c4a65a42 Mon Sep 17 00:00:00 2001 From: Martin Kronbichler Date: Tue, 5 Feb 2019 19:06:12 +0100 Subject: [PATCH 066/507] Fix initialization of LA::d::Vector in multigrid. --- .../deal.II/multigrid/mg_transfer.templates.h | 59 ++- .../parallel_multigrid_adaptive_08.cc | 423 ++++++++++++++++++ ...4est=true.with_lapack=true.mpirun=3.output | 47 ++ 3 files changed, 498 insertions(+), 31 deletions(-) create mode 100644 tests/matrix_free/parallel_multigrid_adaptive_08.cc create mode 100644 tests/matrix_free/parallel_multigrid_adaptive_08.with_mpi=true.with_p4est=true.with_lapack=true.mpirun=3.output diff --git a/include/deal.II/multigrid/mg_transfer.templates.h b/include/deal.II/multigrid/mg_transfer.templates.h index 439f2dda3085..c207fe593ed2 100644 --- a/include/deal.II/multigrid/mg_transfer.templates.h +++ b/include/deal.II/multigrid/mg_transfer.templates.h @@ -104,34 +104,6 @@ namespace internal } } - /** - * Adjust vectors on all levels to correct size. Here, we just count the - * numbers of degrees of freedom on each level and @p reinit each level - * vector to this length. - */ - template - void - reinit_vector(const dealii::DoFHandler &mg_dof, - const std::vector &, - MGLevelObject> &v) - { - const parallel::Triangulation *tria = - (dynamic_cast *>( - &mg_dof.get_triangulation())); - - for (unsigned int level = v.min_level(); level <= v.max_level(); ++level) - { - if (v[level].size() != mg_dof.locally_owned_mg_dofs(level).size() || - v[level].local_size() != - mg_dof.locally_owned_mg_dofs(level).n_elements()) - v[level].reinit(mg_dof.locally_owned_mg_dofs(level), - tria != nullptr ? tria->get_communicator() : - MPI_COMM_SELF); - else - v[level] = 0.; - } - } - #ifdef DEAL_II_WITH_TRILINOS /** @@ -453,12 +425,37 @@ MGLevelGlobalTransfer>::copy_to_mg( solution_transfer ? solution_copy_indices_level_mine : copy_indices_level_mine; + (void)mg_dof_handler; + AssertIndexRange(dst.max_level(), mg_dof_handler.get_triangulation().n_global_levels()); AssertIndexRange(dst.min_level(), dst.max_level() + 1); - internal::MGTransfer::reinit_vector(mg_dof_handler, - component_to_block_map, - dst); + + for (unsigned int level = dst.min_level(); level <= dst.max_level(); ++level) + if (dst[level].size() != mg_dof_handler.n_dofs(level) || + dst[level].local_size() != + mg_dof_handler.locally_owned_mg_dofs(level).n_elements()) + { + // In case a ghosted level vector has been initialized, we can simply + // use that as a template for the vector partitioning. If not, we + // resort to the locally owned range of the dof handler. + if (level <= ghosted_level_vector.max_level() && + ghosted_level_vector[level].size() == mg_dof_handler.n_dofs(level)) + dst[level].reinit(ghosted_level_vector[level], false); + else + { + const parallel::Triangulation *tria = + (dynamic_cast *>( + &mg_dof_handler.get_triangulation())); + dst[level].reinit(mg_dof_handler.locally_owned_mg_dofs(level), + tria != nullptr ? tria->get_communicator() : + MPI_COMM_SELF); + } + } + else if ((perform_plain_copy == false && + perform_renumbered_plain_copy == false) || + level != dst.max_level()) + dst[level] = 0; if (perform_plain_copy) { diff --git a/tests/matrix_free/parallel_multigrid_adaptive_08.cc b/tests/matrix_free/parallel_multigrid_adaptive_08.cc new file mode 100644 index 000000000000..4fb6c2b0c433 --- /dev/null +++ b/tests/matrix_free/parallel_multigrid_adaptive_08.cc @@ -0,0 +1,423 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2016 - 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + + +// similar to parallel_multigrid_adaptive_02 but without using a separate +// transfer class that builds the appropriate vectors. Furthermore, we want to +// avoid setting some vectors to zero in the cell loop. Rather, +// MatrixFreeOperators::LaplaceOperator::adjust_ghost_range_if_necessary() +// will do that - or rather a variant of that, given that we want to modify +// the cell loop of the LaplaceOperator class and provide our own. This forces +// us to reimplement a few things, but all ideas are the same as in the +// matrix-free operators. + +#include + +#include + +#include + +#include +#include + +#include +#include + +#include +#include +#include +#include + +#include +#include +#include + +#include +#include +#include +#include +#include +#include + +#include + +#include "../tests.h" + +std::ofstream logfile("output"); + +using namespace dealii::MatrixFreeOperators; + + +template +class MyLaplaceOperator : public MatrixFreeOperators::LaplaceOperator< + dim, + fe_degree, + fe_degree + 1, + 1, + LinearAlgebra::distributed::Vector> +{ +public: + void + initialize(std::shared_ptr> data, + const MGConstrainedDoFs & mg_constrained_dofs, + const unsigned int level) + { + MatrixFreeOperators::Base>:: + initialize(data, + mg_constrained_dofs, + level, + std::vector({0})); + + std::vector interface_indices; + mg_constrained_dofs.get_refinement_edge_indices(level).fill_index_vector( + interface_indices); + vmult_edge_constrained_indices.clear(); + vmult_edge_constrained_indices.reserve(interface_indices.size()); + vmult_edge_constrained_values.resize(interface_indices.size()); + const IndexSet &locally_owned = + this->data->get_dof_handler(0).locally_owned_mg_dofs(level); + for (unsigned int i = 0; i < interface_indices.size(); ++i) + if (locally_owned.is_element(interface_indices[i])) + vmult_edge_constrained_indices.push_back( + locally_owned.index_within_set(interface_indices[i])); + } + + void + initialize(std::shared_ptr> data, + const std::vector & mask = {}) + { + MatrixFreeOperators::Base>:: + initialize(data, mask); + } + + + void + vmult(LinearAlgebra::distributed::Vector & dst, + const LinearAlgebra::distributed::Vector &src) const + { + adjust_ghost_range_if_necessary(src); + adjust_ghost_range_if_necessary(dst); + + for (unsigned int i = 0; i < vmult_edge_constrained_indices.size(); ++i) + { + vmult_edge_constrained_values[i] = + src.local_element(vmult_edge_constrained_indices[i]); + const_cast &>(src) + .local_element(vmult_edge_constrained_indices[i]) = 0.; + } + + // zero dst within the loop + this->data->cell_loop( + &MyLaplaceOperator::local_apply, this, dst, src, true); + + for (auto i : this->data->get_constrained_dofs(0)) + dst.local_element(i) = src.local_element(i); + for (unsigned int i = 0; i < vmult_edge_constrained_indices.size(); ++i) + { + dst.local_element(vmult_edge_constrained_indices[i]) = + vmult_edge_constrained_values[i]; + const_cast &>(src) + .local_element(vmult_edge_constrained_indices[i]) = + vmult_edge_constrained_values[i]; + } + } + +private: + void + local_apply(const MatrixFree & data, + LinearAlgebra::distributed::Vector & dst, + const LinearAlgebra::distributed::Vector &src, + const std::pair &cell_range) const + { + FEEvaluation phi(data); + + for (unsigned int cell = cell_range.first; cell < cell_range.second; ++cell) + { + phi.reinit(cell); + phi.gather_evaluate(src, false, true); + for (unsigned int q = 0; q < phi.n_q_points; ++q) + phi.submit_gradient(phi.get_gradient(q), q); + phi.integrate_scatter(false, true, dst); + } + } + + void + adjust_ghost_range_if_necessary( + const LinearAlgebra::distributed::Vector &vec) const + { + if (vec.get_partitioner().get() == + this->data->get_dof_info(0).vector_partitioner.get()) + return; + + Assert(vec.get_partitioner()->local_size() == + this->data->get_dof_info(0).vector_partitioner->local_size(), + ExcMessage("The vector passed to the vmult() function does not have " + "the correct size for compatibility with MatrixFree.")); + LinearAlgebra::distributed::Vector copy_vec(vec); + const_cast &>(vec).reinit( + this->data->get_dof_info(0).vector_partitioner); + const_cast &>(vec) + .copy_locally_owned_data_from(copy_vec); + } + + std::vector vmult_edge_constrained_indices; + + mutable std::vector vmult_edge_constrained_values; +}; + + + +template +class MGCoarseIterative + : public MGCoarseGridBase> +{ +public: + MGCoarseIterative() + {} + + void + initialize(const MatrixType &matrix) + { + coarse_matrix = &matrix; + } + + virtual void + operator()(const unsigned int level, + LinearAlgebra::distributed::Vector & dst, + const LinearAlgebra::distributed::Vector &src) const + { + ReductionControl solver_control(1e4, 1e-50, 1e-10); + SolverCG> solver_coarse( + solver_control); + solver_coarse.solve(*coarse_matrix, dst, src, PreconditionIdentity()); + } + + const MatrixType *coarse_matrix; +}; + + + +template +void +do_test(const DoFHandler &dof) +{ + deallog << "Testing " << dof.get_fe().get_name(); + deallog << std::endl; + deallog << "Number of degrees of freedom: " << dof.n_dofs() << std::endl; + + IndexSet locally_relevant_dofs; + DoFTools::extract_locally_relevant_dofs(dof, locally_relevant_dofs); + + // Dirichlet BC + Functions::ZeroFunction zero_function; + std::map *> dirichlet_boundary; + dirichlet_boundary[0] = &zero_function; + + // fine-level constraints + AffineConstraints constraints; + constraints.reinit(locally_relevant_dofs); + DoFTools::make_hanging_node_constraints(dof, constraints); + VectorTools::interpolate_boundary_values(dof, + dirichlet_boundary, + constraints); + constraints.close(); + + // level constraints: + MGConstrainedDoFs mg_constrained_dofs; + mg_constrained_dofs.initialize(dof, dirichlet_boundary); + + MappingQ mapping(fe_degree + 1); + + MyLaplaceOperator fine_matrix; + std::shared_ptr> fine_level_data( + new MatrixFree()); + + typename MatrixFree::AdditionalData fine_level_additional_data; + fine_level_additional_data.tasks_parallel_scheme = + MatrixFree::AdditionalData::none; + fine_level_additional_data.tasks_block_size = 3; + fine_level_data->reinit(mapping, + dof, + constraints, + QGauss<1>(n_q_points_1d), + fine_level_additional_data); + + fine_matrix.initialize(fine_level_data); + fine_matrix.compute_diagonal(); + + + LinearAlgebra::distributed::Vector in, sol; + fine_matrix.initialize_dof_vector(in); + fine_matrix.initialize_dof_vector(sol); + + // set constant rhs vector + { + // this is to make it consistent with parallel_multigrid_adaptive.cc + AffineConstraints hanging_node_constraints; + hanging_node_constraints.reinit(locally_relevant_dofs); + DoFTools::make_hanging_node_constraints(dof, hanging_node_constraints); + hanging_node_constraints.close(); + + for (unsigned int i = 0; i < in.local_size(); ++i) + if (!hanging_node_constraints.is_constrained( + in.get_partitioner()->local_to_global(i))) + in.local_element(i) = 1.; + } + + // set up multigrid in analogy to step-37 + using LevelMatrixType = MyLaplaceOperator; + + MGLevelObject mg_matrices; + MGLevelObject> mg_level_data; + mg_matrices.resize(0, dof.get_triangulation().n_global_levels() - 1); + mg_level_data.resize(0, dof.get_triangulation().n_global_levels() - 1); + for (unsigned int level = 0; + level < dof.get_triangulation().n_global_levels(); + ++level) + { + typename MatrixFree::AdditionalData mg_additional_data; + mg_additional_data.tasks_parallel_scheme = + MatrixFree::AdditionalData::none; + mg_additional_data.tasks_block_size = 3; + mg_additional_data.level_mg_handler = level; + + AffineConstraints level_constraints; + IndexSet relevant_dofs; + DoFTools::extract_locally_relevant_level_dofs(dof, level, relevant_dofs); + level_constraints.reinit(relevant_dofs); + level_constraints.add_lines( + mg_constrained_dofs.get_boundary_indices(level)); + level_constraints.close(); + + mg_level_data[level].reinit(mapping, + dof, + level_constraints, + QGauss<1>(n_q_points_1d), + mg_additional_data); + mg_matrices[level].initialize(std::make_shared>( + mg_level_data[level]), + mg_constrained_dofs, + level); + mg_matrices[level].compute_diagonal(); + } + MGLevelObject> mg_interface_matrices; + mg_interface_matrices.resize(0, + dof.get_triangulation().n_global_levels() - 1); + for (unsigned int level = 0; + level < dof.get_triangulation().n_global_levels(); + ++level) + mg_interface_matrices[level].initialize(mg_matrices[level]); + + MGTransferMatrixFree mg_transfer(mg_constrained_dofs); + mg_transfer.build(dof); + + MGCoarseIterative mg_coarse; + mg_coarse.initialize(mg_matrices[0]); + + typedef PreconditionChebyshev> + SMOOTHER; + MGSmootherPrecondition> + mg_smoother; + + MGLevelObject smoother_data; + smoother_data.resize(0, dof.get_triangulation().n_global_levels() - 1); + for (unsigned int level = 0; + level < dof.get_triangulation().n_global_levels(); + ++level) + { + smoother_data[level].smoothing_range = 15.; + smoother_data[level].degree = 5; + smoother_data[level].eig_cg_n_iterations = 15; + smoother_data[level].preconditioner = + mg_matrices[level].get_matrix_diagonal_inverse(); + } + mg_smoother.initialize(mg_matrices, smoother_data); + + mg::Matrix> mg_matrix(mg_matrices); + mg::Matrix> mg_interface( + mg_interface_matrices); + + Multigrid> mg( + dof, mg_matrix, mg_coarse, mg_transfer, mg_smoother, mg_smoother); + mg.set_edge_matrices(mg_interface, mg_interface); + PreconditionMG, + MGTransferMatrixFree> + preconditioner(dof, mg, mg_transfer); + + { + // avoid output from inner (coarse-level) solver + deallog.depth_file(3); + + ReductionControl control(30, 1e-20, 1e-7); + SolverCG> solver(control); + solver.solve(fine_matrix, sol, in, preconditioner); + } + + fine_matrix.clear(); + for (unsigned int level = 0; + level < dof.get_triangulation().n_global_levels(); + ++level) + mg_matrices[level].clear(); +} + + + +template +void +test() +{ + parallel::distributed::Triangulation tria( + MPI_COMM_WORLD, + Triangulation::limit_level_difference_at_vertices, + parallel::distributed::Triangulation::construct_multigrid_hierarchy); + GridGenerator::hyper_cube(tria); + tria.refine_global(6 - dim); + const unsigned int n_runs = fe_degree == 1 ? 6 - dim : 5 - dim; + for (unsigned int i = 0; i < n_runs; ++i) + { + for (typename Triangulation::active_cell_iterator cell = + tria.begin_active(); + cell != tria.end(); + ++cell) + if (cell->is_locally_owned() && + ((cell->center().norm() < 0.5 && + (cell->level() < 5 || cell->center().norm() > 0.45)) || + (dim == 2 && cell->center().norm() > 1.2))) + cell->set_refine_flag(); + tria.execute_coarsening_and_refinement(); + FE_Q fe(fe_degree); + DoFHandler dof(tria); + dof.distribute_dofs(fe); + dof.distribute_mg_dofs(fe); + + do_test(dof); + } +} + + + +int +main(int argc, char **argv) +{ + Utilities::MPI::MPI_InitFinalize mpi_init(argc, argv, 1); + mpi_initlog(true); + + test<2, 2>(); +} diff --git a/tests/matrix_free/parallel_multigrid_adaptive_08.with_mpi=true.with_p4est=true.with_lapack=true.mpirun=3.output b/tests/matrix_free/parallel_multigrid_adaptive_08.with_mpi=true.with_p4est=true.with_lapack=true.mpirun=3.output new file mode 100644 index 000000000000..f00e1a40b439 --- /dev/null +++ b/tests/matrix_free/parallel_multigrid_adaptive_08.with_mpi=true.with_p4est=true.with_lapack=true.mpirun=3.output @@ -0,0 +1,47 @@ + +DEAL::Testing FE_Q<2>(2) +DEAL::Number of degrees of freedom: 1935 +DEAL:cg::Starting value 43.0929 +DEAL:cg:cg::Starting value 2.63785 +DEAL:cg:cg::Convergence step 1 value 0.00000 +DEAL:cg:cg::Starting value 0.000574845 +DEAL:cg:cg::Convergence step 1 value 0.00000 +DEAL:cg:cg::Starting value 4.62010e-05 +DEAL:cg:cg::Convergence step 1 value 6.77626e-21 +DEAL:cg:cg::Starting value 6.27180e-07 +DEAL:cg:cg::Convergence step 1 value 1.05879e-22 +DEAL:cg:cg::Starting value 3.19916e-08 +DEAL:cg:cg::Convergence step 1 value 0.00000 +DEAL:cg::Convergence step 5 value 2.10775e-06 +DEAL::Testing FE_Q<2>(2) +DEAL::Number of degrees of freedom: 3403 +DEAL:cg::Starting value 55.4346 +DEAL:cg:cg::Starting value 3.96150 +DEAL:cg:cg::Convergence step 1 value 0.00000 +DEAL:cg:cg::Starting value 0.00121318 +DEAL:cg:cg::Convergence step 1 value 0.00000 +DEAL:cg:cg::Starting value 9.44668e-05 +DEAL:cg:cg::Convergence step 1 value 1.35525e-20 +DEAL:cg:cg::Starting value 1.80128e-06 +DEAL:cg:cg::Convergence step 1 value 2.11758e-22 +DEAL:cg:cg::Starting value 1.21766e-07 +DEAL:cg:cg::Convergence step 1 value 2.64698e-23 +DEAL:cg:cg::Starting value 5.04178e-09 +DEAL:cg:cg::Convergence step 1 value 0.00000 +DEAL:cg::Convergence step 6 value 4.24128e-07 +DEAL::Testing FE_Q<2>(2) +DEAL::Number of degrees of freedom: 8417 +DEAL:cg::Starting value 87.1149 +DEAL:cg:cg::Starting value 9.09582 +DEAL:cg:cg::Convergence step 1 value 0.00000 +DEAL:cg:cg::Starting value 0.00294550 +DEAL:cg:cg::Convergence step 1 value 0.00000 +DEAL:cg:cg::Starting value 0.000242151 +DEAL:cg:cg::Convergence step 1 value 0.00000 +DEAL:cg:cg::Starting value 3.21426e-06 +DEAL:cg:cg::Convergence step 1 value 0.00000 +DEAL:cg:cg::Starting value 1.60211e-07 +DEAL:cg:cg::Convergence step 1 value 0.00000 +DEAL:cg:cg::Starting value 3.38024e-09 +DEAL:cg:cg::Convergence step 1 value 4.13590e-25 +DEAL:cg::Convergence step 6 value 2.56705e-07 From 797969ed01c7f685b8495e77f34ea7bf33ce9abb Mon Sep 17 00:00:00 2001 From: Martin Kronbichler Date: Tue, 5 Feb 2019 19:08:36 +0100 Subject: [PATCH 067/507] Add changelog. --- doc/news/changes/minor/20190205MartinKronbichler | 7 +++++++ 1 file changed, 7 insertions(+) create mode 100644 doc/news/changes/minor/20190205MartinKronbichler diff --git a/doc/news/changes/minor/20190205MartinKronbichler b/doc/news/changes/minor/20190205MartinKronbichler new file mode 100644 index 000000000000..711b9588dfb0 --- /dev/null +++ b/doc/news/changes/minor/20190205MartinKronbichler @@ -0,0 +1,7 @@ +Fixed: MGLevelGlobalTransfer::copy_to_mg would initialize the level vectors +without ghosts. When combined with Chebyshev smoother and a DiagonalMatrix as +well as specific matrix-free loops, this could lead to ghosted vectors in +places where they were not supposed to be ghosted, leading to exceptions. This +is now fixed. +
+(Martin Kronbichler, 2019/02/05) From adf0ac2259e3e1943af51e4eeec13b3303989500 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 6 Feb 2019 14:18:56 +0100 Subject: [PATCH 068/507] use binary search in BlockIndices::global_to_local() --- doc/news/changes/minor/20190206DenisDavydov | 4 ++ include/deal.II/lac/block_indices.h | 8 +-- tests/lac/block_indices_02.cc | 60 +++++++++++++++++++++ tests/lac/block_indices_02.output | 11 ++++ 4 files changed, 79 insertions(+), 4 deletions(-) create mode 100644 doc/news/changes/minor/20190206DenisDavydov create mode 100644 tests/lac/block_indices_02.cc create mode 100644 tests/lac/block_indices_02.output diff --git a/doc/news/changes/minor/20190206DenisDavydov b/doc/news/changes/minor/20190206DenisDavydov new file mode 100644 index 000000000000..73aa3ed586bd --- /dev/null +++ b/doc/news/changes/minor/20190206DenisDavydov @@ -0,0 +1,4 @@ +Improved: Use binary search in BlockIndices::global_to_local() to improve performance +for large number of blocks. +
+(Denis Davydov, 2019/02/06) diff --git a/include/deal.II/lac/block_indices.h b/include/deal.II/lac/block_indices.h index 6ada38375a72..ef81f81c6e54 100644 --- a/include/deal.II/lac/block_indices.h +++ b/include/deal.II/lac/block_indices.h @@ -333,11 +333,11 @@ BlockIndices::global_to_local(const size_type i) const Assert(i < total_size(), ExcIndexRangeType(i, 0, total_size())); Assert(n_blocks > 0, ExcLowerRangeType(i, size_type(1))); - unsigned int block = n_blocks - 1; - while (i < start_indices[block]) - --block; + // start_indices[0] == 0 so we might as well start from the next one + const auto it = + --std::upper_bound(++start_indices.begin(), start_indices.end(), i); - return {block, i - start_indices[block]}; + return {std::distance(start_indices.begin(), it), i - *it}; } diff --git a/tests/lac/block_indices_02.cc b/tests/lac/block_indices_02.cc new file mode 100644 index 000000000000..0d2cc2c4bd2f --- /dev/null +++ b/tests/lac/block_indices_02.cc @@ -0,0 +1,60 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + +// Test BlockIndices::global_to_local() for very large number of blocks + +#include + +#include "../tests.h" + + + +void +test() +{ + constexpr unsigned int n_blocks = 10000; + constexpr types::global_dof_index block_size = 3; + constexpr types::global_dof_index size = n_blocks * block_size; + BlockIndices idx(n_blocks, block_size); + + const std::vector is = {{0, + 1, + block_size * 500 + 2, + block_size * 600, + block_size * 701 - 1, + size - 1}}; + + deallog << "n_blocks: " << n_blocks << std::endl + << "block_size: " << block_size << std::endl + << "size: " << idx.size() << std::endl; + for (auto i : is) + { + const auto p = idx.global_to_local(i); + AssertDimension(p.first, i / block_size); + AssertDimension(p.second, i % block_size); + deallog << i << " -> (" << p.first << "," << p.second << ")" << std::endl; + } + + deallog << std::endl; +} + + +int +main() +{ + initlog(); + test(); +} diff --git a/tests/lac/block_indices_02.output b/tests/lac/block_indices_02.output new file mode 100644 index 000000000000..6265aaf46676 --- /dev/null +++ b/tests/lac/block_indices_02.output @@ -0,0 +1,11 @@ + +DEAL::n_blocks: 10000 +DEAL::block_size: 3 +DEAL::size: 10000 +DEAL::0 -> (0,0) +DEAL::1 -> (0,1) +DEAL::1502 -> (500,2) +DEAL::1800 -> (600,0) +DEAL::2102 -> (700,2) +DEAL::29999 -> (9999,2) +DEAL:: From b6cd01769019e600993cbe061aef92df62c370fc Mon Sep 17 00:00:00 2001 From: Bruno Turcksin Date: Wed, 6 Feb 2019 17:00:24 -0500 Subject: [PATCH 069/507] Do not use I in header files due to conflict with The C version of defines the macro I. So when a third-party library such as lapacke include is included before the header the variable I is expanded which trips the compiler. --- include/deal.II/base/patterns.h | 16 ++++++++-------- include/deal.II/physics/transformations.h | 10 ++++++---- 2 files changed, 14 insertions(+), 12 deletions(-) diff --git a/include/deal.II/base/patterns.h b/include/deal.II/base/patterns.h index d4ea6babc0b2..3a8617fc91e0 100644 --- a/include/deal.II/base/patterns.h +++ b/include/deal.II/base/patterns.h @@ -2296,15 +2296,15 @@ namespace Patterns } private: - template + template static std::array::value> to_string_internal_1(const T & t, const Patterns::Tuple &pattern, - std_cxx14::index_sequence) + std_cxx14::index_sequence) { std::array::value> a = { - {Convert::type>::to_string( - std::get(t), pattern.get_pattern(I).clone())...}}; + {Convert::type>::to_string( + std::get(t), pattern.get_pattern(U).clone())...}}; return a; } @@ -2317,15 +2317,15 @@ namespace Patterns std_cxx14::make_index_sequence::value>{}); } - template + template static T to_value_internal_1(const std::vector &s, const Patterns::Tuple & pattern, - std_cxx14::index_sequence) + std_cxx14::index_sequence) { return std::make_tuple( - Convert::type>::to_value( - s[I], pattern.get_pattern(I).clone())...); + Convert::type>::to_value( + s[U], pattern.get_pattern(U).clone())...); } static T diff --git a/include/deal.II/physics/transformations.h b/include/deal.II/physics/transformations.h index 322aa29747fa..12e8fcc8a328 100644 --- a/include/deal.II/physics/transformations.h +++ b/include/deal.II/physics/transformations.h @@ -852,8 +852,9 @@ namespace internal Tensor<2, dim, Number> tmp_1; for (unsigned int i = 0; i < dim; ++i) for (unsigned int J = 0; J < dim; ++J) - for (unsigned int I = 0; I < dim; ++I) - tmp_1[i][J] += F[i][I] * T[I][J]; + // Loop over I but complex.h defines a macro I, so use I_ instead + for (unsigned int I_ = 0; I_ < dim; ++I_) + tmp_1[i][J] += F[i][I_] * T[I_][J]; dealii::SymmetricTensor<2, dim, Number> out; for (unsigned int i = 0; i < dim; ++i) @@ -918,12 +919,13 @@ namespace internal // Push forward (inner) index 1 Tensor<4, dim, Number> tmp; - for (unsigned int I = 0; I < dim; ++I) + // Loop over I but complex.h defines a macro I, so use I_ instead + for (unsigned int I_ = 0; I_ < dim; ++I_) for (unsigned int j = 0; j < dim; ++j) for (unsigned int K = 0; K < dim; ++K) for (unsigned int L = 0; L < dim; ++L) for (unsigned int J = 0; J < dim; ++J) - tmp[I][j][K][L] += F[j][J] * H[I][J][K][L]; + tmp[I_][j][K][L] += F[j][J] * H[I_][J][K][L]; // Push forward (outer) indices 0 and 3 tmp = contract<1, 0>(F, contract<3, 1>(tmp, F)); From 479cd3d51f46b9eac0170f03e78917ed959b8f92 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Thu, 7 Feb 2019 00:22:57 +0100 Subject: [PATCH 070/507] Use size_type for rows in ChunkSparsityPattern --- include/deal.II/lac/chunk_sparsity_pattern.h | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/include/deal.II/lac/chunk_sparsity_pattern.h b/include/deal.II/lac/chunk_sparsity_pattern.h index 4a458f598213..a43a3f9558d6 100644 --- a/include/deal.II/lac/chunk_sparsity_pattern.h +++ b/include/deal.II/lac/chunk_sparsity_pattern.h @@ -64,10 +64,15 @@ namespace ChunkSparsityPatternIterators class Accessor { public: + /** + * Declare the type for container size. + */ + using size_type = types::global_dof_index; + /** * Constructor. */ - Accessor(const ChunkSparsityPattern *matrix, const unsigned int row); + Accessor(const ChunkSparsityPattern *matrix, const size_type row); /** * Constructor. Construct the end accessor for the given sparsity pattern. @@ -165,11 +170,16 @@ namespace ChunkSparsityPatternIterators class Iterator { public: + /** + * Declare the type for container size. + */ + using size_type = types::global_dof_index; + /** * Constructor. Create an iterator into the sparsity pattern @p sp for the * given row and the index within it. */ - Iterator(const ChunkSparsityPattern *sp, const unsigned int row); + Iterator(const ChunkSparsityPattern *sp, const size_type row); /** * Prefix increment. @@ -865,7 +875,7 @@ class ChunkSparsityPattern : public Subscriptor namespace ChunkSparsityPatternIterators { inline Accessor::Accessor(const ChunkSparsityPattern *sparsity_pattern, - const unsigned int row) + const size_type row) : sparsity_pattern(sparsity_pattern) , reduced_accessor(row == sparsity_pattern->n_rows() ? *sparsity_pattern->sparsity_pattern.end() : @@ -1039,7 +1049,7 @@ namespace ChunkSparsityPatternIterators inline Iterator::Iterator(const ChunkSparsityPattern *sparsity_pattern, - const unsigned int row) + const size_type row) : accessor(sparsity_pattern, row) {} From b163e04e589737eba7702e93f648073022b3afc1 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Thu, 7 Feb 2019 10:43:15 +0100 Subject: [PATCH 071/507] Replace all unsigned int by size_type in ChunkSparsityPattern --- include/deal.II/lac/chunk_sparsity_pattern.h | 90 ++++++++++---------- source/lac/chunk_sparsity_pattern.cc | 18 ++-- 2 files changed, 53 insertions(+), 55 deletions(-) diff --git a/include/deal.II/lac/chunk_sparsity_pattern.h b/include/deal.II/lac/chunk_sparsity_pattern.h index a43a3f9558d6..cc0d6969c674 100644 --- a/include/deal.II/lac/chunk_sparsity_pattern.h +++ b/include/deal.II/lac/chunk_sparsity_pattern.h @@ -83,7 +83,7 @@ namespace ChunkSparsityPatternIterators * Row number of the element represented by this object. This function can * only be called for entries for which is_valid_entry() is true. */ - unsigned int + size_type row() const; /** @@ -96,7 +96,7 @@ namespace ChunkSparsityPatternIterators * Column number of the element represented by this object. This function * can only be called for entries for which is_valid_entry() is true. */ - unsigned int + size_type column() const; /** @@ -143,12 +143,12 @@ namespace ChunkSparsityPatternIterators /** * Current chunk row number. */ - unsigned int chunk_row; + size_type chunk_row; /** * Current chunk col number. */ - unsigned int chunk_col; + size_type chunk_col; /** * Move the accessor to the next nonzero entry in the matrix. @@ -443,13 +443,12 @@ class ChunkSparsityPattern : public Subscriptor * these iterators) must be a container itself that provides functions * begin and end designating a range of iterators that * describe the contents of one line. Dereferencing these inner iterators - * must either yield a pair of an unsigned integer as column index and a + * must either yield a pair of a scalar as column index and a * value of arbitrary type (such a type would be used if we wanted to - * describe a sparse matrix with one such object), or simply an unsigned - * integer (of we only wanted to describe a sparsity pattern). The function - * is able to determine itself whether an unsigned integer or a pair is what - * we get after dereferencing the inner iterators, through some template - * magic. + * describe a sparse matrix with one such object), or simply a scalar (if we + * only wanted to describe a sparsity pattern). The function is able to + * determine itself whether a scalar or a pair is what we get after + * dereferencing the inner iterators, through some template magic. * * While the order of the outer iterators denotes the different rows of the * matrix, the order of the inner iterator denoting the columns does not @@ -471,7 +470,7 @@ class ChunkSparsityPattern : public Subscriptor * Note that this example works since the iterators dereferenced yield * containers with functions begin and end (namely * std::vectors), and the inner iterators dereferenced yield - * unsigned integers as column indices. Note that we could have replaced + * scalars as column indices. Note that we could have replaced * each of the two std::vector occurrences by std::list, * and the inner one by std::set as well. * @@ -493,12 +492,12 @@ class ChunkSparsityPattern : public Subscriptor * @endcode * * This example works because dereferencing iterators of the inner type - * yields a pair of unsigned integers and a value, the first of which we + * yields a pair of scalars and a value, the first of which we * take as column index. As previously, the outer std::vector could - * be replaced by std::list, and the inner std::map could be replaced by std::vector >, or a list or set of such pairs, as they all return - * iterators that point to such pairs. + * be replaced by std::list, and the inner + * std::map could be replaced by + * std::vector >, or a list or set of + * such pairs, as they all return iterators that point to such pairs. */ template void @@ -547,11 +546,11 @@ class ChunkSparsityPattern : public Subscriptor */ template void - create_from(const unsigned int m, - const unsigned int n, - const Sparsity & sparsity_pattern_for_chunks, - const unsigned int chunk_size, - const bool optimize_diagonal = true); + create_from(const size_type m, + const size_type n, + const Sparsity &sparsity_pattern_for_chunks, + const size_type chunk_size, + const bool optimize_diagonal = true); /** * Return whether the object is empty. It is empty if no memory is @@ -683,7 +682,7 @@ class ChunkSparsityPattern : public Subscriptor * that case. */ iterator - begin(const unsigned int r) const; + begin(const size_type r) const; /** * Final iterator of row r. It points to the first element past the @@ -694,7 +693,7 @@ class ChunkSparsityPattern : public Subscriptor * matrix. */ iterator - end(const unsigned int r) const; + end(const size_type r) const; /** * Write the data of this object en bloc to a file. This is done in a binary @@ -764,22 +763,22 @@ class ChunkSparsityPattern : public Subscriptor * Exception */ DeclException1(ExcInvalidNumber, - int, + size_type, << "The provided number is invalid here: " << arg1); /** * Exception */ DeclException2(ExcInvalidIndex, - int, - int, + size_type, + size_type, << "The given index " << arg1 << " should be less than " << arg2 << "."); /** * Exception */ DeclException2(ExcNotEnoughSpace, - int, - int, + size_type, + size_type, << "Upon entering a new entry to row " << arg1 << ": there was no free entry any more. " << std::endl << "(Maximum number of entries for this row: " << arg2 @@ -808,8 +807,8 @@ class ChunkSparsityPattern : public Subscriptor * Exception */ DeclException2(ExcIteratorRange, - int, - int, + size_type, + size_type, << "The iterators denote a range of " << arg1 << " elements, but the given number of rows was " << arg2); /** @@ -820,15 +819,15 @@ class ChunkSparsityPattern : public Subscriptor * Exception */ DeclException1(ExcInvalidNumberOfPartitions, - int, + size_type, << "The number of partitions you gave is " << arg1 << ", but must be greater than zero."); /** * Exception */ DeclException2(ExcInvalidArraySize, - int, - int, + size_type, + size_type, << "The array has size " << arg1 << " but should have size " << arg2); //@} @@ -912,7 +911,7 @@ namespace ChunkSparsityPatternIterators - inline unsigned int + inline Accessor::size_type Accessor::row() const { Assert(is_valid_entry() == true, ExcInvalidIterator()); @@ -923,7 +922,7 @@ namespace ChunkSparsityPatternIterators - inline unsigned int + inline Accessor::size_type Accessor::column() const { Assert(is_valid_entry() == true, ExcInvalidIterator()); @@ -970,13 +969,12 @@ namespace ChunkSparsityPatternIterators reduced_accessor.container->n_nonzero_elements()) return true; - const unsigned int global_row = sparsity_pattern->get_chunk_size() * - reduced_accessor.row() + - chunk_row, - other_global_row = - sparsity_pattern->get_chunk_size() * - other.reduced_accessor.row() + - other.chunk_row; + const auto global_row = sparsity_pattern->get_chunk_size() * + reduced_accessor.row() + + chunk_row, + other_global_row = sparsity_pattern->get_chunk_size() * + other.reduced_accessor.row() + + other.chunk_row; if (global_row < other_global_row) return true; else if (global_row > other_global_row) @@ -993,7 +991,7 @@ namespace ChunkSparsityPatternIterators inline void Accessor::advance() { - const unsigned int chunk_size = sparsity_pattern->get_chunk_size(); + const auto chunk_size = sparsity_pattern->get_chunk_size(); Assert(chunk_row < chunk_size && chunk_col < chunk_size, ExcIteratorPastEnd()); Assert(reduced_accessor.row() * chunk_size + chunk_row < @@ -1014,7 +1012,7 @@ namespace ChunkSparsityPatternIterators reduced_accessor.column() * chunk_size + chunk_col == sparsity_pattern->n_cols()) { - const unsigned int reduced_row = reduced_accessor.row(); + const auto reduced_row = reduced_accessor.row(); // end of row if (reduced_accessor.linear_index + 1 == reduced_accessor.container->rowstart[reduced_row + 1]) @@ -1128,7 +1126,7 @@ ChunkSparsityPattern::end() const inline ChunkSparsityPattern::iterator -ChunkSparsityPattern::begin(const unsigned int r) const +ChunkSparsityPattern::begin(const size_type r) const { Assert(r < n_rows(), ExcIndexRange(r, 0, n_rows())); return {this, r}; @@ -1137,7 +1135,7 @@ ChunkSparsityPattern::begin(const unsigned int r) const inline ChunkSparsityPattern::iterator -ChunkSparsityPattern::end(const unsigned int r) const +ChunkSparsityPattern::end(const size_type r) const { Assert(r < n_rows(), ExcIndexRange(r, 0, n_rows())); return {this, r + 1}; diff --git a/source/lac/chunk_sparsity_pattern.cc b/source/lac/chunk_sparsity_pattern.cc index 60b4167a5399..db9cc4bbe47b 100644 --- a/source/lac/chunk_sparsity_pattern.cc +++ b/source/lac/chunk_sparsity_pattern.cc @@ -292,10 +292,10 @@ namespace internal template void -ChunkSparsityPattern::create_from(const unsigned int m, - const unsigned int n, +ChunkSparsityPattern::create_from(const size_type m, + const size_type n, const Sparsity &sparsity_pattern_for_chunks, - const unsigned int chunk_size_in, + const size_type chunk_size_in, const bool) { Assert(m > (sparsity_pattern_for_chunks.n_rows() - 1) * chunk_size_in && @@ -598,17 +598,17 @@ ChunkSparsityPattern::copy_from( const DynamicSparsityPattern &, const size_type); template void -ChunkSparsityPattern::create_from(const unsigned int, - const unsigned int, +ChunkSparsityPattern::create_from(const size_type, + const size_type, const SparsityPattern &, - const unsigned int, + const size_type, const bool); template void ChunkSparsityPattern::create_from( - const unsigned int, - const unsigned int, + const size_type, + const size_type, const DynamicSparsityPattern &, - const unsigned int, + const size_type, const bool); template void ChunkSparsityPattern::copy_from(const FullMatrix &, From 371a71a783fc84f2c4b07852db71ee9ab589af0e Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Thu, 7 Feb 2019 14:00:08 +0100 Subject: [PATCH 072/507] Replace 'scalar' by 'integer' --- include/deal.II/lac/chunk_sparsity_pattern.h | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/include/deal.II/lac/chunk_sparsity_pattern.h b/include/deal.II/lac/chunk_sparsity_pattern.h index cc0d6969c674..e958ecd89a54 100644 --- a/include/deal.II/lac/chunk_sparsity_pattern.h +++ b/include/deal.II/lac/chunk_sparsity_pattern.h @@ -443,11 +443,11 @@ class ChunkSparsityPattern : public Subscriptor * these iterators) must be a container itself that provides functions * begin and end designating a range of iterators that * describe the contents of one line. Dereferencing these inner iterators - * must either yield a pair of a scalar as column index and a + * must either yield a pair of an integer as column index and a * value of arbitrary type (such a type would be used if we wanted to - * describe a sparse matrix with one such object), or simply a scalar (if we + * describe a sparse matrix with one such object), or simply an integer (if we * only wanted to describe a sparsity pattern). The function is able to - * determine itself whether a scalar or a pair is what we get after + * determine itself whether an integer or a pair is what we get after * dereferencing the inner iterators, through some template magic. * * While the order of the outer iterators denotes the different rows of the @@ -470,7 +470,7 @@ class ChunkSparsityPattern : public Subscriptor * Note that this example works since the iterators dereferenced yield * containers with functions begin and end (namely * std::vectors), and the inner iterators dereferenced yield - * scalars as column indices. Note that we could have replaced + * integers as column indices. Note that we could have replaced * each of the two std::vector occurrences by std::list, * and the inner one by std::set as well. * @@ -492,7 +492,7 @@ class ChunkSparsityPattern : public Subscriptor * @endcode * * This example works because dereferencing iterators of the inner type - * yields a pair of scalars and a value, the first of which we + * yields a pair of integers and a value, the first of which we * take as column index. As previously, the outer std::vector could * be replaced by std::list, and the inner * std::map could be replaced by From d4473deb06d77babfd0573ae6c4ce8cb723912c3 Mon Sep 17 00:00:00 2001 From: Matthias Maier Date: Tue, 5 Feb 2019 10:20:26 -0600 Subject: [PATCH 073/507] CMake: Do not automatically rebuild a project when switching build type For a long time the "debug" and "release" targets of our convenience macro DEAL_II_INVOKE_AUTOPILOT automatically rebuild the project when switching to the debug or release flavor. Closes #7693 --- cmake/macros/macro_deal_ii_invoke_autopilot.cmake | 2 -- 1 file changed, 2 deletions(-) diff --git a/cmake/macros/macro_deal_ii_invoke_autopilot.cmake b/cmake/macros/macro_deal_ii_invoke_autopilot.cmake index 94fcbc8a4982..a494f0a9e8f4 100644 --- a/cmake/macros/macro_deal_ii_invoke_autopilot.cmake +++ b/cmake/macros/macro_deal_ii_invoke_autopilot.cmake @@ -141,13 +141,11 @@ MACRO(DEAL_II_INVOKE_AUTOPILOT) # Define custom targets to easily switch the build type: ADD_CUSTOM_TARGET(debug COMMAND ${CMAKE_COMMAND} -DCMAKE_BUILD_TYPE=Debug ${CMAKE_SOURCE_DIR} - COMMAND ${CMAKE_COMMAND} --build ${CMAKE_BINARY_DIR} --target all COMMENT "Switch CMAKE_BUILD_TYPE to Debug" ) ADD_CUSTOM_TARGET(release COMMAND ${CMAKE_COMMAND} -DCMAKE_BUILD_TYPE=Release ${CMAKE_SOURCE_DIR} - COMMAND ${CMAKE_COMMAND} --build ${CMAKE_BINARY_DIR} --target all COMMENT "Switch CMAKE_BUILD_TYPE to Release" ) From 06181108246e8c09c298a91d0730bb8061b7991f Mon Sep 17 00:00:00 2001 From: Matthias Maier Date: Tue, 5 Feb 2019 10:26:28 -0600 Subject: [PATCH 074/507] add a changes entry --- doc/news/changes/incompatibilities/20190205Maier | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 doc/news/changes/incompatibilities/20190205Maier diff --git a/doc/news/changes/incompatibilities/20190205Maier b/doc/news/changes/incompatibilities/20190205Maier new file mode 100644 index 000000000000..207868135824 --- /dev/null +++ b/doc/news/changes/incompatibilities/20190205Maier @@ -0,0 +1,5 @@ +Changed: The "debug" and "release" targets that are created by the +DEAL_II_INVOKE_AUTOPILOT() macro no longer automatically rebuild the +project. +
+(Matthias Maier, 2019/02/05) From 613673a1c0a1470ff7ad2e486b4cf8242636ae5e Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Thu, 7 Feb 2019 18:04:32 +0100 Subject: [PATCH 075/507] Unrestrict ScaLAPACKMatrix::copy_to/from --- include/deal.II/lac/scalapack.h | 3 --- source/lac/scalapack.cc | 40 ++++++++++++--------------------- 2 files changed, 14 insertions(+), 29 deletions(-) diff --git a/include/deal.II/lac/scalapack.h b/include/deal.II/lac/scalapack.h index ebc212f622fd..e44ef1ffe48c 100644 --- a/include/deal.II/lac/scalapack.h +++ b/include/deal.II/lac/scalapack.h @@ -203,8 +203,6 @@ class ScaLAPACKMatrix : protected TransposeTable * The user has to ensure that all processes call this with identical @p rank. * The @p rank refers to a process of the MPI communicator used to create the process grid * of the distributed matrix. - * - * @note This function requires MPI-3.0 support */ void copy_from(const LAPACKFullMatrix &matrix, @@ -215,7 +213,6 @@ class ScaLAPACKMatrix : protected TransposeTable * * @note This function should only be used for relatively small matrix * dimensions. It is primarily intended for debugging purposes. - * This function requires MPI-3.0 support */ void copy_to(FullMatrix &matrix) const; diff --git a/source/lac/scalapack.cc b/source/lac/scalapack.cc index 8651557833d8..89d98c930c22 100644 --- a/source/lac/scalapack.cc +++ b/source/lac/scalapack.cc @@ -361,19 +361,18 @@ void ScaLAPACKMatrix::copy_from(const LAPACKFullMatrix &B, const unsigned int rank) { -# if DEAL_II_MPI_VERSION_GTE(3, 0) if (n_rows * n_columns == 0) return; const unsigned int this_mpi_process( Utilities::MPI::this_mpi_process(this->grid->mpi_communicator)); -# ifdef DEBUG +# ifdef DEBUG Assert(Utilities::MPI::max(rank, this->grid->mpi_communicator) == rank, ExcMessage("All processes have to call routine with identical rank")); Assert(Utilities::MPI::min(rank, this->grid->mpi_communicator) == rank, ExcMessage("All processes have to call routine with identical rank")); -# endif +# endif // root process has to be active in the grid of A if (this_mpi_process == rank) @@ -391,12 +390,12 @@ ScaLAPACKMatrix::copy_from(const LAPACKFullMatrix &B, const int n = 1; const std::vector ranks(n, rank); MPI_Group group_B; - MPI_Group_incl(group_A, n, ranks.data(), &group_B); + MPI_Group_incl(group_A, n, DEAL_II_MPI_CONST_CAST(ranks.data()), &group_B); MPI_Comm communicator_B; - MPI_Comm_create_group(this->grid->mpi_communicator, - group_B, - 0, - &communicator_B); + Utilities::MPI::create_group(this->grid->mpi_communicator, + group_B, + 0, + &communicator_B); int n_proc_rows_B = 1, n_proc_cols_B = 1; int this_process_row_B = -1, this_process_column_B = -1; int blacs_context_B = -1; @@ -485,11 +484,6 @@ ScaLAPACKMatrix::copy_from(const LAPACKFullMatrix &B, MPI_Comm_free(&communicator_B); state = LAPACKSupport::matrix; -# else - (void)B; - (void)rank; - AssertThrow(false, ExcNotImplemented()); -# endif } @@ -534,19 +528,18 @@ void ScaLAPACKMatrix::copy_to(LAPACKFullMatrix &B, const unsigned int rank) const { -# if DEAL_II_MPI_VERSION_GTE(3, 0) if (n_rows * n_columns == 0) return; const unsigned int this_mpi_process( Utilities::MPI::this_mpi_process(this->grid->mpi_communicator)); -# ifdef DEBUG +# ifdef DEBUG Assert(Utilities::MPI::max(rank, this->grid->mpi_communicator) == rank, ExcMessage("All processes have to call routine with identical rank")); Assert(Utilities::MPI::min(rank, this->grid->mpi_communicator) == rank, ExcMessage("All processes have to call routine with identical rank")); -# endif +# endif if (this_mpi_process == rank) { @@ -565,12 +558,12 @@ ScaLAPACKMatrix::copy_to(LAPACKFullMatrix &B, const int n = 1; const std::vector ranks(n, rank); MPI_Group group_B; - MPI_Group_incl(group_A, n, ranks.data(), &group_B); + MPI_Group_incl(group_A, n, DEAL_II_MPI_CONST_CAST(ranks.data()), &group_B); MPI_Comm communicator_B; - MPI_Comm_create_group(this->grid->mpi_communicator, - group_B, - 0, - &communicator_B); + Utilities::MPI::create_group(this->grid->mpi_communicator, + group_B, + 0, + &communicator_B); int n_proc_rows_B = 1, n_proc_cols_B = 1; int this_process_row_B = -1, this_process_column_B = -1; int blacs_context_B = -1; @@ -657,11 +650,6 @@ ScaLAPACKMatrix::copy_to(LAPACKFullMatrix &B, MPI_Group_free(&group_B); if (MPI_COMM_NULL != communicator_B) MPI_Comm_free(&communicator_B); -# else - (void)B; - (void)rank; - AssertThrow(false, ExcNotImplemented()); -# endif } From 9d6dd6845c3bc9eabd4d27ac4e4caa76f3d78436 Mon Sep 17 00:00:00 2001 From: Marc Fehling Date: Tue, 18 Dec 2018 15:23:15 +0100 Subject: [PATCH 076/507] Automatic transfer of active fe indices during refinement and serialization. --- doc/news/changes/major/20190127Fehling | 10 + doc/news/changes/minor/20180723MarcFehling | 6 - .../distributed/active_fe_indices_transfer.h | 211 --------- .../deal.II/distributed/solution_transfer.h | 82 +--- include/deal.II/hp/dof_handler.h | 147 +++++- source/distributed/CMakeLists.txt | 2 - .../distributed/active_fe_indices_transfer.cc | 215 --------- .../active_fe_indices_transfer.inst.in | 30 -- source/hp/dof_handler.cc | 425 ++++++++++++++---- tests/mpi/hp_active_fe_indices_transfer_01.cc | 94 ++-- tests/mpi/hp_active_fe_indices_transfer_02.cc | 127 ++++++ ...ransfer_02.with_p4est=true.mpirun=2.output | 175 ++++++++ ...ransfer_02.with_p4est=true.mpirun=8.output | 223 +++++++++ tests/mpi/hp_cell_weights_01.cc | 5 - tests/mpi/hp_cell_weights_02.cc | 5 - tests/mpi/p4est_save_06.cc | 10 +- tests/mpi/solution_transfer_04.cc | 5 - 17 files changed, 1073 insertions(+), 699 deletions(-) create mode 100644 doc/news/changes/major/20190127Fehling delete mode 100644 doc/news/changes/minor/20180723MarcFehling delete mode 100644 include/deal.II/distributed/active_fe_indices_transfer.h delete mode 100644 source/distributed/active_fe_indices_transfer.cc delete mode 100644 source/distributed/active_fe_indices_transfer.inst.in create mode 100644 tests/mpi/hp_active_fe_indices_transfer_02.cc create mode 100644 tests/mpi/hp_active_fe_indices_transfer_02.with_p4est=true.mpirun=2.output create mode 100644 tests/mpi/hp_active_fe_indices_transfer_02.with_p4est=true.mpirun=8.output diff --git a/doc/news/changes/major/20190127Fehling b/doc/news/changes/major/20190127Fehling new file mode 100644 index 000000000000..74c4c55f9077 --- /dev/null +++ b/doc/news/changes/major/20190127Fehling @@ -0,0 +1,10 @@ +Changed: Class hp::DoFHandler now transfers the active_fe_index of each +cell automatically when refining/coarsening a Triangulation, +parallel::shared::Triangulation, or +parallel::distributed::Triangulation. However, serialization of a +parallel::distributed::Triangulation still requires a user to +explicitly call the functions +hp::DoFHandler::prepare_for_serialization_of_active_fe_indices() and +hp::DoFHandler::deserialize_active_fe_indices(). +
+(Marc Fehling, 2019/01/27) diff --git a/doc/news/changes/minor/20180723MarcFehling b/doc/news/changes/minor/20180723MarcFehling deleted file mode 100644 index fd54c397db88..000000000000 --- a/doc/news/changes/minor/20180723MarcFehling +++ /dev/null @@ -1,6 +0,0 @@ -New: Class parallel::distributed::ActiveFEIndicesTransfer -has been introduced to transfer the active_fe_index of each -cell across meshes in case of refinement/serialization, if a -hp::DoFHandler has been used with a parallel::distributed::Triangulation. -
-(Marc Fehling, 2018/07/23) diff --git a/include/deal.II/distributed/active_fe_indices_transfer.h b/include/deal.II/distributed/active_fe_indices_transfer.h deleted file mode 100644 index c1c8702fe4e7..000000000000 --- a/include/deal.II/distributed/active_fe_indices_transfer.h +++ /dev/null @@ -1,211 +0,0 @@ -// --------------------------------------------------------------------- -// -// Copyright (C) 2018 by the deal.II authors -// -// This file is part of the deal.II library. -// -// The deal.II library is free software; you can use it, redistribute -// it, and/or modify it under the terms of the GNU Lesser General -// Public License as published by the Free Software Foundation; either -// version 2.1 of the License, or (at your option) any later version. -// The full text of the license can be found in the file LICENSE.md at -// the top level directory of deal.II. -// -// --------------------------------------------------------------------- - -#ifndef dealii_distributed_active_fe_indices_transfer_h -#define dealii_distributed_active_fe_indices_transfer_h - -#include - -#include - -#include - - -DEAL_II_NAMESPACE_OPEN - -namespace parallel -{ - namespace distributed - { - /** - * This class transfers each cell's `active_fe_index` of a hp::FECollection - * attached to a hp::DoFHandler while refining and/or coarsening a - * distributed grid and handles the necessary communication. - * - * This class therefore does for the `active_fe_index` information of each - * cell what parallel::distributed::SolutionTransfer does for the values - * of degrees of freedom defined on a parallel::distributed::Triangulation. - * - * If refinement is involved in the data transfer process, the children of - * a refined cell inherit the `active_fe_index` from their parent. If - * cells get coarsened into one, the latter will get the least dominating - * `active_fe_index` amongst its children, as determined by the function - * hp::FECollection::find_least_face_dominating_fe_in_collection(). - * - * @note If you use more than one object to attach data to a - * parallel::distributed::Triangulation at the same time (e.g. a - * parallel::distributed::SolutionTransfer object), the calls to - * parallel::distributed::ActiveFEIndicesTransfer::prepare_for_transfer(), - * parallel::distributed::SolutionTransfer::prepare_for_coarsening_and_refinement() - * and parallel::distributed::SolutionTransfer::prepare_serialization(), - * as well as parallel::distributed::ActiveFEIndicesTransfer::unpack() and - * parallel::distributed::SolutionTransfer::interpolate(), or - * parallel::distributed::ActiveFEIndicesTransfer::deserialize() and - * parallel::distributed::SolutionTransfer::deserialize() for serialization, - * need to be in the same order, respectively. - * - *

Transferring each cell's active_fe_index

- * - * The following code snippet demonstrates how to transfer all active FE - * indices across refinement/coarsening of the triangulation that is - * registered to the hp::DoFHandler member object of this class. - * - * @code - * parallel::distributed::ActiveFEIndicesTransfer - * feidx_trans(hp_dof_handler); - * // flag some cells for refinement and coarsening, e.g. - * GridRefinement::refine_and_coarsen_fixed_fraction(tria, - * error_indicators, - * 0.3, - * 0.05); - * - * // prepare the triangulation, - * tria.prepare_coarsening_and_refinement(); - * - * // prepare the SolutionTransfer object for coarsening and refinement - * // and give the solution vector that we intend to interpolate later, - * feidx_trans.prepare_for_transfer(); - * - * // actually execute the refinement, - * tria.execute_coarsening_and_refinement(); - * - * // unpack all active fe indices, - * feidx_trans.unpack(); - * - * // redistribute dofs for further use, - * // using the active FE indices just restored - * hp_dof_handler.distribute_dofs(fe_collection); - * @endcode - * - * - *

Use for serialization

- * - * This class can be used to serialize and later deserialize a distributed - * mesh with attached data to separate files. If you use more than one - * hp::DoFHandler and therefore more than one - * parallel::distributed::ActiveFEIndicesTransfer object, they need to be - * serialized and deserialized in the same order. - * - * For serialization, the following code snippet saves not only the - * triangulation itself, but also the active FE indices of a hp::DoFHandler - * that works on this triangulation: - * @code - * parallel::distributed::ActiveFEIndicesTransfer - * feidx_trans(hp_dof_handler); - * feidx_trans.prepare_for_transfer(); - * - * triangulation.save(filename); - * @endcode - * - * Later, during deserialization, both the triangulation and all active FE - * indices of the hp::DoFHandler can be restored as follows: - * @code - * //[create coarse mesh...] - * triangulation.load(filename); - * - * parallel::distributed::ActiveFEIndicesTransfer - * feidx_trans(hp_dof_handler); - * feidx_trans.deserialize(); - * - * // distribute dofs for further use, - * // using the active FE indices just restored - * hp_dof_handler.distribute_dofs(fe_collection); - * @endcode - * - * @note See documentation of parallel::distributed::SolutionTransfer for - * matching code snippets in both cases. - * - * @ingroup distributed - * @author Marc Fehling, 2018 - */ - template - class ActiveFEIndicesTransfer - { - public: - /** - * Constructor. - * - * @param[in] dof The hp::DoFHandler on which all - * operations will happen. At the time when this constructor - * is called, the hp::DoFHandler still points to the triangulation - * before the refinement in question happens. - */ - ActiveFEIndicesTransfer(const hp::DoFHandler &dof_handler); - - /** - * Prepare the current object for coarsening and refinement or - * serialization. - */ - void - prepare_for_transfer(); - - /** - * Unpack the information previously stored in this object before - * the mesh was refined or coarsened onto the current set of cells. - */ - void - unpack(); - - /** - * Execute the deserialization of the stored information. - * This needs to be done after calling Triangulation::load(). - */ - void - deserialize(); - - private: - /** - * Pointer to the hp::DoFHandler to work with. - */ - SmartPointer, - ActiveFEIndicesTransfer> - dof_handler; - - /** - * The handle that the parallel::distributed::Triangulation has - * assigned to this object with which we can access our memory - * offset and our pack function. - */ - unsigned int handle; - - /** - * A callback function used to pack the data on the current mesh into - * objects that can later be retrieved after refinement, coarsening and - * repartitioning. - */ - std::vector - pack_callback( - const typename Triangulation::cell_iterator &cell, - const typename Triangulation::CellStatus status); - - /** - * A callback function used to unpack the data on the current mesh that - * has been packed up previously on the mesh before refinement, - * coarsening and repartitioning. - */ - void - unpack_callback( - const typename Triangulation::cell_iterator &cell, - const typename Triangulation::CellStatus status, - const boost::iterator_range::const_iterator> - &data_range); - }; - } // namespace distributed -} // namespace parallel - - -DEAL_II_NAMESPACE_CLOSE - -#endif diff --git a/include/deal.II/distributed/solution_transfer.h b/include/deal.II/distributed/solution_transfer.h index a0d47d7544cc..558ebeed2966 100644 --- a/include/deal.II/distributed/solution_transfer.h +++ b/include/deal.II/distributed/solution_transfer.h @@ -153,32 +153,12 @@ namespace parallel * * If an object of the hp::DoFHandler class is registered with an * instantiation of this parallel::distributed::SolutionTransfer - * class, the following requirements have to be met: - *
    - *
  • - * The hp::DoFHandler needs to be explicitly mentioned - * in the parallel::distributed::SolutionTransfer type, i.e.: - * @code - * parallel::distributed::SolutionsTransfer> sol_trans(hp_dof_handler); - * @endcode - *
    • - *
  • - * The transfer of the active_fe_index of each cell - * has to be scheduled as well in the parallel::distributed case, - * since ownerships of cells change during mesh repartitioning. - * This can be achieved with the - * parallel::distributed::ActiveFEIndicesTransfer class. The order in - * which both objects append data during the packing process does not - * matter. However, the unpacking process after refinement or - * deserialization requires the `active_fe_index` to be distributed - * before interpolating the data of the - * parallel::distributed::SolutionTransfer object, so that the correct - * FiniteElement object is associated with each cell. See the - * documentation on parallel::distributed::ActiveFEIndicesTransfer - * for further instructions. - *
    • - *
+ * class, it is necessary to explicitly specify this in the template + * argument list of this class, i.e.: + * @code + * parallel::distributed::SolutionsTransfer> sol_trans(hp_dof_handler); + * @endcode * * Since data on hp::DoFHandler objects is associated with many different * FiniteElement objects, each cell's data has to be processed with its @@ -190,44 +170,22 @@ namespace parallel * function hp::FECollection::find_least_face_dominating_fe_in_collection(), * and unpacked on the same cell with the same index. * - * Code snippets to demonstrate the usage of the - * parallel::distributed::SolutionTransfer class with hp::DoFHandler - * objects are provided in the following. Here VectorType - * is your favorite vector type, e.g. PETScWrappers::MPI::Vector, - * TrilinosWrappers::MPI::Vector, or corresponding block vectors. - * - * After refinement, the order in which to unpack the transferred data - * is important: - * @code - * //[prepare triangulation for refinement ...] - * - * parallel::distributed::ActiveFEIndicesTransfer - * feidx_trans(hp_dof_handler); - * parallel::distributed:: - * SolutionTransfer> - * sol_trans(hp_dof_handler); - * - * feidx_trans.prepare_for_transfer(); - * sol_trans.prepare_for_coarsening_and_refinement(solution); - * triangulation.execute_coarsening_and_refinement(); - * - * feidx_trans.unpack(); - * hp_dof_handler.distribute_dofs(fe_collection); - * - * VectorType interpolated_solution; - * //[create VectorType in the right size here ...] - * soltrans.interpolate(interpolated_solution); - * @endcode + * Transferring a solution across refinement works exactly like in the + * non-hp case. However, when considering serialization, we also have to + * store the active_fe_indices in an additional step. A code snippet + * demonstrating serialization with the + * parallel::distributed::SolutionTransfer class with hp::DoFHandler objects + * is provided in the following. Here VectorType is your favorite vector + * type, e.g. PETScWrappers::MPI::Vector, TrilinosWrappers::MPI::Vector, or + * corresponding block vectors. * * If vector has the locally relevant DoFs, serialization works as follows: * @code - * parallel::distributed::ActiveFEIndicesTransfer - * feidx_trans(hp_dof_handler); * parallel::distributed:: * SolutionTransfer> * sol_trans(hp_dof_handler); * - * feidx_trans.prepare_for_transfer(); + * hp_dof_handler.prepare_for_serialization_of_active_fe_indices(); * sol_trans.prepare_serialization(vector); * * triangulation.save(filename); @@ -239,14 +197,14 @@ namespace parallel * //[create coarse mesh...] * triangulation.load(filename); * - * hp::DoFHandler hp_dof_handler(triangulation); * hp::FECollection fe_collection; * //[prepare identical fe_collection...] - * hp_dof_handler.distribute_dofs(fe_collection); * - * parallel::distributed::ActiveFEIndicesTransfer - * feidx_trans(hp_dof_handler); - * feidx_trans.deserialize(); + * hp::DoFHandler hp_dof_handler(triangulation); + * // We need to introduce our dof_handler to the fe_collection + * // before setting all active_fe_indices. + * hp_dof_handler.distribute_dofs(fe_collection); + * hp_dof_handler.deserialize_active_fe_indices(); * hp_dof_handler.distribute_dofs(fe_collection); * * parallel::distributed:: diff --git a/include/deal.II/hp/dof_handler.h b/include/deal.II/hp/dof_handler.h index 95c33c30ed5f..29a3746ec89a 100644 --- a/include/deal.II/hp/dof_handler.h +++ b/include/deal.II/hp/dof_handler.h @@ -26,6 +26,8 @@ #include #include +#include + #include #include #include @@ -36,6 +38,7 @@ #include #include +#include #include #include @@ -159,12 +162,23 @@ namespace hp * @ref GlossArtificialCell "the glossary entry on artificial cells" * for more information. * - * Using a parallel::distributed::Triangulation with an hp::DoFHandler - * requires additional attention during coarsening and refinement, since - * no information on active FE indices will be automatically transferred. - * This has to be done manually using the - * parallel::distributed::ActiveFEIndicesTransfer class. Consult its - * documentation for more information. + * During refinement and coarsening, information about the @p active_fe_index + * of each cell will be automatically transferred. + * + * However, using a parallel::distributed::Triangulation with an + * hp::DoFHandler requires additional attention during serialization, since no + * information on active FE indices will be automatically transferred. This + * has to be done manually using the + * prepare_for_serialization_of_active_fe_indices() and + * deserialize_active_fe_indices() functions. The former has to be called + * before parallel::distributed::Triangulation::save() is invoked, and the + * latter needs to be run after parallel::distributed::Triangulation::load(). + * If further data will be attached to the triangulation via the + * parallel::distributed::CellDataTransfer, + * parallel::distributed::SolutionTransfer, or Particles::ParticleHandler + * classes, all corresponding preparation and deserialization function calls + * need to happen in the same order. Consult the documentation of + * parallel::distributed::SolutionTransfer for more information. * * * @ingroup dofs @@ -884,6 +898,43 @@ namespace hp virtual std::size_t memory_consumption() const; + /** + * Whenever serialization with a parallel::distributed::Triangulation as the + * underlying triangulation is considered, we also need to consider storing + * the active_fe_indices on all active cells as well. + * + * This function registers that these indices are to be stored whenever the + * parallel::distributed::Triangulation::save() function is called on the + * underlying triangulation. + * + * @note Currently only implemented for triangulations of type + * parallel::distributed::Triangulation. An assertion will be triggered if + * a different type is registered. + * + * @see The documentation of parallel::distributed::SolutionTransfer has further + * information on serialization. + */ + void + prepare_for_serialization_of_active_fe_indices(); + + /** + * Whenever serialization with a parallel::distributed::Triangulation as the + * underlying triangulation is considered, we also need to consider storing + * the active_fe_indices on all active cells as well. + * + * This function deserializes and distributes the previously stored + * active_fe_indices on all active cells. + * + * @note Currently only implemented for triangulations of type + * parallel::distributed::Triangulation. An assertion will be triggered if + * a different type is registered. + * + * @see The documentation of parallel::distributed::SolutionTransfer has further + * information on serialization. + */ + void + deserialize_active_fe_indices(); + /** * Write the data of this object to a stream for the purpose of * serialization. @@ -1039,17 +1090,70 @@ namespace hp post_refinement_action(); /** - * Functions that will be triggered through signals whenever the - * triangulation is modified, with the restriction that it is not - * a parallel::distributed::Triangulation. + * A function that will be triggered through a triangulation + * signal just before the associated Triangulation is modified. + * + * The function that stores the active_fe_indices of all cells that will + * be refined or coarsened before the refinement happens, so that + * they can be set again after refinement. + */ + void + pre_active_fe_index_transfer(); + + /** + * A function that will be triggered through a triangulation + * signal just before the associated parallel::shared::Triangulation is + * modified. + * + * The function that stores the active_fe_indices of all cells that will + * be refined or coarsened before the refinement happens, so that + * they can be set again after refinement. + */ + void + pre_shared_active_fe_index_transfer(); + + /** + * A function that will be triggered through a triangulation + * signal just before the associated parallel::distributed::Triangulation is + * modified. + * + * The function that stores all active_fe_indices on locally owned cells for + * distribution over all participating processors. + */ + void + pre_distributed_active_fe_index_transfer(); + + /** + * A function that will be triggered through a triangulation + * signal just after the associated Triangulation is modified. + * + * The function that restores the active_fe_indices of all cells that + * were refined or coarsened. + */ + void + post_active_fe_index_transfer(); + + /** + * A function that will be triggered through a triangulation + * signal just after the associated parallel::shared::Triangulation is + * modified. * - * Here they are used to administrate the active_fe_indices during the - * spatial refinement. + * The function that restores the active_fe_indices of all cells that + * were refined or coarsened. */ void - pre_refinement_fe_index_update(); + post_shared_active_fe_index_transfer(); + + /** + * A function that will be triggered through a triangulation + * signal just after the associated parallel::distributed::Triangulation is + * modified. + * + * The function that restores all active_fe_indices on locally owned cells + * that have been communicated. + */ void - post_refinement_fe_index_update(); + post_distributed_active_fe_index_transfer(); /** * Space to store the DoF numbers for the different levels. Analogous to @@ -1120,6 +1224,23 @@ namespace hp */ std::map coarsened_cells_fe_index; + /** + * Container to temporarily store the active_fe_index of every locally + * owned cell for transfer across parallel::distributed::Triangulation + * objects. + */ + std::vector active_fe_indices; + + /** + * Helper object to transfer all active_fe_indices on + * parallel::distributed::Triangulation objects during refinement/coarsening + * and serialization. + */ + std::unique_ptr< + parallel::distributed:: + CellDataTransfer>> + cell_data_transfer; + /** * A list of connections with which this object connects to the * triangulation to get information about when the triangulation changes. diff --git a/source/distributed/CMakeLists.txt b/source/distributed/CMakeLists.txt index ac47675cbe3a..fec5610af2b0 100644 --- a/source/distributed/CMakeLists.txt +++ b/source/distributed/CMakeLists.txt @@ -18,7 +18,6 @@ INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_BINARY_DIR}) SET(_unity_include_src grid_refinement.cc cell_weights.cc - active_fe_indices_transfer.cc cell_data_transfer.cc solution_transfer.cc tria.cc @@ -42,7 +41,6 @@ SETUP_SOURCE_LIST("${_unity_include_src}" SET(_inst grid_refinement.inst.in cell_weights.inst.in - active_fe_indices_transfer.inst.in cell_data_transfer.inst.in solution_transfer.inst.in tria.inst.in diff --git a/source/distributed/active_fe_indices_transfer.cc b/source/distributed/active_fe_indices_transfer.cc deleted file mode 100644 index 60ea718f17ca..000000000000 --- a/source/distributed/active_fe_indices_transfer.cc +++ /dev/null @@ -1,215 +0,0 @@ -// --------------------------------------------------------------------- -// -// Copyright (C) 2018 by the deal.II authors -// -// This file is part of the deal.II library. -// -// The deal.II library is free software; you can use it, redistribute -// it, and/or modify it under the terms of the GNU Lesser General -// Public License as published by the Free Software Foundation; either -// version 2.1 of the License, or (at your option) any later version. -// The full text of the license can be found in the file LICENSE.md at -// the top level directory of deal.II. -// -// --------------------------------------------------------------------- - - -#include - -#ifdef DEAL_II_WITH_P4EST - -# include -# include - -# include - -# include - -DEAL_II_NAMESPACE_OPEN - -namespace parallel -{ - namespace distributed - { - template - ActiveFEIndicesTransfer::ActiveFEIndicesTransfer( - const hp::DoFHandler &dof_handler) - : dof_handler(&dof_handler, typeid(*this).name()) - , handle(numbers::invalid_unsigned_int) - { - Assert( - (dynamic_cast< - const parallel::distributed::Triangulation *>( - &(this->dof_handler)->get_triangulation()) != nullptr), - ExcMessage( - "parallel::distributed::ActiveFEIndicesTransfer requires a parallel::distributed::Triangulation object.")); - } - - - - template - void - ActiveFEIndicesTransfer::prepare_for_transfer() - { - parallel::distributed::Triangulation *tria = - (dynamic_cast *>( - const_cast *>( - &dof_handler->get_triangulation()))); - Assert(tria != nullptr, ExcInternalError()); - - handle = tria->register_data_attach( - std::bind(&ActiveFEIndicesTransfer::pack_callback, - this, - std::placeholders::_1, - std::placeholders::_2), - /*returns_variable_size_data=*/false); - } - - - - template - void - ActiveFEIndicesTransfer::unpack() - { - // TODO: casting away constness is bad - parallel::distributed::Triangulation *tria = - (dynamic_cast *>( - const_cast *>( - &dof_handler->get_triangulation()))); - Assert(tria != nullptr, ExcInternalError()); - - tria->notify_ready_to_unpack( - handle, - std::bind(&ActiveFEIndicesTransfer::unpack_callback, - this, - std::placeholders::_1, - std::placeholders::_2, - std::placeholders::_3)); - } - - - - template - void - ActiveFEIndicesTransfer::deserialize() - { - // For deserialization, we need to register this object - // to the triangulation first to get a valid handle for - // data access. - prepare_for_transfer(); - unpack(); - } - - - - template - std::vector - ActiveFEIndicesTransfer::pack_callback( - const typename Triangulation::cell_iterator &cell_, - const typename Triangulation::CellStatus status) - { - const typename hp::DoFHandler::cell_iterator cell( - *cell_, dof_handler); - - unsigned int fe_index = numbers::invalid_unsigned_int; - - switch (status) - { - case parallel::distributed::Triangulation::CELL_PERSIST: - case parallel::distributed::Triangulation::CELL_REFINE: - fe_index = cell->active_fe_index(); - break; - - case parallel::distributed::Triangulation::CELL_COARSEN: - // In this case, the callback function will be called on the parent - // cell which shall store the packed information. We need to choose - // from its children which ID to store. - { - std::set fe_indices_children; - for (unsigned int child_index = 0; - child_index < GeometryInfo::max_children_per_cell; - ++child_index) - { - typename hp::DoFHandler::cell_iterator child = - cell->child(child_index); - - fe_indices_children.insert(child->active_fe_index()); - } - - fe_index = - dof_handler->get_fe_collection() - .find_least_dominating_fe_in_collection(fe_indices_children, - /*codim=*/0); - - Assert(fe_index != numbers::invalid_unsigned_int, - ExcMessage( - "No FiniteElement has been found in your FECollection " - "that dominates all children of a cell you are trying " - "to coarsen!")); - } - break; - - default: - Assert(false, ExcInternalError()); - break; - } - - return Utilities::pack(fe_index, /*allow_compression=*/false); - } - - - - template - void - ActiveFEIndicesTransfer::unpack_callback( - const typename Triangulation::cell_iterator &cell_, - const typename Triangulation::CellStatus status, - const boost::iterator_range::const_iterator> - &data_range) - { - typename hp::DoFHandler::cell_iterator cell(*cell_, - dof_handler); - - const unsigned int fe_index = - Utilities::unpack(data_range.begin(), - data_range.end(), - /*allow_compression=*/false); - - Assert(fe_index <= dof_handler->get_fe().size(), ExcInternalError()); - - switch (status) - { - case parallel::distributed::Triangulation::CELL_PERSIST: - case parallel::distributed::Triangulation::CELL_COARSEN: - cell->set_active_fe_index(fe_index); - break; - - case parallel::distributed::Triangulation::CELL_REFINE: - // In this case, the callback function will be called on the parent - // cell which stores the packed information. We need to distribute - // it on its children. - for (unsigned int child_index = 0; - child_index < GeometryInfo::max_children_per_cell; - ++child_index) - cell->child(child_index)->set_active_fe_index(fe_index); - break; - - default: - Assert(false, ExcInternalError()); - break; - } - } - } // namespace distributed -} // namespace parallel - - -// explicit instantiations -# include "active_fe_indices_transfer.inst" - -DEAL_II_NAMESPACE_CLOSE - -#endif diff --git a/source/distributed/active_fe_indices_transfer.inst.in b/source/distributed/active_fe_indices_transfer.inst.in deleted file mode 100644 index 4e91a9b682a1..000000000000 --- a/source/distributed/active_fe_indices_transfer.inst.in +++ /dev/null @@ -1,30 +0,0 @@ -// --------------------------------------------------------------------- -// -// Copyright (C) 2018 by the deal.II authors -// -// This file is part of the deal.II library. -// -// The deal.II library is free software; you can use it, redistribute -// it, and/or modify it under the terms of the GNU Lesser General -// Public License as published by the Free Software Foundation; either -// version 2.1 of the License, or (at your option) any later version. -// The full text of the license can be found in the file LICENSE.md at -// the top level directory of deal.II. -// -// --------------------------------------------------------------------- - - - -for (deal_II_dimension : DIMENSIONS; deal_II_space_dimension : SPACE_DIMENSIONS) - { - namespace parallel - \{ - namespace distributed - \{ -#if deal_II_dimension <= deal_II_space_dimension - template class ActiveFEIndicesTransfer; -#endif - \} - \} - } diff --git a/source/hp/dof_handler.cc b/source/hp/dof_handler.cc index c7b5011f89d1..01900459d885 100644 --- a/source/hp/dof_handler.cc +++ b/source/hp/dof_handler.cc @@ -238,6 +238,7 @@ namespace internal } + /** * Do that part of reserving space that pertains to cells, * since this is the same in all space dimensions. @@ -652,6 +653,7 @@ namespace internal } + /** * Reserve enough space in the levels[] objects to * store the numbers of the degrees of freedom needed for the @@ -825,6 +827,7 @@ namespace internal } + /** * Implement the function of same name in the mother class. */ @@ -905,6 +908,7 @@ namespace internal } + template static unsigned int max_couplings_between_dofs(const DoFHandler<3, spacedim> &dof_handler) @@ -938,6 +942,7 @@ namespace internal } + /** * Given a hp::DoFHandler object, make sure that the active_fe_indices * that a user has set for locally owned cells are communicated to all @@ -1037,6 +1042,7 @@ namespace internal } // namespace internal + namespace hp { template @@ -1057,6 +1063,7 @@ namespace hp {} + template DoFHandler::DoFHandler( const Triangulation &tria) @@ -1069,6 +1076,7 @@ namespace hp } + template DoFHandler::~DoFHandler() { @@ -1086,8 +1094,10 @@ namespace hp } + /*------------------------ Cell iterator functions ------------------------*/ + template typename DoFHandler::cell_iterator DoFHandler::begin(const unsigned int level) const @@ -1121,6 +1131,7 @@ namespace hp } + template typename DoFHandler::cell_iterator DoFHandler::end(const unsigned int level) const @@ -1131,6 +1142,7 @@ namespace hp } + template typename DoFHandler::active_cell_iterator DoFHandler::end_active(const unsigned int level) const @@ -1151,6 +1163,7 @@ namespace hp } + template IteratorRange::active_cell_iterator> DoFHandler::active_cell_iterators() const @@ -1329,10 +1342,9 @@ namespace hp // protected data of this object, but for simplicity we use the // cell-wise access. this way we also have to pass some debug-mode // tests which we would have to duplicate ourselves otherwise - active_cell_iterator cell = begin_active(), endc = end(); - for (unsigned int i = 0; cell != endc; ++cell, ++i) + for (const auto &cell : active_cell_iterators()) if (cell->is_locally_owned()) - cell->set_active_fe_index(active_fe_indices[i]); + cell->set_active_fe_index(active_fe_indices[cell->active_cell_index()]); } @@ -1347,11 +1359,13 @@ namespace hp // we could try to extract the values directly, since they are // stored as protected data of this object, but for simplicity we // use the cell-wise access. - active_cell_iterator cell = begin_active(), endc = end(); - for (unsigned int i = 0; cell != endc; ++cell, ++i) - active_fe_indices[i] = cell->active_fe_index(); + for (const auto &cell : active_cell_iterators()) + if (cell->is_locally_owned()) + active_fe_indices[cell->active_cell_index()] = cell->active_fe_index(); } + + template void DoFHandler::initialize( @@ -1375,6 +1389,7 @@ namespace hp } + template void DoFHandler::distribute_dofs( @@ -1490,29 +1505,12 @@ namespace hp } + template void DoFHandler::setup_policy_and_listeners() { - // decide whether we need a sequential or a parallel shared/distributed - // policy - if (dynamic_cast *>( - &*this->tria) != nullptr) - policy = - std_cxx14::make_unique>>( - *this); - else if (dynamic_cast< - const parallel::distributed::Triangulation *>( - &*this->tria) != nullptr) - policy = std_cxx14::make_unique< - internal::DoFHandlerImplementation::Policy::ParallelDistributed< - DoFHandler>>(*this); - else - policy = - std_cxx14::make_unique>>(*this); - + // connect functions to signals of the underlying triangulation tria_listeners.push_back(this->tria->signals.pre_refinement.connect( std::bind(&DoFHandler::pre_refinement_action, std::ref(*this)))); @@ -1522,22 +1520,77 @@ namespace hp tria_listeners.push_back(this->tria->signals.create.connect(std::bind( &DoFHandler::post_refinement_action, std::ref(*this)))); - // Only connect the update of active fe indices if we are not using a - // p::d::Triangulation. In this case, the class ActiveFEIndicesTransfer - // has to be consulted. - if (dynamic_cast - *>(&*this->tria) == nullptr) + // decide whether we need a sequential or a parallel shared/distributed + // policy and attach corresponding callback functions dealing with the + // transfer of active_fe_indices + if (const auto *distributed_tria = dynamic_cast< + const parallel::distributed::Triangulation *>( + &this->get_triangulation())) { + policy = std_cxx14::make_unique< + internal::DoFHandlerImplementation::Policy::ParallelDistributed< + DoFHandler>>(*this); + +#ifdef DEAL_II_WITH_P4EST + cell_data_transfer = std_cxx14::make_unique< + parallel::distributed:: + CellDataTransfer>>( + *distributed_tria, + /*transfer_variable_size_data=*/false, + ¶llel::distributed::CellDataTransfer< + dim, + spacedim, + std::vector>::CoarseningStrategies::check_equality); +#endif + + tria_listeners.push_back( + distributed_tria->signals.pre_distributed_refinement.connect( + std::bind( + &DoFHandler::pre_distributed_active_fe_index_transfer, + std::ref(*this)))); + tria_listeners.push_back( + distributed_tria->signals.post_distributed_refinement.connect( + std::bind( + &DoFHandler::post_distributed_active_fe_index_transfer, + std::ref(*this)))); + } + else if (dynamic_cast + *>(&this->get_triangulation()) != nullptr) + { + policy = + std_cxx14::make_unique>>( + *this); + + tria_listeners.push_back( + this->tria->signals.pre_refinement.connect(std::bind( + &DoFHandler::pre_shared_active_fe_index_transfer, + std::ref(*this)))); + tria_listeners.push_back( + this->tria->signals.post_refinement.connect(std::bind( + &DoFHandler::post_shared_active_fe_index_transfer, + std::ref(*this)))); + } + else + { + policy = + std_cxx14::make_unique>>( + *this); + tria_listeners.push_back(this->tria->signals.pre_refinement.connect( - std::bind(&DoFHandler::pre_refinement_fe_index_update, + std::bind(&DoFHandler::pre_active_fe_index_transfer, std::ref(*this)))); tria_listeners.push_back(this->tria->signals.post_refinement.connect( - std::bind(&DoFHandler::post_refinement_fe_index_update, + std::bind(&DoFHandler::post_active_fe_index_transfer, std::ref(*this)))); } } + template void DoFHandler::clear() @@ -1695,6 +1748,7 @@ namespace hp } + template void DoFHandler::pre_refinement_action() @@ -1703,6 +1757,7 @@ namespace hp } + template void DoFHandler::post_refinement_action() @@ -1727,9 +1782,10 @@ namespace hp } + template void - DoFHandler::pre_refinement_fe_index_update() + DoFHandler::pre_active_fe_index_transfer() { // Finite elements need to be assigned to each cell by calling // distribute_dofs() first to make this functionality available. @@ -1738,6 +1794,74 @@ namespace hp Assert(refined_cells_fe_index.empty(), ExcInternalError()); Assert(coarsened_cells_fe_index.empty(), ExcInternalError()); + // Store active_fe_index information for all cells that will be + // affected by refinement/coarsening. + for (const auto &cell : active_cell_iterators()) + if (cell->is_locally_owned()) + { + if (cell->refine_flag_set()) + { + // Store the active_fe_index of each cell that will be refined + // to and distribute it later on its children. + refined_cells_fe_index.insert( + {cell, cell->active_fe_index()}); + } + else if (cell->coarsen_flag_set()) + { + // From all cells that will be coarsened, determine their + // parent and calculate its proper active_fe_index, so that it + // can be set after refinement. But first, check if that + // particular cell has a parent at all. + Assert(cell->level() > 0, ExcInternalError()); + const auto &parent = cell->parent(); + // Check if the active_fe_index for the current cell has been + // determined already. + if (coarsened_cells_fe_index.find(parent) == + coarsened_cells_fe_index.end()) + { + std::set fe_indices_children; + for (unsigned int child_index = 0; + child_index < parent->n_children(); + ++child_index) + { + Assert(parent->child(child_index)->active(), + ExcInternalError()); + + fe_indices_children.insert( + parent->child(child_index)->active_fe_index()); + } + + const unsigned int fe_index = + fe_collection.find_least_dominating_fe_in_collection( + fe_indices_children, /*codim=*/0); + + Assert( + fe_index != numbers::invalid_unsigned_int, + ExcMessage( + "No FiniteElement has been found in your FECollection " + "that dominates all children of a cell you are trying " + "to coarsen!")); + + coarsened_cells_fe_index.insert({parent, fe_index}); + } + } + } + } + } + + + + template + void + DoFHandler::pre_shared_active_fe_index_transfer() + { +#ifndef DEAL_II_WITH_MPI + Assert(false, ExcInternalError()); +#else + // Finite elements need to be assigned to each cell by calling + // distribute_dofs() first to make this functionality available. + if (fe_collection.size() > 0) + { // If the underlying shared::Tria allows artificial cells, // then save the current set of subdomain ids, and set // subdomain ids to the "true" owner of each cell. We later @@ -1745,9 +1869,10 @@ namespace hp const parallel::shared::Triangulation *shared_tria = (dynamic_cast *>( &(*tria))); + Assert(shared_tria != nullptr, ExcInternalError()); std::vector saved_subdomain_ids; - if (shared_tria != nullptr && shared_tria->with_artificial_cells()) + if (shared_tria->with_artificial_cells()) { saved_subdomain_ids.resize(shared_tria->n_active_cells()); @@ -1767,54 +1892,11 @@ namespace hp communicate_active_fe_indices(*this); } - // Store active_fe_index information for all cells that will be - // affected by refinement/coarsening. - for (const auto &cell : active_cell_iterators()) - { - if (cell->refine_flag_set()) - { - // Store the active_fe_index of each cell that will be refined - // to and distribute it later on its children. - refined_cells_fe_index.insert({cell, cell->active_fe_index()}); - } - else if (cell->coarsen_flag_set()) - { - // From all cells that will be coarsened, determine their parent - // and calculate its proper active_fe_index, so that it can be - // set after refinement. - // But first, check if that particular cell has a parent at all. - Assert(cell->level() > 0, ExcInternalError()); - const auto &parent = cell->parent(); - // Check if the active_fe_index for the current cell has been - // determined already. - if (coarsened_cells_fe_index.find(parent) == - coarsened_cells_fe_index.end()) - { - std::set fe_indices_children; - for (unsigned int child_index = 0; - child_index < parent->n_children(); - ++child_index) - fe_indices_children.insert( - parent->child(child_index)->active_fe_index()); - - const unsigned int fe_index = - fe_collection.find_least_dominating_fe_in_collection( - fe_indices_children, /*codim=*/0); - - Assert( - fe_index != numbers::invalid_unsigned_int, - ExcMessage( - "No FiniteElement has been found in your FECollection " - "that dominates all children of a cell you are trying " - "to coarsen!")); - - coarsened_cells_fe_index.insert({parent, fe_index}); - } - } - } + // Now do what we would do in the sequential case. + pre_active_fe_index_transfer(); // Finally, restore current subdomain_ids. - if (shared_tria != nullptr && shared_tria->with_artificial_cells()) + if (shared_tria->with_artificial_cells()) for (const auto &cell : active_cell_iterators()) { if (cell->is_artificial()) @@ -1824,17 +1906,69 @@ namespace hp saved_subdomain_ids[cell->active_cell_index()]); } } +#endif } + template void - DoFHandler::post_refinement_fe_index_update() + DoFHandler::pre_distributed_active_fe_index_transfer() { +#ifndef DEAL_II_WITH_P4EST + Assert(false, ExcInternalError()); +#else // Finite elements need to be assigned to each cell by calling // distribute_dofs() first to make this functionality available. if (fe_collection.size() > 0) { + // First, do what we would do in the sequential case. + pre_active_fe_index_transfer(); + + // If we work on a p::d::Triangulation, we have to transfer all + // active_fe_indices since ownership of cells may change. We will + // use our p::d::CellDataTransfer member to achieve this. Further, + // we prepare the values in such a way that they will correspond to + // the active_fe_indices on the new mesh. + + // Gather all current active_fe_indices. + get_active_fe_indices(active_fe_indices); + + // Overwrite values of cells that will be coarsened with the + // active_fe_index determined beforehand for their parent. + for (const auto &pair : coarsened_cells_fe_index) + for (unsigned int child_index = 0; + child_index < pair.first->n_children(); + ++child_index) + active_fe_indices[pair.first->child(child_index) + ->active_cell_index()] = pair.second; + + // Attach to transfer object. + cell_data_transfer->prepare_for_coarsening_and_refinement( + active_fe_indices); + + // Free some memory. + refined_cells_fe_index.clear(); + coarsened_cells_fe_index.clear(); + } +#endif + } + + + + template + void + DoFHandler::post_active_fe_index_transfer() + { + // Finite elements need to be assigned to each cell by calling + // distribute_dofs() first to make this functionality available. + if (fe_collection.size() > 0) + { + // For Triangulation and p::s::Triangulation, the old cell iterators + // are still valid. There is no need to transfer data in this case, + // and we can re-use our previously gathered information from the + // container. + // Distribute active_fe_indices from all refined cells on their // respective children. for (const auto &pair : refined_cells_fe_index) @@ -1868,19 +2002,140 @@ namespace hp } } + // Clear stored active_fe_indices. + refined_cells_fe_index.clear(); + coarsened_cells_fe_index.clear(); + } + } + + + + template + void + DoFHandler::post_shared_active_fe_index_transfer() + { +#ifndef DEAL_II_WITH_MPI + Assert(false, ExcInternalError()); +#else + // Finite elements need to be assigned to each cell by calling + // distribute_dofs() first to make this functionality available. + if (fe_collection.size() > 0) + { + // Do what we normally do in the sequential case. + post_active_fe_index_transfer(); + // We have to distribute the information about active_fe_indices // on all processors, if a parallel::shared::Triangulation // has been used. dealii::internal::hp::DoFHandlerImplementation::Implementation:: communicate_active_fe_indices(*this); + } +#endif + } - // Clear stored active_fe_indices. - refined_cells_fe_index.clear(); - coarsened_cells_fe_index.clear(); + + + template + void + DoFHandler::post_distributed_active_fe_index_transfer() + { +#ifndef DEAL_II_WITH_P4EST + Assert(false, ExcInternalError()); +#else + // Finite elements need to be assigned to each cell by calling + // distribute_dofs() first to make this functionality available. + if (fe_collection.size() > 0) + { + // Unpack active_fe_indices. + active_fe_indices.resize(tria->n_active_cells(), + numbers::invalid_unsigned_int); + cell_data_transfer->unpack(active_fe_indices); + + // Update all locally owned active_fe_indices. + set_active_fe_indices(active_fe_indices); + + // Free some memory. + active_fe_indices.clear(); + active_fe_indices.shrink_to_fit(); } +#endif + } + + + + template + void + DoFHandler::prepare_for_serialization_of_active_fe_indices() + { +#ifndef DEAL_II_WITH_P4EST + Assert(false, + ExcMessage( + "You are attempting to use a functionality that is only available " + "if deal.II was configured to use p4est, but cmake did not find a " + "valid p4est library.")); +#else + Assert( + (dynamic_cast + *>(&this->get_triangulation()) != nullptr), + ExcMessage( + "This functionality requires a parallel::distributed::Triangulation object.")); + + // Finite elements need to be assigned to each cell by calling + // distribute_dofs() first to make this functionality available. + if (fe_collection.size() > 0) + { + // If we work on a p::d::Triangulation, we have to transfer all + // active fe indices since ownership of cells may change. + + // Gather all current active_fe_indices + get_active_fe_indices(active_fe_indices); + + // Attach to transfer object + cell_data_transfer->prepare_for_serialization(active_fe_indices); + } +#endif + } + + + + template + void + DoFHandler::deserialize_active_fe_indices() + { +#ifndef DEAL_II_WITH_P4EST + Assert(false, + ExcMessage( + "You are attempting to use a functionality that is only available " + "if deal.II was configured to use p4est, but cmake did not find a " + "valid p4est library.")); +#else + Assert( + (dynamic_cast + *>(&this->get_triangulation()) != nullptr), + ExcMessage( + "This functionality requires a parallel::distributed::Triangulation object.")); + + // Finite elements need to be assigned to each cell by calling + // distribute_dofs() first to make this functionality available. + if (fe_collection.size() > 0) + { + // Unpack active_fe_indices. + active_fe_indices.resize(tria->n_active_cells(), + numbers::invalid_unsigned_int); + cell_data_transfer->deserialize(active_fe_indices); + + // Update all locally owned active_fe_indices. + set_active_fe_indices(active_fe_indices); + + // Free some memory. + active_fe_indices.clear(); + active_fe_indices.shrink_to_fit(); + } +#endif } + template template types::global_dof_index @@ -1894,6 +2149,7 @@ namespace hp } + template template void @@ -1907,6 +2163,7 @@ namespace hp } + template void DoFHandler::clear_space() diff --git a/tests/mpi/hp_active_fe_indices_transfer_01.cc b/tests/mpi/hp_active_fe_indices_transfer_01.cc index 4e0266a1b9a6..2d5cb00ab231 100644 --- a/tests/mpi/hp_active_fe_indices_transfer_01.cc +++ b/tests/mpi/hp_active_fe_indices_transfer_01.cc @@ -15,10 +15,9 @@ -// ActiveFEIndicesTransfer Test +// active fe indices transfer on refinement -#include #include #include @@ -51,65 +50,54 @@ test() for (unsigned int i = 0; i < max_degree; ++i) fe_collection.push_back(FE_Q(max_degree - i)); - typename hp::DoFHandler::active_cell_iterator cell; - unsigned int i = 0; - - for (cell = dh.begin_active(); cell != dh.end(); ++cell) - { - if (cell->is_locally_owned()) - { - // set active fe index - if (!(cell->is_artificial())) - { - if (i >= fe_collection.size()) - i = 0; - cell->set_active_fe_index(i++); - } - - // set refinement/coarsening flags - if (cell->id().to_string() == "0_1:0") - cell->set_refine_flag(); - else if (cell->parent()->id().to_string() == - ((dim == 2) ? "3_0:" : "7_0:")) - cell->set_coarsen_flag(); - - deallog << "myid=" << myid << " cellid=" << cell->id() - << " fe_index=" << cell->active_fe_index() - << " feq_degree=" << max_degree - cell->active_fe_index(); - if (cell->coarsen_flag_set()) - deallog << " coarsening"; - else if (cell->refine_flag_set()) - deallog << " refining"; - deallog << std::endl; - } - } - + // this distribute_dofs() call is necessary + // we need to introduce dof_handler to its fe_collection first dh.distribute_dofs(fe_collection); - // ----- transfer ----- - parallel::distributed::ActiveFEIndicesTransfer feidx_transfer(dh); + unsigned int i = 0; + for (auto &cell : dh.active_cell_iterators()) + if (cell->is_locally_owned()) + { + // set active fe index + if (!(cell->is_artificial())) + { + if (i >= fe_collection.size()) + i = 0; + cell->set_active_fe_index(i++); + } + + // set refinement/coarsening flags + if (cell->id().to_string() == "0_1:0") + cell->set_refine_flag(); + else if (cell->parent()->id().to_string() == + ((dim == 2) ? "3_0:" : "7_0:")) + cell->set_coarsen_flag(); + + deallog << "myid=" << myid << " cellid=" << cell->id() + << " fe_index=" << cell->active_fe_index() + << " feq_degree=" << max_degree - cell->active_fe_index(); + if (cell->coarsen_flag_set()) + deallog << " coarsening"; + else if (cell->refine_flag_set()) + deallog << " refining"; + deallog << std::endl; + } - feidx_transfer.prepare_for_transfer(); + // ----- transfer ----- tria.execute_coarsening_and_refinement(); deallog << "cells after: " << tria.n_global_active_cells() << std::endl; - feidx_transfer.unpack(); - - // for further calculations, distribute dofs after unpacking, i.e. - // dh.distribute_dofs(fe_collection); - // ------ verify ------ // check if all children adopted the correct id - for (cell = dh.begin_active(); cell != dh.end(); ++cell) - { - if (cell->is_locally_owned()) - { - deallog << "myid=" << myid << " cellid=" << cell->id() - << " fe_index=" << cell->active_fe_index() - << " feq_degree=" << max_degree - cell->active_fe_index() - << std::endl; - } - } + for (auto &cell : dh.active_cell_iterators()) + if (cell->is_locally_owned()) + deallog << "myid=" << myid << " cellid=" << cell->id() + << " fe_index=" << cell->active_fe_index() + << " feq_degree=" << max_degree - cell->active_fe_index() + << std::endl; + + // for further calculations, distribute dofs, i.e. + // dh.distribute_dofs(fe_collection); // make sure no processor is hanging MPI_Barrier(MPI_COMM_WORLD); diff --git a/tests/mpi/hp_active_fe_indices_transfer_02.cc b/tests/mpi/hp_active_fe_indices_transfer_02.cc new file mode 100644 index 000000000000..65393457401e --- /dev/null +++ b/tests/mpi/hp_active_fe_indices_transfer_02.cc @@ -0,0 +1,127 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2018 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + + +// active fe indices transfer on serialization + + +#include + +#include + +#include + +#include + +#include "../tests.h" + + +template +void +test() +{ + const unsigned int max_degree = 1 + Utilities::pow(2, dim); + + // prepare FECollection with arbitrary number of entries + hp::FECollection fe_collection; + for (unsigned int i = 0; i < max_degree; ++i) + fe_collection.push_back(FE_Q(max_degree - i)); + + { + deallog << "writing" << std::endl; + + // ------ setup ------ + parallel::distributed::Triangulation tria(MPI_COMM_WORLD); + GridGenerator::subdivided_hyper_cube(tria, 2); + tria.refine_global(1); + + // this distribute_dofs() call is necessary + // we need to introduce dof_handler to its fe_collection first + hp::DoFHandler dh(tria); + dh.distribute_dofs(fe_collection); + + unsigned int i = 0; + for (auto &cell : dh.active_cell_iterators()) + if (cell->is_locally_owned()) + { + // set active fe index + if (!(cell->is_artificial())) + { + if (i >= fe_collection.size()) + i = 0; + cell->set_active_fe_index(i++); + } + + deallog << "cellid=" << cell->id() + << " fe_index=" << cell->active_fe_index() << std::endl; + } + + // ----- transfer ----- + dh.prepare_for_serialization_of_active_fe_indices(); + tria.save("file"); + + // make sure no processor is hanging + MPI_Barrier(MPI_COMM_WORLD); + } + + { + deallog << "reading" << std::endl; + + // ------ setup ------ + parallel::distributed::Triangulation tria(MPI_COMM_WORLD); + GridGenerator::subdivided_hyper_cube(tria, 2); + // triangulation has to be initialized with correct coarse cells + + // this distribute_dofs() call is necessary + // we need to introduce dof_handler to its fe_collection first + hp::DoFHandler dh(tria); + dh.distribute_dofs(fe_collection); + + // ----- transfer ----- + tria.load("file"); + dh.deserialize_active_fe_indices(); + + // ------ verify ------ + // check if all children adopted the correct id + for (auto &cell : dh.active_cell_iterators()) + if (cell->is_locally_owned()) + deallog << "cellid=" << cell->id() + << " fe_index=" << cell->active_fe_index() << std::endl; + + // distribute dofs again for further calculations, i.e. + // dh.distribute_dofs(fe_collection); + + // make sure no processor is hanging + MPI_Barrier(MPI_COMM_WORLD); + } + + deallog << "OK" << std::endl; +} + + +int +main(int argc, char *argv[]) +{ + Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1); + MPILogInitAll log; + + deallog.push("2d"); + test<2>(); + deallog.pop(); + deallog.push("3d"); + test<3>(); + deallog.pop(); +} diff --git a/tests/mpi/hp_active_fe_indices_transfer_02.with_p4est=true.mpirun=2.output b/tests/mpi/hp_active_fe_indices_transfer_02.with_p4est=true.mpirun=2.output new file mode 100644 index 000000000000..a9f6eeb1ba56 --- /dev/null +++ b/tests/mpi/hp_active_fe_indices_transfer_02.with_p4est=true.mpirun=2.output @@ -0,0 +1,175 @@ + +DEAL:0:2d::writing +DEAL:0:2d::cellid=0_1:0 fe_index=0 +DEAL:0:2d::cellid=0_1:1 fe_index=1 +DEAL:0:2d::cellid=0_1:2 fe_index=2 +DEAL:0:2d::cellid=0_1:3 fe_index=3 +DEAL:0:2d::cellid=1_1:0 fe_index=4 +DEAL:0:2d::cellid=1_1:1 fe_index=0 +DEAL:0:2d::cellid=1_1:2 fe_index=1 +DEAL:0:2d::cellid=1_1:3 fe_index=2 +DEAL:0:2d::reading +DEAL:0:2d::cellid=0_1:0 fe_index=0 +DEAL:0:2d::cellid=0_1:1 fe_index=1 +DEAL:0:2d::cellid=0_1:2 fe_index=2 +DEAL:0:2d::cellid=0_1:3 fe_index=3 +DEAL:0:2d::cellid=1_1:0 fe_index=4 +DEAL:0:2d::cellid=1_1:1 fe_index=0 +DEAL:0:2d::cellid=1_1:2 fe_index=1 +DEAL:0:2d::cellid=1_1:3 fe_index=2 +DEAL:0:2d::OK +DEAL:0:3d::writing +DEAL:0:3d::cellid=0_1:0 fe_index=0 +DEAL:0:3d::cellid=0_1:1 fe_index=1 +DEAL:0:3d::cellid=0_1:2 fe_index=2 +DEAL:0:3d::cellid=0_1:3 fe_index=3 +DEAL:0:3d::cellid=0_1:4 fe_index=4 +DEAL:0:3d::cellid=0_1:5 fe_index=5 +DEAL:0:3d::cellid=0_1:6 fe_index=6 +DEAL:0:3d::cellid=0_1:7 fe_index=7 +DEAL:0:3d::cellid=1_1:0 fe_index=8 +DEAL:0:3d::cellid=1_1:1 fe_index=0 +DEAL:0:3d::cellid=1_1:2 fe_index=1 +DEAL:0:3d::cellid=1_1:3 fe_index=2 +DEAL:0:3d::cellid=1_1:4 fe_index=3 +DEAL:0:3d::cellid=1_1:5 fe_index=4 +DEAL:0:3d::cellid=1_1:6 fe_index=5 +DEAL:0:3d::cellid=1_1:7 fe_index=6 +DEAL:0:3d::cellid=2_1:0 fe_index=7 +DEAL:0:3d::cellid=2_1:1 fe_index=8 +DEAL:0:3d::cellid=2_1:2 fe_index=0 +DEAL:0:3d::cellid=2_1:3 fe_index=1 +DEAL:0:3d::cellid=2_1:4 fe_index=2 +DEAL:0:3d::cellid=2_1:5 fe_index=3 +DEAL:0:3d::cellid=2_1:6 fe_index=4 +DEAL:0:3d::cellid=2_1:7 fe_index=5 +DEAL:0:3d::cellid=3_1:0 fe_index=6 +DEAL:0:3d::cellid=3_1:1 fe_index=7 +DEAL:0:3d::cellid=3_1:2 fe_index=8 +DEAL:0:3d::cellid=3_1:3 fe_index=0 +DEAL:0:3d::cellid=3_1:4 fe_index=1 +DEAL:0:3d::cellid=3_1:5 fe_index=2 +DEAL:0:3d::cellid=3_1:6 fe_index=3 +DEAL:0:3d::cellid=3_1:7 fe_index=4 +DEAL:0:3d::reading +DEAL:0:3d::cellid=0_1:0 fe_index=0 +DEAL:0:3d::cellid=0_1:1 fe_index=1 +DEAL:0:3d::cellid=0_1:2 fe_index=2 +DEAL:0:3d::cellid=0_1:3 fe_index=3 +DEAL:0:3d::cellid=0_1:4 fe_index=4 +DEAL:0:3d::cellid=0_1:5 fe_index=5 +DEAL:0:3d::cellid=0_1:6 fe_index=6 +DEAL:0:3d::cellid=0_1:7 fe_index=7 +DEAL:0:3d::cellid=1_1:0 fe_index=8 +DEAL:0:3d::cellid=1_1:1 fe_index=0 +DEAL:0:3d::cellid=1_1:2 fe_index=1 +DEAL:0:3d::cellid=1_1:3 fe_index=2 +DEAL:0:3d::cellid=1_1:4 fe_index=3 +DEAL:0:3d::cellid=1_1:5 fe_index=4 +DEAL:0:3d::cellid=1_1:6 fe_index=5 +DEAL:0:3d::cellid=1_1:7 fe_index=6 +DEAL:0:3d::cellid=2_1:0 fe_index=7 +DEAL:0:3d::cellid=2_1:1 fe_index=8 +DEAL:0:3d::cellid=2_1:2 fe_index=0 +DEAL:0:3d::cellid=2_1:3 fe_index=1 +DEAL:0:3d::cellid=2_1:4 fe_index=2 +DEAL:0:3d::cellid=2_1:5 fe_index=3 +DEAL:0:3d::cellid=2_1:6 fe_index=4 +DEAL:0:3d::cellid=2_1:7 fe_index=5 +DEAL:0:3d::cellid=3_1:0 fe_index=6 +DEAL:0:3d::cellid=3_1:1 fe_index=7 +DEAL:0:3d::cellid=3_1:2 fe_index=8 +DEAL:0:3d::cellid=3_1:3 fe_index=0 +DEAL:0:3d::cellid=3_1:4 fe_index=1 +DEAL:0:3d::cellid=3_1:5 fe_index=2 +DEAL:0:3d::cellid=3_1:6 fe_index=3 +DEAL:0:3d::cellid=3_1:7 fe_index=4 +DEAL:0:3d::OK + +DEAL:1:2d::writing +DEAL:1:2d::cellid=2_1:0 fe_index=0 +DEAL:1:2d::cellid=2_1:1 fe_index=1 +DEAL:1:2d::cellid=2_1:2 fe_index=2 +DEAL:1:2d::cellid=2_1:3 fe_index=3 +DEAL:1:2d::cellid=3_1:0 fe_index=4 +DEAL:1:2d::cellid=3_1:1 fe_index=0 +DEAL:1:2d::cellid=3_1:2 fe_index=1 +DEAL:1:2d::cellid=3_1:3 fe_index=2 +DEAL:1:2d::reading +DEAL:1:2d::cellid=2_1:0 fe_index=0 +DEAL:1:2d::cellid=2_1:1 fe_index=1 +DEAL:1:2d::cellid=2_1:2 fe_index=2 +DEAL:1:2d::cellid=2_1:3 fe_index=3 +DEAL:1:2d::cellid=3_1:0 fe_index=4 +DEAL:1:2d::cellid=3_1:1 fe_index=0 +DEAL:1:2d::cellid=3_1:2 fe_index=1 +DEAL:1:2d::cellid=3_1:3 fe_index=2 +DEAL:1:2d::OK +DEAL:1:3d::writing +DEAL:1:3d::cellid=4_1:0 fe_index=0 +DEAL:1:3d::cellid=4_1:1 fe_index=1 +DEAL:1:3d::cellid=4_1:2 fe_index=2 +DEAL:1:3d::cellid=4_1:3 fe_index=3 +DEAL:1:3d::cellid=4_1:4 fe_index=4 +DEAL:1:3d::cellid=4_1:5 fe_index=5 +DEAL:1:3d::cellid=4_1:6 fe_index=6 +DEAL:1:3d::cellid=4_1:7 fe_index=7 +DEAL:1:3d::cellid=5_1:0 fe_index=8 +DEAL:1:3d::cellid=5_1:1 fe_index=0 +DEAL:1:3d::cellid=5_1:2 fe_index=1 +DEAL:1:3d::cellid=5_1:3 fe_index=2 +DEAL:1:3d::cellid=5_1:4 fe_index=3 +DEAL:1:3d::cellid=5_1:5 fe_index=4 +DEAL:1:3d::cellid=5_1:6 fe_index=5 +DEAL:1:3d::cellid=5_1:7 fe_index=6 +DEAL:1:3d::cellid=6_1:0 fe_index=7 +DEAL:1:3d::cellid=6_1:1 fe_index=8 +DEAL:1:3d::cellid=6_1:2 fe_index=0 +DEAL:1:3d::cellid=6_1:3 fe_index=1 +DEAL:1:3d::cellid=6_1:4 fe_index=2 +DEAL:1:3d::cellid=6_1:5 fe_index=3 +DEAL:1:3d::cellid=6_1:6 fe_index=4 +DEAL:1:3d::cellid=6_1:7 fe_index=5 +DEAL:1:3d::cellid=7_1:0 fe_index=6 +DEAL:1:3d::cellid=7_1:1 fe_index=7 +DEAL:1:3d::cellid=7_1:2 fe_index=8 +DEAL:1:3d::cellid=7_1:3 fe_index=0 +DEAL:1:3d::cellid=7_1:4 fe_index=1 +DEAL:1:3d::cellid=7_1:5 fe_index=2 +DEAL:1:3d::cellid=7_1:6 fe_index=3 +DEAL:1:3d::cellid=7_1:7 fe_index=4 +DEAL:1:3d::reading +DEAL:1:3d::cellid=4_1:0 fe_index=0 +DEAL:1:3d::cellid=4_1:1 fe_index=1 +DEAL:1:3d::cellid=4_1:2 fe_index=2 +DEAL:1:3d::cellid=4_1:3 fe_index=3 +DEAL:1:3d::cellid=4_1:4 fe_index=4 +DEAL:1:3d::cellid=4_1:5 fe_index=5 +DEAL:1:3d::cellid=4_1:6 fe_index=6 +DEAL:1:3d::cellid=4_1:7 fe_index=7 +DEAL:1:3d::cellid=5_1:0 fe_index=8 +DEAL:1:3d::cellid=5_1:1 fe_index=0 +DEAL:1:3d::cellid=5_1:2 fe_index=1 +DEAL:1:3d::cellid=5_1:3 fe_index=2 +DEAL:1:3d::cellid=5_1:4 fe_index=3 +DEAL:1:3d::cellid=5_1:5 fe_index=4 +DEAL:1:3d::cellid=5_1:6 fe_index=5 +DEAL:1:3d::cellid=5_1:7 fe_index=6 +DEAL:1:3d::cellid=6_1:0 fe_index=7 +DEAL:1:3d::cellid=6_1:1 fe_index=8 +DEAL:1:3d::cellid=6_1:2 fe_index=0 +DEAL:1:3d::cellid=6_1:3 fe_index=1 +DEAL:1:3d::cellid=6_1:4 fe_index=2 +DEAL:1:3d::cellid=6_1:5 fe_index=3 +DEAL:1:3d::cellid=6_1:6 fe_index=4 +DEAL:1:3d::cellid=6_1:7 fe_index=5 +DEAL:1:3d::cellid=7_1:0 fe_index=6 +DEAL:1:3d::cellid=7_1:1 fe_index=7 +DEAL:1:3d::cellid=7_1:2 fe_index=8 +DEAL:1:3d::cellid=7_1:3 fe_index=0 +DEAL:1:3d::cellid=7_1:4 fe_index=1 +DEAL:1:3d::cellid=7_1:5 fe_index=2 +DEAL:1:3d::cellid=7_1:6 fe_index=3 +DEAL:1:3d::cellid=7_1:7 fe_index=4 +DEAL:1:3d::OK + diff --git a/tests/mpi/hp_active_fe_indices_transfer_02.with_p4est=true.mpirun=8.output b/tests/mpi/hp_active_fe_indices_transfer_02.with_p4est=true.mpirun=8.output new file mode 100644 index 000000000000..883234fd1c5e --- /dev/null +++ b/tests/mpi/hp_active_fe_indices_transfer_02.with_p4est=true.mpirun=8.output @@ -0,0 +1,223 @@ + +DEAL:0:2d::writing +DEAL:0:2d::cellid=0_1:0 fe_index=0 +DEAL:0:2d::cellid=0_1:1 fe_index=1 +DEAL:0:2d::cellid=0_1:2 fe_index=2 +DEAL:0:2d::cellid=0_1:3 fe_index=3 +DEAL:0:2d::reading +DEAL:0:2d::cellid=0_1:0 fe_index=0 +DEAL:0:2d::cellid=0_1:1 fe_index=1 +DEAL:0:2d::OK +DEAL:0:3d::writing +DEAL:0:3d::cellid=0_1:0 fe_index=0 +DEAL:0:3d::cellid=0_1:1 fe_index=1 +DEAL:0:3d::cellid=0_1:2 fe_index=2 +DEAL:0:3d::cellid=0_1:3 fe_index=3 +DEAL:0:3d::cellid=0_1:4 fe_index=4 +DEAL:0:3d::cellid=0_1:5 fe_index=5 +DEAL:0:3d::cellid=0_1:6 fe_index=6 +DEAL:0:3d::cellid=0_1:7 fe_index=7 +DEAL:0:3d::reading +DEAL:0:3d::cellid=0_1:0 fe_index=0 +DEAL:0:3d::cellid=0_1:1 fe_index=1 +DEAL:0:3d::cellid=0_1:2 fe_index=2 +DEAL:0:3d::cellid=0_1:3 fe_index=3 +DEAL:0:3d::cellid=0_1:4 fe_index=4 +DEAL:0:3d::cellid=0_1:5 fe_index=5 +DEAL:0:3d::cellid=0_1:6 fe_index=6 +DEAL:0:3d::cellid=0_1:7 fe_index=7 +DEAL:0:3d::OK + +DEAL:1:2d::writing +DEAL:1:2d::reading +DEAL:1:2d::cellid=0_1:2 fe_index=2 +DEAL:1:2d::cellid=0_1:3 fe_index=3 +DEAL:1:2d::OK +DEAL:1:3d::writing +DEAL:1:3d::cellid=1_1:0 fe_index=0 +DEAL:1:3d::cellid=1_1:1 fe_index=1 +DEAL:1:3d::cellid=1_1:2 fe_index=2 +DEAL:1:3d::cellid=1_1:3 fe_index=3 +DEAL:1:3d::cellid=1_1:4 fe_index=4 +DEAL:1:3d::cellid=1_1:5 fe_index=5 +DEAL:1:3d::cellid=1_1:6 fe_index=6 +DEAL:1:3d::cellid=1_1:7 fe_index=7 +DEAL:1:3d::reading +DEAL:1:3d::cellid=1_1:0 fe_index=0 +DEAL:1:3d::cellid=1_1:1 fe_index=1 +DEAL:1:3d::cellid=1_1:2 fe_index=2 +DEAL:1:3d::cellid=1_1:3 fe_index=3 +DEAL:1:3d::cellid=1_1:4 fe_index=4 +DEAL:1:3d::cellid=1_1:5 fe_index=5 +DEAL:1:3d::cellid=1_1:6 fe_index=6 +DEAL:1:3d::cellid=1_1:7 fe_index=7 +DEAL:1:3d::OK + + +DEAL:2:2d::writing +DEAL:2:2d::cellid=1_1:0 fe_index=0 +DEAL:2:2d::cellid=1_1:1 fe_index=1 +DEAL:2:2d::cellid=1_1:2 fe_index=2 +DEAL:2:2d::cellid=1_1:3 fe_index=3 +DEAL:2:2d::reading +DEAL:2:2d::cellid=1_1:0 fe_index=0 +DEAL:2:2d::cellid=1_1:1 fe_index=1 +DEAL:2:2d::OK +DEAL:2:3d::writing +DEAL:2:3d::cellid=2_1:0 fe_index=0 +DEAL:2:3d::cellid=2_1:1 fe_index=1 +DEAL:2:3d::cellid=2_1:2 fe_index=2 +DEAL:2:3d::cellid=2_1:3 fe_index=3 +DEAL:2:3d::cellid=2_1:4 fe_index=4 +DEAL:2:3d::cellid=2_1:5 fe_index=5 +DEAL:2:3d::cellid=2_1:6 fe_index=6 +DEAL:2:3d::cellid=2_1:7 fe_index=7 +DEAL:2:3d::reading +DEAL:2:3d::cellid=2_1:0 fe_index=0 +DEAL:2:3d::cellid=2_1:1 fe_index=1 +DEAL:2:3d::cellid=2_1:2 fe_index=2 +DEAL:2:3d::cellid=2_1:3 fe_index=3 +DEAL:2:3d::cellid=2_1:4 fe_index=4 +DEAL:2:3d::cellid=2_1:5 fe_index=5 +DEAL:2:3d::cellid=2_1:6 fe_index=6 +DEAL:2:3d::cellid=2_1:7 fe_index=7 +DEAL:2:3d::OK + + +DEAL:3:2d::writing +DEAL:3:2d::reading +DEAL:3:2d::cellid=1_1:2 fe_index=2 +DEAL:3:2d::cellid=1_1:3 fe_index=3 +DEAL:3:2d::OK +DEAL:3:3d::writing +DEAL:3:3d::cellid=3_1:0 fe_index=0 +DEAL:3:3d::cellid=3_1:1 fe_index=1 +DEAL:3:3d::cellid=3_1:2 fe_index=2 +DEAL:3:3d::cellid=3_1:3 fe_index=3 +DEAL:3:3d::cellid=3_1:4 fe_index=4 +DEAL:3:3d::cellid=3_1:5 fe_index=5 +DEAL:3:3d::cellid=3_1:6 fe_index=6 +DEAL:3:3d::cellid=3_1:7 fe_index=7 +DEAL:3:3d::reading +DEAL:3:3d::cellid=3_1:0 fe_index=0 +DEAL:3:3d::cellid=3_1:1 fe_index=1 +DEAL:3:3d::cellid=3_1:2 fe_index=2 +DEAL:3:3d::cellid=3_1:3 fe_index=3 +DEAL:3:3d::cellid=3_1:4 fe_index=4 +DEAL:3:3d::cellid=3_1:5 fe_index=5 +DEAL:3:3d::cellid=3_1:6 fe_index=6 +DEAL:3:3d::cellid=3_1:7 fe_index=7 +DEAL:3:3d::OK + + +DEAL:4:2d::writing +DEAL:4:2d::cellid=2_1:0 fe_index=0 +DEAL:4:2d::cellid=2_1:1 fe_index=1 +DEAL:4:2d::cellid=2_1:2 fe_index=2 +DEAL:4:2d::cellid=2_1:3 fe_index=3 +DEAL:4:2d::reading +DEAL:4:2d::cellid=2_1:0 fe_index=0 +DEAL:4:2d::cellid=2_1:1 fe_index=1 +DEAL:4:2d::OK +DEAL:4:3d::writing +DEAL:4:3d::cellid=4_1:0 fe_index=0 +DEAL:4:3d::cellid=4_1:1 fe_index=1 +DEAL:4:3d::cellid=4_1:2 fe_index=2 +DEAL:4:3d::cellid=4_1:3 fe_index=3 +DEAL:4:3d::cellid=4_1:4 fe_index=4 +DEAL:4:3d::cellid=4_1:5 fe_index=5 +DEAL:4:3d::cellid=4_1:6 fe_index=6 +DEAL:4:3d::cellid=4_1:7 fe_index=7 +DEAL:4:3d::reading +DEAL:4:3d::cellid=4_1:0 fe_index=0 +DEAL:4:3d::cellid=4_1:1 fe_index=1 +DEAL:4:3d::cellid=4_1:2 fe_index=2 +DEAL:4:3d::cellid=4_1:3 fe_index=3 +DEAL:4:3d::cellid=4_1:4 fe_index=4 +DEAL:4:3d::cellid=4_1:5 fe_index=5 +DEAL:4:3d::cellid=4_1:6 fe_index=6 +DEAL:4:3d::cellid=4_1:7 fe_index=7 +DEAL:4:3d::OK + + +DEAL:5:2d::writing +DEAL:5:2d::reading +DEAL:5:2d::cellid=2_1:2 fe_index=2 +DEAL:5:2d::cellid=2_1:3 fe_index=3 +DEAL:5:2d::OK +DEAL:5:3d::writing +DEAL:5:3d::cellid=5_1:0 fe_index=0 +DEAL:5:3d::cellid=5_1:1 fe_index=1 +DEAL:5:3d::cellid=5_1:2 fe_index=2 +DEAL:5:3d::cellid=5_1:3 fe_index=3 +DEAL:5:3d::cellid=5_1:4 fe_index=4 +DEAL:5:3d::cellid=5_1:5 fe_index=5 +DEAL:5:3d::cellid=5_1:6 fe_index=6 +DEAL:5:3d::cellid=5_1:7 fe_index=7 +DEAL:5:3d::reading +DEAL:5:3d::cellid=5_1:0 fe_index=0 +DEAL:5:3d::cellid=5_1:1 fe_index=1 +DEAL:5:3d::cellid=5_1:2 fe_index=2 +DEAL:5:3d::cellid=5_1:3 fe_index=3 +DEAL:5:3d::cellid=5_1:4 fe_index=4 +DEAL:5:3d::cellid=5_1:5 fe_index=5 +DEAL:5:3d::cellid=5_1:6 fe_index=6 +DEAL:5:3d::cellid=5_1:7 fe_index=7 +DEAL:5:3d::OK + + +DEAL:6:2d::writing +DEAL:6:2d::cellid=3_1:0 fe_index=0 +DEAL:6:2d::cellid=3_1:1 fe_index=1 +DEAL:6:2d::cellid=3_1:2 fe_index=2 +DEAL:6:2d::cellid=3_1:3 fe_index=3 +DEAL:6:2d::reading +DEAL:6:2d::cellid=3_1:0 fe_index=0 +DEAL:6:2d::cellid=3_1:1 fe_index=1 +DEAL:6:2d::OK +DEAL:6:3d::writing +DEAL:6:3d::cellid=6_1:0 fe_index=0 +DEAL:6:3d::cellid=6_1:1 fe_index=1 +DEAL:6:3d::cellid=6_1:2 fe_index=2 +DEAL:6:3d::cellid=6_1:3 fe_index=3 +DEAL:6:3d::cellid=6_1:4 fe_index=4 +DEAL:6:3d::cellid=6_1:5 fe_index=5 +DEAL:6:3d::cellid=6_1:6 fe_index=6 +DEAL:6:3d::cellid=6_1:7 fe_index=7 +DEAL:6:3d::reading +DEAL:6:3d::cellid=6_1:0 fe_index=0 +DEAL:6:3d::cellid=6_1:1 fe_index=1 +DEAL:6:3d::cellid=6_1:2 fe_index=2 +DEAL:6:3d::cellid=6_1:3 fe_index=3 +DEAL:6:3d::cellid=6_1:4 fe_index=4 +DEAL:6:3d::cellid=6_1:5 fe_index=5 +DEAL:6:3d::cellid=6_1:6 fe_index=6 +DEAL:6:3d::cellid=6_1:7 fe_index=7 +DEAL:6:3d::OK + + +DEAL:7:2d::writing +DEAL:7:2d::reading +DEAL:7:2d::cellid=3_1:2 fe_index=2 +DEAL:7:2d::cellid=3_1:3 fe_index=3 +DEAL:7:2d::OK +DEAL:7:3d::writing +DEAL:7:3d::cellid=7_1:0 fe_index=0 +DEAL:7:3d::cellid=7_1:1 fe_index=1 +DEAL:7:3d::cellid=7_1:2 fe_index=2 +DEAL:7:3d::cellid=7_1:3 fe_index=3 +DEAL:7:3d::cellid=7_1:4 fe_index=4 +DEAL:7:3d::cellid=7_1:5 fe_index=5 +DEAL:7:3d::cellid=7_1:6 fe_index=6 +DEAL:7:3d::cellid=7_1:7 fe_index=7 +DEAL:7:3d::reading +DEAL:7:3d::cellid=7_1:0 fe_index=0 +DEAL:7:3d::cellid=7_1:1 fe_index=1 +DEAL:7:3d::cellid=7_1:2 fe_index=2 +DEAL:7:3d::cellid=7_1:3 fe_index=3 +DEAL:7:3d::cellid=7_1:4 fe_index=4 +DEAL:7:3d::cellid=7_1:5 fe_index=5 +DEAL:7:3d::cellid=7_1:6 fe_index=6 +DEAL:7:3d::cellid=7_1:7 fe_index=7 +DEAL:7:3d::OK + diff --git a/tests/mpi/hp_cell_weights_01.cc b/tests/mpi/hp_cell_weights_01.cc index 838e48cc85f5..6d15d5841b32 100644 --- a/tests/mpi/hp_cell_weights_01.cc +++ b/tests/mpi/hp_cell_weights_01.cc @@ -30,7 +30,6 @@ // This test works on a parallel::distributed::Triangulation. -#include #include #include @@ -66,9 +65,6 @@ test() dh.distribute_dofs(fe_collection); - parallel::distributed::ActiveFEIndicesTransfer feidx_transfer(dh); - feidx_transfer.prepare_for_transfer(); - parallel::CellWeights cell_weights(dh); cell_weights.register_ndofs_weighting(100000); @@ -85,7 +81,6 @@ test() tria.repartition(); - feidx_transfer.unpack(); dh.distribute_dofs(fe_collection); diff --git a/tests/mpi/hp_cell_weights_02.cc b/tests/mpi/hp_cell_weights_02.cc index 52b8a6608007..5d13dff77469 100644 --- a/tests/mpi/hp_cell_weights_02.cc +++ b/tests/mpi/hp_cell_weights_02.cc @@ -36,7 +36,6 @@ // to 'cut' its tree on a parent branch that does not exist in this case. -#include #include #include @@ -72,9 +71,6 @@ test() dh.distribute_dofs(fe_collection); - parallel::distributed::ActiveFEIndicesTransfer feidx_transfer(dh); - feidx_transfer.prepare_for_transfer(); - parallel::CellWeights cell_weights(dh); cell_weights.register_ndofs_weighting(100000); @@ -91,7 +87,6 @@ test() tria.repartition(); - feidx_transfer.unpack(); dh.distribute_dofs(fe_collection); diff --git a/tests/mpi/p4est_save_06.cc b/tests/mpi/p4est_save_06.cc index 446242a45410..5af46a86964b 100644 --- a/tests/mpi/p4est_save_06.cc +++ b/tests/mpi/p4est_save_06.cc @@ -21,7 +21,6 @@ #include #include -#include #include #include @@ -93,8 +92,6 @@ test() locally_relevant_dofs, com_small); - parallel::distributed::ActiveFEIndicesTransfer feidx_transfer( - dh); parallel::distributed:: SolutionTransfer> soltrans(dh); @@ -109,7 +106,7 @@ test() x.compress(VectorOperation::insert); rel_x = x; - feidx_transfer.prepare_for_transfer(); + dh.prepare_for_serialization_of_active_fe_indices(); soltrans.prepare_serialization(rel_x); tr.save("file"); @@ -138,10 +135,7 @@ test() fe_collection.push_back(FE_Q(max_degree - i)); dh.distribute_dofs(fe_collection); - - parallel::distributed::ActiveFEIndicesTransfer feidx_transfer(dh); - feidx_transfer.deserialize(); - + dh.deserialize_active_fe_indices(); dh.distribute_dofs(fe_collection); IndexSet locally_owned_dofs = dh.locally_owned_dofs(); diff --git a/tests/mpi/solution_transfer_04.cc b/tests/mpi/solution_transfer_04.cc index 6edb651b388d..6f81c5cf5f24 100644 --- a/tests/mpi/solution_transfer_04.cc +++ b/tests/mpi/solution_transfer_04.cc @@ -19,7 +19,6 @@ // This tests is based on mpi/feindices_transfer.cc -#include #include #include @@ -101,17 +100,13 @@ test() // ----- transfer ----- - parallel::distributed::ActiveFEIndicesTransfer feidx_transfer(dh); parallel::distributed:: SolutionTransfer> soltrans(dh); - feidx_transfer.prepare_for_transfer(); soltrans.prepare_for_coarsening_and_refinement(old_solution); tria.execute_coarsening_and_refinement(); - feidx_transfer.unpack(); - dh.distribute_dofs(fe_collection); locally_owned_dofs = dh.locally_owned_dofs(); DoFTools::extract_locally_relevant_dofs(dh, locally_relevant_dofs); From 3d6616dff1ed167c2e7669dc2d4da99d0d366465 Mon Sep 17 00:00:00 2001 From: Matthias Maier Date: Tue, 5 Feb 2019 15:12:52 -0600 Subject: [PATCH 077/507] CMake: error message + guard target - Add a helpful message to make debug/release targets. - Only create the corresponding debug/release target if the build type is available. --- .../macro_deal_ii_invoke_autopilot.cmake | 34 ++++++++++++++----- 1 file changed, 26 insertions(+), 8 deletions(-) diff --git a/cmake/macros/macro_deal_ii_invoke_autopilot.cmake b/cmake/macros/macro_deal_ii_invoke_autopilot.cmake index a494f0a9e8f4..ca5a1c0832a9 100644 --- a/cmake/macros/macro_deal_ii_invoke_autopilot.cmake +++ b/cmake/macros/macro_deal_ii_invoke_autopilot.cmake @@ -138,19 +138,37 @@ MACRO(DEAL_II_INVOKE_AUTOPILOT) ) ENDIF() + # # Define custom targets to easily switch the build type: - ADD_CUSTOM_TARGET(debug - COMMAND ${CMAKE_COMMAND} -DCMAKE_BUILD_TYPE=Debug ${CMAKE_SOURCE_DIR} - COMMENT "Switch CMAKE_BUILD_TYPE to Debug" - ) + # - ADD_CUSTOM_TARGET(release - COMMAND ${CMAKE_COMMAND} -DCMAKE_BUILD_TYPE=Release ${CMAKE_SOURCE_DIR} - COMMENT "Switch CMAKE_BUILD_TYPE to Release" - ) + IF(${DEAL_II_BUILD_TYPE} MATCHES "Debug") + ADD_CUSTOM_TARGET(debug + COMMAND ${CMAKE_COMMAND} -DCMAKE_BUILD_TYPE=Debug ${CMAKE_SOURCE_DIR} + COMMAND ${CMAKE_COMMAND} -E echo "***" + COMMAND ${CMAKE_COMMAND} -E echo "*** Switched to Debug mode. Now recompile with: ${_make_command}" + COMMAND ${CMAKE_COMMAND} -E echo "***" + COMMENT "Switch CMAKE_BUILD_TYPE to Debug" + VERBATIM + ) + ENDIF() + IF(${DEAL_II_BUILD_TYPE} MATCHES "Release") + ADD_CUSTOM_TARGET(release + COMMAND ${CMAKE_COMMAND} -DCMAKE_BUILD_TYPE=Release ${CMAKE_SOURCE_DIR} + COMMAND ${CMAKE_COMMAND} -E echo "***" + COMMAND ${CMAKE_COMMAND} -E echo "*** Switched to Release mode. Now recompile with: ${_make_command}" + COMMAND ${CMAKE_COMMAND} -E echo "***" + COMMENT "Switch CMAKE_BUILD_TYPE to Release" + VERBATIM + ) + ENDIF() + + # # Only mention release and debug targets if it is actually possible to # switch between them: + # + IF(${DEAL_II_BUILD_TYPE} MATCHES "DebugRelease") SET(_switch_targets "# ${_make_command} debug - to switch the build type to 'Debug' From f7cd45eeda29d4e503057f1bf96c78f894e53d67 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Wed, 30 Jan 2019 21:05:36 +0100 Subject: [PATCH 078/507] Move and fix std::enable_if to a template parameter, fix test --- ...GiovanniAlzettaDanielArndtWolfgangBangerth | 4 ++ include/deal.II/base/point.h | 15 ++++--- tests/base/point_04.cc | 45 ++++++++++++------- tests/base/point_04.output | 4 ++ 4 files changed, 45 insertions(+), 23 deletions(-) create mode 100644 doc/news/changes/minor/20190131GiovanniAlzettaDanielArndtWolfgangBangerth diff --git a/doc/news/changes/minor/20190131GiovanniAlzettaDanielArndtWolfgangBangerth b/doc/news/changes/minor/20190131GiovanniAlzettaDanielArndtWolfgangBangerth new file mode 100644 index 000000000000..882d29c7cba7 --- /dev/null +++ b/doc/news/changes/minor/20190131GiovanniAlzettaDanielArndtWolfgangBangerth @@ -0,0 +1,4 @@ +New: added constructor to the class Point, which converts +a boost::geometry::model::point to a dealii::Point +
+(Giovanni Alzetta, Daniel Arndt, Wolfgang Bangerth, 2019/01/31) diff --git a/include/deal.II/base/point.h b/include/deal.II/base/point.h index d486ae36c858..093c87eaa3d6 100644 --- a/include/deal.II/base/point.h +++ b/include/deal.II/base/point.h @@ -148,11 +148,11 @@ class Point : public Tensor<1, dim, Number> /** * Convert a boost::geometry::point to a dealii::Point. */ - template + template ::type = 0> Point(const boost::geometry::model:: - point &boost_pt, - typename std::enable_if<(dim == dummy_dim) && (dummy_dim != 0), - int>::type = 0); + point &boost_pt); /** * Return a unit vector in coordinate direction i, i.e., a vector @@ -371,11 +371,12 @@ inline Point::Point(const Number x, const Number y, const Number z) template -template +template < + std::size_t dummy_dim, + typename std::enable_if<(dim == dummy_dim) && (dummy_dim != 0), int>::type> inline Point::Point( const boost::geometry::model:: - point &boost_pt, - typename std::enable_if<(dim == dummy_dim) && (dummy_dim != 0), int>::type) + point &boost_pt) { Assert(dim <= 3, ExcNotImplemented()); this->values[0] = boost::geometry::get<0>(boost_pt); diff --git a/tests/base/point_04.cc b/tests/base/point_04.cc index 7dbb62241b5f..97613ae51f9e 100644 --- a/tests/base/point_04.cc +++ b/tests/base/point_04.cc @@ -26,37 +26,50 @@ namespace bg = boost::geometry; -template void -check() +check3d() { - bg::model::point bg_point; + bg::model::point point(-1.0, + 2.0, + 0.15); - constexpr unsigned int y_index = (spacedim < 2) ? 0 : 1; - constexpr unsigned int z_index = (spacedim < 3) ? 0 : 2; + Point<3> p(point); - bg_point.set<0>(42.0); - - if (dim >= 2) - bg_point.set(42.0 + dim); + for (unsigned int i = 0; i < 3; ++i) + deallog << p(i) << ' '; + deallog << std::endl; +} - if (dim >= 3) - bg_point.set(42.0 + dim + 1); +void +check2d() +{ + bg::model::point point(2.0, 3.0); - Point p(bg_point); + Point<2> p(point); - for (unsigned int i = 0; i < dim; ++i) + for (unsigned int i = 0; i < 2; ++i) deallog << p(i) << ' '; deallog << std::endl; } +void +check1d() +{ + bg::model::point point(12.0); + + Point<1> p(point); + + deallog << p(0) << ' '; + deallog << std::endl; +} + int main() { initlog(); deallog << std::setprecision(3); - check<1>(); - check<2>(); - check<3>(); + check1d(); + check2d(); + check3d(); } diff --git a/tests/base/point_04.output b/tests/base/point_04.output index e69de29bb2d1..199099313332 100644 --- a/tests/base/point_04.output +++ b/tests/base/point_04.output @@ -0,0 +1,4 @@ + +DEAL::12.0 +DEAL::2.00 3.00 +DEAL::-1.00 2.00 0.150 From 7ceedf3bfaed059d4d2e354f839fd9a75c7b0c19 Mon Sep 17 00:00:00 2001 From: Martin Kronbichler Date: Fri, 8 Feb 2019 16:28:21 +0100 Subject: [PATCH 079/507] Adjust Chebyshev degree in loop to convention in literature. --- examples/step-37/step-37.cc | 4 +- examples/step-59/step-59.cc | 2 +- include/deal.II/lac/precondition.h | 10 +- tests/lac/precondition_chebyshev_01.cc | 2 +- tests/lac/precondition_chebyshev_02.cc | 2 +- tests/lac/precondition_chebyshev_03.cc | 2 +- tests/lac/precondition_chebyshev_04.cc | 2 +- tests/lac/precondition_chebyshev_05.cc | 2 +- ...h_mpi=true.with_p4est=true.mpirun=1.output | 20 +- ...h_mpi=true.with_p4est=true.mpirun=3.output | 20 +- ...h_mpi=true.with_p4est=true.mpirun=5.output | 20 +- ...h_mpi=true.with_p4est=true.mpirun=1.output | 20 +- ...h_mpi=true.with_p4est=true.mpirun=5.output | 20 +- ...h_mpi=true.with_p4est=true.mpirun=5.output | 20 +- ...inos=true.with_lapack=true.mpirun=3.output | 202 ++++++++++-------- ...inos=true.with_lapack=true.mpirun=7.output | 202 ++++++++++-------- ...inos=true.with_lapack=true.mpirun=3.output | 97 +++++---- ...inos=true.with_lapack=true.mpirun=7.output | 97 +++++---- ...inos=true.with_lapack=true.mpirun=3.output | 14 +- ...inos=true.with_lapack=true.mpirun=7.output | 14 +- ...4est=true.with_lapack=true.mpirun=3.output | 24 +-- ...4est=true.with_lapack=true.mpirun=7.output | 24 +-- ...4est=true.with_lapack=true.mpirun=4.output | 52 ++--- ...4est=true.with_lapack=true.mpirun=7.output | 52 ++--- ...4est=true.with_lapack=true.mpirun=4.output | 8 +- ...4est=true.with_lapack=true.mpirun=7.output | 16 +- ...ogeneous-1.mpirun=4.with_p4est=true.output | 88 ++++---- .../step-37.with_lapack=true.output | 12 +- ...h_mpi=true.with_p4est=true.mpirun=4.output | 6 +- tests/multigrid/step-16-04.cc | 2 +- tests/multigrid/step-16-05.cc | 2 +- tests/multigrid/step-16-06.cc | 2 +- tests/multigrid/step-16-50-serial.cc | 1 + tests/multigrid/step-16-50-serial.output | 20 +- 34 files changed, 567 insertions(+), 514 deletions(-) diff --git a/examples/step-37/step-37.cc b/examples/step-37/step-37.cc index 65d118b59b30..e64baa61b83b 100644 --- a/examples/step-37/step-37.cc +++ b/examples/step-37/step-37.cc @@ -950,7 +950,7 @@ namespace Step37 // do not have the matrix elements available explicitly, and it is // difficult to make it work efficiently in %parallel.) The smoother is // initialized with our level matrices and the mandatory additional data - // for the Chebyshev smoother. We use a relatively high degree here (4), + // for the Chebyshev smoother. We use a relatively high degree here (5), // since matrix-vector products are comparably cheap. We choose to smooth // out a range of $[1.2 \hat{\lambda}_{\max}/15,1.2 \hat{\lambda}_{\max}]$ // in the smoother where $\hat{\lambda}_{\max}$ is an estimate of the @@ -1002,7 +1002,7 @@ namespace Step37 if (level > 0) { smoother_data[level].smoothing_range = 15.; - smoother_data[level].degree = 4; + smoother_data[level].degree = 5; smoother_data[level].eig_cg_n_iterations = 10; } else diff --git a/examples/step-59/step-59.cc b/examples/step-59/step-59.cc index 979488fdde04..5627107ffb57 100644 --- a/examples/step-59/step-59.cc +++ b/examples/step-59/step-59.cc @@ -1235,7 +1235,7 @@ namespace Step59 if (level > 0) { smoother_data[level].smoothing_range = 15.; - smoother_data[level].degree = 2; + smoother_data[level].degree = 3; smoother_data[level].eig_cg_n_iterations = 10; } else diff --git a/include/deal.II/lac/precondition.h b/include/deal.II/lac/precondition.h index e61138208aa6..be50dd34a702 100644 --- a/include/deal.II/lac/precondition.h +++ b/include/deal.II/lac/precondition.h @@ -2250,13 +2250,16 @@ inline void PreconditionChebyshev:: do_chebyshev_loop(VectorType &dst, const VectorType &src) const { + if (data.degree < 2) + return; + // if delta is zero, we do not need to iterate because the updates will be // zero if (std::abs(delta) < 1e-40) return; double rhok = delta / theta, sigma = theta / delta; - for (unsigned int k = 0; k < data.degree; ++k) + for (unsigned int k = 0; k < data.degree - 1; ++k) { matrix_ptr->vmult(update2, dst); const double rhokp = 1. / (2. * sigma - rhok); @@ -2282,8 +2285,11 @@ inline void PreconditionChebyshev:: do_transpose_chebyshev_loop(VectorType &dst, const VectorType &src) const { + if (data.degree < 2) + return; + double rhok = delta / theta, sigma = theta / delta; - for (unsigned int k = 0; k < data.degree; ++k) + for (unsigned int k = 0; k < data.degree - 1; ++k) { matrix_ptr->Tvmult(update2, dst); const double rhokp = 1. / (2. * sigma - rhok); diff --git a/tests/lac/precondition_chebyshev_01.cc b/tests/lac/precondition_chebyshev_01.cc index 14caa3699b8f..494c61b4c5d4 100644 --- a/tests/lac/precondition_chebyshev_01.cc +++ b/tests/lac/precondition_chebyshev_01.cc @@ -56,7 +56,7 @@ check() PreconditionChebyshev>::AdditionalData data; data.smoothing_range = 2 * size; - data.degree = 3; + data.degree = 4; prec.initialize(m, data); deallog << "Exact inverse: "; diff --git a/tests/lac/precondition_chebyshev_02.cc b/tests/lac/precondition_chebyshev_02.cc index 13a179d44fbd..5b029fbcfc91 100644 --- a/tests/lac/precondition_chebyshev_02.cc +++ b/tests/lac/precondition_chebyshev_02.cc @@ -87,7 +87,7 @@ check() Vector, DiagonalMatrixManual>::AdditionalData data; data.smoothing_range = 2 * size; - data.degree = 3; + data.degree = 4; data.preconditioner.reset(new DiagonalMatrixManual()); data.preconditioner->set_vector_one(size); prec.initialize(m, data); diff --git a/tests/lac/precondition_chebyshev_03.cc b/tests/lac/precondition_chebyshev_03.cc index 4a964e85f4f7..c8999d959bca 100644 --- a/tests/lac/precondition_chebyshev_03.cc +++ b/tests/lac/precondition_chebyshev_03.cc @@ -59,7 +59,7 @@ main() SparseILU>::AdditionalData cheby_data; cheby_data.preconditioner.reset(new SparseILU()); cheby_data.preconditioner->initialize(A); - cheby_data.degree = 10; + cheby_data.degree = 11; cheby_data.smoothing_range = 40; cheby.initialize(A, cheby_data); diff --git a/tests/lac/precondition_chebyshev_04.cc b/tests/lac/precondition_chebyshev_04.cc index a4ba314794d0..484e93c22986 100644 --- a/tests/lac/precondition_chebyshev_04.cc +++ b/tests/lac/precondition_chebyshev_04.cc @@ -87,7 +87,7 @@ check() Vector, DiagonalMatrixManual>::AdditionalData data; data.smoothing_range = 2 * size; - data.degree = 3; + data.degree = 4; data.preconditioner.reset(new DiagonalMatrixManual()); data.preconditioner->set_vector_one(size); prec.initialize(m, data); diff --git a/tests/lac/precondition_chebyshev_05.cc b/tests/lac/precondition_chebyshev_05.cc index 8e6d2c1b1218..c65114d273f1 100644 --- a/tests/lac/precondition_chebyshev_05.cc +++ b/tests/lac/precondition_chebyshev_05.cc @@ -67,7 +67,7 @@ main(int argc, char **argv) cheby_data.preconditioner.reset( new TrilinosWrappers::PreconditionJacobi()); cheby_data.preconditioner->initialize(AA); - cheby_data.degree = 10; + cheby_data.degree = 11; cheby_data.smoothing_range = 40; cheby.initialize(AA, cheby_data); diff --git a/tests/matrix_free/multigrid_dg_periodic.with_trilinos=true.with_mpi=true.with_p4est=true.mpirun=1.output b/tests/matrix_free/multigrid_dg_periodic.with_trilinos=true.with_mpi=true.with_p4est=true.mpirun=1.output index 9465de82032c..4624baa08f23 100644 --- a/tests/matrix_free/multigrid_dg_periodic.with_trilinos=true.with_mpi=true.with_p4est=true.mpirun=1.output +++ b/tests/matrix_free/multigrid_dg_periodic.with_trilinos=true.with_mpi=true.with_p4est=true.mpirun=1.output @@ -2,40 +2,40 @@ DEAL:2d::Testing FE_DGQ<2>(1) DEAL:2d::Number of degrees of freedom: 256 DEAL:2d:cg::Starting value 16.0000 -DEAL:2d:cg::Convergence step 6 value 3.31973e-12 +DEAL:2d:cg::Convergence step 7 value 1.80729e-11 DEAL:2d::Testing FE_DGQ<2>(1) DEAL:2d::Number of degrees of freedom: 1024 DEAL:2d:cg::Starting value 32.0000 -DEAL:2d:cg::Convergence step 6 value 1.50088e-09 +DEAL:2d:cg::Convergence step 8 value 8.73511e-11 DEAL:2d::Testing FE_DGQ<2>(1) DEAL:2d::Number of degrees of freedom: 4096 DEAL:2d:cg::Starting value 64.0000 -DEAL:2d:cg::Convergence step 7 value 7.89595e-10 +DEAL:2d:cg::Convergence step 8 value 4.57619e-10 DEAL:2d::Testing FE_DGQ<2>(2) DEAL:2d::Number of degrees of freedom: 576 DEAL:2d:cg::Starting value 24.0000 -DEAL:2d:cg::Convergence step 6 value 2.18769e-10 +DEAL:2d:cg::Convergence step 7 value 1.07430e-09 DEAL:2d::Testing FE_DGQ<2>(2) DEAL:2d::Number of degrees of freedom: 2304 DEAL:2d:cg::Starting value 48.0000 -DEAL:2d:cg::Convergence step 6 value 1.04858e-09 +DEAL:2d:cg::Convergence step 8 value 1.87005e-10 DEAL:3d::Testing FE_DGQ<3>(1) DEAL:3d::Number of degrees of freedom: 512 DEAL:3d:cg::Starting value 22.6274 -DEAL:3d:cg::Convergence step 4 value 1.39603e-17 +DEAL:3d:cg::Convergence step 4 value 7.99677e-17 DEAL:3d::Testing FE_DGQ<3>(1) DEAL:3d::Number of degrees of freedom: 4096 DEAL:3d:cg::Starting value 64.0000 -DEAL:3d:cg::Convergence step 6 value 2.68072e-11 +DEAL:3d:cg::Convergence step 6 value 2.27740e-11 DEAL:3d::Testing FE_DGQ<3>(1) DEAL:3d::Number of degrees of freedom: 32768 DEAL:3d:cg::Starting value 181.019 -DEAL:3d:cg::Convergence step 7 value 8.70647e-10 +DEAL:3d:cg::Convergence step 7 value 2.41331e-09 DEAL:3d::Testing FE_DGQ<3>(2) DEAL:3d::Number of degrees of freedom: 1728 DEAL:3d:cg::Starting value 41.5692 -DEAL:3d:cg::Convergence step 7 value 1.39310e-09 +DEAL:3d:cg::Convergence step 8 value 1.14978e-09 DEAL:3d::Testing FE_DGQ<3>(2) DEAL:3d::Number of degrees of freedom: 13824 DEAL:3d:cg::Starting value 117.576 -DEAL:3d:cg::Convergence step 8 value 1.40299e-09 +DEAL:3d:cg::Convergence step 9 value 1.16347e-09 diff --git a/tests/matrix_free/multigrid_dg_periodic.with_trilinos=true.with_mpi=true.with_p4est=true.mpirun=3.output b/tests/matrix_free/multigrid_dg_periodic.with_trilinos=true.with_mpi=true.with_p4est=true.mpirun=3.output index 07dcc3520536..7630f429b145 100644 --- a/tests/matrix_free/multigrid_dg_periodic.with_trilinos=true.with_mpi=true.with_p4est=true.mpirun=3.output +++ b/tests/matrix_free/multigrid_dg_periodic.with_trilinos=true.with_mpi=true.with_p4est=true.mpirun=3.output @@ -2,40 +2,40 @@ DEAL:2d::Testing FE_DGQ<2>(1) DEAL:2d::Number of degrees of freedom: 256 DEAL:2d:cg::Starting value 16.0000 -DEAL:2d:cg::Convergence step 6 value 3.31973e-12 +DEAL:2d:cg::Convergence step 7 value 1.80729e-11 DEAL:2d::Testing FE_DGQ<2>(1) DEAL:2d::Number of degrees of freedom: 1024 DEAL:2d:cg::Starting value 32.0000 -DEAL:2d:cg::Convergence step 6 value 1.50088e-09 +DEAL:2d:cg::Convergence step 8 value 8.73511e-11 DEAL:2d::Testing FE_DGQ<2>(1) DEAL:2d::Number of degrees of freedom: 4096 DEAL:2d:cg::Starting value 64.0000 -DEAL:2d:cg::Convergence step 7 value 7.89595e-10 +DEAL:2d:cg::Convergence step 8 value 4.57619e-10 DEAL:2d::Testing FE_DGQ<2>(2) DEAL:2d::Number of degrees of freedom: 576 DEAL:2d:cg::Starting value 24.0000 -DEAL:2d:cg::Convergence step 6 value 2.18769e-10 +DEAL:2d:cg::Convergence step 7 value 1.07430e-09 DEAL:2d::Testing FE_DGQ<2>(2) DEAL:2d::Number of degrees of freedom: 2304 DEAL:2d:cg::Starting value 48.0000 -DEAL:2d:cg::Convergence step 6 value 1.04858e-09 +DEAL:2d:cg::Convergence step 8 value 1.87005e-10 DEAL:3d::Testing FE_DGQ<3>(1) DEAL:3d::Number of degrees of freedom: 512 DEAL:3d:cg::Starting value 22.6274 -DEAL:3d:cg::Convergence step 4 value 1.45014e-17 +DEAL:3d:cg::Convergence step 4 value 9.91449e-17 DEAL:3d::Testing FE_DGQ<3>(1) DEAL:3d::Number of degrees of freedom: 4096 DEAL:3d:cg::Starting value 64.0000 -DEAL:3d:cg::Convergence step 6 value 2.68072e-11 +DEAL:3d:cg::Convergence step 6 value 2.27740e-11 DEAL:3d::Testing FE_DGQ<3>(1) DEAL:3d::Number of degrees of freedom: 32768 DEAL:3d:cg::Starting value 181.019 -DEAL:3d:cg::Convergence step 7 value 8.70647e-10 +DEAL:3d:cg::Convergence step 7 value 2.41331e-09 DEAL:3d::Testing FE_DGQ<3>(2) DEAL:3d::Number of degrees of freedom: 1728 DEAL:3d:cg::Starting value 41.5692 -DEAL:3d:cg::Convergence step 7 value 1.39310e-09 +DEAL:3d:cg::Convergence step 8 value 1.14978e-09 DEAL:3d::Testing FE_DGQ<3>(2) DEAL:3d::Number of degrees of freedom: 13824 DEAL:3d:cg::Starting value 117.576 -DEAL:3d:cg::Convergence step 8 value 1.40299e-09 +DEAL:3d:cg::Convergence step 9 value 1.16347e-09 diff --git a/tests/matrix_free/multigrid_dg_periodic.with_trilinos=true.with_mpi=true.with_p4est=true.mpirun=5.output b/tests/matrix_free/multigrid_dg_periodic.with_trilinos=true.with_mpi=true.with_p4est=true.mpirun=5.output index 6d3556b543b8..e2e33e652a97 100644 --- a/tests/matrix_free/multigrid_dg_periodic.with_trilinos=true.with_mpi=true.with_p4est=true.mpirun=5.output +++ b/tests/matrix_free/multigrid_dg_periodic.with_trilinos=true.with_mpi=true.with_p4est=true.mpirun=5.output @@ -2,40 +2,40 @@ DEAL:2d::Testing FE_DGQ<2>(1) DEAL:2d::Number of degrees of freedom: 256 DEAL:2d:cg::Starting value 16.0000 -DEAL:2d:cg::Convergence step 6 value 3.31973e-12 +DEAL:2d:cg::Convergence step 7 value 1.80729e-11 DEAL:2d::Testing FE_DGQ<2>(1) DEAL:2d::Number of degrees of freedom: 1024 DEAL:2d:cg::Starting value 32.0000 -DEAL:2d:cg::Convergence step 6 value 1.50088e-09 +DEAL:2d:cg::Convergence step 8 value 8.73511e-11 DEAL:2d::Testing FE_DGQ<2>(1) DEAL:2d::Number of degrees of freedom: 4096 DEAL:2d:cg::Starting value 64.0000 -DEAL:2d:cg::Convergence step 7 value 7.89595e-10 +DEAL:2d:cg::Convergence step 8 value 4.57619e-10 DEAL:2d::Testing FE_DGQ<2>(2) DEAL:2d::Number of degrees of freedom: 576 DEAL:2d:cg::Starting value 24.0000 -DEAL:2d:cg::Convergence step 6 value 2.18769e-10 +DEAL:2d:cg::Convergence step 7 value 1.07430e-09 DEAL:2d::Testing FE_DGQ<2>(2) DEAL:2d::Number of degrees of freedom: 2304 DEAL:2d:cg::Starting value 48.0000 -DEAL:2d:cg::Convergence step 6 value 1.04858e-09 +DEAL:2d:cg::Convergence step 8 value 1.87005e-10 DEAL:3d::Testing FE_DGQ<3>(1) DEAL:3d::Number of degrees of freedom: 512 DEAL:3d:cg::Starting value 22.6274 -DEAL:3d:cg::Convergence step 4 value 1.18679e-17 +DEAL:3d:cg::Convergence step 4 value 7.23452e-17 DEAL:3d::Testing FE_DGQ<3>(1) DEAL:3d::Number of degrees of freedom: 4096 DEAL:3d:cg::Starting value 64.0000 -DEAL:3d:cg::Convergence step 6 value 2.68072e-11 +DEAL:3d:cg::Convergence step 6 value 2.27740e-11 DEAL:3d::Testing FE_DGQ<3>(1) DEAL:3d::Number of degrees of freedom: 32768 DEAL:3d:cg::Starting value 181.019 -DEAL:3d:cg::Convergence step 7 value 8.70647e-10 +DEAL:3d:cg::Convergence step 7 value 2.41331e-09 DEAL:3d::Testing FE_DGQ<3>(2) DEAL:3d::Number of degrees of freedom: 1728 DEAL:3d:cg::Starting value 41.5692 -DEAL:3d:cg::Convergence step 7 value 1.39310e-09 +DEAL:3d:cg::Convergence step 8 value 1.14978e-09 DEAL:3d::Testing FE_DGQ<3>(2) DEAL:3d::Number of degrees of freedom: 13824 DEAL:3d:cg::Starting value 117.576 -DEAL:3d:cg::Convergence step 8 value 1.40299e-09 +DEAL:3d:cg::Convergence step 9 value 1.16347e-09 diff --git a/tests/matrix_free/multigrid_dg_sip_01.with_mpi=true.with_p4est=true.mpirun=1.output b/tests/matrix_free/multigrid_dg_sip_01.with_mpi=true.with_p4est=true.mpirun=1.output index 29dbbfae2dc3..3755b9b07c24 100644 --- a/tests/matrix_free/multigrid_dg_sip_01.with_mpi=true.with_p4est=true.mpirun=1.output +++ b/tests/matrix_free/multigrid_dg_sip_01.with_mpi=true.with_p4est=true.mpirun=1.output @@ -2,40 +2,40 @@ DEAL:2d::Testing FE_DGQ<2>(1) DEAL:2d::Number of degrees of freedom: 256 DEAL:2d:cg::Starting value 16.0000 -DEAL:2d:cg::Convergence step 4 value 1.45213e-06 +DEAL:2d:cg::Convergence step 5 value 3.60502e-07 DEAL:2d::Testing FE_DGQ<2>(1) DEAL:2d::Number of degrees of freedom: 1024 DEAL:2d:cg::Starting value 32.0000 -DEAL:2d:cg::Convergence step 5 value 8.09074e-08 +DEAL:2d:cg::Convergence step 5 value 2.14074e-06 DEAL:2d::Testing FE_DGQ<2>(1) DEAL:2d::Number of degrees of freedom: 4096 DEAL:2d:cg::Starting value 64.0000 -DEAL:2d:cg::Convergence step 5 value 9.08540e-07 +DEAL:2d:cg::Convergence step 5 value 5.99637e-06 DEAL:2d::Testing FE_DGQ<2>(2) DEAL:2d::Number of degrees of freedom: 576 DEAL:2d:cg::Starting value 24.0000 -DEAL:2d:cg::Convergence step 5 value 4.02774e-08 +DEAL:2d:cg::Convergence step 5 value 1.81901e-06 DEAL:2d::Testing FE_DGQ<2>(2) DEAL:2d::Number of degrees of freedom: 2304 DEAL:2d:cg::Starting value 48.0000 -DEAL:2d:cg::Convergence step 5 value 7.58404e-08 +DEAL:2d:cg::Convergence step 6 value 1.94976e-07 DEAL:3d::Testing FE_DGQ<3>(1) DEAL:3d::Number of degrees of freedom: 512 DEAL:3d:cg::Starting value 22.6274 -DEAL:3d:cg::Convergence step 5 value 2.70681e-07 +DEAL:3d:cg::Convergence step 6 value 7.43327e-08 DEAL:3d::Testing FE_DGQ<3>(1) DEAL:3d::Number of degrees of freedom: 4096 DEAL:3d:cg::Starting value 64.0000 -DEAL:3d:cg::Convergence step 5 value 3.69638e-06 +DEAL:3d:cg::Convergence step 6 value 2.28298e-06 DEAL:3d::Testing FE_DGQ<3>(1) DEAL:3d::Number of degrees of freedom: 32768 DEAL:3d:cg::Starting value 181.019 -DEAL:3d:cg::Convergence step 5 value 5.56024e-06 +DEAL:3d:cg::Convergence step 6 value 5.09300e-06 DEAL:3d::Testing FE_DGQ<3>(2) DEAL:3d::Number of degrees of freedom: 1728 DEAL:3d:cg::Starting value 41.5692 -DEAL:3d:cg::Convergence step 5 value 5.30416e-07 +DEAL:3d:cg::Convergence step 6 value 1.73456e-07 DEAL:3d::Testing FE_DGQ<3>(2) DEAL:3d::Number of degrees of freedom: 13824 DEAL:3d:cg::Starting value 117.576 -DEAL:3d:cg::Convergence step 6 value 8.58800e-07 +DEAL:3d:cg::Convergence step 7 value 5.35539e-07 diff --git a/tests/matrix_free/multigrid_dg_sip_01.with_mpi=true.with_p4est=true.mpirun=5.output b/tests/matrix_free/multigrid_dg_sip_01.with_mpi=true.with_p4est=true.mpirun=5.output index 29dbbfae2dc3..3755b9b07c24 100644 --- a/tests/matrix_free/multigrid_dg_sip_01.with_mpi=true.with_p4est=true.mpirun=5.output +++ b/tests/matrix_free/multigrid_dg_sip_01.with_mpi=true.with_p4est=true.mpirun=5.output @@ -2,40 +2,40 @@ DEAL:2d::Testing FE_DGQ<2>(1) DEAL:2d::Number of degrees of freedom: 256 DEAL:2d:cg::Starting value 16.0000 -DEAL:2d:cg::Convergence step 4 value 1.45213e-06 +DEAL:2d:cg::Convergence step 5 value 3.60502e-07 DEAL:2d::Testing FE_DGQ<2>(1) DEAL:2d::Number of degrees of freedom: 1024 DEAL:2d:cg::Starting value 32.0000 -DEAL:2d:cg::Convergence step 5 value 8.09074e-08 +DEAL:2d:cg::Convergence step 5 value 2.14074e-06 DEAL:2d::Testing FE_DGQ<2>(1) DEAL:2d::Number of degrees of freedom: 4096 DEAL:2d:cg::Starting value 64.0000 -DEAL:2d:cg::Convergence step 5 value 9.08540e-07 +DEAL:2d:cg::Convergence step 5 value 5.99637e-06 DEAL:2d::Testing FE_DGQ<2>(2) DEAL:2d::Number of degrees of freedom: 576 DEAL:2d:cg::Starting value 24.0000 -DEAL:2d:cg::Convergence step 5 value 4.02774e-08 +DEAL:2d:cg::Convergence step 5 value 1.81901e-06 DEAL:2d::Testing FE_DGQ<2>(2) DEAL:2d::Number of degrees of freedom: 2304 DEAL:2d:cg::Starting value 48.0000 -DEAL:2d:cg::Convergence step 5 value 7.58404e-08 +DEAL:2d:cg::Convergence step 6 value 1.94976e-07 DEAL:3d::Testing FE_DGQ<3>(1) DEAL:3d::Number of degrees of freedom: 512 DEAL:3d:cg::Starting value 22.6274 -DEAL:3d:cg::Convergence step 5 value 2.70681e-07 +DEAL:3d:cg::Convergence step 6 value 7.43327e-08 DEAL:3d::Testing FE_DGQ<3>(1) DEAL:3d::Number of degrees of freedom: 4096 DEAL:3d:cg::Starting value 64.0000 -DEAL:3d:cg::Convergence step 5 value 3.69638e-06 +DEAL:3d:cg::Convergence step 6 value 2.28298e-06 DEAL:3d::Testing FE_DGQ<3>(1) DEAL:3d::Number of degrees of freedom: 32768 DEAL:3d:cg::Starting value 181.019 -DEAL:3d:cg::Convergence step 5 value 5.56024e-06 +DEAL:3d:cg::Convergence step 6 value 5.09300e-06 DEAL:3d::Testing FE_DGQ<3>(2) DEAL:3d::Number of degrees of freedom: 1728 DEAL:3d:cg::Starting value 41.5692 -DEAL:3d:cg::Convergence step 5 value 5.30416e-07 +DEAL:3d:cg::Convergence step 6 value 1.73456e-07 DEAL:3d::Testing FE_DGQ<3>(2) DEAL:3d::Number of degrees of freedom: 13824 DEAL:3d:cg::Starting value 117.576 -DEAL:3d:cg::Convergence step 6 value 8.58800e-07 +DEAL:3d:cg::Convergence step 7 value 5.35539e-07 diff --git a/tests/matrix_free/multigrid_dg_sip_02.with_mpi=true.with_p4est=true.mpirun=5.output b/tests/matrix_free/multigrid_dg_sip_02.with_mpi=true.with_p4est=true.mpirun=5.output index 29dbbfae2dc3..3755b9b07c24 100644 --- a/tests/matrix_free/multigrid_dg_sip_02.with_mpi=true.with_p4est=true.mpirun=5.output +++ b/tests/matrix_free/multigrid_dg_sip_02.with_mpi=true.with_p4est=true.mpirun=5.output @@ -2,40 +2,40 @@ DEAL:2d::Testing FE_DGQ<2>(1) DEAL:2d::Number of degrees of freedom: 256 DEAL:2d:cg::Starting value 16.0000 -DEAL:2d:cg::Convergence step 4 value 1.45213e-06 +DEAL:2d:cg::Convergence step 5 value 3.60502e-07 DEAL:2d::Testing FE_DGQ<2>(1) DEAL:2d::Number of degrees of freedom: 1024 DEAL:2d:cg::Starting value 32.0000 -DEAL:2d:cg::Convergence step 5 value 8.09074e-08 +DEAL:2d:cg::Convergence step 5 value 2.14074e-06 DEAL:2d::Testing FE_DGQ<2>(1) DEAL:2d::Number of degrees of freedom: 4096 DEAL:2d:cg::Starting value 64.0000 -DEAL:2d:cg::Convergence step 5 value 9.08540e-07 +DEAL:2d:cg::Convergence step 5 value 5.99637e-06 DEAL:2d::Testing FE_DGQ<2>(2) DEAL:2d::Number of degrees of freedom: 576 DEAL:2d:cg::Starting value 24.0000 -DEAL:2d:cg::Convergence step 5 value 4.02774e-08 +DEAL:2d:cg::Convergence step 5 value 1.81901e-06 DEAL:2d::Testing FE_DGQ<2>(2) DEAL:2d::Number of degrees of freedom: 2304 DEAL:2d:cg::Starting value 48.0000 -DEAL:2d:cg::Convergence step 5 value 7.58404e-08 +DEAL:2d:cg::Convergence step 6 value 1.94976e-07 DEAL:3d::Testing FE_DGQ<3>(1) DEAL:3d::Number of degrees of freedom: 512 DEAL:3d:cg::Starting value 22.6274 -DEAL:3d:cg::Convergence step 5 value 2.70681e-07 +DEAL:3d:cg::Convergence step 6 value 7.43327e-08 DEAL:3d::Testing FE_DGQ<3>(1) DEAL:3d::Number of degrees of freedom: 4096 DEAL:3d:cg::Starting value 64.0000 -DEAL:3d:cg::Convergence step 5 value 3.69638e-06 +DEAL:3d:cg::Convergence step 6 value 2.28298e-06 DEAL:3d::Testing FE_DGQ<3>(1) DEAL:3d::Number of degrees of freedom: 32768 DEAL:3d:cg::Starting value 181.019 -DEAL:3d:cg::Convergence step 5 value 5.56024e-06 +DEAL:3d:cg::Convergence step 6 value 5.09300e-06 DEAL:3d::Testing FE_DGQ<3>(2) DEAL:3d::Number of degrees of freedom: 1728 DEAL:3d:cg::Starting value 41.5692 -DEAL:3d:cg::Convergence step 5 value 5.30416e-07 +DEAL:3d:cg::Convergence step 6 value 1.73456e-07 DEAL:3d::Testing FE_DGQ<3>(2) DEAL:3d::Number of degrees of freedom: 13824 DEAL:3d:cg::Starting value 117.576 -DEAL:3d:cg::Convergence step 6 value 8.58800e-07 +DEAL:3d:cg::Convergence step 7 value 5.35539e-07 diff --git a/tests/matrix_free/parallel_multigrid.with_mpi=true.with_p4est=true.with_trilinos=true.with_lapack=true.mpirun=3.output b/tests/matrix_free/parallel_multigrid.with_mpi=true.with_p4est=true.with_trilinos=true.with_lapack=true.mpirun=3.output index cd85abb36828..3c079a9e5332 100644 --- a/tests/matrix_free/parallel_multigrid.with_mpi=true.with_p4est=true.with_trilinos=true.with_lapack=true.mpirun=3.output +++ b/tests/matrix_free/parallel_multigrid.with_mpi=true.with_p4est=true.with_trilinos=true.with_lapack=true.mpirun=3.output @@ -2,130 +2,144 @@ DEAL:2d::Testing FE_Q<2>(1) DEAL:2d::Number of degrees of freedom: 81 DEAL:2d:cg::Starting value 9.000 -DEAL:2d:cg:cg::Starting value 0.008804 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg:cg::Starting value 1.035e-05 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg:cg::Starting value 9.380e-08 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg::Convergence step 3 value 4.632e-07 +DEAL:2d:cg:cg::Starting value 0.02203 +DEAL:2d:cg:cg::Convergence step 1 value 0.000 +DEAL:2d:cg:cg::Starting value 0.0001585 +DEAL:2d:cg:cg::Convergence step 1 value 2.711e-20 +DEAL:2d:cg:cg::Starting value 8.884e-07 +DEAL:2d:cg:cg::Convergence step 1 value 0.000 +DEAL:2d:cg:cg::Starting value 3.123e-09 +DEAL:2d:cg:cg::Convergence step 1 value 8.272e-25 +DEAL:2d:cg::Convergence step 4 value 2.071e-08 DEAL:2d::Testing FE_Q<2>(1) DEAL:2d::Number of degrees of freedom: 289 DEAL:2d:cg::Starting value 17.00 -DEAL:2d:cg:cg::Starting value 0.02904 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg:cg::Starting value 5.542e-06 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg:cg::Starting value 3.318e-09 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg::Convergence step 3 value 4.000e-07 +DEAL:2d:cg:cg::Starting value 0.005310 +DEAL:2d:cg:cg::Convergence step 1 value 0.000 +DEAL:2d:cg:cg::Starting value 5.163e-06 +DEAL:2d:cg:cg::Convergence step 1 value 0.000 +DEAL:2d:cg:cg::Starting value 2.182e-08 +DEAL:2d:cg:cg::Convergence step 1 value 0.000 +DEAL:2d:cg:cg::Starting value 9.610e-10 +DEAL:2d:cg:cg::Convergence step 1 value 0.000 +DEAL:2d:cg::Convergence step 4 value 2.778e-08 DEAL:2d::Testing FE_Q<2>(1) DEAL:2d::Number of degrees of freedom: 1089 DEAL:2d:cg::Starting value 33.00 -DEAL:2d:cg:cg::Starting value 0.1041 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg:cg::Starting value 3.041e-06 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg:cg::Starting value 1.133e-07 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg:cg::Starting value 1.824e-10 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg::Convergence step 4 value 1.222e-08 +DEAL:2d:cg:cg::Starting value 0.008242 +DEAL:2d:cg:cg::Convergence step 1 value 0.000 +DEAL:2d:cg:cg::Starting value 2.754e-06 +DEAL:2d:cg:cg::Convergence step 1 value 0.000 +DEAL:2d:cg:cg::Starting value 9.820e-09 +DEAL:2d:cg:cg::Convergence step 1 value 0.000 +DEAL:2d:cg:cg::Starting value 8.188e-12 +DEAL:2d:cg:cg::Convergence step 1 value 0.000 +DEAL:2d:cg::Convergence step 4 value 8.029e-08 DEAL:2d::Testing FE_Q<2>(2) DEAL:2d::Number of degrees of freedom: 289 DEAL:2d:cg::Starting value 17.00 -DEAL:2d:cg:cg::Starting value 0.4928 -DEAL:2d:cg:cg::Convergence step 2 value 0 -DEAL:2d:cg:cg::Starting value 7.433e-05 -DEAL:2d:cg:cg::Convergence step 2 value 0 -DEAL:2d:cg:cg::Starting value 4.269e-07 -DEAL:2d:cg:cg::Convergence step 2 value 0 -DEAL:2d:cg:cg::Starting value 1.107e-09 -DEAL:2d:cg:cg::Convergence step 2 value 0 -DEAL:2d:cg::Convergence step 4 value 1.339e-08 +DEAL:2d:cg:cg::Starting value 3.849 +DEAL:2d:cg:cg::Convergence step 2 value 4.030e-15 +DEAL:2d:cg:cg::Starting value 0.0007035 +DEAL:2d:cg:cg::Convergence step 2 value 5.474e-20 +DEAL:2d:cg:cg::Starting value 4.286e-06 +DEAL:2d:cg:cg::Convergence step 2 value 4.924e-21 +DEAL:2d:cg:cg::Starting value 2.909e-08 +DEAL:2d:cg:cg::Convergence step 2 value 6.440e-24 +DEAL:2d:cg::Convergence step 4 value 3.931e-08 DEAL:2d::Testing FE_Q<2>(2) DEAL:2d::Number of degrees of freedom: 1089 DEAL:2d:cg::Starting value 33.00 -DEAL:2d:cg:cg::Starting value 1.857 -DEAL:2d:cg:cg::Convergence step 2 value 0 -DEAL:2d:cg:cg::Starting value 6.915e-05 -DEAL:2d:cg:cg::Convergence step 2 value 0 -DEAL:2d:cg:cg::Starting value 9.008e-07 -DEAL:2d:cg:cg::Convergence step 2 value 0 -DEAL:2d:cg:cg::Starting value 2.272e-09 -DEAL:2d:cg:cg::Convergence step 2 value 0 -DEAL:2d:cg::Convergence step 4 value 1.555e-08 +DEAL:2d:cg:cg::Starting value 14.69 +DEAL:2d:cg:cg::Convergence step 2 value 1.477e-14 +DEAL:2d:cg:cg::Starting value 0.002915 +DEAL:2d:cg:cg::Convergence step 2 value 8.995e-19 +DEAL:2d:cg:cg::Starting value 3.439e-06 +DEAL:2d:cg:cg::Convergence step 2 value 3.178e-21 +DEAL:2d:cg:cg::Starting value 1.212e-08 +DEAL:2d:cg:cg::Convergence step 2 value 1.500e-23 +DEAL:2d:cg::Convergence step 4 value 8.121e-08 DEAL:2d::Testing FE_Q<2>(2) DEAL:2d::Number of degrees of freedom: 4225 DEAL:2d:cg::Starting value 65.00 -DEAL:2d:cg:cg::Starting value 7.324 -DEAL:2d:cg:cg::Convergence step 2 value 0 -DEAL:2d:cg:cg::Starting value 0.0003835 -DEAL:2d:cg:cg::Convergence step 2 value 0 -DEAL:2d:cg:cg::Starting value 5.631e-07 -DEAL:2d:cg:cg::Convergence step 2 value 0 -DEAL:2d:cg:cg::Starting value 8.812e-09 -DEAL:2d:cg:cg::Convergence step 2 value 0 -DEAL:2d:cg::Convergence step 4 value 3.108e-08 +DEAL:2d:cg:cg::Starting value 58.09 +DEAL:2d:cg:cg::Convergence step 2 value 5.909e-15 +DEAL:2d:cg:cg::Starting value 0.01056 +DEAL:2d:cg:cg::Convergence step 2 value 5.646e-18 +DEAL:2d:cg:cg::Starting value 2.588e-05 +DEAL:2d:cg:cg::Convergence step 2 value 8.081e-21 +DEAL:2d:cg:cg::Starting value 6.672e-08 +DEAL:2d:cg:cg::Convergence step 2 value 4.727e-23 +DEAL:2d:cg::Convergence step 4 value 1.695e-07 DEAL:3d::Testing FE_Q<3>(1) DEAL:3d::Number of degrees of freedom: 125 DEAL:3d:cg::Starting value 11.18 -DEAL:3d:cg:cg::Starting value 0.1411 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg:cg::Starting value 7.053e-05 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg:cg::Starting value 4.822e-09 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg::Convergence step 3 value 9.057e-09 +DEAL:3d:cg:cg::Starting value 0.5164 +DEAL:3d:cg:cg::Convergence step 1 value 0.000 +DEAL:3d:cg:cg::Starting value 0.02357 +DEAL:3d:cg:cg::Convergence step 1 value 4.907e-18 +DEAL:3d:cg:cg::Starting value 5.322e-05 +DEAL:3d:cg:cg::Convergence step 1 value 0.000 +DEAL:3d:cg:cg::Starting value 1.537e-07 +DEAL:3d:cg:cg::Convergence step 1 value 0.000 +DEAL:3d:cg::Convergence step 4 value 3.460e-07 DEAL:3d::Testing FE_Q<3>(1) DEAL:3d::Number of degrees of freedom: 729 DEAL:3d:cg::Starting value 27.00 -DEAL:3d:cg:cg::Starting value 0.03502 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg:cg::Starting value 0.0002864 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg:cg::Starting value 1.471e-07 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg::Convergence step 3 value 1.321e-06 +DEAL:3d:cg:cg::Starting value 0.1824 +DEAL:3d:cg:cg::Convergence step 1 value 0.000 +DEAL:3d:cg:cg::Starting value 0.004902 +DEAL:3d:cg:cg::Convergence step 1 value 6.133e-19 +DEAL:3d:cg:cg::Starting value 5.629e-06 +DEAL:3d:cg:cg::Convergence step 1 value 0.000 +DEAL:3d:cg:cg::Starting value 3.386e-10 +DEAL:3d:cg:cg::Convergence step 1 value 0.000 +DEAL:3d:cg::Convergence step 4 value 1.074e-07 DEAL:3d::Testing FE_Q<3>(1) DEAL:3d::Number of degrees of freedom: 4913 DEAL:3d:cg::Starting value 70.09 -DEAL:3d:cg:cg::Starting value 0.06187 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg:cg::Starting value 7.069e-05 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg:cg::Starting value 8.132e-07 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg:cg::Starting value 1.153e-09 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg::Convergence step 4 value 6.546e-08 +DEAL:3d:cg:cg::Starting value 0.1633 +DEAL:3d:cg:cg::Convergence step 1 value 0.000 +DEAL:3d:cg:cg::Starting value 0.0001064 +DEAL:3d:cg:cg::Convergence step 1 value 1.917e-20 +DEAL:3d:cg:cg::Starting value 1.367e-06 +DEAL:3d:cg:cg::Convergence step 1 value 2.995e-22 +DEAL:3d:cg:cg::Starting value 1.607e-08 +DEAL:3d:cg:cg::Convergence step 1 value 4.679e-24 +DEAL:3d:cg::Convergence step 4 value 5.067e-08 DEAL:3d::Testing FE_Q<3>(2) DEAL:3d::Number of degrees of freedom: 729 DEAL:3d:cg::Starting value 27.00 -DEAL:3d:cg:cg::Starting value 1.198 -DEAL:3d:cg:cg::Convergence step 2 value 0 -DEAL:3d:cg:cg::Starting value 0.0001874 -DEAL:3d:cg:cg::Convergence step 2 value 0 -DEAL:3d:cg:cg::Starting value 8.519e-08 -DEAL:3d:cg:cg::Convergence step 2 value 0 -DEAL:3d:cg::Convergence step 3 value 4.352e-08 +DEAL:3d:cg:cg::Starting value 1.696 +DEAL:3d:cg:cg::Convergence step 2 value 3.019e-16 +DEAL:3d:cg:cg::Starting value 0.1038 +DEAL:3d:cg:cg::Convergence step 2 value 1.281e-17 +DEAL:3d:cg:cg::Starting value 0.0001778 +DEAL:3d:cg:cg::Convergence step 2 value 2.774e-20 +DEAL:3d:cg:cg::Starting value 5.289e-06 +DEAL:3d:cg:cg::Convergence step 2 value 5.235e-22 +DEAL:3d:cg::Convergence step 4 value 2.355e-06 DEAL:3d::Testing FE_Q<3>(2) DEAL:3d::Number of degrees of freedom: 4913 DEAL:3d:cg::Starting value 70.09 -DEAL:3d:cg:cg::Starting value 6.688 -DEAL:3d:cg:cg::Convergence step 2 value 0 -DEAL:3d:cg:cg::Starting value 0.0005904 -DEAL:3d:cg:cg::Convergence step 2 value 0 -DEAL:3d:cg:cg::Starting value 2.187e-06 -DEAL:3d:cg:cg::Convergence step 2 value 0 -DEAL:3d:cg::Convergence step 3 value 2.196e-06 +DEAL:3d:cg:cg::Starting value 2.313 +DEAL:3d:cg:cg::Convergence step 2 value 3.056e-16 +DEAL:3d:cg:cg::Starting value 0.04486 +DEAL:3d:cg:cg::Convergence step 2 value 9.479e-18 +DEAL:3d:cg:cg::Starting value 0.0007197 +DEAL:3d:cg:cg::Convergence step 2 value 1.099e-19 +DEAL:3d:cg:cg::Starting value 2.909e-06 +DEAL:3d:cg:cg::Convergence step 2 value 1.507e-22 +DEAL:3d:cg::Convergence step 4 value 4.578e-06 DEAL:3d::Testing FE_Q<3>(2) DEAL:3d::Number of degrees of freedom: 35937 DEAL:3d:cg::Starting value 189.6 -DEAL:3d:cg:cg::Starting value 49.17 -DEAL:3d:cg:cg::Convergence step 2 value 0 -DEAL:3d:cg:cg::Starting value 0.006462 -DEAL:3d:cg:cg::Convergence step 2 value 0 -DEAL:3d:cg:cg::Starting value 8.640e-06 -DEAL:3d:cg:cg::Convergence step 2 value 0 -DEAL:3d:cg::Convergence step 3 value 9.302e-06 +DEAL:3d:cg:cg::Starting value 17.40 +DEAL:3d:cg:cg::Convergence step 2 value 1.067e-14 +DEAL:3d:cg:cg::Starting value 0.01679 +DEAL:3d:cg:cg::Convergence step 2 value 2.474e-18 +DEAL:3d:cg:cg::Starting value 0.001098 +DEAL:3d:cg:cg::Convergence step 2 value 8.085e-20 +DEAL:3d:cg:cg::Starting value 1.006e-06 +DEAL:3d:cg:cg::Convergence step 2 value 9.940e-23 +DEAL:3d:cg::Convergence step 4 value 1.784e-05 diff --git a/tests/matrix_free/parallel_multigrid.with_mpi=true.with_p4est=true.with_trilinos=true.with_lapack=true.mpirun=7.output b/tests/matrix_free/parallel_multigrid.with_mpi=true.with_p4est=true.with_trilinos=true.with_lapack=true.mpirun=7.output index cd85abb36828..03fd053a904c 100644 --- a/tests/matrix_free/parallel_multigrid.with_mpi=true.with_p4est=true.with_trilinos=true.with_lapack=true.mpirun=7.output +++ b/tests/matrix_free/parallel_multigrid.with_mpi=true.with_p4est=true.with_trilinos=true.with_lapack=true.mpirun=7.output @@ -2,130 +2,144 @@ DEAL:2d::Testing FE_Q<2>(1) DEAL:2d::Number of degrees of freedom: 81 DEAL:2d:cg::Starting value 9.000 -DEAL:2d:cg:cg::Starting value 0.008804 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg:cg::Starting value 1.035e-05 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg:cg::Starting value 9.380e-08 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg::Convergence step 3 value 4.632e-07 +DEAL:2d:cg:cg::Starting value 0.02203 +DEAL:2d:cg:cg::Convergence step 1 value 3.469e-18 +DEAL:2d:cg:cg::Starting value 0.0001585 +DEAL:2d:cg:cg::Convergence step 1 value 2.711e-20 +DEAL:2d:cg:cg::Starting value 8.884e-07 +DEAL:2d:cg:cg::Convergence step 1 value 0.000 +DEAL:2d:cg:cg::Starting value 3.123e-09 +DEAL:2d:cg:cg::Convergence step 1 value 4.136e-25 +DEAL:2d:cg::Convergence step 4 value 2.071e-08 DEAL:2d::Testing FE_Q<2>(1) DEAL:2d::Number of degrees of freedom: 289 DEAL:2d:cg::Starting value 17.00 -DEAL:2d:cg:cg::Starting value 0.02904 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg:cg::Starting value 5.542e-06 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg:cg::Starting value 3.318e-09 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg::Convergence step 3 value 4.000e-07 +DEAL:2d:cg:cg::Starting value 0.005310 +DEAL:2d:cg:cg::Convergence step 1 value 8.674e-19 +DEAL:2d:cg:cg::Starting value 5.163e-06 +DEAL:2d:cg:cg::Convergence step 1 value 0.000 +DEAL:2d:cg:cg::Starting value 2.182e-08 +DEAL:2d:cg:cg::Convergence step 1 value 0.000 +DEAL:2d:cg:cg::Starting value 9.610e-10 +DEAL:2d:cg:cg::Convergence step 1 value 2.068e-25 +DEAL:2d:cg::Convergence step 4 value 2.778e-08 DEAL:2d::Testing FE_Q<2>(1) DEAL:2d::Number of degrees of freedom: 1089 DEAL:2d:cg::Starting value 33.00 -DEAL:2d:cg:cg::Starting value 0.1041 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg:cg::Starting value 3.041e-06 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg:cg::Starting value 1.133e-07 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg:cg::Starting value 1.824e-10 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg::Convergence step 4 value 1.222e-08 +DEAL:2d:cg:cg::Starting value 0.008242 +DEAL:2d:cg:cg::Convergence step 1 value 0.000 +DEAL:2d:cg:cg::Starting value 2.754e-06 +DEAL:2d:cg:cg::Convergence step 1 value 0.000 +DEAL:2d:cg:cg::Starting value 9.820e-09 +DEAL:2d:cg:cg::Convergence step 1 value 0.000 +DEAL:2d:cg:cg::Starting value 8.188e-12 +DEAL:2d:cg:cg::Convergence step 1 value 0.000 +DEAL:2d:cg::Convergence step 4 value 8.029e-08 DEAL:2d::Testing FE_Q<2>(2) DEAL:2d::Number of degrees of freedom: 289 DEAL:2d:cg::Starting value 17.00 -DEAL:2d:cg:cg::Starting value 0.4928 -DEAL:2d:cg:cg::Convergence step 2 value 0 -DEAL:2d:cg:cg::Starting value 7.433e-05 -DEAL:2d:cg:cg::Convergence step 2 value 0 -DEAL:2d:cg:cg::Starting value 4.269e-07 -DEAL:2d:cg:cg::Convergence step 2 value 0 -DEAL:2d:cg:cg::Starting value 1.107e-09 -DEAL:2d:cg:cg::Convergence step 2 value 0 -DEAL:2d:cg::Convergence step 4 value 1.339e-08 +DEAL:2d:cg:cg::Starting value 3.849 +DEAL:2d:cg:cg::Convergence step 2 value 2.944e-15 +DEAL:2d:cg:cg::Starting value 0.0007035 +DEAL:2d:cg:cg::Convergence step 2 value 9.681e-20 +DEAL:2d:cg:cg::Starting value 4.286e-06 +DEAL:2d:cg:cg::Convergence step 2 value 3.549e-21 +DEAL:2d:cg:cg::Starting value 2.909e-08 +DEAL:2d:cg:cg::Convergence step 2 value 1.182e-23 +DEAL:2d:cg::Convergence step 4 value 3.931e-08 DEAL:2d::Testing FE_Q<2>(2) DEAL:2d::Number of degrees of freedom: 1089 DEAL:2d:cg::Starting value 33.00 -DEAL:2d:cg:cg::Starting value 1.857 -DEAL:2d:cg:cg::Convergence step 2 value 0 -DEAL:2d:cg:cg::Starting value 6.915e-05 -DEAL:2d:cg:cg::Convergence step 2 value 0 -DEAL:2d:cg:cg::Starting value 9.008e-07 -DEAL:2d:cg:cg::Convergence step 2 value 0 -DEAL:2d:cg:cg::Starting value 2.272e-09 -DEAL:2d:cg:cg::Convergence step 2 value 0 -DEAL:2d:cg::Convergence step 4 value 1.555e-08 +DEAL:2d:cg:cg::Starting value 14.69 +DEAL:2d:cg:cg::Convergence step 2 value 4.231e-15 +DEAL:2d:cg:cg::Starting value 0.002915 +DEAL:2d:cg:cg::Convergence step 2 value 5.424e-18 +DEAL:2d:cg:cg::Starting value 3.439e-06 +DEAL:2d:cg:cg::Convergence step 2 value 1.113e-21 +DEAL:2d:cg:cg::Starting value 1.212e-08 +DEAL:2d:cg:cg::Convergence step 2 value 7.249e-24 +DEAL:2d:cg::Convergence step 4 value 8.121e-08 DEAL:2d::Testing FE_Q<2>(2) DEAL:2d::Number of degrees of freedom: 4225 DEAL:2d:cg::Starting value 65.00 -DEAL:2d:cg:cg::Starting value 7.324 -DEAL:2d:cg:cg::Convergence step 2 value 0 -DEAL:2d:cg:cg::Starting value 0.0003835 -DEAL:2d:cg:cg::Convergence step 2 value 0 -DEAL:2d:cg:cg::Starting value 5.631e-07 -DEAL:2d:cg:cg::Convergence step 2 value 0 -DEAL:2d:cg:cg::Starting value 8.812e-09 -DEAL:2d:cg:cg::Convergence step 2 value 0 -DEAL:2d:cg::Convergence step 4 value 3.108e-08 +DEAL:2d:cg:cg::Starting value 58.09 +DEAL:2d:cg:cg::Convergence step 2 value 5.109e-14 +DEAL:2d:cg:cg::Starting value 0.01056 +DEAL:2d:cg:cg::Convergence step 2 value 7.258e-19 +DEAL:2d:cg:cg::Starting value 2.588e-05 +DEAL:2d:cg:cg::Convergence step 2 value 8.491e-21 +DEAL:2d:cg:cg::Starting value 6.672e-08 +DEAL:2d:cg:cg::Convergence step 2 value 1.252e-23 +DEAL:2d:cg::Convergence step 4 value 1.695e-07 DEAL:3d::Testing FE_Q<3>(1) DEAL:3d::Number of degrees of freedom: 125 DEAL:3d:cg::Starting value 11.18 -DEAL:3d:cg:cg::Starting value 0.1411 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg:cg::Starting value 7.053e-05 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg:cg::Starting value 4.822e-09 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg::Convergence step 3 value 9.057e-09 +DEAL:3d:cg:cg::Starting value 0.5164 +DEAL:3d:cg:cg::Convergence step 1 value 0.000 +DEAL:3d:cg:cg::Starting value 0.02357 +DEAL:3d:cg:cg::Convergence step 1 value 0.000 +DEAL:3d:cg:cg::Starting value 5.322e-05 +DEAL:3d:cg:cg::Convergence step 1 value 0.000 +DEAL:3d:cg:cg::Starting value 1.537e-07 +DEAL:3d:cg:cg::Convergence step 1 value 3.743e-23 +DEAL:3d:cg::Convergence step 4 value 3.460e-07 DEAL:3d::Testing FE_Q<3>(1) DEAL:3d::Number of degrees of freedom: 729 DEAL:3d:cg::Starting value 27.00 -DEAL:3d:cg:cg::Starting value 0.03502 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg:cg::Starting value 0.0002864 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg:cg::Starting value 1.471e-07 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg::Convergence step 3 value 1.321e-06 +DEAL:3d:cg:cg::Starting value 0.1824 +DEAL:3d:cg:cg::Convergence step 1 value 3.925e-17 +DEAL:3d:cg:cg::Starting value 0.004902 +DEAL:3d:cg:cg::Convergence step 1 value 6.133e-19 +DEAL:3d:cg:cg::Starting value 5.629e-06 +DEAL:3d:cg:cg::Convergence step 1 value 1.198e-21 +DEAL:3d:cg:cg::Starting value 3.386e-10 +DEAL:3d:cg:cg::Convergence step 1 value 0.000 +DEAL:3d:cg::Convergence step 4 value 1.074e-07 DEAL:3d::Testing FE_Q<3>(1) DEAL:3d::Number of degrees of freedom: 4913 DEAL:3d:cg::Starting value 70.09 -DEAL:3d:cg:cg::Starting value 0.06187 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg:cg::Starting value 7.069e-05 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg:cg::Starting value 8.132e-07 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg:cg::Starting value 1.153e-09 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg::Convergence step 4 value 6.546e-08 +DEAL:3d:cg:cg::Starting value 0.1633 +DEAL:3d:cg:cg::Convergence step 1 value 0.000 +DEAL:3d:cg:cg::Starting value 0.0001064 +DEAL:3d:cg:cg::Convergence step 1 value 0.000 +DEAL:3d:cg:cg::Starting value 1.367e-06 +DEAL:3d:cg:cg::Convergence step 1 value 2.995e-22 +DEAL:3d:cg:cg::Starting value 1.607e-08 +DEAL:3d:cg:cg::Convergence step 1 value 4.679e-24 +DEAL:3d:cg::Convergence step 4 value 5.067e-08 DEAL:3d::Testing FE_Q<3>(2) DEAL:3d::Number of degrees of freedom: 729 DEAL:3d:cg::Starting value 27.00 -DEAL:3d:cg:cg::Starting value 1.198 -DEAL:3d:cg:cg::Convergence step 2 value 0 -DEAL:3d:cg:cg::Starting value 0.0001874 -DEAL:3d:cg:cg::Convergence step 2 value 0 -DEAL:3d:cg:cg::Starting value 8.519e-08 -DEAL:3d:cg:cg::Convergence step 2 value 0 -DEAL:3d:cg::Convergence step 3 value 4.352e-08 +DEAL:3d:cg:cg::Starting value 1.696 +DEAL:3d:cg:cg::Convergence step 2 value 2.866e-16 +DEAL:3d:cg:cg::Starting value 0.1038 +DEAL:3d:cg:cg::Convergence step 2 value 2.373e-17 +DEAL:3d:cg:cg::Starting value 0.0001778 +DEAL:3d:cg:cg::Convergence step 2 value 2.322e-20 +DEAL:3d:cg:cg::Starting value 5.289e-06 +DEAL:3d:cg:cg::Convergence step 2 value 3.474e-22 +DEAL:3d:cg::Convergence step 4 value 2.355e-06 DEAL:3d::Testing FE_Q<3>(2) DEAL:3d::Number of degrees of freedom: 4913 DEAL:3d:cg::Starting value 70.09 -DEAL:3d:cg:cg::Starting value 6.688 -DEAL:3d:cg:cg::Convergence step 2 value 0 -DEAL:3d:cg:cg::Starting value 0.0005904 -DEAL:3d:cg:cg::Convergence step 2 value 0 -DEAL:3d:cg:cg::Starting value 2.187e-06 -DEAL:3d:cg:cg::Convergence step 2 value 0 -DEAL:3d:cg::Convergence step 3 value 2.196e-06 +DEAL:3d:cg:cg::Starting value 2.313 +DEAL:3d:cg:cg::Convergence step 2 value 2.276e-15 +DEAL:3d:cg:cg::Starting value 0.04486 +DEAL:3d:cg:cg::Convergence step 2 value 8.352e-19 +DEAL:3d:cg:cg::Starting value 0.0007197 +DEAL:3d:cg:cg::Convergence step 2 value 7.308e-20 +DEAL:3d:cg:cg::Starting value 2.909e-06 +DEAL:3d:cg:cg::Convergence step 2 value 1.373e-22 +DEAL:3d:cg::Convergence step 4 value 4.578e-06 DEAL:3d::Testing FE_Q<3>(2) DEAL:3d::Number of degrees of freedom: 35937 DEAL:3d:cg::Starting value 189.6 -DEAL:3d:cg:cg::Starting value 49.17 -DEAL:3d:cg:cg::Convergence step 2 value 0 -DEAL:3d:cg:cg::Starting value 0.006462 -DEAL:3d:cg:cg::Convergence step 2 value 0 -DEAL:3d:cg:cg::Starting value 8.640e-06 -DEAL:3d:cg:cg::Convergence step 2 value 0 -DEAL:3d:cg::Convergence step 3 value 9.302e-06 +DEAL:3d:cg:cg::Starting value 17.40 +DEAL:3d:cg:cg::Convergence step 2 value 1.045e-14 +DEAL:3d:cg:cg::Starting value 0.01679 +DEAL:3d:cg:cg::Convergence step 2 value 2.190e-18 +DEAL:3d:cg:cg::Starting value 0.001098 +DEAL:3d:cg:cg::Convergence step 2 value 1.752e-19 +DEAL:3d:cg:cg::Starting value 1.006e-06 +DEAL:3d:cg:cg::Convergence step 2 value 7.732e-22 +DEAL:3d:cg::Convergence step 4 value 1.784e-05 diff --git a/tests/matrix_free/parallel_multigrid_02.with_mpi=true.with_p4est=true.with_trilinos=true.with_lapack=true.mpirun=3.output b/tests/matrix_free/parallel_multigrid_02.with_mpi=true.with_p4est=true.with_trilinos=true.with_lapack=true.mpirun=3.output index 7b27e1ef5971..107753528473 100644 --- a/tests/matrix_free/parallel_multigrid_02.with_mpi=true.with_p4est=true.with_trilinos=true.with_lapack=true.mpirun=3.output +++ b/tests/matrix_free/parallel_multigrid_02.with_mpi=true.with_p4est=true.with_trilinos=true.with_lapack=true.mpirun=3.output @@ -2,68 +2,77 @@ DEAL:2d::Testing FE_Q<2>(1) DEAL:2d::Number of degrees of freedom: 81 DEAL:2d:cg::Starting value 9.000 -DEAL:2d:cg:cg::Convergence step 0 value 0 -DEAL:2d:cg:cg::Convergence step 0 value 0 -DEAL:2d:cg:cg::Convergence step 0 value 0 -DEAL:2d:cg::Convergence step 3 value 3.515e-08 +DEAL:2d:cg:cg::Convergence step 0 value 0.000 +DEAL:2d:cg:cg::Convergence step 0 value 0.000 +DEAL:2d:cg:cg::Convergence step 0 value 0.000 +DEAL:2d:cg::Convergence step 3 value 6.753e-07 DEAL:2d::Testing FE_Q<2>(1) DEAL:2d::Number of degrees of freedom: 289 DEAL:2d:cg::Starting value 17.00 -DEAL:2d:cg:cg::Convergence step 0 value 0 -DEAL:2d:cg:cg::Convergence step 0 value 0 -DEAL:2d:cg:cg::Convergence step 0 value 0 -DEAL:2d:cg::Convergence step 3 value 2.831e-08 +DEAL:2d:cg:cg::Convergence step 0 value 0.000 +DEAL:2d:cg:cg::Convergence step 0 value 0.000 +DEAL:2d:cg:cg::Convergence step 0 value 0.000 +DEAL:2d:cg:cg::Convergence step 0 value 0.000 +DEAL:2d:cg::Convergence step 4 value 2.625e-09 DEAL:2d::Testing FE_Q<2>(2) DEAL:2d::Number of degrees of freedom: 289 DEAL:2d:cg::Starting value 17.00 -DEAL:2d:cg:cg::Starting value 0.4815 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg:cg::Starting value 9.432e-05 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg:cg::Starting value 2.174e-07 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg::Convergence step 3 value 3.366e-07 +DEAL:2d:cg:cg::Starting value 3.765 +DEAL:2d:cg:cg::Convergence step 1 value 0.000 +DEAL:2d:cg:cg::Starting value 0.0005314 +DEAL:2d:cg:cg::Convergence step 1 value 0.000 +DEAL:2d:cg:cg::Starting value 3.806e-06 +DEAL:2d:cg:cg::Convergence step 1 value 4.235e-22 +DEAL:2d:cg:cg::Starting value 1.628e-08 +DEAL:2d:cg:cg::Convergence step 1 value 3.309e-24 +DEAL:2d:cg::Convergence step 4 value 1.712e-08 DEAL:2d::Testing FE_Q<2>(2) DEAL:2d::Number of degrees of freedom: 1089 DEAL:2d:cg::Starting value 33.00 -DEAL:2d:cg:cg::Starting value 1.818 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg:cg::Starting value 0.0001408 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg:cg::Starting value 3.548e-08 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg::Convergence step 3 value 8.040e-07 +DEAL:2d:cg:cg::Starting value 14.37 +DEAL:2d:cg:cg::Convergence step 1 value 0.000 +DEAL:2d:cg:cg::Starting value 0.002280 +DEAL:2d:cg:cg::Convergence step 1 value 0.000 +DEAL:2d:cg:cg::Starting value 6.550e-06 +DEAL:2d:cg:cg::Convergence step 1 value 8.470e-22 +DEAL:2d:cg:cg::Starting value 5.084e-08 +DEAL:2d:cg:cg::Convergence step 1 value 0.000 +DEAL:2d:cg::Convergence step 4 value 4.315e-08 DEAL:3d::Testing FE_Q<3>(1) DEAL:3d::Number of degrees of freedom: 125 DEAL:3d:cg::Starting value 11.18 -DEAL:3d:cg:cg::Convergence step 0 value 0 -DEAL:3d:cg:cg::Convergence step 0 value 0 -DEAL:3d:cg:cg::Convergence step 0 value 0 -DEAL:3d:cg::Convergence step 3 value 9.624e-10 +DEAL:3d:cg:cg::Convergence step 0 value 0.000 +DEAL:3d:cg:cg::Convergence step 0 value 0.000 +DEAL:3d:cg:cg::Convergence step 0 value 0.000 +DEAL:3d:cg::Convergence step 3 value 4.383e-07 DEAL:3d::Testing FE_Q<3>(1) DEAL:3d::Number of degrees of freedom: 729 DEAL:3d:cg::Starting value 27.00 -DEAL:3d:cg:cg::Convergence step 0 value 0 -DEAL:3d:cg:cg::Convergence step 0 value 0 -DEAL:3d:cg:cg::Convergence step 0 value 0 -DEAL:3d:cg::Convergence step 3 value 1.308e-07 +DEAL:3d:cg:cg::Convergence step 0 value 0.000 +DEAL:3d:cg:cg::Convergence step 0 value 0.000 +DEAL:3d:cg:cg::Convergence step 0 value 0.000 +DEAL:3d:cg::Convergence step 3 value 1.025e-06 DEAL:3d::Testing FE_Q<3>(2) DEAL:3d::Number of degrees of freedom: 729 DEAL:3d:cg::Starting value 27.00 -DEAL:3d:cg:cg::Starting value 1.147 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg:cg::Starting value 4.360e-05 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg:cg::Starting value 1.203e-07 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg::Convergence step 3 value 2.611e-08 +DEAL:3d:cg:cg::Starting value 0.3913 +DEAL:3d:cg:cg::Convergence step 1 value 0.000 +DEAL:3d:cg:cg::Starting value 0.0006066 +DEAL:3d:cg:cg::Convergence step 1 value 0.000 +DEAL:3d:cg:cg::Starting value 3.469e-07 +DEAL:3d:cg:cg::Convergence step 1 value 0.000 +DEAL:3d:cg:cg::Starting value 5.798e-10 +DEAL:3d:cg:cg::Convergence step 1 value 0.000 +DEAL:3d:cg::Convergence step 4 value 5.998e-09 DEAL:3d::Testing FE_Q<3>(2) DEAL:3d::Number of degrees of freedom: 4913 DEAL:3d:cg::Starting value 70.09 -DEAL:3d:cg:cg::Starting value 6.424 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg:cg::Starting value 0.0006099 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg:cg::Starting value 1.980e-06 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg::Convergence step 3 value 1.197e-06 +DEAL:3d:cg:cg::Starting value 2.274 +DEAL:3d:cg:cg::Convergence step 1 value 0.000 +DEAL:3d:cg:cg::Starting value 0.0007566 +DEAL:3d:cg:cg::Convergence step 1 value 0.000 +DEAL:3d:cg:cg::Starting value 3.302e-06 +DEAL:3d:cg:cg::Convergence step 1 value 4.235e-22 +DEAL:3d:cg:cg::Starting value 1.183e-08 +DEAL:3d:cg:cg::Convergence step 1 value 1.654e-24 +DEAL:3d:cg::Convergence step 4 value 5.811e-08 diff --git a/tests/matrix_free/parallel_multigrid_02.with_mpi=true.with_p4est=true.with_trilinos=true.with_lapack=true.mpirun=7.output b/tests/matrix_free/parallel_multigrid_02.with_mpi=true.with_p4est=true.with_trilinos=true.with_lapack=true.mpirun=7.output index 7b27e1ef5971..9b87149d9d44 100644 --- a/tests/matrix_free/parallel_multigrid_02.with_mpi=true.with_p4est=true.with_trilinos=true.with_lapack=true.mpirun=7.output +++ b/tests/matrix_free/parallel_multigrid_02.with_mpi=true.with_p4est=true.with_trilinos=true.with_lapack=true.mpirun=7.output @@ -2,68 +2,77 @@ DEAL:2d::Testing FE_Q<2>(1) DEAL:2d::Number of degrees of freedom: 81 DEAL:2d:cg::Starting value 9.000 -DEAL:2d:cg:cg::Convergence step 0 value 0 -DEAL:2d:cg:cg::Convergence step 0 value 0 -DEAL:2d:cg:cg::Convergence step 0 value 0 -DEAL:2d:cg::Convergence step 3 value 3.515e-08 +DEAL:2d:cg:cg::Convergence step 0 value 0.000 +DEAL:2d:cg:cg::Convergence step 0 value 0.000 +DEAL:2d:cg:cg::Convergence step 0 value 0.000 +DEAL:2d:cg::Convergence step 3 value 6.753e-07 DEAL:2d::Testing FE_Q<2>(1) DEAL:2d::Number of degrees of freedom: 289 DEAL:2d:cg::Starting value 17.00 -DEAL:2d:cg:cg::Convergence step 0 value 0 -DEAL:2d:cg:cg::Convergence step 0 value 0 -DEAL:2d:cg:cg::Convergence step 0 value 0 -DEAL:2d:cg::Convergence step 3 value 2.831e-08 +DEAL:2d:cg:cg::Convergence step 0 value 0.000 +DEAL:2d:cg:cg::Convergence step 0 value 0.000 +DEAL:2d:cg:cg::Convergence step 0 value 0.000 +DEAL:2d:cg:cg::Convergence step 0 value 0.000 +DEAL:2d:cg::Convergence step 4 value 2.625e-09 DEAL:2d::Testing FE_Q<2>(2) DEAL:2d::Number of degrees of freedom: 289 DEAL:2d:cg::Starting value 17.00 -DEAL:2d:cg:cg::Starting value 0.4815 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg:cg::Starting value 9.432e-05 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg:cg::Starting value 2.174e-07 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg::Convergence step 3 value 3.366e-07 +DEAL:2d:cg:cg::Starting value 3.765 +DEAL:2d:cg:cg::Convergence step 1 value 4.441e-16 +DEAL:2d:cg:cg::Starting value 0.0005314 +DEAL:2d:cg:cg::Convergence step 1 value 0.000 +DEAL:2d:cg:cg::Starting value 3.806e-06 +DEAL:2d:cg:cg::Convergence step 1 value 0.000 +DEAL:2d:cg:cg::Starting value 1.628e-08 +DEAL:2d:cg:cg::Convergence step 1 value 0.000 +DEAL:2d:cg::Convergence step 4 value 1.712e-08 DEAL:2d::Testing FE_Q<2>(2) DEAL:2d::Number of degrees of freedom: 1089 DEAL:2d:cg::Starting value 33.00 -DEAL:2d:cg:cg::Starting value 1.818 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg:cg::Starting value 0.0001408 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg:cg::Starting value 3.548e-08 -DEAL:2d:cg:cg::Convergence step 1 value 0 -DEAL:2d:cg::Convergence step 3 value 8.040e-07 +DEAL:2d:cg:cg::Starting value 14.37 +DEAL:2d:cg:cg::Convergence step 1 value 1.776e-15 +DEAL:2d:cg:cg::Starting value 0.002280 +DEAL:2d:cg:cg::Convergence step 1 value 0.000 +DEAL:2d:cg:cg::Starting value 6.550e-06 +DEAL:2d:cg:cg::Convergence step 1 value 8.470e-22 +DEAL:2d:cg:cg::Starting value 5.084e-08 +DEAL:2d:cg:cg::Convergence step 1 value 0.000 +DEAL:2d:cg::Convergence step 4 value 4.315e-08 DEAL:3d::Testing FE_Q<3>(1) DEAL:3d::Number of degrees of freedom: 125 DEAL:3d:cg::Starting value 11.18 -DEAL:3d:cg:cg::Convergence step 0 value 0 -DEAL:3d:cg:cg::Convergence step 0 value 0 -DEAL:3d:cg:cg::Convergence step 0 value 0 -DEAL:3d:cg::Convergence step 3 value 9.624e-10 +DEAL:3d:cg:cg::Convergence step 0 value 0.000 +DEAL:3d:cg:cg::Convergence step 0 value 0.000 +DEAL:3d:cg:cg::Convergence step 0 value 0.000 +DEAL:3d:cg::Convergence step 3 value 4.383e-07 DEAL:3d::Testing FE_Q<3>(1) DEAL:3d::Number of degrees of freedom: 729 DEAL:3d:cg::Starting value 27.00 -DEAL:3d:cg:cg::Convergence step 0 value 0 -DEAL:3d:cg:cg::Convergence step 0 value 0 -DEAL:3d:cg:cg::Convergence step 0 value 0 -DEAL:3d:cg::Convergence step 3 value 1.308e-07 +DEAL:3d:cg:cg::Convergence step 0 value 0.000 +DEAL:3d:cg:cg::Convergence step 0 value 0.000 +DEAL:3d:cg:cg::Convergence step 0 value 0.000 +DEAL:3d:cg::Convergence step 3 value 1.025e-06 DEAL:3d::Testing FE_Q<3>(2) DEAL:3d::Number of degrees of freedom: 729 DEAL:3d:cg::Starting value 27.00 -DEAL:3d:cg:cg::Starting value 1.147 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg:cg::Starting value 4.360e-05 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg:cg::Starting value 1.203e-07 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg::Convergence step 3 value 2.611e-08 +DEAL:3d:cg:cg::Starting value 0.3913 +DEAL:3d:cg:cg::Convergence step 1 value 5.551e-17 +DEAL:3d:cg:cg::Starting value 0.0006066 +DEAL:3d:cg:cg::Convergence step 1 value 0.000 +DEAL:3d:cg:cg::Starting value 3.469e-07 +DEAL:3d:cg:cg::Convergence step 1 value 0.000 +DEAL:3d:cg:cg::Starting value 5.798e-10 +DEAL:3d:cg:cg::Convergence step 1 value 0.000 +DEAL:3d:cg::Convergence step 4 value 5.998e-09 DEAL:3d::Testing FE_Q<3>(2) DEAL:3d::Number of degrees of freedom: 4913 DEAL:3d:cg::Starting value 70.09 -DEAL:3d:cg:cg::Starting value 6.424 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg:cg::Starting value 0.0006099 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg:cg::Starting value 1.980e-06 -DEAL:3d:cg:cg::Convergence step 1 value 0 -DEAL:3d:cg::Convergence step 3 value 1.197e-06 +DEAL:3d:cg:cg::Starting value 2.274 +DEAL:3d:cg:cg::Convergence step 1 value 0.000 +DEAL:3d:cg:cg::Starting value 0.0007566 +DEAL:3d:cg:cg::Convergence step 1 value 1.084e-19 +DEAL:3d:cg:cg::Starting value 3.302e-06 +DEAL:3d:cg:cg::Convergence step 1 value 0.000 +DEAL:3d:cg:cg::Starting value 1.183e-08 +DEAL:3d:cg:cg::Convergence step 1 value 0.000 +DEAL:3d:cg::Convergence step 4 value 5.811e-08 diff --git a/tests/matrix_free/parallel_multigrid_adaptive_01.with_mpi=true.with_p4est=true.with_trilinos=true.with_lapack=true.mpirun=3.output b/tests/matrix_free/parallel_multigrid_adaptive_01.with_mpi=true.with_p4est=true.with_trilinos=true.with_lapack=true.mpirun=3.output index 34ea63ce0d82..4e020c6122be 100644 --- a/tests/matrix_free/parallel_multigrid_adaptive_01.with_mpi=true.with_p4est=true.with_trilinos=true.with_lapack=true.mpirun=3.output +++ b/tests/matrix_free/parallel_multigrid_adaptive_01.with_mpi=true.with_p4est=true.with_trilinos=true.with_lapack=true.mpirun=3.output @@ -2,28 +2,28 @@ DEAL:2d::Testing FE_Q<2>(1) DEAL:2d::Number of degrees of freedom: 507 DEAL:2d:cg::Starting value 21.93 -DEAL:2d:cg::Convergence step 5 value 7.800e-07 +DEAL:2d:cg::Convergence step 5 value 1.167e-06 DEAL:2d::Testing FE_Q<2>(1) DEAL:2d::Number of degrees of freedom: 881 DEAL:2d:cg::Starting value 27.77 -DEAL:2d:cg::Convergence step 6 value 9.250e-07 +DEAL:2d:cg::Convergence step 6 value 1.190e-06 DEAL:2d::Testing FE_Q<2>(1) DEAL:2d::Number of degrees of freedom: 2147 DEAL:2d:cg::Starting value 43.26 -DEAL:2d:cg::Convergence step 6 value 1.135e-06 +DEAL:2d:cg::Convergence step 6 value 1.886e-06 DEAL:2d::Testing FE_Q<2>(1) DEAL:2d::Number of degrees of freedom: 6517 DEAL:2d:cg::Starting value 76.92 -DEAL:2d:cg::Convergence step 6 value 1.557e-06 +DEAL:2d:cg::Convergence step 6 value 3.143e-06 DEAL:3d::Testing FE_Q<3>(1) DEAL:3d::Number of degrees of freedom: 1103 DEAL:3d:cg::Starting value 31.21 -DEAL:3d:cg::Convergence step 6 value 3.602e-08 +DEAL:3d:cg::Convergence step 6 value 2.139e-07 DEAL:3d::Testing FE_Q<3>(1) DEAL:3d::Number of degrees of freedom: 3694 DEAL:3d:cg::Starting value 55.00 -DEAL:3d:cg::Convergence step 7 value 3.930e-06 +DEAL:3d:cg::Convergence step 7 value 4.724e-06 DEAL:3d::Testing FE_Q<3>(1) DEAL:3d::Number of degrees of freedom: 9566 DEAL:3d:cg::Starting value 76.18 -DEAL:3d:cg::Convergence step 8 value 5.370e-06 +DEAL:3d:cg::Convergence step 8 value 6.234e-06 diff --git a/tests/matrix_free/parallel_multigrid_adaptive_01.with_mpi=true.with_p4est=true.with_trilinos=true.with_lapack=true.mpirun=7.output b/tests/matrix_free/parallel_multigrid_adaptive_01.with_mpi=true.with_p4est=true.with_trilinos=true.with_lapack=true.mpirun=7.output index 34ea63ce0d82..cd898e3eaf2b 100644 --- a/tests/matrix_free/parallel_multigrid_adaptive_01.with_mpi=true.with_p4est=true.with_trilinos=true.with_lapack=true.mpirun=7.output +++ b/tests/matrix_free/parallel_multigrid_adaptive_01.with_mpi=true.with_p4est=true.with_trilinos=true.with_lapack=true.mpirun=7.output @@ -2,28 +2,28 @@ DEAL:2d::Testing FE_Q<2>(1) DEAL:2d::Number of degrees of freedom: 507 DEAL:2d:cg::Starting value 21.93 -DEAL:2d:cg::Convergence step 5 value 7.800e-07 +DEAL:2d:cg::Convergence step 5 value 1.145e-06 DEAL:2d::Testing FE_Q<2>(1) DEAL:2d::Number of degrees of freedom: 881 DEAL:2d:cg::Starting value 27.77 -DEAL:2d:cg::Convergence step 6 value 9.250e-07 +DEAL:2d:cg::Convergence step 6 value 1.176e-06 DEAL:2d::Testing FE_Q<2>(1) DEAL:2d::Number of degrees of freedom: 2147 DEAL:2d:cg::Starting value 43.26 -DEAL:2d:cg::Convergence step 6 value 1.135e-06 +DEAL:2d:cg::Convergence step 6 value 1.884e-06 DEAL:2d::Testing FE_Q<2>(1) DEAL:2d::Number of degrees of freedom: 6517 DEAL:2d:cg::Starting value 76.92 -DEAL:2d:cg::Convergence step 6 value 1.557e-06 +DEAL:2d:cg::Convergence step 6 value 3.090e-06 DEAL:3d::Testing FE_Q<3>(1) DEAL:3d::Number of degrees of freedom: 1103 DEAL:3d:cg::Starting value 31.21 -DEAL:3d:cg::Convergence step 6 value 3.602e-08 +DEAL:3d:cg::Convergence step 6 value 2.139e-07 DEAL:3d::Testing FE_Q<3>(1) DEAL:3d::Number of degrees of freedom: 3694 DEAL:3d:cg::Starting value 55.00 -DEAL:3d:cg::Convergence step 7 value 3.930e-06 +DEAL:3d:cg::Convergence step 7 value 4.739e-06 DEAL:3d::Testing FE_Q<3>(1) DEAL:3d::Number of degrees of freedom: 9566 DEAL:3d:cg::Starting value 76.18 -DEAL:3d:cg::Convergence step 8 value 5.370e-06 +DEAL:3d:cg::Convergence step 8 value 6.236e-06 diff --git a/tests/matrix_free/parallel_multigrid_adaptive_02.with_mpi=true.with_p4est=true.with_lapack=true.mpirun=3.output b/tests/matrix_free/parallel_multigrid_adaptive_02.with_mpi=true.with_p4est=true.with_lapack=true.mpirun=3.output index 16d865c56ac6..57d068da86c1 100644 --- a/tests/matrix_free/parallel_multigrid_adaptive_02.with_mpi=true.with_p4est=true.with_lapack=true.mpirun=3.output +++ b/tests/matrix_free/parallel_multigrid_adaptive_02.with_mpi=true.with_p4est=true.with_lapack=true.mpirun=3.output @@ -2,48 +2,48 @@ DEAL:2d::Testing FE_Q<2>(1) DEAL:2d::Number of degrees of freedom: 507 DEAL:2d:cg::Starting value 21.93 -DEAL:2d:cg::Convergence step 5 value 7.781e-07 +DEAL:2d:cg::Convergence step 5 value 1.167e-06 DEAL:2d::Testing FE_Q<2>(1) DEAL:2d::Number of degrees of freedom: 881 DEAL:2d:cg::Starting value 27.77 -DEAL:2d:cg::Convergence step 6 value 9.215e-07 +DEAL:2d:cg::Convergence step 6 value 1.190e-06 DEAL:2d::Testing FE_Q<2>(1) DEAL:2d::Number of degrees of freedom: 2147 DEAL:2d:cg::Starting value 43.26 -DEAL:2d:cg::Convergence step 6 value 1.142e-06 +DEAL:2d:cg::Convergence step 6 value 1.886e-06 DEAL:2d::Testing FE_Q<2>(1) DEAL:2d::Number of degrees of freedom: 6517 DEAL:2d:cg::Starting value 76.92 -DEAL:2d:cg::Convergence step 6 value 1.563e-06 +DEAL:2d:cg::Convergence step 6 value 3.143e-06 DEAL:2d::Testing FE_Q<2>(3) DEAL:2d::Number of degrees of freedom: 4259 DEAL:2d:cg::Starting value 64.26 -DEAL:2d:cg::Convergence step 5 value 1.632e-06 +DEAL:2d:cg::Convergence step 5 value 2.131e-06 DEAL:2d::Testing FE_Q<2>(3) DEAL:2d::Number of degrees of freedom: 7457 DEAL:2d:cg::Starting value 83.11 -DEAL:2d:cg::Convergence step 5 value 7.695e-06 +DEAL:2d:cg::Convergence step 6 value 5.783e-07 DEAL:2d::Testing FE_Q<2>(3) DEAL:2d::Number of degrees of freedom: 18535 DEAL:2d:cg::Starting value 131.0 -DEAL:2d:cg::Convergence step 5 value 6.059e-06 +DEAL:2d:cg::Convergence step 6 value 6.147e-07 DEAL:3d::Testing FE_Q<3>(1) DEAL:3d::Number of degrees of freedom: 1103 DEAL:3d:cg::Starting value 31.21 -DEAL:3d:cg::Convergence step 6 value 3.615e-08 +DEAL:3d:cg::Convergence step 6 value 2.139e-07 DEAL:3d::Testing FE_Q<3>(1) DEAL:3d::Number of degrees of freedom: 3694 DEAL:3d:cg::Starting value 55.00 -DEAL:3d:cg::Convergence step 7 value 3.941e-06 +DEAL:3d:cg::Convergence step 7 value 4.724e-06 DEAL:3d::Testing FE_Q<3>(1) DEAL:3d::Number of degrees of freedom: 9566 DEAL:3d:cg::Starting value 76.18 -DEAL:3d:cg::Convergence step 8 value 5.362e-06 +DEAL:3d:cg::Convergence step 8 value 6.234e-06 DEAL:3d::Testing FE_Q<3>(2) DEAL:3d::Number of degrees of freedom: 7494 DEAL:3d:cg::Starting value 82.90 -DEAL:3d:cg::Convergence step 7 value 8.682e-07 +DEAL:3d:cg::Convergence step 7 value 1.038e-06 DEAL:3d::Testing FE_Q<3>(2) DEAL:3d::Number of degrees of freedom: 26548 DEAL:3d:cg::Starting value 152.6 -DEAL:3d:cg::Convergence step 7 value 3.969e-06 +DEAL:3d:cg::Convergence step 7 value 4.360e-06 diff --git a/tests/matrix_free/parallel_multigrid_adaptive_02.with_mpi=true.with_p4est=true.with_lapack=true.mpirun=7.output b/tests/matrix_free/parallel_multigrid_adaptive_02.with_mpi=true.with_p4est=true.with_lapack=true.mpirun=7.output index 16d865c56ac6..e5e72f230291 100644 --- a/tests/matrix_free/parallel_multigrid_adaptive_02.with_mpi=true.with_p4est=true.with_lapack=true.mpirun=7.output +++ b/tests/matrix_free/parallel_multigrid_adaptive_02.with_mpi=true.with_p4est=true.with_lapack=true.mpirun=7.output @@ -2,48 +2,48 @@ DEAL:2d::Testing FE_Q<2>(1) DEAL:2d::Number of degrees of freedom: 507 DEAL:2d:cg::Starting value 21.93 -DEAL:2d:cg::Convergence step 5 value 7.781e-07 +DEAL:2d:cg::Convergence step 5 value 1.145e-06 DEAL:2d::Testing FE_Q<2>(1) DEAL:2d::Number of degrees of freedom: 881 DEAL:2d:cg::Starting value 27.77 -DEAL:2d:cg::Convergence step 6 value 9.215e-07 +DEAL:2d:cg::Convergence step 6 value 1.176e-06 DEAL:2d::Testing FE_Q<2>(1) DEAL:2d::Number of degrees of freedom: 2147 DEAL:2d:cg::Starting value 43.26 -DEAL:2d:cg::Convergence step 6 value 1.142e-06 +DEAL:2d:cg::Convergence step 6 value 1.884e-06 DEAL:2d::Testing FE_Q<2>(1) DEAL:2d::Number of degrees of freedom: 6517 DEAL:2d:cg::Starting value 76.92 -DEAL:2d:cg::Convergence step 6 value 1.563e-06 +DEAL:2d:cg::Convergence step 6 value 3.090e-06 DEAL:2d::Testing FE_Q<2>(3) DEAL:2d::Number of degrees of freedom: 4259 DEAL:2d:cg::Starting value 64.26 -DEAL:2d:cg::Convergence step 5 value 1.632e-06 +DEAL:2d:cg::Convergence step 5 value 2.131e-06 DEAL:2d::Testing FE_Q<2>(3) DEAL:2d::Number of degrees of freedom: 7457 DEAL:2d:cg::Starting value 83.11 -DEAL:2d:cg::Convergence step 5 value 7.695e-06 +DEAL:2d:cg::Convergence step 6 value 5.788e-07 DEAL:2d::Testing FE_Q<2>(3) DEAL:2d::Number of degrees of freedom: 18535 DEAL:2d:cg::Starting value 131.0 -DEAL:2d:cg::Convergence step 5 value 6.059e-06 +DEAL:2d:cg::Convergence step 6 value 6.134e-07 DEAL:3d::Testing FE_Q<3>(1) DEAL:3d::Number of degrees of freedom: 1103 DEAL:3d:cg::Starting value 31.21 -DEAL:3d:cg::Convergence step 6 value 3.615e-08 +DEAL:3d:cg::Convergence step 6 value 2.139e-07 DEAL:3d::Testing FE_Q<3>(1) DEAL:3d::Number of degrees of freedom: 3694 DEAL:3d:cg::Starting value 55.00 -DEAL:3d:cg::Convergence step 7 value 3.941e-06 +DEAL:3d:cg::Convergence step 7 value 4.739e-06 DEAL:3d::Testing FE_Q<3>(1) DEAL:3d::Number of degrees of freedom: 9566 DEAL:3d:cg::Starting value 76.18 -DEAL:3d:cg::Convergence step 8 value 5.362e-06 +DEAL:3d:cg::Convergence step 8 value 6.236e-06 DEAL:3d::Testing FE_Q<3>(2) DEAL:3d::Number of degrees of freedom: 7494 DEAL:3d:cg::Starting value 82.90 -DEAL:3d:cg::Convergence step 7 value 8.682e-07 +DEAL:3d:cg::Convergence step 7 value 1.039e-06 DEAL:3d::Testing FE_Q<3>(2) DEAL:3d::Number of degrees of freedom: 26548 DEAL:3d:cg::Starting value 152.6 -DEAL:3d:cg::Convergence step 7 value 3.969e-06 +DEAL:3d:cg::Convergence step 7 value 4.352e-06 diff --git a/tests/matrix_free/parallel_multigrid_adaptive_03.with_mpi=true.with_p4est=true.with_lapack=true.mpirun=4.output b/tests/matrix_free/parallel_multigrid_adaptive_03.with_mpi=true.with_p4est=true.with_lapack=true.mpirun=4.output index c7cff64778d9..877c9af81ae8 100644 --- a/tests/matrix_free/parallel_multigrid_adaptive_03.with_mpi=true.with_p4est=true.with_lapack=true.mpirun=4.output +++ b/tests/matrix_free/parallel_multigrid_adaptive_03.with_mpi=true.with_p4est=true.with_lapack=true.mpirun=4.output @@ -2,104 +2,104 @@ DEAL:nothread::Testing FE_Q<2>(1) DEAL:nothread::Number of degrees of freedom: 507 DEAL:nothread:cg::Starting value 21.9317 -DEAL:nothread:cg::Convergence step 5 value 7.78558e-07 +DEAL:nothread:cg::Convergence step 5 value 1.14537e-06 DEAL:threaded::Testing FE_Q<2>(1) DEAL:threaded::Number of degrees of freedom: 507 DEAL:threaded:cg::Starting value 21.9317 -DEAL:threaded:cg::Convergence step 5 value 7.78558e-07 +DEAL:threaded:cg::Convergence step 5 value 1.14537e-06 DEAL:nothread::Testing FE_Q<2>(1) DEAL:nothread::Number of degrees of freedom: 881 DEAL:nothread:cg::Starting value 27.7669 -DEAL:nothread:cg::Convergence step 6 value 9.22164e-07 +DEAL:nothread:cg::Convergence step 6 value 1.18996e-06 DEAL:threaded::Testing FE_Q<2>(1) DEAL:threaded::Number of degrees of freedom: 881 DEAL:threaded:cg::Starting value 27.7669 -DEAL:threaded:cg::Convergence step 6 value 9.22164e-07 +DEAL:threaded:cg::Convergence step 6 value 1.18996e-06 DEAL:nothread::Testing FE_Q<2>(1) DEAL:nothread::Number of degrees of freedom: 2147 DEAL:nothread:cg::Starting value 43.2551 -DEAL:nothread:cg::Convergence step 6 value 1.15108e-06 +DEAL:nothread:cg::Convergence step 6 value 1.86235e-06 DEAL:threaded::Testing FE_Q<2>(1) DEAL:threaded::Number of degrees of freedom: 2147 DEAL:threaded:cg::Starting value 43.2551 -DEAL:threaded:cg::Convergence step 6 value 1.15108e-06 +DEAL:threaded:cg::Convergence step 6 value 1.86235e-06 DEAL:nothread::Testing FE_Q<2>(1) DEAL:nothread::Number of degrees of freedom: 6517 DEAL:nothread:cg::Starting value 76.9220 -DEAL:nothread:cg::Convergence step 6 value 1.56831e-06 +DEAL:nothread:cg::Convergence step 6 value 3.14118e-06 DEAL:threaded::Testing FE_Q<2>(1) DEAL:threaded::Number of degrees of freedom: 6517 DEAL:threaded:cg::Starting value 76.9220 -DEAL:threaded:cg::Convergence step 6 value 1.56831e-06 +DEAL:threaded:cg::Convergence step 6 value 3.14118e-06 DEAL:nothread::Testing FE_Q<2>(2) DEAL:nothread::Number of degrees of freedom: 1935 DEAL:nothread:cg::Starting value 43.0929 -DEAL:nothread:cg::Convergence step 5 value 2.13384e-06 +DEAL:nothread:cg::Convergence step 5 value 3.22495e-06 DEAL:threaded::Testing FE_Q<2>(2) DEAL:threaded::Number of degrees of freedom: 1935 DEAL:threaded:cg::Starting value 43.0929 -DEAL:threaded:cg::Convergence step 5 value 2.13388e-06 +DEAL:threaded:cg::Convergence step 5 value 3.22504e-06 DEAL:nothread::Testing FE_Q<2>(2) DEAL:nothread::Number of degrees of freedom: 3403 DEAL:nothread:cg::Starting value 55.4346 -DEAL:nothread:cg::Convergence step 6 value 4.27828e-07 +DEAL:nothread:cg::Convergence step 6 value 8.67853e-07 DEAL:threaded::Testing FE_Q<2>(2) DEAL:threaded::Number of degrees of freedom: 3403 DEAL:threaded:cg::Starting value 55.4346 -DEAL:threaded:cg::Convergence step 6 value 4.27798e-07 +DEAL:threaded:cg::Convergence step 6 value 8.67861e-07 DEAL:nothread::Testing FE_Q<2>(2) DEAL:nothread::Number of degrees of freedom: 8417 DEAL:nothread:cg::Starting value 87.1149 -DEAL:nothread:cg::Convergence step 6 value 2.55138e-07 +DEAL:nothread:cg::Convergence step 6 value 5.47715e-07 DEAL:threaded::Testing FE_Q<2>(2) DEAL:threaded::Number of degrees of freedom: 8417 DEAL:threaded:cg::Starting value 87.1149 -DEAL:threaded:cg::Convergence step 6 value 2.55129e-07 +DEAL:threaded:cg::Convergence step 6 value 5.47726e-07 DEAL:nothread::Testing FE_Q<3>(1) DEAL:nothread::Number of degrees of freedom: 186 DEAL:nothread:cg::Starting value 12.3693 -DEAL:nothread:cg::Convergence step 3 value 2.26211e-07 +DEAL:nothread:cg::Convergence step 4 value 2.87808e-08 DEAL:threaded::Testing FE_Q<3>(1) DEAL:threaded::Number of degrees of freedom: 186 DEAL:threaded:cg::Starting value 12.3693 -DEAL:threaded:cg::Convergence step 3 value 2.26211e-07 +DEAL:threaded:cg::Convergence step 4 value 2.87808e-08 DEAL:nothread::Testing FE_Q<3>(1) DEAL:nothread::Number of degrees of freedom: 648 DEAL:nothread:cg::Starting value 21.1424 -DEAL:nothread:cg::Convergence step 6 value 1.11426e-07 +DEAL:nothread:cg::Convergence step 6 value 6.44935e-07 DEAL:threaded::Testing FE_Q<3>(1) DEAL:threaded::Number of degrees of freedom: 648 DEAL:threaded:cg::Starting value 21.1424 -DEAL:threaded:cg::Convergence step 6 value 1.11426e-07 +DEAL:threaded:cg::Convergence step 6 value 6.44935e-07 DEAL:nothread::Testing FE_Q<3>(1) DEAL:nothread::Number of degrees of freedom: 2930 DEAL:nothread:cg::Starting value 47.1699 -DEAL:nothread:cg::Convergence step 7 value 1.63079e-06 +DEAL:nothread:cg::Convergence step 7 value 2.56010e-06 DEAL:threaded::Testing FE_Q<3>(1) DEAL:threaded::Number of degrees of freedom: 2930 DEAL:threaded:cg::Starting value 47.1699 -DEAL:threaded:cg::Convergence step 7 value 1.63079e-06 +DEAL:threaded:cg::Convergence step 7 value 2.56010e-06 DEAL:nothread::Testing FE_Q<3>(1) DEAL:nothread::Number of degrees of freedom: 186 DEAL:nothread:cg::Starting value 12.3693 -DEAL:nothread:cg::Convergence step 3 value 2.24462e-07 +DEAL:nothread:cg::Convergence step 4 value 2.88983e-08 DEAL:threaded::Testing FE_Q<3>(1) DEAL:threaded::Number of degrees of freedom: 186 DEAL:threaded:cg::Starting value 12.3693 -DEAL:threaded:cg::Convergence step 3 value 2.24473e-07 +DEAL:threaded:cg::Convergence step 4 value 2.88980e-08 DEAL:nothread::Testing FE_Q<3>(1) DEAL:nothread::Number of degrees of freedom: 648 DEAL:nothread:cg::Starting value 21.1424 -DEAL:nothread:cg::Convergence step 6 value 1.06988e-07 +DEAL:nothread:cg::Convergence step 6 value 6.40524e-07 DEAL:threaded::Testing FE_Q<3>(1) DEAL:threaded::Number of degrees of freedom: 648 DEAL:threaded:cg::Starting value 21.1424 -DEAL:threaded:cg::Convergence step 6 value 1.06988e-07 +DEAL:threaded:cg::Convergence step 6 value 6.40523e-07 DEAL:nothread::Testing FE_Q<3>(1) DEAL:nothread::Number of degrees of freedom: 2930 DEAL:nothread:cg::Starting value 47.1699 -DEAL:nothread:cg::Convergence step 7 value 1.63550e-06 +DEAL:nothread:cg::Convergence step 7 value 2.56010e-06 DEAL:threaded::Testing FE_Q<3>(1) DEAL:threaded::Number of degrees of freedom: 2930 DEAL:threaded:cg::Starting value 47.1699 -DEAL:threaded:cg::Convergence step 7 value 1.63550e-06 +DEAL:threaded:cg::Convergence step 7 value 2.56010e-06 diff --git a/tests/matrix_free/parallel_multigrid_adaptive_03.with_mpi=true.with_p4est=true.with_lapack=true.mpirun=7.output b/tests/matrix_free/parallel_multigrid_adaptive_03.with_mpi=true.with_p4est=true.with_lapack=true.mpirun=7.output index fae3b8e1a7d2..d176be1ecf49 100644 --- a/tests/matrix_free/parallel_multigrid_adaptive_03.with_mpi=true.with_p4est=true.with_lapack=true.mpirun=7.output +++ b/tests/matrix_free/parallel_multigrid_adaptive_03.with_mpi=true.with_p4est=true.with_lapack=true.mpirun=7.output @@ -2,104 +2,104 @@ DEAL:nothread::Testing FE_Q<2>(1) DEAL:nothread::Number of degrees of freedom: 507 DEAL:nothread:cg::Starting value 21.9317 -DEAL:nothread:cg::Convergence step 5 value 7.76680e-07 +DEAL:nothread:cg::Convergence step 5 value 1.14539e-06 DEAL:threaded::Testing FE_Q<2>(1) DEAL:threaded::Number of degrees of freedom: 507 DEAL:threaded:cg::Starting value 21.9317 -DEAL:threaded:cg::Convergence step 5 value 7.76680e-07 +DEAL:threaded:cg::Convergence step 5 value 1.14539e-06 DEAL:nothread::Testing FE_Q<2>(1) DEAL:nothread::Number of degrees of freedom: 881 DEAL:nothread:cg::Starting value 27.7669 -DEAL:nothread:cg::Convergence step 6 value 9.25965e-07 +DEAL:nothread:cg::Convergence step 6 value 1.17649e-06 DEAL:threaded::Testing FE_Q<2>(1) DEAL:threaded::Number of degrees of freedom: 881 DEAL:threaded:cg::Starting value 27.7669 -DEAL:threaded:cg::Convergence step 6 value 9.25965e-07 +DEAL:threaded:cg::Convergence step 6 value 1.17649e-06 DEAL:nothread::Testing FE_Q<2>(1) DEAL:nothread::Number of degrees of freedom: 2147 DEAL:nothread:cg::Starting value 43.2551 -DEAL:nothread:cg::Convergence step 6 value 1.14972e-06 +DEAL:nothread:cg::Convergence step 6 value 1.88354e-06 DEAL:threaded::Testing FE_Q<2>(1) DEAL:threaded::Number of degrees of freedom: 2147 DEAL:threaded:cg::Starting value 43.2551 -DEAL:threaded:cg::Convergence step 6 value 1.14972e-06 +DEAL:threaded:cg::Convergence step 6 value 1.88354e-06 DEAL:nothread::Testing FE_Q<2>(1) DEAL:nothread::Number of degrees of freedom: 6517 DEAL:nothread:cg::Starting value 76.9220 -DEAL:nothread:cg::Convergence step 6 value 1.56712e-06 +DEAL:nothread:cg::Convergence step 6 value 3.08982e-06 DEAL:threaded::Testing FE_Q<2>(1) DEAL:threaded::Number of degrees of freedom: 6517 DEAL:threaded:cg::Starting value 76.9220 -DEAL:threaded:cg::Convergence step 6 value 1.56712e-06 +DEAL:threaded:cg::Convergence step 6 value 3.08982e-06 DEAL:nothread::Testing FE_Q<2>(2) DEAL:nothread::Number of degrees of freedom: 1935 DEAL:nothread:cg::Starting value 43.0929 -DEAL:nothread:cg::Convergence step 5 value 2.13377e-06 +DEAL:nothread:cg::Convergence step 5 value 3.19333e-06 DEAL:threaded::Testing FE_Q<2>(2) DEAL:threaded::Number of degrees of freedom: 1935 DEAL:threaded:cg::Starting value 43.0929 -DEAL:threaded:cg::Convergence step 5 value 2.13371e-06 +DEAL:threaded:cg::Convergence step 5 value 3.19334e-06 DEAL:nothread::Testing FE_Q<2>(2) DEAL:nothread::Number of degrees of freedom: 3403 DEAL:nothread:cg::Starting value 55.4346 -DEAL:nothread:cg::Convergence step 6 value 4.27767e-07 +DEAL:nothread:cg::Convergence step 6 value 8.71780e-07 DEAL:threaded::Testing FE_Q<2>(2) DEAL:threaded::Number of degrees of freedom: 3403 DEAL:threaded:cg::Starting value 55.4346 -DEAL:threaded:cg::Convergence step 6 value 4.27807e-07 +DEAL:threaded:cg::Convergence step 6 value 8.71685e-07 DEAL:nothread::Testing FE_Q<2>(2) DEAL:nothread::Number of degrees of freedom: 8417 DEAL:nothread:cg::Starting value 87.1149 -DEAL:nothread:cg::Convergence step 6 value 2.55168e-07 +DEAL:nothread:cg::Convergence step 6 value 5.47238e-07 DEAL:threaded::Testing FE_Q<2>(2) DEAL:threaded::Number of degrees of freedom: 8417 DEAL:threaded:cg::Starting value 87.1149 -DEAL:threaded:cg::Convergence step 6 value 2.55163e-07 +DEAL:threaded:cg::Convergence step 6 value 5.47227e-07 DEAL:nothread::Testing FE_Q<3>(1) DEAL:nothread::Number of degrees of freedom: 186 DEAL:nothread:cg::Starting value 12.3693 -DEAL:nothread:cg::Convergence step 3 value 2.28324e-07 +DEAL:nothread:cg::Convergence step 4 value 2.87808e-08 DEAL:threaded::Testing FE_Q<3>(1) DEAL:threaded::Number of degrees of freedom: 186 DEAL:threaded:cg::Starting value 12.3693 -DEAL:threaded:cg::Convergence step 3 value 2.28324e-07 +DEAL:threaded:cg::Convergence step 4 value 2.87808e-08 DEAL:nothread::Testing FE_Q<3>(1) DEAL:nothread::Number of degrees of freedom: 648 DEAL:nothread:cg::Starting value 21.1424 -DEAL:nothread:cg::Convergence step 6 value 1.11195e-07 +DEAL:nothread:cg::Convergence step 6 value 6.44905e-07 DEAL:threaded::Testing FE_Q<3>(1) DEAL:threaded::Number of degrees of freedom: 648 DEAL:threaded:cg::Starting value 21.1424 -DEAL:threaded:cg::Convergence step 6 value 1.11195e-07 +DEAL:threaded:cg::Convergence step 6 value 6.44905e-07 DEAL:nothread::Testing FE_Q<3>(1) DEAL:nothread::Number of degrees of freedom: 2930 DEAL:nothread:cg::Starting value 47.1699 -DEAL:nothread:cg::Convergence step 7 value 1.63163e-06 +DEAL:nothread:cg::Convergence step 7 value 2.56063e-06 DEAL:threaded::Testing FE_Q<3>(1) DEAL:threaded::Number of degrees of freedom: 2930 DEAL:threaded:cg::Starting value 47.1699 -DEAL:threaded:cg::Convergence step 7 value 1.63163e-06 +DEAL:threaded:cg::Convergence step 7 value 2.56063e-06 DEAL:nothread::Testing FE_Q<3>(1) DEAL:nothread::Number of degrees of freedom: 186 DEAL:nothread:cg::Starting value 12.3693 -DEAL:nothread:cg::Convergence step 3 value 1.58643e-07 +DEAL:nothread:cg::Convergence step 4 value 2.88986e-08 DEAL:threaded::Testing FE_Q<3>(1) DEAL:threaded::Number of degrees of freedom: 186 DEAL:threaded:cg::Starting value 12.3693 -DEAL:threaded:cg::Convergence step 3 value 1.58660e-07 +DEAL:threaded:cg::Convergence step 4 value 2.88984e-08 DEAL:nothread::Testing FE_Q<3>(1) DEAL:nothread::Number of degrees of freedom: 648 DEAL:nothread:cg::Starting value 21.1424 -DEAL:nothread:cg::Convergence step 6 value 1.06758e-07 +DEAL:nothread:cg::Convergence step 6 value 6.39127e-07 DEAL:threaded::Testing FE_Q<3>(1) DEAL:threaded::Number of degrees of freedom: 648 DEAL:threaded:cg::Starting value 21.1424 -DEAL:threaded:cg::Convergence step 6 value 1.06760e-07 +DEAL:threaded:cg::Convergence step 6 value 6.39130e-07 DEAL:nothread::Testing FE_Q<3>(1) DEAL:nothread::Number of degrees of freedom: 2930 DEAL:nothread:cg::Starting value 47.1699 -DEAL:nothread:cg::Convergence step 7 value 1.63203e-06 +DEAL:nothread:cg::Convergence step 7 value 2.55900e-06 DEAL:threaded::Testing FE_Q<3>(1) DEAL:threaded::Number of degrees of freedom: 2930 DEAL:threaded:cg::Starting value 47.1699 -DEAL:threaded:cg::Convergence step 7 value 1.63203e-06 +DEAL:threaded:cg::Convergence step 7 value 2.55899e-06 diff --git a/tests/matrix_free/parallel_multigrid_adaptive_05.with_mpi=true.with_p4est=true.with_lapack=true.mpirun=4.output b/tests/matrix_free/parallel_multigrid_adaptive_05.with_mpi=true.with_p4est=true.with_lapack=true.mpirun=4.output index 7916f86cb3b6..5563de929413 100644 --- a/tests/matrix_free/parallel_multigrid_adaptive_05.with_mpi=true.with_p4est=true.with_lapack=true.mpirun=4.output +++ b/tests/matrix_free/parallel_multigrid_adaptive_05.with_mpi=true.with_p4est=true.with_lapack=true.mpirun=4.output @@ -2,16 +2,16 @@ DEAL:threaded::Testing FE_Q<2>(1) DEAL:threaded::Number of degrees of freedom: 507 DEAL:threaded:cg::Starting value 21.9317 -DEAL:threaded:cg::Convergence step 5 value 7.81205e-07 +DEAL:threaded:cg::Convergence step 5 value 1.14537e-06 DEAL:threaded::Testing FE_Q<2>(1) DEAL:threaded::Number of degrees of freedom: 881 DEAL:threaded:cg::Starting value 27.7669 -DEAL:threaded:cg::Convergence step 6 value 9.24482e-07 +DEAL:threaded:cg::Convergence step 6 value 1.18996e-06 DEAL:threaded::Testing FE_Q<2>(1) DEAL:threaded::Number of degrees of freedom: 2147 DEAL:threaded:cg::Starting value 43.2551 -DEAL:threaded:cg::Convergence step 6 value 1.14520e-06 +DEAL:threaded:cg::Convergence step 6 value 1.86235e-06 DEAL:threaded::Testing FE_Q<2>(1) DEAL:threaded::Number of degrees of freedom: 6517 DEAL:threaded:cg::Starting value 76.9220 -DEAL:threaded:cg::Convergence step 6 value 1.55925e-06 +DEAL:threaded:cg::Convergence step 6 value 3.14118e-06 diff --git a/tests/matrix_free/parallel_multigrid_mf.with_mpi=true.with_p4est=true.with_lapack=true.mpirun=7.output b/tests/matrix_free/parallel_multigrid_mf.with_mpi=true.with_p4est=true.with_lapack=true.mpirun=7.output index aa47ee8f4d2a..cd88f52b6e0d 100644 --- a/tests/matrix_free/parallel_multigrid_mf.with_mpi=true.with_p4est=true.with_lapack=true.mpirun=7.output +++ b/tests/matrix_free/parallel_multigrid_mf.with_mpi=true.with_p4est=true.with_lapack=true.mpirun=7.output @@ -2,32 +2,32 @@ DEAL::Testing FE_Q<2>(1) DEAL::Number of degrees of freedom: 81 DEAL:cg::Starting value 9.00000 -DEAL:cg::Convergence step 3 value 3.51890e-08 +DEAL:cg::Convergence step 3 value 6.75256e-07 DEAL::Testing FE_Q<2>(1) DEAL::Number of degrees of freedom: 289 DEAL:cg::Starting value 17.0000 -DEAL:cg::Convergence step 3 value 2.90115e-08 +DEAL:cg::Convergence step 4 value 2.62465e-09 DEAL::Testing FE_Q<2>(2) DEAL::Number of degrees of freedom: 289 DEAL:cg::Starting value 17.0000 -DEAL:cg::Convergence step 3 value 2.86879e-07 +DEAL:cg::Convergence step 4 value 1.71224e-08 DEAL::Testing FE_Q<2>(2) DEAL::Number of degrees of freedom: 1089 DEAL:cg::Starting value 33.0000 -DEAL:cg::Convergence step 3 value 7.11331e-07 +DEAL:cg::Convergence step 4 value 4.31534e-08 DEAL::Testing FE_Q<3>(1) DEAL::Number of degrees of freedom: 125 DEAL:cg::Starting value 11.1803 -DEAL:cg::Convergence step 3 value 0 +DEAL:cg::Convergence step 3 value 4.38307e-07 DEAL::Testing FE_Q<3>(1) DEAL::Number of degrees of freedom: 729 DEAL:cg::Starting value 27.0000 -DEAL:cg::Convergence step 3 value 1.30374e-07 +DEAL:cg::Convergence step 3 value 1.02520e-06 DEAL::Testing FE_Q<3>(2) DEAL::Number of degrees of freedom: 729 DEAL:cg::Starting value 27.0000 -DEAL:cg::Convergence step 3 value 2.75558e-08 +DEAL:cg::Convergence step 4 value 5.99244e-09 DEAL::Testing FE_Q<3>(2) DEAL::Number of degrees of freedom: 4913 DEAL:cg::Starting value 70.0928 -DEAL:cg::Convergence step 3 value 1.14078e-06 +DEAL:cg::Convergence step 4 value 5.81100e-08 diff --git a/tests/matrix_free/step-37-inhomogeneous-1.mpirun=4.with_p4est=true.output b/tests/matrix_free/step-37-inhomogeneous-1.mpirun=4.with_p4est=true.output index 6121bdd29e31..59dbf7d1ff29 100644 --- a/tests/matrix_free/step-37-inhomogeneous-1.mpirun=4.with_p4est=true.output +++ b/tests/matrix_free/step-37-inhomogeneous-1.mpirun=4.with_p4est=true.output @@ -2,149 +2,149 @@ Cycle 0 Number of degrees of freedom: 81 DEAL:0:cg::Starting value 45.0807 -DEAL:0:cg::Convergence step 6 value 2.23481e-13 +DEAL:0:cg::Convergence step 7 value 2.65304e-12 max error: 0.00772526 error ratio: 1.00000 Cycle 1 Number of degrees of freedom: 289 DEAL:0:cg::Starting value 68.5863 -DEAL:0:cg::Convergence step 6 value 4.06929e-13 +DEAL:0:cg::Convergence step 7 value 3.81082e-12 max error: 0.000971239 error ratio: 7.95402 Cycle 2 Number of degrees of freedom: 1089 DEAL:0:cg::Starting value 95.4381 -DEAL:0:cg::Convergence step 6 value 5.78305e-13 +DEAL:0:cg::Convergence step 7 value 7.14371e-12 max error: 0.000120278 error ratio: 8.07497 Cycle 3 Number of degrees of freedom: 4225 DEAL:0:cg::Starting value 131.732 -DEAL:0:cg::Convergence step 6 value 1.31602e-12 +DEAL:0:cg::Convergence step 7 value 1.44204e-11 max error: 1.49228e-05 error ratio: 8.05998 Cycle 4 Number of degrees of freedom: 16641 DEAL:0:cg::Starting value 183.473 -DEAL:0:cg::Convergence step 6 value 2.60867e-12 +DEAL:0:cg::Convergence step 7 value 2.54095e-11 max error: 1.85713e-06 error ratio: 8.03544 Cycle 5 Number of degrees of freedom: 66049 DEAL:0:cg::Starting value 257.379 -DEAL:0:cg::Convergence step 6 value 4.17156e-12 +DEAL:0:cg::Convergence step 7 value 3.94318e-11 max error: 2.31590e-07 error ratio: 8.01904 Cycle 0 Number of degrees of freedom: 125 DEAL:0:cg::Starting value 6.44073 -DEAL:0:cg::Convergence step 6 value 2.97002e-14 +DEAL:0:cg::Convergence step 7 value 4.64523e-13 max error: 0.0499110 error ratio: 1.00000 Cycle 1 Number of degrees of freedom: 729 DEAL:0:cg::Starting value 8.68642 -DEAL:0:cg::Convergence step 6 value 6.80139e-14 +DEAL:0:cg::Convergence step 7 value 5.79753e-13 max error: 0.00756448 error ratio: 6.59807 Cycle 2 Number of degrees of freedom: 4913 DEAL:0:cg::Starting value 9.47362 -DEAL:0:cg::Convergence step 6 value 6.56927e-14 +DEAL:0:cg::Convergence step 7 value 6.67651e-13 max error: 0.000965192 error ratio: 7.83728 Cycle 3 Number of degrees of freedom: 35937 DEAL:0:cg::Starting value 9.30402 -DEAL:0:cg::Convergence step 6 value 7.06917e-14 +DEAL:0:cg::Convergence step 7 value 9.36336e-13 max error: 0.000120048 error ratio: 8.04008 Cycle 4 Number of degrees of freedom: 274625 DEAL:0:cg::Starting value 8.99023 -DEAL:0:cg::Convergence step 6 value 8.15983e-14 +DEAL:0:cg::Convergence step 7 value 1.22268e-12 max error: 1.49140e-05 error ratio: 8.04933 DEAL:1:cg::Starting value 45.0807 -DEAL:1:cg::Convergence step 6 value 2.23481e-13 +DEAL:1:cg::Convergence step 7 value 2.65304e-12 DEAL:1:cg::Starting value 68.5863 -DEAL:1:cg::Convergence step 6 value 4.06929e-13 +DEAL:1:cg::Convergence step 7 value 3.81082e-12 DEAL:1:cg::Starting value 95.4381 -DEAL:1:cg::Convergence step 6 value 5.78305e-13 +DEAL:1:cg::Convergence step 7 value 7.14371e-12 DEAL:1:cg::Starting value 131.732 -DEAL:1:cg::Convergence step 6 value 1.31602e-12 +DEAL:1:cg::Convergence step 7 value 1.44204e-11 DEAL:1:cg::Starting value 183.473 -DEAL:1:cg::Convergence step 6 value 2.60867e-12 +DEAL:1:cg::Convergence step 7 value 2.54095e-11 DEAL:1:cg::Starting value 257.379 -DEAL:1:cg::Convergence step 6 value 4.17156e-12 +DEAL:1:cg::Convergence step 7 value 3.94318e-11 DEAL:1:cg::Starting value 6.44073 -DEAL:1:cg::Convergence step 6 value 2.97002e-14 +DEAL:1:cg::Convergence step 7 value 4.64523e-13 DEAL:1:cg::Starting value 8.68642 -DEAL:1:cg::Convergence step 6 value 6.80139e-14 +DEAL:1:cg::Convergence step 7 value 5.79753e-13 DEAL:1:cg::Starting value 9.47362 -DEAL:1:cg::Convergence step 6 value 6.56927e-14 +DEAL:1:cg::Convergence step 7 value 6.67651e-13 DEAL:1:cg::Starting value 9.30402 -DEAL:1:cg::Convergence step 6 value 7.06917e-14 +DEAL:1:cg::Convergence step 7 value 9.36336e-13 DEAL:1:cg::Starting value 8.99023 -DEAL:1:cg::Convergence step 6 value 8.15983e-14 +DEAL:1:cg::Convergence step 7 value 1.22268e-12 DEAL:2:cg::Starting value 45.0807 -DEAL:2:cg::Convergence step 6 value 2.23481e-13 +DEAL:2:cg::Convergence step 7 value 2.65304e-12 DEAL:2:cg::Starting value 68.5863 -DEAL:2:cg::Convergence step 6 value 4.06929e-13 +DEAL:2:cg::Convergence step 7 value 3.81082e-12 DEAL:2:cg::Starting value 95.4381 -DEAL:2:cg::Convergence step 6 value 5.78305e-13 +DEAL:2:cg::Convergence step 7 value 7.14371e-12 DEAL:2:cg::Starting value 131.732 -DEAL:2:cg::Convergence step 6 value 1.31602e-12 +DEAL:2:cg::Convergence step 7 value 1.44204e-11 DEAL:2:cg::Starting value 183.473 -DEAL:2:cg::Convergence step 6 value 2.60867e-12 +DEAL:2:cg::Convergence step 7 value 2.54095e-11 DEAL:2:cg::Starting value 257.379 -DEAL:2:cg::Convergence step 6 value 4.17156e-12 +DEAL:2:cg::Convergence step 7 value 3.94318e-11 DEAL:2:cg::Starting value 6.44073 -DEAL:2:cg::Convergence step 6 value 2.97002e-14 +DEAL:2:cg::Convergence step 7 value 4.64523e-13 DEAL:2:cg::Starting value 8.68642 -DEAL:2:cg::Convergence step 6 value 6.80139e-14 +DEAL:2:cg::Convergence step 7 value 5.79753e-13 DEAL:2:cg::Starting value 9.47362 -DEAL:2:cg::Convergence step 6 value 6.56927e-14 +DEAL:2:cg::Convergence step 7 value 6.67651e-13 DEAL:2:cg::Starting value 9.30402 -DEAL:2:cg::Convergence step 6 value 7.06917e-14 +DEAL:2:cg::Convergence step 7 value 9.36336e-13 DEAL:2:cg::Starting value 8.99023 -DEAL:2:cg::Convergence step 6 value 8.15983e-14 +DEAL:2:cg::Convergence step 7 value 1.22268e-12 DEAL:3:cg::Starting value 45.0807 -DEAL:3:cg::Convergence step 6 value 2.23481e-13 +DEAL:3:cg::Convergence step 7 value 2.65304e-12 DEAL:3:cg::Starting value 68.5863 -DEAL:3:cg::Convergence step 6 value 4.06929e-13 +DEAL:3:cg::Convergence step 7 value 3.81082e-12 DEAL:3:cg::Starting value 95.4381 -DEAL:3:cg::Convergence step 6 value 5.78305e-13 +DEAL:3:cg::Convergence step 7 value 7.14371e-12 DEAL:3:cg::Starting value 131.732 -DEAL:3:cg::Convergence step 6 value 1.31602e-12 +DEAL:3:cg::Convergence step 7 value 1.44204e-11 DEAL:3:cg::Starting value 183.473 -DEAL:3:cg::Convergence step 6 value 2.60867e-12 +DEAL:3:cg::Convergence step 7 value 2.54095e-11 DEAL:3:cg::Starting value 257.379 -DEAL:3:cg::Convergence step 6 value 4.17156e-12 +DEAL:3:cg::Convergence step 7 value 3.94318e-11 DEAL:3:cg::Starting value 6.44073 -DEAL:3:cg::Convergence step 6 value 2.97002e-14 +DEAL:3:cg::Convergence step 7 value 4.64523e-13 DEAL:3:cg::Starting value 8.68642 -DEAL:3:cg::Convergence step 6 value 6.80139e-14 +DEAL:3:cg::Convergence step 7 value 5.79753e-13 DEAL:3:cg::Starting value 9.47362 -DEAL:3:cg::Convergence step 6 value 6.56927e-14 +DEAL:3:cg::Convergence step 7 value 6.67651e-13 DEAL:3:cg::Starting value 9.30402 -DEAL:3:cg::Convergence step 6 value 7.06917e-14 +DEAL:3:cg::Convergence step 7 value 9.36336e-13 DEAL:3:cg::Starting value 8.99023 -DEAL:3:cg::Convergence step 6 value 8.15983e-14 +DEAL:3:cg::Convergence step 7 value 1.22268e-12 diff --git a/tests/matrix_free/step-37.with_lapack=true.output b/tests/matrix_free/step-37.with_lapack=true.output index f67b52a7ea0b..d4c371622ad2 100644 --- a/tests/matrix_free/step-37.with_lapack=true.output +++ b/tests/matrix_free/step-37.with_lapack=true.output @@ -2,30 +2,30 @@ DEAL:2d::Cycle 0 DEAL:2d::Number of degrees of freedom: 81 DEAL:2d:cg::Starting value 0.132 -DEAL:2d:cg::Convergence step 4 value 0 +DEAL:2d:cg::Convergence step 5 value 4.87e-15 DEAL:2d:: DEAL:2d::Cycle 1 DEAL:2d::Number of degrees of freedom: 289 DEAL:2d:cg::Starting value 0.0677 -DEAL:2d:cg::Convergence step 5 value 0 +DEAL:2d:cg::Convergence step 5 value 6.38e-14 DEAL:2d:: DEAL:2d::Cycle 2 DEAL:2d::Number of degrees of freedom: 1089 DEAL:2d:cg::Starting value 0.0343 -DEAL:2d:cg::Convergence step 5 value 0 +DEAL:2d:cg::Convergence step 6 value 8.43e-16 DEAL:2d:: DEAL:3d::Cycle 0 DEAL:3d::Number of degrees of freedom: 125 DEAL:3d:cg::Starting value 0.125 -DEAL:3d:cg::Convergence step 5 value 0 +DEAL:3d:cg::Convergence step 4 value 2.35e-14 DEAL:3d:: DEAL:3d::Cycle 1 DEAL:3d::Number of degrees of freedom: 729 DEAL:3d:cg::Starting value 0.0479 -DEAL:3d:cg::Convergence step 4 value 0 +DEAL:3d:cg::Convergence step 5 value 1.75e-17 DEAL:3d:: DEAL:3d::Cycle 2 DEAL:3d::Number of degrees of freedom: 4913 DEAL:3d:cg::Starting value 0.0176 -DEAL:3d:cg::Convergence step 4 value 0 +DEAL:3d:cg::Convergence step 5 value 1.68e-16 DEAL:3d:: diff --git a/tests/matrix_free/stokes_computation.with_mpi=true.with_p4est=true.mpirun=4.output b/tests/matrix_free/stokes_computation.with_mpi=true.with_p4est=true.mpirun=4.output index c33433cf2546..1f2687b42cdf 100644 --- a/tests/matrix_free/stokes_computation.with_mpi=true.with_p4est=true.mpirun=4.output +++ b/tests/matrix_free/stokes_computation.with_mpi=true.with_p4est=true.mpirun=4.output @@ -4,16 +4,16 @@ DEAL:2d::n_sinker: 4 max/min viscosity ratio: 1000.00 DEAL:2d:: DEAL:2d::Number of active cells: 1024 (on 6 levels) DEAL:2d::Number of degrees of freedom: 9539 (8450+1089) -DEAL:2d::Solved-in 62 iterations, final residual: 5.37736e-08 +DEAL:2d::Solved-in 69 iterations, final residual: 5.58979e-08 DEAL:2d:: DEAL:2d::Number of active cells: 4096 (on 7 levels) DEAL:2d::Number of degrees of freedom: 37507 (33282+4225) -DEAL:2d::Solved-in 61 iterations, final residual: 2.94930e-08 +DEAL:2d::Solved-in 69 iterations, final residual: 2.58019e-08 DEAL:2d:: DEAL:3d::Sinker problem in 3D. DEAL:3d::n_sinker: 4 max/min viscosity ratio: 1000.00 DEAL:3d:: DEAL:3d::Number of active cells: 512 (on 4 levels) DEAL:3d::Number of degrees of freedom: 15468 (14739+729) -DEAL:3d::Solved-in 54 iterations, final residual: 2.12652e-08 +DEAL:3d::Solved-in 62 iterations, final residual: 1.99453e-08 DEAL:3d:: diff --git a/tests/multigrid/step-16-04.cc b/tests/multigrid/step-16-04.cc index 39ddbad30c97..631b29fba58b 100644 --- a/tests/multigrid/step-16-04.cc +++ b/tests/multigrid/step-16-04.cc @@ -397,7 +397,7 @@ LaplaceProblem::solve() mg_smoother; typename Smoother::AdditionalData smoother_data; smoother_data.smoothing_range = 20.; - smoother_data.degree = 2; + smoother_data.degree = 3; smoother_data.eig_cg_n_iterations = 20; mg_smoother.initialize(mg_matrices, smoother_data); diff --git a/tests/multigrid/step-16-05.cc b/tests/multigrid/step-16-05.cc index dd7057ae91d3..3b3441a98905 100644 --- a/tests/multigrid/step-16-05.cc +++ b/tests/multigrid/step-16-05.cc @@ -398,7 +398,7 @@ LaplaceProblem::solve() mg_smoother; typename Smoother::AdditionalData smoother_data; smoother_data.smoothing_range = 20.; - smoother_data.degree = 2; + smoother_data.degree = 3; smoother_data.eig_cg_n_iterations = 20; mg_smoother.initialize(mg_matrices, smoother_data); diff --git a/tests/multigrid/step-16-06.cc b/tests/multigrid/step-16-06.cc index aa46cd7dba8e..d6a90ea82440 100644 --- a/tests/multigrid/step-16-06.cc +++ b/tests/multigrid/step-16-06.cc @@ -398,7 +398,7 @@ LaplaceProblem::solve() mg_smoother; typename Smoother::AdditionalData smoother_data; smoother_data.smoothing_range = 20.; - smoother_data.degree = 2; + smoother_data.degree = 3; smoother_data.eig_cg_n_iterations = 20; mg_smoother.initialize(mg_matrices, smoother_data); diff --git a/tests/multigrid/step-16-50-serial.cc b/tests/multigrid/step-16-50-serial.cc index 736b86d15a93..baa48db33bb3 100644 --- a/tests/multigrid/step-16-50-serial.cc +++ b/tests/multigrid/step-16-50-serial.cc @@ -470,6 +470,7 @@ int main() { initlog(); + deallog << std::setprecision(10); try { diff --git a/tests/multigrid/step-16-50-serial.output b/tests/multigrid/step-16-50-serial.output index 3f3684cfb080..42daab35f86c 100644 --- a/tests/multigrid/step-16-50-serial.output +++ b/tests/multigrid/step-16-50-serial.output @@ -2,25 +2,25 @@ DEAL::Cycle 0: DEAL:: Number of active cells: 256 DEAL:: Number of degrees of freedom: 289 (by level: 4, 9, 25, 81, 289) -DEAL:cg::Starting value 0.585938 -DEAL:cg::Convergence step 7 value 4.58200e-09 +DEAL:cg::Starting value 0.5859375000 +DEAL:cg::Convergence step 7 value 4.581996212e-09 DEAL::Cycle 1: DEAL:: Number of active cells: 418 DEAL:: Number of degrees of freedom: 495 (by level: 4, 9, 25, 81, 289, 305) -DEAL:cg::Starting value 0.533937 -DEAL:cg::Convergence step 10 value 7.40543e-10 +DEAL:cg::Starting value 0.5339372772 +DEAL:cg::Convergence step 10 value 7.405430549e-10 DEAL::Cycle 2: DEAL:: Number of active cells: 865 DEAL:: Number of degrees of freedom: 952 (by level: 4, 9, 25, 81, 289, 769, 153) -DEAL:cg::Starting value 0.378780 -DEAL:cg::Convergence step 11 value 1.39894e-09 +DEAL:cg::Starting value 0.3787800687 +DEAL:cg::Convergence step 11 value 1.398936158e-09 DEAL::Cycle 3: DEAL:: Number of active cells: 1219 DEAL:: Number of degrees of freedom: 1354 (by level: 4, 9, 25, 81, 289, 953, 277, 261) -DEAL:cg::Starting value 0.343729 -DEAL:cg::Convergence step 13 value 6.16552e-10 +DEAL:cg::Starting value 0.3437292109 +DEAL:cg::Convergence step 13 value 6.165515097e-10 DEAL::Cycle 4: DEAL:: Number of active cells: 1297 DEAL:: Number of degrees of freedom: 1446 (by level: 4, 9, 25, 81, 289, 961, 313, 349) -DEAL:cg::Starting value 0.339440 -DEAL:cg::Convergence step 13 value 7.00850e-10 +DEAL:cg::Starting value 0.3394403283 +DEAL:cg::Convergence step 13 value 7.008502779e-10 From 13c5efbcede00de082417c32f23925cd46b5afb3 Mon Sep 17 00:00:00 2001 From: Martin Kronbichler Date: Fri, 8 Feb 2019 16:33:10 +0100 Subject: [PATCH 080/507] Add changelog. --- doc/news/changes/minor/20190208MartinKronbichler | 8 ++++++++ 1 file changed, 8 insertions(+) create mode 100644 doc/news/changes/minor/20190208MartinKronbichler diff --git a/doc/news/changes/minor/20190208MartinKronbichler b/doc/news/changes/minor/20190208MartinKronbichler new file mode 100644 index 000000000000..3a12e97374da --- /dev/null +++ b/doc/news/changes/minor/20190208MartinKronbichler @@ -0,0 +1,8 @@ +Fixed: PreconditionChebyshev would previously run one iteration more than +requested, i.e., perform `degree+1` matrix-vector products rather than +`degree` which is the convention in literature. This is now fixed. Note that +the quality of PreconditionChebyshev is obviously slightly reduced by this +change, and some solvers might need more outer iterations due to a ligher +Chebyshev iteration. +
+(Martin Kronbichler, 2019/02/08) From 8fb857bde477c48e3db19a59875261e73502719b Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Fri, 8 Feb 2019 16:37:18 +0100 Subject: [PATCH 081/507] Add default constructor to SparsityPatternIterators::Accessor --- doc/news/changes/minor/20190208DenisDavydov | 3 +++ include/deal.II/lac/sparsity_pattern.h | 26 +++++++++++++++++++++ 2 files changed, 29 insertions(+) create mode 100644 doc/news/changes/minor/20190208DenisDavydov diff --git a/doc/news/changes/minor/20190208DenisDavydov b/doc/news/changes/minor/20190208DenisDavydov new file mode 100644 index 000000000000..3d8c7ce6cd5f --- /dev/null +++ b/doc/news/changes/minor/20190208DenisDavydov @@ -0,0 +1,3 @@ +New: Add default constructor to SparsityPatternIterators::Accessor(). +
+(Denis Davydov, 2019/02/08) diff --git a/include/deal.II/lac/sparsity_pattern.h b/include/deal.II/lac/sparsity_pattern.h index 4182a1fd7349..89c507a31e16 100644 --- a/include/deal.II/lac/sparsity_pattern.h +++ b/include/deal.II/lac/sparsity_pattern.h @@ -146,6 +146,13 @@ namespace SparsityPatternIterators */ Accessor(const SparsityPattern *matrix); + /** + * Default constructor creating a dummy accessor. This constructor is here + * only to be able to store accessors in STL containers such as + * `std::vector`. + */ + Accessor(); + /** * Row number of the element represented by this object. This function can * only be called for entries for which is_valid_entry() is true. @@ -209,6 +216,12 @@ namespace SparsityPatternIterators operator<(const Accessor &) const; protected: + DeclExceptionMsg(DummyAccessor, + "The instance of this class was initialized" + " without SparsityPattern object, which" + " means that it is a dummy accessor that can" + " not do any operations."); + /** * The sparsity pattern we operate on accessed. */ @@ -1162,9 +1175,17 @@ namespace SparsityPatternIterators + inline Accessor::Accessor() + : container(nullptr) + , linear_index(numbers::invalid_size_type) + {} + + + inline bool Accessor::is_valid_entry() const { + Assert(container != nullptr, DummyAccessor()); return (linear_index < container->rowstart[container->rows] && container->colnums[linear_index] != SparsityPattern::invalid_entry); } @@ -1218,6 +1239,8 @@ namespace SparsityPatternIterators inline bool Accessor::operator==(const Accessor &other) const { + Assert(container != nullptr, DummyAccessor()); + Assert(other.container != nullptr, DummyAccessor()); return (container == other.container && linear_index == other.linear_index); } @@ -1226,6 +1249,8 @@ namespace SparsityPatternIterators inline bool Accessor::operator<(const Accessor &other) const { + Assert(container != nullptr, DummyAccessor()); + Assert(other.container != nullptr, DummyAccessor()); Assert(container == other.container, ExcInternalError()); return linear_index < other.linear_index; @@ -1236,6 +1261,7 @@ namespace SparsityPatternIterators inline void Accessor::advance() { + Assert(container != nullptr, DummyAccessor()); Assert(linear_index < container->rowstart[container->rows], ExcIteratorPastEnd()); ++linear_index; From 05d5673e3adf15c9844760ea9561e63b0bb82dcd Mon Sep 17 00:00:00 2001 From: Martin Kronbichler Date: Wed, 6 Feb 2019 12:53:20 +0100 Subject: [PATCH 082/507] Avoid underflow in MF::ShapeInfo for very large number of q points. --- .../matrix_free/shape_info.templates.h | 83 ++++++++++--------- 1 file changed, 45 insertions(+), 38 deletions(-) diff --git a/include/deal.II/matrix_free/shape_info.templates.h b/include/deal.II/matrix_free/shape_info.templates.h index 18ed6fba80fe..af18d30c80d5 100644 --- a/include/deal.II/matrix_free/shape_info.templates.h +++ b/include/deal.II/matrix_free/shape_info.templates.h @@ -266,44 +266,51 @@ namespace internal } // get gradient and Hessian transformation matrix for the polynomial - // space associated with the quadrature rule (collocation space) - { - const unsigned int stride = (n_q_points_1d + 1) / 2; - shape_gradients_collocation_eo.resize(n_q_points_1d * stride); - shape_hessians_collocation_eo.resize(n_q_points_1d * stride); - FE_DGQArbitraryNodes<1> fe(quad.get_points()); - for (unsigned int i = 0; i < n_q_points_1d / 2; ++i) - for (unsigned int q = 0; q < stride; ++q) - { - shape_gradients_collocation_eo[i * stride + q] = - 0.5 * - (fe.shape_grad(i, quad.get_points()[q])[0] + - fe.shape_grad(i, quad.get_points()[n_q_points_1d - 1 - q])[0]); - shape_gradients_collocation_eo[(n_q_points_1d - 1 - i) * stride + - q] = - 0.5 * - (fe.shape_grad(i, quad.get_points()[q])[0] - - fe.shape_grad(i, quad.get_points()[n_q_points_1d - 1 - q])[0]); - shape_hessians_collocation_eo[i * stride + q] = - 0.5 * (fe.shape_grad_grad(i, quad.get_points()[q])[0][0] + - fe.shape_grad_grad( - i, quad.get_points()[n_q_points_1d - 1 - q])[0][0]); - shape_hessians_collocation_eo[(n_q_points_1d - 1 - i) * stride + - q] = - 0.5 * (fe.shape_grad_grad(i, quad.get_points()[q])[0][0] - - fe.shape_grad_grad( - i, quad.get_points()[n_q_points_1d - 1 - q])[0][0]); - } - if (n_q_points_1d % 2 == 1) - for (unsigned int q = 0; q < stride; ++q) - { - shape_gradients_collocation_eo[n_q_points_1d / 2 * stride + q] = - fe.shape_grad(n_q_points_1d / 2, quad.get_points()[q])[0]; - shape_hessians_collocation_eo[n_q_points_1d / 2 * stride + q] = - fe.shape_grad_grad(n_q_points_1d / 2, - quad.get_points()[q])[0][0]; - } - } + // space associated with the quadrature rule (collocation space). We + // need to avoid the case with more than a few hundreds of quadrature + // points when the Lagrange polynomials constructed in + // FE_DGQArbitraryNodes underflow. + if (n_q_points_1d < 200) + { + const unsigned int stride = (n_q_points_1d + 1) / 2; + shape_gradients_collocation_eo.resize(n_q_points_1d * stride); + shape_hessians_collocation_eo.resize(n_q_points_1d * stride); + FE_DGQArbitraryNodes<1> fe(quad.get_points()); + for (unsigned int i = 0; i < n_q_points_1d / 2; ++i) + for (unsigned int q = 0; q < stride; ++q) + { + shape_gradients_collocation_eo[i * stride + q] = + 0.5 * + (fe.shape_grad(i, quad.get_points()[q])[0] + + fe.shape_grad(i, + quad.get_points()[n_q_points_1d - 1 - q])[0]); + shape_gradients_collocation_eo[(n_q_points_1d - 1 - i) * + stride + + q] = + 0.5 * + (fe.shape_grad(i, quad.get_points()[q])[0] - + fe.shape_grad(i, + quad.get_points()[n_q_points_1d - 1 - q])[0]); + shape_hessians_collocation_eo[i * stride + q] = + 0.5 * (fe.shape_grad_grad(i, quad.get_points()[q])[0][0] + + fe.shape_grad_grad( + i, quad.get_points()[n_q_points_1d - 1 - q])[0][0]); + shape_hessians_collocation_eo[(n_q_points_1d - 1 - i) * stride + + q] = + 0.5 * (fe.shape_grad_grad(i, quad.get_points()[q])[0][0] - + fe.shape_grad_grad( + i, quad.get_points()[n_q_points_1d - 1 - q])[0][0]); + } + if (n_q_points_1d % 2 == 1) + for (unsigned int q = 0; q < stride; ++q) + { + shape_gradients_collocation_eo[n_q_points_1d / 2 * stride + q] = + fe.shape_grad(n_q_points_1d / 2, quad.get_points()[q])[0]; + shape_hessians_collocation_eo[n_q_points_1d / 2 * stride + q] = + fe.shape_grad_grad(n_q_points_1d / 2, + quad.get_points()[q])[0][0]; + } + } if (element_type == tensor_general && check_1d_shapes_symmetric(n_q_points_1d)) From 856007a732bef1484b2eb540714e9c78b2ad3c08 Mon Sep 17 00:00:00 2001 From: Martin Kronbichler Date: Wed, 6 Feb 2019 12:53:59 +0100 Subject: [PATCH 083/507] Do not use transformation to collocation for large n_q_points. --- .../deal.II/matrix_free/evaluation_kernels.h | 14 +++++- .../deal.II/matrix_free/evaluation_selector.h | 44 ++++++++++++++----- 2 files changed, 46 insertions(+), 12 deletions(-) diff --git a/include/deal.II/matrix_free/evaluation_kernels.h b/include/deal.II/matrix_free/evaluation_kernels.h index 7cfa435b6ad3..3f47fbe06eb1 100644 --- a/include/deal.II/matrix_free/evaluation_kernels.h +++ b/include/deal.II/matrix_free/evaluation_kernels.h @@ -1337,6 +1337,16 @@ namespace internal typename Number> struct FEFaceEvaluationImpl { + // We enable a transformation to collocation for derivatives if it gives + // correct results (first two conditions), if it is the most efficient + // choice in terms of operation counts (third condition) and if we were + // able to initialize the fields in shape_info.templates.h from the + // polynomials (fourth condition). + static constexpr bool use_collocation = + symmetric_evaluate && + n_q_points_1d > fe_degree &&n_q_points_1d <= 3 * fe_degree / 2 + 1 && + n_q_points_1d < 200; + static void evaluate_in_face(const MatrixFreeFunctions::ShapeInfo &data, Number * values_dofs, @@ -1431,7 +1441,7 @@ namespace internal switch (dim) { case 3: - if (symmetric_evaluate && n_q_points_1d > fe_degree) + if (use_collocation) { eval1.template values<0, true, false>(values_dofs, values_quad); @@ -1590,7 +1600,7 @@ namespace internal 2 * n_q_points); eval1.template values<0, false, false>( gradients_quad + 2 * n_q_points, values_dofs + size_deg); - if (symmetric_evaluate && n_q_points_1d > fe_degree) + if (use_collocation) { internal::EvaluatorTensorProduct< internal::evaluate_evenodd, diff --git a/include/deal.II/matrix_free/evaluation_selector.h b/include/deal.II/matrix_free/evaluation_selector.h index 2fd382aa0647..30115e481be1 100644 --- a/include/deal.II/matrix_free/evaluation_selector.h +++ b/include/deal.II/matrix_free/evaluation_selector.h @@ -251,6 +251,17 @@ namespace internal n_q_points_1d, typename std::enable_if<(n_q_points_1d < degree + 3)>::type> { + /** + * We enable a transformation to collocation for derivatives if it gives + * correct results (first condition), if it is the most efficient choice + * in terms of operation counts (second condition) and if we were able + * to initialize the fields in shape_info.templates.h from the + * polynomials (third condition). + */ + static constexpr bool use_collocation = + n_q_points_1d > degree &&n_q_points_1d <= 3 * degree / 2 + 1 && + n_q_points_1d < 200; + static inline void evaluate( const internal::MatrixFreeFunctions::ShapeInfo &shape_info, @@ -280,7 +291,7 @@ namespace internal evaluate_values, evaluate_gradients, evaluate_hessians); - else if (degree < n_q_points_1d) + else if (use_collocation) internal::FEEvaluationImplTransformToCollocation< dim, degree, @@ -352,7 +363,7 @@ namespace internal integrate_values, integrate_gradients, sum_into_values_array); - else if (degree < n_q_points_1d) + else if (use_collocation) internal::FEEvaluationImplTransformToCollocation< dim, degree, @@ -481,6 +492,17 @@ template struct SelectEvaluator { + /** + * We enable a transformation to collocation for derivatives if it gives + * correct results (first condition), if it is the most efficient choice in + * terms of operation counts (second condition) and if we were able to + * initialize the fields in shape_info.templates.h from the polynomials + * (third condition). + */ + static constexpr bool use_collocation = + n_q_points_1d > fe_degree &&n_q_points_1d <= 3 * fe_degree / 2 + 1 && + n_q_points_1d < 200; + /** * Chooses an appropriate evaluation strategy for the evaluate function, i.e. * this calls internal::FEEvaluationImpl::evaluate(), @@ -606,9 +628,10 @@ SelectEvaluator::evaluate( evaluate_gradients, evaluate_hessians); } - else if (fe_degree < n_q_points_1d && - shape_info.element_type <= - internal::MatrixFreeFunctions::tensor_symmetric) + // '<=' on type means tensor_symmetric or tensor_symmetric_hermite, see + // shape_info.h for more details + else if (use_collocation && shape_info.element_type <= + internal::MatrixFreeFunctions::tensor_symmetric) { internal::FEEvaluationImplTransformToCollocation< dim, @@ -625,7 +648,7 @@ SelectEvaluator::evaluate( evaluate_gradients, evaluate_hessians); } - else if (shape_info.element_type == + else if (shape_info.element_type <= internal::MatrixFreeFunctions::tensor_symmetric) { internal::FEEvaluationImpl< @@ -739,9 +762,10 @@ SelectEvaluator::integrate( integrate_gradients, sum_into_values_array); } - else if (fe_degree < n_q_points_1d && - shape_info.element_type <= - internal::MatrixFreeFunctions::tensor_symmetric) + // '<=' on type means tensor_symmetric or tensor_symmetric_hermite, see + // shape_info.h for more details + else if (use_collocation && shape_info.element_type <= + internal::MatrixFreeFunctions::tensor_symmetric) { internal::FEEvaluationImplTransformToCollocation< dim, @@ -757,7 +781,7 @@ SelectEvaluator::integrate( integrate_gradients, sum_into_values_array); } - else if (shape_info.element_type == + else if (shape_info.element_type <= internal::MatrixFreeFunctions::tensor_symmetric) { internal::FEEvaluationImpl< From 054d440c7b363f2000a62d5b04238acdea09692d Mon Sep 17 00:00:00 2001 From: Martin Kronbichler Date: Wed, 6 Feb 2019 12:54:07 +0100 Subject: [PATCH 084/507] Add changelog. --- doc/news/changes/minor/20190206MartinKronbichler | 9 +++++++++ 1 file changed, 9 insertions(+) create mode 100644 doc/news/changes/minor/20190206MartinKronbichler diff --git a/doc/news/changes/minor/20190206MartinKronbichler b/doc/news/changes/minor/20190206MartinKronbichler new file mode 100644 index 000000000000..ef651a9a6687 --- /dev/null +++ b/doc/news/changes/minor/20190206MartinKronbichler @@ -0,0 +1,9 @@ +Improved: The FEEvaluation::evaluate() and FEEvaluation::integrate() routines +would previously unconditionally use an evaluation routine with a +transformation to a collocation basis and subsequent collocation derivative +for `n_q_points_1d > fe_degree` because it is faster for the usual case of +`n_q_points_1d` close to the polynomial degree. Now, we switch back to the +standard evaluation if `n_q_points_1d > 3 * (fe_degree+1) / 2` where that +variant is faster. +
+(Martin Kronbichler, 2019/02/06) From 0e6ce56b46adbe4c05ecfe39e8871937ee1de210 Mon Sep 17 00:00:00 2001 From: Martin Kronbichler Date: Wed, 6 Feb 2019 12:55:09 +0100 Subject: [PATCH 085/507] Add test case --- .../matrix_vector_large_degree_03.cc | 140 ++++++++++++++++++ .../matrix_vector_large_degree_03.output | 7 + 2 files changed, 147 insertions(+) create mode 100644 tests/matrix_free/matrix_vector_large_degree_03.cc create mode 100644 tests/matrix_free/matrix_vector_large_degree_03.output diff --git a/tests/matrix_free/matrix_vector_large_degree_03.cc b/tests/matrix_free/matrix_vector_large_degree_03.cc new file mode 100644 index 000000000000..36e945ab9ef9 --- /dev/null +++ b/tests/matrix_free/matrix_vector_large_degree_03.cc @@ -0,0 +1,140 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2017 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + + +// test that FEEvaluation can correctly handle large polynomial degrees of 20 +// with 100, 200, 500 and 1000 quadrature points per direction in 2D. Since we +// have a constant-coefficient Laplacian, we can verify the implementation by +// comparing to the result with 21 quadrature points. + +#include "../tests.h" + +std::ofstream logfile("output"); + +#include + +#include +#include + +#include +#include +#include + +#include +#include + +#include "matrix_vector_mf.h" + + +template +void +test() +{ + Triangulation tria; + GridGenerator::hyper_cube(tria); + tria.refine_global(1); + + FE_Q fe(fe_degree); + DoFHandler dof(tria); + dof.distribute_dofs(fe); + AffineConstraints constraints; + constraints.close(); + + deallog << "Testing " << dof.get_fe().get_name() << std::endl; + + Vector in(dof.n_dofs()), out(dof.n_dofs()), ref(dof.n_dofs()); + + for (unsigned int i = 0; i < dof.n_dofs(); ++i) + { + if (constraints.is_constrained(i)) + continue; + in(i) = static_cast(i % 13) / 11.; + } + + { + MatrixFree mf_data; + { + const QGauss<1> quad(fe_degree + 1); + typename MatrixFree::AdditionalData data; + data.tasks_parallel_scheme = + MatrixFree::AdditionalData::none; + mf_data.reinit(dof, constraints, quad, data); + } + + MatrixFreeTest, fe_degree + 1> mf( + mf_data); + mf.vmult(ref, in); + } + + typename MatrixFree::AdditionalData data; + data.tasks_parallel_scheme = MatrixFree::AdditionalData::none; + MatrixFree mf_data; + + { + mf_data.reinit(dof, constraints, QGauss<1>(fe_degree + 2), data); + MatrixFreeTest, fe_degree + 2> mf( + mf_data); + mf.vmult(out, in); + out -= ref; + deallog << "Error with " << fe_degree + 2 << "^" << dim + << " quadrature points: " << out.l2_norm() << std::endl; + } + + // unfortunately we cannot use for loops due to the template, so duplicate + // some code here + { + mf_data.reinit(dof, constraints, QGauss<1>(100), data); + MatrixFreeTest, 100> mf(mf_data); + mf.vmult(out, in); + out -= ref; + deallog << "Error with " << 100 << "^" << dim + << " quadrature points: " << out.l2_norm() << std::endl; + } + { + mf_data.reinit(dof, constraints, QGauss<1>(200), data); + MatrixFreeTest, 200> mf(mf_data); + mf.vmult(out, in); + out -= ref; + deallog << "Error with " << 200 << "^" << dim + << " quadrature points: " << out.l2_norm() << std::endl; + } + { + mf_data.reinit(dof, constraints, QGauss<1>(500), data); + MatrixFreeTest, 500> mf(mf_data); + mf.vmult(out, in); + out -= ref; + deallog << "Error with " << 500 << "^" << dim + << " quadrature points: " << out.l2_norm() << std::endl; + } + { + mf_data.reinit(dof, constraints, QGauss<1>(1000), data); + MatrixFreeTest, 1000> mf(mf_data); + mf.vmult(out, in); + out -= ref; + deallog << "Error with " << 1000 << "^" << dim + << " quadrature points: " << out.l2_norm() << std::endl; + } +} + + + +int +main() +{ + initlog(); + + test<2, 20>(); +} diff --git a/tests/matrix_free/matrix_vector_large_degree_03.output b/tests/matrix_free/matrix_vector_large_degree_03.output new file mode 100644 index 000000000000..d5272b9136b3 --- /dev/null +++ b/tests/matrix_free/matrix_vector_large_degree_03.output @@ -0,0 +1,7 @@ + +DEAL::Testing FE_Q<2>(20) +DEAL::Error with 22^2 quadrature points: 7.12679e-13 +DEAL::Error with 100^2 quadrature points: 3.09514e-13 +DEAL::Error with 200^2 quadrature points: 3.05924e-13 +DEAL::Error with 500^2 quadrature points: 3.28960e-13 +DEAL::Error with 1000^2 quadrature points: 3.39364e-13 From efcbebec5ef0c0ce1ddaa324df9a6965726f3392 Mon Sep 17 00:00:00 2001 From: Martin Kronbichler Date: Sat, 9 Feb 2019 11:44:41 +0100 Subject: [PATCH 086/507] Comment on <= comparison for MatrixFree::ElementType. --- include/deal.II/matrix_free/shape_info.h | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/include/deal.II/matrix_free/shape_info.h b/include/deal.II/matrix_free/shape_info.h index 9533c9c94d4c..89c1f2902d0f 100644 --- a/include/deal.II/matrix_free/shape_info.h +++ b/include/deal.II/matrix_free/shape_info.h @@ -36,6 +36,15 @@ namespace internal * initialization. FEEvaluation will select the most efficient algorithm * based on the given element type. * + * There is an implied ordering in the type ElementType::tensor_symmetric + * in the sense that both ElementType::tensor_symmetric_collocation and + * ElementType::tensor_symmetric_hermite are also of type + * ElementType::tensor_symmetric. Likewise, a configuration of type + * ElementType::tensor_symmetric is also of type + * ElementType::tensor_general. As a consequence, we support `<=` + * operations between the types with this sorting, but not against the + * even higher indexed types such as ElementType::truncated_tensor. + * * @ingroup matrixfree */ enum ElementType From 666d0580a97aa250c0ad1c2e2270e804189b8f12 Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Sun, 10 Feb 2019 17:23:56 -0700 Subject: [PATCH 087/507] [CI]: cleanup workspaces, document, simplify tidy - tidy job: use only one agent - add documentation - add cleanup of workspace (otherwise we run out of disk space, yay) --- contrib/ci/Jenkinsfile.mark | 16 +++++++++++----- contrib/ci/Jenkinsfile.osx | 10 ++++++++++ contrib/ci/Jenkinsfile.tidy | 33 +++++++++++++++++---------------- 3 files changed, 38 insertions(+), 21 deletions(-) diff --git a/contrib/ci/Jenkinsfile.mark b/contrib/ci/Jenkinsfile.mark index 37aa15478cd7..78f8e02c676c 100644 --- a/contrib/ci/Jenkinsfile.mark +++ b/contrib/ci/Jenkinsfile.mark @@ -1,10 +1,14 @@ #!groovy -// This Jenkinsfile is used to mark jobs as "pending" as quickly as -// possible. The other longer running jobs only set the status to pending once -// they start running. -// -// See https://jenkins.tjhei.info/job/dealii-mark/ for details. +/* + +This Jenkinsfile is used to mark jobs as "pending" as quickly as possible. The +other longer running jobs only set the status to pending once they start +running. + +See https://jenkins.tjhei.info/job/dealii-mark/ for details. + +*/ /* Settings to apply inside Jenkins: @@ -28,6 +32,8 @@ pipeline } } + post { cleanup { cleanWs() } } + stages { stage("check") diff --git a/contrib/ci/Jenkinsfile.osx b/contrib/ci/Jenkinsfile.osx index fbee05a7686f..5a404aabb774 100644 --- a/contrib/ci/Jenkinsfile.osx +++ b/contrib/ci/Jenkinsfile.osx @@ -1,5 +1,13 @@ #!groovy +/* + +This Jenkins job runs a build on OSX + +See https://jenkins.tjhei.info/job/dealii-osx/ for details. + +*/ + /* Settings to apply inside Jenkins: - discover pull requests (remove branches/master) @@ -19,6 +27,8 @@ pipeline } } + post { cleanup { cleanWs() } } + stages { stage("check") diff --git a/contrib/ci/Jenkinsfile.tidy b/contrib/ci/Jenkinsfile.tidy index 05c013482631..82d7e69a39f2 100644 --- a/contrib/ci/Jenkinsfile.tidy +++ b/contrib/ci/Jenkinsfile.tidy @@ -1,5 +1,13 @@ #!groovy +/* + +This Jenkins job runs clang-tidy on the code base + +See https://jenkins.tjhei.info/job/dealii-tidy/ for details. + +*/ + /* Settings to apply inside Jenkins: - discover pull requests (remove branches/master) @@ -13,7 +21,15 @@ Settings to apply inside Jenkins: pipeline { - agent none + agent + { + docker + { + image 'tjhei/candi-base-clang' + } + } + + post { cleanup { cleanWs() } } stages { @@ -25,14 +41,6 @@ pipeline } } - agent - { - docker - { - image 'dealii/indent' - } - } - steps { githubNotify context: 'tidy', description: 'pending...', status: 'PENDING' @@ -56,13 +64,6 @@ pipeline stage('build') { - agent - { - docker - { - image 'tjhei/candi-base-clang' - } - } steps { timeout(time: 2, unit: 'HOURS') From 64e934f2579478844ae950ce2dc1ccf8f11d5a3a Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Mon, 11 Feb 2019 01:52:05 +0100 Subject: [PATCH 088/507] Remove warnings generated by step-61 --- examples/step-61/step-61.cc | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/examples/step-61/step-61.cc b/examples/step-61/step-61.cc index 90ed9c019bee..13866adf300f 100644 --- a/examples/step-61/step-61.cc +++ b/examples/step-61/step-61.cc @@ -113,6 +113,7 @@ class Coefficient : public TensorFunction<2, dim> Coefficient() : TensorFunction<2, dim>() {} + virtual void value_list(const std::vector> &points, std::vector> & values) const override; }; @@ -138,6 +139,7 @@ class BoundaryValues : public Function BoundaryValues() : Function(2) {} + virtual double value(const Point & p, const unsigned int component = 0) const override; }; @@ -156,8 +158,9 @@ class RightHandSide : public Function RightHandSide() : Function() {} + virtual double value(const Point & p, - const unsigned int component = 0) const; + const unsigned int component = 0) const override; }; template @@ -176,7 +179,8 @@ class Solution : public Function Solution() : Function(1) {} - virtual double value(const Point &p, const unsigned int) const; + + virtual double value(const Point &p, const unsigned int) const override; }; template @@ -194,6 +198,7 @@ class Velocity : public TensorFunction<1, dim> Velocity() : TensorFunction<1, dim>() {} + virtual Tensor<1, dim> value(const Point &p) const override; }; From 1cc8f8e0ba6fb442598ed2fa7801fb57383e2404 Mon Sep 17 00:00:00 2001 From: Wolfgang Bangerth Date: Sun, 10 Feb 2019 21:47:30 -0700 Subject: [PATCH 089/507] Use the usual grammar for make targets. --- cmake/macros/macro_deal_ii_invoke_autopilot.cmake | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/cmake/macros/macro_deal_ii_invoke_autopilot.cmake b/cmake/macros/macro_deal_ii_invoke_autopilot.cmake index ca5a1c0832a9..e93e95a0cf75 100644 --- a/cmake/macros/macro_deal_ii_invoke_autopilot.cmake +++ b/cmake/macros/macro_deal_ii_invoke_autopilot.cmake @@ -148,7 +148,7 @@ MACRO(DEAL_II_INVOKE_AUTOPILOT) COMMAND ${CMAKE_COMMAND} -E echo "***" COMMAND ${CMAKE_COMMAND} -E echo "*** Switched to Debug mode. Now recompile with: ${_make_command}" COMMAND ${CMAKE_COMMAND} -E echo "***" - COMMENT "Switch CMAKE_BUILD_TYPE to Debug" + COMMENT "Switching CMAKE_BUILD_TYPE to Debug" VERBATIM ) ENDIF() @@ -159,7 +159,7 @@ MACRO(DEAL_II_INVOKE_AUTOPILOT) COMMAND ${CMAKE_COMMAND} -E echo "***" COMMAND ${CMAKE_COMMAND} -E echo "*** Switched to Release mode. Now recompile with: ${_make_command}" COMMAND ${CMAKE_COMMAND} -E echo "***" - COMMENT "Switch CMAKE_BUILD_TYPE to Release" + COMMENT "Switching CMAKE_BUILD_TYPE to Release" VERBATIM ) ENDIF() From 53bdfa8752c64cca0e640034063d4237442bc7e1 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Sat, 9 Feb 2019 15:20:44 +0100 Subject: [PATCH 090/507] Add make_const_array_view --- doc/news/changes/minor/20190209Arndt | 3 ++ include/deal.II/base/array_view.h | 19 +++++++++++ tests/base/array_view_07.cc | 50 ++++++++++++++++++++++++++++ tests/base/array_view_07.output | 3 ++ 4 files changed, 75 insertions(+) create mode 100644 doc/news/changes/minor/20190209Arndt create mode 100644 tests/base/array_view_07.cc create mode 100644 tests/base/array_view_07.output diff --git a/doc/news/changes/minor/20190209Arndt b/doc/news/changes/minor/20190209Arndt new file mode 100644 index 000000000000..d8bdf8fff554 --- /dev/null +++ b/doc/news/changes/minor/20190209Arndt @@ -0,0 +1,3 @@ +New: make_const_array_view creates a constant view from a non-const object. +
+(Daniel Arndt, 2019/02/09) diff --git a/include/deal.II/base/array_view.h b/include/deal.II/base/array_view.h index 9fdcbb3b6b20..130e693f4bef 100644 --- a/include/deal.II/base/array_view.h +++ b/include/deal.II/base/array_view.h @@ -1134,6 +1134,25 @@ make_array_view(const Table<2, ElementType> & table, +/* + * Create a view that doesn't allow the container it points to to be modified. + * This is useful if the object passed in is not `const` already and a function + * requires a view to constant memory in its signature. + * + * This function returns an object of type `ArrayView` where `T` is the + * element type of the container. + * + * @relatesalso ArrayView + */ +template +inline auto +make_const_array_view(const Container &container) + -> decltype(make_array_view(container)) +{ + return make_array_view(container); +} + + DEAL_II_NAMESPACE_CLOSE #endif diff --git a/tests/base/array_view_07.cc b/tests/base/array_view_07.cc new file mode 100644 index 000000000000..06d844ad8d2a --- /dev/null +++ b/tests/base/array_view_07.cc @@ -0,0 +1,50 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2017 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + +// test make_const_array_view + +#include + +#include "../tests.h" + +template +void +const_foo(const ArrayView> &view) +{ + AssertThrow(view[0][0] == 1, ExcInternalError()); + deallog << "OK" << std::endl; +} + +template +void +foo(const ArrayView> &view) +{ + AssertThrow(view[0][0] == 1, ExcInternalError()); + deallog << "OK" << std::endl; +} + +int +main() +{ + initlog(); + std::vector> v(1, std::vector(1, 1)); + // this doesn't work + // const_foo(make_array_view(v)); + const_foo(make_const_array_view(v)); + foo(make_array_view(v)); + // this doesn't work + // foo(make_const_array_view(v)); +} diff --git a/tests/base/array_view_07.output b/tests/base/array_view_07.output new file mode 100644 index 000000000000..8b3b075900ce --- /dev/null +++ b/tests/base/array_view_07.output @@ -0,0 +1,3 @@ + +DEAL::OK +DEAL::OK From 4c84273983e81741f8eb6e987159a4ed5909167d Mon Sep 17 00:00:00 2001 From: Giovanni Alzetta Date: Fri, 11 Jan 2019 20:16:45 +0100 Subject: [PATCH 091/507] NonMatching::coupling_matrix now also skips useless cells --- source/non_matching/coupling.cc | 169 +++++++++++++++++++++++--------- 1 file changed, 124 insertions(+), 45 deletions(-) diff --git a/source/non_matching/coupling.cc b/source/non_matching/coupling.cc index 6673a1af544d..d8d31cf2d3c9 100644 --- a/source/non_matching/coupling.cc +++ b/source/non_matching/coupling.cc @@ -40,6 +40,92 @@ DEAL_II_NAMESPACE_OPEN namespace NonMatching { + namespace internal + { + /** + * Given two triangulations, the first immersed inside the other, this + * function computes and returns the real-space quadrature points of the + * immersed triangulation. + * + * For reference: + * cache->triangulation() is the imbdedding triangulation, which contains + * immersed_dh->get_triangulation() the embedded triangulation + * + * Mapping and quadrature are those of this second triangulation. + * + * If the triangulation inside @p cache is parallel, only points lying over + * locally onwed cells are returned. This is why a vector of unsigned int + * is returned: it describes the indices of cells from the immersed + * triangulation which have been used (relative to a loop over al cells). If + * embedding triangulation is not parallel, all cells shall be used. + */ + template + std::pair>, std::vector> + qpoints_over_locally_owned_cells( + const GridTools::Cache &cache, + const DoFHandler & immersed_dh, + const Quadrature & quad, + const Mapping & immersed_mapping, + const bool tria_is_parallel) + { + const auto & immersed_fe = immersed_dh.get_fe(); + std::vector> points_over_local_cells; + // Keep track of which cells we actually used + std::vector used_cells_ids; + { + FEValues fe_v(immersed_mapping, + immersed_fe, + quad, + update_quadrature_points); + unsigned int cell_id = 0; + for (const auto &cell : immersed_dh.active_cell_iterators()) + { + bool use_cell = false; + if (tria_is_parallel) + { + const auto bbox = cell->bounding_box(); + std::vector, + typename Triangulation::active_cell_iterator>> + out_vals; + cache.get_cell_bounding_boxes_rtree().query( + boost::geometry::index::intersects(bbox), + std::back_inserter(out_vals)); + // Each bounding box corresponds to an active cell + // of the imbedding triangulation: we now check if + // the current cell, of the imbedded triangulation, + // overlaps a locally owned cell of the imbedding one + for (const auto &bbox_it : out_vals) + if (bbox_it.second->is_locally_owned()) + { + use_cell = true; + used_cells_ids.emplace_back(cell_id); + break; + } + } + else + // for sequential triangulations, simply use all cells + use_cell = true; + + if (use_cell) + { + // Reinitialize the cell and the fe_values + fe_v.reinit(cell); + const std::vector> &x_points = + fe_v.get_quadrature_points(); + + // Insert the points to the vector + points_over_local_cells.insert(points_over_local_cells.end(), + x_points.begin(), + x_points.end()); + } + ++cell_id; + } + } + return {std::move(points_over_local_cells), std::move(used_cells_ids)}; + } + } // namespace internal + template *>( + &space_dh.get_triangulation()) != nullptr); const auto &space_fe = space_dh.get_fe(); const auto &immersed_fe = immersed_dh.get_fe(); @@ -134,27 +223,13 @@ namespace NonMatching const unsigned int n_q_points = quad.size(); const unsigned int n_active_c = immersed_dh.get_triangulation().n_active_cells(); - std::vector> all_points(n_active_c * n_q_points); - { - FEValues fe_v(immersed_mapping, - immersed_fe, - quad, - update_quadrature_points); - unsigned int c = 0; - for (const auto &cell : immersed_dh.active_cell_iterators()) - { - // Reinitialize the cell and the fe_values - fe_v.reinit(cell); - const std::vector> &x_points = - fe_v.get_quadrature_points(); - - // Copy the points to the vector - std::copy(x_points.begin(), - x_points.end(), - all_points.begin() + c * n_q_points); - ++c; - } - } + + const auto qpoints_cells_data = internal::qpoints_over_locally_owned_cells( + cache, immersed_dh, quad, immersed_mapping, tria_is_parallel); + + const auto &points_over_local_cells = std::get<0>(qpoints_cells_data); + const auto &used_cells_ids = std::get<1>(qpoints_cells_data); + // [TODO]: when the add_entries_local_to_global below will implement // the version with the dof_mask, this should be uncommented. // @@ -177,7 +252,8 @@ namespace NonMatching // Get a list of outer cells, qpoints and maps. - const auto cpm = GridTools::compute_point_locations(cache, all_points); + const auto cpm = + GridTools::compute_point_locations(cache, points_over_local_cells); const auto &all_cells = std::get<0>(cpm); const auto &maps = std::get<2>(cpm); @@ -191,10 +267,15 @@ namespace NonMatching // the following index keeps track of the last id // where the current cell was inserted unsigned int last_id = std::numeric_limits::max(); + unsigned int cell_id; for (const unsigned int idx : maps[i]) { - // Find in which cell the point lies - unsigned int cell_id = idx / n_q_points; + // Find in which cell of immersed triangulation the point lies + if (tria_is_parallel) + cell_id = used_cells_ids[idx / n_q_points]; + else + cell_id = idx / n_q_points; + if (last_id != cell_id) { cell_sets[cell_id].insert(all_cells[i]); @@ -285,6 +366,10 @@ namespace NonMatching &immersed_dh.get_triangulation()) == nullptr), ExcNotImplemented()); + const bool tria_is_parallel = + (dynamic_cast *>( + &space_dh.get_triangulation()) != nullptr); + const auto &space_fe = space_dh.get_fe(); const auto &immersed_fe = immersed_dh.get_fe(); @@ -330,28 +415,16 @@ namespace NonMatching const unsigned int n_q_points = quad.size(); const unsigned int n_active_c = immersed_dh.get_triangulation().n_active_cells(); - std::vector> all_points(n_active_c * n_q_points); - // Collecting all points - { - unsigned int c = 0; - for (const auto &cell : immersed_dh.active_cell_iterators()) - { - // Reinitialize the cell and the fe_values - fe_v.reinit(cell); - const std::vector> &x_points = - fe_v.get_quadrature_points(); - - // Copy the points to the vector - std::copy(x_points.begin(), - x_points.end(), - all_points.begin() + c * n_q_points); - ++c; - } - } + const auto used_cells_data = internal::qpoints_over_locally_owned_cells( + cache, immersed_dh, quad, immersed_mapping, tria_is_parallel); + + const auto &points_over_local_cells = std::get<0>(used_cells_data); + const auto &used_cells_ids = std::get<1>(used_cells_data); // Get a list of outer cells, qpoints and maps. - const auto cpm = GridTools::compute_point_locations(cache, all_points); + const auto cpm = + GridTools::compute_point_locations(cache, points_over_local_cells); const auto &all_cells = std::get<0>(cpm); const auto &all_qpoints = std::get<1>(cpm); const auto &all_maps = std::get<2>(cpm); @@ -372,8 +445,14 @@ namespace NonMatching { // Find the index of the "owner" cell and qpoint // with regard to the immersed mesh - const unsigned int cell_id = all_maps[o][j] / n_q_points; - const unsigned int n_pt = all_maps[o][j] % n_q_points; + // Find in which cell of immersed triangulation the point lies + unsigned int cell_id; + if (tria_is_parallel) + cell_id = used_cells_ids[all_maps[o][j] / n_q_points]; + else + cell_id = all_maps[o][j] / n_q_points; + + const unsigned int n_pt = all_maps[o][j] % n_q_points; // If there are no cells, we just add our data if (cell_container[cell_id].empty()) From b74d9d5ac89674e4ed0627f51aa8e93d3035d0cf Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Mon, 11 Feb 2019 18:43:54 +0100 Subject: [PATCH 092/507] Improve some documentation --- include/deal.II/differentiation/ad/ad_helpers.h | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/include/deal.II/differentiation/ad/ad_helpers.h b/include/deal.II/differentiation/ad/ad_helpers.h index ff94ee962f1b..ba21b90be59e 100644 --- a/include/deal.II/differentiation/ad/ad_helpers.h +++ b/include/deal.II/differentiation/ad/ad_helpers.h @@ -934,8 +934,9 @@ namespace Differentiation * auto-differentiable numbers. These are the independent * variables $\mathbf{X}$ about which the solution is linearized. * - * It is indicated to the AD library that operations performed with these - * numbers are to be tracked, so they are considered "sensitive" + * This function indicates to the AD library that implements the + * auto-differentiable number type that operations performed on these + * numbers are to be tracked so they are considered "sensitive" * variables. This is, therefore, the set of variables with which one * would then perform computations, and based on which one can then * extract both the value of the function and its derivatives with the From 33fe4a9974851ce841b1f3ce9300646498ec08c3 Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Mon, 11 Feb 2019 18:44:32 +0100 Subject: [PATCH 093/507] Mark a function as constant. --- include/deal.II/differentiation/ad/ad_helpers.h | 2 +- source/differentiation/ad/ad_helpers.cc | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/include/deal.II/differentiation/ad/ad_helpers.h b/include/deal.II/differentiation/ad/ad_helpers.h index ba21b90be59e..61bb85daeb07 100644 --- a/include/deal.II/differentiation/ad/ad_helpers.h +++ b/include/deal.II/differentiation/ad/ad_helpers.h @@ -950,7 +950,7 @@ namespace Differentiation * @note For taped AD numbers, this operation is only valid in recording mode. */ const std::vector & - get_sensitive_dof_values(); + get_sensitive_dof_values() const; //@} diff --git a/source/differentiation/ad/ad_helpers.cc b/source/differentiation/ad/ad_helpers.cc index e259ab6019c6..98f90b0aedf6 100644 --- a/source/differentiation/ad/ad_helpers.cc +++ b/source/differentiation/ad/ad_helpers.cc @@ -738,7 +738,7 @@ namespace Differentiation const std::vector< typename ADHelperCellLevelBase::ad_type> & ADHelperCellLevelBase::get_sensitive_dof_values() + ScalarType>::get_sensitive_dof_values() const { if (ADNumberTraits::is_taped == true) { From bfe7446fa892c036d63b9aa3c259895fe03bafe5 Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Mon, 11 Feb 2019 18:45:09 +0100 Subject: [PATCH 094/507] ADHelpers: Remove an unnecessary function --- .../deal.II/differentiation/ad/ad_helpers.h | 30 ------------------- source/differentiation/ad/ad_helpers.cc | 24 --------------- 2 files changed, 54 deletions(-) diff --git a/include/deal.II/differentiation/ad/ad_helpers.h b/include/deal.II/differentiation/ad/ad_helpers.h index 61bb85daeb07..bf3ea90c62f3 100644 --- a/include/deal.II/differentiation/ad/ad_helpers.h +++ b/include/deal.II/differentiation/ad/ad_helpers.h @@ -954,36 +954,6 @@ namespace Differentiation //@} - /** - * @name Post-processing - */ - //@{ - - /* - * Return the complete set of degree of freedom values of - * auto-differentiable number type. These store the same scalar values as - * the independent variables $\mathbf{X}$ about which the solution is - * linearized. - * - * Operations performed with these numbers are not tracked by the AD, - * libraries so they are considered "non-sensitive" variables. - * The values of the components of the returned object are initialized to - * the values set with register_dof_values(). - * - * @return An array of auto-differentiable type numbers representing the - * local degree of freedom values. - * - * @note This function is not typically used within the context of automatic - * differentation computations, but can make performing substutitions in - * other post-processing computations more straight forward. - * - * @note For taped AD numbers, this operation is only valid outside recording mode. - */ - std::vector - get_non_sensitive_dof_values() const; - - //@} - /** * @name Operations specific to taped mode: Reusing tapes */ diff --git a/source/differentiation/ad/ad_helpers.cc b/source/differentiation/ad/ad_helpers.cc index 98f90b0aedf6..2c3a9a5a47bd 100644 --- a/source/differentiation/ad/ad_helpers.cc +++ b/source/differentiation/ad/ad_helpers.cc @@ -760,30 +760,6 @@ namespace Differentiation - template - std::vector< - typename ADHelperCellLevelBase::ad_type> - ADHelperCellLevelBase::get_non_sensitive_dof_values() const - { - if (ADNumberTraits::is_taped == true) - { - Assert(this->active_tape_index() != - Numbers::invalid_tape_index, - ExcMessage("Invalid tape index")); - } - - std::vector out(this->n_independent_variables(), - dealii::internal::NumberType::value( - 0.0)); - for (unsigned int i = 0; i < this->n_independent_variables(); ++i) - this->initialize_non_sensitive_independent_variable(i, out[i]); - - return out; - } - - - template void ADHelperCellLevelBase::set_dof_values( From 9bac38c6ecafe3da017b9b49b013bd603866dc94 Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Mon, 11 Feb 2019 18:46:21 +0100 Subject: [PATCH 095/507] AD Helpers: Add some internal functions to assist when using Extractors --- .../deal.II/differentiation/ad/ad_helpers.h | 970 ++++++++++++++++++ 1 file changed, 970 insertions(+) diff --git a/include/deal.II/differentiation/ad/ad_helpers.h b/include/deal.II/differentiation/ad/ad_helpers.h index bf3ea90c62f3..5460362a72bf 100644 --- a/include/deal.II/differentiation/ad/ad_helpers.h +++ b/include/deal.II/differentiation/ad/ad_helpers.h @@ -21,6 +21,8 @@ #if defined(DEAL_II_WITH_ADOLC) || defined(DEAL_II_TRILINOS_WITH_SACADO) # include +# include +# include # include # include @@ -29,6 +31,8 @@ # include # include +# include + # include # include @@ -1647,6 +1651,972 @@ namespace Differentiation }; // class ADHelperResidualLinearization + + namespace internal + { + /** + * A helper struct that assists with the extraction of data associated + * with fields that are defined by FEExtractors. + */ + template + struct Extractor; + + + /** + * A helper struct that assists with the extraction of data associated + * with fields that are defined by FEExtractors. + * This particular specialization is for scalar fields. + */ + template + struct Extractor + { + /** + * The number of components of the field. + */ + static const unsigned int n_components = 1; + + /** + * The tensor rank of the field. + */ + static const unsigned int rank = 0; + + /** + * The tensor type associated with this field. + */ + template + using tensor_type = Tensor; + + static_assert( + n_components == tensor_type::n_independent_components, + "The number of components doesn't match that of the corresponding tensor type."); + static_assert( + rank == tensor_type::rank, + "The rank doesn't match that of the corresponding tensor type."); + + /** + * The value type associated with this field. + */ + // Note: FEValuesViews::Scalar::tensor_type is double, so we can't + // use it (FEValuesViews) in this context. + // In fact, sadly, all FEValuesViews objects expect doubles as value + // types. + template + using value_type = NumberType; + + /** + * The gradient type associated with this field. + */ + template + using gradient_type = Tensor; // NumberType; + + /** + * Return the first global component of this field. + */ + static inline unsigned int + first_component(const FEValuesExtractors::Scalar &extractor) + { + return extractor.component; + } + + /** + * Return a flag that indicates if the input @p unrolled_index + * corresponds to a symmetric component of the field. + * + * For a scalar field, the single component is defined + * to not have a symmetric counterpart. + */ + static bool + symmetric_component(const unsigned int unrolled_index) + { + (void)unrolled_index; + return false; + } + + /** + * Return the local unrolled component corresponding to + * @p column_offset entry of the @p table_indices. + * + * For a scalar field, the local component is always + * equal to zero. + */ + template + static IndexType + local_component(const TableIndices &table_indices, + const unsigned int column_offset) + { + Assert(column_offset <= rank_in, ExcInternalError()); + (void)table_indices; + (void)column_offset; + return 0; + } + }; + + + /** + * A helper struct that assists with the extraction of data associated + * with fields that are defined by FEExtractors. + * This particular specialization is for vector fields. + */ + template + struct Extractor + { + /** + * The number of components of the field. + */ + static const unsigned int n_components = dim; + + /** + * The tensor rank of the field. + */ + static const unsigned int rank = 1; + + /** + * The tensor type associated with this field. + */ + template + using tensor_type = Tensor; + + static_assert( + n_components == tensor_type::n_independent_components, + "The number of components doesn't match that of the corresponding tensor type."); + static_assert( + rank == tensor_type::rank, + "The rank doesn't match that of the corresponding tensor type."); + + /** + * The value type associated with this field. + */ + template + using value_type = tensor_type; + + /** + * The gradient type associated with this field. + */ + template + using gradient_type = Tensor; + + /** + * Return the first global component of this field. + */ + static inline unsigned int + first_component(const FEValuesExtractors::Vector &extractor) + { + return extractor.first_vector_component; + } + + /** + * + * Return a flag that indicates if the input @p unrolled_index + * corresponds to a symmetric component of the field. + * + * For a vector field, the none of the vector components + * have a symmetric counterpart. + */ + static bool + symmetric_component(const unsigned int unrolled_index) + { + (void)unrolled_index; + return false; + } + + /** + * Return the table index corresponding to + * @p column_offset entry of the input @p table_indices. + */ + template + static TableIndices + table_index_view(const TableIndices &table_indices, + const unsigned int column_offset) + { + Assert(0 + column_offset < rank_in, ExcInternalError()); + return TableIndices(table_indices[column_offset]); + } + + /** + * Return the local unrolled component corresponding to + * @p column_offset entry of the @p table_indices. + * + * This function computes and returns a local component + * associated with the extractor's @p tensor_type from a + * set of @p table_indices that are generally associated + * with a tensor of equal or greater order. In effect, it + * creates a view of a selected number of indices of the + * input table, and interprets that subtable's indices as + * the local index to be returned. Since the @p table_indices + * may be of size greater than the extractor's @p rank, + * the @p column_offset specifies the first index of the + * input table to create the view from. + */ + template + static IndexType + local_component(const TableIndices &table_indices, + const unsigned int column_offset) + { + static_assert( + rank_in >= rank, + "Cannot extract more table indices than the input table has!"); + using TensorType = tensor_type; + return TensorType::component_to_unrolled_index( + table_index_view(table_indices, column_offset)); + } + }; + + + /** + * A helper struct that assists with the extraction of data associated + * with fields that are defined by FEExtractors. + * This particular specialization is for rank-1 tensor fields. + */ + template + struct Extractor> + { + /** + * The number of components of the field. + */ + static const unsigned int n_components = + Tensor<1, dim>::n_independent_components; + + /** + * The tensor rank of the field. + */ + static const unsigned int rank = 1; + + /** + * The tensor type associated with this field. + */ + template + using tensor_type = Tensor; + + /** + * The value type associated with this field. + */ + template + using value_type = tensor_type; + + /** + * The gradient type associated with this field. + */ + template + using gradient_type = Tensor; + + /** + * Return the first global component of this field. + */ + static inline unsigned int + first_component(const FEValuesExtractors::Tensor<1> &extractor) + { + return extractor.first_tensor_component; + } + + /** + * Return a flag that indicates if the input @p unrolled_index + * corresponds to a symmetric component of the field. + * + * For a vector field, the none of the vector components + * have a symmetric counterpart. + */ + static bool + symmetric_component(const unsigned int unrolled_index) + { + (void)unrolled_index; + return false; + } + + /** + * Return the table index corresponding to + * @p column_offset entry of the input @p table_indices. + */ + template + static TableIndices + table_index_view(const TableIndices &table_indices, + const unsigned int column_offset) + { + Assert(column_offset < rank_in, ExcInternalError()); + return TableIndices(table_indices[column_offset]); + } + + /** + * Return the local unrolled component corresponding to + * a subset of table indices from the input @p table_indices. + * + * This function computes and returns a local component + * associated with the extractor's @p tensor_type from a + * set of @p table_indices that are generally associated + * with a tensor of equal or greater order. In effect, it + * creates a view of a selected number of indices of the + * input table, and interprets that subtable's indices as + * the local index to be returned. Since the @p table_indices + * may be of size greater than the extractor's @p rank, + * the @p column_offset specifies the first index of the + * input table to create the view from. + */ + template + static IndexType + local_component(const TableIndices &table_indices, + const unsigned int column_offset) + { + static_assert( + rank_in >= rank, + "Cannot extract more table indices than the input table has!"); + using TensorType = tensor_type; + return TensorType::component_to_unrolled_index( + table_index_view(table_indices, column_offset)); + } + }; + + + /** + * A helper struct that assists with the extraction of data associated + * with fields that are defined by FEExtractors. + * This particular specialization is for rank-2 tensor fields. + */ + template + struct Extractor> + { + /** + * The number of components of the field. + */ + static const unsigned int n_components = + Tensor<2, dim>::n_independent_components; + + /** + * The tensor rank of the field. + */ + static const unsigned int rank = Tensor<2, dim>::rank; + + /** + * The tensor type associated with this field. + */ + template + using tensor_type = Tensor; + + /** + * The value type associated with this field. + */ + template + using value_type = tensor_type; + + /** + * The gradient type associated with this field. + */ + template + using gradient_type = Tensor; + + /** + * Return the first global component of this field. + */ + static inline unsigned int + first_component(const FEValuesExtractors::Tensor<2> &extractor) + { + return extractor.first_tensor_component; + } + + /** + * Return a flag that indicates if the input @p unrolled_index + * corresponds to a symmetric component of the field. + * + * For a rank-2 tensor field, the none of the tensor + * components have a symmetric counterpart. + */ + static bool + symmetric_component(const unsigned int unrolled_index) + { + (void)unrolled_index; + return false; + } + + /** + * Return the table indices corresponding to + * @p column_offset entry of the input @p table_indices. + */ + template + static TableIndices + table_index_view(const TableIndices &table_indices, + const unsigned int column_offset) + { + Assert(column_offset < rank_in, ExcInternalError()); + Assert(column_offset + 1 < rank_in, ExcInternalError()); + return TableIndices(table_indices[column_offset], + table_indices[column_offset + 1]); + } + + /** + * Return the local unrolled component corresponding to + * @p column_offset entry of the @p table_indices. + * + * This function computes and returns a local component + * associated with the extractor's @p tensor_type from a + * set of @p table_indices that are generally associated + * with a tensor of equal or greater order. In effect, it + * creates a view of a selected number of indices of the + * input table, and interprets that subtable's indices as + * the local index to be returned. Since the @p table_indices + * may be of size greater than the extractor's @p rank, + * the @p column_offset specifies the first index of the + * input table to create the view from. + */ + template + static IndexType + local_component(const TableIndices &table_indices, + const unsigned int column_offset) + { + static_assert( + rank_in >= rank, + "Cannot extract more table indices than the input table has!"); + using TensorType = tensor_type; + return TensorType::component_to_unrolled_index( + table_index_view(table_indices, column_offset)); + } + }; + + + /** + * A helper struct that assists with the extraction of data associated + * with fields that are defined by FEExtractors. + * This particular specialization is for rank-2 symmetric tensor fields. + */ + template + struct Extractor> + { + /** + * The number of components of the field. + */ + static const unsigned int n_components = + SymmetricTensor<2, dim>::n_independent_components; + + /** + * The tensor rank of the field. + */ + static const unsigned int rank = SymmetricTensor<2, dim>::rank; + + /** + * The tensor type associated with this field. + */ + template + using tensor_type = SymmetricTensor; + + /** + * The value type associated with this field. + */ + template + using value_type = tensor_type; + + /** + * The gradient type associated with this field. + */ + template + using gradient_type = Tensor; + + /** + * Return the first global component of this field. + */ + static inline unsigned int + first_component(const FEValuesExtractors::SymmetricTensor<2> &extractor) + { + return extractor.first_tensor_component; + } + + /** + * Return a flag that indicates if the input @p unrolled_index + * corresponds to a symmetric component of the field. + * + * For a rank-2 symmetric tensor field, each of the + * off-diagonal components have a symmetric counterpart, + * while the diagonal components do not. + */ + static bool + symmetric_component(const unsigned int unrolled_index) + { + const TableIndices<2> table_indices = + tensor_type::unrolled_to_component_indices(unrolled_index); + return table_indices[0] != table_indices[1]; + } + + /** + * Return the table indices corresponding to + * @p column_offset entry of the input @p table_indices. + */ + template + static TableIndices + table_index_view(const TableIndices &table_indices, + const unsigned int column_offset) + { + Assert(column_offset < rank_in, ExcInternalError()); + Assert(column_offset + 1 < rank_in, ExcInternalError()); + return TableIndices(table_indices[column_offset], + table_indices[column_offset + 1]); + } + + /** + * Return the local unrolled component corresponding to + * @p column_offset entry of the @p table_indices. + * + * This function computes and returns a local component + * associated with the extractor's @p tensor_type from a + * set of @p table_indices that are generally associated + * with a tensor of equal or greater order. In effect, it + * creates a view of a selected number of indices of the + * input table, and interprets that subtable's indices as + * the local index to be returned. Since the @p table_indices + * may be of size greater than the extractor's @p rank, + * the @p column_offset specifies the first index of the + * input table to create the view from. + */ + template + static IndexType + local_component(const TableIndices &table_indices, + const unsigned int column_offset) + { + static_assert( + rank_in >= rank, + "Cannot extract more table indices than the input table has!"); + using TensorType = tensor_type; + return TensorType::component_to_unrolled_index( + table_index_view(table_indices, column_offset)); + } + }; + + + /** + * A helper struct that defines the return type of gradient (first + * derivative) calculations of scalar fields with respect to a field + * defined by the @p ExtractorType template parameter. + */ + template + struct ScalarFieldGradient + { + /** + * The type associated with computing the gradient of a scalar + * field with respect to the given @p ExtractorType. + */ + using type = + typename Extractor::template tensor_type; + }; + + + /** + * An intermediate helper struct that defines the return type of Hessian + * (second derivative) calculations of scalar fields with respect to + * fields defined by the two extractor-type template parameters. + * The first, @p ExtractorType_Row, defines the field that the first + * derivatives are taken with respect to while the second, + * @p ExtractorType_Col, defines the field that the second derivatives + * are taken with respect to. + */ + template + struct HessianType + { + /** + * The type associated with computing the gradient of a scalar + * field with respect to the given @p ExtractorType_Row + * followed by the @p ExtractorType_Col. + * + * @note We set the return type for + * HessianType + * as a normal Tensor. This is because if one has two vector components, + * the coupling tensor (i.e. Hessian component) is in + * general not symmetric. + */ + template + using type = Tensor; + }; + + + /** + * An intermediate helper struct that defines the return type of Hessian + * (second derivative) calculations of scalar fields with respect to + * fields defined by the two extractor-type template parameters. This + * particular specialization is for taking the first derivative with + * respect to a symmetric tensor field, and the second with respect to a + * scalar field. + */ + template <> + struct HessianType, + FEValuesExtractors::Scalar> + { + /** + * The type associated with computing the gradient of a scalar + * field with respect to the given + * ExtractorType_Row = + * FEValuesExtractors::SymmetricTensor<2> followed by the + * ExtractorType_Col = FEValuesExtractors::Scalar. + */ + template + using type = SymmetricTensor<2 /*rank*/, dim, NumberType>; + }; + + + /** + * An intermediate helper struct that defines the return type of Hessian + * (second derivative) calculations of scalar fields with respect to + * fields defined by the two extractor-type template parameters. This + * particular specialization is for taking the first derivative with + * respect to a scalar field, and the second with respect to a symmetric + * tensor field. + */ + template <> + struct HessianType> + { + /** + * The type associated with computing the gradient of a scalar + * field with respect to the given + * ExtractorType_Row = FEValuesExtractors::Scalar + * followed by the + * ExtractorType_Col = + * FEValuesExtractors::SymmetricTensor<2>. + */ + template + using type = SymmetricTensor<2 /*rank*/, dim, NumberType>; + }; + + + /** + * An intermediate helper struct that defines the return type of Hessian + * (second derivative) calculations of scalar fields with respect to + * fields defined by the two extractor-type template parameters. This + * particular specialization is for taking both the first and second + * derivatives with respect to symmetric tensor fields. + */ + template <> + struct HessianType, + FEValuesExtractors::SymmetricTensor<2>> + { + /** + * The type associated with computing the gradient of a scalar + * field with respect to the given + * ExtractorType_Row = + * FEValuesExtractors::SymmetricTensor<2> followed by the + * ExtractorType_Col = + * FEValuesExtractors::SymmetricTensor<2>. + */ + template + using type = SymmetricTensor<4 /*rank*/, dim, NumberType>; + }; + + + /** + * A helper struct that defines the final return type of Hessian + * (second derivative) calculations of scalar fields with respect to + * fields defined by the two extractor-type + * template parameters. The first, @p ExtractorType_Row, defines the field + * that the first derivatives are taken with respect to while the second, + * @p ExtractorType_Col, defines the field that the second derivatives + * are taken with respect to. + */ + template + struct ScalarFieldHessian + { + /** + * The tensor rank of the resulting derivative computation. + */ + static const int rank = Extractor::rank + + Extractor::rank; + + /** + * The type associated with computing the Hessian of a scalar + * field with first respect to the field defined by the + * @p ExtractorType_Row and then with respect to the field defined by + * the @p ExtractorType_Col. + */ + using type = + typename HessianType:: + template type; + }; + + + /** + * A helper struct that defines the return type of value computations + * of vector fields the @p ExtractorType_Field template parameter. + */ + template + using VectorFieldValue = + ScalarFieldGradient; + + + /** + * A helper struct that defines the final return type of Jacobian + * (first derivative) calculations of vector fields with respect to + * fields as defined by the two extractor-type template parameters. + * The first, @p ExtractorType_Field, defines the field from which + * the initial field values are computed while the second, + * @p ExtractorType_Derivative, defines the field that the derivatives + * are taken with respect to. + */ + template + using VectorFieldJacobian = ScalarFieldHessian; + + + /** + * Return a global view of the field component indices that correspond to + * the input @p extractor. For this general function the + * @p ignore_symmetries flag has no effect. + */ + template + std::vector + extract_field_component_indices(const ExtractorType &extractor, + const bool ignore_symmetries = true) + { + (void)ignore_symmetries; + const IndexType n_components = + internal::Extractor::n_components; + const IndexType comp_first = + internal::Extractor::first_component(extractor); + std::vector indices(n_components); + std::iota(indices.begin(), indices.end(), comp_first); + return indices; + } + + + /** + * Return a global view of the field component indices that correspond to + * the input FEValuesExtractors::SymmetricTensor @p extractor_symm_tensor. + * If the @p ignore_symmetries is set true, then all + * component of the tensor are considered to be independent. If set to + * code>false, then the set of returned indices will contain + * duplicate entries for components that are symmetric. + */ + template + std::vector + extract_field_component_indices( + const FEValuesExtractors::SymmetricTensor<2> &extractor_symm_tensor, + const bool ignore_symmetries = true) + { + using ExtractorType = FEValuesExtractors::SymmetricTensor<2>; + const IndexType n_components = + internal::Extractor::n_components; + if (ignore_symmetries == true) + { + const IndexType comp_first = + internal::Extractor::first_component( + extractor_symm_tensor); + std::vector indices(n_components); + std::iota(indices.begin(), indices.end(), comp_first); + return indices; + } + else + { + // First get all of the indices of the non-symmetric tensor + const FEValuesExtractors::Tensor<2> extractor_tensor( + extractor_symm_tensor.first_tensor_component); + std::vector indices = + extract_field_component_indices(extractor_tensor, true); + + // Then we overwrite any illegal entries with the equivalent indices + // from the symmetric tensor + for (unsigned int i = 0; i < indices.size(); ++i) + { + if (indices[i] >= n_components) + { + const TableIndices<2> ti_tensor = + Tensor<2, dim>::unrolled_to_component_indices(indices[i]); + const IndexType sti_new_index = + SymmetricTensor<2, dim>::component_to_unrolled_index( + ti_tensor); + indices[i] = sti_new_index; + } + } + + return indices; + } + } + + + /** + * Set the unrolled component given by @p index in the generic tensor + * @p t to the given @p value. + */ + template + inline void + set_tensor_entry(TensorType & t, + const unsigned int &unrolled_index, + const NumberType & value) + { + // Where possible, set values using TableIndices + Assert(unrolled_index < t.n_independent_components, + ExcIndexRange(unrolled_index, 0, t.n_independent_components)); + t[TensorType::unrolled_to_component_indices(unrolled_index)] = value; + } + + + /** + * Set the unrolled component given by @p index in the rank-0 tensor + * @p t to the given @p value. + */ + template + inline void set_tensor_entry(Tensor<0, dim, NumberType> &t, + const unsigned int & unrolled_index, + const NumberType & value) + { + Assert(unrolled_index == 0, ExcIndexRange(unrolled_index, 0, 1)); + (void)unrolled_index; + t = value; + } + + + /** + * Set the value of @p t to the given @p value. + * This function exists to provide compatibility with similar functions + * that exist for use with the tensor classes. + */ + template + inline void + set_tensor_entry(NumberType & t, + const unsigned int &unrolled_index, + const NumberType & value) + { + Assert(unrolled_index == 0, ExcIndexRange(unrolled_index, 0, 1)); + (void)unrolled_index; + t = value; + } + + + /** + * Set the unrolled component given by the @p index_row and + * the @p index_col in the fourth-order symmetric tensor + * @p t to the given @p value. + */ + template + inline void set_tensor_entry(SymmetricTensor<4, dim, NumberType> &t, + const unsigned int &unrolled_index_row, + const unsigned int &unrolled_index_col, + const NumberType & value) + { + // Fourth order symmetric tensors require a specialized interface + // to extract values. + using SubTensorType = SymmetricTensor<2, dim, NumberType>; + Assert(unrolled_index_row < SubTensorType::n_independent_components, + ExcIndexRange(unrolled_index_row, + 0, + SubTensorType::n_independent_components)); + Assert(unrolled_index_col < SubTensorType::n_independent_components, + ExcIndexRange(unrolled_index_col, + 0, + SubTensorType::n_independent_components)); + const TableIndices<2> indices_row = + SubTensorType::unrolled_to_component_indices(unrolled_index_row); + const TableIndices<2> indices_col = + SubTensorType::unrolled_to_component_indices(unrolled_index_col); + t[indices_row[0]][indices_row[1]][indices_col[0]][indices_col[1]] = + value; + } + + + /** + * Return the value of the @p index'th unrolled component of the + * generic tensor @p t. + */ + template class TensorType> + inline NumberType + get_tensor_entry(const TensorType &t, + const unsigned int & unrolled_index) + { + // Where possible, get values using TableIndices + Assert(unrolled_index < t.n_independent_components, + ExcIndexRange(unrolled_index, 0, t.n_independent_components)); + return t[TensorType:: + unrolled_to_component_indices(unrolled_index)]; + } + + + /** + * Return the value of the @p index'th unrolled component of the + * rank-0 tensor @p t. + */ + template class TensorType> + inline NumberType + get_tensor_entry(const TensorType<0, dim, NumberType> &t, + const unsigned int & unrolled_index) + { + Assert(unrolled_index == 0, ExcIndexRange(unrolled_index, 0, 1)); + (void)unrolled_index; + return t; + } + + + /** + * Return the value of @p t. + * This function exists to provide compatibility with similar functions + * that exist for use with the tensor classes. + */ + template + inline const NumberType & + get_tensor_entry(const NumberType &t, const unsigned int &unrolled_index) + { + Assert(unrolled_index == 0, ExcIndexRange(unrolled_index, 0, 1)); + (void)unrolled_index; + return t; + } + + + /** + * Return a reference to the entry stored in the @p index'th unrolled + * component of the generic tensor @p t. + */ + template class TensorType> + inline NumberType & + get_tensor_entry(TensorType &t, + const unsigned int & unrolled_index) + { + // Where possible, get values using TableIndices + Assert(unrolled_index < t.n_independent_components, + ExcIndexRange(unrolled_index, 0, t.n_independent_components)); + return t[TensorType:: + unrolled_to_component_indices(unrolled_index)]; + } + + + /** + * Return a reference to the entry stored in the @p index'th unrolled + * component of the rank-0 tensor @p t. + */ + template class TensorType> + NumberType &get_tensor_entry(TensorType<0, dim, NumberType> &t, + const unsigned int & index) + { + Assert(index == 0, ExcIndexRange(index, 0, 1)); + (void)index; + return t; + } + + + /** + * Return a reference to @p t. + * This function exists to provide compatibility with similar functions + * that exist for use with the tensor classes. + */ + template + inline NumberType & + get_tensor_entry(NumberType &t, const unsigned int &index) + { + Assert(index == 0, ExcIndexRange(index, 0, 1)); + (void)index; + return t; + } + + } // namespace internal } // namespace AD } // namespace Differentiation From b001e6dfcda04dfacc64e20dc48f3bb31d3e808b Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Mon, 11 Feb 2019 18:47:04 +0100 Subject: [PATCH 096/507] AD Helpers: Introduce base class for QP-level helper classes --- .../deal.II/differentiation/ad/ad_helpers.h | 424 ++++++++++++++++++ source/differentiation/ad/ad_helpers.cc | 169 +++++++ source/differentiation/ad/ad_helpers.inst1.in | 39 ++ source/differentiation/ad/ad_helpers.inst2.in | 52 +++ 4 files changed, 684 insertions(+) diff --git a/include/deal.II/differentiation/ad/ad_helpers.h b/include/deal.II/differentiation/ad/ad_helpers.h index 5460362a72bf..4f36c1dbfe11 100644 --- a/include/deal.II/differentiation/ad/ad_helpers.h +++ b/include/deal.II/differentiation/ad/ad_helpers.h @@ -2617,6 +2617,323 @@ namespace Differentiation } } // namespace internal + + + + /** + * A base helper class that facilitates the evaluation of point-wise defined + * functions. This is the point-wise counterpart of the + * ADHelperCellLevelBase class, and was conceived for computations at a + * continuum point, or quadrature point, rather than for finite-element + * level calculations. That being said, the interface to this and the + * derived classes are sufficiently generic that the dependent function(s) + * and their argument(s), that are the independent variables, can be + * interpreted in any manner that the user may choose. + * + * As it offers a field-based interface, this class would + * typically be used to compute the derivatives of a constitutive law + * defined at a quadrature point; however, it may also be used in other + * contexts, such as to compute the linearization of a set of local + * nonlinear equations. + * + * @warning ADOL-C does not support the standard threading models used by + * deal.II, so this class should @b not be embedded within a multithreaded + * function when using ADOL-C number types. It is, however, suitable for use + * in both serial and MPI routines. + * + * @author Jean-Paul Pelteret, 2016, 2017, 2018 + */ + template + class ADHelperPointLevelFunctionsBase + : public ADHelperBase + { + public: + /** + * Type definition for the dimension of the associated input and output + * tensor types. + */ + static const unsigned int dimension = dim; + + /** + * Type definition for the floating point number type that is used in, + * and results from, all computations. + */ + using scalar_type = + typename ADHelperBase::scalar_type; + + /** + * Type definition for the auto-differentiation number type that is used + * in all computations. + */ + using ad_type = + typename ADHelperBase::ad_type; + + /** + * @name Constructor / destructor + */ + //@{ + + /** + * The constructor for the class. + * + * @param[in] n_independent_variables The number of independent variables + * that will be used in the definition of the functions that it is + * desired to compute the sensitivities of. In the computation of + * $\mathbf{f}(\mathbf{X})$, this will be the number of inputs + * $\mathbf{X}$, i.e. the dimension of the domain space. + * @param[in] n_dependent_variables The number of scalar functions to be + * defined that will have a sensitivity to the given independent + * variables. In the computation of $\mathbf{f}(\mathbf{X})$, this will + * be the number of outputs $\mathbf{f}$, i.e. the dimension of the + * image space. + */ + ADHelperPointLevelFunctionsBase( + const unsigned int n_independent_variables, + const unsigned int n_dependent_variables); + + /** + * Destructor + */ + virtual ~ADHelperPointLevelFunctionsBase() = default; + + //@} + + /** + * @name Independent variables + */ + //@{ + + /** + * @copydoc ADHelperBase::reset() + */ + virtual void + reset(const unsigned int n_independent_variables = + dealii::numbers::invalid_unsigned_int, + const unsigned int n_dependent_variables = + dealii::numbers::invalid_unsigned_int, + const bool clear_registered_tapes = true) override; + + /** + * Register the complete set of independent variables $\mathbf{X}$. + * + * @param[in] values A field that defines the values of all independent + * variables. When considering taped AD numbers with branching functions, + * to avoid potential issues with branch switching it may be a good idea + * to choose these values close or equal to those that will be later + * evaluated and differentiated around. + * + * @note The input value type must correspond to this class's @p scalar_type. + * Depending on the selected @p ADNumberTypeCode, this may or may not + * correspond with the @p ScalarType prescribed as a template argument. + * + * @note For taped AD numbers, this operation is only valid in recording mode. + */ + void + register_independent_variables(const std::vector &values); + + /** + * Register the subset of independent variables + * $\mathbf{A} \subset \mathbf{X}$. + * + * @param[in] value A field that defines a number of independent + * variables. When considering taped AD numbers with branching functions, + * to avoid potential issues with branch switching it may be a good idea + * to choose these values close or equal to those that will be later + * evaluated and differentiated around. + * @param[in] extractor An extractor associated with the input field + * variables. This effectively defines which components of the global set + * of independent variables this field is associated with. + * + * @note The input value type must correspond to this class's @p scalar_type. + * Depending on the selected @p ADNumberTypeCode, this may or may not + * correspond with the @p ScalarType prescribed as a template argument. + * + * @note The input extractor must correspond to the input @p ValueType. + * So, for example, if a value is a rank-1 tensor + * (i.e. of type Tensor<1,dim,scalar_type>), then the extractor must + * be an FEValuesExtractors::Vector or FEValuesExtractors::Tensor<1>. + * + * @note This function may be repeatedly used until a call to + * finalize_sensitive_independent_variables() or + * get_sensitive_variables() is made. + * + * @note For taped AD numbers, this operation is only valid in recording mode. + */ + template + void + register_independent_variable(const ValueType & value, + const ExtractorType &extractor); + + /** + * Return the complete set of independent variables as represented by + * auto-differentiable numbers. These are the independent + * variables $\mathbf{X}$ at which the dependent values are evaluated + * and differentiated. + * + * This function indicates to the AD library that implements the + * auto-differentiable number type that operations performed on these + * numbers are to be tracked so they are considered "sensitive" + * variables. This is, therefore, the set of variables with which one + * would then perform computations, and based on which one can then + * extract both the value of the function and its derivatives with the + * member functions below. The values of the components of the returned + * object are initialized to the values set with + * register_independent_variable(). + * + * @return An array of auto-differentiable type numbers. + * + * @note For taped AD numbers, this operation is only valid in recording mode. + */ + const std::vector & + get_sensitive_variables() const; + + /* + * Extract a subset of the independent variables as represented by + * auto-differentiable numbers. These are the independent + * variables $\mathbf{A} \subset \mathbf{X}$ at which the dependent values + * are evaluated and differentiated. + * + * This function indicates to the AD library that implements the + * auto-differentiable number type that operations performed on these + * numbers are to be tracked so they are considered "sensitive" + * variables. This is, therefore, the set of variables with which one + * would then perform computations, and based on which one can then + * extract both the value of the function and its derivatives with the + * member functions below. The values of the components of the returned + * object are initialized to the values set with + * register_independent_variable(). + * + * @param[in] extractor An extractor associated with the input field + * variables. This effectively defines which components of the global set + * of independent variables this field is associated with. + * @return An object of auto-differentiable type numbers. The return type is + * based on the input extractor, and will be either a scalar, + * Tensor<1,dim>, Tensor<2,dim>, or SymmetricTensor<2,dim>. + * + * @note For taped AD numbers, this operation is only valid in recording mode. + */ + template + typename internal::Extractor::template tensor_type + get_sensitive_variables(const ExtractorType &extractor) const; + + //@} + + /** + * @name Operations specific to taped mode: Reusing tapes + */ + //@{ + + /** + * Set the values for the independent variables $\mathbf{X}$. + * + * @param[in] values A vector that defines the values of all + * independent variables. + * + * @note The input value type must correspond to this class's @p scalar_type. + * Depending on the selected @p ADNumberTypeCode, this may or may not + * correspond with the @p ScalarType prescribed as a template argument. + * + * @note If the @p keep_independent_values flag has been set when + * ADHelperBase::start_recording_operations() is called then the tape is + * immediately usable after creation, and the values of the independent + * variables set by register_independent_variables() are those at which + * the function is to be evaluated. In this case, a separate call to this + * function is not strictly necessary. + */ + void + set_independent_variables(const std::vector &values); + + /** + * Set the values for a subset of independent variables + * $\mathbf{A} \subset \mathbf{X}$. + * + * @param[in] value A field that defines the values of a number of + * independent variables. + * @param[in] extractor An extractor associated with the input field + * variables. This effectively defines which components of the global set + * of independent variables this field is associated with. + * + * @note The input value type must correspond to this class's @p scalar_type. + * Depending on the selected @p ADNumberTypeCode, this may or may not + * correspond with the @p ScalarType prescribed as a template argument. + * + * @note The input extractor must correspond to the input @p ValueType. + * So, for example, if a value is a rank-1 tensor + * (i.e. of type Tensor<1,dim,scalar_type>), then the extractor must + * be an FEValuesExtractors::Vector or FEValuesExtractors::Tensor<1>. + * + * @note If the @p keep_independent_values flag has been set when + * ADHelperBase::start_recording_operations() is called then the tape is + * immediately usable after creation, and the values of the independent + * variables set by register_independent_variable() are those at which the + * function is to be evaluated. In this case, a separate call to this + * function is not strictly necessary. + */ + template + void + set_independent_variable(const ValueType & value, + const ExtractorType &extractor); + + //@} + + protected: + /** + * @name Independent variables + */ + //@{ + + /** + * Set the actual value of the independent variable $X_{i}$. + * + * @param[in] index The index in the vector of independent variables. + * @param[in] symmetric_component Mark whether this index relates to a + * component of a field that has a symmetric counterpart + * (e.g. if @p index represents an off-diagonal entry in a symmetric + * tensor). + * @param[in] value The value to set the index'd independent variable to. + */ + void + set_sensitivity_value(const unsigned int index, + const bool symmetric_component, + const scalar_type &value); + + /** + * Return whether the @p index'th independent variables is one for which + * we must take into account symmetry when extracting their gradient or + * Hessian values. + */ + bool + is_symmetric_independent_variable(const unsigned int index) const; + + /** + * Return the number of independent variables that have been marked as + * being components of a symmetric field. + */ + unsigned int + n_symmetric_independent_variables() const; + + //@} + + private: + /** + * @name Independent variables + */ + //@{ + + /** + * The independent variables for which we must take into account symmetry + * when extracting their gradient or Hessian values. + */ + std::vector symmetric_independent_variables; + + //@} + + }; // class ADHelperPointLevelFunctionsBase + + } // namespace AD } // namespace Differentiation @@ -2675,6 +2992,113 @@ namespace Differentiation } + + /* ----------------- ADHelperPointLevelFunctionsBase ----------------- */ + + + + template + template + void + ADHelperPointLevelFunctionsBase:: + register_independent_variable(const ValueType & value, + const ExtractorType &extractor) + { + // This is actually the same thing as the set_independent_variable + // function, in the sense that we simply populate our array of independent + // values with a meaningful number. However, in this case we need to + // double check that we're not registering these variables twice +# ifdef DEBUG + const std::vector index_set( + internal::extract_field_component_indices(extractor)); + for (unsigned int i = 0; i < index_set.size(); ++i) + { + Assert( + this->registered_independent_variable_values[index_set[i]] == false, + ExcMessage( + "Overlapping indices for independent variables. " + "One or more indices associated with the field that " + "is being registered as an independent variable have " + "already been associated with another field. This suggests " + "that the component offsets used to construct their counterpart " + "extractors are incompatible with one another. Make sure that " + "the first component for each extractor properly takes into " + "account the dimensionality of the preceeding fields.")); + } +# endif + set_independent_variable(value, extractor); + } + + + + template + template + void + ADHelperPointLevelFunctionsBase:: + set_independent_variable(const ValueType & value, + const ExtractorType &extractor) + { + const std::vector index_set( + internal::extract_field_component_indices(extractor)); + for (unsigned int i = 0; i < index_set.size(); ++i) + { + set_sensitivity_value( + index_set[i], + internal::Extractor::symmetric_component(i), + internal::get_tensor_entry(value, i)); + } + } + + + + template + template + typename internal::Extractor::template tensor_type< + typename ADHelperBase::ad_type> + ADHelperPointLevelFunctionsBase:: + get_sensitive_variables(const ExtractorType &extractor) const + { + if (ADNumberTraits::is_taped == true) + { + Assert(this->active_tape_index() != + Numbers::invalid_tape_index, + ExcMessage("Invalid tape index")); + } + + // If necessary, finalize the internally stored vector of + // AD numbers that represents the independent variables + this->finalize_sensitive_independent_variables(); + Assert(this->independent_variables.size() == + this->n_independent_variables(), + ExcDimensionMismatch(this->independent_variables.size(), + this->n_independent_variables())); + + const std::vector index_set( + internal::extract_field_component_indices(extractor)); + typename internal::Extractor::template tensor_type + out; + + for (unsigned int i = 0; i < index_set.size(); ++i) + { + const unsigned int index = index_set[i]; + Assert(index < this->n_independent_variables(), ExcInternalError()); + Assert(this->registered_independent_variable_values[index] == true, + ExcInternalError()); + internal::get_tensor_entry(out, i) = + this->independent_variables[index]; + } + + return out; + } + + } // namespace AD } // namespace Differentiation diff --git a/source/differentiation/ad/ad_helpers.cc b/source/differentiation/ad/ad_helpers.cc index 2c3a9a5a47bd..7789a475430b 100644 --- a/source/differentiation/ad/ad_helpers.cc +++ b/source/differentiation/ad/ad_helpers.cc @@ -1143,6 +1143,175 @@ namespace Differentiation } + + /* ----------------- ADHelperPointLevelFunctionsBase ----------------- */ + + + + template + ADHelperPointLevelFunctionsBase:: + ADHelperPointLevelFunctionsBase( + const unsigned int n_independent_variables, + const unsigned int n_dependent_variables) + : ADHelperBase(n_independent_variables, + n_dependent_variables) + , symmetric_independent_variables(n_independent_variables, false) + {} + + + + template + void + ADHelperPointLevelFunctionsBase::reset( + const unsigned int n_independent_variables, + const unsigned int n_dependent_variables, + const bool clear_registered_tapes) + { + ADHelperBase::reset(n_independent_variables, + n_dependent_variables, + clear_registered_tapes); + + const unsigned int new_n_independent_variables = + (n_independent_variables != dealii::numbers::invalid_unsigned_int ? + n_independent_variables : + this->n_independent_variables()); + symmetric_independent_variables = + std::vector(new_n_independent_variables, false); + } + + + + template + bool + ADHelperPointLevelFunctionsBase:: + is_symmetric_independent_variable(const unsigned int index) const + { + Assert(index < symmetric_independent_variables.size(), + ExcInternalError()); + return symmetric_independent_variables[index]; + } + + + + template + unsigned int + ADHelperPointLevelFunctionsBase:: + n_symmetric_independent_variables() const + { + return std::count(symmetric_independent_variables.begin(), + symmetric_independent_variables.end(), + true); + } + + + + template + void + ADHelperPointLevelFunctionsBase:: + register_independent_variables(const std::vector &values) + { + // This is actually the same thing the set_independent_variable function, + // in the sense that we simply populate our array of independent values + // with a meaningful number. However, in this case we need to double check + // that we're not registering these variables twice + Assert(values.size() == this->n_independent_variables(), + ExcMessage( + "Vector size does not match number of independent variables")); + for (unsigned int i = 0; i < this->n_independent_variables(); ++i) + { + Assert(this->registered_independent_variable_values[i] == false, + ExcMessage("Independent variable value already registered.")); + } + set_independent_variables(values); + } + + + + template + const std::vector< + typename ADHelperPointLevelFunctionsBase::ad_type> & + ADHelperPointLevelFunctionsBase:: + get_sensitive_variables() const + { + if (ADNumberTraits::is_taped == true) + { + Assert(this->active_tape_index() != + Numbers::invalid_tape_index, + ExcMessage("Invalid tape index")); + } + + // Just in case the user has not done so, we repeat the call to + // initialize the internally stored vector of AD numbers that + // represents the independent variables. + this->finalize_sensitive_independent_variables(); + Assert(this->independent_variables.size() == + this->n_independent_variables(), + ExcDimensionMismatch(this->independent_variables.size(), + this->n_independent_variables())); + + return this->independent_variables; + } + + + + template + void + ADHelperPointLevelFunctionsBase:: + set_sensitivity_value(const unsigned int index, + const bool symmetric_component, + const scalar_type &value) + { + ADHelperBase::set_sensitivity_value(index, + value); + Assert( + index < this->n_independent_variables(), + ExcMessage( + "Trying to set the symmetry flag of a non-existent independent variable.")); + Assert(index < symmetric_independent_variables.size(), + ExcInternalError()); + symmetric_independent_variables[index] = symmetric_component; + } + + + + template + void + ADHelperPointLevelFunctionsBase:: + set_independent_variables(const std::vector &values) + { + if (ADNumberTraits::is_taped == true) + { + Assert(this->active_tape_index() != + Numbers::invalid_tape_index, + ExcMessage("Invalid tape index")); + } + Assert(values.size() == this->n_independent_variables(), + ExcMessage( + "Vector size does not match number of independent variables")); + for (unsigned int i = 0; i < this->n_independent_variables(); ++i) + ADHelperBase::set_sensitivity_value( + i, values[i]); + } + + } // namespace AD } // namespace Differentiation diff --git a/source/differentiation/ad/ad_helpers.inst1.in b/source/differentiation/ad/ad_helpers.inst1.in index bf91f88855b7..ef44c9398496 100644 --- a/source/differentiation/ad/ad_helpers.inst1.in +++ b/source/differentiation/ad/ad_helpers.inst1.in @@ -101,3 +101,42 @@ for () \} \} } + + +for (deal_II_dimension : DIMENSIONS ; number : REAL_SCALARS) +{ + namespace Differentiation + \{ + namespace AD + \{ + // -------------------------- ADHelperPointLevelFunctionsBase ---------------------- + + template + class ADHelperPointLevelFunctionsBase; + + template + class ADHelperPointLevelFunctionsBase; + + \} + \} +} + +// Instantiations for ADHelpers for which the underlying number type is fixed +for (deal_II_dimension : DIMENSIONS) +{ + namespace Differentiation + \{ + namespace AD + \{ + + // -------------------------- ADHelperPointLevelFunctionsBase ---------------------- + + template + class ADHelperPointLevelFunctionsBase::ad_type>; + + template + class ADHelperPointLevelFunctionsBase::ad_type>; + + \} + \} +} diff --git a/source/differentiation/ad/ad_helpers.inst2.in b/source/differentiation/ad/ad_helpers.inst2.in index 30c30a054ce3..5fa4b2511e37 100644 --- a/source/differentiation/ad/ad_helpers.inst2.in +++ b/source/differentiation/ad/ad_helpers.inst2.in @@ -149,3 +149,55 @@ for () \} \} } + + +for (deal_II_dimension : DIMENSIONS ; number : REAL_SCALARS) +{ + namespace Differentiation + \{ + namespace AD + \{ + + // -------------------------- ADHelperPointLevelFunctionsBase ---------------------- + + template + class ADHelperPointLevelFunctionsBase; + + template + class ADHelperPointLevelFunctionsBase; + + template + class ADHelperPointLevelFunctionsBase; + + template + class ADHelperPointLevelFunctionsBase; + + \} + \} +} + +// Instantiations for ADHelpers for which the underlying number type is fixed +for (deal_II_dimension : DIMENSIONS) +{ + namespace Differentiation + \{ + namespace AD + \{ + + // -------------------------- ADHelperPointLevelFunctionsBase ---------------------- + + template + class ADHelperPointLevelFunctionsBase::ad_type>; + + template + class ADHelperPointLevelFunctionsBase::ad_type>; + + template + class ADHelperPointLevelFunctionsBase::ad_type>; + + template + class ADHelperPointLevelFunctionsBase::ad_type>; + + \} + \} +} From 5f482f9cdd1a822f6a7b7f1bb3458d68382ad6ec Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Tue, 12 Feb 2019 01:21:37 +0100 Subject: [PATCH 097/507] Fix changelog entry --- doc/news/changes/minor/20190209Arndt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/news/changes/minor/20190209Arndt b/doc/news/changes/minor/20190209Arndt index d8bdf8fff554..b781c4394355 100644 --- a/doc/news/changes/minor/20190209Arndt +++ b/doc/news/changes/minor/20190209Arndt @@ -1,3 +1,3 @@ -New: make_const_array_view creates a constant view from a non-const object. +New: make_const_array_view() creates a constant view from a non-const object.
(Daniel Arndt, 2019/02/09) From 62db86d737aaa557822b411340268352d25e8ada Mon Sep 17 00:00:00 2001 From: Matthias Maier Date: Fri, 8 Feb 2019 13:50:16 -0600 Subject: [PATCH 098/507] examples/step-20: Update introduction - Introduce LinearOperator and PackagedOperation - Explain in detail how to solve the Schur complement using this functionality. --- examples/step-20/doc/intro.dox | 380 ++++++++++++++++----------------- 1 file changed, 185 insertions(+), 195 deletions(-) diff --git a/examples/step-20/doc/intro.dox b/examples/step-20/doc/intro.dox index b9a7bde9cf4e..f090523b020d 100644 --- a/examples/step-20/doc/intro.dox +++ b/examples/step-20/doc/intro.dox @@ -249,7 +249,7 @@ program we do that in the following way: for (unsigned int i=0; i phi_j_u = fe_values[velocities].value (j, q); - const double div_phi_j_u = fe_values[velocities].divergence (j, q); - const double phi_j_p = fe_values[pressure].value (j, q); + const Tensor<1,dim> phi_j_u = fe_values[velocities].value (j, q); + const double div_phi_j_u = fe_values[velocities].divergence (j, q); + const double phi_j_p = fe_values[pressure].value (j, q); local_matrix(i,j) += (phi_i_u * k_inverse_values[q] * phi_j_u - div_phi_i_u * phi_j_p @@ -333,23 +333,23 @@ the same way as above, i.e. the extractor classes also work on FEFaceValues obje @code for (unsigned int face_no=0; - face_no::faces_per_cell; - ++face_no) - if (cell->at_boundary(face_no)) - { - fe_face_values.reinit (cell, face_no); - - pressure_boundary_values - .value_list (fe_face_values.get_quadrature_points(), - boundary_values); - - for (unsigned int q=0; q::faces_per_cell; + ++face_no) + if (cell->at_boundary(face_no)) + { + fe_face_values.reinit (cell, face_no); + + pressure_boundary_values + .value_list (fe_face_values.get_quadrature_points(), + boundary_values); + + for (unsigned int q=0; qblocks that correspond to the individual operators that appear in -the system. We note that the resulting solver is not optimal -- there are much -better ways, for example those explained in the results section of step-22 or -the one we use in step-43 for a problem rather similar to the current one -- -but that the goal is to introduce techniques rather than optimal solvers. +the system. We note that the resulting solver is not optimal -- there are +much better ways to efficiently compute the system, for example those +explained in the results section of step-22 or the one we use in step-43 +for a problem similar to the current one. Here, our goal shall be to +introduce new solution techniques how they can be implemented in deal.II.

Solving using the Schur complement

@@ -439,115 +440,162 @@ matrix-vector products. @note The key point in this consideration is to recognize that to implement an iterative solver such as CG or GMRES, we never actually need the actual elements of a matrix! All that is required is that we can form -matrix-vector products. The same is true for preconditioners. In deal.II -we encode this requirement by only requiring that matrices and preconditioners -given to solver classes have a vmult() member function that does -the matrix-vector product. How a class chooses to implement this function is -not important to the solver. Consequently, classes can implement it by, -for example, doing a sequence of products and linear solves as discussed -above. - -Using this strategy, we can then implement a class that provides the -function vmult() that is all that the SolverCG class -requires from an object representing a matrix. We can make our life a -bit easier by also introducing an object that represents $M^{-1}$ and -that has its own vmult() function that, if called, solves -the linear system with $M$. Using this (which we will implement as the -InverseMatrix class in the body of the program), the class -that implements the Schur only needs to offer the vmult() -function to perform a matrix-vector multiplication, using the algorithm -above. Here are again the relevant parts of the code: - +matrix-vector products. The same is true for preconditioners. In deal.II we +encode this requirement by only requiring that matrices and preconditioners +given to solver classes have a vmult() member function that +does the matrix-vector product. How a class chooses to implement this +function is not important to the solver. Consequently, classes can +implement it by, for example, doing a sequence of products and linear +solves as discussed above. + + +

The LinearOperator framework in deal.II

+ +deal.II includes support for describing such linear operations in a very +general way. This is done with the LinearOperator class that, like +@ref ConceptMatrixType "the MatrixType concept", +defines a minimal interface for applying a linear operation to a +vector: @code -class SchurComplement : public Subscriptor -{ - public: - SchurComplement (const BlockSparseMatrix &A, - const InverseMatrix > &inverse_mass); - - void vmult (Vector &dst, - const Vector &src) const; - - private: - const SmartPointer > system_matrix; - const SmartPointer > > inverse_mass; - - mutable Vector tmp1, tmp2; -}; - - -void SchurComplement::vmult (Vector &dst, - const Vector &src) const -{ - system_matrix->block(0,1).vmult (tmp1, src); // multiply with the top right block: B - inverse_mass->vmult (tmp2, tmp1); // multiply with M^-1 - system_matrix->block(1,0).vmult (dst, tmp2); // multiply with the bottom left block: B^T -} + std::function vmult; + std::function vmult_add; + std::function Tvmult; + std::function Tvmult_add; @endcode +The key difference between a LinearOperator and an ordinary matrix is +however that a LinearOperator does not allow any further access to the +underlying object. All you can do with a LinearOperator is to apply its +"action" to a vector! We take the opportunity to introduce the +LinearOperator concept at this point because it is a very useful tool that +allows you to construct complex solvers and preconditioners in a very +intuitive manner. + +As a first example let us construct a LinearOperator object that represents +$M^{-1}$. This means that whenever the vmult() function of +this operator is called it has to solve a linear system. This requires us +to specify a solver (and corresponding) preconditioner. Assuming that +M is a reference to the upper left block of the system matrix +we can write: +@code + const auto op_M = linear_operator(M); -In this code, the constructor takes a reference to a block sparse matrix for -the entire system, and a reference to the object representing the inverse of -the mass matrix. It stores these using SmartPointer objects (see -step-7), and additionally allocates two temporary vectors tmp1 and -tmp2 for the vectors labeled $w,y$ in the list above. + PreconditionJacobi<> preconditioner_M; + preconditioner_M.initialize(M); -In the matrix-vector multiplication function, the product $Sv$ is performed in -exactly the order outlined above. Note how we access the blocks $B$ and $B^T$ -by calling system_matrix->block(0,1) and -system_matrix->block(1,0) respectively, thereby picking out -individual blocks of the block system. Multiplication by $M^{-1}$ happens -using the object introduced above. + ReductionControl reduction_control_M(2000, 1.0e-18, 1.0e-10); + SolverCG<> solver_M(reduction_control_M); -With all this, we can go ahead and write down the solver we are going to -use. Essentially, all we need to do is form the right hand sides of the two -equations defining $P$ and $U$, and then solve them with the Schur complement -matrix and the mass matrix, respectively: + const auto op_M_inv = inverse_operator(op_M, solver_M, preconditioner_M); +@endcode +Rather than using a SolverControl we use the ReductionControl class here +that stops iterations when either an absolute tolerance is reached (for +which we choose $10^{-18}$) or when the residual is reduced by a certain +factor (here, $10^{-10}$). In contrast the SolverControl class only checks +for absolute tolerances. We have to use ReductionControl in our case to +work around a minor issue: The right hand sides that we will feed to +op_M_inv are essentially formed by residuals that naturally +have vastly differing norms. This makes control by an absolute tolerance +very error prone. + +We now have a LinearOperator op_M_inv that we can use to +construct more complicated operators such as the Schur complement $S$. +Assuming that B is a reference to the upper right block +constructing a LinearOperator op_S is a matter of two lines: +@code + const auto op_B = linear_operator(B); + const auto op_S = transpose_operator(op_B) * op_M_inv * op_B; +@endcode +Here, the multiplication of three LinearOperator objects yields a composite +object op_S whose vmult() function first applies +$B$, then $M^{-1}$ (i.e. solving an equation with $M$), and finally $B^T$ +to any given input vector. In that sense op_S.vmult() is +similar to the following code: +@code + B.vmult (tmp1, src); // multiply with the top right block: B + solver_M(M, tmp2, tmp1, preconditioner_M); // multiply with M^-1 + B.Tvmult (dst, tmp2); // multiply with the bottom left block: B^T +@endcode +(tmp1 and tmp2 are two temporary vectors). +@note We could have achieved the same goal of creating a "matrix like" +object by implementing a specialized class SchurComplement +that provides a suitable vmult() function. Skipping over some +details this might have looked like the following: @code -template -void MixedLaplaceProblem::solve () +class SchurComplement { - InverseMatrix > inverse_mass (system_matrix.block(0,0)); - Vector tmp (solution.block(0).size()); + public: - { - SchurComplement schur_complement (system_matrix, inverse_mass); - Vector schur_rhs (solution.block(1).size()); - inverse_mass.vmult (tmp, system_rhs.block(0)); - system_matrix.block(1,0).vmult (schur_rhs, tmp); - schur_rhs -= system_rhs.block(1); - - SolverControl solver_control (solution.block(1).size(), - 1e-12*schur_rhs.l2_norm()); - SolverCG<> cg (solver_control); - - PreconditionIdentity preconditioner; - cg.solve (schur_complement, solution.block(1), schur_rhs, - preconditioner); - } + // ... + void SchurComplement::vmult (Vector &dst, + const Vector &src) const { - system_matrix.block(0,1).vmult (tmp, solution.block(1)); - tmp *= -1; - tmp += system_rhs.block(0); - - inverse_mass.vmult (solution.block(0), tmp); + B.vmult (tmp1, src); + solver_M(M, tmp2, tmp1, preconditioner_M); + B.Tvmult (dst, tmp2); } -} +}; +@endcode +Even though both approaches are exactly equivalent, the LinearOperator +class has a big advantage over this manual approach. +It provides so-called syntactic sugar: Mathematically, we think +about $S$ as being the composite matrix $S=B^TM^{-1}B$ and the +LinearOperator class allows you to write this out more or less verbatim, +@code +const auto op_M_inv = inverse_operator(op_M, solver_M, preconditioner_M); +const auto op_S = transpose_operator(op_B) * op_M_inv * op_B; @endcode +The manual approach on the other hand obscures this fact. -This code looks more impressive than it actually is. At the beginning, we -declare an object representing $M^{-1}$ and a temporary vector (of the size of -the first block of the solution, i.e. with as many entries as there are -velocity unknowns), and the two blocks surrounded by braces then solve the two -equations for $P$ and $U$, in this order. Most of the code in each of the two -blocks is actually devoted to constructing the proper right hand sides. For -the first equation, this would be $B^TM^{-1}F-G$, and $-BP+F$ for the second -one. The first hand side is then solved with the Schur complement matrix, and -the second simply multiplied with $M^{-1}$. The code as shown uses no -preconditioner (i.e. the identity matrix as preconditioner) for the Schur -complement. +All that is left for us to do now is to form the right hand sides of the +two equations defining $P$ and $U$, and then solve them with the Schur +complement matrix and the mass matrix, respectively. For example the right +hand side of the first equation reads $B^TM^{-1}F-G$. This could be +implemented as follows: +@code + Vector schur_rhs (U.size()); + Vector tmp (P.size()); + op_M_inv.vmult (tmp, F); + transpose_operator(op_B).vmult (schur_rhs, tmp); + schur_rhs -= G; +@endcode +Again, this is a perfectly valid approach, but the fact that deal.II +requires us to manually resize the final and temporary vector, and that +every operation takes up a new line makes this hard to read. This is the +point where a second class in the linear operator framework can will help +us. Similarly in spirit to LinearOperator, a PackagedOperation stores a +"computation": +@code + std::function apply; + std::function apply_add; +@endcode +The class allows lazy evaluation of expressions involving vectors and +linear operators. This is done by storing the computational expression and +only performing the computation when either the object is converted to a +vector object, or PackagedOperation::apply() (or +PackagedOperation::apply_add()) is invoked by hand. Assuming that +F and G are the two vectors of the right hand +side we can simply write: +@code + const auto schur_rhs = transpose_operator(op_B) * op_M_inv * F - G; +@endcode +Here, schur_rhs is a PackagedOperation that records the +computation we specified. It does not create a vector with the actual +result immediately. +With these prerequisites at hand, solving for $P$ and $U$ is a matter of +creating another solver and inverse: +@code + SolverControl solver_control_S(2000, 1.e-12); + SolverCG<> solver_S(solver_control_S); + PreconditionIdentity preconditioner_S; + + const auto op_S_inv = inverse_operator(op_S, solver_S, preconditioner_S); + + P = op_S_inv * schur_rhs; + U = op_M_inv * (F - op_B * P); +@endcode

A preconditioner for the Schur complement

@@ -579,82 +627,34 @@ this looks almost as expensive as solving with $S$ right away. However, note that in the inner iteration, we do not have to calculate $M^{-1}$, but only the inverse of its diagonal, which is cheap. -The next step is to define a class that represents this approximate Schur -complement. This should look very much like the Schur complement class itself, -except that it doesn't need the object representing $M^{-1}$ any more -since we can compute the inverse of the diagonal of $M$ on the fly: - +Thankfully, the LinearOperator framework makes this very easy to write out. +We already used a Jacobi preconditioner (preconditioner_M) for +the $M$ matrix earlier. So all that is left to do is to write out how the +approximate Schur complement should look like: @code -class ApproximateSchurComplement : public Subscriptor -{ -public: - ApproximateSchurComplement (const BlockSparseMatrix &A); - - void vmult (Vector &dst, - const Vector &src) const; - -private: - const SmartPointer > system_matrix; - - mutable Vector tmp1, tmp2; -}; - - -void -ApproximateSchurComplement::vmult - (Vector &dst, - const Vector &src) const - { - system_matrix->block(0,1).vmult (tmp1, src); - system_matrix->block(0,0).precondition_Jacobi (tmp2, tmp1); - system_matrix->block(1,0).vmult (dst, tmp2); - } + const auto op_aS = + transpose_operator(op_B) * linear_operator(preconditioner_M) * op_B; @endcode - -Note how the vmult function differs in simply doing one Jacobi sweep +Note how this operator differs in simply doing one Jacobi sweep (i.e. multiplying with the inverses of the diagonal) instead of multiplying -with the full $M^{-1}$. (This is how a single Jacobi preconditioner -step with $M$ is defined: it is the multiplication with the inverse of -the diagonal of $M$; in other words, the operation $({\textrm{diag}\ -}M)^{-1}x$ on a vector $x$ is exactly what the function -SparseMatrix::precondition_Jacobi above does.) +with the full $M^{-1}$. (This is how a single Jacobi preconditioner step +with $M$ is defined: it is the multiplication with the inverse of the +diagonal of $M$; in other words, the operation $({\textrm{diag}\ }M)^{-1}x$ +on a vector $x$ is exactly what PreconditionJacobi does.) With all this, we nearly already have the preconditioner: it should be the -inverse of the approximate Schur complement. We implement this with -the InverseMatrix class: - +inverse of the approximate Schur complement. We implement this again with +the inverse_operator() function @code - ApproximateSchurComplement approximate_schur (system_matrix); - InverseMatrix approximate_inverse - (approximate_schur); + ReductionControl reduction_control_aS(2000, 1.e-18, 1.0e-6); + SolverCG<> solver_aS(reduction_control_aS); + PreconditionIdentity preconditioner_aS; + const auto preconditioner_S = + inverse_operator(op_aS, solver_aS, preconditioner_aS); @endcode That's all! -Taken together, the first block of our solve() function will then -look like this: - -@code - SchurComplement schur_complement (system_matrix, inverse_mass); - Vector schur_rhs (solution.block(1).size()); - inverse_mass.vmult (tmp, system_rhs.block(0)); - system_matrix.block(1,0).vmult (schur_rhs, tmp); - schur_rhs -= system_rhs.block(1); - - SolverControl solver_control (solution.block(1).size(), - 1e-12*schur_rhs.l2_norm()); - SolverCG<> cg (solver_control); - - ApproximateSchurComplement approximate_schur (system_matrix); - InverseMatrix approximate_inverse - (approximate_schur); - cg.solve (schur_complement, solution.block(1), schur_rhs, - approximate_inverse); -@endcode - -Note how we pass the so-defined preconditioner to the solver working on the -Schur complement matrix. - Obviously, applying this inverse of the approximate Schur complement is a very expensive preconditioner, almost as expensive as inverting the Schur complement itself. We can expect it to significantly reduce the number of @@ -670,16 +670,6 @@ six times refined mesh and using elements of order 2 yields an improvement of earth shattering, but significant. -

A remark on similar functionality in deal.II

- -As a final remark about solvers and preconditioners, let us note that a -significant amount of functionality introduced above is actually also present -in the library itself. It probably even is more powerful and general, but we -chose to introduce this material here anyway to demonstrate how to work with -block matrices and to develop solvers and preconditioners, rather than using -black box components from the library. - -

Definition of the test case

In this tutorial program, we will solve the Laplace equation in mixed From f21656e3fd265a36fd53616888bffca7601600e5 Mon Sep 17 00:00:00 2001 From: Matthias Maier Date: Fri, 8 Feb 2019 13:51:36 -0600 Subject: [PATCH 099/507] examples/step-20: Actually use LinearOperator in the example step --- examples/step-20/step-20.cc | 240 ++++++++++-------------------------- 1 file changed, 66 insertions(+), 174 deletions(-) diff --git a/examples/step-20/step-20.cc b/examples/step-20/step-20.cc index 8710392acae2..20ddcb621d42 100644 --- a/examples/step-20/step-20.cc +++ b/examples/step-20/step-20.cc @@ -14,7 +14,8 @@ * --------------------------------------------------------------------- * - * Author: Wolfgang Bangerth, Texas A&M University, 2005, 2006 + * Authors: Wolfgang Bangerth, Texas A&M University, 2005, 2006; + * (port to LinearOperator:) Matthias Maier, 2019 */ @@ -27,12 +28,18 @@ #include #include #include + #include #include #include #include #include +// The only two new header files that deserve some attention are those for +// the LinearOperator and PackagedOperation classes: +#include +#include + #include #include #include @@ -559,206 +566,91 @@ namespace Step20 // @sect3{Linear solvers and preconditioners} - // The linear solvers and preconditioners we use in this example have been - // discussed in significant detail already in the introduction. We will - // therefore not discuss the rationale for these classes here any more, but - // rather only comment on implementational aspects. - - // @sect4{The InverseMatrix class template} - - // There are a few places in this program where we will need either the - // action of the inverse of the mass matrix or the action of the inverse of - // the approximate Schur complement. Rather than explicitly calling - // SolverCG::solve every time that we need to solve such a system, we will - // wrap the action of either inverse in a simple class. The only things we - // would like to note are that this class is derived from - // Subscriptor and, as mentioned above, it stores a pointer to - // the underlying matrix with a SmartPointer object. This class - // also appears in step-21 and a more advanced version of it appears in - // step-22. - template - class InverseMatrix : public Subscriptor - { - public: - InverseMatrix(const MatrixType &m); - - void vmult(Vector &dst, const Vector &src) const; - - private: - const SmartPointer matrix; - }; - - - template - InverseMatrix::InverseMatrix(const MatrixType &m) - : matrix(&m) - {} - + // The linear solvers and preconditioners we use in this example have + // been discussed in significant detail already in the introduction. We + // will therefore not discuss the rationale for our approach here any + // more, but rather only comment on some remaining implementational + // aspects. - template - void InverseMatrix::vmult(Vector & dst, - const Vector &src) const - { - // To make the control flow simpler, we recreate both the ReductionControl - // and SolverCG objects every time this is called. This is not the most - // efficient choice because SolverCG instances allocate memory whenever - // they are created; this is just a tutorial so such inefficiencies are - // acceptable for the sake of exposition. - SolverControl solver_control(std::max(src.size(), 200), - 1e-8 * src.l2_norm()); - SolverCG<> cg(solver_control); - - dst = 0; - - cg.solve(*matrix, dst, src, PreconditionIdentity()); - } - - - // @sect4{The SchurComplement class} + // @sect4{MixedLaplace::solve} - // The next class is the Schur complement class. Its rationale has also been - // discussed in length in the introduction. Like InverseMatrix, - // this class is derived from Subscriptor and stores SmartPointer s - // pointing to the system matrix and InverseMatrix wrapper. - // - // The vmult function requires two temporary vectors that we do - // not want to re-allocate and free every time we call this function. Since - // here, we have full control over the use of these vectors (unlike above, - // where a class called by the vmult function required these - // vectors, not the vmult function itself), we allocate them - // directly, rather than going through the VectorMemory - // mechanism. However, again, these member variables do not carry any state - // between successive calls to the member functions of this class (i.e., we - // never care what values they were set to the last time a member function - // was called), we mark these vectors as mutable. - // - // The rest of the (short) implementation of this class is straightforward - // if you know the order of matrix-vector multiplications performed by the - // vmult function: - class SchurComplement : public Subscriptor + // As already outlined in the introduction, the solve function consists + // essentially of two steps. First, we have to form the first equation + // involving the Schur complement and solve for the pressure (component 1 + // of the solution). Then, we can reconstruct the velocities from the + // second equation (component 0 of the solution). + template + void MixedLaplaceProblem::solve() { - public: - SchurComplement(const BlockSparseMatrix & A, - const InverseMatrix> &Minv); - - void vmult(Vector &dst, const Vector &src) const; - - private: - const SmartPointer> system_matrix; - const SmartPointer>> m_inverse; - - mutable Vector tmp1, tmp2; - }; + // As a first step we declare references to all block components of the + // matrix, the right hand side and the solution vector that we will + // need. + const auto &M = system_matrix.block(0, 0); + const auto &B = system_matrix.block(0, 1); + const auto &F = system_rhs.block(0); + const auto &G = system_rhs.block(1); - SchurComplement ::SchurComplement( - const BlockSparseMatrix & A, - const InverseMatrix> &Minv) - : system_matrix(&A) - , m_inverse(&Minv) - , tmp1(A.block(0, 0).m()) - , tmp2(A.block(0, 0).m()) - {} + auto &U = solution.block(0); + auto &P = solution.block(1); + // Then, we will create corresponding LinearOperator objects and create + // the op_M_inv operator: - void SchurComplement::vmult(Vector & dst, - const Vector &src) const - { - system_matrix->block(0, 1).vmult(tmp1, src); - m_inverse->vmult(tmp2, tmp1); - system_matrix->block(1, 0).vmult(dst, tmp2); - } + const auto op_M = linear_operator(M); + const auto op_B = linear_operator(B); + ReductionControl reduction_control_M(2000, 1.0e-18, 1.0e-10); + SolverCG<> solver_M(reduction_control_M); + PreconditionJacobi<> preconditioner_M; - // @sect4{The ApproximateSchurComplement class} + preconditioner_M.initialize(M); - // The third component of our solver and preconditioner system is the class - // that approximates the Schur complement with the method described in the - // introduction. We will use this class to build a preconditioner for our - // system matrix. - class ApproximateSchurComplement : public Subscriptor - { - public: - ApproximateSchurComplement(const BlockSparseMatrix &A); + const auto op_M_inv = inverse_operator(op_M, solver_M, preconditioner_M); - void vmult(Vector &dst, const Vector &src) const; + // This puts us in the position to be able to declare the Schur + // complement op_S and the approximate Schur complement + // op_aS: - private: - const SmartPointer> system_matrix; + const auto op_S = transpose_operator(op_B) * op_M_inv * op_B; + const auto op_aS = + transpose_operator(op_B) * linear_operator(preconditioner_M) * op_B; - mutable Vector tmp1, tmp2; - }; + // We now create a preconditioner out of op_aS that + // applies a few number of CG iterations (until a very modest relative + // reduction of $10^{-16}$ is reached): + ReductionControl reduction_control_aS(2000, 1.e-18, 1.0e-6); + SolverCG<> solver_aS(reduction_control_aS); + PreconditionIdentity preconditioner_aS; + const auto preconditioner_S = + inverse_operator(op_aS, solver_aS, preconditioner_aS); - ApproximateSchurComplement::ApproximateSchurComplement( - const BlockSparseMatrix &A) - : system_matrix(&A) - , tmp1(A.block(0, 0).m()) - , tmp2(A.block(0, 0).m()) - {} + // Now on to the first equation. The right hand side of it is + // $B^TM^{-1}F-G$, which is what we compute in the first few lines. We + // then solve the first equation with a CG solver and the + // preconditioner we just declared. + const auto schur_rhs = transpose_operator(op_B) * op_M_inv * F - G; - void ApproximateSchurComplement::vmult(Vector & dst, - const Vector &src) const - { - system_matrix->block(0, 1).vmult(tmp1, src); - system_matrix->block(0, 0).precondition_Jacobi(tmp2, tmp1); - system_matrix->block(1, 0).vmult(dst, tmp2); - } + SolverControl solver_control_S(2000, 1.e-12); + SolverCG<> solver_S(solver_control_S); - // @sect4{MixedLaplace::solve} + const auto op_S_inv = inverse_operator(op_S, solver_S, preconditioner_S); - // After all these preparations, we can finally write the function that - // actually solves the linear problem. We will go through the two parts it - // has that each solve one of the two equations, the first one for the - // pressure (component 1 of the solution), then the velocities (component 0 - // of the solution). - template - void MixedLaplaceProblem::solve() - { - InverseMatrix> inverse_mass(system_matrix.block(0, 0)); - Vector tmp(solution.block(0).size()); + P = op_S_inv * schur_rhs; - // Now on to the first equation. The right hand side of it is - // $B^TM^{-1}F-G$, which is what we compute in the first few lines: - { - SchurComplement schur_complement(system_matrix, inverse_mass); - Vector schur_rhs(solution.block(1).size()); - inverse_mass.vmult(tmp, system_rhs.block(0)); - system_matrix.block(1, 0).vmult(schur_rhs, tmp); - schur_rhs -= system_rhs.block(1); - - // Now that we have the right hand side we can go ahead and solve for the - // pressure, using our approximation of the inverse as a preconditioner: - SolverControl solver_control(solution.block(1).size(), - 1e-12 * schur_rhs.l2_norm()); - SolverCG<> cg(solver_control); - - ApproximateSchurComplement approximate_schur(system_matrix); - InverseMatrix approximate_inverse( - approximate_schur); - cg.solve(schur_complement, - solution.block(1), - schur_rhs, - approximate_inverse); - - std::cout << solver_control.last_step() - << " CG Schur complement iterations to obtain convergence." - << std::endl; - } + std::cout << solver_control_S.last_step() + << " CG Schur complement iterations to obtain convergence." + << std::endl; // After we have the pressure, we can compute the velocity. The equation // reads $MU=-BP+F$, and we solve it by first computing the right hand // side, and then multiplying it with the object that represents the // inverse of the mass matrix: - { - system_matrix.block(0, 1).vmult(tmp, solution.block(1)); - tmp *= -1; - tmp += system_rhs.block(0); - inverse_mass.vmult(solution.block(0), tmp); - } + U = op_M_inv * (F - op_B * P); } From e2b7c60bcbde35ad934d38d29a30137f6a6a5d6e Mon Sep 17 00:00:00 2001 From: Matthias Maier Date: Fri, 8 Feb 2019 14:09:50 -0600 Subject: [PATCH 100/507] doc: add a changes entry --- doc/news/changes/major/20190208MatthiasMaier | 4 ++++ 1 file changed, 4 insertions(+) create mode 100644 doc/news/changes/major/20190208MatthiasMaier diff --git a/doc/news/changes/major/20190208MatthiasMaier b/doc/news/changes/major/20190208MatthiasMaier new file mode 100644 index 000000000000..b1cd3de01f22 --- /dev/null +++ b/doc/news/changes/major/20190208MatthiasMaier @@ -0,0 +1,4 @@ +Improved: The preconditioner and solver setup in step-20 has been rewritten +to highlight the new LinearOperator and PackagedOperation classes. +
+(2019/02/08, Matthias Maier) From 6836468408ed5ecfdc2c4ffd0336cce70a9dde55 Mon Sep 17 00:00:00 2001 From: Matthias Maier Date: Fri, 8 Feb 2019 14:36:08 -0600 Subject: [PATCH 101/507] remove unnecessary whitespace --- examples/step-20/step-20.cc | 5 ----- 1 file changed, 5 deletions(-) diff --git a/examples/step-20/step-20.cc b/examples/step-20/step-20.cc index 20ddcb621d42..7c6d13494ecb 100644 --- a/examples/step-20/step-20.cc +++ b/examples/step-20/step-20.cc @@ -596,7 +596,6 @@ namespace Step20 // Then, we will create corresponding LinearOperator objects and create // the op_M_inv operator: - const auto op_M = linear_operator(M); const auto op_B = linear_operator(B); @@ -611,7 +610,6 @@ namespace Step20 // This puts us in the position to be able to declare the Schur // complement op_S and the approximate Schur complement // op_aS: - const auto op_S = transpose_operator(op_B) * op_M_inv * op_B; const auto op_aS = transpose_operator(op_B) * linear_operator(preconditioner_M) * op_B; @@ -619,7 +617,6 @@ namespace Step20 // We now create a preconditioner out of op_aS that // applies a few number of CG iterations (until a very modest relative // reduction of $10^{-16}$ is reached): - ReductionControl reduction_control_aS(2000, 1.e-18, 1.0e-6); SolverCG<> solver_aS(reduction_control_aS); PreconditionIdentity preconditioner_aS; @@ -631,7 +628,6 @@ namespace Step20 // $B^TM^{-1}F-G$, which is what we compute in the first few lines. We // then solve the first equation with a CG solver and the // preconditioner we just declared. - const auto schur_rhs = transpose_operator(op_B) * op_M_inv * F - G; SolverControl solver_control_S(2000, 1.e-12); @@ -649,7 +645,6 @@ namespace Step20 // reads $MU=-BP+F$, and we solve it by first computing the right hand // side, and then multiplying it with the object that represents the // inverse of the mass matrix: - U = op_M_inv * (F - op_B * P); } From 3d625c92024b0b1e92e7d1be300d52f5e6294696 Mon Sep 17 00:00:00 2001 From: Matthias Maier Date: Fri, 8 Feb 2019 16:40:03 -0600 Subject: [PATCH 102/507] Address Martin's comments - Change preconditioner reduction to a relative tolerance of 10^-3 - Increase initial resolution to 5 global refinement steps - Update results section to reflect changes --- examples/step-20/doc/intro.dox | 4 ++-- examples/step-20/doc/results.dox | 35 ++++++++++++++++---------------- examples/step-20/step-20.cc | 8 ++++---- 3 files changed, 24 insertions(+), 23 deletions(-) diff --git a/examples/step-20/doc/intro.dox b/examples/step-20/doc/intro.dox index f090523b020d..2f3209618b80 100644 --- a/examples/step-20/doc/intro.dox +++ b/examples/step-20/doc/intro.dox @@ -554,8 +554,8 @@ complement matrix and the mass matrix, respectively. For example the right hand side of the first equation reads $B^TM^{-1}F-G$. This could be implemented as follows: @code - Vector schur_rhs (U.size()); - Vector tmp (P.size()); + Vector schur_rhs (P.size()); + Vector tmp (U.size()); op_M_inv.vmult (tmp, F); transpose_operator(op_B).vmult (schur_rhs, tmp); schur_rhs -= G; diff --git a/examples/step-20/doc/results.dox b/examples/step-20/doc/results.dox index 42dbf4517127..85700efea3e6 100644 --- a/examples/step-20/doc/results.dox +++ b/examples/step-20/doc/results.dox @@ -3,33 +3,34 @@

Output of the program and graphical visualization

-If we run the program as is, we get this output for the $8\times 8$ -mesh we use (for a total of 64 cells with 64 pressure degrees of -freedom since we use piecewise constants, and 144 velocities because +If we run the program as is, we get this output for the $32\times 32$ +mesh we use (for a total of 1024 cells with 1024 pressure degrees of +freedom since we use piecewise constants, and 2112 velocities because the Raviart-Thomas element defines one degree per freedom per face and -there are 72 faces parallel to the $x$-axis and the same number -parallel to the $y$-axis): +there are $1024 + 32 = 1056$ faces parallel to the $x$-axis and the same +number parallel to the $y$-axis): @verbatim \$ make run [ 66%] Built target \step-20 Scanning dependencies of target run [100%] Run \step-20 with Release configuration -Number of active cells: 64 -Total number of cells: 85 -Number of degrees of freedom: 208 (144+64) -15 CG Schur complement iterations to obtain convergence. -Errors: ||e_p||_L2 = 0.178055, ||e_u||_L2 = 0.0433435 +Number of active cells: 1024 +Total number of cells: 1365 +Number of degrees of freedom: 3136 (2112+1024) +24 CG Schur complement iterations to obtain convergence. +Errors: ||e_p||_L2 = 0.0445032, ||e_u||_L2 = 0.010826 [100%] Built target run @endverbatim -The fact that the number of iterations is so small, of course, is due to good -(but expensive!) preconditioner we have developed. To get confidence in the -solution, let us take a look at it. The following three images show (from left -to right) the x-velocity, the y-velocity, and the pressure: +The fact that the number of iterations is so small, of course, is due to +the good (but expensive!) preconditioner we have developed. To get +confidence in the solution, let us take a look at it. The following three +images show (from left to right) the x-velocity, the y-velocity, and the +pressure: - - - + + + diff --git a/examples/step-20/step-20.cc b/examples/step-20/step-20.cc index 7c6d13494ecb..2c4ef1733f02 100644 --- a/examples/step-20/step-20.cc +++ b/examples/step-20/step-20.cc @@ -327,7 +327,7 @@ namespace Step20 void MixedLaplaceProblem::make_grid_and_dofs() { GridGenerator::hyper_cube(triangulation, -1, 1); - triangulation.refine_global(3); + triangulation.refine_global(5); dof_handler.distribute_dofs(fe); @@ -615,9 +615,9 @@ namespace Step20 transpose_operator(op_B) * linear_operator(preconditioner_M) * op_B; // We now create a preconditioner out of op_aS that - // applies a few number of CG iterations (until a very modest relative - // reduction of $10^{-16}$ is reached): - ReductionControl reduction_control_aS(2000, 1.e-18, 1.0e-6); + // applies a few CG iterations (until a very modest relative reduction + // of $10^{-3}$ is reached): + ReductionControl reduction_control_aS(2000, 1.e-18, 1.0e-3); SolverCG<> solver_aS(reduction_control_aS); PreconditionIdentity preconditioner_aS; From 6c3aa3848b44d9405e05ca11064cf1de090f02ce Mon Sep 17 00:00:00 2001 From: Matthias Maier Date: Mon, 11 Feb 2019 18:27:15 -0600 Subject: [PATCH 103/507] Update discussion about preconditioner performance The numbers here were seriously outdated :-D (For example with a modern CPU the refinement step of 5 global refinement and lowest order elements converges nowadays in about 0.8 total runtime seconds instead of 28 seconds (0.4 seconds of thise total runtime is by the way the dynamic linker starting up the program...) --- examples/step-20/doc/intro.dox | 19 ++++++++++--------- 1 file changed, 10 insertions(+), 9 deletions(-) diff --git a/examples/step-20/doc/intro.dox b/examples/step-20/doc/intro.dox index 2f3209618b80..97bcb989cfaf 100644 --- a/examples/step-20/doc/intro.dox +++ b/examples/step-20/doc/intro.dox @@ -659,15 +659,16 @@ Obviously, applying this inverse of the approximate Schur complement is a very expensive preconditioner, almost as expensive as inverting the Schur complement itself. We can expect it to significantly reduce the number of outer iterations required for the Schur complement. In fact it does: in a -typical run on 5 times refined meshes using elements of order 0, the number of -outer iterations drops from 164 to 12. On the other hand, we now have to apply -a very expensive preconditioner 12 times. A better measure is therefore simply -the run-time of the program: on my laptop, it drops from 28 to 23 seconds for -this test case. That doesn't seem too impressive, but the savings become more -pronounced on finer meshes and with elements of higher order. For example, a -six times refined mesh and using elements of order 2 yields an improvement of -318 to 12 outer iterations, at a runtime of 338 seconds to 229 seconds. Not -earth shattering, but significant. +typical run on 7 times refined meshes using elements of order 0, the number of +outer iterations drops from 592 to 25. On the other hand, we now have to apply +a very expensive preconditioner 25 times. A better measure is therefore simply +the run-time of the program: on a current laptop (as of January 2019), it +drops from 3.57 to 2.48 seconds for this test case. That doesn't seem too +impressive, but the savings become more pronounced on finer meshes and with +elements of higher order. For example, an seven times refined mesh and +using elements of order 2 (which amounts to about 0.4 million degrees of +freedom) yields an improvement of 1134 to 28 outer iterations, at a runtime +of 168 seconds to 78 seconds. Not earth shattering, but significant.

Definition of the test case

From c09b8083217dbf2a06ba4af9b6223a45f3218bed Mon Sep 17 00:00:00 2001 From: Matthias Maier Date: Mon, 11 Feb 2019 18:42:10 -0600 Subject: [PATCH 104/507] Address Wolfgang's comments - fix wording - remove author statement (the generic copyright is enough). --- examples/step-20/doc/intro.dox | 36 +++++++++++++++++++++------------- examples/step-20/step-20.cc | 15 +++++--------- 2 files changed, 27 insertions(+), 24 deletions(-) diff --git a/examples/step-20/doc/intro.dox b/examples/step-20/doc/intro.dox index 97bcb989cfaf..7a836f0edf1f 100644 --- a/examples/step-20/doc/intro.dox +++ b/examples/step-20/doc/intro.dox @@ -384,7 +384,8 @@ the system. We note that the resulting solver is not optimal -- there are much better ways to efficiently compute the system, for example those explained in the results section of step-22 or the one we use in step-43 for a problem similar to the current one. Here, our goal shall be to -introduce new solution techniques how they can be implemented in deal.II. +introduce new solution techniques and how they can be implemented in +deal.II.

Solving using the Schur complement

@@ -494,8 +495,8 @@ factor (here, $10^{-10}$). In contrast the SolverControl class only checks for absolute tolerances. We have to use ReductionControl in our case to work around a minor issue: The right hand sides that we will feed to op_M_inv are essentially formed by residuals that naturally -have vastly differing norms. This makes control by an absolute tolerance -very error prone. +decrease vastly in norm as the outer iterations progress. This makes +control by an absolute tolerance very error prone. We now have a LinearOperator op_M_inv that we can use to construct more complicated operators such as the Schur complement $S$. @@ -515,7 +516,11 @@ similar to the following code: solver_M(M, tmp2, tmp1, preconditioner_M); // multiply with M^-1 B.Tvmult (dst, tmp2); // multiply with the bottom left block: B^T @endcode -(tmp1 and tmp2 are two temporary vectors). +(tmp1 and tmp2 are two temporary vectors). The +key point behind this approach is the fact that we never actually create an +inner product of matrices. Instead, whenever we have to perform a matrix +vector multiplication with op_S we simply run all individual +vmult operations in above sequence. @note We could have achieved the same goal of creating a "matrix like" object by implementing a specialized class SchurComplement @@ -539,9 +544,11 @@ class SchurComplement @endcode Even though both approaches are exactly equivalent, the LinearOperator class has a big advantage over this manual approach. -It provides so-called syntactic sugar: Mathematically, we think -about $S$ as being the composite matrix $S=B^TM^{-1}B$ and the -LinearOperator class allows you to write this out more or less verbatim, +It provides so-called +syntactic sugar: +Mathematically, we think about $S$ as being the composite matrix +$S=B^TM^{-1}B$ and the LinearOperator class allows you to write this out +more or less verbatim, @code const auto op_M_inv = inverse_operator(op_M, solver_M, preconditioner_M); const auto op_S = transpose_operator(op_B) * op_M_inv * op_B; @@ -570,13 +577,14 @@ us. Similarly in spirit to LinearOperator, a PackagedOperation stores a std::function apply; std::function apply_add; @endcode -The class allows lazy evaluation of expressions involving vectors and -linear operators. This is done by storing the computational expression and -only performing the computation when either the object is converted to a -vector object, or PackagedOperation::apply() (or -PackagedOperation::apply_add()) is invoked by hand. Assuming that -F and G are the two vectors of the right hand -side we can simply write: +The class allows +lazy evaluation +of expressions involving vectors and linear operators. This is done by +storing the computational expression and only performing the computation +when either the object is converted to a vector object, or +PackagedOperation::apply() (or PackagedOperation::apply_add()) is invoked +by hand. Assuming that F and G are the two +vectors of the right hand side we can simply write: @code const auto schur_rhs = transpose_operator(op_B) * op_M_inv * F - G; @endcode diff --git a/examples/step-20/step-20.cc b/examples/step-20/step-20.cc index 2c4ef1733f02..5879d3b6a1f9 100644 --- a/examples/step-20/step-20.cc +++ b/examples/step-20/step-20.cc @@ -1,6 +1,6 @@ /* --------------------------------------------------------------------- * - * Copyright (C) 2005 - 2018 by the deal.II authors + * Copyright (C) 2005 - 2019 by the deal.II authors * * This file is part of the deal.II library. * @@ -12,10 +12,6 @@ * the top level directory of deal.II. * * --------------------------------------------------------------------- - - * - * Authors: Wolfgang Bangerth, Texas A&M University, 2005, 2006; - * (port to LinearOperator:) Matthias Maier, 2019 */ @@ -607,16 +603,15 @@ namespace Step20 const auto op_M_inv = inverse_operator(op_M, solver_M, preconditioner_M); - // This puts us in the position to be able to declare the Schur - // complement op_S and the approximate Schur complement - // op_aS: + // This allows us to declare the Schur complement op_S and + // the approximate Schur complement op_aS: const auto op_S = transpose_operator(op_B) * op_M_inv * op_B; const auto op_aS = transpose_operator(op_B) * linear_operator(preconditioner_M) * op_B; // We now create a preconditioner out of op_aS that - // applies a few CG iterations (until a very modest relative reduction - // of $10^{-3}$ is reached): + // applies a small number of CG iterations (until a very modest + // relative reduction of $10^{-3}$ is reached): ReductionControl reduction_control_aS(2000, 1.e-18, 1.0e-3); SolverCG<> solver_aS(reduction_control_aS); PreconditionIdentity preconditioner_aS; From 8443f7fe715e0a6f44e87e0cb2f4bc10ff2dc3b6 Mon Sep 17 00:00:00 2001 From: Matthias Maier Date: Mon, 11 Feb 2019 18:46:19 -0600 Subject: [PATCH 105/507] Address J.-P.'s comments --- examples/step-20/doc/intro.dox | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/examples/step-20/doc/intro.dox b/examples/step-20/doc/intro.dox index 7a836f0edf1f..844507e93f30 100644 --- a/examples/step-20/doc/intro.dox +++ b/examples/step-20/doc/intro.dox @@ -605,6 +605,10 @@ creating another solver and inverse: U = op_M_inv * (F - op_B * P); @endcode +@note The functionality that we developed in this example step by hand is +already readily available in the library. Have a look at +schur_complement(), condense_schur_rhs(), and postprocess_schur_solution(). +

A preconditioner for the Schur complement

From 20e6c36535105ed10156388384573eaf51b29d94 Mon Sep 17 00:00:00 2001 From: Matthias Maier Date: Mon, 11 Feb 2019 18:53:20 -0600 Subject: [PATCH 106/507] examples/step-22: adjust sizes of pictures showing result --- examples/step-20/doc/results.dox | 10 +++++++--- 1 file changed, 7 insertions(+), 3 deletions(-) diff --git a/examples/step-20/doc/results.dox b/examples/step-20/doc/results.dox index 85700efea3e6..573fe46f9f09 100644 --- a/examples/step-20/doc/results.dox +++ b/examples/step-20/doc/results.dox @@ -28,9 +28,13 @@ confidence in the solution, let us take a look at it. The following three images show (from left to right) the x-velocity, the y-velocity, and the pressure: - - - + + + + + + +
From 42021d3a02ff37efd241e0b77b1ebd05bb01daa8 Mon Sep 17 00:00:00 2001 From: Bruno Turcksin Date: Fri, 8 Feb 2019 14:36:02 +0000 Subject: [PATCH 107/507] Change API of a few functions cuda_kernel for consistency --- include/deal.II/base/partitioner.templates.h | 2 +- include/deal.II/lac/cuda_kernels.h | 14 ++-- include/deal.II/lac/cuda_kernels.templates.h | 14 ++-- .../lac/la_parallel_vector.templates.h | 6 +- source/lac/cuda_kernels.cu | 64 +++++++++---------- 5 files changed, 50 insertions(+), 50 deletions(-) diff --git a/include/deal.II/base/partitioner.templates.h b/include/deal.II/base/partitioner.templates.h index 7ccedad7379a..582034a7bc35 100644 --- a/include/deal.II/base/partitioner.templates.h +++ b/include/deal.II/base/partitioner.templates.h @@ -161,8 +161,8 @@ namespace Utilities ::dealii::LinearAlgebra::CUDAWrappers::kernel:: gather<<>>( temp_array_ptr, - locally_owned_array.data(), import_indices_plain_dev[i].first.get(), + locally_owned_array.data(), import_indices_plain_dev[i].second); } else diff --git a/include/deal.II/lac/cuda_kernels.h b/include/deal.II/lac/cuda_kernels.h index 20c5c361ec33..963a9461702a 100644 --- a/include/deal.II/lac/cuda_kernels.h +++ b/include/deal.II/lac/cuda_kernels.h @@ -451,12 +451,12 @@ namespace LinearAlgebra * * @ingroup CUDAWrappers */ - template + template __global__ void - set_permutated(Number * val, + set_permutated(const IndexType *indices, + Number * val, const Number * v, - const size_type *indices, - const size_type N); + const IndexType N); @@ -469,8 +469,8 @@ namespace LinearAlgebra template __global__ void gather(Number * val, - const Number * v, const IndexType *indices, + const Number * v, const IndexType N); @@ -483,9 +483,9 @@ namespace LinearAlgebra */ template __global__ void - add_permutated(Number * val, + add_permutated(const size_type *indices, + Number * val, const Number * v, - const size_type *indices, const size_type N); } // namespace kernel } // namespace CUDAWrappers diff --git a/include/deal.II/lac/cuda_kernels.templates.h b/include/deal.II/lac/cuda_kernels.templates.h index 5d196ddc5cfc..cd522131ba9c 100644 --- a/include/deal.II/lac/cuda_kernels.templates.h +++ b/include/deal.II/lac/cuda_kernels.templates.h @@ -533,12 +533,12 @@ namespace LinearAlgebra - template + template __global__ void - set_permutated(Number * val, + set_permutated(const IndexType *indices, + Number * val, const Number * v, - const size_type *indices, - const size_type N) + const IndexType N) { const size_type idx_base = threadIdx.x + blockIdx.x * (blockDim.x * chunk_size); @@ -555,8 +555,8 @@ namespace LinearAlgebra template __global__ void gather(Number * val, - const Number * v, const IndexType *indices, + const Number * v, const IndexType N) { const IndexType idx_base = @@ -573,9 +573,9 @@ namespace LinearAlgebra template __global__ void - add_permutated(Number * val, + add_permutated(const size_type *indices, + Number * val, const Number * v, - const size_type *indices, const size_type N) { const size_type idx_base = diff --git a/include/deal.II/lac/la_parallel_vector.templates.h b/include/deal.II/lac/la_parallel_vector.templates.h index ae0ec7c9612a..b2e890c30ee5 100644 --- a/include/deal.II/lac/la_parallel_vector.templates.h +++ b/include/deal.II/lac/la_parallel_vector.templates.h @@ -301,7 +301,7 @@ namespace LinearAlgebra ::dealii::CUDAWrappers::block_size); ::dealii::LinearAlgebra::CUDAWrappers::kernel::set_permutated <<>>( - tmp_vector.begin(), V_dev, indices_dev, n_elements); + indices_dev, tmp_vector.begin(), V_dev, n_elements); tmp_vector.compress(operation); @@ -319,16 +319,16 @@ namespace LinearAlgebra if (operation == VectorOperation::add) ::dealii::LinearAlgebra::CUDAWrappers::kernel::add_permutated< Number><<>>( + indices_dev, data.values_dev.get(), tmp_vector.begin(), - indices_dev, tmp_n_elements); else ::dealii::LinearAlgebra::CUDAWrappers::kernel::set_permutated< Number><<>>( + indices_dev, data.values_dev.get(), tmp_vector.begin(), - indices_dev, tmp_n_elements); ::dealii::Utilities::CUDA::free(indices_dev); diff --git a/source/lac/cuda_kernels.cu b/source/lac/cuda_kernels.cu index 317399c74d42..a1c83d59352d 100644 --- a/source/lac/cuda_kernels.cu +++ b/source/lac/cuda_kernels.cu @@ -94,12 +94,12 @@ namespace LinearAlgebra const float * V_val, const size_type N); template __global__ void - equ(float * val, - const float a, - const float * V_val, - const float b, - const float * W_val, - const size_type N); + equ(float * val, + const float a, + const float * V_val, + const float b, + const float * W_val, + const size_type N); template __global__ void add_and_dot(float * res, float * v1, @@ -110,19 +110,19 @@ namespace LinearAlgebra template __global__ void set(float *val, const float s, const size_type N); template __global__ void - set_permutated(float * val, - const float * v, - const size_type *indices, - const size_type N); + set_permutated(const size_type *indices, + float * val, + const float * v, + const size_type N); template __global__ void - gather(float * val, - const float * v, - const size_type *indices, - const size_type N); + gather(float * val, + const size_type *indices, + const float * v, + const size_type N); template __global__ void - add_permutated(float * val, + add_permutated(const size_type *indices, + float * val, const float * v, - const size_type *indices, const size_type N); @@ -194,12 +194,12 @@ namespace LinearAlgebra const double * V_val, const size_type N); template __global__ void - equ(double * val, - const double a, - const double * V_val, - const double b, - const double * W_val, - const size_type N); + equ(double * val, + const double a, + const double * V_val, + const double b, + const double * W_val, + const size_type N); template __global__ void add_and_dot(double * res, double * v1, @@ -210,19 +210,19 @@ namespace LinearAlgebra template __global__ void set(double *val, const double s, const size_type N); template __global__ void - set_permutated(double * val, - const double * v, - const size_type *indices, - const size_type N); + set_permutated(const size_type *indices, + double * val, + const double * v, + const size_type N); template __global__ void - gather(double * val, - const double * v, - const size_type *indices, - const size_type N); + gather(double * val, + const size_type *indices, + const double * v, + const size_type N); template __global__ void - add_permutated(double * val, + add_permutated(const size_type *indices, + double * val, const double * v, - const size_type *indices, const size_type N); } // namespace kernel } // namespace CUDAWrappers From 17a59dbcc69f88d87e048c515cd276619671f7b3 Mon Sep 17 00:00:00 2001 From: Bruno Turcksin Date: Fri, 8 Feb 2019 14:44:36 +0000 Subject: [PATCH 108/507] Move initialization of import_indices_plain_dev into a separate function --- include/deal.II/base/partitioner.h | 7 ++++ include/deal.II/base/partitioner.templates.h | 44 ++------------------ source/base/partitioner.cu | 44 ++++++++++++++++++++ 3 files changed, 54 insertions(+), 41 deletions(-) diff --git a/include/deal.II/base/partitioner.h b/include/deal.II/base/partitioner.h index 2c0db0955f33..c98454dcbec5 100644 --- a/include/deal.II/base/partitioner.h +++ b/include/deal.II/base/partitioner.h @@ -571,6 +571,13 @@ namespace Utilities << " elements for this partitioner."); private: + /** + * Initialize import_indices_plain_dev from import_indices_data. This + * function is only used when using CUDA-aware MPI. + */ + void + initialize_import_indices_plain_dev() const; + /** * The global size of the vector over all processors */ diff --git a/include/deal.II/base/partitioner.templates.h b/include/deal.II/base/partitioner.templates.h index 582034a7bc35..48432cfcbc5f 100644 --- a/include/deal.II/base/partitioner.templates.h +++ b/include/deal.II/base/partitioner.templates.h @@ -105,47 +105,9 @@ namespace Utilities // performance reasons as this can significantly decrease the number of // kernel launched. The indices are expanded the first time the function // is called. - if (std::is_same::value) - { - if (import_indices_plain_dev.size() == 0) - { - import_indices_plain_dev.reserve(n_import_targets); - for (unsigned int i = 0; i < n_import_targets; i++) - { - // Expand the indices on the host - std::vector>:: - const_iterator my_imports = - import_indices_data.begin() + - import_indices_chunks_by_rank_data[i], - end_my_imports = - import_indices_data.begin() + - import_indices_chunks_by_rank_data[i + 1]; - std::vector import_indices_plain_host; - for (; my_imports != end_my_imports; ++my_imports) - { - const unsigned int chunk_size = - my_imports->second - my_imports->first; - for (unsigned int j = 0; j < chunk_size; ++j) - import_indices_plain_host.push_back(my_imports->first + - j); - } - - // Move the indices to the device - import_indices_plain_dev.emplace_back(std::make_pair( - std::unique_ptr( - nullptr, - Utilities::CUDA::delete_device_data), - import_indices_plain_host.size())); - - import_indices_plain_dev[i].first.reset( - Utilities::CUDA::allocate_device_data( - import_indices_plain_dev[i].second)); - Utilities::CUDA::copy_to_dev( - import_indices_plain_host, - import_indices_plain_dev[i].first.get()); - } - } - } + if ((std::is_same::value) && + (import_indices_plain_dev.size() == 0)) + initialize_import_indices_plain_dev(); # endif for (unsigned int i = 0; i < n_import_targets; i++) diff --git a/source/base/partitioner.cu b/source/base/partitioner.cu index ed02193e8914..4788e7571d01 100644 --- a/source/base/partitioner.cu +++ b/source/base/partitioner.cu @@ -18,6 +18,50 @@ DEAL_II_NAMESPACE_OPEN + + +namespace Utilities +{ + namespace MPI + { + void + Partitioner::initialize_import_indices_plain_dev() const + { + const unsigned int n_import_targets = import_targets_data.size(); + import_indices_plain_dev.reserve(n_import_targets); + for (unsigned int i = 0; i < n_import_targets; i++) + { + // Expand the indices on the host + std::vector>::const_iterator + my_imports = import_indices_data.begin() + + import_indices_chunks_by_rank_data[i], + end_my_imports = import_indices_data.begin() + + import_indices_chunks_by_rank_data[i + 1]; + std::vector import_indices_plain_host; + for (; my_imports != end_my_imports; ++my_imports) + { + const unsigned int chunk_size = + my_imports->second - my_imports->first; + for (unsigned int j = 0; j < chunk_size; ++j) + import_indices_plain_host.push_back(my_imports->first + j); + } + + // Move the indices to the device + import_indices_plain_dev.emplace_back(std::make_pair( + std::unique_ptr( + nullptr, Utilities::CUDA::delete_device_data), + import_indices_plain_host.size())); + + import_indices_plain_dev[i].first.reset( + Utilities::CUDA::allocate_device_data( + import_indices_plain_dev[i].second)); + Utilities::CUDA::copy_to_dev(import_indices_plain_host, + import_indices_plain_dev[i].first.get()); + } + } + } // namespace MPI +} // namespace Utilities + // explicit instantiations from .templates.h file #include "partitioner.cuda.inst" From 5cb0fe6b2dcc72ded68ec91519e388382c184fe0 Mon Sep 17 00:00:00 2001 From: Bruno Turcksin Date: Fri, 8 Feb 2019 14:47:25 +0000 Subject: [PATCH 109/507] Add new cuda kernel function to execute a binary operation on a subset of the vector --- include/deal.II/lac/cuda_kernels.h | 17 +++++++++++++++++ include/deal.II/lac/cuda_kernels.templates.h | 18 ++++++++++++++++++ source/lac/cuda_kernels.cu | 20 ++++++++++++++++++++ 3 files changed, 55 insertions(+) diff --git a/include/deal.II/lac/cuda_kernels.h b/include/deal.II/lac/cuda_kernels.h index 963a9461702a..c3470a5749d9 100644 --- a/include/deal.II/lac/cuda_kernels.h +++ b/include/deal.II/lac/cuda_kernels.h @@ -181,6 +181,23 @@ namespace LinearAlgebra + /** + * Apply the functor @tparam Binop to the elements of @p v1 that have + * indices in @p mask and @p v2. The size of @p mask should be greater + * than the size of @p v1. @p mask and @p v2 should have the same size @p + * N. + * + * @ingroup CUDAWrappers + */ + template class Binop> + __global__ void + masked_vector_bin_op(const unsigned int *mask, + Number * v1, + const Number * v2, + const size_type N); + + + /** * Structure implementing the functions used to add elements when * using a reduction. diff --git a/include/deal.II/lac/cuda_kernels.templates.h b/include/deal.II/lac/cuda_kernels.templates.h index cd522131ba9c..cadeb4d11a39 100644 --- a/include/deal.II/lac/cuda_kernels.templates.h +++ b/include/deal.II/lac/cuda_kernels.templates.h @@ -60,6 +60,24 @@ namespace LinearAlgebra + template class Binop> + __global__ void + masked_vector_bin_op(const unsigned int *mask, + Number * v1, + const Number * v2, + const size_type N) + { + const size_type idx_base = + threadIdx.x + blockIdx.x * (blockDim.x * chunk_size); + for (unsigned int i = 0; i < chunk_size; ++i) + { + const size_type idx = idx_base + i * block_size; + if (idx < N) + v1[mask[idx]] = Binop::operation(v1[mask[idx]], v2[idx]); + } + } + + template __device__ Number ElemSum::reduction_op(const Number a, const Number b) diff --git a/source/lac/cuda_kernels.cu b/source/lac/cuda_kernels.cu index a1c83d59352d..c7bfb9b020e3 100644 --- a/source/lac/cuda_kernels.cu +++ b/source/lac/cuda_kernels.cu @@ -37,6 +37,16 @@ namespace LinearAlgebra vector_bin_op(float * v1, const float * v2, const size_type N); + template __global__ void + masked_vector_bin_op(const unsigned int *mask, + float * v1, + const float * v2, + const size_type N); + template __global__ void + masked_vector_bin_op(const unsigned int *mask, + float * v1, + const float * v2, + const size_type N); template struct ElemSum; template struct L1Norm; template struct LInfty; @@ -137,6 +147,16 @@ namespace LinearAlgebra vector_bin_op(double * v1, const double * v2, const size_type N); + template __global__ void + masked_vector_bin_op(const unsigned int *mask, + double * v1, + const double * v2, + const size_type N); + template __global__ void + masked_vector_bin_op(const unsigned int *mask, + double * v1, + const double * v2, + const size_type N); template struct ElemSum; template struct L1Norm; template struct LInfty; From 55026d64f095b6214e9b8635ab83c427345c3758 Mon Sep 17 00:00:00 2001 From: Bruno Turcksin Date: Fri, 8 Feb 2019 14:49:12 +0000 Subject: [PATCH 110/507] Improve compress when using CUDA-aware MPI Reduce the number of kernel launch in a way similar to what is done for update_ghost. --- include/deal.II/base/partitioner.templates.h | 128 +++++++++++-------- 1 file changed, 76 insertions(+), 52 deletions(-) diff --git a/include/deal.II/base/partitioner.templates.h b/include/deal.II/base/partitioner.templates.h index 48432cfcbc5f..4d4b55108dc8 100644 --- a/include/deal.II/base/partitioner.templates.h +++ b/include/deal.II/base/partitioner.templates.h @@ -530,6 +530,18 @@ namespace Utilities const unsigned int n_import_targets = import_targets_data.size(); const unsigned int n_ghost_targets = ghost_targets_data.size(); +# if (defined(DEAL_II_COMPILER_CUDA_AWARE) && \ + defined(DEAL_II_WITH_CUDA_AWARE_MPI)) + // When using CUDAs-aware MPI, the set of local indices that are ghosts + // indices on other processors is expanded in arrays. This is for + // performance reasons as this can significantly decrease the number of + // kernel launched. The indices are expanded the first time the function + // is called. + if ((std::is_same::value) && + (import_indices_plain_dev.size() == 0)) + initialize_import_indices_plain_dev(); +# endif + if (vector_operation != dealii::VectorOperation::insert) AssertDimension(n_ghost_targets + n_import_targets, requests.size()); // first wait for the receive to complete @@ -595,70 +607,82 @@ namespace Utilities # else if (vector_operation == dealii::VectorOperation::add) { - for (const auto &import_range : import_indices_data) + for (auto const &import_indices_plain : import_indices_plain_dev) { - const auto chunk_size = - import_range.second - import_range.first; + const auto chunk_size = import_indices_plain.second; const int n_blocks = 1 + (chunk_size - 1) / (::dealii::CUDAWrappers::chunk_size * ::dealii::CUDAWrappers::block_size); - dealii::LinearAlgebra::CUDAWrappers::kernel::vector_bin_op< - Number, - dealii::LinearAlgebra::CUDAWrappers::kernel::Binop_Addition> + dealii::LinearAlgebra::CUDAWrappers::kernel:: + masked_vector_bin_op <<>>( - locally_owned_array.data() + import_range.first, + import_indices_plain.first.get(), + locally_owned_array.data(), read_position, chunk_size); read_position += chunk_size; } } else if (vector_operation == dealii::VectorOperation::min) - for (const auto &import_range : import_indices_data) - { - const auto chunk_size = - import_range.second - import_range.first; - const int n_blocks = - 1 + (chunk_size - 1) / (::dealii::CUDAWrappers::chunk_size * - ::dealii::CUDAWrappers::block_size); - dealii::LinearAlgebra::CUDAWrappers::kernel::vector_bin_op< - Number, - dealii::LinearAlgebra::CUDAWrappers::kernel::Binop_Min> - <<>>( - locally_owned_array.data() + import_range.first, - read_position, - chunk_size); - read_position += chunk_size; - } + { + for (auto const &import_indices_plain : import_indices_plain_dev) + { + const auto chunk_size = import_indices_plain.second; + const int n_blocks = + 1 + (chunk_size - 1) / (::dealii::CUDAWrappers::chunk_size * + ::dealii::CUDAWrappers::block_size); + dealii::LinearAlgebra::CUDAWrappers::kernel:: + masked_vector_bin_op< + Number, + dealii::LinearAlgebra::CUDAWrappers::kernel::Binop_Min> + <<>>( + import_indices_plain.first.get(), + locally_owned_array.data(), + read_position, + chunk_size); + read_position += chunk_size; + } + } else if (vector_operation == dealii::VectorOperation::max) - for (const auto &import_range : import_indices_data) - { - const auto chunk_size = - import_range.second - import_range.first; - const int n_blocks = - 1 + (chunk_size - 1) / (::dealii::CUDAWrappers::chunk_size * - ::dealii::CUDAWrappers::block_size); - dealii::LinearAlgebra::CUDAWrappers::kernel::vector_bin_op< - Number, - dealii::LinearAlgebra::CUDAWrappers::kernel::Binop_Max> - <<>>( - locally_owned_array.data() + import_range.first, - read_position, - chunk_size); - read_position += chunk_size; - } - else // TODO - for (const auto &import_range : import_indices_data) - { - const auto chunk_size = - import_range.second - import_range.first; - const cudaError_t cuda_error_code = - cudaMemcpy(locally_owned_array.data() + import_range.first, - read_position, - chunk_size * sizeof(Number), - cudaMemcpyDeviceToDevice); - AssertCuda(cuda_error_code); - read_position += chunk_size; - } + { + for (auto const &import_indices_plain : import_indices_plain_dev) + { + const auto chunk_size = import_indices_plain.second; + const int n_blocks = + 1 + (chunk_size - 1) / (::dealii::CUDAWrappers::chunk_size * + ::dealii::CUDAWrappers::block_size); + dealii::LinearAlgebra::CUDAWrappers::kernel:: + masked_vector_bin_op< + Number, + dealii::LinearAlgebra::CUDAWrappers::kernel::Binop_Max> + <<>>( + import_indices_plain.first.get(), + locally_owned_array.data(), + read_position, + chunk_size); + read_position += chunk_size; + } + } + else + { + for (auto const &import_indices_plain : import_indices_plain_dev) + { + const auto chunk_size = import_indices_plain.second; + const int n_blocks = + 1 + (chunk_size - 1) / (::dealii::CUDAWrappers::chunk_size * + ::dealii::CUDAWrappers::block_size); + dealii::LinearAlgebra::CUDAWrappers::kernel:: + set_permutated<<>>( + import_indices_plain.first.get(), + locally_owned_array.data(), + read_position, + chunk_size); + read_position += chunk_size; + } + } # endif AssertDimension(read_position - temporary_storage.data(), n_import_indices()); From 6dd31bf3b49e405dce3c4f66e85d575cccd24b25 Mon Sep 17 00:00:00 2001 From: Matthias Maier Date: Tue, 12 Feb 2019 00:19:47 -0600 Subject: [PATCH 111/507] examples/step-20: Change preconditioner to a fixed number of iterations This improves the total runtime performance with preconditioner significantly! (Even though the total number of iterations increases significantly.) --- examples/step-20/doc/intro.dox | 27 ++++++++++++++++++--------- examples/step-20/step-20.cc | 9 ++++----- 2 files changed, 22 insertions(+), 14 deletions(-) diff --git a/examples/step-20/doc/intro.dox b/examples/step-20/doc/intro.dox index 844507e93f30..773141dfcc73 100644 --- a/examples/step-20/doc/intro.dox +++ b/examples/step-20/doc/intro.dox @@ -654,12 +654,21 @@ with $M$ is defined: it is the multiplication with the inverse of the diagonal of $M$; in other words, the operation $({\textrm{diag}\ }M)^{-1}x$ on a vector $x$ is exactly what PreconditionJacobi does.) -With all this, we nearly already have the preconditioner: it should be the -inverse of the approximate Schur complement. We implement this again with -the inverse_operator() function +With all this we almost have the preconditioner completed: it should be the +inverse of the approximate Schur complement. We implement this again by +creating a linear operator with inverse_operator() function. This time +however we would like to choose a relatively modest tolerance for the CG +solver (that inverts op_aS). The reasoning is that +op_aS is only coarse approximation to op_S, so we +actually do not need to invert it exactly. This, however creates a subtle +problem: preconditioner_S will be used in the final outer CG +iteration to create an orthogonal basis. But for this to work, it must be +precisely the same linear operation for every invocation. We ensure this by +using an IterationNumberControl that allows us to fix the number of CG +iterations that are performed to a fixed small number (in our case 30): @code - ReductionControl reduction_control_aS(2000, 1.e-18, 1.0e-6); - SolverCG<> solver_aS(reduction_control_aS); + IterationNumberControl iteration_number_control_aS(30, 1.e-18); + SolverCG<> solver_aS(iteration_number_control_aS); PreconditionIdentity preconditioner_aS; const auto preconditioner_S = inverse_operator(op_aS, solver_aS, preconditioner_aS); @@ -672,15 +681,15 @@ expensive preconditioner, almost as expensive as inverting the Schur complement itself. We can expect it to significantly reduce the number of outer iterations required for the Schur complement. In fact it does: in a typical run on 7 times refined meshes using elements of order 0, the number of -outer iterations drops from 592 to 25. On the other hand, we now have to apply +outer iterations drops from 592 to 39. On the other hand, we now have to apply a very expensive preconditioner 25 times. A better measure is therefore simply the run-time of the program: on a current laptop (as of January 2019), it -drops from 3.57 to 2.48 seconds for this test case. That doesn't seem too +drops from 3.57 to 2.05 seconds for this test case. That doesn't seem too impressive, but the savings become more pronounced on finer meshes and with elements of higher order. For example, an seven times refined mesh and using elements of order 2 (which amounts to about 0.4 million degrees of -freedom) yields an improvement of 1134 to 28 outer iterations, at a runtime -of 168 seconds to 78 seconds. Not earth shattering, but significant. +freedom) yields an improvement of 1134 to 83 outer iterations, at a runtime +of 168 seconds to 40 seconds. Not earth shattering, but significant.

Definition of the test case

diff --git a/examples/step-20/step-20.cc b/examples/step-20/step-20.cc index 5879d3b6a1f9..f1b12f6e185d 100644 --- a/examples/step-20/step-20.cc +++ b/examples/step-20/step-20.cc @@ -610,11 +610,10 @@ namespace Step20 transpose_operator(op_B) * linear_operator(preconditioner_M) * op_B; // We now create a preconditioner out of op_aS that - // applies a small number of CG iterations (until a very modest - // relative reduction of $10^{-3}$ is reached): - ReductionControl reduction_control_aS(2000, 1.e-18, 1.0e-3); - SolverCG<> solver_aS(reduction_control_aS); - PreconditionIdentity preconditioner_aS; + // applies a fixed number of 30 (inexpensive) CG iterations: + IterationNumberControl iteration_number_control_aS(30, 1.e-18); + SolverCG<> solver_aS(iteration_number_control_aS); + PreconditionIdentity preconditioner_aS; const auto preconditioner_S = inverse_operator(op_aS, solver_aS, preconditioner_aS); From 8a6f81ce9302d587b878abcdf390dd42b72e8fad Mon Sep 17 00:00:00 2001 From: Martin Kronbichler Date: Thu, 7 Feb 2019 12:23:56 +0100 Subject: [PATCH 112/507] Clean up iteration of PreconditionChebyshev. --- include/deal.II/lac/precondition.h | 523 ++++++++++++++++------------- 1 file changed, 284 insertions(+), 239 deletions(-) diff --git a/include/deal.II/lac/precondition.h b/include/deal.II/lac/precondition.h index be50dd34a702..94ecb0e76f65 100644 --- a/include/deal.II/lac/precondition.h +++ b/include/deal.II/lac/precondition.h @@ -871,13 +871,26 @@ class PreconditionPSOR : public PreconditionRelaxation * matrices. This preconditioner is based on an iteration of an inner * preconditioner of type @p PreconditionerType with coefficients that are * adapted to optimally cover an eigenvalue range between the largest - * eigenvalue down to a given lower eigenvalue specified by the optional - * parameter @p smoothing_range. The typical use case for the preconditioner - * is a Jacobi preconditioner specified through DiagonalMatrix, which is also - * the default value for the preconditioner. Note that if the degree variable - * is set to zero, the Chebyshev iteration corresponds to a Jacobi - * preconditioner (or the underlying preconditioner type) with relaxation - * parameter according to the specified smoothing range. + * eigenvalue $\lambda_{\max{}}$ down to a given lower eigenvalue + * $\lambda_{\min{}}$ specified by the optional parameter + * @p smoothing_range. The algorithm is based on the following three-term + * recurrence: + * @f[ + * x^{n+1} = x^{n} + \rho_n \rho_{n-1} (x^{n} - x^{n-1}) + + * \frac{\rho_n}{\lambda_{\max{}}-\lambda_{\min{}}} P^{-1} (b-Ax^n). + * @f] + * where the parameter $rho_0$ is set to $rho_0 = + * \frac{\lambda_{\max{}}-\lambda_{\min{}}}{\lambda_{\max{}}+\lambda_{\min{}}}$ + * for the maximal eigenvalue $\lambda_{\max{}}$ and updated via $\rho_n = + * \left(2\frac{\lambda_{\max{}}+\lambda_{\min{}}} + * {\lambda_{\max{}}-\lambda_{\min{}}} - \rho_{n-1}\right)^{-1}$. + * + * The typical use case for the preconditioner is a Jacobi preconditioner + * specified through DiagonalMatrix, which is also the default value for the + * preconditioner. Note that if the degree variable is set to zero, the + * Chebyshev iteration corresponds to a Jacobi preconditioner (or the + * underlying preconditioner type) with relaxation parameter according to the + * specified smoothing range. * * Besides the default choice of a pointwise Jacobi preconditioner, this class * also allows for more advanced types of preconditioners, for example @@ -895,11 +908,13 @@ class PreconditionPSOR : public PreconditionRelaxation * The Chebyshev method relies on an estimate of the eigenvalues of the matrix * which are computed during the first invocation of vmult(). The algorithm * invokes a conjugate gradient solver so symmetry and positive definiteness - * of the (preconditioned) matrix system are strong requirements. The - * computation of eigenvalues needs to be deferred until the first vmult() - * invocation because temporary vectors of the same layout as the source and - * destination vectors are necessary for these computations and this - * information gets only available through vmult(). + * of the (preconditioned) matrix system are strong requirements. As a + * consequence, this class only makes sense if it is applied repeatedly, + * e.g. in a smoother for a multigrid algorithm. The computation of + * eigenvalues needs to be deferred until the first vmult() invocation because + * temporary vectors of the same layout as the source and destination vectors + * are necessary for these computations and this information gets only + * available through vmult(). * * The estimation of eigenvalues can also be bypassed by setting * PreconditionChebyshev::AdditionalData::eig_cg_n_iterations to zero and @@ -976,7 +991,7 @@ class PreconditionChebyshev : public Subscriptor /** * Constructor. */ - AdditionalData(const unsigned int degree = 0, + AdditionalData(const unsigned int degree = 1, const double smoothing_range = 0., const bool nonzero_starting = false, const unsigned int eig_cg_n_iterations = 8, @@ -986,7 +1001,7 @@ class PreconditionChebyshev : public Subscriptor /** * This determines the degree of the Chebyshev polynomial. The degree of * the polynomial gives the number of matrix-vector products to be - * performed for one application of the vmult() operation. Degree zero + * performed for one application of the vmult() operation. Degree one * corresponds to a damped Jacobi method. * * If the degree is set to numbers::invalid_unsigned_int, the algorithm @@ -1132,17 +1147,17 @@ class PreconditionChebyshev : public Subscriptor /** * Internal vector used for the vmult operation. */ - mutable VectorType update1; + mutable VectorType solution_old; /** * Internal vector used for the vmult operation. */ - mutable VectorType update2; + mutable VectorType temp_vector1; /** * Internal vector used for the vmult operation. */ - mutable VectorType update3; + mutable VectorType temp_vector2; /** * Stores the additional data passed to the initialize function, obtained @@ -1173,22 +1188,6 @@ class PreconditionChebyshev : public Subscriptor */ mutable Threads::Mutex mutex; - /** - * Runs the inner loop of the Chebyshev preconditioner that is the same for - * vmult() and step() methods. - */ - void - do_chebyshev_loop(VectorType &dst, const VectorType &src) const; - - /** - * Runs the inner loop of the Chebyshev preconditioner that is the same for - * vmult() and step() methods. Uses a separate function to not force users - * to provide both vmult() and Tvmult() in case only one variant is - * requested in subsequent calls. - */ - void - do_transpose_chebyshev_loop(VectorType &dst, const VectorType &src) const; - /** * Initializes the factors theta and delta based on an eigenvalue * computation. If the user set provided values for the largest eigenvalue @@ -1760,33 +1759,42 @@ namespace internal // generic part for non-deal.II vectors template inline void - vector_updates(const VectorType & src, + vector_updates(const VectorType & rhs, const PreconditionerType &preconditioner, - const bool start_zero, + const unsigned int iteration_index, const double factor1, const double factor2, - VectorType & update1, - VectorType & update2, - VectorType & update3, - VectorType & dst) + VectorType & solution_old, + VectorType & temp_vector1, + VectorType & temp_vector2, + VectorType & solution) { - if (start_zero) + if (iteration_index == 0) { - update1.equ(factor2, src); - preconditioner.vmult(dst, update1); - update1.equ(-1., dst); + solution.equ(factor2, rhs); + preconditioner.vmult(solution_old, solution); + } + else if (iteration_index == 1) + { + // compute t = P^{-1} * (b-A*x^{n}) + temp_vector1.sadd(-1.0, 1.0, rhs); + preconditioner.vmult(solution_old, temp_vector1); + + // compute x^{n+1} = x^{n} + f_1 * x^{n} + f_2 * t + solution_old.sadd(factor2, 1 + factor1, solution); } else { - update2 -= src; - preconditioner.vmult(update3, update2); - update2 = update3; - if (factor1 == 0.) - update1.equ(factor2, update2); - else - update1.sadd(factor1, factor2, update2); - dst -= update1; + // compute t = P^{-1} * (b-A*x^{n}) + temp_vector1.sadd(-1.0, 1.0, rhs); + preconditioner.vmult(temp_vector2, temp_vector1); + + // compute x^{n+1} = x^{n} + f_1 * (x^{n}-x^{n-1}) + f_2 * t + solution_old.sadd(-factor1, factor2, temp_vector2); + solution_old.add(1 + factor1, solution); } + + solution.swap(solution_old); } // worker routine for deal.II vectors. Because of vectorization, we need @@ -1795,23 +1803,22 @@ namespace internal template struct VectorUpdater { - VectorUpdater(const Number *src, - const Number *matrix_diagonal_inverse, - const bool start_zero, - const Number factor1, - const Number factor2, - Number * update1, - Number * update2, - Number * dst) - : src(src) + VectorUpdater(const Number * rhs, + const Number * matrix_diagonal_inverse, + const unsigned int iteration_index, + const Number factor1, + const Number factor2, + Number * solution_old, + Number * tmp_vector, + Number * solution) + : rhs(rhs) , matrix_diagonal_inverse(matrix_diagonal_inverse) - , do_startup(factor1 == Number()) - , start_zero(start_zero) + , iteration_index(iteration_index) , factor1(factor1) , factor2(factor2) - , update1(update1) - , update2(update2) - , dst(dst) + , solution_old(solution_old) + , tmp_vector(tmp_vector) + , solution(solution) {} void @@ -1821,46 +1828,46 @@ namespace internal // (https://gcc.gnu.org/bugzilla/show_bug.cgi?id=63945), we create // copies of the variables factor1 and factor2 and do not check based on // factor1. - const Number factor1 = this->factor1; - const Number factor2 = this->factor2; - if (do_startup) + const Number factor1 = this->factor1; + const Number factor1_plus_1 = 1. + this->factor1; + const Number factor2 = this->factor2; + if (iteration_index == 0) { - if (start_zero) - DEAL_II_OPENMP_SIMD_PRAGMA + DEAL_II_OPENMP_SIMD_PRAGMA for (std::size_t i = begin; i < end; ++i) - { - dst[i] = factor2 * src[i] * matrix_diagonal_inverse[i]; - update1[i] = -dst[i]; - } - else DEAL_II_OPENMP_SIMD_PRAGMA for (std::size_t i = begin; i < end; - ++i) - { - update1[i] = - ((update2[i] - src[i]) * factor2 * matrix_diagonal_inverse[i]); - dst[i] -= update1[i]; - } + solution[i] = factor2 * matrix_diagonal_inverse[i] * rhs[i]; + } + else if (iteration_index == 1) + { + // x^{n+1} = x^{n} + f_1 * x^{n} + f_2 * P^{-1} * (b-A*x^{n}) + DEAL_II_OPENMP_SIMD_PRAGMA + for (std::size_t i = begin; i < end; ++i) + // for efficiency reason, write back to temp_vector that is + // already read (avoid read-for-ownership) + tmp_vector[i] = + factor1_plus_1 * solution[i] + + factor2 * matrix_diagonal_inverse[i] * (rhs[i] - tmp_vector[i]); } else - DEAL_II_OPENMP_SIMD_PRAGMA - for (std::size_t i = begin; i < end; ++i) { - const Number update = - factor1 * update1[i] + - factor2 * ((update2[i] - src[i]) * matrix_diagonal_inverse[i]); - update1[i] = update; - dst[i] -= update; + // x^{n+1} = x^{n} + f_1 * (x^{n}-x^{n-1}) + // + f_2 * P^{-1} * (b-A*x^{n}) + DEAL_II_OPENMP_SIMD_PRAGMA + for (std::size_t i = begin; i < end; ++i) + solution_old[i] = + factor1_plus_1 * solution[i] - factor1 * solution_old[i] + + factor2 * matrix_diagonal_inverse[i] * (rhs[i] - tmp_vector[i]); } } - const Number * src; - const Number * matrix_diagonal_inverse; - const bool do_startup; - const bool start_zero; - const Number factor1; - const Number factor2; - mutable Number *update1; - mutable Number *update2; - mutable Number *dst; + const Number * rhs; + const Number * matrix_diagonal_inverse; + const unsigned int iteration_index; + const Number factor1; + const Number factor2; + mutable Number * solution_old; + mutable Number * tmp_vector; + mutable Number * solution; }; template @@ -1894,51 +1901,69 @@ namespace internal // selection for diagonal matrix around deal.II vector template inline void - vector_updates(const ::dealii::Vector & src, + vector_updates(const ::dealii::Vector & rhs, const DiagonalMatrix<::dealii::Vector> &jacobi, - const bool start_zero, - const double factor1, - const double factor2, - ::dealii::Vector & update1, - ::dealii::Vector & update2, + const unsigned int iteration_index, + const double factor1, + const double factor2, + ::dealii::Vector &solution_old, + ::dealii::Vector &temp_vector1, ::dealii::Vector &, - ::dealii::Vector &dst) + ::dealii::Vector &solution) { - VectorUpdater upd(src.begin(), + VectorUpdater upd(rhs.begin(), jacobi.get_vector().begin(), - start_zero, + iteration_index, factor1, factor2, - update1.begin(), - update2.begin(), - dst.begin()); - VectorUpdatesRange(upd, src.size()); + solution_old.begin(), + temp_vector1.begin(), + solution.begin()); + VectorUpdatesRange(upd, rhs.size()); + + // swap vectors x^{n+1}->x^{n}, given the updates in the function above + if (iteration_index == 1) + { + solution.swap(temp_vector1); + solution_old.swap(temp_vector1); + } + else if (iteration_index > 1) + solution.swap(solution_old); } // selection for diagonal matrix around parallel deal.II vector template inline void vector_updates( - const LinearAlgebra::distributed::Vector &src, + const LinearAlgebra::distributed::Vector &rhs, const DiagonalMatrix< LinearAlgebra::distributed::Vector> &jacobi, - const bool start_zero, - const double factor1, - const double factor2, - LinearAlgebra::distributed::Vector & update1, - LinearAlgebra::distributed::Vector & update2, + const unsigned int iteration_index, + const double factor1, + const double factor2, + LinearAlgebra::distributed::Vector &solution_old, + LinearAlgebra::distributed::Vector &temp_vector1, LinearAlgebra::distributed::Vector &, - LinearAlgebra::distributed::Vector &dst) + LinearAlgebra::distributed::Vector &solution) { - VectorUpdater upd(src.begin(), + VectorUpdater upd(rhs.begin(), jacobi.get_vector().begin(), - start_zero, + iteration_index, factor1, factor2, - update1.begin(), - update2.begin(), - dst.begin()); - VectorUpdatesRange(upd, src.local_size()); + solution_old.begin(), + temp_vector1.begin(), + solution.begin()); + VectorUpdatesRange(upd, rhs.local_size()); + + // swap vectors x^{n+1}->x^{n}, given the updates in the function above + if (iteration_index == 1) + { + solution.swap(temp_vector1); + solution_old.swap(temp_vector1); + } + else if (iteration_index > 1) + solution.swap(solution_old); } template ::initialize( { matrix_ptr = &matrix; data = additional_data; + Assert(data.degree > 0, + ExcMessage("The degree of the Chebyshev method must be positive.")); internal::PreconditionChebyshevImplementation::initialize_preconditioner( matrix, data.preconditioner, data.matrix_diagonal_inverse); eigenvalues_are_initialized = false; @@ -2112,9 +2139,9 @@ PreconditionChebyshev::clear() { VectorType empty_vector; data.matrix_diagonal_inverse.reinit(empty_vector); - update1.reinit(empty_vector); - update2.reinit(empty_vector); - update3.reinit(empty_vector); + solution_old.reinit(empty_vector); + temp_vector1.reinit(empty_vector); + temp_vector2.reinit(empty_vector); } data.preconditioner.reset(); } @@ -2129,8 +2156,8 @@ PreconditionChebyshev:: Assert(eigenvalues_are_initialized == false, ExcInternalError()); Assert(data.preconditioner.get() != nullptr, ExcNotInitialized()); - update1.reinit(src); - update2.reinit(src, true); + solution_old.reinit(src); + temp_vector1.reinit(src, true); // calculate largest eigenvalue using a hand-tuned CG iteration on the // matrix weighted by its diagonal. we start with a vector that consists of @@ -2161,11 +2188,15 @@ PreconditionChebyshev:: // set an initial guess which is close to the constant vector but where // one entry is different to trigger high frequencies - internal::PreconditionChebyshevImplementation::set_initial_guess(update2); + internal::PreconditionChebyshevImplementation::set_initial_guess( + temp_vector1); try { - solver.solve(*matrix_ptr, update1, update2, *data.preconditioner); + solver.solve(*matrix_ptr, + solution_old, + temp_vector1, + *data.preconditioner); } catch (SolverControl::NoConvergence &) {} @@ -2219,24 +2250,21 @@ PreconditionChebyshev:: PreconditionChebyshev *>(this) ->theta = (max_eigenvalue + alpha) * 0.5; - // We do not need the third auxiliary vector in case we have a + // We do not need the second temporary vector in case we have a // DiagonalMatrix as preconditioner and use deal.II's own vectors + using NumberType = typename VectorType::value_type; if (std::is_same>::value == false || - (std::is_same>::value == - false && - ((std::is_same< - VectorType, - LinearAlgebra::distributed::Vector>::value == + (std::is_same>::value == false && + ((std::is_same>::value == false) || - (std::is_same< - VectorType, - LinearAlgebra::distributed::Vector>::value == + (std::is_same>::value == false)))) - update3.reinit(src, true); + temp_vector2.reinit(src, true); const_cast< PreconditionChebyshev *>(this) @@ -2247,34 +2275,47 @@ PreconditionChebyshev:: template inline void -PreconditionChebyshev:: - do_chebyshev_loop(VectorType &dst, const VectorType &src) const +PreconditionChebyshev::vmult( + VectorType & solution, + const VectorType &rhs) const { - if (data.degree < 2) - return; + std::lock_guard lock(mutex); + if (eigenvalues_are_initialized == false) + estimate_eigenvalues(rhs); + + internal::PreconditionChebyshevImplementation::vector_updates( + rhs, + *data.preconditioner, + 0, + 0., + 1. / theta, + solution_old, + temp_vector1, + temp_vector2, + solution); // if delta is zero, we do not need to iterate because the updates will be // zero - if (std::abs(delta) < 1e-40) + if (data.degree < 2 || std::abs(delta) < 1e-40) return; double rhok = delta / theta, sigma = theta / delta; for (unsigned int k = 0; k < data.degree - 1; ++k) { - matrix_ptr->vmult(update2, dst); + matrix_ptr->vmult(temp_vector1, solution); const double rhokp = 1. / (2. * sigma - rhok); const double factor1 = rhokp * rhok, factor2 = 2. * rhokp / delta; rhok = rhokp; internal::PreconditionChebyshevImplementation::vector_updates( - src, + rhs, *data.preconditioner, - false, + k + 1, factor1, factor2, - update1, - update2, - update3, - dst); + solution_old, + temp_vector1, + temp_vector2, + solution); } } @@ -2282,109 +2323,93 @@ PreconditionChebyshev:: template inline void -PreconditionChebyshev:: - do_transpose_chebyshev_loop(VectorType &dst, const VectorType &src) const +PreconditionChebyshev::Tvmult( + VectorType & solution, + const VectorType &rhs) const { - if (data.degree < 2) + std::lock_guard lock(mutex); + if (eigenvalues_are_initialized == false) + estimate_eigenvalues(rhs); + + internal::PreconditionChebyshevImplementation::vector_updates( + rhs, + *data.preconditioner, + 0, + 0., + 1. / theta, + solution_old, + temp_vector1, + temp_vector2, + solution); + + if (data.degree < 2 || std::abs(delta) < 1e-40) return; double rhok = delta / theta, sigma = theta / delta; for (unsigned int k = 0; k < data.degree - 1; ++k) { - matrix_ptr->Tvmult(update2, dst); + matrix_ptr->Tvmult(temp_vector1, solution); const double rhokp = 1. / (2. * sigma - rhok); const double factor1 = rhokp * rhok, factor2 = 2. * rhokp / delta; rhok = rhokp; internal::PreconditionChebyshevImplementation::vector_updates( - src, + rhs, *data.preconditioner, - false, + k + 1, factor1, factor2, - update1, - update2, - update3, - dst); + solution_old, + temp_vector1, + temp_vector2, + solution); } } -template -inline void -PreconditionChebyshev::vmult( - VectorType & dst, - const VectorType &src) const -{ - std::lock_guard lock(mutex); - if (eigenvalues_are_initialized == false) - estimate_eigenvalues(src); - - internal::PreconditionChebyshevImplementation::vector_updates( - src, - *data.preconditioner, - true, - 0., - 1. / theta, - update1, - update2, - update3, - dst); - - do_chebyshev_loop(dst, src); -} - - - -template -inline void -PreconditionChebyshev::Tvmult( - VectorType & dst, - const VectorType &src) const -{ - std::lock_guard lock(mutex); - if (eigenvalues_are_initialized == false) - estimate_eigenvalues(src); - - internal::PreconditionChebyshevImplementation::vector_updates( - src, - *data.preconditioner, - true, - 0., - 1. / theta, - update1, - update2, - update3, - dst); - - do_transpose_chebyshev_loop(dst, src); -} - - - template inline void PreconditionChebyshev::step( - VectorType & dst, - const VectorType &src) const + VectorType & solution, + const VectorType &rhs) const { std::lock_guard lock(mutex); if (eigenvalues_are_initialized == false) - estimate_eigenvalues(src); + estimate_eigenvalues(rhs); - matrix_ptr->vmult(update2, dst); + matrix_ptr->vmult(temp_vector1, solution); internal::PreconditionChebyshevImplementation::vector_updates( - src, + rhs, *data.preconditioner, - false, + 1, 0., 1. / theta, - update1, - update2, - update3, - dst); + solution_old, + temp_vector1, + temp_vector2, + solution); + + if (data.degree < 2 || std::abs(delta) < 1e-40) + return; - do_chebyshev_loop(dst, src); + double rhok = delta / theta, sigma = theta / delta; + for (unsigned int k = 0; k < data.degree - 1; ++k) + { + matrix_ptr->vmult(temp_vector1, solution); + const double rhokp = 1. / (2. * sigma - rhok); + const double factor1 = rhokp * rhok, factor2 = 2. * rhokp / delta; + rhok = rhokp; + internal::PreconditionChebyshevImplementation::vector_updates( + rhs, + *data.preconditioner, + k + 2, + factor1, + factor2, + solution_old, + temp_vector1, + temp_vector2, + solution); + } } @@ -2392,26 +2417,46 @@ PreconditionChebyshev::step( template inline void PreconditionChebyshev::Tstep( - VectorType & dst, - const VectorType &src) const + VectorType & solution, + const VectorType &rhs) const { std::lock_guard lock(mutex); if (eigenvalues_are_initialized == false) - estimate_eigenvalues(src); + estimate_eigenvalues(rhs); - matrix_ptr->Tvmult(update2, dst); + matrix_ptr->Tvmult(temp_vector1, solution); internal::PreconditionChebyshevImplementation::vector_updates( - src, + rhs, *data.preconditioner, - false, + 1, 0., 1. / theta, - update1, - update2, - update3, - dst); + solution_old, + temp_vector1, + temp_vector2, + solution); + + if (data.degree < 2 || std::abs(delta) < 1e-40) + return; - do_transpose_chebyshev_loop(dst, src); + double rhok = delta / theta, sigma = theta / delta; + for (unsigned int k = 0; k < data.degree - 1; ++k) + { + matrix_ptr->Tvmult(temp_vector1, solution); + const double rhokp = 1. / (2. * sigma - rhok); + const double factor1 = rhokp * rhok, factor2 = 2. * rhokp / delta; + rhok = rhokp; + internal::PreconditionChebyshevImplementation::vector_updates( + rhs, + *data.preconditioner, + k + 2, + factor1, + factor2, + solution_old, + temp_vector1, + temp_vector2, + solution); + } } From 63f795652168082d5ed2124258500b8e454e2d5b Mon Sep 17 00:00:00 2001 From: Martin Kronbichler Date: Thu, 7 Feb 2019 12:26:11 +0100 Subject: [PATCH 113/507] Add changelog. --- doc/news/changes/minor/20190207MartinKronbichler | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 doc/news/changes/minor/20190207MartinKronbichler diff --git a/doc/news/changes/minor/20190207MartinKronbichler b/doc/news/changes/minor/20190207MartinKronbichler new file mode 100644 index 000000000000..3785b7f5ab22 --- /dev/null +++ b/doc/news/changes/minor/20190207MartinKronbichler @@ -0,0 +1,5 @@ +Improved: The iteration of PreconditionChebyshev has been overhauled to reduce +the number of vectors written per iteration to one, leading to slightly faster +execution of the vector updates. +
+(Martin Kronbichler, 2019/02/07) From 1b3760abe97fe7dbe6efaaccebd356ccc7a35402 Mon Sep 17 00:00:00 2001 From: Martin Kronbichler Date: Thu, 7 Feb 2019 18:09:54 +0100 Subject: [PATCH 114/507] Augment documentation about eigenvalue computation. --- include/deal.II/lac/precondition.h | 73 ++++++++++++++++++++++-------- 1 file changed, 53 insertions(+), 20 deletions(-) diff --git a/include/deal.II/lac/precondition.h b/include/deal.II/lac/precondition.h index 94ecb0e76f65..7d21d2cc0c95 100644 --- a/include/deal.II/lac/precondition.h +++ b/include/deal.II/lac/precondition.h @@ -883,7 +883,10 @@ class PreconditionPSOR : public PreconditionRelaxation * \frac{\lambda_{\max{}}-\lambda_{\min{}}}{\lambda_{\max{}}+\lambda_{\min{}}}$ * for the maximal eigenvalue $\lambda_{\max{}}$ and updated via $\rho_n = * \left(2\frac{\lambda_{\max{}}+\lambda_{\min{}}} - * {\lambda_{\max{}}-\lambda_{\min{}}} - \rho_{n-1}\right)^{-1}$. + * {\lambda_{\max{}}-\lambda_{\min{}}} - \rho_{n-1}\right)^{-1}$. The + * Chebyshev polynomial is constructed to strongly damp the eigenvalue range + * between $\lambda_{\min{}}$ and $\lambda_{\max{}}$ and is visualized e.g. in + * Utilities::LinearAlgebra::chebyshev_filter(). * * The typical use case for the preconditioner is a Jacobi preconditioner * specified through DiagonalMatrix, which is also the default value for the @@ -903,28 +906,52 @@ class PreconditionPSOR : public PreconditionRelaxation * products are %parallel and the inner preconditioner is %parallel). Its use * is demonstrated in the step-37 tutorial program. * - *

Algorithm execution

+ *

Estimation of the eigenvalues

* * The Chebyshev method relies on an estimate of the eigenvalues of the matrix * which are computed during the first invocation of vmult(). The algorithm * invokes a conjugate gradient solver so symmetry and positive definiteness - * of the (preconditioned) matrix system are strong requirements. As a - * consequence, this class only makes sense if it is applied repeatedly, - * e.g. in a smoother for a multigrid algorithm. The computation of - * eigenvalues needs to be deferred until the first vmult() invocation because + * of the (preconditioned) matrix system are requirements. The eigenvalue + * algorithm can be controlled by + * PreconditionChebyshev::AdditionalData::eig_cg_n_iterations specifying how + * many iterations should be performed. The iterations are started from an + * initial vector that depends on the vector type. For the classes + * dealii::Vector or dealii::LinearAlgebra::distributed::Vector, which have + * fast element access, it is either a vector with entries `(-5.5, -4.5, -3.5, + * -2.5, ..., 3.5, 4.5, 5.5)` with appropriate epilogue and adjusted such that + * its mean is always zero, which works well for the Laplacian. For other + * vector types, the initial vector contains all ones, scaled by the length of + * the vector, except for the very first entry that is zero, triggering + * high-frequency content again. + * + * The computation of eigenvalues happens the first time one of the + * vmult(), Tvmult(), step() or Tstep() functions is called. This is because * temporary vectors of the same layout as the source and destination vectors * are necessary for these computations and this information gets only * available through vmult(). * - * The estimation of eigenvalues can also be bypassed by setting - * PreconditionChebyshev::AdditionalData::eig_cg_n_iterations to zero and - * providing sensible values for the largest eigenvalues in the field - * PreconditionChebyshev::AdditionalData::max_eigenvalue. If the range - * [max_eigenvalue/smoothing_range, max_eigenvalue] contains all - * eigenvalues of the preconditioned matrix system and the degree (i.e., - * number of iterations) is high enough, this class can also be used as a - * direct solver. For an error estimation of the Chebyshev iteration that can - * be used to determine the number of iteration, see Varga (2009). + * Due to the cost of the eigenvalue estimate in the first vmult(), this class + * is most appropriate if it is applied repeatedly, e.g. in a smoother for a + * algorithm. + * + *

Bypassing the eigenvalue computation

+ * + * In some contexts, the automatic eigenvalue computation of this class may + * result in bad quality, or it may be unstable when used in parallel with + * different enumerations of the degrees of freedom, making computations + * strongly dependent on the parallel configuration. It is possible to bypass + * the automatic eigenvalue computation by setting + * AdditionalData::eig_cg_n_iterations to zero, and provide the variable + * AdditionalData::max_eigenvalue instead. The minimal eigenvalue is + * implicitly specified via `max_eigenvalue/smoothing_range`. + + *

Using the PreconditionChebyshev as a solver

+ * + * If the range [max_eigenvalue/smoothing_range, max_eigenvalue] + * contains all eigenvalues of the preconditioned matrix system and the degree + * (i.e., number of iterations) is high enough, this class can also be used as + * a direct solver. For an error estimation of the Chebyshev iteration that + * can be used to determine the number of iteration, see Varga (2009). * * In order to use Chebyshev as a solver, set the degree to * numbers::invalid_unsigned_int to force the automatic computation of the @@ -953,11 +980,11 @@ class PreconditionPSOR : public PreconditionRelaxation * PreconditionChebyshev. The preconditioner is held in a shared_ptr that is * copied into the AdditionalData member variable of the class, so the * variable used for initialization can safely be discarded after calling - * initialize(). Both the matrix and the preconditioner need to provide @p - * vmult functions for the matrix-vector product and @p m functions for + * initialize(). Both the matrix and the preconditioner need to provide + * @p vmult() functions for the matrix-vector product and @p m() functions for * accessing the number of rows in the (square) matrix. Furthermore, the * matrix must provide el(i,i) methods for accessing the matrix - * diagonal in case the preconditioner type is a diagonal matrix. Even though + * diagonal in case the preconditioner type is DiagonalMatrix. Even though * it is highly recommended to pass the inverse diagonal entries inside a * separate preconditioner object for implementing the Jacobi method (which is * the only possible way to operate this class when computing in %parallel @@ -1040,8 +1067,9 @@ class PreconditionChebyshev : public Subscriptor /** * Maximum number of CG iterations performed for finding the maximum - * eigenvalue. If set to zero, no computations are performed and the - * eigenvalues according to the given input are used instead. + * eigenvalue. If set to zero, no computations are performed. Instead, the + * user must supply a largest eigenvalue via the variable + * PreconditionChebyshev::AdditionalData::max_eigenvalue. */ unsigned int eig_cg_n_iterations; @@ -2265,6 +2293,11 @@ PreconditionChebyshev:: Vector>::value == false)))) temp_vector2.reinit(src, true); + else + { + VectorType empty_vector; + temp_vector2.reinit(empty_vector); + } const_cast< PreconditionChebyshev *>(this) From d3b96e1585d4a698ff9684fc3225d24cb9dabb3f Mon Sep 17 00:00:00 2001 From: Martin Kronbichler Date: Sat, 9 Feb 2019 11:02:01 +0100 Subject: [PATCH 115/507] Adjust test to definition of Chebyshev degree. --- tests/matrix_free/parallel_multigrid_adaptive_08.cc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/matrix_free/parallel_multigrid_adaptive_08.cc b/tests/matrix_free/parallel_multigrid_adaptive_08.cc index 4fb6c2b0c433..8c6b201129c1 100644 --- a/tests/matrix_free/parallel_multigrid_adaptive_08.cc +++ b/tests/matrix_free/parallel_multigrid_adaptive_08.cc @@ -342,7 +342,7 @@ do_test(const DoFHandler &dof) ++level) { smoother_data[level].smoothing_range = 15.; - smoother_data[level].degree = 5; + smoother_data[level].degree = 6; smoother_data[level].eig_cg_n_iterations = 15; smoother_data[level].preconditioner = mg_matrices[level].get_matrix_diagonal_inverse(); From 75eec859751d6275780b23015c6943087acbc5ed Mon Sep 17 00:00:00 2001 From: Martin Kronbichler Date: Sat, 9 Feb 2019 18:48:16 +0100 Subject: [PATCH 116/507] Add a comment about iteration 0. --- include/deal.II/lac/precondition.h | 18 ++++++++++++++---- 1 file changed, 14 insertions(+), 4 deletions(-) diff --git a/include/deal.II/lac/precondition.h b/include/deal.II/lac/precondition.h index 7d21d2cc0c95..900c474fc7a6 100644 --- a/include/deal.II/lac/precondition.h +++ b/include/deal.II/lac/precondition.h @@ -1950,12 +1950,17 @@ namespace internal VectorUpdatesRange(upd, rhs.size()); // swap vectors x^{n+1}->x^{n}, given the updates in the function above - if (iteration_index == 1) + if (iteration_index == 0) + { + // nothing to do here because we can immediately write into the + // solution vector without remembering any of the other vectors + } + else if (iteration_index == 1) { solution.swap(temp_vector1); solution_old.swap(temp_vector1); } - else if (iteration_index > 1) + else solution.swap(solution_old); } @@ -1985,12 +1990,17 @@ namespace internal VectorUpdatesRange(upd, rhs.local_size()); // swap vectors x^{n+1}->x^{n}, given the updates in the function above - if (iteration_index == 1) + if (iteration_index == 0) + { + // nothing to do here because we can immediately write into the + // solution vector without remembering any of the other vectors + } + else if (iteration_index == 1) { solution.swap(temp_vector1); solution_old.swap(temp_vector1); } - else if (iteration_index > 1) + else solution.swap(solution_old); } From 286a2d867a44c85e83dc60b5dafff424f35ebcbe Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Mon, 11 Feb 2019 16:11:08 -0700 Subject: [PATCH 117/507] reserve step-63 --- examples/step-63/CMakeLists.txt | 39 ++ examples/step-63/doc/builds-on | 1 + examples/step-63/doc/intro.dox | 9 + examples/step-63/doc/kind | 1 + examples/step-63/doc/results.dox | 2 + examples/step-63/doc/tooltip | 1 + examples/step-63/step-63.cc | 715 +++++++++++++++++++++++++++++++ 7 files changed, 768 insertions(+) create mode 100644 examples/step-63/CMakeLists.txt create mode 100644 examples/step-63/doc/builds-on create mode 100644 examples/step-63/doc/intro.dox create mode 100644 examples/step-63/doc/kind create mode 100644 examples/step-63/doc/results.dox create mode 100644 examples/step-63/doc/tooltip create mode 100644 examples/step-63/step-63.cc diff --git a/examples/step-63/CMakeLists.txt b/examples/step-63/CMakeLists.txt new file mode 100644 index 000000000000..476f55c11e5c --- /dev/null +++ b/examples/step-63/CMakeLists.txt @@ -0,0 +1,39 @@ +## +# CMake script for the step-63 tutorial program: +## + +# Set the name of the project and target: +SET(TARGET "step-63") + +# Declare all source files the target consists of. Here, this is only +# the one step-X.cc file, but as you expand your project you may wish +# to add other source files as well. If your project becomes much larger, +# you may want to either replace the following statement by something like +# FILE(GLOB_RECURSE TARGET_SRC "source/*.cc") +# FILE(GLOB_RECURSE TARGET_INC "include/*.h") +# SET(TARGET_SRC ${TARGET_SRC} ${TARGET_INC}) +# or switch altogether to the large project CMakeLists.txt file discussed +# in the "CMake in user projects" page accessible from the "User info" +# page of the documentation. +SET(TARGET_SRC + ${TARGET}.cc + ) + +# Usually, you will not need to modify anything beyond this point... + +CMAKE_MINIMUM_REQUIRED(VERSION 2.8.12) + +FIND_PACKAGE(deal.II 9.1.0 QUIET + HINTS ${deal.II_DIR} ${DEAL_II_DIR} ../ ../../ $ENV{DEAL_II_DIR} + ) +IF(NOT ${deal.II_FOUND}) + MESSAGE(FATAL_ERROR "\n" + "*** Could not locate a (sufficiently recent) version of deal.II. ***\n\n" + "You may want to either pass a flag -DDEAL_II_DIR=/path/to/deal.II to cmake\n" + "or set an environment variable \"DEAL_II_DIR\" that contains this path." + ) +ENDIF() + +DEAL_II_INITIALIZE_CACHED_VARIABLES() +PROJECT(${TARGET}) +DEAL_II_INVOKE_AUTOPILOT() diff --git a/examples/step-63/doc/builds-on b/examples/step-63/doc/builds-on new file mode 100644 index 000000000000..42c284692101 --- /dev/null +++ b/examples/step-63/doc/builds-on @@ -0,0 +1 @@ +step-16 diff --git a/examples/step-63/doc/intro.dox b/examples/step-63/doc/intro.dox new file mode 100644 index 000000000000..b8535c110b50 --- /dev/null +++ b/examples/step-63/doc/intro.dox @@ -0,0 +1,9 @@ +
+ +This program was contributed by Thomas Clevenger and Timo Heister. + + +

Introduction

+ +Please note: This is work in progress and will be an example for block +smoothers in geometric multigrid. For now, this is just step-16. diff --git a/examples/step-63/doc/kind b/examples/step-63/doc/kind new file mode 100644 index 000000000000..6816e9090f56 --- /dev/null +++ b/examples/step-63/doc/kind @@ -0,0 +1 @@ +unfinished diff --git a/examples/step-63/doc/results.dox b/examples/step-63/doc/results.dox new file mode 100644 index 000000000000..b5eaba9377b6 --- /dev/null +++ b/examples/step-63/doc/results.dox @@ -0,0 +1,2 @@ +

Results

+ diff --git a/examples/step-63/doc/tooltip b/examples/step-63/doc/tooltip new file mode 100644 index 000000000000..9aad4b39bba7 --- /dev/null +++ b/examples/step-63/doc/tooltip @@ -0,0 +1 @@ +Block smoothers for Geometric Multigrid. diff --git a/examples/step-63/step-63.cc b/examples/step-63/step-63.cc new file mode 100644 index 000000000000..86234e2ac7b0 --- /dev/null +++ b/examples/step-63/step-63.cc @@ -0,0 +1,715 @@ +/* --------------------------------------------------------------------- + * + * Copyright (C) 2003 - 2018 by the deal.II authors + * + * This file is part of the deal.II library. + * + * The deal.II library is free software; you can use it, redistribute + * it, and/or modify it under the terms of the GNU Lesser General + * Public License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * The full text of the license can be found in the file LICENSE.md at + * the top level directory of deal.II. + * + * --------------------------------------------------------------------- + * + * Authors: Thomas Clevenger, Clemson University + * Timo Heister, University of Utah + */ + +// @note: This is work in progress and will be an example for block smoothers +// in geometric multigrid. For now, this is just step-16. + +// @sect3{Include files} + +// Again, the first few include files are already known, so we won't comment +// on them: +#include +#include +#include +#include + +#include +#include +#include +#include +#include +#include + +#include +#include +#include +#include +#include + +#include +#include + +#include +#include + +#include +#include +#include + +// These, now, are the include necessary for the multilevel methods. The first +// one declares how to handle Dirichlet boundary conditions on each of the +// levels of the multigrid method. For the actual description of the degrees +// of freedom, we do not need any new include file because DoFHandler already +// has all necessary methods implemented. We will only need to distribute the +// DoFs for the levels further down. +// +// The rest of the include files deals with the mechanics of multigrid as a +// linear operator (solver or preconditioner). +#include +#include +#include +#include +#include +#include +#include + +// We will be using MeshWorker::mesh_loop to loop over the cells, so include it +// here: +#include + + +// This is C++: +#include +#include + +using namespace dealii; + +namespace Step16 +{ + // @sect3{The Scratch and Copy objects} + // + // We use MeshWorker::mesh_loop() to assemble our matrices. For this, we + // need a ScratchData object to store temporary data on each cell (this is + // just the FEValues object) and a CopyData object that will contain the + // output of each cell assembly. For more details about the usage of scratch + // and copy objects, see the WorkStream namespace. + template + struct ScratchData + { + ScratchData(const Mapping & mapping, + const FiniteElement &fe, + const unsigned int quadrature_degree, + const UpdateFlags update_flags) + : fe_values(mapping, fe, QGauss(quadrature_degree), update_flags) + {} + + ScratchData(const ScratchData &scratch_data) + : fe_values(scratch_data.fe_values.get_mapping(), + scratch_data.fe_values.get_fe(), + scratch_data.fe_values.get_quadrature(), + scratch_data.fe_values.get_update_flags()) + {} + + FEValues fe_values; + }; + + struct CopyData + { + unsigned int level; + FullMatrix cell_matrix; + Vector cell_rhs; + std::vector local_dof_indices; + + template + void reinit(const Iterator &cell, unsigned int dofs_per_cell) + { + cell_matrix.reinit(dofs_per_cell, dofs_per_cell); + cell_rhs.reinit(dofs_per_cell); + + local_dof_indices.resize(dofs_per_cell); + cell->get_active_or_mg_dof_indices(local_dof_indices); + level = cell->level(); + } + }; + + // @sect3{The LaplaceProblem class template} + + // This main class is similar to the same class in step-6. As far as + // member functions is concerned, the only additions are: + // - The assemble_multigrid function that assembles the matrices + // that correspond to the discrete operators on intermediate levels. + // - The cell_worker function that assembles our PDE on a single + // cell. + template + class LaplaceProblem + { + public: + LaplaceProblem(const unsigned int degree); + void run(); + + private: + template + void cell_worker(const Iterator & cell, + ScratchData &scratch_data, + CopyData & copy_data); + + void setup_system(); + void assemble_system(); + void assemble_multigrid(); + void solve(); + void refine_grid(); + void output_results(const unsigned int cycle) const; + + Triangulation triangulation; + FE_Q fe; + DoFHandler dof_handler; + + SparsityPattern sparsity_pattern; + SparseMatrix system_matrix; + + AffineConstraints constraints; + + Vector solution; + Vector system_rhs; + + const unsigned int degree; + + // The following members are the essential data structures for the multigrid + // method. The first four represent the sparsity patterns and the matrices + // on individual levels of the multilevel hierarchy, very much like the + // objects for the global mesh above. + // + // Then we have two new matrices only needed for multigrid methods with + // local smoothing on adaptive meshes. They convey data between the interior + // part of the refined region and the refinement edge, as outlined in detail + // in the @ref mg_paper "multigrid paper". + // + // The last object stores information about the boundary indices on each + // level and information about indices lying on a refinement edge between + // two different refinement levels. It thus serves a similar purpose as + // AffineConstraints, but on each level. + MGLevelObject mg_sparsity_patterns; + MGLevelObject mg_interface_sparsity_patterns; + + MGLevelObject> mg_matrices; + MGLevelObject> mg_interface_matrices; + MGConstrainedDoFs mg_constrained_dofs; + }; + + + // @sect3{The LaplaceProblem class implementation} + + // Just one short remark about the constructor of the Triangulation: + // by convention, all adaptively refined triangulations in deal.II never + // change by more than one level across a face between cells. For our + // multigrid algorithms, however, we need a slightly stricter guarantee, + // namely that the mesh also does not change by more than refinement level + // across vertices that might connect two cells. In other words, we must + // prevent the following situation: + // + // @image html limit_level_difference_at_vertices.png "" + // + // This is achieved by passing the + // Triangulation::limit_level_difference_at_vertices flag to the constructor + // of the triangulation class. + template + LaplaceProblem::LaplaceProblem(const unsigned int degree) + : triangulation(Triangulation::limit_level_difference_at_vertices) + , fe(degree) + , dof_handler(triangulation) + , degree(degree) + {} + + + + // @sect4{LaplaceProblem::setup_system} + + // In addition to just distributing the degrees of freedom in + // the DoFHandler, we do the same on each level. Then, we follow the + // same procedure as before to set up the system on the leaf mesh. + template + void LaplaceProblem::setup_system() + { + dof_handler.distribute_dofs(fe); + dof_handler.distribute_mg_dofs(); + + std::cout << " Number of degrees of freedom: " << dof_handler.n_dofs() + << " (by level: "; + for (unsigned int level = 0; level < triangulation.n_levels(); ++level) + std::cout << dof_handler.n_dofs(level) + << (level == triangulation.n_levels() - 1 ? ")" : ", "); + std::cout << std::endl; + + + solution.reinit(dof_handler.n_dofs()); + system_rhs.reinit(dof_handler.n_dofs()); + + constraints.clear(); + DoFTools::make_hanging_node_constraints(dof_handler, constraints); + + std::set dirichlet_boundary_ids = {0}; + Functions::ZeroFunction homogeneous_dirichlet_bc; + const std::map *> + dirichlet_boundary_functions = { + {types::boundary_id(0), &homogeneous_dirichlet_bc}}; + VectorTools::interpolate_boundary_values(dof_handler, + dirichlet_boundary_functions, + constraints); + constraints.close(); + + { + DynamicSparsityPattern dsp(dof_handler.n_dofs(), dof_handler.n_dofs()); + DoFTools::make_sparsity_pattern(dof_handler, dsp, constraints); + sparsity_pattern.copy_from(dsp); + } + system_matrix.reinit(sparsity_pattern); + + // The multigrid constraints have to be initialized. They need to know + // where Dirichlet boundary conditions are prescribed. + mg_constrained_dofs.clear(); + mg_constrained_dofs.initialize(dof_handler); + mg_constrained_dofs.make_zero_boundary_constraints(dof_handler, + dirichlet_boundary_ids); + + + // Now for the things that concern the multigrid data structures. First, we + // resize the multilevel objects to hold matrices and sparsity patterns for + // every level. The coarse level is zero (this is mandatory right now but + // may change in a future revision). Note that these functions take a + // complete, inclusive range here (not a starting index and size), so the + // finest level is n_levels-1. We first have to resize the + // container holding the SparseMatrix classes, since they have to release + // their SparsityPattern before the can be destroyed upon resizing. + const unsigned int n_levels = triangulation.n_levels(); + + mg_interface_matrices.resize(0, n_levels - 1); + mg_matrices.resize(0, n_levels - 1); + mg_sparsity_patterns.resize(0, n_levels - 1); + mg_interface_sparsity_patterns.resize(0, n_levels - 1); + + // Now, we have to provide a matrix on each level. To this end, we first use + // the MGTools::make_sparsity_pattern function to generate a preliminary + // compressed sparsity pattern on each level (see the @ref Sparsity module + // for more information on this topic) and then copy it over to the one we + // really want. The next step is to initialize the interface matrices with + // the fitting sparsity pattern. + // + // It may be worth pointing out that the interface matrices only have + // entries for degrees of freedom that sit at or next to the interface + // between coarser and finer levels of the mesh. They are therefore even + // sparser than the matrices on the individual levels of our multigrid + // hierarchy. Therefore, we use a function specifically build for this + // purpose to generate it. + for (unsigned int level = 0; level < n_levels; ++level) + { + { + DynamicSparsityPattern dsp(dof_handler.n_dofs(level), + dof_handler.n_dofs(level)); + MGTools::make_sparsity_pattern(dof_handler, dsp, level); + + mg_sparsity_patterns[level].copy_from(dsp); + mg_matrices[level].reinit(mg_sparsity_patterns[level]); + } + { + DynamicSparsityPattern dsp(dof_handler.n_dofs(level), + dof_handler.n_dofs(level)); + MGTools::make_interface_sparsity_pattern(dof_handler, + mg_constrained_dofs, + dsp, + level); + mg_interface_sparsity_patterns[level].copy_from(dsp); + mg_interface_matrices[level].reinit( + mg_interface_sparsity_patterns[level]); + } + } + } + + + // @sect4{LaplaceProblem::cell_worker} + + // The cell_worker function is used to assemble the matrix and right-hand side + // on the given cell. This function is used for the active cells to generate + // the system_matrix and on each level to build the level matrices. + // + // Note that we also assemble a right-hand side when called from + // assemble_multigrid() even though it is not used. + template + template + void LaplaceProblem::cell_worker(const Iterator & cell, + ScratchData &scratch_data, + CopyData & copy_data) + { + FEValues &fe_values = scratch_data.fe_values; + fe_values.reinit(cell); + + const unsigned int dofs_per_cell = fe_values.get_fe().dofs_per_cell; + const unsigned int n_q_points = fe_values.get_quadrature().size(); + + copy_data.reinit(cell, dofs_per_cell); + + const std::vector &JxW = fe_values.get_JxW_values(); + + for (unsigned int q = 0; q < n_q_points; ++q) + { + const double coefficient = + (fe_values.get_quadrature_points()[q][0] < 0.0) ? 1.0 : 0.1; + //(cell->center().square() < 0.5 * 0.5) ? 10.0:1.0; + + for (unsigned int i = 0; i < dofs_per_cell; ++i) + { + for (unsigned int j = 0; j < dofs_per_cell; ++j) + { + copy_data.cell_matrix(i, j) += + coefficient * + (fe_values.shape_grad(i, q) * fe_values.shape_grad(j, q)) * + JxW[q]; + } + copy_data.cell_rhs(i) += 1.0 * fe_values.shape_value(i, q) * JxW[q]; + } + } + } + + + + // @sect4{LaplaceProblem::assemble_system} + + // The following function assembles the linear system on the active cells of + // the mesh. For this, we pass two lambda functions to the mesh_loop() + // function. The cell_worker function redirects to the class member function + // of the same name, while the copier is specific to this function and copies + // local matrix and vector to the corresponding global ones using the + // constraints. + template + void LaplaceProblem::assemble_system() + { + MappingQ1 mapping; + + auto cell_worker = + [&](const typename DoFHandler::active_cell_iterator &cell, + ScratchData & scratch_data, + CopyData & copy_data) { + this->cell_worker(cell, scratch_data, copy_data); + }; + + auto copier = [&](const CopyData &cd) { + this->constraints.distribute_local_to_global(cd.cell_matrix, + cd.cell_rhs, + cd.local_dof_indices, + system_matrix, + system_rhs); + }; + + const unsigned int n_gauss_points = degree + 1; + + ScratchData scratch_data(mapping, + fe, + n_gauss_points, + update_values | update_gradients | + update_JxW_values | + update_quadrature_points); + + MeshWorker::mesh_loop(dof_handler.begin_active(), + dof_handler.end(), + cell_worker, + copier, + scratch_data, + CopyData(), + MeshWorker::assemble_own_cells); + } + + + // @sect4{LaplaceProblem::assemble_multigrid} + + // The next function is the one that builds the matrices + // that define the multigrid method on each level of the mesh. The integration + // core is the same as above, but the loop below will go over all existing + // cells instead of just the active ones, and the results must be entered into + // the correct level matrices. Fortunately, MeshWorker hides most of that from + // us, and thus the difference between this function and the previous lies + // only in the setup of the assembler and the different iterators in the loop. + // + // We generate an AffineConstraints<> object for each level containing the + // boundary and interface dofs as constrained entries. The corresponding + // object is then used to generate the level matrices. + template + void LaplaceProblem::assemble_multigrid() + { + MappingQ1 mapping; + const unsigned int n_levels = triangulation.n_levels(); + + std::vector> boundary_constraints(n_levels); + for (unsigned int level = 0; level < n_levels; ++level) + { + IndexSet dofset; + DoFTools::extract_locally_relevant_level_dofs(dof_handler, + level, + dofset); + boundary_constraints[level].reinit(dofset); + boundary_constraints[level].add_lines( + mg_constrained_dofs.get_refinement_edge_indices(level)); + boundary_constraints[level].add_lines( + mg_constrained_dofs.get_boundary_indices(level)); + boundary_constraints[level].close(); + } + + auto cell_worker = + [&](const typename DoFHandler::level_cell_iterator &cell, + ScratchData & scratch_data, + CopyData & copy_data) { + this->cell_worker(cell, scratch_data, copy_data); + }; + + auto copier = [&](const CopyData &cd) { + boundary_constraints[cd.level].distribute_local_to_global( + cd.cell_matrix, cd.local_dof_indices, mg_matrices[cd.level]); + + const unsigned int dofs_per_cell = cd.local_dof_indices.size(); + + // TODO EXPLAIN: + + for (unsigned int i = 0; i < dofs_per_cell; ++i) + for (unsigned int j = 0; j < dofs_per_cell; ++j) + if (mg_constrained_dofs.is_interface_matrix_entry( + cd.level, cd.local_dof_indices[i], cd.local_dof_indices[j])) + { + mg_interface_matrices[cd.level].add(cd.local_dof_indices[i], + cd.local_dof_indices[j], + cd.cell_matrix(i, j)); + } + }; + + const unsigned int n_gauss_points = degree + 1; + + ScratchData scratch_data(mapping, + fe, + n_gauss_points, + update_values | update_gradients | + update_JxW_values | + update_quadrature_points); + + MeshWorker::mesh_loop(dof_handler.begin_mg(), + dof_handler.end_mg(), + cell_worker, + copier, + scratch_data, + CopyData(), + MeshWorker::assemble_own_cells); + } + + + + // @sect4{LaplaceProblem::solve} + + // This is the other function that is significantly different in support of + // the multigrid solver (or, in fact, the preconditioner for which we use + // the multigrid method). + // + // Let us start out by setting up two of the components of multilevel + // methods: transfer operators between levels, and a solver on the coarsest + // level. In finite element methods, the transfer operators are derived from + // the finite element function spaces involved and can often be computed in + // a generic way independent of the problem under consideration. In that + // case, we can use the MGTransferPrebuilt class that, given the constraints + // of the final linear system and the MGConstrainedDoFs object that knows + // about the boundary conditions on the each level and the degrees of + // freedom on interfaces between different refinement level can build the + // matrices for those transfer operations from a DoFHandler object with + // level degrees of freedom. + // + // The second part of the following lines deals with the coarse grid + // solver. Since our coarse grid is very coarse indeed, we decide for a + // direct solver (a Householder decomposition of the coarsest level matrix), + // even if its implementation is not particularly sophisticated. If our + // coarse mesh had many more cells than the five we have here, something + // better suited would obviously be necessary here. + template + void LaplaceProblem::solve() + { + MGTransferPrebuilt> mg_transfer(mg_constrained_dofs); + mg_transfer.build_matrices(dof_handler); + + FullMatrix coarse_matrix; + coarse_matrix.copy_from(mg_matrices[0]); + MGCoarseGridHouseholder<> coarse_grid_solver; + coarse_grid_solver.initialize(coarse_matrix); + + // The next component of a multilevel solver or preconditioner is that we + // need a smoother on each level. A common choice for this is to use the + // application of a relaxation method (such as the SOR, Jacobi or Richardson + // method) or a small number of iterations of a solver method (such as CG or + // GMRES). The mg::SmootherRelaxation and MGSmootherPrecondition classes + // provide support for these two kinds of smoothers. Here, we opt for the + // application of a single SOR iteration. To this end, we define an + // appropriate alias and then setup a smoother object. + // + // The last step is to initialize the smoother object with our level + // matrices and to set some smoothing parameters. The + // initialize() function can optionally take additional + // arguments that will be passed to the smoother object on each level. In + // the current case for the SOR smoother, this could, for example, include + // a relaxation parameter. However, we here leave these at their default + // values. The call to set_steps() indicates that we will use + // two pre- and two post-smoothing steps on each level; to use a variable + // number of smoother steps on different levels, more options can be set + // in the constructor call to the mg_smoother object. + // + // The last step results from the fact that we use the SOR method as a + // smoother - which is not symmetric - but we use the conjugate gradient + // iteration (which requires a symmetric preconditioner) below, we need to + // let the multilevel preconditioner make sure that we get a symmetric + // operator even for nonsymmetric smoothers: + using Smoother = PreconditionSOR>; + mg::SmootherRelaxation> mg_smoother; + mg_smoother.initialize(mg_matrices); + mg_smoother.set_steps(2); + mg_smoother.set_symmetric(true); + + // The next preparatory step is that we must wrap our level and interface + // matrices in an object having the required multiplication functions. We + // will create two objects for the interface objects going from coarse to + // fine and the other way around; the multigrid algorithm will later use + // the transpose operator for the latter operation, allowing us to + // initialize both up and down versions of the operator with the matrices + // we already built: + mg::Matrix> mg_matrix(mg_matrices); + mg::Matrix> mg_interface_up(mg_interface_matrices); + mg::Matrix> mg_interface_down(mg_interface_matrices); + + // Now, we are ready to set up the V-cycle operator and the multilevel + // preconditioner. + Multigrid> mg( + mg_matrix, coarse_grid_solver, mg_transfer, mg_smoother, mg_smoother); + mg.set_edge_matrices(mg_interface_down, mg_interface_up); + + PreconditionMG, MGTransferPrebuilt>> + preconditioner(dof_handler, mg, mg_transfer); + + // With all this together, we can finally get about solving the linear + // system in the usual way: + SolverControl solver_control(1000, 1e-12); + SolverCG<> solver(solver_control); + + solution = 0; + + solver.solve(system_matrix, solution, system_rhs, preconditioner); + std::cout << " Number of CG iterations: " << solver_control.last_step() + << "\n" + << std::endl; + constraints.distribute(solution); + } + + + + // @sect4{Postprocessing} + + // The following two functions postprocess a solution once it is + // computed. In particular, the first one refines the mesh at the beginning + // of each cycle while the second one outputs results at the end of each + // such cycle. The functions are almost unchanged from those in step-6. + template + void LaplaceProblem::refine_grid() + { + Vector estimated_error_per_cell(triangulation.n_active_cells()); + + KellyErrorEstimator::estimate( + dof_handler, + QGauss(degree + 2), + std::map *>(), + solution, + estimated_error_per_cell); + GridRefinement::refine_and_coarsen_fixed_number(triangulation, + estimated_error_per_cell, + 0.3, + 0.03); + triangulation.execute_coarsening_and_refinement(); + } + + + + template + void LaplaceProblem::output_results(const unsigned int cycle) const + { + DataOut data_out; + + data_out.attach_dof_handler(dof_handler); + data_out.add_data_vector(solution, "solution"); + data_out.build_patches(); + + std::ofstream output("solution-" + std::to_string(cycle) + ".vtk"); + data_out.write_vtk(output); + } + + + // @sect4{LaplaceProblem::run} + + // Like several of the functions above, this is almost exactly a copy of + // the corresponding function in step-6. The only difference is the call to + // assemble_multigrid that takes care of forming the matrices + // on every level that we need in the multigrid method. + template + void LaplaceProblem::run() + { + for (unsigned int cycle = 0; cycle < 8; ++cycle) + { + std::cout << "Cycle " << cycle << std::endl; + + if (cycle == 0) + { + GridGenerator::hyper_ball(triangulation); + triangulation.refine_global(2); + } + else + refine_grid(); + + std::cout << " Number of active cells: " + << triangulation.n_active_cells() << std::endl; + + setup_system(); + + assemble_system(); + assemble_multigrid(); + + solve(); + output_results(cycle); + } + } +} // namespace Step16 + + +// @sect3{The main() function} +// +// This is again the same function as in step-6: +int main() +{ + try + { + using namespace Step16; + + LaplaceProblem<2> laplace_problem(1); + laplace_problem.run(); + } + catch (std::exception &exc) + { + std::cerr << std::endl + << std::endl + << "----------------------------------------------------" + << std::endl; + std::cerr << "Exception on processing: " << std::endl + << exc.what() << std::endl + << "Aborting!" << std::endl + << "----------------------------------------------------" + << std::endl; + + return 1; + } + catch (...) + { + std::cerr << std::endl + << std::endl + << "----------------------------------------------------" + << std::endl; + std::cerr << "Unknown exception!" << std::endl + << "Aborting!" << std::endl + << "----------------------------------------------------" + << std::endl; + return 1; + } + + return 0; +} From 81c110c254b5fbfb9c40410220543641f1367e04 Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Tue, 12 Feb 2019 10:20:02 -0700 Subject: [PATCH 118/507] make example empty --- examples/step-63/step-63.cc | 664 +----------------------------------- 1 file changed, 4 insertions(+), 660 deletions(-) diff --git a/examples/step-63/step-63.cc b/examples/step-63/step-63.cc index 86234e2ac7b0..d2b9a18715f6 100644 --- a/examples/step-63/step-63.cc +++ b/examples/step-63/step-63.cc @@ -1,6 +1,6 @@ /* --------------------------------------------------------------------- * - * Copyright (C) 2003 - 2018 by the deal.II authors + * Copyright (C) 2018 - 2019 by the deal.II authors * * This file is part of the deal.II library. * @@ -18,671 +18,15 @@ */ // @note: This is work in progress and will be an example for block smoothers -// in geometric multigrid. For now, this is just step-16. +// in geometric multigrid. -// @sect3{Include files} +#include -// Again, the first few include files are already known, so we won't comment -// on them: -#include -#include -#include -#include - -#include -#include -#include -#include -#include -#include - -#include -#include -#include -#include -#include - -#include -#include - -#include -#include - -#include -#include -#include - -// These, now, are the include necessary for the multilevel methods. The first -// one declares how to handle Dirichlet boundary conditions on each of the -// levels of the multigrid method. For the actual description of the degrees -// of freedom, we do not need any new include file because DoFHandler already -// has all necessary methods implemented. We will only need to distribute the -// DoFs for the levels further down. -// -// The rest of the include files deals with the mechanics of multigrid as a -// linear operator (solver or preconditioner). -#include -#include -#include -#include -#include -#include -#include - -// We will be using MeshWorker::mesh_loop to loop over the cells, so include it -// here: -#include - - -// This is C++: -#include -#include - -using namespace dealii; - -namespace Step16 -{ - // @sect3{The Scratch and Copy objects} - // - // We use MeshWorker::mesh_loop() to assemble our matrices. For this, we - // need a ScratchData object to store temporary data on each cell (this is - // just the FEValues object) and a CopyData object that will contain the - // output of each cell assembly. For more details about the usage of scratch - // and copy objects, see the WorkStream namespace. - template - struct ScratchData - { - ScratchData(const Mapping & mapping, - const FiniteElement &fe, - const unsigned int quadrature_degree, - const UpdateFlags update_flags) - : fe_values(mapping, fe, QGauss(quadrature_degree), update_flags) - {} - - ScratchData(const ScratchData &scratch_data) - : fe_values(scratch_data.fe_values.get_mapping(), - scratch_data.fe_values.get_fe(), - scratch_data.fe_values.get_quadrature(), - scratch_data.fe_values.get_update_flags()) - {} - - FEValues fe_values; - }; - - struct CopyData - { - unsigned int level; - FullMatrix cell_matrix; - Vector cell_rhs; - std::vector local_dof_indices; - - template - void reinit(const Iterator &cell, unsigned int dofs_per_cell) - { - cell_matrix.reinit(dofs_per_cell, dofs_per_cell); - cell_rhs.reinit(dofs_per_cell); - - local_dof_indices.resize(dofs_per_cell); - cell->get_active_or_mg_dof_indices(local_dof_indices); - level = cell->level(); - } - }; - - // @sect3{The LaplaceProblem class template} - - // This main class is similar to the same class in step-6. As far as - // member functions is concerned, the only additions are: - // - The assemble_multigrid function that assembles the matrices - // that correspond to the discrete operators on intermediate levels. - // - The cell_worker function that assembles our PDE on a single - // cell. - template - class LaplaceProblem - { - public: - LaplaceProblem(const unsigned int degree); - void run(); - - private: - template - void cell_worker(const Iterator & cell, - ScratchData &scratch_data, - CopyData & copy_data); - - void setup_system(); - void assemble_system(); - void assemble_multigrid(); - void solve(); - void refine_grid(); - void output_results(const unsigned int cycle) const; - - Triangulation triangulation; - FE_Q fe; - DoFHandler dof_handler; - - SparsityPattern sparsity_pattern; - SparseMatrix system_matrix; - - AffineConstraints constraints; - - Vector solution; - Vector system_rhs; - - const unsigned int degree; - - // The following members are the essential data structures for the multigrid - // method. The first four represent the sparsity patterns and the matrices - // on individual levels of the multilevel hierarchy, very much like the - // objects for the global mesh above. - // - // Then we have two new matrices only needed for multigrid methods with - // local smoothing on adaptive meshes. They convey data between the interior - // part of the refined region and the refinement edge, as outlined in detail - // in the @ref mg_paper "multigrid paper". - // - // The last object stores information about the boundary indices on each - // level and information about indices lying on a refinement edge between - // two different refinement levels. It thus serves a similar purpose as - // AffineConstraints, but on each level. - MGLevelObject mg_sparsity_patterns; - MGLevelObject mg_interface_sparsity_patterns; - - MGLevelObject> mg_matrices; - MGLevelObject> mg_interface_matrices; - MGConstrainedDoFs mg_constrained_dofs; - }; - - - // @sect3{The LaplaceProblem class implementation} - - // Just one short remark about the constructor of the Triangulation: - // by convention, all adaptively refined triangulations in deal.II never - // change by more than one level across a face between cells. For our - // multigrid algorithms, however, we need a slightly stricter guarantee, - // namely that the mesh also does not change by more than refinement level - // across vertices that might connect two cells. In other words, we must - // prevent the following situation: - // - // @image html limit_level_difference_at_vertices.png "" - // - // This is achieved by passing the - // Triangulation::limit_level_difference_at_vertices flag to the constructor - // of the triangulation class. - template - LaplaceProblem::LaplaceProblem(const unsigned int degree) - : triangulation(Triangulation::limit_level_difference_at_vertices) - , fe(degree) - , dof_handler(triangulation) - , degree(degree) - {} - - - - // @sect4{LaplaceProblem::setup_system} - - // In addition to just distributing the degrees of freedom in - // the DoFHandler, we do the same on each level. Then, we follow the - // same procedure as before to set up the system on the leaf mesh. - template - void LaplaceProblem::setup_system() - { - dof_handler.distribute_dofs(fe); - dof_handler.distribute_mg_dofs(); - - std::cout << " Number of degrees of freedom: " << dof_handler.n_dofs() - << " (by level: "; - for (unsigned int level = 0; level < triangulation.n_levels(); ++level) - std::cout << dof_handler.n_dofs(level) - << (level == triangulation.n_levels() - 1 ? ")" : ", "); - std::cout << std::endl; - - - solution.reinit(dof_handler.n_dofs()); - system_rhs.reinit(dof_handler.n_dofs()); - - constraints.clear(); - DoFTools::make_hanging_node_constraints(dof_handler, constraints); - - std::set dirichlet_boundary_ids = {0}; - Functions::ZeroFunction homogeneous_dirichlet_bc; - const std::map *> - dirichlet_boundary_functions = { - {types::boundary_id(0), &homogeneous_dirichlet_bc}}; - VectorTools::interpolate_boundary_values(dof_handler, - dirichlet_boundary_functions, - constraints); - constraints.close(); - - { - DynamicSparsityPattern dsp(dof_handler.n_dofs(), dof_handler.n_dofs()); - DoFTools::make_sparsity_pattern(dof_handler, dsp, constraints); - sparsity_pattern.copy_from(dsp); - } - system_matrix.reinit(sparsity_pattern); - - // The multigrid constraints have to be initialized. They need to know - // where Dirichlet boundary conditions are prescribed. - mg_constrained_dofs.clear(); - mg_constrained_dofs.initialize(dof_handler); - mg_constrained_dofs.make_zero_boundary_constraints(dof_handler, - dirichlet_boundary_ids); - - - // Now for the things that concern the multigrid data structures. First, we - // resize the multilevel objects to hold matrices and sparsity patterns for - // every level. The coarse level is zero (this is mandatory right now but - // may change in a future revision). Note that these functions take a - // complete, inclusive range here (not a starting index and size), so the - // finest level is n_levels-1. We first have to resize the - // container holding the SparseMatrix classes, since they have to release - // their SparsityPattern before the can be destroyed upon resizing. - const unsigned int n_levels = triangulation.n_levels(); - - mg_interface_matrices.resize(0, n_levels - 1); - mg_matrices.resize(0, n_levels - 1); - mg_sparsity_patterns.resize(0, n_levels - 1); - mg_interface_sparsity_patterns.resize(0, n_levels - 1); - - // Now, we have to provide a matrix on each level. To this end, we first use - // the MGTools::make_sparsity_pattern function to generate a preliminary - // compressed sparsity pattern on each level (see the @ref Sparsity module - // for more information on this topic) and then copy it over to the one we - // really want. The next step is to initialize the interface matrices with - // the fitting sparsity pattern. - // - // It may be worth pointing out that the interface matrices only have - // entries for degrees of freedom that sit at or next to the interface - // between coarser and finer levels of the mesh. They are therefore even - // sparser than the matrices on the individual levels of our multigrid - // hierarchy. Therefore, we use a function specifically build for this - // purpose to generate it. - for (unsigned int level = 0; level < n_levels; ++level) - { - { - DynamicSparsityPattern dsp(dof_handler.n_dofs(level), - dof_handler.n_dofs(level)); - MGTools::make_sparsity_pattern(dof_handler, dsp, level); - - mg_sparsity_patterns[level].copy_from(dsp); - mg_matrices[level].reinit(mg_sparsity_patterns[level]); - } - { - DynamicSparsityPattern dsp(dof_handler.n_dofs(level), - dof_handler.n_dofs(level)); - MGTools::make_interface_sparsity_pattern(dof_handler, - mg_constrained_dofs, - dsp, - level); - mg_interface_sparsity_patterns[level].copy_from(dsp); - mg_interface_matrices[level].reinit( - mg_interface_sparsity_patterns[level]); - } - } - } - - - // @sect4{LaplaceProblem::cell_worker} - - // The cell_worker function is used to assemble the matrix and right-hand side - // on the given cell. This function is used for the active cells to generate - // the system_matrix and on each level to build the level matrices. - // - // Note that we also assemble a right-hand side when called from - // assemble_multigrid() even though it is not used. - template - template - void LaplaceProblem::cell_worker(const Iterator & cell, - ScratchData &scratch_data, - CopyData & copy_data) - { - FEValues &fe_values = scratch_data.fe_values; - fe_values.reinit(cell); - - const unsigned int dofs_per_cell = fe_values.get_fe().dofs_per_cell; - const unsigned int n_q_points = fe_values.get_quadrature().size(); - - copy_data.reinit(cell, dofs_per_cell); - - const std::vector &JxW = fe_values.get_JxW_values(); - - for (unsigned int q = 0; q < n_q_points; ++q) - { - const double coefficient = - (fe_values.get_quadrature_points()[q][0] < 0.0) ? 1.0 : 0.1; - //(cell->center().square() < 0.5 * 0.5) ? 10.0:1.0; - - for (unsigned int i = 0; i < dofs_per_cell; ++i) - { - for (unsigned int j = 0; j < dofs_per_cell; ++j) - { - copy_data.cell_matrix(i, j) += - coefficient * - (fe_values.shape_grad(i, q) * fe_values.shape_grad(j, q)) * - JxW[q]; - } - copy_data.cell_rhs(i) += 1.0 * fe_values.shape_value(i, q) * JxW[q]; - } - } - } - - - - // @sect4{LaplaceProblem::assemble_system} - - // The following function assembles the linear system on the active cells of - // the mesh. For this, we pass two lambda functions to the mesh_loop() - // function. The cell_worker function redirects to the class member function - // of the same name, while the copier is specific to this function and copies - // local matrix and vector to the corresponding global ones using the - // constraints. - template - void LaplaceProblem::assemble_system() - { - MappingQ1 mapping; - - auto cell_worker = - [&](const typename DoFHandler::active_cell_iterator &cell, - ScratchData & scratch_data, - CopyData & copy_data) { - this->cell_worker(cell, scratch_data, copy_data); - }; - - auto copier = [&](const CopyData &cd) { - this->constraints.distribute_local_to_global(cd.cell_matrix, - cd.cell_rhs, - cd.local_dof_indices, - system_matrix, - system_rhs); - }; - - const unsigned int n_gauss_points = degree + 1; - - ScratchData scratch_data(mapping, - fe, - n_gauss_points, - update_values | update_gradients | - update_JxW_values | - update_quadrature_points); - - MeshWorker::mesh_loop(dof_handler.begin_active(), - dof_handler.end(), - cell_worker, - copier, - scratch_data, - CopyData(), - MeshWorker::assemble_own_cells); - } - - - // @sect4{LaplaceProblem::assemble_multigrid} - - // The next function is the one that builds the matrices - // that define the multigrid method on each level of the mesh. The integration - // core is the same as above, but the loop below will go over all existing - // cells instead of just the active ones, and the results must be entered into - // the correct level matrices. Fortunately, MeshWorker hides most of that from - // us, and thus the difference between this function and the previous lies - // only in the setup of the assembler and the different iterators in the loop. - // - // We generate an AffineConstraints<> object for each level containing the - // boundary and interface dofs as constrained entries. The corresponding - // object is then used to generate the level matrices. - template - void LaplaceProblem::assemble_multigrid() - { - MappingQ1 mapping; - const unsigned int n_levels = triangulation.n_levels(); - - std::vector> boundary_constraints(n_levels); - for (unsigned int level = 0; level < n_levels; ++level) - { - IndexSet dofset; - DoFTools::extract_locally_relevant_level_dofs(dof_handler, - level, - dofset); - boundary_constraints[level].reinit(dofset); - boundary_constraints[level].add_lines( - mg_constrained_dofs.get_refinement_edge_indices(level)); - boundary_constraints[level].add_lines( - mg_constrained_dofs.get_boundary_indices(level)); - boundary_constraints[level].close(); - } - - auto cell_worker = - [&](const typename DoFHandler::level_cell_iterator &cell, - ScratchData & scratch_data, - CopyData & copy_data) { - this->cell_worker(cell, scratch_data, copy_data); - }; - - auto copier = [&](const CopyData &cd) { - boundary_constraints[cd.level].distribute_local_to_global( - cd.cell_matrix, cd.local_dof_indices, mg_matrices[cd.level]); - - const unsigned int dofs_per_cell = cd.local_dof_indices.size(); - - // TODO EXPLAIN: - - for (unsigned int i = 0; i < dofs_per_cell; ++i) - for (unsigned int j = 0; j < dofs_per_cell; ++j) - if (mg_constrained_dofs.is_interface_matrix_entry( - cd.level, cd.local_dof_indices[i], cd.local_dof_indices[j])) - { - mg_interface_matrices[cd.level].add(cd.local_dof_indices[i], - cd.local_dof_indices[j], - cd.cell_matrix(i, j)); - } - }; - - const unsigned int n_gauss_points = degree + 1; - - ScratchData scratch_data(mapping, - fe, - n_gauss_points, - update_values | update_gradients | - update_JxW_values | - update_quadrature_points); - - MeshWorker::mesh_loop(dof_handler.begin_mg(), - dof_handler.end_mg(), - cell_worker, - copier, - scratch_data, - CopyData(), - MeshWorker::assemble_own_cells); - } - - - - // @sect4{LaplaceProblem::solve} - - // This is the other function that is significantly different in support of - // the multigrid solver (or, in fact, the preconditioner for which we use - // the multigrid method). - // - // Let us start out by setting up two of the components of multilevel - // methods: transfer operators between levels, and a solver on the coarsest - // level. In finite element methods, the transfer operators are derived from - // the finite element function spaces involved and can often be computed in - // a generic way independent of the problem under consideration. In that - // case, we can use the MGTransferPrebuilt class that, given the constraints - // of the final linear system and the MGConstrainedDoFs object that knows - // about the boundary conditions on the each level and the degrees of - // freedom on interfaces between different refinement level can build the - // matrices for those transfer operations from a DoFHandler object with - // level degrees of freedom. - // - // The second part of the following lines deals with the coarse grid - // solver. Since our coarse grid is very coarse indeed, we decide for a - // direct solver (a Householder decomposition of the coarsest level matrix), - // even if its implementation is not particularly sophisticated. If our - // coarse mesh had many more cells than the five we have here, something - // better suited would obviously be necessary here. - template - void LaplaceProblem::solve() - { - MGTransferPrebuilt> mg_transfer(mg_constrained_dofs); - mg_transfer.build_matrices(dof_handler); - - FullMatrix coarse_matrix; - coarse_matrix.copy_from(mg_matrices[0]); - MGCoarseGridHouseholder<> coarse_grid_solver; - coarse_grid_solver.initialize(coarse_matrix); - - // The next component of a multilevel solver or preconditioner is that we - // need a smoother on each level. A common choice for this is to use the - // application of a relaxation method (such as the SOR, Jacobi or Richardson - // method) or a small number of iterations of a solver method (such as CG or - // GMRES). The mg::SmootherRelaxation and MGSmootherPrecondition classes - // provide support for these two kinds of smoothers. Here, we opt for the - // application of a single SOR iteration. To this end, we define an - // appropriate alias and then setup a smoother object. - // - // The last step is to initialize the smoother object with our level - // matrices and to set some smoothing parameters. The - // initialize() function can optionally take additional - // arguments that will be passed to the smoother object on each level. In - // the current case for the SOR smoother, this could, for example, include - // a relaxation parameter. However, we here leave these at their default - // values. The call to set_steps() indicates that we will use - // two pre- and two post-smoothing steps on each level; to use a variable - // number of smoother steps on different levels, more options can be set - // in the constructor call to the mg_smoother object. - // - // The last step results from the fact that we use the SOR method as a - // smoother - which is not symmetric - but we use the conjugate gradient - // iteration (which requires a symmetric preconditioner) below, we need to - // let the multilevel preconditioner make sure that we get a symmetric - // operator even for nonsymmetric smoothers: - using Smoother = PreconditionSOR>; - mg::SmootherRelaxation> mg_smoother; - mg_smoother.initialize(mg_matrices); - mg_smoother.set_steps(2); - mg_smoother.set_symmetric(true); - - // The next preparatory step is that we must wrap our level and interface - // matrices in an object having the required multiplication functions. We - // will create two objects for the interface objects going from coarse to - // fine and the other way around; the multigrid algorithm will later use - // the transpose operator for the latter operation, allowing us to - // initialize both up and down versions of the operator with the matrices - // we already built: - mg::Matrix> mg_matrix(mg_matrices); - mg::Matrix> mg_interface_up(mg_interface_matrices); - mg::Matrix> mg_interface_down(mg_interface_matrices); - - // Now, we are ready to set up the V-cycle operator and the multilevel - // preconditioner. - Multigrid> mg( - mg_matrix, coarse_grid_solver, mg_transfer, mg_smoother, mg_smoother); - mg.set_edge_matrices(mg_interface_down, mg_interface_up); - - PreconditionMG, MGTransferPrebuilt>> - preconditioner(dof_handler, mg, mg_transfer); - - // With all this together, we can finally get about solving the linear - // system in the usual way: - SolverControl solver_control(1000, 1e-12); - SolverCG<> solver(solver_control); - - solution = 0; - - solver.solve(system_matrix, solution, system_rhs, preconditioner); - std::cout << " Number of CG iterations: " << solver_control.last_step() - << "\n" - << std::endl; - constraints.distribute(solution); - } - - - - // @sect4{Postprocessing} - - // The following two functions postprocess a solution once it is - // computed. In particular, the first one refines the mesh at the beginning - // of each cycle while the second one outputs results at the end of each - // such cycle. The functions are almost unchanged from those in step-6. - template - void LaplaceProblem::refine_grid() - { - Vector estimated_error_per_cell(triangulation.n_active_cells()); - - KellyErrorEstimator::estimate( - dof_handler, - QGauss(degree + 2), - std::map *>(), - solution, - estimated_error_per_cell); - GridRefinement::refine_and_coarsen_fixed_number(triangulation, - estimated_error_per_cell, - 0.3, - 0.03); - triangulation.execute_coarsening_and_refinement(); - } - - - - template - void LaplaceProblem::output_results(const unsigned int cycle) const - { - DataOut data_out; - - data_out.attach_dof_handler(dof_handler); - data_out.add_data_vector(solution, "solution"); - data_out.build_patches(); - - std::ofstream output("solution-" + std::to_string(cycle) + ".vtk"); - data_out.write_vtk(output); - } - - - // @sect4{LaplaceProblem::run} - - // Like several of the functions above, this is almost exactly a copy of - // the corresponding function in step-6. The only difference is the call to - // assemble_multigrid that takes care of forming the matrices - // on every level that we need in the multigrid method. - template - void LaplaceProblem::run() - { - for (unsigned int cycle = 0; cycle < 8; ++cycle) - { - std::cout << "Cycle " << cycle << std::endl; - - if (cycle == 0) - { - GridGenerator::hyper_ball(triangulation); - triangulation.refine_global(2); - } - else - refine_grid(); - - std::cout << " Number of active cells: " - << triangulation.n_active_cells() << std::endl; - - setup_system(); - - assemble_system(); - assemble_multigrid(); - - solve(); - output_results(cycle); - } - } -} // namespace Step16 - - -// @sect3{The main() function} -// -// This is again the same function as in step-6: int main() { try { - using namespace Step16; - - LaplaceProblem<2> laplace_problem(1); - laplace_problem.run(); + // do nothing. } catch (std::exception &exc) { From 583b5acc874e6e36b591801c508828f82c8d269b Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Sat, 9 Feb 2019 10:48:12 -0700 Subject: [PATCH 119/507] [CI]: expose tests in Jenkins --- Jenkinsfile | 25 +++++++++++++++++++++---- 1 file changed, 21 insertions(+), 4 deletions(-) diff --git a/Jenkinsfile b/Jenkinsfile index 9e3e48848fc8..e6f70559f4e0 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -76,7 +76,15 @@ pipeline image 'tjhei/candi:v9.0.1-r4' } } - post { cleanup { cleanWs() } } + post { + always { + sh "cp /home/dealii/build/Testing/*/*.xml $WORKSPACE/serial.xml || true" + xunit tools: [CTest(pattern: '*.xml')] + } + cleanup { + cleanWs() + } + } steps { @@ -97,7 +105,7 @@ pipeline $WORKSPACE/ time ninja -j $NP time ninja setup_tests - time ctest --output-on-failure -DDESCRIPTION="CI-$JOB_NAME" -j $NP + time ctest --output-on-failure -DDESCRIPTION="CI-$JOB_NAME" -j $NP --no-compress-output -T test ''' } } @@ -113,7 +121,15 @@ pipeline image 'tjhei/candi:v9.0.1-r4' } } - post { cleanup { cleanWs() } } + post { + always { + sh "cp /home/dealii/build/Testing/*/*.xml $WORKSPACE/mpi.xml || true" + xunit tools: [CTest(pattern: '*.xml')] + } + cleanup { + cleanWs() + } + } steps { @@ -132,10 +148,11 @@ pipeline $WORKSPACE/ time ninja -j $NP time ninja setup_tests - time ctest -R "all-headers|multigrid/transfer" --output-on-failure -DDESCRIPTION="CI-$JOB_NAME" -j $NP + time ctest -R "all-headers|multigrid/transfer" --output-on-failure -DDESCRIPTION="CI-$JOB_NAME" -j $NP --no-compress-output -T test ''' } } + } } From 9d41443da1975f5c0ae8fe55c86558863b2e4fa5 Mon Sep 17 00:00:00 2001 From: Giovanni Alzetta Date: Wed, 13 Feb 2019 09:30:53 +0100 Subject: [PATCH 120/507] Adding cell_hint to GridTools::compute_point_locations documentation --- include/deal.II/grid/grid_tools.h | 2 ++ 1 file changed, 2 insertions(+) diff --git a/include/deal.II/grid/grid_tools.h b/include/deal.II/grid/grid_tools.h index 3a89f434b751..420ec05376d5 100644 --- a/include/deal.II/grid/grid_tools.h +++ b/include/deal.II/grid/grid_tools.h @@ -698,6 +698,8 @@ namespace GridTools * * @param[in] cache The triangulation's GridTools::Cache . * @param[in] points The point's vector. + * @param[in] cell_hint (optional) A cell iterator for a cell which likely + * contains the first point of @p points. * * @return A tuple containing the following information: * - Cells, is a vector of a vector cells of the all cells From 229e27b92360196e6371306d65e87f0db0ab5ba9 Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Wed, 13 Feb 2019 08:31:48 -0700 Subject: [PATCH 121/507] add include --- examples/step-63/step-63.cc | 2 ++ 1 file changed, 2 insertions(+) diff --git a/examples/step-63/step-63.cc b/examples/step-63/step-63.cc index d2b9a18715f6..2534596dc665 100644 --- a/examples/step-63/step-63.cc +++ b/examples/step-63/step-63.cc @@ -20,8 +20,10 @@ // @note: This is work in progress and will be an example for block smoothers // in geometric multigrid. +#include #include + int main() { try From cd914279550bebc954c219c4e072e4e64246f2f7 Mon Sep 17 00:00:00 2001 From: Matthias Maier Date: Wed, 13 Feb 2019 19:00:48 -0600 Subject: [PATCH 122/507] Documentation: add some pointers to step-20 --- doc/doxygen/headers/laoperators.h | 6 ++++++ include/deal.II/lac/linear_operator.h | 3 +++ include/deal.II/lac/packaged_operation.h | 3 +++ 3 files changed, 12 insertions(+) diff --git a/doc/doxygen/headers/laoperators.h b/doc/doxygen/headers/laoperators.h index 64d8bfe40fad..49d2a122bda0 100644 --- a/doc/doxygen/headers/laoperators.h +++ b/doc/doxygen/headers/laoperators.h @@ -89,6 +89,9 @@ * encapsulation of individual linear operators into blocked linear * operator variants. * + * The step-20 tutorial program has a detailed usage example of the + * LinearOperator class. + * * @note As explained below, when using LinearOperator as res = op_a*x * a PackagedOperation class instance is generated behind-the-curtains. * Consequently, the user program has to include header files for both classes @@ -175,6 +178,9 @@ * Vector residual = b - op_a * x; // computes the residual at this point * @endcode * + * The step-20 tutorial program has a detailed usage example of the + * PackagedOperation class. + * * * @ingroup LAC * @ingroup MATRICES diff --git a/include/deal.II/lac/linear_operator.h b/include/deal.II/lac/linear_operator.h index e066190781cd..ef84db6e253c 100644 --- a/include/deal.II/lac/linear_operator.h +++ b/include/deal.II/lac/linear_operator.h @@ -151,6 +151,9 @@ null_operator(const LinearOperator &); * for linear operators have been provided within the respective * TrilinosWrappers (and, in the future, PETScWrappers) namespaces. * + * @note The step-20 tutorial program has a detailed usage example of the + * LinearOperator class. + * * @author Luca Heltai, Matthias Maier, 2015; Jean-Paul Pelteret, 2016 * * @ingroup LAOperators diff --git a/include/deal.II/lac/packaged_operation.h b/include/deal.II/lac/packaged_operation.h index 8c73828e2ad1..f4da9786afef 100644 --- a/include/deal.II/lac/packaged_operation.h +++ b/include/deal.II/lac/packaged_operation.h @@ -93,6 +93,9 @@ class PackagedOperation; * y -= residual; * @endcode * + * @note The step-20 tutorial program has a detailed usage example of the + * LinearOperator class. + * * @author Matthias Maier, 2015 * * @ingroup LAOperators From c46ca30fe9b73ae1c4ac13010f8377705b6e285e Mon Sep 17 00:00:00 2001 From: Bruno Turcksin Date: Thu, 14 Feb 2019 02:31:17 +0000 Subject: [PATCH 123/507] Do not use cudaDeviceSynchronize in release mode --- .../deal.II/lac/vector_operations_internal.h | 26 +++++++++++++++++++ source/lac/cuda_sparse_matrix.cu | 10 +++++++ source/lac/cuda_vector.cu | 23 ++++++++++++++++ 3 files changed, 59 insertions(+) diff --git a/include/deal.II/lac/vector_operations_internal.h b/include/deal.II/lac/vector_operations_internal.h index c78df10c9433..5d98e3f23a6b 100644 --- a/include/deal.II/lac/vector_operations_internal.h +++ b/include/deal.II/lac/vector_operations_internal.h @@ -2026,10 +2026,12 @@ namespace internal ::dealii::LinearAlgebra::CUDAWrappers::kernel::set <<>>(data.values_dev.get(), s, size); +# ifdef DEBUG // Check that the kernel was launched correctly AssertCuda(cudaGetLastError()); // Check that there was no problem during the execution of the kernel AssertCuda(cudaDeviceSynchronize()); +# endif } static void @@ -2049,10 +2051,12 @@ namespace internal v_data.values_dev.get(), size); +# ifdef DEBUG // Check that the kernel was launched correctly AssertCuda(cudaGetLastError()); // Check that there was no problem during the execution of the kernel AssertCuda(cudaDeviceSynchronize()); +# endif } static void @@ -2072,10 +2076,12 @@ namespace internal v_data.values_dev.get(), size); +# ifdef DEBUG // Check that the kernel was launched correctly AssertCuda(cudaGetLastError()); // Check that there was no problem during the execution of the kernel AssertCuda(cudaDeviceSynchronize()); +# endif } static void @@ -2091,10 +2097,12 @@ namespace internal ::dealii::LinearAlgebra::CUDAWrappers::kernel::vec_add <<>>(data.values_dev.get(), a, size); +# ifdef DEBUG // Check that the kernel was launched correctly AssertCuda(cudaGetLastError()); // Check that there was no problem during the execution of the kernel AssertCuda(cudaDeviceSynchronize()); +# endif } static void @@ -2115,10 +2123,12 @@ namespace internal v_data.values_dev.get(), size); +# ifdef DEBUG // Check that the kernel was launched correctly AssertCuda(cudaGetLastError()); // Check that there was no problem during the execution of the kernel AssertCuda(cudaDeviceSynchronize()); +# endif } static void @@ -2144,10 +2154,12 @@ namespace internal w_data.values_dev.get(), size); +# ifdef DEBUG // Check that the kernel was launched correctly AssertCuda(cudaGetLastError()); // Check that there was no problem during the execution of the kernel AssertCuda(cudaDeviceSynchronize()); +# endif } static void @@ -2166,10 +2178,12 @@ namespace internal <<>>( x, data.values_dev.get(), 1., v_data.values_dev.get(), size); +# ifdef DEBUG // Check that the kernel was launched correctly AssertCuda(cudaGetLastError()); // Check that there was no problem during the execution of the kernel AssertCuda(cudaDeviceSynchronize()); +# endif } static void @@ -2189,10 +2203,12 @@ namespace internal <<>>( x, data.values_dev.get(), a, v_data.values_dev.get(), size); +# ifdef DEBUG // Check that the kernel was launched correctly AssertCuda(cudaGetLastError()); // Check that there was no problem during the execution of the kernel AssertCuda(cudaDeviceSynchronize()); +# endif } static void @@ -2220,10 +2236,12 @@ namespace internal w_data.values_dev.get(), size); +# ifdef DEBUG // Check that the kernel was launched correctly AssertCuda(cudaGetLastError()); // Check that there was no problem during the execution of the kernel AssertCuda(cudaDeviceSynchronize()); +# endif } static void @@ -2239,10 +2257,12 @@ namespace internal ::dealii::LinearAlgebra::CUDAWrappers::kernel::vec_scale <<>>(data.values_dev.get(), factor, size); +# ifdef DEBUG // Check that the kernel was launched correctly AssertCuda(cudaGetLastError()); // Check that there was no problem during the execution of the kernel AssertCuda(cudaDeviceSynchronize()); +# endif } static void @@ -2261,10 +2281,12 @@ namespace internal v_data.values_dev.get(), size); +# ifdef DEBUG // Check that the kernel was launched correctly AssertCuda(cudaGetLastError()); // Check that there was no problem during the execution of the kernel AssertCuda(cudaDeviceSynchronize()); +# endif } static void @@ -2285,10 +2307,12 @@ namespace internal v_data.values_dev.get(), size); +# ifdef DEBUG // Check that the kernel was launched correctly AssertCuda(cudaGetLastError()); // Check that there was no problem during the execution of the kernel AssertCuda(cudaDeviceSynchronize()); +# endif } static void @@ -2314,10 +2338,12 @@ namespace internal w_data.values_dev.get(), size); +# ifdef DEBUG // Check that the kernel was launched correctly AssertCuda(cudaGetLastError()); // Check that there was no problem during the execution of the kernel AssertCuda(cudaDeviceSynchronize()); +# endif } static Number diff --git a/source/lac/cuda_sparse_matrix.cu b/source/lac/cuda_sparse_matrix.cu index 6756e9d97ded..687e565d26ec 100644 --- a/source/lac/cuda_sparse_matrix.cu +++ b/source/lac/cuda_sparse_matrix.cu @@ -343,10 +343,12 @@ namespace CUDAWrappers internal::scale <<>>(val_dev.get(), factor, nnz); +# ifdef DEBUG // Check that the kernel was launched correctly AssertCuda(cudaGetLastError()); // Check that there was no problem during the execution of the kernel AssertCuda(cudaDeviceSynchronize()); +# endif return *this; } @@ -363,10 +365,12 @@ namespace CUDAWrappers internal::scale <<>>(val_dev.get(), 1. / factor, nnz); +# ifdef DEBUG // Check that the kernel was launched correctly AssertCuda(cudaGetLastError()); // Check that there was no problem during the execution of the kernel AssertCuda(cudaDeviceSynchronize()); +# endif return *this; } @@ -515,10 +519,13 @@ namespace CUDAWrappers column_index_dev.get(), row_ptr_dev.get(), column_sums.get_values()); + +# ifdef DEBUG // Check that the kernel was launched correctly AssertCuda(cudaGetLastError()); // Check that there was no problem during the execution of the kernel AssertCuda(cudaDeviceSynchronize()); +# endif return column_sums.linfty_norm(); } @@ -537,10 +544,13 @@ namespace CUDAWrappers column_index_dev.get(), row_ptr_dev.get(), row_sums.get_values()); + +# ifdef DEUG // Check that the kernel was launched correctly AssertCuda(cudaGetLastError()); // Check that there was no problem during the execution of the kernel AssertCuda(cudaDeviceSynchronize()); +# endif return row_sums.linfty_norm(); } diff --git a/source/lac/cuda_vector.cu b/source/lac/cuda_vector.cu index 4f12a49740db..0787cb679c70 100644 --- a/source/lac/cuda_vector.cu +++ b/source/lac/cuda_vector.cu @@ -158,10 +158,13 @@ namespace LinearAlgebra kernel::vector_bin_op <<>>(val.get(), tmp, n_elements); + +# ifdef DEBUG // Check that the kernel was launched correctly AssertCuda(cudaGetLastError()); // Check that there was no problem during the execution of the kernel AssertCuda(cudaDeviceSynchronize()); +# endif // Delete the temporary vector Utilities::CUDA::free(tmp); @@ -197,10 +200,12 @@ namespace LinearAlgebra kernel::vec_scale <<>>(val.get(), factor, n_elements); +# ifdef DEBUG // Check that the kernel was launched correctly AssertCuda(cudaGetLastError()); // Check that there was no problem during the execution of the kernel AssertCuda(cudaDeviceSynchronize()); +# endif return *this; } @@ -217,10 +222,12 @@ namespace LinearAlgebra kernel::vec_scale <<>>(val.get(), 1. / factor, n_elements); +# ifdef DEBUG // Check that the kernel was launched correctly AssertCuda(cudaGetLastError()); // Check that there was no problem during the execution of the kernel AssertCuda(cudaDeviceSynchronize()); +# endif return *this; } @@ -246,10 +253,12 @@ namespace LinearAlgebra kernel::vector_bin_op <<>>(val.get(), down_V.val.get(), n_elements); +# ifdef DEBUG // Check that the kernel was launched correctly AssertCuda(cudaGetLastError()); // Check that there was no problem during the execution of the kernel AssertCuda(cudaDeviceSynchronize()); +# endif return *this; } @@ -275,10 +284,12 @@ namespace LinearAlgebra kernel::vector_bin_op <<>>(val.get(), down_V.val.get(), n_elements); +# ifdef DEBUG // Check that the kernel was launched correctly AssertCuda(cudaGetLastError()); // Check that there was no problem during the execution of the kernel AssertCuda(cudaDeviceSynchronize()); +# endif return *this; } @@ -336,10 +347,12 @@ namespace LinearAlgebra kernel::vec_add <<>>(val.get(), a, n_elements); +# ifdef DEBUG // Check that the kernel was launched correctly AssertCuda(cudaGetLastError()); // Check that there was no problem during the execution of the kernel AssertCuda(cudaDeviceSynchronize()); +# endif } @@ -364,10 +377,12 @@ namespace LinearAlgebra kernel::add_aV<<>>( val.get(), a, down_V.val.get(), n_elements); +# ifdef DEBUG // Check that the kernel was launched correctly AssertCuda(cudaGetLastError()); // Check that there was no problem during the execution of the kernel AssertCuda(cudaDeviceSynchronize()); +# endif } @@ -406,10 +421,12 @@ namespace LinearAlgebra kernel::add_aVbW<<>>( val.get(), a, down_V.val.get(), b, down_W.val.get(), n_elements); +# ifdef DEBUG // Check that the kernel was launched correctly AssertCuda(cudaGetLastError()); // Check that there was no problem during the execution of the kernel AssertCuda(cudaDeviceSynchronize()); +# endif } @@ -437,10 +454,12 @@ namespace LinearAlgebra kernel::sadd<<>>( s, val.get(), a, down_V.val.get(), n_elements); +# ifdef DEBUG // Check that the kernel was launched correctly AssertCuda(cudaGetLastError()); // Check that there was no problem during the execution of the kernel AssertCuda(cudaDeviceSynchronize()); +# endif } @@ -464,10 +483,12 @@ namespace LinearAlgebra kernel::scale<<>>( val.get(), down_scaling_factors.val.get(), n_elements); +# ifdef DEBUG // Check that the kernel was launched correctly AssertCuda(cudaGetLastError()); // Check that there was no problem during the execution of the kernel AssertCuda(cudaDeviceSynchronize()); +# endif } @@ -493,10 +514,12 @@ namespace LinearAlgebra kernel::equ<<>>( val.get(), a, down_V.val.get(), n_elements); +# ifdef DEBUG // Check that the kernel was launched correctly AssertCuda(cudaGetLastError()); // Check that there was no problem during the execution of the kernel AssertCuda(cudaDeviceSynchronize()); +# endif } From b2bac494a46b5322fa7d2507c937b1b200bf5491 Mon Sep 17 00:00:00 2001 From: Giovanni Alzetta Date: Wed, 9 Jan 2019 15:32:24 +0100 Subject: [PATCH 124/507] Added new function compute point locations try all --- include/deal.II/grid/grid_tools.h | 41 +++++ source/grid/grid_tools.cc | 120 ++++++++++++--- source/grid/grid_tools.inst.in | 13 ++ .../compute_point_locations_try_all_01.cc | 143 ++++++++++++++++++ .../compute_point_locations_try_all_01.output | 12 ++ 5 files changed, 311 insertions(+), 18 deletions(-) create mode 100644 tests/grid/compute_point_locations_try_all_01.cc create mode 100644 tests/grid/compute_point_locations_try_all_01.output diff --git a/include/deal.II/grid/grid_tools.h b/include/deal.II/grid/grid_tools.h index 3a89f434b751..809de1bccad4 100644 --- a/include/deal.II/grid/grid_tools.h +++ b/include/deal.II/grid/grid_tools.h @@ -720,6 +720,9 @@ namespace GridTools * they belong are the best case. Pre-sorting points, trying to minimize * distances between them, might make the function extremely faster. * + * @note If a point is not found inside the mesh, or is lying inside an + * artificial cell of a parallel::Triangulation, an exception is thrown. + * * @note The actual return type of this function, i.e., the type referenced * above as @p return_type, is * @code @@ -750,6 +753,44 @@ namespace GridTools &cell_hint = typename Triangulation::active_cell_iterator()); + /** + * This function is similar to GridTools::compute_point_locations(), + * but it tries to find and transform every point of @p points. + * + * @return A tuple containing four elements; the first three + * are documented in GridTools::compute_point_locations(). + * The last element of the @p return_type contains the + * indices of points which are not not found inside the mesh + * or lie on artificial cells. + * + * @code + * std::tuple< + * std::vector::active_cell_iterator>, std::vector>>, + * std::vector>, + * std::vector> + * @endcode + * + * For a more detailed documentation see + * GridTools::compute_point_locations(). + */ + template +# ifndef DOXYGEN + std::tuple< + std::vector::active_cell_iterator>, + std::vector>>, + std::vector>, + std::vector> +# else + return_type +# endif + compute_point_locations_try_all( + const Cache & cache, + const std::vector> &points, + const typename Triangulation::active_cell_iterator + &cell_hint = + typename Triangulation::active_cell_iterator()); + /** * Given a @p cache and a list of * @p local_points for each process, find the points lying on the locally diff --git a/source/grid/grid_tools.cc b/source/grid/grid_tools.cc index 201dfe03f9ee..bd97f63dc4b9 100644 --- a/source/grid/grid_tools.cc +++ b/source/grid/grid_tools.cc @@ -4193,14 +4193,50 @@ namespace GridTools const std::vector> &points, const typename Triangulation::active_cell_iterator &cell_hint) + { + const auto cqmp = compute_point_locations_try_all(cache, points, cell_hint); + // Splitting the tuple's components + auto &cells = std::get<0>(cqmp); + auto &qpoints = std::get<1>(cqmp); + auto &maps = std::get<2>(cqmp); + auto &missing_points = std::get<3>(cqmp); + // If a point was not found, throwing an error, as the old + // implementation of compute_point_locations would have done + AssertThrow(std::get<3>(cqmp).size() == 0, + ExcPointNotFound(points[missing_points[0]])); + + (void)missing_points; + + return {std::move(cells), std::move(qpoints), std::move(maps)}; + } + + + + template +#ifndef DOXYGEN + std::tuple< + std::vector::active_cell_iterator>, + std::vector>>, + std::vector>, + std::vector> +#else + return_type +#endif + compute_point_locations_try_all( + const Cache & cache, + const std::vector> &points, + const typename Triangulation::active_cell_iterator + &cell_hint) { // How many points are here? - const unsigned int np = points.size(); + const unsigned int np = points.size(); + std::vector points_outside; std::tuple< std::vector::active_cell_iterator>, std::vector>>, - std::vector>> + std::vector>, + std::vector> cell_qpoint_map; // Now the easy case. @@ -4211,18 +4247,53 @@ namespace GridTools std::pair::active_cell_iterator, Point> my_pair; + + bool found = false; + unsigned int points_checked = 0; if (cell_hint.state() == IteratorState::valid) - my_pair = - GridTools::find_active_cell_around_point(cache, points[0], cell_hint); - else - my_pair = GridTools::find_active_cell_around_point(cache, points[0]); + { + try + { + my_pair = GridTools::find_active_cell_around_point(cache, + points[0], + cell_hint); + found = true; + } + catch (const GridTools::ExcPointNotFound &) + { + points_outside.emplace_back(0); + } + ++points_checked; + } + - std::get<0>(cell_qpoint_map).emplace_back(my_pair.first); - std::get<1>(cell_qpoint_map).emplace_back(1, my_pair.second); - std::get<2>(cell_qpoint_map).emplace_back(1, 0); + while (!found && points_checked < np) + { + try + { + my_pair = + GridTools::find_active_cell_around_point(cache, + points[points_checked]); + found = true; + } + catch (const GridTools::ExcPointNotFound &) + { + points_outside.emplace_back(points_checked); + } + // Updating the position of the analyzed points + ++points_checked; + } + + // If the point has been found in a cell, adding it + if (found) + { + std::get<0>(cell_qpoint_map).emplace_back(my_pair.first); + std::get<1>(cell_qpoint_map).emplace_back(1, my_pair.second); + std::get<2>(cell_qpoint_map).emplace_back(1, points_checked - 1); + } // Now the second easy case. - if (np == 1) + if (np == points_outside.size()) return cell_qpoint_map; // Computing the cell center and diameter Point cell_center = std::get<0>(cell_qpoint_map)[0]->center(); @@ -4230,15 +4301,24 @@ namespace GridTools (0.5 + std::numeric_limits::epsilon()); // Cycle over all points left - for (unsigned int p = 1; p < np; ++p) + for (unsigned int p = points_checked; p < np; ++p) { // Checking if the point is close to the cell center, in which // case calling find active cell with a cell hint - if (cell_center.distance(points[p]) < cell_diameter) - my_pair = GridTools::find_active_cell_around_point( - cache, points[p], std::get<0>(cell_qpoint_map).back()); - else - my_pair = GridTools::find_active_cell_around_point(cache, points[p]); + try + { + if (cell_center.distance(points[p]) < cell_diameter) + my_pair = GridTools::find_active_cell_around_point( + cache, points[p], std::get<0>(cell_qpoint_map).back()); + else + my_pair = + GridTools::find_active_cell_around_point(cache, points[p]); + } + catch (const GridTools::ExcPointNotFound &) + { + points_outside.push_back(p); + continue; + } // Assuming the cell is probably the last cell added if (my_pair.first == std::get<0>(cell_qpoint_map).back()) @@ -4298,7 +4378,8 @@ namespace GridTools // The number of points in all // the cells must be the same as // the number of points we - // started off from. + // started off from, + // plus the points which were ignored for (unsigned int n = 0; n < c; ++n) { Assert(std::get<1>(cell_qpoint_map)[n].size() == @@ -4307,9 +4388,12 @@ namespace GridTools std::get<2>(cell_qpoint_map)[n].size())); qps += std::get<1>(cell_qpoint_map)[n].size(); } - Assert(qps == np, ExcDimensionMismatch(qps, np)); + + Assert(qps + points_outside.size() == np, + ExcDimensionMismatch(qps + points_outside.size(), np)); #endif + std::get<3>(cell_qpoint_map) = points_outside; return cell_qpoint_map; } diff --git a/source/grid/grid_tools.inst.in b/source/grid/grid_tools.inst.in index c8b0ce9120e1..23dd04b907b6 100644 --- a/source/grid/grid_tools.inst.in +++ b/source/grid/grid_tools.inst.in @@ -93,6 +93,19 @@ for (deal_II_dimension : DIMENSIONS; deal_II_space_dimension : SPACE_DIMENSIONS) deal_II_space_dimension>::active_cell_iterator &, const std::vector &); + template std::tuple::active_cell_iterator>, + std::vector>>, + std::vector>, + std::vector> + compute_point_locations_try_all( + const Cache &, + const std::vector> &, + const typename Triangulation< + deal_II_dimension, + deal_II_space_dimension>::active_cell_iterator &); + template std::tuple::active_cell_iterator>, diff --git a/tests/grid/compute_point_locations_try_all_01.cc b/tests/grid/compute_point_locations_try_all_01.cc new file mode 100644 index 000000000000..ddb72f2e3f77 --- /dev/null +++ b/tests/grid/compute_point_locations_try_all_01.cc @@ -0,0 +1,143 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + +// Test GridTools::compute_point_locations_try_all +// Test for corner case: vector of points, some of which +// lie outside the mesh + +#include + +#include +#include +#include + +#include +#include +#include + +#include +#include +#include +#include + +#include + +#include + +#include "../tests.h" + +using namespace dealii; + +template +void +test_compute_pt_loc(unsigned int n_points) +{ + deallog << "Testing for dim = " << dim << std::endl; + deallog << "Testing on: " << n_points << " points." << std::endl; + + // Creating a grid in the square [0,1]x[0,1] + Triangulation tria; + GridGenerator::hyper_cube(tria); + tria.refine_global(std::max(6 - dim, 2)); + + // Creating the finite elements needed: + FE_Q fe(1); + DoFHandler dof_handler(tria); + dof_handler.distribute_dofs(fe); + + // Creating the random points + std::vector> points; + + for (size_t i = 0; i < n_points; ++i) + { + points.push_back(random_point()); + // One every three points is + // shifted outside the mesh + if (points.size() % 3 == dim - 1) + { + points.back()[0] += 5.0; + } + } + + // Initializing the cache + GridTools::Cache cache(tria); + + auto cell_qpoint_map = + GridTools::compute_point_locations_try_all(cache, points); + const auto &cells = std::get<0>(cell_qpoint_map); + const auto &qpoints = std::get<1>(cell_qpoint_map); + const auto &maps = std::get<2>(cell_qpoint_map); + const auto &other_p = std::get<3>(cell_qpoint_map); + size_t n_cells = cells.size(); + + deallog << "Points found in " << n_cells << " cells" << std::endl; + + unsigned int checked_points = 0; + // testing if the transformation is correct: + for (unsigned int i = 0; i < n_cells; ++i) + { + const auto &cell = cells[i]; + const auto &quad = qpoints[i]; + const auto &local_map = maps[i]; + + // Given the std::get<1>(cell_qpoint_map) of the current cell, compute the + // real points + FEValues fev(fe, quad, update_quadrature_points); + fev.reinit(cell); + const auto &real_quad = fev.get_quadrature_points(); + + for (unsigned int q = 0; q < real_quad.size(); ++q) + { + // Check if points are the same as real points + if (real_quad[q].distance(points[local_map[q]]) > 1e-10) + deallog << "Error on cell : " << cell << " at local point " << i + << ", corresponding to real point " << points[local_map[q]] + << ", that got transformed to " << real_quad[q] + << " instead." << std::endl; + else + ++checked_points; + } + } + for (auto i : other_p) + if (i % 3 != dim - 2) + { + deallog << "Error: point index " << i << " was not found!" << std::endl; + } + + if (checked_points + other_p.size() == points.size()) + deallog << "All points where processed correctly" << std::endl; + else + { + deallog << "Error: some points where not processed correctly" + << std::endl; + deallog << "Points found inside the mesh: " << checked_points + << std::endl; + deallog << "Discarded points: " << points.size() - checked_points + << std::endl; + deallog << "Points outside the mesh: " << other_p.size() << std::endl; + deallog << "Total points processed: " << points.size() << std::endl; + } + deallog << "Test finished" << std::endl; +} + +int +main() +{ + initlog(); + + deallog << "Deal.II compute_pt_loc_try_all:" << std::endl; + test_compute_pt_loc<2>(101); + test_compute_pt_loc<3>(202); +} diff --git a/tests/grid/compute_point_locations_try_all_01.output b/tests/grid/compute_point_locations_try_all_01.output new file mode 100644 index 000000000000..1272686f8528 --- /dev/null +++ b/tests/grid/compute_point_locations_try_all_01.output @@ -0,0 +1,12 @@ + +DEAL::Deal.II compute_pt_loc_try_all: +DEAL::Testing for dim = 2 +DEAL::Testing on: 101 points. +DEAL::Points found in 58 cells +DEAL::All points where processed correctly +DEAL::Test finished +DEAL::Testing for dim = 3 +DEAL::Testing on: 202 points. +DEAL::Points found in 119 cells +DEAL::All points where processed correctly +DEAL::Test finished From 5cca395fd110d6d30112aca0f157133c92cc9dfd Mon Sep 17 00:00:00 2001 From: Sebastian Stark Date: Wed, 13 Feb 2019 13:33:09 +0200 Subject: [PATCH 125/507] Fix bug in distribute_local_to_global If a local matrix with all diagonal elements equal to zero is distributed to a global matrix, the l1 norm of the local matrix divided by the size of the local matrix is now added to those diagonal elements of the global matrix which correspond to a constrained dof. In case the entire local matrix is zero, 1 is added. Previously zero was added for both cases, possibly resulting in singular global matrices. Additionally, a test for the patched version of distribute_local_to_global has been added. Fixes #7658 --- doc/news/changes/minor/20190213SebastianStark | 3 + .../lac/affine_constraints.templates.h | 20 ++++- ...nstraint_matrix_distribute_local_global.cc | 78 +++++++++++++++++++ ...aint_matrix_distribute_local_global.output | 7 ++ 4 files changed, 105 insertions(+), 3 deletions(-) create mode 100644 doc/news/changes/minor/20190213SebastianStark create mode 100644 tests/lac/constraint_matrix_distribute_local_global.cc create mode 100644 tests/lac/constraint_matrix_distribute_local_global.output diff --git a/doc/news/changes/minor/20190213SebastianStark b/doc/news/changes/minor/20190213SebastianStark new file mode 100644 index 000000000000..44710517f535 --- /dev/null +++ b/doc/news/changes/minor/20190213SebastianStark @@ -0,0 +1,3 @@ +Fixed: Handle the case properly that a local matrix with all diagonal elements equal to zero is distributed with AffineConstraints::distribute_local_to_global() to the global matrix while constraints apply. +
+(Sebastian Stark, 2019/02/13) diff --git a/include/deal.II/lac/affine_constraints.templates.h b/include/deal.II/lac/affine_constraints.templates.h index dc0df47d7f5a..9eb936ec9f73 100644 --- a/include/deal.II/lac/affine_constraints.templates.h +++ b/include/deal.II/lac/affine_constraints.templates.h @@ -3325,9 +3325,13 @@ namespace internals } // to make sure that the global matrix remains invertible, we need to do - // something with the diagonal elements. add the absolute value of the local - // matrix, so the resulting entry will always be positive and furthermore be - // in the same order of magnitude as the other elements of the matrix + // something with the diagonal elements. Add the average of the + // absolute values of the local matrix diagonals, so the resulting entry + // will always be positive and furthermore be in the same order of magnitude + // as the other elements of the matrix. If all local matrix diagonals are + // zero, add the l1 norm of the local matrix divided by the matrix size + // to the diagonal of the global matrix. If the entire local matrix is zero, + // add 1 to the diagonal of the global matrix. // // note that this also captures the special case that a dof is both // constrained and fixed (this can happen for hanging nodes in 3d that also @@ -3355,6 +3359,16 @@ namespace internals average_diagonal += std::abs(local_matrix(i, i)); average_diagonal /= static_cast(local_matrix.m()); + // handle the case that all diagonal elements are zero + if (average_diagonal == static_cast(0.)) + { + average_diagonal = static_cast(local_matrix.l1_norm()) / + static_cast(local_matrix.m()); + // if the entire matrix is zero, use 1. for the diagonal + if (average_diagonal == static_cast(0.)) + average_diagonal = static_cast(1.); + } + for (size_type i = 0; i < global_rows.n_constraints(); i++) { const size_type local_row = global_rows.constraint_origin(i); diff --git a/tests/lac/constraint_matrix_distribute_local_global.cc b/tests/lac/constraint_matrix_distribute_local_global.cc new file mode 100644 index 000000000000..c76d1372cd68 --- /dev/null +++ b/tests/lac/constraint_matrix_distribute_local_global.cc @@ -0,0 +1,78 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2005 - 2016 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + +#include +#include +#include + +#include + +#include + +#include "../tests.h" + +// Tests distribute_local_to_global for +// (1) the case that a local matrix +// with all diagonals equal to zero is +// distributed while a dof is +// constrained, and +// (2) the case that all entries of the local matrix +// are zero while a dof is constrained. + +using namespace dealii; + +int +main() +{ + initlog(); + + // set up constraint + AffineConstraints constraints; + constraints.add_line(0); + constraints.close(); + + // global matrix and vector + FullMatrix global_matrix(2); + Vector global_vector(2); + + // first test: add matrix with all diagonals zero + FullMatrix local_matrix(2); + local_matrix(1, 0) = local_matrix(0, 1) = 1.; + Vector local_vector(2); + constraints.distribute_local_to_global( + local_matrix, local_vector, {0, 1}, global_matrix, global_vector, true); + // output result + for (unsigned int m = 0; m < global_matrix.m(); ++m) + { + for (unsigned int n = 0; n < global_matrix.n(); ++n) + deallog << global_matrix(m, n) << " "; + deallog << std::endl; + } + deallog << std::endl; + + // second test: add matrix with all entries zero + global_matrix = 0.; + local_matrix = 0.; + constraints.distribute_local_to_global( + local_matrix, local_vector, {0, 1}, global_matrix, global_vector, true); + // output result + for (unsigned int m = 0; m < global_matrix.m(); ++m) + { + for (unsigned int n = 0; n < global_matrix.n(); ++n) + deallog << global_matrix(m, n) << " "; + deallog << std::endl; + } + deallog << std::endl; +} diff --git a/tests/lac/constraint_matrix_distribute_local_global.output b/tests/lac/constraint_matrix_distribute_local_global.output new file mode 100644 index 000000000000..6e129c4244cb --- /dev/null +++ b/tests/lac/constraint_matrix_distribute_local_global.output @@ -0,0 +1,7 @@ + +DEAL::0.500000 0.00000 +DEAL::0.00000 0.00000 +DEAL:: +DEAL::1.00000 0.00000 +DEAL::0.00000 0.00000 +DEAL:: From c7a3e6a787f0a1ddc8eb5ae5d43a77df2680eec8 Mon Sep 17 00:00:00 2001 From: Matthias Maier Date: Tue, 12 Feb 2019 14:34:17 -0600 Subject: [PATCH 126/507] lac/linear_operator.h: Add rvalue-reference variant of inverse_operator --- include/deal.II/lac/linear_operator.h | 106 ++++++++++++++++++++++++++ 1 file changed, 106 insertions(+) diff --git a/include/deal.II/lac/linear_operator.h b/include/deal.II/lac/linear_operator.h index ef84db6e253c..f0115ff2578d 100644 --- a/include/deal.II/lac/linear_operator.h +++ b/include/deal.II/lac/linear_operator.h @@ -41,6 +41,8 @@ namespace internal template class Vector; +class PreconditionIdentity; + template , typename Domain = Range, typename Payload = @@ -71,6 +73,10 @@ template < LinearOperator null_operator(const LinearOperator &); +template +LinearOperator +identity_operator(const LinearOperator &); + /** * A class to store the abstract concept of a linear operator. @@ -629,6 +635,7 @@ operator*(const LinearOperator & first_op, } } + /** * @relatesalso LinearOperator * @@ -725,6 +732,105 @@ inverse_operator(const LinearOperator &op, return return_op; } + +/** + * @relatesalso LinearOperator + * + * Variant of above function that takes a LinearOperator @p preconditioner + * as preconditioner argument. + * + * @ingroup LAOperators + */ +template +LinearOperator +inverse_operator(const LinearOperator &op, + Solver & solver, + const LinearOperator &preconditioner) +{ + LinearOperator return_op( + op.inverse_payload(solver, preconditioner)); + + return_op.reinit_range_vector = op.reinit_domain_vector; + return_op.reinit_domain_vector = op.reinit_range_vector; + + return_op.vmult = [op, &solver, preconditioner](Range &v, const Domain &u) { + op.reinit_range_vector(v, /*bool omit_zeroing_entries =*/false); + solver.solve(op, v, u, preconditioner); + }; + + return_op.vmult_add = [op, &solver, preconditioner](Range & v, + const Domain &u) { + GrowingVectorMemory vector_memory; + + typename VectorMemory::Pointer v2(vector_memory); + op.reinit_range_vector(*v2, /*bool omit_zeroing_entries =*/false); + solver.solve(op, *v2, u, preconditioner); + v += *v2; + }; + + return_op.Tvmult = [op, &solver, preconditioner](Range &v, const Domain &u) { + op.reinit_range_vector(v, /*bool omit_zeroing_entries =*/false); + solver.solve(transpose_operator(op), v, u, preconditioner); + }; + + return_op.Tvmult_add = [op, &solver, preconditioner](Range & v, + const Domain &u) { + GrowingVectorMemory vector_memory; + + typename VectorMemory::Pointer v2(vector_memory); + op.reinit_range_vector(*v2, /*bool omit_zeroing_entries =*/false); + solver.solve(transpose_operator(op), *v2, u, preconditioner); + v += *v2; + }; + + return return_op; +} + + +/** + * @relatesalso LinearOperator + * + * Variant of above function without a preconditioner argument. In this + * case the identity_operator() of the @p op argument is used as a + * preconditioner. This is equivalent to using PreconditionIdentity. + * + * @ingroup LAOperators + */ +template +LinearOperator +inverse_operator(const LinearOperator &op, + Solver & solver) +{ + return inverse_operator(op, solver, identity_operator(op)); +} + + +/** + * @relatesalso LinearOperator + * + * Special overload of above function that takes a PreconditionIdentity + * argument. + * + * @ingroup LAOperators + */ +template +LinearOperator +inverse_operator(const LinearOperator &op, + Solver & solver, + const PreconditionIdentity &) +{ + return inverse_operator(op, solver); +} + //@} From fadf55490d527d8c03b74bc3f11382f766b20369 Mon Sep 17 00:00:00 2001 From: Matthias Maier Date: Wed, 13 Feb 2019 16:46:32 -0600 Subject: [PATCH 127/507] add a test --- tests/lac/linear_operator_01d.cc | 90 ++++++++++++++++++++++++++++ tests/lac/linear_operator_01d.output | 2 + 2 files changed, 92 insertions(+) create mode 100644 tests/lac/linear_operator_01d.cc create mode 100644 tests/lac/linear_operator_01d.output diff --git a/tests/lac/linear_operator_01d.cc b/tests/lac/linear_operator_01d.cc new file mode 100644 index 000000000000..b5482f5a9d44 --- /dev/null +++ b/tests/lac/linear_operator_01d.cc @@ -0,0 +1,90 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2015 - 2016 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + +// Verify that the inverse_operator function signature without a +// preconditioner argument and the one with PreconditionIdentity() as a +// temporary works correctly. + +#include +#include +#include +#include +#include +#include +#include + +#include "../tests.h" + +using namespace dealii; + +int +main() +{ + initlog(); + + Vector answer(2); + answer[0] = 0.25; + answer[1] = 0.25; + + SparsityPattern sparsity_pattern(2, 2, 1); + sparsity_pattern.add(0, 0); + sparsity_pattern.add(1, 1); + sparsity_pattern.compress(); + + SparseMatrix A(sparsity_pattern); + A.set(0, 0, 4.0); + A.set(1, 1, 4.0); + + Vector b(2); + b[0] = 1.0; + b[1] = 1.0; + + const auto lo_A = linear_operator(A); + + // As we all remember from numerical analysis class, CG will converge in + // at most two iterations + SolverControl solver_control_A(2, 1.0e-15); + + SolverCG> solver_A(solver_control_A); + + const auto lo_A_inv = inverse_operator(lo_A, solver_A); + const auto lo_A_inv_t = transpose_operator(lo_A_inv); + + deallog.depth_file(0); + + unsigned int n_mistakes{0}; + + Vector residual; // keep storage location to trigger bug. + + for (unsigned int j = 0; j < 1000; ++j) + { + // test Tvmult: + residual = lo_A_inv_t * b; + residual -= answer; + if (residual.l2_norm() > 1e-10) + ++n_mistakes; + + // test Tvmult_add: + residual = lo_A_inv_t * b - answer; + if (residual.l2_norm() > 1e-10) + ++n_mistakes; + } + + deallog.depth_file(3); + + deallog << "number of mistakes: " << n_mistakes << std::endl; + if (n_mistakes != 0) + deallog << "Ooops!" << std::endl; +} diff --git a/tests/lac/linear_operator_01d.output b/tests/lac/linear_operator_01d.output new file mode 100644 index 000000000000..9694fcba7f0e --- /dev/null +++ b/tests/lac/linear_operator_01d.output @@ -0,0 +1,2 @@ + +DEAL::number of mistakes: 0 From 49717f7bbe7e2299544ee11a45c90cbe387b3710 Mon Sep 17 00:00:00 2001 From: Matthias Maier Date: Wed, 13 Feb 2019 16:50:21 -0600 Subject: [PATCH 128/507] add a changelog entry --- doc/news/changes/minor/20190213MatthiasMaier | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 doc/news/changes/minor/20190213MatthiasMaier diff --git a/doc/news/changes/minor/20190213MatthiasMaier b/doc/news/changes/minor/20190213MatthiasMaier new file mode 100644 index 000000000000..6d3a30db0f87 --- /dev/null +++ b/doc/news/changes/minor/20190213MatthiasMaier @@ -0,0 +1,5 @@ +Fixed: inverse_operator() now handles a (composite) LinearOperator, the +temporary PreconditionIdentity(), or no argument as preconditioner argument +correctly. +
+(Matthias Maier 2018/06/11) From 094a1d2acb10c2fc946e5e9728427c9790f30744 Mon Sep 17 00:00:00 2001 From: Matthias Maier Date: Wed, 13 Feb 2019 16:51:16 -0600 Subject: [PATCH 129/507] examples/step-20: Simplify code by using a temporary --- examples/step-20/step-20.cc | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/examples/step-20/step-20.cc b/examples/step-20/step-20.cc index f1b12f6e185d..89ed11124b16 100644 --- a/examples/step-20/step-20.cc +++ b/examples/step-20/step-20.cc @@ -613,10 +613,9 @@ namespace Step20 // applies a fixed number of 30 (inexpensive) CG iterations: IterationNumberControl iteration_number_control_aS(30, 1.e-18); SolverCG<> solver_aS(iteration_number_control_aS); - PreconditionIdentity preconditioner_aS; const auto preconditioner_S = - inverse_operator(op_aS, solver_aS, preconditioner_aS); + inverse_operator(op_aS, solver_aS, PreconditionIdentity()); // Now on to the first equation. The right hand side of it is // $B^TM^{-1}F-G$, which is what we compute in the first few lines. We From 2c2d43580f7cfc06e8551b88de783eeec70fb6df Mon Sep 17 00:00:00 2001 From: Matthias Maier Date: Thu, 14 Feb 2019 13:12:06 -0600 Subject: [PATCH 130/507] lac/linear_operator.h: Prevent users from creating LinearOperators with temoporaries --- include/deal.II/lac/linear_operator.h | 119 ++++++++++++++++++++++++++ tests/lac/linear_operator_18.cc | 55 ++++++++++++ tests/lac/linear_operator_18.output | 6 ++ 3 files changed, 180 insertions(+) create mode 100644 tests/lac/linear_operator_18.cc create mode 100644 tests/lac/linear_operator_18.output diff --git a/include/deal.II/lac/linear_operator.h b/include/deal.II/lac/linear_operator.h index f0115ff2578d..64dff9a09960 100644 --- a/include/deal.II/lac/linear_operator.h +++ b/include/deal.II/lac/linear_operator.h @@ -1473,6 +1473,125 @@ linear_operator(const LinearOperator &operator_exemplar, //@} +#ifndef DOXYGEN + +// +// Ensure that we never capture a reference to a temporary by accident. +// This ensures that instead of silently allowing a "stack use after free", +// we at least bail out with a runtime error message that is slightly more +// understandable. +// + +template < + typename Range = Vector, + typename Domain = Range, + typename Payload = internal::LinearOperatorImplementation::EmptyPayload, + typename OperatorExemplar, + typename Matrix, + typename = + typename std::enable_if::value>::type> +LinearOperator +linear_operator(const OperatorExemplar &, Matrix &&) +{ + Assert(false, + ExcMessage( + "You are trying to construct a linear operator from a temporary " + "matrix object.")); +} + +template < + typename Range = Vector, + typename Domain = Range, + typename Payload = internal::LinearOperatorImplementation::EmptyPayload, + typename OperatorExemplar, + typename Matrix, + typename = typename std::enable_if< + !std::is_lvalue_reference::value>::type> +LinearOperator +linear_operator(OperatorExemplar &&, const Matrix &) +{ + Assert(false, + ExcMessage( + "You are trying to construct a linear operator with a temporary " + "operator_exemplar object.")); +} + +template < + typename Range = Vector, + typename Domain = Range, + typename Payload = internal::LinearOperatorImplementation::EmptyPayload, + typename OperatorExemplar, + typename Matrix, + typename = + typename std::enable_if::value>::type, + typename = typename std::enable_if< + !std::is_lvalue_reference::value>::type> +LinearOperator +linear_operator(OperatorExemplar &&, Matrix &&) +{ + Assert(false, + ExcMessage( + "You are trying to construct a linear operator from a temporary " + "matrix object.")); +} + + +template < + typename Range = Vector, + typename Domain = Range, + typename Payload = internal::LinearOperatorImplementation::EmptyPayload, + typename Matrix, + typename = + typename std::enable_if::value>::type> +LinearOperator +linear_operator(const LinearOperator &, Matrix &&) +{ + Assert(false, + ExcMessage( + "You are trying to construct a linear operator from a temporary " + "matrix object.")); +} + +template < + typename Range = Vector, + typename Domain = Range, + typename Payload = internal::LinearOperatorImplementation::EmptyPayload, + typename Matrix, + typename = + typename std::enable_if::value>::type> +LinearOperator +linear_operator(Matrix &&) +{ + Assert(false, + ExcMessage( + "You are trying to construct a linear operator from a temporary " + "matrix object.")); +} + +template ::value>::type, + typename = typename std::enable_if< + !std::is_same::value>::type, + typename = typename std::enable_if< + !std::is_same>::value>::type> +LinearOperator +inverse_operator(const LinearOperator &, + Solver &, + Preconditioner &&) +{ + Assert(false, + ExcMessage( + "You are trying to construct an inverse operator with a temporary " + "preconditioner object.")); +} + +#endif // DOXYGEN DEAL_II_NAMESPACE_CLOSE diff --git a/tests/lac/linear_operator_18.cc b/tests/lac/linear_operator_18.cc new file mode 100644 index 000000000000..08fbfb180152 --- /dev/null +++ b/tests/lac/linear_operator_18.cc @@ -0,0 +1,55 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2015 - 2018 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + +// Test that we cannot accidentally create a linear operator from a +// temporary object + +#include +#include +#include + +#include "../tests.h" + +#define CATCH(call) \ + try \ + { \ + call; \ + deallog << "Error: Something went wrong!" << std::endl; \ + } \ + catch (ExceptionBase & e) \ + { \ + deallog << e.get_exc_name() << std::endl; \ + } + +using namespace dealii; + +int +main() +{ + initlog(); + deal_II_exceptions::disable_abort_on_exception(); + + SparseMatrix A; + const auto op_A = linear_operator(A); + + CATCH(linear_operator(SparseMatrix())) + CATCH(linear_operator(SparseMatrix(), A)) + CATCH(linear_operator(A, SparseMatrix())) + CATCH(linear_operator(SparseMatrix(), SparseMatrix())) + + SolverControl solver_control; + SolverCG> solver(solver_control); + CATCH(inverse_operator(op_A, solver, SparseMatrix())) +} diff --git a/tests/lac/linear_operator_18.output b/tests/lac/linear_operator_18.output new file mode 100644 index 000000000000..8aad5753bce2 --- /dev/null +++ b/tests/lac/linear_operator_18.output @@ -0,0 +1,6 @@ + +DEAL::ExcMessage( "You are trying to construct a linear operator from a temporary " "matrix object.") +DEAL::ExcMessage( "You are trying to construct a linear operator with a temporary " "operator_exemplar object.") +DEAL::ExcMessage( "You are trying to construct a linear operator from a temporary " "matrix object.") +DEAL::ExcMessage( "You are trying to construct a linear operator from a temporary " "matrix object.") +DEAL::ExcMessage( "You are trying to construct an inverse operator with a temporary " "preconditioner object.") From 225cc0c87449c6c1baaa88e694c223560e353308 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Thu, 14 Feb 2019 22:50:50 +0100 Subject: [PATCH 131/507] Delete the disallowed functions instead --- include/deal.II/lac/linear_operator.h | 64 +++++++-------------------- tests/lac/linear_operator_18.cc | 55 ----------------------- tests/lac/linear_operator_18.output | 6 --- 3 files changed, 16 insertions(+), 109 deletions(-) delete mode 100644 tests/lac/linear_operator_18.cc delete mode 100644 tests/lac/linear_operator_18.output diff --git a/include/deal.II/lac/linear_operator.h b/include/deal.II/lac/linear_operator.h index 64dff9a09960..b8e118fe112c 100644 --- a/include/deal.II/lac/linear_operator.h +++ b/include/deal.II/lac/linear_operator.h @@ -1477,9 +1477,7 @@ linear_operator(const LinearOperator &operator_exemplar, // // Ensure that we never capture a reference to a temporary by accident. -// This ensures that instead of silently allowing a "stack use after free", -// we at least bail out with a runtime error message that is slightly more -// understandable. +// to avoid "stack use after free". // template < @@ -1491,13 +1489,7 @@ template < typename = typename std::enable_if::value>::type> LinearOperator -linear_operator(const OperatorExemplar &, Matrix &&) -{ - Assert(false, - ExcMessage( - "You are trying to construct a linear operator from a temporary " - "matrix object.")); -} +linear_operator(const OperatorExemplar &, Matrix &&) = delete; template < typename Range = Vector, @@ -1506,15 +1498,12 @@ template < typename OperatorExemplar, typename Matrix, typename = typename std::enable_if< - !std::is_lvalue_reference::value>::type> + !std::is_lvalue_reference::value>::type, + typename = typename std::enable_if< + !std::is_same>::value>::type> LinearOperator -linear_operator(OperatorExemplar &&, const Matrix &) -{ - Assert(false, - ExcMessage( - "You are trying to construct a linear operator with a temporary " - "operator_exemplar object.")); -} +linear_operator(OperatorExemplar &&, const Matrix &) = delete; template < typename Range = Vector, @@ -1525,16 +1514,12 @@ template < typename = typename std::enable_if::value>::type, typename = typename std::enable_if< - !std::is_lvalue_reference::value>::type> + !std::is_lvalue_reference::value>::type, + typename = typename std::enable_if< + !std::is_same>::value>::type> LinearOperator -linear_operator(OperatorExemplar &&, Matrix &&) -{ - Assert(false, - ExcMessage( - "You are trying to construct a linear operator from a temporary " - "matrix object.")); -} - +linear_operator(OperatorExemplar &&, Matrix &&) = delete; template < typename Range = Vector, @@ -1544,13 +1529,8 @@ template < typename = typename std::enable_if::value>::type> LinearOperator -linear_operator(const LinearOperator &, Matrix &&) -{ - Assert(false, - ExcMessage( - "You are trying to construct a linear operator from a temporary " - "matrix object.")); -} +linear_operator(const LinearOperator &, + Matrix &&) = delete; template < typename Range = Vector, @@ -1560,13 +1540,7 @@ template < typename = typename std::enable_if::value>::type> LinearOperator -linear_operator(Matrix &&) -{ - Assert(false, - ExcMessage( - "You are trying to construct a linear operator from a temporary " - "matrix object.")); -} +linear_operator(Matrix &&) = delete; template inverse_operator(const LinearOperator &, Solver &, - Preconditioner &&) -{ - Assert(false, - ExcMessage( - "You are trying to construct an inverse operator with a temporary " - "preconditioner object.")); -} + Preconditioner &&) = delete; #endif // DOXYGEN diff --git a/tests/lac/linear_operator_18.cc b/tests/lac/linear_operator_18.cc deleted file mode 100644 index 08fbfb180152..000000000000 --- a/tests/lac/linear_operator_18.cc +++ /dev/null @@ -1,55 +0,0 @@ -// --------------------------------------------------------------------- -// -// Copyright (C) 2015 - 2018 by the deal.II authors -// -// This file is part of the deal.II library. -// -// The deal.II library is free software; you can use it, redistribute -// it, and/or modify it under the terms of the GNU Lesser General -// Public License as published by the Free Software Foundation; either -// version 2.1 of the License, or (at your option) any later version. -// The full text of the license can be found in the file LICENSE.md at -// the top level directory of deal.II. -// -// --------------------------------------------------------------------- - -// Test that we cannot accidentally create a linear operator from a -// temporary object - -#include -#include -#include - -#include "../tests.h" - -#define CATCH(call) \ - try \ - { \ - call; \ - deallog << "Error: Something went wrong!" << std::endl; \ - } \ - catch (ExceptionBase & e) \ - { \ - deallog << e.get_exc_name() << std::endl; \ - } - -using namespace dealii; - -int -main() -{ - initlog(); - deal_II_exceptions::disable_abort_on_exception(); - - SparseMatrix A; - const auto op_A = linear_operator(A); - - CATCH(linear_operator(SparseMatrix())) - CATCH(linear_operator(SparseMatrix(), A)) - CATCH(linear_operator(A, SparseMatrix())) - CATCH(linear_operator(SparseMatrix(), SparseMatrix())) - - SolverControl solver_control; - SolverCG> solver(solver_control); - CATCH(inverse_operator(op_A, solver, SparseMatrix())) -} diff --git a/tests/lac/linear_operator_18.output b/tests/lac/linear_operator_18.output deleted file mode 100644 index 8aad5753bce2..000000000000 --- a/tests/lac/linear_operator_18.output +++ /dev/null @@ -1,6 +0,0 @@ - -DEAL::ExcMessage( "You are trying to construct a linear operator from a temporary " "matrix object.") -DEAL::ExcMessage( "You are trying to construct a linear operator with a temporary " "operator_exemplar object.") -DEAL::ExcMessage( "You are trying to construct a linear operator from a temporary " "matrix object.") -DEAL::ExcMessage( "You are trying to construct a linear operator from a temporary " "matrix object.") -DEAL::ExcMessage( "You are trying to construct an inverse operator with a temporary " "preconditioner object.") From cfdd06c2bd8388581be15e2f8e825a7bb44341d9 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Thu, 14 Feb 2019 00:40:26 +0100 Subject: [PATCH 132/507] Fix return value --- include/deal.II/grid/grid_tools.h | 9 +++++---- source/grid/grid_tools.cc | 4 +++- 2 files changed, 8 insertions(+), 5 deletions(-) diff --git a/include/deal.II/grid/grid_tools.h b/include/deal.II/grid/grid_tools.h index 809de1bccad4..d8e9050b414e 100644 --- a/include/deal.II/grid/grid_tools.h +++ b/include/deal.II/grid/grid_tools.h @@ -765,10 +765,11 @@ namespace GridTools * * @code * std::tuple< - * std::vector::active_cell_iterator>, std::vector>>, - * std::vector>, - * std::vector> + * std::vector< + * typename Triangulation::active_cell_iterator>, + * std::vector>>, + * std::vector>, + * std::vector > * @endcode * * For a more detailed documentation see diff --git a/source/grid/grid_tools.cc b/source/grid/grid_tools.cc index bd97f63dc4b9..58d12d3a94fc 100644 --- a/source/grid/grid_tools.cc +++ b/source/grid/grid_tools.cc @@ -4207,7 +4207,9 @@ namespace GridTools (void)missing_points; - return {std::move(cells), std::move(qpoints), std::move(maps)}; + return std::make_tuple(std::move(cells), + std::move(qpoints), + std::move(maps)); } From bc7358286f2f2614713ea2735d53cd01b0259639 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Fri, 15 Feb 2019 18:00:02 +0100 Subject: [PATCH 133/507] allow zero padding in plate_with_a_hole --- include/deal.II/grid/grid_generator.h | 3 +- source/grid/grid_generator.cc | 129 +++++---- .../grid_generator_plate_with_a_hole_4.cc | 121 ++++++++ .../grid_generator_plate_with_a_hole_4.output | 261 ++++++++++++++++++ 4 files changed, 451 insertions(+), 63 deletions(-) create mode 100644 tests/grid/grid_generator_plate_with_a_hole_4.cc create mode 100644 tests/grid/grid_generator_plate_with_a_hole_4.output diff --git a/include/deal.II/grid/grid_generator.h b/include/deal.II/grid/grid_generator.h index 318646b14c96..caa95daf80dc 100644 --- a/include/deal.II/grid/grid_generator.h +++ b/include/deal.II/grid/grid_generator.h @@ -327,8 +327,7 @@ namespace GridGenerator * All cells in this region will have a FlatManifold attached to them. * The final width of the plate will be padding_left + 2*outer_radius + * padding_right, while its length is padding_top + - * 2*outer_radius + padding_bottom. Three out of four paddings are - * allowed to be zero. + * 2*outer_radius + padding_bottom. * * Here is the non-symmetric grid (after one global refinement, colored * according to manifold id) in 2D and 3D, respectively: diff --git a/source/grid/grid_generator.cc b/source/grid/grid_generator.cc index 08eb9c701fb2..e774a7368ae2 100644 --- a/source/grid/grid_generator.cc +++ b/source/grid/grid_generator.cc @@ -1966,8 +1966,9 @@ namespace GridGenerator const unsigned int /*n_slices*/, const bool colorize) { - Assert((pad_bottom > 0 || pad_top > 0 || pad_left > 0 || pad_right > 0), - ExcMessage("At least one padding parameter has to be non-zero.")); + const bool with_padding = + pad_bottom > 0 || pad_top > 0 || pad_left > 0 || pad_right > 0; + Assert(pad_bottom >= 0., ExcMessage("Negative bottom padding.")); Assert(pad_top >= 0., ExcMessage("Negative top padding.")); Assert(pad_left >= 0., ExcMessage("Negative left padding.")); @@ -1984,7 +1985,8 @@ namespace GridGenerator }; // start by setting up the cylinder triangulation - Triangulation<2> cylinder_tria; + Triangulation<2> cylinder_tria_maybe; + Triangulation<2> &cylinder_tria = with_padding ? cylinder_tria_maybe : tria; GridGenerator::hyper_cube_with_cylindrical_hole(cylinder_tria, inner_radius, outer_radius, @@ -1996,65 +1998,70 @@ namespace GridGenerator for (const auto &cell : cylinder_tria.active_cell_iterators()) cell->set_manifold_id(tfi_manifold_id); - // hyper_cube_with_cylindrical_hole will have 2 cells along - // each face, so he element size is outer_radius - - auto add_sizes = [](std::vector &step_sizes, - const double padding, - const double h) -> void { - // use std::round instead of std::ceil to improve aspect ratio - // in case padding is only slightly larger than h. - const auto rounded = static_cast(std::round(padding / h)); - // in case padding is much smaller than h, make sure we - // have at least 1 element - const unsigned int num = (padding > 0. && rounded == 0) ? 1 : rounded; - for (unsigned int i = 0; i < num; ++i) - step_sizes.push_back(padding / num); - }; - - std::vector> step_sizes(2); - // x-coord - // left: - add_sizes(step_sizes[0], pad_left, outer_radius); - // center - step_sizes[0].push_back(outer_radius); - step_sizes[0].push_back(outer_radius); - // right - add_sizes(step_sizes[0], pad_right, outer_radius); - // y-coord - // bottom - add_sizes(step_sizes[1], pad_bottom, outer_radius); - // center - step_sizes[1].push_back(outer_radius); - step_sizes[1].push_back(outer_radius); - // top - add_sizes(step_sizes[1], pad_top, outer_radius); - - // now create bulk - Triangulation<2> bulk_tria; - const Point<2> bl(-outer_radius - pad_left, -outer_radius - pad_bottom); - const Point<2> tr(outer_radius + pad_right, outer_radius + pad_top); - GridGenerator::subdivided_hyper_rectangle( - bulk_tria, step_sizes, bl, tr, colorize); - - // now remove cells reserved from the cylindrical hole - std::set::active_cell_iterator> cells_to_remove; - for (const auto &cell : bulk_tria.active_cell_iterators()) - if (internal::point_in_2d_box(cell->center(), center, outer_radius)) - cells_to_remove.insert(cell); - - Triangulation<2> tria_without_cylinder; - GridGenerator::create_triangulation_with_removed_cells( - bulk_tria, cells_to_remove, tria_without_cylinder); - - const double tolerance = std::min(min_line_length(tria_without_cylinder), - min_line_length(cylinder_tria)) / - 2.0; + const Point<2> bl(-outer_radius - pad_left, -outer_radius - pad_bottom); + const Point<2> tr(outer_radius + pad_right, outer_radius + pad_top); + if (with_padding) + { + // hyper_cube_with_cylindrical_hole will have 2 cells along + // each face, so he element size is outer_radius + + auto add_sizes = [](std::vector &step_sizes, + const double padding, + const double h) -> void { + // use std::round instead of std::ceil to improve aspect ratio + // in case padding is only slightly larger than h. + const auto rounded = + static_cast(std::round(padding / h)); + // in case padding is much smaller than h, make sure we + // have at least 1 element + const unsigned int num = (padding > 0. && rounded == 0) ? 1 : rounded; + for (unsigned int i = 0; i < num; ++i) + step_sizes.push_back(padding / num); + }; - GridGenerator::merge_triangulations(tria_without_cylinder, - cylinder_tria, - tria, - tolerance); + std::vector> step_sizes(2); + // x-coord + // left: + add_sizes(step_sizes[0], pad_left, outer_radius); + // center + step_sizes[0].push_back(outer_radius); + step_sizes[0].push_back(outer_radius); + // right + add_sizes(step_sizes[0], pad_right, outer_radius); + // y-coord + // bottom + add_sizes(step_sizes[1], pad_bottom, outer_radius); + // center + step_sizes[1].push_back(outer_radius); + step_sizes[1].push_back(outer_radius); + // top + add_sizes(step_sizes[1], pad_top, outer_radius); + + // now create bulk + Triangulation<2> bulk_tria; + GridGenerator::subdivided_hyper_rectangle( + bulk_tria, step_sizes, bl, tr, colorize); + + // now remove cells reserved from the cylindrical hole + std::set::active_cell_iterator> cells_to_remove; + for (const auto &cell : bulk_tria.active_cell_iterators()) + if (internal::point_in_2d_box(cell->center(), center, outer_radius)) + cells_to_remove.insert(cell); + + Triangulation<2> tria_without_cylinder; + GridGenerator::create_triangulation_with_removed_cells( + bulk_tria, cells_to_remove, tria_without_cylinder); + + const double tolerance = + std::min(min_line_length(tria_without_cylinder), + min_line_length(cylinder_tria)) / + 2.0; + + GridGenerator::merge_triangulations(tria_without_cylinder, + cylinder_tria, + tria, + tolerance); + } // now set manifold ids: for (const auto &cell : tria.active_cell_iterators()) diff --git a/tests/grid/grid_generator_plate_with_a_hole_4.cc b/tests/grid/grid_generator_plate_with_a_hole_4.cc new file mode 100644 index 000000000000..7631d240d393 --- /dev/null +++ b/tests/grid/grid_generator_plate_with_a_hole_4.cc @@ -0,0 +1,121 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + + +// Test GridGenerator::plate_with_a_hole() with zero padding + +#include + +#include + +#include +#include + +#include + +#include "../tests.h" + +template +void +test() +{ + Triangulation triangulation; + GridGenerator::plate_with_a_hole( + triangulation, 0.4, 1., 0, 0, 0, 0, Point(), 0, 1, 1., 2, true); + + triangulation.refine_global(1); + + using Tuple = std::tuple, types::boundary_id, types::manifold_id>; + std::vector boundary_faces; + + for (const auto &cell : triangulation.active_cell_iterators()) + for (unsigned int face_n = 0; face_n < GeometryInfo::faces_per_cell; + ++face_n) + if (cell->face(face_n)->at_boundary()) + boundary_faces.push_back( + std::make_tuple(cell->face(face_n)->center(), + cell->face(face_n)->boundary_id(), + cell->face(face_n)->manifold_id())); + + // see dof_tools.cc internal::ComparisonHelper + std::sort(begin(boundary_faces), + end(boundary_faces), + [](const Tuple &t1, const Tuple &t2) { + const auto &b1 = std::get<1>(t1); + const auto &b2 = std::get<1>(t2); + if (b1 != b2) + return b1 < b2; + + const auto &p1 = std::get<0>(t1); + const auto &p2 = std::get<0>(t2); + + for (unsigned int d = 0; d < dim; ++d) + if (std::abs(p1[d] - p2[d]) > 1e-8) + return p1[d] < p2[d]; + + return std::get<2>(t1) < std::get<2>(t2); + }); + + for (const auto el : boundary_faces) + deallog << "center: " << std::get<0>(el) + << " boundary id: " << std::get<1>(el) + << " manifold id: " << std::get<2>(el) << std::endl; + + deallog << std::endl << std::endl; + Vector manifold_id(triangulation.n_active_cells()); + unsigned int index = 0; + for (const auto &cell : triangulation.active_cell_iterators()) + { + deallog << "center: " << cell->center() + << " manifold id: " << cell->manifold_id() << std::endl; + manifold_id[index] = cell->manifold_id(); + index++; + } + + // write in vtk for visual inspection + if (false) + { + DoFHandler dof_handler(triangulation); + FE_Q fe(1); + dof_handler.distribute_dofs(fe); + + DataOut data_out; + + data_out.attach_dof_handler(dof_handler); + data_out.add_data_vector(manifold_id, "manifold_id"); + data_out.build_patches(); + + const std::string filename = + "output_" + Utilities::int_to_string(dim) + ".vtu"; + std::ofstream output(filename.c_str()); + data_out.write_vtu(output); + } +} + + +int +main() +{ + initlog(); + + deallog.push("2d"); + test<2>(); + deallog.pop(); + + deallog.push("3d"); + test<3>(); + deallog.pop(); +} diff --git a/tests/grid/grid_generator_plate_with_a_hole_4.output b/tests/grid/grid_generator_plate_with_a_hole_4.output new file mode 100644 index 000000000000..8f7500c6a4da --- /dev/null +++ b/tests/grid/grid_generator_plate_with_a_hole_4.output @@ -0,0 +1,261 @@ + +DEAL:2d::center: -1.00000 -0.750000 boundary id: 0 manifold id: 1 +DEAL:2d::center: -1.00000 -0.250000 boundary id: 0 manifold id: 1 +DEAL:2d::center: -1.00000 0.250000 boundary id: 0 manifold id: 1 +DEAL:2d::center: -1.00000 0.750000 boundary id: 0 manifold id: 1 +DEAL:2d::center: 1.00000 -0.750000 boundary id: 1 manifold id: 1 +DEAL:2d::center: 1.00000 -0.250000 boundary id: 1 manifold id: 1 +DEAL:2d::center: 1.00000 0.250000 boundary id: 1 manifold id: 1 +DEAL:2d::center: 1.00000 0.750000 boundary id: 1 manifold id: 1 +DEAL:2d::center: -0.750000 -1.00000 boundary id: 2 manifold id: 1 +DEAL:2d::center: -0.250000 -1.00000 boundary id: 2 manifold id: 1 +DEAL:2d::center: 0.250000 -1.00000 boundary id: 2 manifold id: 1 +DEAL:2d::center: 0.750000 -1.00000 boundary id: 2 manifold id: 1 +DEAL:2d::center: -0.750000 1.00000 boundary id: 3 manifold id: 1 +DEAL:2d::center: -0.250000 1.00000 boundary id: 3 manifold id: 1 +DEAL:2d::center: 0.250000 1.00000 boundary id: 3 manifold id: 1 +DEAL:2d::center: 0.750000 1.00000 boundary id: 3 manifold id: 1 +DEAL:2d::center: -0.384776 -0.0765367 boundary id: 4 manifold id: 0 +DEAL:2d::center: -0.384776 0.0765367 boundary id: 4 manifold id: 0 +DEAL:2d::center: -0.326197 -0.217958 boundary id: 4 manifold id: 0 +DEAL:2d::center: -0.326197 0.217958 boundary id: 4 manifold id: 0 +DEAL:2d::center: -0.217958 -0.326197 boundary id: 4 manifold id: 0 +DEAL:2d::center: -0.217958 0.326197 boundary id: 4 manifold id: 0 +DEAL:2d::center: -0.0765367 -0.384776 boundary id: 4 manifold id: 0 +DEAL:2d::center: -0.0765367 0.384776 boundary id: 4 manifold id: 0 +DEAL:2d::center: 0.0765367 -0.384776 boundary id: 4 manifold id: 0 +DEAL:2d::center: 0.0765367 0.384776 boundary id: 4 manifold id: 0 +DEAL:2d::center: 0.217958 -0.326197 boundary id: 4 manifold id: 0 +DEAL:2d::center: 0.217958 0.326197 boundary id: 4 manifold id: 0 +DEAL:2d::center: 0.326197 -0.217958 boundary id: 4 manifold id: 0 +DEAL:2d::center: 0.326197 0.217958 boundary id: 4 manifold id: 0 +DEAL:2d::center: 0.384776 -0.0765367 boundary id: 4 manifold id: 0 +DEAL:2d::center: 0.384776 0.0765367 boundary id: 4 manifold id: 0 +DEAL:2d:: +DEAL:2d:: +DEAL:2d::center: 0.846194 0.206634 manifold id: 1 +DEAL:2d::center: 0.831549 0.616990 manifold id: 1 +DEAL:2d::center: 0.538582 0.119903 manifold id: 1 +DEAL:2d::center: 0.494648 0.350969 manifold id: 1 +DEAL:2d::center: 0.616990 0.831549 manifold id: 1 +DEAL:2d::center: 0.206634 0.846194 manifold id: 1 +DEAL:2d::center: 0.350969 0.494648 manifold id: 1 +DEAL:2d::center: 0.119903 0.538582 manifold id: 1 +DEAL:2d::center: -0.206634 0.846194 manifold id: 1 +DEAL:2d::center: -0.616990 0.831549 manifold id: 1 +DEAL:2d::center: -0.119903 0.538582 manifold id: 1 +DEAL:2d::center: -0.350969 0.494648 manifold id: 1 +DEAL:2d::center: -0.831549 0.616990 manifold id: 1 +DEAL:2d::center: -0.846194 0.206634 manifold id: 1 +DEAL:2d::center: -0.494648 0.350969 manifold id: 1 +DEAL:2d::center: -0.538582 0.119903 manifold id: 1 +DEAL:2d::center: -0.846194 -0.206634 manifold id: 1 +DEAL:2d::center: -0.831549 -0.616990 manifold id: 1 +DEAL:2d::center: -0.538582 -0.119903 manifold id: 1 +DEAL:2d::center: -0.494648 -0.350969 manifold id: 1 +DEAL:2d::center: -0.616990 -0.831549 manifold id: 1 +DEAL:2d::center: -0.206634 -0.846194 manifold id: 1 +DEAL:2d::center: -0.350969 -0.494648 manifold id: 1 +DEAL:2d::center: -0.119903 -0.538582 manifold id: 1 +DEAL:2d::center: 0.206634 -0.846194 manifold id: 1 +DEAL:2d::center: 0.616990 -0.831549 manifold id: 1 +DEAL:2d::center: 0.119903 -0.538582 manifold id: 1 +DEAL:2d::center: 0.350969 -0.494648 manifold id: 1 +DEAL:2d::center: 0.831549 -0.616990 manifold id: 1 +DEAL:2d::center: 0.846194 -0.206634 manifold id: 1 +DEAL:2d::center: 0.494648 -0.350969 manifold id: 1 +DEAL:2d::center: 0.538582 -0.119903 manifold id: 1 +DEAL:3d::center: -1.00000 -0.750000 -0.250000 boundary id: 0 manifold id: 1 +DEAL:3d::center: -1.00000 -0.750000 0.250000 boundary id: 0 manifold id: 1 +DEAL:3d::center: -1.00000 -0.250000 -0.250000 boundary id: 0 manifold id: 1 +DEAL:3d::center: -1.00000 -0.250000 0.250000 boundary id: 0 manifold id: 1 +DEAL:3d::center: -1.00000 0.250000 -0.250000 boundary id: 0 manifold id: 1 +DEAL:3d::center: -1.00000 0.250000 0.250000 boundary id: 0 manifold id: 1 +DEAL:3d::center: -1.00000 0.750000 -0.250000 boundary id: 0 manifold id: 1 +DEAL:3d::center: -1.00000 0.750000 0.250000 boundary id: 0 manifold id: 1 +DEAL:3d::center: 1.00000 -0.750000 -0.250000 boundary id: 1 manifold id: 1 +DEAL:3d::center: 1.00000 -0.750000 0.250000 boundary id: 1 manifold id: 1 +DEAL:3d::center: 1.00000 -0.250000 -0.250000 boundary id: 1 manifold id: 1 +DEAL:3d::center: 1.00000 -0.250000 0.250000 boundary id: 1 manifold id: 1 +DEAL:3d::center: 1.00000 0.250000 -0.250000 boundary id: 1 manifold id: 1 +DEAL:3d::center: 1.00000 0.250000 0.250000 boundary id: 1 manifold id: 1 +DEAL:3d::center: 1.00000 0.750000 -0.250000 boundary id: 1 manifold id: 1 +DEAL:3d::center: 1.00000 0.750000 0.250000 boundary id: 1 manifold id: 1 +DEAL:3d::center: -0.750000 -1.00000 -0.250000 boundary id: 2 manifold id: 1 +DEAL:3d::center: -0.750000 -1.00000 0.250000 boundary id: 2 manifold id: 1 +DEAL:3d::center: -0.250000 -1.00000 -0.250000 boundary id: 2 manifold id: 1 +DEAL:3d::center: -0.250000 -1.00000 0.250000 boundary id: 2 manifold id: 1 +DEAL:3d::center: 0.250000 -1.00000 -0.250000 boundary id: 2 manifold id: 1 +DEAL:3d::center: 0.250000 -1.00000 0.250000 boundary id: 2 manifold id: 1 +DEAL:3d::center: 0.750000 -1.00000 -0.250000 boundary id: 2 manifold id: 1 +DEAL:3d::center: 0.750000 -1.00000 0.250000 boundary id: 2 manifold id: 1 +DEAL:3d::center: -0.750000 1.00000 -0.250000 boundary id: 3 manifold id: 1 +DEAL:3d::center: -0.750000 1.00000 0.250000 boundary id: 3 manifold id: 1 +DEAL:3d::center: -0.250000 1.00000 -0.250000 boundary id: 3 manifold id: 1 +DEAL:3d::center: -0.250000 1.00000 0.250000 boundary id: 3 manifold id: 1 +DEAL:3d::center: 0.250000 1.00000 -0.250000 boundary id: 3 manifold id: 1 +DEAL:3d::center: 0.250000 1.00000 0.250000 boundary id: 3 manifold id: 1 +DEAL:3d::center: 0.750000 1.00000 -0.250000 boundary id: 3 manifold id: 1 +DEAL:3d::center: 0.750000 1.00000 0.250000 boundary id: 3 manifold id: 1 +DEAL:3d::center: -0.384776 -0.0765367 -0.250000 boundary id: 4 manifold id: 0 +DEAL:3d::center: -0.384776 -0.0765367 0.250000 boundary id: 4 manifold id: 0 +DEAL:3d::center: -0.384776 0.0765367 -0.250000 boundary id: 4 manifold id: 0 +DEAL:3d::center: -0.384776 0.0765367 0.250000 boundary id: 4 manifold id: 0 +DEAL:3d::center: -0.326197 -0.217958 -0.250000 boundary id: 4 manifold id: 0 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-0.206634 -0.250000 manifold id: 1 +DEAL:3d::center: -0.831549 -0.616990 -0.250000 manifold id: 1 +DEAL:3d::center: -0.538582 -0.119903 -0.250000 manifold id: 1 +DEAL:3d::center: -0.494648 -0.350969 -0.250000 manifold id: 1 +DEAL:3d::center: -0.846194 -0.206634 0.250000 manifold id: 1 +DEAL:3d::center: -0.831549 -0.616990 0.250000 manifold id: 1 +DEAL:3d::center: -0.538582 -0.119903 0.250000 manifold id: 1 +DEAL:3d::center: -0.494648 -0.350969 0.250000 manifold id: 1 +DEAL:3d::center: -0.616990 -0.831549 -0.250000 manifold id: 1 +DEAL:3d::center: -0.206634 -0.846194 -0.250000 manifold id: 1 +DEAL:3d::center: -0.350969 -0.494648 -0.250000 manifold id: 1 +DEAL:3d::center: -0.119903 -0.538582 -0.250000 manifold id: 1 +DEAL:3d::center: -0.616990 -0.831549 0.250000 manifold id: 1 +DEAL:3d::center: -0.206634 -0.846194 0.250000 manifold id: 1 +DEAL:3d::center: -0.350969 -0.494648 0.250000 manifold id: 1 +DEAL:3d::center: -0.119903 -0.538582 0.250000 manifold id: 1 +DEAL:3d::center: 0.206634 -0.846194 -0.250000 manifold id: 1 +DEAL:3d::center: 0.616990 -0.831549 -0.250000 manifold id: 1 +DEAL:3d::center: 0.119903 -0.538582 -0.250000 manifold id: 1 +DEAL:3d::center: 0.350969 -0.494648 -0.250000 manifold id: 1 +DEAL:3d::center: 0.206634 -0.846194 0.250000 manifold id: 1 +DEAL:3d::center: 0.616990 -0.831549 0.250000 manifold id: 1 +DEAL:3d::center: 0.119903 -0.538582 0.250000 manifold id: 1 +DEAL:3d::center: 0.350969 -0.494648 0.250000 manifold id: 1 +DEAL:3d::center: 0.831549 -0.616990 -0.250000 manifold id: 1 +DEAL:3d::center: 0.846194 -0.206634 -0.250000 manifold id: 1 +DEAL:3d::center: 0.494648 -0.350969 -0.250000 manifold id: 1 +DEAL:3d::center: 0.538582 -0.119903 -0.250000 manifold id: 1 +DEAL:3d::center: 0.831549 -0.616990 0.250000 manifold id: 1 +DEAL:3d::center: 0.846194 -0.206634 0.250000 manifold id: 1 +DEAL:3d::center: 0.494648 -0.350969 0.250000 manifold id: 1 +DEAL:3d::center: 0.538582 -0.119903 0.250000 manifold id: 1 From 9296119dcb0888f4a9bed2f3e72b08a3fec3edca Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Fri, 15 Feb 2019 09:42:02 -0700 Subject: [PATCH 134/507] [CI]: mark main status in github as failed --- Jenkinsfile | 52 +++++++++++++++++++++++++++++++++++----------------- 1 file changed, 35 insertions(+), 17 deletions(-) diff --git a/Jenkinsfile b/Jenkinsfile index e6f70559f4e0..c2b78f390a13 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -40,6 +40,12 @@ pipeline stage("indent") { + post { + failure { + githubNotify context: 'indent', description: 'failed', status: 'FAILURE' + } + } + steps { // we are finally running, so we can mark the 'ready' context from Jenkinsfile.mark as success: @@ -76,15 +82,21 @@ pipeline image 'tjhei/candi:v9.0.1-r4' } } + post { - always { - sh "cp /home/dealii/build/Testing/*/*.xml $WORKSPACE/serial.xml || true" - xunit tools: [CTest(pattern: '*.xml')] - } - cleanup { - cleanWs() - } - } + always { + sh "cp /home/dealii/build/Testing/*/*.xml $WORKSPACE/serial.xml || true" + xunit tools: [CTest(pattern: '*.xml')] + } + + cleanup { + cleanWs() + } + + failure { + githubNotify context: 'CI', description: 'serial build failed', status: 'FAILURE' + } + } steps { @@ -93,7 +105,7 @@ pipeline sh "echo \"building on node ${env.NODE_NAME}\"" sh '''#!/bin/bash export NP=`grep -c ^processor /proc/cpuinfo` - export TEST_TIME_LIMIT=1200 + export TEST_TIME_LIMIT=1200 echo $NP mkdir -p /home/dealii/build cd /home/dealii/build @@ -121,15 +133,21 @@ pipeline image 'tjhei/candi:v9.0.1-r4' } } + post { - always { - sh "cp /home/dealii/build/Testing/*/*.xml $WORKSPACE/mpi.xml || true" - xunit tools: [CTest(pattern: '*.xml')] - } - cleanup { - cleanWs() - } - } + always { + sh "cp /home/dealii/build/Testing/*/*.xml $WORKSPACE/mpi.xml || true" + xunit tools: [CTest(pattern: '*.xml')] + } + + cleanup { + cleanWs() + } + + failure { + githubNotify context: 'CI', description: 'mpi build failed', status: 'FAILURE' + } + } steps { From 2489cfc0e7f32f863709f4c63ea32b9570f0e5f7 Mon Sep 17 00:00:00 2001 From: Logan Harbour Date: Tue, 19 Feb 2019 12:20:08 -0600 Subject: [PATCH 135/507] Fix doxygen docstring for DoFInfo indices --- include/deal.II/meshworker/dof_info.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/include/deal.II/meshworker/dof_info.h b/include/deal.II/meshworker/dof_info.h index 34a54fe076ae..1b3bf0825a27 100644 --- a/include/deal.II/meshworker/dof_info.h +++ b/include/deal.II/meshworker/dof_info.h @@ -96,7 +96,7 @@ namespace MeshWorker */ unsigned int sub_number; - /* + /** * The DoF indices of the * current cell */ From f81049e0e89c85b1ba1b19f1b1de6e6a4a88ecb5 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Tue, 19 Feb 2019 19:21:50 +0100 Subject: [PATCH 136/507] Remove redundant switch in MatrixFree::TaskInfo --- source/matrix_free/task_info.cc | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/source/matrix_free/task_info.cc b/source/matrix_free/task_info.cc index 1fd323d2cfa6..d60db786c86b 100644 --- a/source/matrix_free/task_info.cc +++ b/source/matrix_free/task_info.cc @@ -363,10 +363,7 @@ namespace internal worker[j]->set_ref_count(2); blocked_worker[j - 1]->dummy = new (worker[j]->allocate_child()) tbb::empty_task; - if (j > 1) - tbb::task::spawn(*blocked_worker[j - 1]); - else - tbb::task::spawn(*blocked_worker[j - 1]); + tbb::task::spawn(*blocked_worker[j - 1]); } else { From a1ba1042970bfbb815774dc4866bb3e6c6a5abff Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Tue, 19 Feb 2019 19:26:55 +0100 Subject: [PATCH 137/507] Provide step-61 with the usual exception catching harness --- examples/step-61/step-61.cc | 33 ++++++++++++++++++++++++++++++--- 1 file changed, 30 insertions(+), 3 deletions(-) diff --git a/examples/step-61/step-61.cc b/examples/step-61/step-61.cc index 13866adf300f..d62b125a7b8c 100644 --- a/examples/step-61/step-61.cc +++ b/examples/step-61/step-61.cc @@ -912,9 +912,36 @@ void WGDarcyEquation::run() // This is the main function. We can change the dimension here to run in 3d. int main() { - deallog.depth_console(2); - WGDarcyEquation<2> WGDarcyEquationTest; - WGDarcyEquationTest.run(); + try + { + deallog.depth_console(2); + WGDarcyEquation<2> WGDarcyEquationTest; + WGDarcyEquationTest.run(); + } + catch (std::exception &exc) + { + std::cerr << std::endl + << std::endl + << "----------------------------------------------------" + << std::endl; + std::cerr << "Exception on processing: " << std::endl + << exc.what() << std::endl + << "Aborting!" << std::endl + << "----------------------------------------------------" + << std::endl; + } + catch (...) + { + std::cerr << std::endl + << std::endl + << "----------------------------------------------------" + << std::endl; + std::cerr << "Unknown exception!" << std::endl + << "Aborting!" << std::endl + << "----------------------------------------------------" + << std::endl; + throw; + } return 0; } From 531bd4307253266c0d3772c4eab6e0c76b4053fa Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Tue, 19 Feb 2019 18:58:32 +0100 Subject: [PATCH 138/507] More HDF5 checks --- source/base/hdf5.cc | 73 ++++++++++++++++++++++++++++++--------------- 1 file changed, 49 insertions(+), 24 deletions(-) diff --git a/source/base/hdf5.cc b/source/base/hdf5.cc index b8c958679012..9e061c766432 100644 --- a/source/base/hdf5.cc +++ b/source/base/hdf5.cc @@ -68,8 +68,10 @@ namespace HDF5 else if (std::is_same>::value) { t_type = std::shared_ptr(new hid_t, [](hid_t *pointer) { - // Relase the HDF5 resource - H5Tclose(*pointer); + // Release the HDF5 resource + const herr_t ret = H5Tclose(*pointer); + Assert(ret >= 0, ExcInternalError()); + (void)ret; delete pointer; }); *t_type = H5Tcreate(H5T_COMPOUND, sizeof(std::complex)); @@ -77,15 +79,20 @@ namespace HDF5 // format used for the std::complex type be binary-compatible with // the C99 type, i.e. an array T[2] with consecutive real [0] and // imaginary [1] parts. - H5Tinsert(*t_type, "r", 0, H5T_NATIVE_FLOAT); - H5Tinsert(*t_type, "i", sizeof(float), H5T_NATIVE_FLOAT); + herr_t ret = H5Tinsert(*t_type, "r", 0, H5T_NATIVE_FLOAT); + Assert(ret >= 0, ExcInternalError()); + ret = H5Tinsert(*t_type, "i", sizeof(float), H5T_NATIVE_FLOAT); + Assert(ret >= 0, ExcInternalError()); + (void)ret; return t_type; } else if (std::is_same>::value) { t_type = std::shared_ptr(new hid_t, [](hid_t *pointer) { - // Relase the HDF5 resource - H5Tclose(*pointer); + // Release the HDF5 resource + const herr_t ret = H5Tclose(*pointer); + Assert(ret >= 0, ExcInternalError()); + (void)ret; delete pointer; }); *t_type = H5Tcreate(H5T_COMPOUND, sizeof(std::complex)); @@ -93,8 +100,11 @@ namespace HDF5 // format used for the std::complex type be binary-compatible with // the C99 type, i.e. an array T[2] with consecutive real [0] and // imaginary [1] parts. - H5Tinsert(*t_type, "r", 0, H5T_NATIVE_DOUBLE); - H5Tinsert(*t_type, "i", sizeof(double), H5T_NATIVE_DOUBLE); + herr_t ret = H5Tinsert(*t_type, "r", 0, H5T_NATIVE_DOUBLE); + Assert(ret >= 0, ExcInternalError()); + ret = H5Tinsert(*t_type, "i", sizeof(double), H5T_NATIVE_DOUBLE); + Assert(ret >= 0, ExcInternalError()); + (void)ret; return t_type; } @@ -434,7 +444,7 @@ namespace HDF5 // https://support.hdfgroup.org/ftp/HDF5/examples/misc-examples/vlstratt.c // // In the case of a variable length string the user does not have to reserve - // memory for string_out. The call HAread will reserve the memory and the + // memory for string_out. H5Aread will reserve the memory and the // user has to free the memory. // // Todo: @@ -466,8 +476,11 @@ namespace HDF5 // The memory of the variable length string has to be freed. // H5Dvlen_reclaim could be also used free(string_out); - H5Tclose(type); - H5Aclose(attr); + ret = H5Tclose(type); + Assert(ret >= 0, ExcInternalError()); + + ret = H5Aclose(attr); + Assert(ret >= 0, ExcInternalError()); (void)ret; return string_value; @@ -588,13 +601,17 @@ namespace HDF5 , global_no_collective_cause(H5D_MPIO_SET_INDEPENDENT) { hdf5_reference = std::shared_ptr(new hid_t, [](hid_t *pointer) { - // Relase the HDF5 resource - H5Dclose(*pointer); + // Release the HDF5 resource + const herr_t ret = H5Dclose(*pointer); + Assert(ret >= 0, ExcInternalError()); + (void)ret; delete pointer; }); dataspace = std::shared_ptr(new hid_t, [](hid_t *pointer) { - // Relase the HDF5 resource - H5Sclose(*pointer); + // Release the HDF5 resource + const herr_t ret = H5Sclose(*pointer); + Assert(ret >= 0, ExcInternalError()); + (void)ret; delete pointer; }); @@ -639,13 +656,17 @@ namespace HDF5 , global_no_collective_cause(H5D_MPIO_SET_INDEPENDENT) { hdf5_reference = std::shared_ptr(new hid_t, [](hid_t *pointer) { - // Relase the HDF5 resource - H5Dclose(*pointer); + // Release the HDF5 resource + const herr_t ret = H5Dclose(*pointer); + Assert(ret >= 0, ExcInternalError()); + (void)ret; delete pointer; }); dataspace = std::shared_ptr(new hid_t, [](hid_t *pointer) { - // Relase the HDF5 resource - H5Sclose(*pointer); + // Release the HDF5 resource + const herr_t ret = H5Sclose(*pointer); + Assert(ret >= 0, ExcInternalError()); + (void)ret; delete pointer; }); @@ -1273,8 +1294,10 @@ namespace HDF5 : HDF5Object(name, mpi) { hdf5_reference = std::shared_ptr(new hid_t, [](hid_t *pointer) { - // Relase the HDF5 resource - H5Gclose(*pointer); + // Release the HDF5 resource + const herr_t ret = H5Gclose(*pointer); + Assert(ret >= 0, ExcInternalError()); + (void)ret; delete pointer; }); switch (mode) @@ -1374,8 +1397,10 @@ namespace HDF5 : Group(name, mpi) { hdf5_reference = std::shared_ptr(new hid_t, [](hid_t *pointer) { - // Relase the HDF5 resource - H5Fclose(*pointer); + // Release the HDF5 resource + const herr_t err = H5Fclose(*pointer); + Assert(err >= 0, ExcInternalError()); + (void)err; delete pointer; }); @@ -1419,7 +1444,7 @@ namespace HDF5 if (mpi) { - // Relase the HDF5 resource + // Release the HDF5 resource ret = H5Pclose(plist); Assert(ret >= 0, ExcMessage("Error at H5Pclose")); } From 44cd2cedb50036b8e19fd5cd4fd85413b02cd2e7 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Tue, 19 Feb 2019 21:00:48 +0100 Subject: [PATCH 139/507] Use AssertNothrow in custom deleters --- source/base/hdf5.cc | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/source/base/hdf5.cc b/source/base/hdf5.cc index 9e061c766432..d32555839966 100644 --- a/source/base/hdf5.cc +++ b/source/base/hdf5.cc @@ -70,7 +70,7 @@ namespace HDF5 t_type = std::shared_ptr(new hid_t, [](hid_t *pointer) { // Release the HDF5 resource const herr_t ret = H5Tclose(*pointer); - Assert(ret >= 0, ExcInternalError()); + AssertNothrow(ret >= 0, ExcInternalError()); (void)ret; delete pointer; }); @@ -91,7 +91,7 @@ namespace HDF5 t_type = std::shared_ptr(new hid_t, [](hid_t *pointer) { // Release the HDF5 resource const herr_t ret = H5Tclose(*pointer); - Assert(ret >= 0, ExcInternalError()); + AssertNothrow(ret >= 0, ExcInternalError()); (void)ret; delete pointer; }); @@ -603,14 +603,14 @@ namespace HDF5 hdf5_reference = std::shared_ptr(new hid_t, [](hid_t *pointer) { // Release the HDF5 resource const herr_t ret = H5Dclose(*pointer); - Assert(ret >= 0, ExcInternalError()); + AssertNothrow(ret >= 0, ExcInternalError()); (void)ret; delete pointer; }); dataspace = std::shared_ptr(new hid_t, [](hid_t *pointer) { // Release the HDF5 resource const herr_t ret = H5Sclose(*pointer); - Assert(ret >= 0, ExcInternalError()); + AssertNothrow(ret >= 0, ExcInternalError()); (void)ret; delete pointer; }); @@ -658,14 +658,14 @@ namespace HDF5 hdf5_reference = std::shared_ptr(new hid_t, [](hid_t *pointer) { // Release the HDF5 resource const herr_t ret = H5Dclose(*pointer); - Assert(ret >= 0, ExcInternalError()); + AssertNothrow(ret >= 0, ExcInternalError()); (void)ret; delete pointer; }); dataspace = std::shared_ptr(new hid_t, [](hid_t *pointer) { // Release the HDF5 resource const herr_t ret = H5Sclose(*pointer); - Assert(ret >= 0, ExcInternalError()); + AssertNothrow(ret >= 0, ExcInternalError()); (void)ret; delete pointer; }); @@ -1296,7 +1296,7 @@ namespace HDF5 hdf5_reference = std::shared_ptr(new hid_t, [](hid_t *pointer) { // Release the HDF5 resource const herr_t ret = H5Gclose(*pointer); - Assert(ret >= 0, ExcInternalError()); + AssertNothrow(ret >= 0, ExcInternalError()); (void)ret; delete pointer; }); @@ -1399,7 +1399,7 @@ namespace HDF5 hdf5_reference = std::shared_ptr(new hid_t, [](hid_t *pointer) { // Release the HDF5 resource const herr_t err = H5Fclose(*pointer); - Assert(err >= 0, ExcInternalError()); + AssertNothrow(err >= 0, ExcInternalError()); (void)err; delete pointer; }); From f0ddc3b56bdbc002c2176ac347bf9463ec779766 Mon Sep 17 00:00:00 2001 From: Wolfgang Bangerth Date: Tue, 19 Feb 2019 16:04:29 -0700 Subject: [PATCH 140/507] Update the indentation of a documentation snippet. --- include/deal.II/grid/grid_tools.h | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/include/deal.II/grid/grid_tools.h b/include/deal.II/grid/grid_tools.h index d8e9050b414e..6eb080fe7233 100644 --- a/include/deal.II/grid/grid_tools.h +++ b/include/deal.II/grid/grid_tools.h @@ -761,15 +761,16 @@ namespace GridTools * are documented in GridTools::compute_point_locations(). * The last element of the @p return_type contains the * indices of points which are not not found inside the mesh - * or lie on artificial cells. - * + * or lie on artificial cells. The @p return_type equals the + * following tuple type: * @code * std::tuple< * std::vector< * typename Triangulation::active_cell_iterator>, - * std::vector>>, - * std::vector>, - * std::vector > + * std::vector>>, + * std::vector>, + * std::vector + * > * @endcode * * For a more detailed documentation see From 87179579f0aa07beeb41b9a7fb942c600eee9b32 Mon Sep 17 00:00:00 2001 From: tcclevenger Date: Tue, 19 Feb 2019 16:48:34 -0700 Subject: [PATCH 141/507] add random renumbering --- .../changes/minor/20190219ConradClevenger | 4 + include/deal.II/dofs/dof_renumbering.h | 21 ++++ source/dofs/dof_renumbering.cc | 49 ++++++++ source/dofs/dof_renumbering.inst.in | 10 ++ tests/dofs/dof_renumbering_09.cc | 108 ++++++++++++++++++ tests/dofs/dof_renumbering_09.output | 68 +++++++++++ 6 files changed, 260 insertions(+) create mode 100644 doc/news/changes/minor/20190219ConradClevenger create mode 100644 tests/dofs/dof_renumbering_09.cc create mode 100644 tests/dofs/dof_renumbering_09.output diff --git a/doc/news/changes/minor/20190219ConradClevenger b/doc/news/changes/minor/20190219ConradClevenger new file mode 100644 index 000000000000..aa560d10d9b8 --- /dev/null +++ b/doc/news/changes/minor/20190219ConradClevenger @@ -0,0 +1,4 @@ +New: Function DoFRenumbering::random(dof_handler, level) which allows for a random renumbering +of degrees of freedom on a level in a mutilevel hierarchy. +
+(Conrad Clevenger, 2019/02/19) diff --git a/include/deal.II/dofs/dof_renumbering.h b/include/deal.II/dofs/dof_renumbering.h index d94420c66e78..445fedd07883 100644 --- a/include/deal.II/dofs/dof_renumbering.h +++ b/include/deal.II/dofs/dof_renumbering.h @@ -1133,6 +1133,16 @@ namespace DoFRenumbering void random(DoFHandlerType &dof_handler); + /** + * Renumber the degrees of freedom in a random way. It does the same thing as + * the above function, only that it does this for one single level of a + * multilevel discretization. The non-multigrid part of the DoFHandler + * is not touched. + */ + template + void + random(DoFHandlerType &dof_handler, const unsigned int level); + /** * Compute the renumbering vector needed by the random() function. See * there for more information on the computed random renumbering. @@ -1145,6 +1155,17 @@ namespace DoFRenumbering compute_random(std::vector &new_dof_indices, const DoFHandlerType & dof_handler); + /** + * Compute the renumbering vector needed by the random() function. Same + * as the above function but for a single level of a multilevel + * discretization. + */ + template + void + compute_random(std::vector &new_dof_indices, + const DoFHandlerType & dof_handler, + const unsigned int level); + /** * @} */ diff --git a/source/dofs/dof_renumbering.cc b/source/dofs/dof_renumbering.cc index bd96818aca41..adc401e0f70d 100644 --- a/source/dofs/dof_renumbering.cc +++ b/source/dofs/dof_renumbering.cc @@ -2129,6 +2129,24 @@ namespace DoFRenumbering + template + void + random(DoFHandlerType &dof_handler, const unsigned int level) + { + Assert(dof_handler.n_dofs(level) != numbers::invalid_dof_index, + ExcDoFHandlerNotInitialized()); + + std::vector renumbering( + dof_handler.locally_owned_mg_dofs(level).n_elements(), + numbers::invalid_dof_index); + + compute_random(renumbering, dof_handler, level); + + dof_handler.renumber_dofs(level, renumbering); + } + + + template void compute_random(std::vector &new_indices, @@ -2159,6 +2177,37 @@ namespace DoFRenumbering + template + void + compute_random(std::vector &new_indices, + const DoFHandlerType & dof_handler, + const unsigned int level) + { + const types::global_dof_index n_dofs = dof_handler.n_dofs(level); + Assert(new_indices.size() == n_dofs, + ExcDimensionMismatch(new_indices.size(), n_dofs)); + + for (unsigned int i = 0; i < n_dofs; ++i) + new_indices[i] = i; + + // shuffle the elements; the following is essentially std::shuffle (which + // is new in C++11) but with a boost URNG + ::boost::mt19937 random_number_generator; + for (unsigned int i = 1; i < n_dofs; ++i) + { + // get a random number between 0 and i (inclusive) + const unsigned int j = + ::boost::random::uniform_int_distribution<>(0, i)( + random_number_generator); + + // if possible, swap the elements + if (i != j) + std::swap(new_indices[i], new_indices[j]); + } + } + + + template void subdomain_wise(DoFHandlerType &dof_handler) diff --git a/source/dofs/dof_renumbering.inst.in b/source/dofs/dof_renumbering.inst.in index f7667f4b8316..7ff6480386ef 100644 --- a/source/dofs/dof_renumbering.inst.in +++ b/source/dofs/dof_renumbering.inst.in @@ -293,6 +293,16 @@ for (deal_II_dimension : DIMENSIONS; deal_II_space_dimension : SPACE_DIMENSIONS) std::vector &, const DoFHandler &); + template void + random>(DoFHandler &, + const unsigned int); + + template void + compute_random>( + std::vector &, + const DoFHandler &, + const unsigned int); + template void sort_selected_dofs_back>( DoFHandler &, diff --git a/tests/dofs/dof_renumbering_09.cc b/tests/dofs/dof_renumbering_09.cc new file mode 100644 index 000000000000..7d3e0dcc3b0c --- /dev/null +++ b/tests/dofs/dof_renumbering_09.cc @@ -0,0 +1,108 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2000 - 2018 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + + +// tests DoFRenumbering::random function for levels + + + +#include + +#include +#include +#include + +#include +#include +#include +#include + +#include +#include +#include + +#include + +#include "../tests.h" + + + +template +void +print_dofs(const DoFHandler &dof, unsigned int level) +{ + std::vector v(dof.get_fe().dofs_per_cell); + for (typename DoFHandler::cell_iterator cell = dof.begin(level); + cell != dof.end(level); + ++cell) + { + deallog << "Cell " << cell << " -- "; + cell->get_mg_dof_indices(v); + for (unsigned int i = 0; i < v.size(); ++i) + deallog << v[i] << ' '; + deallog << std::endl; + } +} + + +template +void +test() +{ + Triangulation tr(Triangulation::limit_level_difference_at_vertices); + GridGenerator::hyper_cube(tr); + tr.refine_global((dim == 1 ? 2 : 1)); + + DoFHandler dof_handler(tr); + + FE_Q fe(1); + dof_handler.distribute_dofs(fe); + dof_handler.distribute_mg_dofs(fe); + + + // Print dofs before reordering + deallog << "Before reorder: " << std::endl; + for (unsigned int level = 0; level < tr.n_levels(); ++level) + { + deallog << "Level " << level << std::endl; + print_dofs(dof_handler, level); + } + + for (unsigned int level = 0; level < tr.n_levels(); ++level) + DoFRenumbering::random(dof_handler, level); + + // Print dofs after reordering + deallog << "After reorder: " << std::endl; + for (unsigned int level = 0; level < tr.n_levels(); ++level) + { + deallog << "Level " << level << std::endl; + print_dofs(dof_handler, level); + } +} + + +int +main() +{ + initlog(); + + deallog << "1D" << std::endl; + test<1>(); + deallog << std::endl << "2D" << std::endl; + test<2>(); + deallog << std::endl << "3D" << std::endl; + test<3>(); +} diff --git a/tests/dofs/dof_renumbering_09.output b/tests/dofs/dof_renumbering_09.output new file mode 100644 index 000000000000..a82919a5f96f --- /dev/null +++ b/tests/dofs/dof_renumbering_09.output @@ -0,0 +1,68 @@ + +DEAL::1D +DEAL::Before reorder: +DEAL::Level 0 +DEAL::Cell 0.0 -- 0 1 +DEAL::Level 1 +DEAL::Cell 1.0 -- 0 1 +DEAL::Cell 1.1 -- 1 2 +DEAL::Level 2 +DEAL::Cell 2.0 -- 0 1 +DEAL::Cell 2.1 -- 1 2 +DEAL::Cell 2.2 -- 2 3 +DEAL::Cell 2.3 -- 3 4 +DEAL::After reorder: +DEAL::Level 0 +DEAL::Cell 0.0 -- 0 1 +DEAL::Level 1 +DEAL::Cell 1.0 -- 2 1 +DEAL::Cell 1.1 -- 1 0 +DEAL::Level 2 +DEAL::Cell 2.0 -- 2 1 +DEAL::Cell 2.1 -- 1 0 +DEAL::Cell 2.2 -- 0 3 +DEAL::Cell 2.3 -- 3 4 +DEAL:: +DEAL::2D +DEAL::Before reorder: +DEAL::Level 0 +DEAL::Cell 0.0 -- 0 1 2 3 +DEAL::Level 1 +DEAL::Cell 1.0 -- 0 1 2 3 +DEAL::Cell 1.1 -- 1 4 3 5 +DEAL::Cell 1.2 -- 2 3 6 7 +DEAL::Cell 1.3 -- 3 5 7 8 +DEAL::After reorder: +DEAL::Level 0 +DEAL::Cell 0.0 -- 2 1 0 3 +DEAL::Level 1 +DEAL::Cell 1.0 -- 5 8 0 3 +DEAL::Cell 1.1 -- 8 4 3 2 +DEAL::Cell 1.2 -- 0 3 6 7 +DEAL::Cell 1.3 -- 3 2 7 1 +DEAL:: +DEAL::3D +DEAL::Before reorder: +DEAL::Level 0 +DEAL::Cell 0.0 -- 0 1 2 3 4 5 6 7 +DEAL::Level 1 +DEAL::Cell 1.0 -- 0 1 2 3 4 5 6 7 +DEAL::Cell 1.1 -- 1 8 3 9 5 10 7 11 +DEAL::Cell 1.2 -- 2 3 12 13 6 7 14 15 +DEAL::Cell 1.3 -- 3 9 13 16 7 11 15 17 +DEAL::Cell 1.4 -- 4 5 6 7 18 19 20 21 +DEAL::Cell 1.5 -- 5 10 7 11 19 22 21 23 +DEAL::Cell 1.6 -- 6 7 14 15 20 21 24 25 +DEAL::Cell 1.7 -- 7 11 15 17 21 23 25 26 +DEAL::After reorder: +DEAL::Level 0 +DEAL::Cell 0.0 -- 5 1 0 3 4 2 6 7 +DEAL::Level 1 +DEAL::Cell 1.0 -- 5 11 26 21 4 2 9 12 +DEAL::Cell 1.1 -- 11 15 21 6 2 3 12 8 +DEAL::Cell 1.2 -- 26 21 7 10 9 12 0 1 +DEAL::Cell 1.3 -- 21 6 10 22 12 8 1 17 +DEAL::Cell 1.4 -- 4 2 9 12 18 19 20 13 +DEAL::Cell 1.5 -- 2 3 12 8 19 16 13 23 +DEAL::Cell 1.6 -- 9 12 0 1 20 13 25 24 +DEAL::Cell 1.7 -- 12 8 1 17 13 23 24 14 From 23412344473e67a86effd12b85ec8f63d20a5e70 Mon Sep 17 00:00:00 2001 From: Wolfgang Bangerth Date: Tue, 19 Feb 2019 18:12:28 -0700 Subject: [PATCH 142/507] Edits to the intro and results sections of step-61. --- examples/step-61/doc/intro.dox | 101 ++++++++++++++++++++++--------- examples/step-61/doc/results.dox | 85 ++++++++++++++++++-------- 2 files changed, 134 insertions(+), 52 deletions(-) diff --git a/examples/step-61/doc/intro.dox b/examples/step-61/doc/intro.dox index f5ca096683c0..5cc7c2120e3c 100644 --- a/examples/step-61/doc/intro.dox +++ b/examples/step-61/doc/intro.dox @@ -11,9 +11,11 @@ This tutorial program presents an implementation of the "weak Galerkin" finite element method for the Poisson equation. In some sense, the motivation for considering this method starts from the same point as in step-51: We would like to consider discontinuous shape functions, but then need to address the fact that -the resulting problem has a large number of degrees of freedom (because, for +the resulting problem has a much larger number of degrees of freedom compared to +the usual continuous Galerkin method (because, for example, each vertex carries as many degrees of freedom as there are adjacent cells). -We also have to address the fact that, in general, every degree of freedom +We also have to address the fact that, unlike in the continuous +Galerkin method, every degree of freedom on one cell couples with all of the degrees of freedom on each of its face neighbor cells. Consequently, the matrix one gets from the "traditional" discontinuous Galerkin methods are both large and relatively dense. @@ -25,13 +27,15 @@ cells (i.e., on the "skeleton" of the mesh), and which therefore "insulate" the degrees of freedom on the adjacent cells from each other: cell degrees of freedom only couple with other cell degrees of freedom on the same cell, as well as face degrees of freedom, but not with cell degrees of freedom on neighboring cells. -Consequently, the shape functions for these cell degrees of freedom are -discontinuous and only "live" on exactly one cell. +Consequently, the coupling of shape functions for these cell degrees of freedom +indeed local to on exactly one cell and the degrees of freedom defined on its +faces. For a given equation, say the second order Poisson equation, -the difference between the HDG and the WG method is how exactly one formulates -the problem that connects all of these different shape functions. The HDG does -things by reformulating second order problems in terms of a system of first +the difference between the HDG and the WG method is how precisely one formulates +the problem that connects all of these different shape functions. (Indeed, +for some WG and HDG formulation, it is possible to show that they are equivalent.) +The HDG does things by reformulating second order problems in terms of a system of first order equations and then conceptually considers the face degrees of freedom to be "fluxes" of this first order system. In contrast, the WG method keeps things in second order form and considers the face degrees of freedom as of the same @@ -48,19 +52,21 @@ additional effort is not prohibitive.

Weak Galerkin finite element methods

Weak Galerkin Finite Element Methods (WGFEMs) use discrete weak functions -to approximate scalar unknowns and discrete weak gradients to +to approximate scalar unknowns, and discrete weak gradients to approximate classical gradients. -It was introduced by Junping Wang and Xiu Ye -in the paper: A weak Galerkin finite element method for second order elliptic problems, -J. Comput. Appl. Math., 2013, 103-115. +The method was originally introduced by Junping Wang and Xiu Ye +in the paper + +A weak Galerkin finite element method for second order elliptic problems, +J. Comput. Appl. Math., 103-115, 2013. Compared to the continuous Galerkin method, the weak Galerkin method satisfies important physical properties, namely local mass conservation and bulk normal flux continuity. -It results in a SPD linear system, and expected convergence rates can +It results in a SPD linear system, and optimal convergence rates can be obtained with mesh refinement. -

WGFEM applied to the Poisson equation

+

The equation to solve

This program solves the Poisson equation using the weak Galerkin finite element method: @f{eqnarray*} @@ -74,38 +80,77 @@ using the weak Galerkin finite element method: where $\Omega \subset \mathbb{R}^n (n=2,3)$ is a bounded domain. In the context of the flow of a fluid through a porous medium, $p$ is the pressure, $\mathbf{K}$ is a permeability tensor, -$ f $ is the source term, and -$ p_D, u_N $ represent Dirichlet and Neumann boundary conditions. +$f$ is the source term, and +$p_D, u_N$ represent Dirichlet and Neumann boundary conditions. We can introduce a flux, $\mathbf{u} = -\mathbf{K} \nabla p$, that corresponds to the Darcy velocity (in the way we did in step-20) and this variable will be important in the considerations below. In this program, we will consider a test case where the exact pressure -is $p = \sin \left( \pi x)\sin(\pi y \right)$ on the unit square domain, -with homogenous Dirichelet boundary conditions and identity matrix $\mathbf{K}$. -Then we will calculate $L_2$ errors of pressure, velocity and flux. +is $p = \sin \left( \pi x\right)\sin\left(\pi y \right)$ on the unit square domain, +with homogenous Dirichelet boundary conditions and $\mathbf{K}$ the identity matrix. +Then we will calculate $L_2$ errors of pressure, velocity, and flux.

Weak Galerkin scheme

-Via integration by parts, the weak Galerkin scheme for the Poisson equation is +The Poisson equation above has a solution $p$ that needs to satisfy the weak +formulation of the problem, @f{equation*} -\mathcal{A}_h\left(p_h,q \right) = \mathcal{F} \left(q \right), +\mathcal{A}\left(p,q \right) = \mathcal{F} \left(q \right), @f} -where +for all test functions $q$, where @f{equation*} -\mathcal{A}_h\left(p_h,q\right) - := \sum_{T \in \mathcal{T}_h} - \int_T \mathbf{K} \nabla_{w,d} p_h \cdot \nabla_{w,d} q \mathrm{d}x, +\mathcal{A}\left(p,q\right) + := \int_\Omega \mathbf{K} \nabla p \cdot \nabla q \;\mathrm{d}x, @f} and @f{equation*} \mathcal{F}\left(q\right) - := \sum_{T \in \mathcal{T}_h} \int_T f \, q^\circ \mathrm{d}x - - \sum_{\gamma \in \Gamma_h^N} \int_\gamma u_N q^\partial \mathrm{d}x, + := \int_\Omega f \, q \;\mathrm{d}x + - \int_{\Gamma^N} u_N q \; \mathrm{d}x. +@f} +Here, we have integrated by parts in the bilinear form, and we are evaluating +the gradient of $p,p$ in the interior and the values of $q$ on the boundary +of the domain. All of this is well defined because we assume that the solution +is in $H^1$ for which taking the gradient and evaluating boundary values +are valid operations. + +The idea of the weak Galerkin method is now to approximate the exact $p$ +solution with a discontinuous function $p_h$. This function may only be +discontinuous along interfaces between cells, and because we will want to +evaluate this function also along interfaces, we have to +prescribe not only what values it is supposed to have in the cell interiors +but also its values along interfaces. We do this by saying that $p_h$ is +actually a tuple, $p_h=(p^\circ,p^\partial)$, though it's really just +a single function that is either equal to $p^\circ(x)$ or $p^\partial(x)$, +depending on whether it is evaluated at a point $x$ that lies in the cell +interior or on cell interfaces. + +We would then like to simply stick this approximation into the bilinear +form above. This works for the case where we have to evaluate the +test function $q_h$ on the boundary (where we would simply take its interface +part $q_h^\partial$) but we have to be careful with the gradient because +that is only defined in cell interiors. Consequently, + the weak Galerkin scheme for the Poisson equation is defined by +@f{equation*} +\mathcal{A}_h\left(p_h,q \right) = \mathcal{F} \left(q_h \right), +@f} +for all discrete test functions $q_h$, where +@f{equation*} +\mathcal{A}_h\left(p_h,q_h\right) + := \sum_{T \in \mathcal{T}_h} + \int_T \mathbf{K} \nabla_{w,d} p_h \cdot \nabla_{w,d} q_h \;\mathrm{d}x, +@f} +and +@f{equation*} +\mathcal{F}\left(q_h\right) + := \sum_{T \in \mathcal{T}_h} \int_T f \, q_h^\circ \;\mathrm{d}x + - \sum_{\gamma \in \Gamma_h^N} \int_\gamma u_N q_h^\partial \;\mathrm{d}x, @f} -$q^\circ$ is the shape function of the polynomial space in the interior, -$q^\partial$ is the shape function of the polynomial space on faces, $ \nabla_{w,d} $ means the discrete weak gradient used to approximate the classical gradient. +The key point is that here, we have replaced the gradient $\nabla p_h$ by the +discrete weak gradient + $ \nabla_{w,d} p_h $ that is defined for our peculiarly defined approximation $p_h$. We use FE_DGQ as the interior polynomial space, FE_FaceQ as the face polynomial space, and Raviart-Thomas elements for the velocity $\mathbf{u} = -{\mathbf{K}} \nabla_{w,d} p$. diff --git a/examples/step-61/doc/results.dox b/examples/step-61/doc/results.dox index b71c57abb177..6d21bb519c00 100644 --- a/examples/step-61/doc/results.dox +++ b/examples/step-61/doc/results.dox @@ -24,14 +24,27 @@ Since the mesh is a rectangular mesh and numbers of refinement are even, we have We run the code with finer meshes and get the following convergence rates of pressure, velocity and flux. -@code -number of refinements $\|p-p_h^\circ\|$ $\|\mathbf{u}-\mathbf{u}_h\|$ $\|(\mathbf{u}-\mathbf{u}_h) \cdot \mathbf{n}\|$ - 2 1.587e-01 5.113e-01 7.062e-01 - 3 8.000e-02 2.529e-01 3.554e-01 - 4 4.006e-02 1.260e-01 1.780e-01 - 5 2.004e-02 6.297e-02 8.902e-02 -Conv.rate 1.00 1.00 1.00 -@endcode + + + + + + + + + + + + + + + + + + + +
number of refinements $\|p-p_h^\circ\|$ $\|\mathbf{u}-\mathbf{u}_h\|$ $\|(\mathbf{u}-\mathbf{u}_h) \cdot \mathbf{n}\|$
2 1.587e-01 5.113e-01 7.062e-01
3 8.000e-02 2.529e-01 3.554e-01
4 4.006e-02 1.260e-01 1.780e-01
5 2.004e-02 6.297e-02 8.902e-02
Conv.rate 1.00 1.00 1.00
+ We can see that the convergence rates of $\mbox{WG}(Q_0,Q_0;RT_{[0]})$ are around 1. @@ -52,14 +65,26 @@ to divide each cell interior into 4 subcells. These are the convergence rates of pressure, velocity and flux on $\mbox{WG}(Q_1,Q_1;RT_{[1]})$ -@code -number of refinements $\|p-p_h^\circ\|$ $\|\mathbf{u}-\mathbf{u}_h\|$ $\|(\mathbf{u}-\mathbf{u}_h) \cdot \mathbf{n}\|$ - 2 1.613e-02 5.093e-02 7.167e-02 - 3 4.056e-03 1.276e-02 1.802e-02 - 4 1.015e-03 3.191e-03 4.512e-03 - 5 2.540e-04 7.979e-04 1.128e-03 -Conv.rate 2.00 2.00 2.00 -@endcode + + + + + + + + + + + + + + + + + + + +
number of refinements $\|p-p_h^\circ\|$ $\|\mathbf{u}-\mathbf{u}_h\|$ $\|(\mathbf{u}-\mathbf{u}_h) \cdot \mathbf{n}\|$
2 1.613e-02 5.093e-02 7.167e-02
3 4.056e-03 1.276e-02 1.802e-02
4 1.015e-03 3.191e-03 4.512e-03
5 2.540e-04 7.979e-04 1.128e-03
Conv.rate 2.00 2.00 2.00
The convergence rates of $WG(Q_1,Q_1;RT_{[1]})$ are around 2.

Test results on $WG(Q_2,Q_2;RT_{[2]})$

@@ -77,12 +102,24 @@ These are interior pressures and face pressures implemented on $WG(Q_2,Q_2;RT_{[ This is the convergence table of $L_2$ errors of pressure, velocity and flux on $\mbox{WG}(Q_2,Q_2;RT_{[2]})$ -@code -number of refinements $\|p-p_h^\circ\|$ $\|\mathbf{u}-\mathbf{u}_h\|$ $\|(\mathbf{u}-\mathbf{u}_h) \cdot \mathbf{n}\|$ - 2 1.072e-03 3.375e-03 4.762e-03 - 3 1.347e-04 4.233e-04 5.982e-04 - 4 1.685e-05 5.295e-05 7.487e-05 - 5 2.107e-06 6.620e-06 9.362e-06 -Conv.rate 3.00 3.00 3.00 -@endcode + + + + + + + + + + + + + + + + + + + +
number of refinements $\|p-p_h^\circ\|$ $\|\mathbf{u}-\mathbf{u}_h\|$ $\|(\mathbf{u}-\mathbf{u}_h) \cdot \mathbf{n}\|$
2 1.072e-03 3.375e-03 4.762e-03
3 1.347e-04 4.233e-04 5.982e-04
4 1.685e-05 5.295e-05 7.487e-05
5 2.107e-06 6.620e-06 9.362e-06
Conv.rate 3.00 3.00 3.00
The convergence rates of $\mbox{WG}(Q_2,Q_2;RT_{[2]})$ are around 3. From 8dd953d299423f8f0dc292d57378b9d5a9734440 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Wed, 20 Feb 2019 11:36:56 +0100 Subject: [PATCH 143/507] Escape preprocessor commands for doxygen --- include/deal.II/base/exceptions.h | 54 +++++++++++++++---------------- 1 file changed, 27 insertions(+), 27 deletions(-) diff --git a/include/deal.II/base/exceptions.h b/include/deal.II/base/exceptions.h index 2f254faf9020..7ae5571d7d91 100644 --- a/include/deal.II/base/exceptions.h +++ b/include/deal.II/base/exceptions.h @@ -185,7 +185,7 @@ class ExceptionBase : public std::exception * them unique to deal.II. As a consequence, it is possible that other * libraries your code interfaces with define the same name, and the result * will be name collisions (see - * https://en.wikipedia.org/wiki/Name_collision). One can #undef + * https://en.wikipedia.org/wiki/Name_collision). One can \#undef * this macro, as well as all other macros defined by deal.II that are not * prefixed with either DEAL or deal, by including * the header deal.II/base/undefine_macros.h after all other @@ -210,7 +210,7 @@ class ExceptionBase : public std::exception * them unique to deal.II. As a consequence, it is possible that other * libraries your code interfaces with define the same name, and the result * will be name collisions (see - * https://en.wikipedia.org/wiki/Name_collision). One can #undef + * https://en.wikipedia.org/wiki/Name_collision). One can \#undef * this macro, as well as all other macros defined by deal.II that are not * prefixed with either DEAL or deal, by including * the header deal.II/base/undefine_macros.h after all other @@ -246,7 +246,7 @@ class ExceptionBase : public std::exception * them unique to deal.II. As a consequence, it is possible that other * libraries your code interfaces with define the same name, and the result * will be name collisions (see - * https://en.wikipedia.org/wiki/Name_collision). One can #undef + * https://en.wikipedia.org/wiki/Name_collision). One can \#undef * this macro, as well as all other macros defined by deal.II that are not * prefixed with either DEAL or deal, by including * the header deal.II/base/undefine_macros.h after all other @@ -283,7 +283,7 @@ class ExceptionBase : public std::exception * them unique to deal.II. As a consequence, it is possible that other * libraries your code interfaces with define the same name, and the result * will be name collisions (see - * https://en.wikipedia.org/wiki/Name_collision). One can #undef + * https://en.wikipedia.org/wiki/Name_collision). One can \#undef * this macro, as well as all other macros defined by deal.II that are not * prefixed with either DEAL or deal, by including * the header deal.II/base/undefine_macros.h after all other @@ -322,7 +322,7 @@ class ExceptionBase : public std::exception * them unique to deal.II. As a consequence, it is possible that other * libraries your code interfaces with define the same name, and the result * will be name collisions (see - * https://en.wikipedia.org/wiki/Name_collision). One can #undef + * https://en.wikipedia.org/wiki/Name_collision). One can \#undef * this macro, as well as all other macros defined by deal.II that are not * prefixed with either DEAL or deal, by including * the header deal.II/base/undefine_macros.h after all other @@ -363,7 +363,7 @@ class ExceptionBase : public std::exception * them unique to deal.II. As a consequence, it is possible that other * libraries your code interfaces with define the same name, and the result * will be name collisions (see - * https://en.wikipedia.org/wiki/Name_collision). One can #undef + * https://en.wikipedia.org/wiki/Name_collision). One can \#undef * this macro, as well as all other macros defined by deal.II that are not * prefixed with either DEAL or deal, by including * the header deal.II/base/undefine_macros.h after all other @@ -409,7 +409,7 @@ class ExceptionBase : public std::exception * them unique to deal.II. As a consequence, it is possible that other * libraries your code interfaces with define the same name, and the result * will be name collisions (see - * https://en.wikipedia.org/wiki/Name_collision). One can #undef + * https://en.wikipedia.org/wiki/Name_collision). One can \#undef * this macro, as well as all other macros defined by deal.II that are not * prefixed with either DEAL or deal, by including * the header deal.II/base/undefine_macros.h after all other @@ -461,7 +461,7 @@ class ExceptionBase : public std::exception * them unique to deal.II. As a consequence, it is possible that other * libraries your code interfaces with define the same name, and the result * will be name collisions (see - * https://en.wikipedia.org/wiki/Name_collision). One can #undef + * https://en.wikipedia.org/wiki/Name_collision). One can \#undef * this macro, as well as all other macros defined by deal.II that are not * prefixed with either DEAL or deal, by including * the header deal.II/base/undefine_macros.h after all other @@ -485,7 +485,7 @@ class ExceptionBase : public std::exception * them unique to deal.II. As a consequence, it is possible that other * libraries your code interfaces with define the same name, and the result * will be name collisions (see - * https://en.wikipedia.org/wiki/Name_collision). One can #undef + * https://en.wikipedia.org/wiki/Name_collision). One can \#undef * this macro, as well as all other macros defined by deal.II that are not * prefixed with either DEAL or deal, by including * the header deal.II/base/undefine_macros.h after all other @@ -507,7 +507,7 @@ class ExceptionBase : public std::exception * them unique to deal.II. As a consequence, it is possible that other * libraries your code interfaces with define the same name, and the result * will be name collisions (see - * https://en.wikipedia.org/wiki/Name_collision). One can #undef + * https://en.wikipedia.org/wiki/Name_collision). One can \#undef * this macro, as well as all other macros defined by deal.II that are not * prefixed with either DEAL or deal, by including * the header deal.II/base/undefine_macros.h after all other @@ -530,7 +530,7 @@ class ExceptionBase : public std::exception * them unique to deal.II. As a consequence, it is possible that other * libraries your code interfaces with define the same name, and the result * will be name collisions (see - * https://en.wikipedia.org/wiki/Name_collision). One can #undef + * https://en.wikipedia.org/wiki/Name_collision). One can \#undef * this macro, as well as all other macros defined by deal.II that are not * prefixed with either DEAL or deal, by including * the header deal.II/base/undefine_macros.h after all other @@ -553,7 +553,7 @@ class ExceptionBase : public std::exception * them unique to deal.II. As a consequence, it is possible that other * libraries your code interfaces with define the same name, and the result * will be name collisions (see - * https://en.wikipedia.org/wiki/Name_collision). One can #undef + * https://en.wikipedia.org/wiki/Name_collision). One can \#undef * this macro, as well as all other macros defined by deal.II that are not * prefixed with either DEAL or deal, by including * the header deal.II/base/undefine_macros.h after all other @@ -576,7 +576,7 @@ class ExceptionBase : public std::exception * them unique to deal.II. As a consequence, it is possible that other * libraries your code interfaces with define the same name, and the result * will be name collisions (see - * https://en.wikipedia.org/wiki/Name_collision). One can #undef + * https://en.wikipedia.org/wiki/Name_collision). One can \#undef * this macro, as well as all other macros defined by deal.II that are not * prefixed with either DEAL or deal, by including * the header deal.II/base/undefine_macros.h after all other @@ -602,7 +602,7 @@ class ExceptionBase : public std::exception * them unique to deal.II. As a consequence, it is possible that other * libraries your code interfaces with define the same name, and the result * will be name collisions (see - * https://en.wikipedia.org/wiki/Name_collision). One can #undef + * https://en.wikipedia.org/wiki/Name_collision). One can \#undef * this macro, as well as all other macros defined by deal.II that are not * prefixed with either DEAL or deal, by including * the header deal.II/base/undefine_macros.h after all other @@ -1393,7 +1393,7 @@ namespace deal_II_exceptions * them unique to deal.II. As a consequence, it is possible that other * libraries your code interfaces with define the same name, and the result * will be name collisions (see - * https://en.wikipedia.org/wiki/Name_collision). One can #undef + * https://en.wikipedia.org/wiki/Name_collision). One can \#undef * this macro, as well as all other macros defined by deal.II that are not * prefixed with either DEAL or deal, by including * the header deal.II/base/undefine_macros.h after all other @@ -1456,7 +1456,7 @@ namespace deal_II_exceptions * them unique to deal.II. As a consequence, it is possible that other * libraries your code interfaces with define the same name, and the result * will be name collisions (see - * https://en.wikipedia.org/wiki/Name_collision). One can #undef + * https://en.wikipedia.org/wiki/Name_collision). One can \#undef * this macro, as well as all other macros defined by deal.II that are not * prefixed with either DEAL or deal, by including * the header deal.II/base/undefine_macros.h after all other @@ -1505,7 +1505,7 @@ namespace deal_II_exceptions * them unique to deal.II. As a consequence, it is possible that other * libraries your code interfaces with define the same name, and the result * will be name collisions (see - * https://en.wikipedia.org/wiki/Name_collision). One can #undef + * https://en.wikipedia.org/wiki/Name_collision). One can \#undef * this macro, as well as all other macros defined by deal.II that are not * prefixed with either DEAL or deal, by including * the header deal.II/base/undefine_macros.h after all other @@ -1555,7 +1555,7 @@ namespace deal_II_exceptions * them unique to deal.II. As a consequence, it is possible that other * libraries your code interfaces with define the same name, and the result * will be name collisions (see - * https://en.wikipedia.org/wiki/Name_collision). One can #undef + * https://en.wikipedia.org/wiki/Name_collision). One can \#undef * this macro, as well as all other macros defined by deal.II that are not * prefixed with either DEAL or deal, by including * the header deal.II/base/undefine_macros.h after all other @@ -1583,7 +1583,7 @@ namespace deal_II_exceptions * them unique to deal.II. As a consequence, it is possible that other * libraries your code interfaces with define the same name, and the result * will be name collisions (see - * https://en.wikipedia.org/wiki/Name_collision). One can #undef + * https://en.wikipedia.org/wiki/Name_collision). One can \#undef * this macro, as well as all other macros defined by deal.II that are not * prefixed with either DEAL or deal, by including * the header deal.II/base/undefine_macros.h after all other @@ -1625,7 +1625,7 @@ namespace internal * them unique to deal.II. As a consequence, it is possible that other * libraries your code interfaces with define the same name, and the result * will be name collisions (see - * https://en.wikipedia.org/wiki/Name_collision). One can #undef + * https://en.wikipedia.org/wiki/Name_collision). One can \#undef * this macro, as well as all other macros defined by deal.II that are not * prefixed with either DEAL or deal, by including * the header deal.II/base/undefine_macros.h after all other @@ -1657,7 +1657,7 @@ namespace internal * them unique to deal.II. As a consequence, it is possible that other * libraries your code interfaces with define the same name, and the result * will be name collisions (see - * https://en.wikipedia.org/wiki/Name_collision). One can #undef + * https://en.wikipedia.org/wiki/Name_collision). One can \#undef * this macro, as well as all other macros defined by deal.II that are not * prefixed with either DEAL or deal, by including * the header deal.II/base/undefine_macros.h after all other @@ -1682,7 +1682,7 @@ namespace internal * them unique to deal.II. As a consequence, it is possible that other * libraries your code interfaces with define the same name, and the result * will be name collisions (see - * https://en.wikipedia.org/wiki/Name_collision). One can #undef + * https://en.wikipedia.org/wiki/Name_collision). One can \#undef * this macro, as well as all other macros defined by deal.II that are not * prefixed with either DEAL or deal, by including * the header deal.II/base/undefine_macros.h after all other @@ -1709,7 +1709,7 @@ namespace internal * them unique to deal.II. As a consequence, it is possible that other * libraries your code interfaces with define the same name, and the result * will be name collisions (see - * https://en.wikipedia.org/wiki/Name_collision). One can #undef + * https://en.wikipedia.org/wiki/Name_collision). One can \#undef * this macro, as well as all other macros defined by deal.II that are not * prefixed with either DEAL or deal, by including * the header deal.II/base/undefine_macros.h after all other @@ -1737,7 +1737,7 @@ namespace internal * them unique to deal.II. As a consequence, it is possible that other * libraries your code interfaces with define the same name, and the result * will be name collisions (see - * https://en.wikipedia.org/wiki/Name_collision). One can #undef + * https://en.wikipedia.org/wiki/Name_collision). One can \#undef * this macro, as well as all other macros defined by deal.II that are not * prefixed with either DEAL or deal, by including * the header deal.II/base/undefine_macros.h after all other @@ -1766,7 +1766,7 @@ namespace internal * them unique to deal.II. As a consequence, it is possible that other * libraries your code interfaces with define the same name, and the result * will be name collisions (see - * https://en.wikipedia.org/wiki/Name_collision). One can #undef + * https://en.wikipedia.org/wiki/Name_collision). One can \#undef * this macro, as well as all other macros defined by deal.II that are not * prefixed with either DEAL or deal, by including * the header deal.II/base/undefine_macros.h after all other @@ -1797,7 +1797,7 @@ namespace internal * them unique to deal.II. As a consequence, it is possible that other * libraries your code interfaces with define the same name, and the result * will be name collisions (see - * https://en.wikipedia.org/wiki/Name_collision). One can #undef + * https://en.wikipedia.org/wiki/Name_collision). One can \#undef * this macro, as well as all other macros defined by deal.II that are not * prefixed with either DEAL or deal, by including * the header deal.II/base/undefine_macros.h after all other @@ -1829,7 +1829,7 @@ namespace internal * them unique to deal.II. As a consequence, it is possible that other * libraries your code interfaces with define the same name, and the result * will be name collisions (see - * https://en.wikipedia.org/wiki/Name_collision). One can #undef + * https://en.wikipedia.org/wiki/Name_collision). One can \#undef * this macro, as well as all other macros defined by deal.II that are not * prefixed with either DEAL or deal, by including * the header deal.II/base/undefine_macros.h after all other From 2db0688995602a45ae67d742e3585968735b4280 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Wed, 20 Feb 2019 11:38:19 +0100 Subject: [PATCH 144/507] Improve QR documentation --- include/deal.II/lac/qr.h | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/include/deal.II/lac/qr.h b/include/deal.II/lac/qr.h index 1898d6fb1438..7625f7935799 100644 --- a/include/deal.II/lac/qr.h +++ b/include/deal.II/lac/qr.h @@ -127,8 +127,8 @@ class BaseQR * Connect a slot to retrieve a notification when the Givens rotations * are performed. * - * The function takes @p i'th and @p j'th indices of the plane of rotation - * and a triplet of numbers @p csr (cosine, sine and radius, see + * The function takes two indices, @p i and @p j, describing the plane of + * rotation, and a triplet of numbers @p csr (cosine, sine and radius, see * Utilities::LinearAlgebra::givens_rotation()) which represents the rotation * matrix. */ @@ -169,7 +169,7 @@ class BaseQR /** * Signal used to retrieve a notification - * when Givens rotations are performed in plane @p i and @p j. + * when Givens rotations are performed in the `(i,j)`-plane. */ boost::signals2::signal virtual ~QR() = default; /** - * @copyfrom BaseQR::append_column + * @copydoc BaseQR::append_column * * @note Currently this function always returns true. */ @@ -310,7 +310,7 @@ class QR : public BaseQR private: /** - * Apply givens rotation in plane @p i @p k to @p Q and @p R so that + * Apply givens rotation in the `(i,j)`-plane to @p Q and @p R so that * R(k,k) is zeroed. * * See Chapter 5.1.9 of Golub 2013, Matrix computations. @@ -396,7 +396,7 @@ class ImplicitQR : public BaseQR * Connect a slot to implement a custom check of linear dependency * during addition of a column. * - * Here, @p u is the last column of the to-be R matrix , @p rho + * Here, @p u is the last column of the to-be R matrix, @p rho * is its diagonal and @p col_norm_sqr is the square of the $l2$ norm of the column. * The function should return true if the new column is * linearly independent. @@ -409,7 +409,7 @@ class ImplicitQR : public BaseQR private: /** - * Apply givens rotation in plane @i @p k to zero out $R(k,k)$. + * Apply givens rotation in the `(i,k)`-plane to zero out $R(k,k)$. */ void apply_givens_rotation(const unsigned int i, const unsigned int k); @@ -417,7 +417,7 @@ class ImplicitQR : public BaseQR /** * Signal used to decide if the new column is linear dependent. * - * Here, @p u is the last column of the to-be R matrix , @p rho + * Here, @p u is the last column of the to-be R matrix, @p rho * is its diagonal and @p col_norm_sqr is the square of the $l2$ norm of the column. * The function should return true if the new column is * linearly independent. From 366c7497712e5269ffc533e94da7ef6ee15541a3 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Wed, 20 Feb 2019 11:38:53 +0100 Subject: [PATCH 145/507] Fix doxygen problem in VectorTools::create_point_source_vector --- include/deal.II/numerics/vector_tools.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/include/deal.II/numerics/vector_tools.h b/include/deal.II/numerics/vector_tools.h index ec060968c17b..37b43f49ed51 100644 --- a/include/deal.II/numerics/vector_tools.h +++ b/include/deal.II/numerics/vector_tools.h @@ -2184,7 +2184,7 @@ namespace VectorTools * function for the problem you are solving. This is because the * Green's function $G(x,p)$ is defined by * @f{align*}{ - * L G(x,p) &= \delta(x-p)$ + * L G(x,p) &= \delta(x-p) * @f} * where $L$ is the differential operator of your problem. The discrete * version then requires computing the right hand side vector From ba314705d507e7d318bf544c969c3799f03be5b2 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Mon, 27 Aug 2018 17:14:38 +0200 Subject: [PATCH 146/507] Implement TpetraWrappers::Vector --- cmake/config/template-arguments.in | 5 + cmake/configure/configure_2_trilinos.cmake | 3 +- doc/external-libs/trilinos.html | 2 + include/deal.II/base/index_set.h | 5 + include/deal.II/base/utilities.h | 3 + include/deal.II/dofs/dof_accessor.templates.h | 27 + .../fe/fe_tools_extrapolate.templates.h | 15 + .../fe/fe_tools_interpolate.templates.h | 16 + include/deal.II/lac/read_write_vector.h | 39 +- .../deal.II/lac/read_write_vector.templates.h | 121 +++- include/deal.II/lac/trilinos_sparse_matrix.h | 1 + .../trilinos_tpetra_communication_pattern.h | 106 +++ include/deal.II/lac/trilinos_tpetra_vector.h | 406 +++++++++++ include/deal.II/lac/vector_element_access.h | 70 +- include/deal.II/multigrid/mg_transfer.h | 32 + .../deal.II/numerics/vector_tools.templates.h | 1 + source/base/index_set.cc | 66 ++ source/base/time_stepping.cc | 1 + source/base/utilities.cc | 14 + source/dofs/dof_accessor_get.cc | 1 + source/dofs/dof_accessor_set.cc | 1 + source/fe/fe_values.cc | 1 + source/fe/mapping_fe_field.cc | 1 + source/lac/CMakeLists.txt | 2 + source/lac/solver.cc | 1 + source/lac/trilinos_sparse_matrix.cc | 50 ++ .../trilinos_tpetra_communication_pattern.cc | 104 +++ source/lac/trilinos_tpetra_vector.cc | 632 ++++++++++++++++++ source/lac/vector_memory.cc | 1 + source/multigrid/mg_base.cc | 1 + source/numerics/data_out_dof_data_codim.cc | 1 + source/numerics/derivative_approximation.cc | 1 + tests/trilinos/tpetra_vector_01.cc | 225 +++++++ .../trilinos/tpetra_vector_01.mpirun=2.output | 2 + tests/trilinos/tpetra_vector_02.cc | 216 ++++++ .../trilinos/tpetra_vector_02.mpirun=2.output | 2 + tests/trilinos/tpetra_vector_03.cc | 101 +++ .../trilinos/tpetra_vector_03.mpirun=2.output | 70 ++ .../trilinos/tpetra_vector_03.mpirun=4.output | 146 ++++ 39 files changed, 2488 insertions(+), 4 deletions(-) create mode 100644 include/deal.II/lac/trilinos_tpetra_communication_pattern.h create mode 100644 include/deal.II/lac/trilinos_tpetra_vector.h create mode 100644 source/lac/trilinos_tpetra_communication_pattern.cc create mode 100644 source/lac/trilinos_tpetra_vector.cc create mode 100644 tests/trilinos/tpetra_vector_01.cc create mode 100644 tests/trilinos/tpetra_vector_01.mpirun=2.output create mode 100644 tests/trilinos/tpetra_vector_02.cc create mode 100644 tests/trilinos/tpetra_vector_02.mpirun=2.output create mode 100644 tests/trilinos/tpetra_vector_03.cc create mode 100644 tests/trilinos/tpetra_vector_03.mpirun=2.output create mode 100644 tests/trilinos/tpetra_vector_03.mpirun=4.output diff --git a/cmake/config/template-arguments.in b/cmake/config/template-arguments.in index 551fdd08d3cc..17a9f2ba9477 100644 --- a/cmake/config/template-arguments.in +++ b/cmake/config/template-arguments.in @@ -95,6 +95,7 @@ VECTOR_TYPES := { Vector; @DEAL_II_EXPAND_TRILINOS_MPI_VECTOR@; @DEAL_II_EXPAND_EPETRA_VECTOR@; + @DEAL_II_EXPAND_TPETRA_VECTOR@; @DEAL_II_EXPAND_PETSC_MPI_VECTOR@; @DEAL_II_EXPAND_TRILINOS_MPI_BLOCKVECTOR@; @@ -120,6 +121,7 @@ REAL_VECTOR_TYPES := { Vector; @DEAL_II_EXPAND_TRILINOS_MPI_VECTOR@; @DEAL_II_EXPAND_EPETRA_VECTOR@; + @DEAL_II_EXPAND_TPETRA_VECTOR@; @DEAL_II_EXPAND_PETSC_MPI_VECTOR_REAL@; @DEAL_II_EXPAND_TRILINOS_MPI_BLOCKVECTOR@; @@ -138,6 +140,7 @@ REAL_NONBLOCK_VECTORS := { Vector; @DEAL_II_EXPAND_TRILINOS_MPI_VECTOR@; @DEAL_II_EXPAND_EPETRA_VECTOR@; + @DEAL_II_EXPAND_TPETRA_VECTOR@; @DEAL_II_EXPAND_PETSC_MPI_VECTOR_REAL@; } @@ -145,6 +148,7 @@ REAL_NONBLOCK_VECTORS := { Vector; EXTERNAL_PARALLEL_VECTORS := { @DEAL_II_EXPAND_TRILINOS_MPI_VECTOR@; @DEAL_II_EXPAND_TRILINOS_MPI_BLOCKVECTOR@; @DEAL_II_EXPAND_EPETRA_VECTOR@; + @DEAL_II_EXPAND_TPETRA_VECTOR@; @DEAL_II_EXPAND_PETSC_MPI_VECTOR@; @DEAL_II_EXPAND_PETSC_MPI_BLOCKVECTOR@ } @@ -163,6 +167,7 @@ VECTORS_WITH_MATRIX := { Vector; @DEAL_II_EXPAND_TRILINOS_MPI_VECTOR@; @DEAL_II_EXPAND_EPETRA_VECTOR@; + @DEAL_II_EXPAND_TPETRA_VECTOR@; @DEAL_II_EXPAND_PETSC_MPI_VECTOR@; } diff --git a/cmake/configure/configure_2_trilinos.cmake b/cmake/configure/configure_2_trilinos.cmake index c53f105c0995..abe66905d82c 100644 --- a/cmake/configure/configure_2_trilinos.cmake +++ b/cmake/configure/configure_2_trilinos.cmake @@ -42,7 +42,7 @@ MACRO(FEATURE_TRILINOS_FIND_EXTERNAL var) ) FOREACH(_module - Amesos Epetra Ifpack AztecOO Teuchos ML MueLu + Amesos Epetra Ifpack AztecOO Teuchos Tpetra ML MueLu ) ITEM_MATCHES(_module_found ${_module} ${Trilinos_PACKAGE_LIST}) IF(_module_found) @@ -227,6 +227,7 @@ MACRO(FEATURE_TRILINOS_CONFIGURE_EXTERNAL) SET(DEAL_II_EXPAND_TRILINOS_MPI_VECTOR "TrilinosWrappers::MPI::Vector") IF (TRILINOS_WITH_MPI) SET(DEAL_II_EXPAND_EPETRA_VECTOR "LinearAlgebra::EpetraWrappers::Vector") + SET(DEAL_II_EXPAND_TPETRA_VECTOR "LinearAlgebra::TpetraWrappers::Vector") ENDIF() IF(${DEAL_II_TRILINOS_WITH_SACADO}) # Note: Only CMake 3.0 and greater support line continuation with the "\" character diff --git a/doc/external-libs/trilinos.html b/doc/external-libs/trilinos.html index 9579c9a62a0a..d950f55b11c0 100644 --- a/doc/external-libs/trilinos.html +++ b/doc/external-libs/trilinos.html @@ -67,6 +67,7 @@
Installing Trilinos
  • ROL (optional),
  • Sacado (optional),
  • Teuchos, +
  • Tpetra,
  • Zoltan (optional). @@ -92,6 +93,7 @@
    Installing Trilinos
    -DTrilinos_ENABLE_MueLu=ON \ -DTrilinos_ENABLE_ML=ON \ -DTrilinos_ENABLE_ROL=ON \ + -DTrilinos_ENABLE_Tpetra=ON \ -DTrilinos_ENABLE_Zoltan=ON \ -DTrilinos_VERBOSE_CONFIGURE=OFF \ -DTPL_ENABLE_MPI=ON \ diff --git a/include/deal.II/base/index_set.h b/include/deal.II/base/index_set.h index fec38b883f22..2e21fab64498 100644 --- a/include/deal.II/base/index_set.h +++ b/include/deal.II/base/index_set.h @@ -31,6 +31,7 @@ #ifdef DEAL_II_WITH_TRILINOS # include +# include #endif #if defined(DEAL_II_WITH_MPI) || defined(DEAL_II_WITH_PETSC) @@ -446,6 +447,10 @@ class IndexSet Epetra_Map make_trilinos_map(const MPI_Comm &communicator = MPI_COMM_WORLD, const bool overlapping = false) const; + + Tpetra::Map<> + make_tpetra_map(const MPI_Comm &communicator = MPI_COMM_WORLD, + const bool overlapping = false) const; #endif diff --git a/include/deal.II/base/utilities.h b/include/deal.II/base/utilities.h index f49c3021321b..71d05faf24ea 100644 --- a/include/deal.II/base/utilities.h +++ b/include/deal.II/base/utilities.h @@ -888,6 +888,9 @@ namespace Utilities const Epetra_Comm & comm_self(); + const Teuchos::RCP> & + tpetra_comm_self(); + /** * Given a communicator, duplicate it. If the given communicator is * serial, that means to just return a copy of itself. On the other hand, diff --git a/include/deal.II/dofs/dof_accessor.templates.h b/include/deal.II/dofs/dof_accessor.templates.h index a7c898c9537f..73b77c07a57d 100644 --- a/include/deal.II/dofs/dof_accessor.templates.h +++ b/include/deal.II/dofs/dof_accessor.templates.h @@ -1534,6 +1534,33 @@ namespace internal + template + static void + extract_subvector_to(const LinearAlgebra::TpetraWrappers::Vector &values, + const types::global_dof_index *cache_begin, + const types::global_dof_index *cache_end, + ForwardIterator local_values_begin) + { + std::vector sorted_indices_pos = + sort_indices(cache_begin, cache_end); + const unsigned int cache_size = cache_end - cache_begin; + std::vector cache_indices(cache_size); + for (unsigned int i = 0; i < cache_size; ++i) + cache_indices[i] = *(cache_begin + sorted_indices_pos[i]); + + IndexSet index_set(cache_indices.back() + 1); + index_set.add_indices(cache_indices.begin(), cache_indices.end()); + index_set.compress(); + LinearAlgebra::ReadWriteVector read_write_vector(index_set); + read_write_vector.import(values, VectorOperation::insert); + + // Copy the elements from read_write_vector and reorder them. + for (unsigned int i = 0; i < cache_size; ++i, ++local_values_begin) + *local_values_begin = read_write_vector[sorted_indices_pos[i]]; + } + + + template static void extract_subvector_to(const LinearAlgebra::EpetraWrappers::Vector &values, diff --git a/include/deal.II/fe/fe_tools_extrapolate.templates.h b/include/deal.II/fe/fe_tools_extrapolate.templates.h index f2acc692d7ae..850a4c6216ca 100644 --- a/include/deal.II/fe/fe_tools_extrapolate.templates.h +++ b/include/deal.II/fe/fe_tools_extrapolate.templates.h @@ -1581,6 +1581,21 @@ namespace FETools # ifdef DEAL_II_WITH_MPI + template + void + reinit_distributed(const DoFHandler & dh, + LinearAlgebra::TpetraWrappers::Vector &vector) + { + const parallel::distributed::Triangulation *parallel_tria = + dynamic_cast< + const parallel::distributed::Triangulation *>( + &dh.get_triangulation()); + Assert(parallel_tria != nullptr, ExcNotImplemented()); + + const IndexSet &locally_owned_dofs = dh.locally_owned_dofs(); + vector.reinit(locally_owned_dofs, parallel_tria->get_communicator()); + } + template void reinit_distributed(const DoFHandler & dh, diff --git a/include/deal.II/fe/fe_tools_interpolate.templates.h b/include/deal.II/fe/fe_tools_interpolate.templates.h index 82460f14bb24..e2e9b417fe02 100644 --- a/include/deal.II/fe/fe_tools_interpolate.templates.h +++ b/include/deal.II/fe/fe_tools_interpolate.templates.h @@ -46,6 +46,7 @@ #include #include #include +#include #include #include @@ -511,6 +512,21 @@ namespace FETools { AssertThrow(false, ExcNotImplemented()); } + + template + void + back_interpolate( + const DoFHandler &, + const AffineConstraints< + typename LinearAlgebra::TpetraWrappers::Vector::value_type> &, + const LinearAlgebra::TpetraWrappers::Vector &, + const DoFHandler &, + const AffineConstraints< + typename LinearAlgebra::TpetraWrappers::Vector::value_type> &, + LinearAlgebra::TpetraWrappers::Vector &) + { + AssertThrow(false, ExcNotImplemented()); + } #endif diff --git a/include/deal.II/lac/read_write_vector.h b/include/deal.II/lac/read_write_vector.h index 9e67f981787d..70d89ade7a1c 100644 --- a/include/deal.II/lac/read_write_vector.h +++ b/include/deal.II/lac/read_write_vector.h @@ -35,6 +35,7 @@ #ifdef DEAL_II_WITH_TRILINOS # include # include +# include # include @@ -334,6 +335,21 @@ namespace LinearAlgebra std::shared_ptr()); # ifdef DEAL_II_WITH_MPI + /** + * Imports all the elements present in the vector's IndexSet from the input + * vector @p tpetra_vec. VectorOperation::values @p operation is used to + * decide if the elements in @p V should be added to the current vector or + * replace the current elements. The last parameter can be used if the same + * communication pattern is used multiple times. This can be used to improve + * performance. + */ + void + import(const TpetraWrappers::Vector &tpetra_vec, + VectorOperation::values operation, + const std::shared_ptr + &communication_pattern = + std::shared_ptr()); + /** * Imports all the elements present in the vector's IndexSet from the input * vector @p epetra_vec. VectorOperation::values @p operation is used to @@ -593,6 +609,19 @@ namespace LinearAlgebra protected: #ifdef DEAL_II_WITH_TRILINOS + /** + * Import all the elements present in the vector's IndexSet from the input + * vector @p tpetra_vector. This is an helper function and it should not be + * used directly. + */ + void + import(const Tpetra::Vector<> &tpetra_vector, + const IndexSet & locally_owned_elements, + VectorOperation::values operation, + const MPI_Comm & mpi_comm, + const std::shared_ptr + &communication_pattern); + /** * Import all the elements present in the vector's IndexSet from the input * vector @p multivector. This is an helper function and it should not be @@ -627,7 +656,15 @@ namespace LinearAlgebra #if defined(DEAL_II_WITH_TRILINOS) && defined(DEAL_II_WITH_MPI) /** - * Return a EpetraWrappers::Communication pattern and store it for future + * Return a TpetraWrappers::CommunicationPattern and store it for future + * use. + */ + TpetraWrappers::CommunicationPattern + create_tpetra_comm_pattern(const IndexSet &source_index_set, + const MPI_Comm &mpi_comm); + + /** + * Return a EpetraWrappers::CommunicationPattern and store it for future * use. */ EpetraWrappers::CommunicationPattern diff --git a/include/deal.II/lac/read_write_vector.templates.h b/include/deal.II/lac/read_write_vector.templates.h index 9a8022648168..b4437cfd3fbf 100644 --- a/include/deal.II/lac/read_write_vector.templates.h +++ b/include/deal.II/lac/read_write_vector.templates.h @@ -34,7 +34,6 @@ #ifdef DEAL_II_WITH_TRILINOS # include -# include # include # include @@ -507,6 +506,93 @@ namespace LinearAlgebra #if defined(DEAL_II_WITH_TRILINOS) && defined(DEAL_II_WITH_MPI) + template + void + ReadWriteVector::import( + const Tpetra::Vector<> &vector, + const IndexSet & source_elements, + VectorOperation::values operation, + const MPI_Comm & mpi_comm, + const std::shared_ptr + &communication_pattern) + { + std::shared_ptr + tpetra_comm_pattern; + + // If no communication pattern is given, create one. Otherwise, use the one + // given. + if (communication_pattern == nullptr) + { + // The first time import is called, we create a communication pattern. + // Check if the communication pattern already exists and if it can be + // reused. + if ((source_elements.size() == source_stored_elements.size()) && + (source_elements == source_stored_elements)) + { + tpetra_comm_pattern = std::dynamic_pointer_cast< + const TpetraWrappers::CommunicationPattern>(comm_pattern); + if (tpetra_comm_pattern == nullptr) + tpetra_comm_pattern = + std::make_shared( + create_tpetra_comm_pattern(source_elements, mpi_comm)); + } + else + tpetra_comm_pattern = + std::make_shared( + create_tpetra_comm_pattern(source_elements, mpi_comm)); + } + else + { + tpetra_comm_pattern = + std::dynamic_pointer_cast( + communication_pattern); + AssertThrow(tpetra_comm_pattern != nullptr, + ExcMessage( + std::string("The communication pattern is not of type ") + + "LinearAlgebra::TpetraWrappers::CommunicationPattern.")); + } + + Tpetra::Export<> tpetra_export(tpetra_comm_pattern->get_tpetra_export()); + + Tpetra::Vector<> target_vector(tpetra_export.getSourceMap()); + target_vector.doImport(vector, tpetra_export, Tpetra::REPLACE); + + const auto *new_values = target_vector.getData().get(); + const auto size = target_vector.getLocalLength(); + + using size_type = std::decay::type; + + Assert(size == 0 || values != nullptr, ExcInternalError("Export failed.")); + AssertDimension(size, stored_elements.n_elements()); + + if (operation == VectorOperation::insert) + { + for (size_type i = 0; i < size; ++i) + values[i] = new_values[i]; + } + else if (operation == VectorOperation::add) + { + for (size_type i = 0; i < size; ++i) + values[i] += new_values[i]; + } + else if (operation == VectorOperation::min) + { + for (size_type i = 0; i < size; ++i) + if (std::real(new_values[i]) - std::real(values[i]) < 0.0) + values[i] = new_values[i]; + } + else if (operation == VectorOperation::max) + { + for (size_type i = 0; i < size; ++i) + if (std::real(new_values[i]) - std::real(values[i]) > 0.0) + values[i] = new_values[i]; + } + else + AssertThrow(false, ExcNotImplemented()); + } + + + template void ReadWriteVector::import( @@ -652,6 +738,23 @@ namespace LinearAlgebra + template + void + ReadWriteVector::import( + const LinearAlgebra::TpetraWrappers::Vector &trilinos_vec, + VectorOperation::values operation, + const std::shared_ptr + &communication_pattern) + { + import(trilinos_vec.trilinos_vector(), + trilinos_vec.locally_owned_elements(), + operation, + trilinos_vec.get_mpi_communicator(), + communication_pattern); + } + + + template void ReadWriteVector::import( @@ -793,6 +896,22 @@ namespace LinearAlgebra #if defined(DEAL_II_WITH_TRILINOS) && defined(DEAL_II_WITH_MPI) + template + TpetraWrappers::CommunicationPattern + ReadWriteVector::create_tpetra_comm_pattern( + const IndexSet &source_index_set, + const MPI_Comm &mpi_comm) + { + source_stored_elements = source_index_set; + TpetraWrappers::CommunicationPattern epetra_comm_pattern( + source_stored_elements, stored_elements, mpi_comm); + comm_pattern = std::make_shared( + source_stored_elements, stored_elements, mpi_comm); + + return epetra_comm_pattern; + } + + template EpetraWrappers::CommunicationPattern ReadWriteVector::create_epetra_comm_pattern( diff --git a/include/deal.II/lac/trilinos_sparse_matrix.h b/include/deal.II/lac/trilinos_sparse_matrix.h index 25478951f673..006dc3171219 100644 --- a/include/deal.II/lac/trilinos_sparse_matrix.h +++ b/include/deal.II/lac/trilinos_sparse_matrix.h @@ -27,6 +27,7 @@ # include # include # include +# include # include # include # include diff --git a/include/deal.II/lac/trilinos_tpetra_communication_pattern.h b/include/deal.II/lac/trilinos_tpetra_communication_pattern.h new file mode 100644 index 000000000000..8dc7cf787472 --- /dev/null +++ b/include/deal.II/lac/trilinos_tpetra_communication_pattern.h @@ -0,0 +1,106 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2015 - 2018 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + +#ifndef dealii_trilinos_tpetra_communication_pattern_h +#define dealii_trilinos_tpetra_communication_pattern_h + + +#include + +#ifdef DEAL_II_WITH_TRILINOS + +# ifdef DEAL_II_WITH_MPI + +# include + +# include + +# include + +DEAL_II_NAMESPACE_OPEN + +namespace LinearAlgebra +{ + namespace TpetraWrappers + { + /** + * This class implements a wrapper to Tpetra::Import and Tpetra::Export. + */ + class CommunicationPattern : public CommunicationPatternBase + { + public: + /** + * Reinitialize the communication pattern. The first argument @p + * vector_space_vector_index_set is the index set associated to a + * VectorSpaceVector object. The second argument @p + * read_write_vector_index_set is the index set associated to a + * ReadWriteVector object. + */ + CommunicationPattern(const IndexSet &vector_space_vector_index_set, + const IndexSet &read_write_vector_index_set, + const MPI_Comm &communicator); + + /** + * Reinitialize the object. + */ + virtual void + reinit(const IndexSet &vector_space_vector_index_set, + const IndexSet &read_write_vector_index_set, + const MPI_Comm &communicator) override; + + /** + * Return the underlying MPI communicator. + */ + virtual const MPI_Comm & + get_mpi_communicator() const override; + + /** + * Return the underlying Tpetra::Import object. + */ + const Tpetra::Import<> & + get_tpetra_import() const; + + /** + * Return the underlying Tpetra::Export object. + */ + const Tpetra::Export<> & + get_tpetra_export() const; + + private: + /** + * Shared pointer to the MPI communicator used. + */ + std::shared_ptr comm; + + /** + * Shared pointer to the Tpetra::Import object used. + */ + std::unique_ptr> tpetra_import; + + /** + * Shared pointer to the Tpetra::Export object used. + */ + std::unique_ptr> tpetra_export; + }; + } // end of namespace TpetraWrappers +} // end of namespace LinearAlgebra + +DEAL_II_NAMESPACE_CLOSE + +# endif + +#endif + +#endif diff --git a/include/deal.II/lac/trilinos_tpetra_vector.h b/include/deal.II/lac/trilinos_tpetra_vector.h new file mode 100644 index 000000000000..df0b0c99c581 --- /dev/null +++ b/include/deal.II/lac/trilinos_tpetra_vector.h @@ -0,0 +1,406 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2015 - 2018 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + +#ifndef dealii_trilinos_tpetra_vector_h +#define dealii_trilinos_tpetra_vector_h + + +#include + +#if defined(DEAL_II_WITH_TRILINOS) && defined(DEAL_II_WITH_MPI) + +# include +# include + +# include +# include +# include +# include + +# include +# include +# include +# include +# include +# include + +# include + +DEAL_II_NAMESPACE_OPEN + +namespace LinearAlgebra +{ + // Forward declaration + template + class ReadWriteVector; + + namespace TpetraWrappers + { + /** + * This class implements a wrapper to the Trilinos distributed vector + * class Tpetra::Vector. This class is derived from the + * LinearAlgebra::VectorSpaceVector class. Note however that Tpetra only + * works with Number = double. + * + * @ingroup TrilinosWrappers + * @ingroup Vectors + * @author Daniel Arndt, 2018 + */ + class Vector : public VectorSpaceVector, public Subscriptor + { + public: + /** + * Constructor. Create a vector of dimension zero. + */ + Vector(); + + /** + * Copy constructor. Sets the dimension and the partitioning to that of + * the given vector and copies all elements. + */ + Vector(const Vector &V); + + /** + * This constructor takes an IndexSet that defines how to distribute the + * individual components among the MPI processors. Since it also + * includes information about the size of the vector, this is all we + * need to generate a %parallel vector. + */ + explicit Vector(const IndexSet ¶llel_partitioner, + const MPI_Comm &communicator); + + /** + * Reinit functionality. This function destroys the old vector content + * and generates a new one based on the input partitioning. The flag + * omit_zeroing_entries determines whether the vector should be + * filled with zero (false) or left untouched (true). + */ + void + reinit(const IndexSet ¶llel_partitioner, + const MPI_Comm &communicator, + const bool omit_zeroing_entries = false); + + /** + * Change the dimension to that of the vector V. The elements of V are not + * copied. + */ + virtual void + reinit(const VectorSpaceVector &V, + const bool omit_zeroing_entries = false) override; + + /** + * Copy function. This function takes a Vector and copies all the + * elements. The Vector will have the same parallel distribution as @p + * V. + */ + Vector & + operator=(const Vector &V); + + /** + * Sets all elements of the vector to the scalar @p s. This operation is + * only allowed if @p s is equal to zero. + */ + virtual Vector & + operator=(const double s) override; + + /** + * Imports all the elements present in the vector's IndexSet from the + * input + * vector @p V. VectorOperation::values @p operation is used to decide if + * the elements in @p V should be added to the current vector or replace the + * current elements. The last parameter can be used if the same + * communication pattern is used multiple times. This can be used to + * improve performance. + */ + virtual void + import( + const ReadWriteVector & V, + VectorOperation::values operation, + std::shared_ptr communication_pattern = + std::shared_ptr()) override; + + /** + * Multiply the entire vector by a fixed factor. + */ + virtual Vector & + operator*=(const double factor) override; + + /** + * Divide the entire vector by a fixed factor. + */ + virtual Vector & + operator/=(const double factor) override; + + /** + * Add the vector @p V to the present one. + */ + virtual Vector & + operator+=(const VectorSpaceVector &V) override; + + /** + * Subtract the vector @p V from the present one. + */ + virtual Vector & + operator-=(const VectorSpaceVector &V) override; + + /** + * Return the scalar product of two vectors. The vectors need to have the + * same layout. + */ + virtual double + operator*(const VectorSpaceVector &V) const override; + + /** + * Add @p a to all components. Note that @p is a scalar not a vector. + */ + virtual void + add(const double a) override; + + /** + * Simple addition of a multiple of a vector, i.e. *this += + * a*V. The vectors need to have the same layout. + */ + virtual void + add(const double a, const VectorSpaceVector &V) override; + + /** + * Multiple addition of multiple of a vector, i.e. *this> += + * a*V+b*W. The vectors need to have the same layout. + */ + virtual void + add(const double a, + const VectorSpaceVector &V, + const double b, + const VectorSpaceVector &W) override; + + /** + * Scaling and simple addition of a multiple of a vector, i.e. *this + * = s*(*this)+a*V. + */ + virtual void + sadd(const double s, + const double a, + const VectorSpaceVector &V) override; + + /** + * Scale each element of this vector by the corresponding element in the + * argument. This function is mostly meant to simulate multiplication + * (and immediate re-assignment) by a diagonal scaling matrix. The + * vectors need to have the same layout. + */ + virtual void + scale(const VectorSpaceVector &scaling_factors) override; + + /** + * Assignment *this = a*V. + */ + virtual void + equ(const double a, const VectorSpaceVector &V) override; + + /** + * Return whether the vector contains only elements with value zero. + */ + virtual bool + all_zero() const override; + + /** + * Return the mean value of the element of this vector. + */ + virtual double + mean_value() const override; + + /** + * Return the l1 norm of the vector (i.e., the sum of the + * absolute values of all entries among all processors). + */ + virtual double + l1_norm() const override; + + /** + * Return the l2 norm of the vector (i.e., the square root of + * the sum of the square of all entries among all processors). + */ + virtual double + l2_norm() const override; + + /** + * Return the maximum norm of the vector (i.e., the maximum absolute value + * among all entries and among all processors). + */ + virtual double + linfty_norm() const override; + + /** + * Performs a combined operation of a vector addition and a subsequent + * inner product, returning the value of the inner product. In other + * words, the result of this function is the same as if the user called + * @code + * this->add(a, V); + * return_value = *this * W; + * @endcode + * + * The reason this function exists is that this operation involves less + * memory transfer than calling the two functions separately. This + * method only needs to load three vectors, @p this, @p V, @p W, whereas + * calling separate methods means to load the calling vector @p this + * twice. Since most vector operations are memory transfer limited, this + * reduces the time by 25\% (or 50\% if @p W equals @p this). + * + * The vectors need to have the same layout. + * + * For complex-valued vectors, the scalar product in the second step is + * implemented as + * $\left=\sum_i v_i \bar{w_i}$. + */ + virtual double + add_and_dot(const double a, + const VectorSpaceVector &V, + const VectorSpaceVector &W) override; + /** + * This function always returns false and is present only for backward + * compatibility. + */ + bool + has_ghost_elements() const; + + /** + * Return the global size of the vector, equal to the sum of the number of + * locally owned indices among all processors. + */ + virtual size_type + size() const override; + + /** + * Return the MPI communicator object in use with this object. + */ + MPI_Comm + get_mpi_communicator() const; + + /** + * Return an index set that describes which elements of this vector are + * owned by the current processor. As a consequence, the index sets + * returned on different processors if this is a distributed vector will + * form disjoint sets that add up to the complete index set. Obviously, if + * a vector is created on only one processor, then the result would + * satisfy + * @code + * vec.locally_owned_elements() == complete_index_set(vec.size()) + * @endcode + */ + virtual ::dealii::IndexSet + locally_owned_elements() const override; + + /** + * Return a const reference to the underlying Trilinos + * Tpetra::Vector class. + */ + const Tpetra::Vector<> & + trilinos_vector() const; + + /** + * Return a (modifyable) reference to the underlying Trilinos + * Tpetra::Vector class. + */ + Tpetra::Vector<> & + trilinos_vector(); + + /** + * Prints the vector to the output stream @p out. + */ + virtual void + print(std::ostream & out, + const unsigned int precision = 3, + const bool scientific = true, + const bool across = true) const override; + + /** + * Return the memory consumption of this class in bytes. + */ + virtual std::size_t + memory_consumption() const override; + + /** + * The vectors have different partitioning, i.e. they have use different + * IndexSet. + */ + DeclException0(ExcDifferentParallelPartitioning); + + /** + * Attempt to perform an operation between two incompatible vector types. + * + * @ingroup Exceptions + */ + DeclException0(ExcVectorTypeNotCompatible); + + /** + * Exception thrown by an error in Trilinos. + * + * @ingroup Exceptions + */ + DeclException1(ExcTrilinosError, + int, + << "An error with error number " << arg1 + << " occurred while calling a Trilinos function"); + + private: + /** + * Create the CommunicationPattern for the communication between the + * IndexSet @p source_index_set and the current vector based + * on the communicator @p mpi_comm. + */ + void + create_tpetra_comm_pattern(const IndexSet &source_index_set, + const MPI_Comm &mpi_comm); + + /** + * Pointer to the actual Tpetra vector object. + */ + std::unique_ptr> vector; + + /** + * IndexSet of the elements of the last imported vector. + */ + ::dealii::IndexSet source_stored_elements; + + /** + * CommunicationPattern for the communication between the + * source_stored_elements IndexSet and the current vector. + */ + std::shared_ptr + tpetra_comm_pattern; + }; + + + inline bool + Vector::has_ghost_elements() const + { + return false; + } + } // namespace TpetraWrappers +} // namespace LinearAlgebra + + +/** + * Declare dealii::LinearAlgebra::TpetraWrappers::Vector as distributed vector. + */ +template <> +struct is_serial_vector : std::false_type +{}; + +DEAL_II_NAMESPACE_CLOSE + +#endif + +#endif diff --git a/include/deal.II/lac/vector_element_access.h b/include/deal.II/lac/vector_element_access.h index 791f6894c375..b16826058885 100644 --- a/include/deal.II/lac/vector_element_access.h +++ b/include/deal.II/lac/vector_element_access.h @@ -18,6 +18,7 @@ #include +#include DEAL_II_NAMESPACE_OPEN @@ -108,7 +109,6 @@ namespace internal vector[0][trilinos_i] = value; } - template <> inline double ElementAccess::get( @@ -122,6 +122,74 @@ namespace internal return vector[0][trilinos_i]; } + + + + template <> + inline void + ElementAccess::add( + const double value, + const types::global_dof_index i, + LinearAlgebra::TpetraWrappers::Vector &V) + { + // Extract local indices in the vector. + Tpetra::Vector<> vector = V.trilinos_vector(); + TrilinosWrappers::types::int_type trilinos_i = + vector.getMap()->getLocalElement( + static_cast(i)); + + vector.sync(); + auto vector_2d = vector.getLocalView(); + auto vector_1d = Kokkos::subview(vector_2d, Kokkos::ALL(), 0); + // We're going to modify the data on host. + vector.modify(); + vector_1d(trilinos_i) += value; + vector.sync::device_type::memory_space>(); + } + + + + template <> + inline void + ElementAccess::set( + const double value, + const types::global_dof_index i, + LinearAlgebra::TpetraWrappers::Vector &V) + { + // Extract local indices in the vector. + Tpetra::Vector<> vector = V.trilinos_vector(); + TrilinosWrappers::types::int_type trilinos_i = + vector.getMap()->getLocalElement( + static_cast(i)); + + vector.sync(); + auto vector_2d = vector.getLocalView(); + auto vector_1d = Kokkos::subview(vector_2d, Kokkos::ALL(), 0); + // We're going to modify the data on host. + vector.modify(); + vector_1d(trilinos_i) = value; + vector.sync::device_type::memory_space>(); + } + + + template <> + inline double + ElementAccess::get( + const LinearAlgebra::TpetraWrappers::Vector &V, + const types::global_dof_index i) + { + // Extract local indices in the vector. + Tpetra::Vector<> vector = V.trilinos_vector(); + TrilinosWrappers::types::int_type trilinos_i = + vector.getMap()->getLocalElement( + static_cast(i)); + + vector.sync(); + auto vector_2d = vector.getLocalView(); + auto vector_1d = Kokkos::subview(vector_2d, Kokkos::ALL(), 0); + // We're going to modify the data on host. + return vector_1d(trilinos_i); + } #endif } // namespace internal diff --git a/include/deal.II/multigrid/mg_transfer.h b/include/deal.II/multigrid/mg_transfer.h index a88bf028846b..e4b4f3db2ac9 100644 --- a/include/deal.II/multigrid/mg_transfer.h +++ b/include/deal.II/multigrid/mg_transfer.h @@ -132,6 +132,38 @@ namespace internal }; # ifdef DEAL_II_WITH_MPI + template <> + struct MatrixSelector + { + using Sparsity = ::dealii::TrilinosWrappers::SparsityPattern; + using Matrix = ::dealii::TrilinosWrappers::SparseMatrix; + + static const bool requires_distributed_sparsity_pattern = false; + + template + static void + reinit(Matrix &matrix, + Sparsity &, + int level, + const SparsityPatternType &sp, + DoFHandlerType & dh) + { + const parallel::Triangulation + *dist_tria = dynamic_cast< + const parallel::Triangulation *>( + &(dh.get_triangulation())); + MPI_Comm communicator = + dist_tria != nullptr ? dist_tria->get_communicator() : MPI_COMM_SELF; + matrix.reinit(dh.locally_owned_mg_dofs(level + 1), + dh.locally_owned_mg_dofs(level), + sp, + communicator, + true); + } + }; + template <> struct MatrixSelector { diff --git a/include/deal.II/numerics/vector_tools.templates.h b/include/deal.II/numerics/vector_tools.templates.h index 30e5fa5f1fe5..aebdafb33768 100644 --- a/include/deal.II/numerics/vector_tools.templates.h +++ b/include/deal.II/numerics/vector_tools.templates.h @@ -70,6 +70,7 @@ #include #include #include +#include #include #include #include diff --git a/source/base/index_set.cc b/source/base/index_set.cc index 3e7f0914cf35..6fe2920ffe39 100644 --- a/source/base/index_set.cc +++ b/source/base/index_set.cc @@ -520,6 +520,72 @@ IndexSet::fill_index_vector(std::vector &indices) const #ifdef DEAL_II_WITH_TRILINOS +Tpetra::Map<> +IndexSet::make_tpetra_map(const MPI_Comm &communicator, + const bool overlapping) const +{ + compress(); + (void)communicator; + +# ifdef DEBUG + if (!overlapping) + { + const size_type n_global_elements = + Utilities::MPI::sum(n_elements(), communicator); + Assert(n_global_elements == size(), + ExcMessage("You are trying to create an Tpetra::Map object " + "that partitions elements of an index set " + "between processors. However, the union of the " + "index sets on different processors does not " + "contain all indices exactly once: the sum of " + "the number of entries the various processors " + "want to store locally is " + + Utilities::to_string(n_global_elements) + + " whereas the total size of the object to be " + "allocated is " + + Utilities::to_string(size()) + + ". In other words, there are " + "either indices that are not spoken for " + "by any processor, or there are indices that are " + "claimed by multiple processors.")); + } +# endif + + // Find out if the IndexSet is ascending and 1:1. This corresponds to a + // linear Tpetra::Map. Overlapping IndexSets are never 1:1. + const bool linear = + overlapping ? false : is_ascending_and_one_to_one(communicator); + if (linear) + return Tpetra::Map<>(size(), + n_elements(), + 0, +# ifdef DEAL_II_WITH_MPI + Teuchos::rcp(new Teuchos::MpiComm(communicator)) +# else + Teuchos::rcp(new Teuchos::Comm()) +# endif + ); + else + { + std::vector indices; + fill_index_vector(indices); + std::vector int_indices(indices.size()); + std::copy(indices.begin(), indices.end(), int_indices.begin()); + return Tpetra::Map<>(size(), + (n_elements() > 0 ? int_indices.data() : nullptr), + n_elements(), + 0, +# ifdef DEAL_II_WITH_MPI + Teuchos::rcp(new Teuchos::MpiComm(communicator)) +# else + Teuchos::rcp(new Teuchos::Comm()) +# endif + ); + } +} + + + Epetra_Map IndexSet::make_trilinos_map(const MPI_Comm &communicator, const bool overlapping) const diff --git a/source/base/time_stepping.cc b/source/base/time_stepping.cc index 9bb02320eb63..3e4d6bed678b 100644 --- a/source/base/time_stepping.cc +++ b/source/base/time_stepping.cc @@ -22,6 +22,7 @@ #include #include #include +#include #include #include diff --git a/source/base/utilities.cc b/source/base/utilities.cc index 27b798cc124b..ff4d0d957322 100644 --- a/source/base/utilities.cc +++ b/source/base/utilities.cc @@ -979,6 +979,20 @@ namespace Utilities + const Teuchos::RCP> & + tpetra_comm_self() + { +# ifdef DEAL_II_WITH_MPI + static auto communicator = Teuchos::RCP>( + new Teuchos::MpiComm(MPI_COMM_SELF)); +# else + static auto communicator = + Teuchos::RCP>(new Teuchos::Comm()); +# endif + + return communicator; + } + const Epetra_Comm & comm_self() { diff --git a/source/dofs/dof_accessor_get.cc b/source/dofs/dof_accessor_get.cc index 4f1bdc2b0316..53b47d2238ad 100644 --- a/source/dofs/dof_accessor_get.cc +++ b/source/dofs/dof_accessor_get.cc @@ -32,6 +32,7 @@ #include #include #include +#include #include #include diff --git a/source/dofs/dof_accessor_set.cc b/source/dofs/dof_accessor_set.cc index 556dcd48c8f7..a116ab0858e9 100644 --- a/source/dofs/dof_accessor_set.cc +++ b/source/dofs/dof_accessor_set.cc @@ -32,6 +32,7 @@ #include #include #include +#include #include #include diff --git a/source/fe/fe_values.cc b/source/fe/fe_values.cc index 920f57a61ae0..b2c44908a6b8 100644 --- a/source/fe/fe_values.cc +++ b/source/fe/fe_values.cc @@ -39,6 +39,7 @@ #include #include #include +#include #include #include #include diff --git a/source/fe/mapping_fe_field.cc b/source/fe/mapping_fe_field.cc index 5289c9d1e7ce..1659ccfb3a65 100644 --- a/source/fe/mapping_fe_field.cc +++ b/source/fe/mapping_fe_field.cc @@ -44,6 +44,7 @@ #include #include #include +#include #include #include diff --git a/source/lac/CMakeLists.txt b/source/lac/CMakeLists.txt index a6ce60360fe8..973837219e1b 100644 --- a/source/lac/CMakeLists.txt +++ b/source/lac/CMakeLists.txt @@ -132,6 +132,8 @@ IF(DEAL_II_WITH_TRILINOS) trilinos_solver.cc trilinos_sparse_matrix.cc trilinos_sparsity_pattern.cc + trilinos_tpetra_communication_pattern.cc + trilinos_tpetra_vector.cc trilinos_vector.cc ) diff --git a/source/lac/solver.cc b/source/lac/solver.cc index 6d432ae184b8..7bf9e30c3e86 100644 --- a/source/lac/solver.cc +++ b/source/lac/solver.cc @@ -22,6 +22,7 @@ #include #include #include +#include #include #include #include diff --git a/source/lac/trilinos_sparse_matrix.cc b/source/lac/trilinos_sparse_matrix.cc index 291929c5c359..350006da3cca 100644 --- a/source/lac/trilinos_sparse_matrix.cc +++ b/source/lac/trilinos_sparse_matrix.cc @@ -103,6 +103,36 @@ namespace TrilinosWrappers { return V.trilinos_vector()[0] + V.trilinos_vector().MyLength(); } + + template <> + double * + begin(LinearAlgebra::TpetraWrappers::Vector &V) + { + return V.trilinos_vector().getDataNonConst().get(); + } + + template <> + const double * + begin(const LinearAlgebra::TpetraWrappers::Vector &V) + { + return V.trilinos_vector().getData().get(); + } + + template <> + double * + end(LinearAlgebra::TpetraWrappers::Vector &V) + { + return V.trilinos_vector().getDataNonConst().get() + + V.trilinos_vector().getLocalLength(); + } + + template <> + const double * + end(const LinearAlgebra::TpetraWrappers::Vector &V) + { + return V.trilinos_vector().getData().get() + + V.trilinos_vector().getLocalLength(); + } # endif } // namespace internal @@ -3454,6 +3484,11 @@ namespace TrilinosWrappers dealii::LinearAlgebra::distributed::Vector &, const dealii::LinearAlgebra::distributed::Vector &) const; # ifdef DEAL_II_WITH_MPI + template void + SparseMatrix::vmult( + dealii::LinearAlgebra::TpetraWrappers::Vector &, + const dealii::LinearAlgebra::TpetraWrappers::Vector &) const; + template void SparseMatrix::vmult( dealii::LinearAlgebra::EpetraWrappers::Vector &, @@ -3469,6 +3504,11 @@ namespace TrilinosWrappers dealii::LinearAlgebra::distributed::Vector &, const dealii::LinearAlgebra::distributed::Vector &) const; # ifdef DEAL_II_WITH_MPI + template void + SparseMatrix::Tvmult( + dealii::LinearAlgebra::TpetraWrappers::Vector &, + const dealii::LinearAlgebra::TpetraWrappers::Vector &) const; + template void SparseMatrix::Tvmult( dealii::LinearAlgebra::EpetraWrappers::Vector &, @@ -3484,6 +3524,11 @@ namespace TrilinosWrappers dealii::LinearAlgebra::distributed::Vector &, const dealii::LinearAlgebra::distributed::Vector &) const; # ifdef DEAL_II_WITH_MPI + template void + SparseMatrix::vmult_add( + dealii::LinearAlgebra::TpetraWrappers::Vector &, + const dealii::LinearAlgebra::TpetraWrappers::Vector &) const; + template void SparseMatrix::vmult_add( dealii::LinearAlgebra::EpetraWrappers::Vector &, @@ -3499,6 +3544,11 @@ namespace TrilinosWrappers dealii::LinearAlgebra::distributed::Vector &, const dealii::LinearAlgebra::distributed::Vector &) const; # ifdef DEAL_II_WITH_MPI + template void + SparseMatrix::Tvmult_add( + dealii::LinearAlgebra::TpetraWrappers::Vector &, + const dealii::LinearAlgebra::TpetraWrappers::Vector &) const; + template void SparseMatrix::Tvmult_add( dealii::LinearAlgebra::EpetraWrappers::Vector &, diff --git a/source/lac/trilinos_tpetra_communication_pattern.cc b/source/lac/trilinos_tpetra_communication_pattern.cc new file mode 100644 index 000000000000..e78dfda3d3d1 --- /dev/null +++ b/source/lac/trilinos_tpetra_communication_pattern.cc @@ -0,0 +1,104 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2015 - 2018 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + +#include + +#include + +#ifdef DEAL_II_WITH_TRILINOS + +# ifdef DEAL_II_WITH_MPI + +# include + +# include + +# include + +DEAL_II_NAMESPACE_OPEN + +namespace LinearAlgebra +{ + namespace TpetraWrappers + { + CommunicationPattern::CommunicationPattern( + const IndexSet &vector_space_vector_index_set, + const IndexSet &read_write_vector_index_set, + const MPI_Comm &communicator) + { + // virtual functions called in constructors and destructors never use the + // override in a derived class + // for clarity be explicit on which function is called + CommunicationPattern::reinit(vector_space_vector_index_set, + read_write_vector_index_set, + communicator); + } + + + + void + CommunicationPattern::reinit(const IndexSet &vector_space_vector_index_set, + const IndexSet &read_write_vector_index_set, + const MPI_Comm &communicator) + { + comm = std::make_shared(communicator); + + auto vector_space_vector_map = Teuchos::rcp(new Tpetra::Map<>( + vector_space_vector_index_set.make_tpetra_map(*comm, false))); + auto read_write_vector_map = Teuchos::rcp(new Tpetra::Map<>( + read_write_vector_index_set.make_tpetra_map(*comm, true))); + + // Target map is read_write_vector_map + // Source map is vector_space_vector_map. This map must have uniquely + // owned GID. + tpetra_import = + std_cxx14::make_unique>(read_write_vector_map, + vector_space_vector_map); + tpetra_export = + std_cxx14::make_unique>(read_write_vector_map, + vector_space_vector_map); + } + + + + const MPI_Comm & + CommunicationPattern::get_mpi_communicator() const + { + return *comm; + } + + + + const Tpetra::Import<> & + CommunicationPattern::get_tpetra_import() const + { + return *tpetra_import; + } + + + + const Tpetra::Export<> & + CommunicationPattern::get_tpetra_export() const + { + return *tpetra_export; + } + } // namespace TpetraWrappers +} // namespace LinearAlgebra + +DEAL_II_NAMESPACE_CLOSE + +# endif + +#endif diff --git a/source/lac/trilinos_tpetra_vector.cc b/source/lac/trilinos_tpetra_vector.cc new file mode 100644 index 000000000000..0a52aa1972e6 --- /dev/null +++ b/source/lac/trilinos_tpetra_vector.cc @@ -0,0 +1,632 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2015 - 2018 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + +#include + +#include + +#ifdef DEAL_II_WITH_TRILINOS + +# ifdef DEAL_II_WITH_MPI + +# include + +# include + +# include + +# include +# include +# include + +# include + + +DEAL_II_NAMESPACE_OPEN + +namespace LinearAlgebra +{ + namespace TpetraWrappers + { + Vector::Vector() + : vector(new Tpetra::Vector<>(Teuchos::RCP>( + new Tpetra::Map<>(0, 0, Utilities::Trilinos::tpetra_comm_self())))) + {} + + + + Vector::Vector(const Vector &V) + : Subscriptor() + , vector(new Tpetra::Vector<>(V.trilinos_vector(), Teuchos::Copy)) + {} + + + + Vector::Vector(const IndexSet ¶llel_partitioner, + const MPI_Comm &communicator) + : vector(new Tpetra::Vector<>(Teuchos::rcp(new Tpetra::Map<>( + parallel_partitioner.make_tpetra_map(communicator, false))))) + {} + + + + void + Vector::reinit(const IndexSet ¶llel_partitioner, + const MPI_Comm &communicator, + const bool omit_zeroing_entries) + { + Tpetra::Map<> input_map = + parallel_partitioner.make_tpetra_map(communicator, false); + if (vector->getMap()->isSameAs(input_map) == false) + vector = std_cxx14::make_unique>( + Teuchos::rcp(new Tpetra::Map<>(input_map))); + else if (omit_zeroing_entries == false) + { + vector->putScalar(0.); + } + } + + + + void + Vector::reinit(const VectorSpaceVector &V, + const bool omit_zeroing_entries) + { + // Check that casting will work. + Assert(dynamic_cast(&V) != nullptr, + ExcVectorTypeNotCompatible()); + + // Downcast V. If fails, throws an exception. + const Vector &down_V = dynamic_cast(V); + + reinit(down_V.locally_owned_elements(), + down_V.get_mpi_communicator(), + omit_zeroing_entries); + } + + + + Vector & + Vector::operator=(const Vector &V) + { + // Distinguish three cases: + // - First case: both vectors have the same layout. + // - Second case: both vectors have the same size but different layout. + // - Third case: the vectors have different size. + if (vector->getMap()->isSameAs(*(V.trilinos_vector().getMap()))) + *vector = V.trilinos_vector(); + else + { + if (size() == V.size()) + { + Tpetra::Import<> data_exchange(vector->getMap(), + V.trilinos_vector().getMap()); + + vector->doImport(V.trilinos_vector(), + data_exchange, + Tpetra::REPLACE); + } + else + vector = + std_cxx14::make_unique>(V.trilinos_vector()); + } + + return *this; + } + + + + Vector & + Vector::operator=(const double s) + { + Assert(s == 0., ExcMessage("Only 0 can be assigned to a vector.")); + + vector->putScalar(s); + + return *this; + } + + + + void + Vector::import( + const ReadWriteVector & V, + VectorOperation::values operation, + std::shared_ptr communication_pattern) + { + // If no communication pattern is given, create one. Otherwsie, use the + // one given. + if (communication_pattern == nullptr) + { + // The first time import is called, a communication pattern is + // created. Check if the communication pattern already exists and if + // it can be reused. + if ((source_stored_elements.size() != + V.get_stored_elements().size()) || + (source_stored_elements != V.get_stored_elements())) + { + const Teuchos::MpiComm *mpi_comm = + dynamic_cast *>( + vector->getMap()->getComm().get()); + Assert(mpi_comm != nullptr, ExcInternalError()); + create_tpetra_comm_pattern(V.get_stored_elements(), + *(mpi_comm->getRawMpiComm())()); + } + } + else + { + tpetra_comm_pattern = std::dynamic_pointer_cast< + const TpetraWrappers::CommunicationPattern>(communication_pattern); + AssertThrow( + tpetra_comm_pattern != nullptr, + ExcMessage( + std::string("The communication pattern is not of type ") + + "LinearAlgebra::TpetraWrappers::CommunicationPattern.")); + } + + Tpetra::Export<> tpetra_export(tpetra_comm_pattern->get_tpetra_export()); + Tpetra::Vector<> source_vector(tpetra_export.getSourceMap()); + + source_vector.sync(); + auto x_2d = source_vector.getLocalView(); + auto x_1d = Kokkos::subview(x_2d, Kokkos::ALL(), 0); + source_vector.modify(); + const size_t localLength = source_vector.getLocalLength(); + auto values_it = V.begin(); + for (size_t k = 0; k < localLength; ++k) + x_1d(k) = *values_it++; + source_vector.sync::device_type::memory_space>(); + if (operation == VectorOperation::insert) + vector->doExport(source_vector, tpetra_export, Tpetra::REPLACE); + else if (operation == VectorOperation::add) + vector->doExport(source_vector, tpetra_export, Tpetra::ADD); + else + AssertThrow(false, ExcNotImplemented()); + } + + + + Vector & + Vector::operator*=(const double factor) + { + AssertIsFinite(factor); + vector->scale(factor); + + return *this; + } + + + + Vector & + Vector::operator/=(const double factor) + { + AssertIsFinite(factor); + Assert(factor != 0., ExcZero()); + *this *= 1. / factor; + + return *this; + } + + + + Vector & + Vector::operator+=(const VectorSpaceVector &V) + { + // Check that casting will work. + Assert(dynamic_cast(&V) != nullptr, + ExcVectorTypeNotCompatible()); + + // Downcast V. If fails, throws an exception. + const Vector &down_V = dynamic_cast(V); + // If the maps are the same we can Update right away. + if (vector->getMap()->isSameAs(*(down_V.trilinos_vector().getMap()))) + { + vector->update(1., down_V.trilinos_vector(), 1.); + } + else + { + Assert(this->size() == down_V.size(), + ExcDimensionMismatch(this->size(), down_V.size())); + + // TODO: The code doesn't work as expected so we use a workaround. + /*Tpetra::Export<> data_exchange(vector->getMap(), + down_V.trilinos_vector().getMap()); + vector->doExport(down_V.trilinos_vector(), + data_exchange, + Tpetra::ADD);*/ + + Tpetra::Vector<> dummy(vector->getMap(), false); + Tpetra::Import<> data_exchange(dummy.getMap(), + down_V.trilinos_vector().getMap()); + + dummy.doExport(down_V.trilinos_vector(), + data_exchange, + Tpetra::REPLACE); + + vector->update(1.0, dummy, 1.0); + } + + return *this; + } + + + + Vector & + Vector::operator-=(const VectorSpaceVector &V) + { + this->add(-1., V); + + return *this; + } + + + + double Vector::operator*(const VectorSpaceVector &V) const + { + // Check that casting will work. + Assert(dynamic_cast(&V) != nullptr, + ExcVectorTypeNotCompatible()); + + // Downcast V. If fails, throws an exception. + const Vector &down_V = dynamic_cast(V); + Assert(this->size() == down_V.size(), + ExcDimensionMismatch(this->size(), down_V.size())); + Assert(vector->getMap()->isSameAs(*down_V.trilinos_vector().getMap()), + ExcDifferentParallelPartitioning()); + + return vector->dot(down_V.trilinos_vector()); + } + + + + void + Vector::add(const double a) + { + AssertIsFinite(a); + + vector->sync(); + auto vector_2d = vector->getLocalView(); + auto vector_1d = Kokkos::subview(vector_2d, Kokkos::ALL(), 0); + vector->modify(); + const size_t localLength = vector->getLocalLength(); + for (size_t k = 0; k < localLength; ++k) + { + vector_1d(k) += a; + } + vector->sync::device_type::memory_space>(); + } + + + + void + Vector::add(const double a, const VectorSpaceVector &V) + { + // Check that casting will work. + Assert(dynamic_cast(&V) != nullptr, + ExcVectorTypeNotCompatible()); + + // Downcast V. If fails, throws an exception. + const Vector &down_V = dynamic_cast(V); + AssertIsFinite(a); + Assert(vector->getMap()->isSameAs(*(down_V.trilinos_vector().getMap())), + ExcDifferentParallelPartitioning()); + + vector->update(a, down_V.trilinos_vector(), 1.); + } + + + + void + Vector::add(const double a, + const VectorSpaceVector &V, + const double b, + const VectorSpaceVector &W) + { + // Check that casting will work. + Assert(dynamic_cast(&V) != nullptr, + ExcVectorTypeNotCompatible()); + // Check that casting will work. + Assert(dynamic_cast(&W) != nullptr, + ExcVectorTypeNotCompatible()); + + // Downcast V. If fails, throws an exception. + const Vector &down_V = dynamic_cast(V); + // Downcast W. If fails, throws an exception. + const Vector &down_W = dynamic_cast(W); + Assert(vector->getMap()->isSameAs(*(down_V.trilinos_vector().getMap())), + ExcDifferentParallelPartitioning()); + Assert(vector->getMap()->isSameAs(*(down_W.trilinos_vector().getMap())), + ExcDifferentParallelPartitioning()); + AssertIsFinite(a); + AssertIsFinite(b); + + vector->update( + a, down_V.trilinos_vector(), b, down_W.trilinos_vector(), 1.); + } + + + + void + Vector::sadd(const double s, + const double a, + const VectorSpaceVector &V) + { + // Check that casting will work. + Assert(dynamic_cast(&V) != nullptr, + ExcVectorTypeNotCompatible()); + + *this *= s; + // Downcast V. It fails, throws an exception. + const Vector &down_V = dynamic_cast(V); + Vector tmp(down_V); + tmp *= a; + *this += tmp; + } + + + + void + Vector::scale(const VectorSpaceVector &scaling_factors) + { + // Check that casting will work. + Assert(dynamic_cast(&scaling_factors) != nullptr, + ExcVectorTypeNotCompatible()); + + // Downcast scaling_factors. If fails, throws an exception. + const Vector &down_scaling_factors = + dynamic_cast(scaling_factors); + Assert(vector->getMap()->isSameAs( + *(down_scaling_factors.trilinos_vector().getMap())), + ExcDifferentParallelPartitioning()); + + vector->elementWiseMultiply(1., + *down_scaling_factors.vector, + *vector, + 0.); + } + + + + void + Vector::equ(const double a, const VectorSpaceVector &V) + { + // Check that casting will work. + Assert(dynamic_cast(&V) != nullptr, + ExcVectorTypeNotCompatible()); + + // Downcast V. If fails, throws an exception. + const Vector &down_V = dynamic_cast(V); + // If we don't have the same map, copy. + if (vector->getMap()->isSameAs(*down_V.trilinos_vector().getMap()) == + false) + this->sadd(0., a, V); + else + { + // Otherwise, just update + vector->update(a, down_V.trilinos_vector(), 0.); + } + } + + + + bool + Vector::all_zero() const + { + // get a representation of the vector and + // loop over all the elements + double * start_ptr = vector->getDataNonConst().get(); + const double *ptr = start_ptr, + *eptr = start_ptr + vector->getLocalLength(); + unsigned int flag = 0; + while (ptr != eptr) + { + if (*ptr != 0) + { + flag = 1; + break; + } + ++ptr; + } + + // Check that the vector is zero on _all_ processors. + const Teuchos::MpiComm *mpi_comm = + dynamic_cast *>( + vector->getMap()->getComm().get()); + Assert(mpi_comm != nullptr, ExcInternalError()); + unsigned int num_nonzero = + Utilities::MPI::sum(flag, *(mpi_comm->getRawMpiComm())()); + + return num_nonzero == 0; + } + + + + double + Vector::mean_value() const + { + return vector->meanValue(); + } + + + + double + Vector::l1_norm() const + { + return vector->norm1(); + } + + + + double + Vector::l2_norm() const + { + return vector->norm2(); + } + + + + double + Vector::linfty_norm() const + { + return vector->normInf(); + } + + + + double + Vector::add_and_dot(const double a, + const VectorSpaceVector &V, + const VectorSpaceVector &W) + { + this->add(a, V); + + return *this * W; + } + + + + Vector::size_type + Vector::size() const + { + return vector->getGlobalLength(); + } + + + + MPI_Comm + Vector::get_mpi_communicator() const + { + const auto tpetra_comm = dynamic_cast *>( + vector->getMap()->getComm().get()); + Assert(tpetra_comm != nullptr, ExcInternalError()); + return *(tpetra_comm->getRawMpiComm())(); + } + + + + ::dealii::IndexSet + Vector::locally_owned_elements() const + { + IndexSet is(size()); + + // easy case: local range is contiguous + if (vector->getMap()->isContiguous()) + { +# ifndef DEAL_II_WITH_64BIT_INDICES + is.add_range(vector->getMap()->getMinGlobalIndex(), + vector->getMap()->getMaxGlobalIndex() + 1); +# else + is.add_range(vector->getMap()->getMinGlobalIndex(), + vector->getMap()->getMaxGlobalIndex() + 1); +# endif + } + else if (vector->getLocalLength() > 0) + { + const size_type n_indices = vector->getLocalLength(); + auto vector_indices = vector->getMap()->getMyGlobalIndices(); + is.add_indices((unsigned int *)&vector_indices[0], + (unsigned int *)&vector_indices[0] + n_indices); + } + is.compress(); + + return is; + } + + + + const Tpetra::Vector<> & + Vector::trilinos_vector() const + { + return *vector; + } + + + + Tpetra::Vector<> & + Vector::trilinos_vector() + { + return *vector; + } + + + + void + Vector::print(std::ostream & out, + const unsigned int precision, + const bool scientific, + const bool across) const + { + AssertThrow(out, ExcIO()); + boost::io::ios_flags_saver restore_flags(out); + + // Get a representation of the vector and loop over all + // the elements + const auto val = vector->get1dView(); + + out.precision(precision); + if (scientific) + out.setf(std::ios::scientific, std::ios::floatfield); + else + out.setf(std::ios::fixed, std::ios::floatfield); + + vector->sync(); + auto vector_2d = vector->getLocalView(); + auto vector_1d = Kokkos::subview(vector_2d, Kokkos::ALL(), 0); + const size_t local_length = vector->getLocalLength(); + + if (across) + for (unsigned int i = 0; i < local_length; ++i) + out << i << "->" << vector->getMap()->getGlobalElement(i) << ": " + << vector_1d(i) << std::endl; + // out << val[i] << ' '; + else + for (unsigned int i = 0; i < local_length; ++i) + out << val[i] << std::endl; + out << std::endl; + + // restore the representation + // of the vector + AssertThrow(out, ExcIO()); + } + + + + std::size_t + Vector::memory_consumption() const + { + return sizeof(*this) + + vector->getLocalLength() * + (sizeof(double) + sizeof(TrilinosWrappers::types::int_type)); + } + + + + void + Vector::create_tpetra_comm_pattern(const IndexSet &source_index_set, + const MPI_Comm &mpi_comm) + { + source_stored_elements = source_index_set; + tpetra_comm_pattern = + std::make_shared( + locally_owned_elements(), source_index_set, mpi_comm); + } + } // namespace TpetraWrappers +} // namespace LinearAlgebra + +DEAL_II_NAMESPACE_CLOSE + +# endif + +#endif diff --git a/source/lac/vector_memory.cc b/source/lac/vector_memory.cc index f15f32800e75..3fa5affd9bd9 100644 --- a/source/lac/vector_memory.cc +++ b/source/lac/vector_memory.cc @@ -21,6 +21,7 @@ #include #include #include +#include #include #include #include diff --git a/source/multigrid/mg_base.cc b/source/multigrid/mg_base.cc index 8744c6cf4049..a32b68a09688 100644 --- a/source/multigrid/mg_base.cc +++ b/source/multigrid/mg_base.cc @@ -19,6 +19,7 @@ #include #include #include +#include #include #include diff --git a/source/numerics/data_out_dof_data_codim.cc b/source/numerics/data_out_dof_data_codim.cc index e085c3d3825b..676a33714ecb 100644 --- a/source/numerics/data_out_dof_data_codim.cc +++ b/source/numerics/data_out_dof_data_codim.cc @@ -21,6 +21,7 @@ #include #include #include +#include #include #include #include diff --git a/source/numerics/derivative_approximation.cc b/source/numerics/derivative_approximation.cc index 73f574bdc116..d062b4ec2bd9 100644 --- a/source/numerics/derivative_approximation.cc +++ b/source/numerics/derivative_approximation.cc @@ -39,6 +39,7 @@ #include #include #include +#include #include #include diff --git a/tests/trilinos/tpetra_vector_01.cc b/tests/trilinos/tpetra_vector_01.cc new file mode 100644 index 000000000000..c10ac87bb1e3 --- /dev/null +++ b/tests/trilinos/tpetra_vector_01.cc @@ -0,0 +1,225 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2015 - 2018 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + +#include + +#include +#include + +#include +#include + +#include "../tests.h" + +// Check LinearAlgebra::TpetraWrappers::Vector assignment and import + + +void +test() +{ + IndexSet parallel_partitioner_1(10); + IndexSet parallel_partitioner_2(10); + unsigned int rank = Utilities::MPI::this_mpi_process(MPI_COMM_WORLD); + if (rank == 0) + { + parallel_partitioner_1.add_range(0, 5); + parallel_partitioner_2.add_range(0, 3); + } + else + { + parallel_partitioner_1.add_range(5, 10); + parallel_partitioner_2.add_range(3, 10); + } + parallel_partitioner_1.compress(); + parallel_partitioner_2.compress(); + LinearAlgebra::TpetraWrappers::Vector a; + LinearAlgebra::TpetraWrappers::Vector b(parallel_partitioner_1, + MPI_COMM_WORLD); + LinearAlgebra::TpetraWrappers::Vector c(b); + + AssertThrow(a.size() == 0, ExcMessage("Vector has the wrong size.")); + AssertThrow(b.size() == 10, ExcMessage("Vector has the wrong size.")); + AssertThrow(c.size() == 10, ExcMessage("Vector has the wrong size.")); + + a.reinit(parallel_partitioner_2, MPI_COMM_WORLD); + AssertThrow(a.size() == 10, ExcMessage("Vector has the wrong size.")); + + AssertThrow(parallel_partitioner_1 == b.locally_owned_elements(), + ExcMessage("IndexSet has been modified.")); + AssertThrow(parallel_partitioner_2 == a.locally_owned_elements(), + ExcMessage("IndexSet has been modified.")); + + IndexSet read_write_index_set(10); + if (rank == 0) + read_write_index_set.add_range(0, 6); + else + read_write_index_set.add_range(4, 10); + read_write_index_set.compress(); + + LinearAlgebra::ReadWriteVector read_write_1(read_write_index_set); + LinearAlgebra::ReadWriteVector read_write_2(read_write_index_set); + LinearAlgebra::ReadWriteVector read_write_3(read_write_index_set); + if (rank == 0) + { + for (unsigned int i = 0; i < 6; ++i) + { + read_write_1[i] = i; + read_write_2[i] = 5. + i; + } + } + else + { + for (unsigned int i = 4; i < 10; ++i) + { + read_write_1[i] = i; + read_write_2[i] = 5. + i; + } + } + + a.import(read_write_2, VectorOperation::insert); + AssertThrow(a.size() == 10, ExcMessage("Vector has the wrong size.")); + + read_write_3.import(a, VectorOperation::insert); + if (rank == 0) + { + for (unsigned int i = 0; i < 6; ++i) + { + AssertThrow(read_write_2[i] == read_write_3[i], + ExcMessage("Vector a has been modified.")); + } + } + else + { + for (unsigned int i = 4; i < 10; ++i) + AssertThrow(read_write_2[i] == read_write_3[i], + ExcMessage("Vector a has been modified.")); + } + + b.import(read_write_1, VectorOperation::insert); + AssertThrow(b.size() == 10, ExcMessage("Vector has the wrong size.")); + + read_write_3.import(b, VectorOperation::insert); + if (rank == 0) + { + for (unsigned int i = 0; i < 6; ++i) + AssertThrow(read_write_1[i] == read_write_3[i], + ExcMessage("Vector b has been modified.")); + } + else + { + for (unsigned int i = 4; i < 10; ++i) + AssertThrow(read_write_1[i] == read_write_3[i], + ExcMessage("Vector b has been modified.")); + } + + c.import(read_write_2, VectorOperation::insert); + AssertThrow(c.size() == 10, ExcMessage("Vector has the wrong size.")); + + read_write_3.import(c, VectorOperation::insert); + if (rank == 0) + { + for (unsigned int i = 0; i < 6; ++i) + AssertThrow(read_write_2[i] == read_write_3[i], + ExcMessage("Vector c has been modified.")); + } + else + { + for (unsigned int i = 4; i < 10; ++i) + AssertThrow(read_write_2[i] == read_write_3[i], + ExcMessage("Vector c has been modified.")); + } + + a *= 2; + read_write_3.import(a, VectorOperation::insert); + if (rank == 0) + { + for (unsigned int i = 0; i < 6; ++i) + AssertThrow(2. * read_write_2[i] == read_write_3[i], + ExcMessage("Problem in operator *=.")); + } + else + { + for (unsigned int i = 4; i < 10; ++i) + AssertThrow(2. * read_write_2[i] == read_write_3[i], + ExcMessage("Problem in operator *=.")); + } + + c /= 2.; + read_write_3.import(c, VectorOperation::insert); + if (rank == 0) + { + for (unsigned int i = 0; i < 6; ++i) + AssertThrow(0.5 * read_write_2[i] == read_write_3[i], + ExcMessage("Problem in operator /=.")); + } + else + { + for (unsigned int i = 4; i < 10; ++i) + AssertThrow(0.5 * read_write_2[i] == read_write_3[i], + ExcMessage("Problem in operator /=.")); + } + + b += a; + read_write_3.import(b, VectorOperation::insert); + if (rank == 0) + { + for (unsigned int i = 0; i < 6; ++i) + AssertThrow(2. * read_write_2[i] + read_write_1[i] == read_write_3[i], + ExcMessage("Problem in operator +=.")); + } + else + { + for (unsigned int i = 4; i < 10; ++i) + AssertThrow(2. * read_write_2[i] + read_write_1[i] == read_write_3[i], + ExcMessage("Problem in operator +=.")); + } + + b -= c; + read_write_3.import(b, VectorOperation::insert); + if (rank == 0) + { + for (unsigned int i = 0; i < 6; ++i) + AssertThrow(1.5 * read_write_2[i] + read_write_1[i] == read_write_3[i], + ExcMessage("Problem in operator -=.")); + } + else + { + for (unsigned int i = 4; i < 10; ++i) + AssertThrow(1.5 * read_write_2[i] + read_write_1[i] == read_write_3[i], + ExcMessage("Problem in operator -=.")); + } + + b.import(read_write_1, VectorOperation::insert); + c.import(read_write_1, VectorOperation::insert); + const double val = b * c; + AssertThrow(val == 285., ExcMessage("Problem in operator *.")); +} + + +int +main(int argc, char **argv) +{ + initlog(); + deallog.depth_console(0); + + Utilities::MPI::MPI_InitFinalize mpi_init(argc, argv, 1); + + test(); + + deallog << "OK" << std::endl; + + return 0; +} diff --git a/tests/trilinos/tpetra_vector_01.mpirun=2.output b/tests/trilinos/tpetra_vector_01.mpirun=2.output new file mode 100644 index 000000000000..0fd8fc12f0b4 --- /dev/null +++ b/tests/trilinos/tpetra_vector_01.mpirun=2.output @@ -0,0 +1,2 @@ + +DEAL::OK diff --git a/tests/trilinos/tpetra_vector_02.cc b/tests/trilinos/tpetra_vector_02.cc new file mode 100644 index 000000000000..8e4875353044 --- /dev/null +++ b/tests/trilinos/tpetra_vector_02.cc @@ -0,0 +1,216 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2015 - 2017 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + +#include + +#include +#include + +#include +#include + +#include "../tests.h" + +// Check LinearAlgebra::TpetraWrappers::Vector add and sadd. + +void +test() +{ + IndexSet parallel_partitioner_1(10); + IndexSet parallel_partitioner_2(10); + unsigned int rank = Utilities::MPI::this_mpi_process(MPI_COMM_WORLD); + if (rank == 0) + { + parallel_partitioner_1.add_range(0, 5); + parallel_partitioner_2.add_range(0, 3); + } + else + { + parallel_partitioner_1.add_range(5, 10); + parallel_partitioner_2.add_range(3, 10); + } + parallel_partitioner_1.compress(); + parallel_partitioner_2.compress(); + LinearAlgebra::TpetraWrappers::Vector a(parallel_partitioner_1, + MPI_COMM_WORLD); + LinearAlgebra::TpetraWrappers::Vector b(parallel_partitioner_1, + MPI_COMM_WORLD); + LinearAlgebra::TpetraWrappers::Vector c(parallel_partitioner_2, + MPI_COMM_WORLD); + + IndexSet read_write_index_set(10); + if (rank == 0) + read_write_index_set.add_range(0, 5); + else + read_write_index_set.add_range(5, 10); + read_write_index_set.compress(); + + LinearAlgebra::ReadWriteVector read_write_1(read_write_index_set); + LinearAlgebra::ReadWriteVector read_write_2(read_write_index_set); + LinearAlgebra::ReadWriteVector read_write_3(read_write_index_set); + if (rank == 0) + { + for (unsigned int i = 0; i < 5; ++i) + { + read_write_1[i] = i; + read_write_2[i] = 5. + i; + } + } + else + { + for (unsigned int i = 5; i < 10; ++i) + { + read_write_1[i] = i; + read_write_2[i] = 5. + i; + } + } + + a.import(read_write_1, VectorOperation::insert); + b.import(read_write_2, VectorOperation::insert); + c.import(read_write_2, VectorOperation::insert); + + a.add(1.); + read_write_3.import(a, VectorOperation::insert); + if (rank == 0) + { + for (unsigned int i = 0; i < 5; ++i) + AssertThrow(1. + read_write_1[i] == read_write_3[i], + ExcMessage("Problem in add(scalar).")); + } + else + { + for (unsigned int i = 5; i < 10; ++i) + AssertThrow(1. + read_write_1[i] == read_write_3[i], + ExcMessage("Problem in add(scalar).")); + } + + a.add(2., b); + read_write_3.import(a, VectorOperation::insert); + if (rank == 0) + { + for (unsigned int i = 0; i < 5; ++i) + AssertThrow(1. + read_write_1[i] + 2. * read_write_2[i] == + read_write_3[i], + ExcMessage("Problem in add(scalar,Vector).")); + } + else + { + for (unsigned int i = 5; i < 10; ++i) + AssertThrow(1. + read_write_1[i] + 2. * read_write_2[i] == + read_write_3[i], + ExcMessage("Problem in add(scalar,Vector).")); + } + + + LinearAlgebra::TpetraWrappers::Vector d(a); + a.add(2., b, 3., d); + read_write_3.import(a, VectorOperation::insert); + if (rank == 0) + { + for (unsigned int i = 0; i < 5; ++i) + AssertThrow(4. + 4. * read_write_1[i] + 10. * read_write_2[i] == + read_write_3[i], + ExcMessage("Problem in add(scalar,Vector,scalar,Vector).")); + } + else + { + for (unsigned int i = 5; i < 10; ++i) + AssertThrow(4. + 4. * read_write_1[i] + 10. * read_write_2[i] == + read_write_3[i], + ExcMessage("Problem in add(scalar,Vector,scalar,Vector).")); + } + + + a.import(read_write_1, VectorOperation::insert); + a.sadd(3., 2., c); + read_write_3.import(a, VectorOperation::insert); + if (rank == 0) + { + for (unsigned int i = 0; i < 5; ++i) + AssertThrow(3. * read_write_1[i] + 2. * read_write_2[i] == + read_write_3[i], + ExcMessage("Problem in sadd(scalar,scalar,Vector).")); + } + else + { + for (unsigned int i = 5; i < 10; ++i) + AssertThrow(3. * read_write_1[i] + 2. * read_write_2[i] == + read_write_3[i], + ExcMessage("Problem in sadd(scalar,scalar,Vector).")); + } + + + a.import(read_write_1, VectorOperation::insert); + a.scale(b); + read_write_3.import(a, VectorOperation::insert); + if (rank == 0) + { + for (unsigned int i = 0; i < 5; ++i) + AssertThrow(read_write_1[i] * read_write_2[i] == read_write_3[i], + ExcMessage("Problem in scale.")); + } + else + { + for (unsigned int i = 5; i < 10; ++i) + AssertThrow(read_write_1[i] * read_write_2[i] == read_write_3[i], + ExcMessage("Problem in scale.")); + } + + + a.equ(2., c); + read_write_3.import(a, VectorOperation::insert); + if (rank == 0) + { + for (unsigned int i = 0; i < 5; ++i) + AssertThrow(2. * read_write_2[i] == read_write_3[i], + ExcMessage("Problem in scale.")); + } + else + { + for (unsigned int i = 5; i < 10; ++i) + AssertThrow(2. * read_write_2[i] == read_write_3[i], + ExcMessage("Problem in equ.")); + } + + + AssertThrow(b.l1_norm() == 95., ExcMessage("Problem in l1_norm.")); + + const double eps = 1e-6; + AssertThrow(std::fabs(b.l2_norm() - 31.3847096) < eps, + ExcMessage("Problem in l2_norm")); + + AssertThrow(b.linfty_norm() == 14., ExcMessage("Problem in linfty_norm.")); + + a.import(read_write_1, VectorOperation::insert); + const double val = a.add_and_dot(2., a, b); + AssertThrow(val == 1530., ExcMessage("Problem in add_and_dot")); +} + + +int +main(int argc, char **argv) +{ + initlog(); + deallog.depth_console(0); + + Utilities::MPI::MPI_InitFinalize mpi_init(argc, argv, 1); + + test(); + + deallog << "OK" << std::endl; + + return 0; +} diff --git a/tests/trilinos/tpetra_vector_02.mpirun=2.output b/tests/trilinos/tpetra_vector_02.mpirun=2.output new file mode 100644 index 000000000000..0fd8fc12f0b4 --- /dev/null +++ b/tests/trilinos/tpetra_vector_02.mpirun=2.output @@ -0,0 +1,2 @@ + +DEAL::OK diff --git a/tests/trilinos/tpetra_vector_03.cc b/tests/trilinos/tpetra_vector_03.cc new file mode 100644 index 000000000000..4927aaedb82a --- /dev/null +++ b/tests/trilinos/tpetra_vector_03.cc @@ -0,0 +1,101 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2018 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + +// Check LinearAlgebra::TpetraWrappers::Vector::import +// for VectorOperation::add and check LinearAlgebra::ReadWriteVector +// for VectorOperation::add/min/max. + +#include +#include + +#include +#include + +#include +#include + +#include "../tests.h" + +void +test() +{ + unsigned int my_id = Utilities::MPI::this_mpi_process(MPI_COMM_WORLD); + unsigned int n_procs = Utilities::MPI::n_mpi_processes(MPI_COMM_WORLD); + + IndexSet locally_owned(n_procs * 2); + locally_owned.add_range(my_id * 2, my_id * 2 + 2); + locally_owned.compress(); + + LinearAlgebra::TpetraWrappers::Vector v(locally_owned, MPI_COMM_WORLD); + + IndexSet workaround_set(n_procs * 2); + unsigned int my_first_index = (my_id * 2 + 2) % (n_procs * 2); + unsigned int my_second_index = my_id * 2 + 1; + workaround_set.add_index(my_first_index); + workaround_set.add_index(my_second_index); + workaround_set.add_index(0); + workaround_set.compress(); + LinearAlgebra::ReadWriteVector rw_vector(workaround_set); + + rw_vector(my_first_index) = my_id + 10; + rw_vector(my_second_index) = my_id + 100; + rw_vector(0) = 1.; + // rw_vector(2) = 1.; + v.import(rw_vector, VectorOperation::add); + deallog << "Tpetra first import add:" << std::endl; + v.print(deallog.get_file_stream()); + rw_vector.print(deallog.get_file_stream()); + + rw_vector(my_first_index) = my_id + 20; + rw_vector(my_second_index) = my_id + 200; + rw_vector(0) = 2.; + // rw_vector(2) = 3.; + v.import(rw_vector, VectorOperation::add); + deallog << "Tpetra second import add:" << std::endl; + v.print(deallog.get_file_stream()); + rw_vector.print(deallog.get_file_stream()); + + rw_vector.import(v, VectorOperation::add); + deallog << "ReadWrite import add:" << std::endl; + rw_vector.print(deallog.get_file_stream()); + + rw_vector(my_first_index) = my_id + 100; + rw_vector(my_second_index) = 1; + rw_vector(0) = 4.; + // rw_vector(2) = 3.; + rw_vector.import(v, VectorOperation::min); + deallog << "ReadWrite import min:" << std::endl; + rw_vector.print(deallog.get_file_stream()); + + rw_vector(my_first_index) = my_id + 100; + rw_vector(my_second_index) = 1; + rw_vector(0) = 4.; + // rw_vector(2) = 3.; + rw_vector.import(v, VectorOperation::max); + deallog << "ReadWrite import max:" << std::endl; + rw_vector.print(deallog.get_file_stream()); +} + + + +int +main(int argc, char **argv) +{ + Utilities::MPI::MPI_InitFinalize mpi_initialization( + argc, argv, testing_max_num_threads()); + + MPILogInitAll log; + test(); +} diff --git a/tests/trilinos/tpetra_vector_03.mpirun=2.output b/tests/trilinos/tpetra_vector_03.mpirun=2.output new file mode 100644 index 000000000000..5d5f9c0afb64 --- /dev/null +++ b/tests/trilinos/tpetra_vector_03.mpirun=2.output @@ -0,0 +1,70 @@ + +DEAL:0::Tpetra first import add: +0->0: 2.000e+00 +1->1: 1.000e+02 + +IndexSet: {[0,2]} + +[0]: 1.000e+00 +[1]: 1.000e+02 +[2]: 1.000e+01 +DEAL:0::Tpetra second import add: +0->0: 4.000e+00 +1->1: 2.000e+02 + +IndexSet: {[0,2]} + +[0]: 2.000e+00 +[1]: 2.000e+02 +[2]: 2.000e+01 +DEAL:0::ReadWrite import add: +IndexSet: {[0,2]} + +[0]: 6.000e+00 +[1]: 4.000e+02 +[2]: 5.000e+01 +DEAL:0::ReadWrite import min: +IndexSet: {[0,2]} + +[0]: 4.000e+00 +[1]: 1.000e+00 +[2]: 3.000e+01 +DEAL:0::ReadWrite import max: +IndexSet: {[0,2]} + +[0]: 4.000e+00 +[1]: 2.000e+02 +[2]: 1.000e+02 + +DEAL:1::Tpetra first import add: +0->2: 1.000e+01 +1->3: 1.010e+02 + +IndexSet: {0, 3} + +[0]: 1.000e+00 +[3]: 1.010e+02 +DEAL:1::Tpetra second import add: +0->2: 3.000e+01 +1->3: 2.010e+02 + +IndexSet: {0, 3} + +[0]: 2.000e+00 +[3]: 2.010e+02 +DEAL:1::ReadWrite import add: +IndexSet: {0, 3} + +[0]: 6.000e+00 +[3]: 4.020e+02 +DEAL:1::ReadWrite import min: +IndexSet: {0, 3} + +[0]: 4.000e+00 +[3]: 1.000e+00 +DEAL:1::ReadWrite import max: +IndexSet: {0, 3} + +[0]: 4.000e+00 +[3]: 2.010e+02 + diff --git a/tests/trilinos/tpetra_vector_03.mpirun=4.output b/tests/trilinos/tpetra_vector_03.mpirun=4.output new file mode 100644 index 000000000000..bb8d36da886b --- /dev/null +++ b/tests/trilinos/tpetra_vector_03.mpirun=4.output @@ -0,0 +1,146 @@ + +DEAL:0::Tpetra first import add: +0->0: 4.000e+00 +1->1: 1.000e+02 + +IndexSet: {[0,2]} + +[0]: 1.000e+00 +[1]: 1.000e+02 +[2]: 1.000e+01 +DEAL:0::Tpetra second import add: +0->0: 8.000e+00 +1->1: 2.000e+02 + +IndexSet: {[0,2]} + +[0]: 2.000e+00 +[1]: 2.000e+02 +[2]: 2.000e+01 +DEAL:0::ReadWrite import add: +IndexSet: {[0,2]} + +[0]: 1.000e+01 +[1]: 4.000e+02 +[2]: 5.000e+01 +DEAL:0::ReadWrite import min: +IndexSet: {[0,2]} + +[0]: 4.000e+00 +[1]: 1.000e+00 +[2]: 3.000e+01 +DEAL:0::ReadWrite import max: +IndexSet: {[0,2]} + +[0]: 8.000e+00 +[1]: 2.000e+02 +[2]: 1.000e+02 + +DEAL:1::Tpetra first import add: +0->2: 1.000e+01 +1->3: 1.010e+02 + +IndexSet: {0, [3,4]} + +[0]: 1.000e+00 +[3]: 1.010e+02 +[4]: 1.100e+01 +DEAL:1::Tpetra second import add: +0->2: 3.000e+01 +1->3: 2.010e+02 + +IndexSet: {0, [3,4]} + +[0]: 2.000e+00 +[3]: 2.010e+02 +[4]: 2.100e+01 +DEAL:1::ReadWrite import add: +IndexSet: {0, [3,4]} + +[0]: 1.000e+01 +[3]: 4.020e+02 +[4]: 5.300e+01 +DEAL:1::ReadWrite import min: +IndexSet: {0, [3,4]} + +[0]: 4.000e+00 +[3]: 1.000e+00 +[4]: 3.200e+01 +DEAL:1::ReadWrite import max: +IndexSet: {0, [3,4]} + +[0]: 8.000e+00 +[3]: 2.010e+02 +[4]: 1.010e+02 + + +DEAL:2::Tpetra first import add: +0->4: 1.100e+01 +1->5: 1.020e+02 + +IndexSet: {0, [5,6]} + +[0]: 1.000e+00 +[5]: 1.020e+02 +[6]: 1.200e+01 +DEAL:2::Tpetra second import add: +0->4: 3.200e+01 +1->5: 2.020e+02 + +IndexSet: {0, [5,6]} + +[0]: 2.000e+00 +[5]: 2.020e+02 +[6]: 2.200e+01 +DEAL:2::ReadWrite import add: +IndexSet: {0, [5,6]} + +[0]: 1.000e+01 +[5]: 4.040e+02 +[6]: 5.600e+01 +DEAL:2::ReadWrite import min: +IndexSet: {0, [5,6]} + +[0]: 4.000e+00 +[5]: 1.000e+00 +[6]: 3.400e+01 +DEAL:2::ReadWrite import max: +IndexSet: {0, [5,6]} + +[0]: 8.000e+00 +[5]: 2.020e+02 +[6]: 1.020e+02 + + +DEAL:3::Tpetra first import add: +0->6: 1.200e+01 +1->7: 1.030e+02 + +IndexSet: {0, 7} + +[0]: 1.000e+00 +[7]: 1.030e+02 +DEAL:3::Tpetra second import add: +0->6: 3.400e+01 +1->7: 2.030e+02 + +IndexSet: {0, 7} + +[0]: 2.000e+00 +[7]: 2.030e+02 +DEAL:3::ReadWrite import add: +IndexSet: {0, 7} + +[0]: 1.000e+01 +[7]: 4.060e+02 +DEAL:3::ReadWrite import min: +IndexSet: {0, 7} + +[0]: 4.000e+00 +[7]: 1.000e+00 +DEAL:3::ReadWrite import max: +IndexSet: {0, 7} + +[0]: 8.000e+00 +[7]: 2.030e+02 + From dbbe12525f2b0c396212ba5258f5d513fcaf1a55 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Thu, 13 Sep 2018 02:30:37 +0200 Subject: [PATCH 147/507] Change output format --- source/lac/trilinos_tpetra_vector.cc | 6 ++-- .../trilinos/tpetra_vector_03.mpirun=2.output | 16 +++------- .../trilinos/tpetra_vector_03.mpirun=4.output | 32 +++++-------------- 3 files changed, 14 insertions(+), 40 deletions(-) diff --git a/source/lac/trilinos_tpetra_vector.cc b/source/lac/trilinos_tpetra_vector.cc index 0a52aa1972e6..5e3c00b53ad4 100644 --- a/source/lac/trilinos_tpetra_vector.cc +++ b/source/lac/trilinos_tpetra_vector.cc @@ -588,12 +588,10 @@ namespace LinearAlgebra if (across) for (unsigned int i = 0; i < local_length; ++i) - out << i << "->" << vector->getMap()->getGlobalElement(i) << ": " - << vector_1d(i) << std::endl; - // out << val[i] << ' '; + out << vector_1d(i) << ' '; else for (unsigned int i = 0; i < local_length; ++i) - out << val[i] << std::endl; + out << vector_1d(i) << std::endl; out << std::endl; // restore the representation diff --git a/tests/trilinos/tpetra_vector_03.mpirun=2.output b/tests/trilinos/tpetra_vector_03.mpirun=2.output index 5d5f9c0afb64..638319c2f1c3 100644 --- a/tests/trilinos/tpetra_vector_03.mpirun=2.output +++ b/tests/trilinos/tpetra_vector_03.mpirun=2.output @@ -1,17 +1,13 @@ DEAL:0::Tpetra first import add: -0->0: 2.000e+00 -1->1: 1.000e+02 - +2.000e+00 1.000e+02 IndexSet: {[0,2]} [0]: 1.000e+00 [1]: 1.000e+02 [2]: 1.000e+01 DEAL:0::Tpetra second import add: -0->0: 4.000e+00 -1->1: 2.000e+02 - +4.000e+00 2.000e+02 IndexSet: {[0,2]} [0]: 2.000e+00 @@ -37,17 +33,13 @@ IndexSet: {[0,2]} [2]: 1.000e+02 DEAL:1::Tpetra first import add: -0->2: 1.000e+01 -1->3: 1.010e+02 - +1.000e+01 1.010e+02 IndexSet: {0, 3} [0]: 1.000e+00 [3]: 1.010e+02 DEAL:1::Tpetra second import add: -0->2: 3.000e+01 -1->3: 2.010e+02 - +3.000e+01 2.010e+02 IndexSet: {0, 3} [0]: 2.000e+00 diff --git a/tests/trilinos/tpetra_vector_03.mpirun=4.output b/tests/trilinos/tpetra_vector_03.mpirun=4.output index bb8d36da886b..f70ed13b09e8 100644 --- a/tests/trilinos/tpetra_vector_03.mpirun=4.output +++ b/tests/trilinos/tpetra_vector_03.mpirun=4.output @@ -1,17 +1,13 @@ DEAL:0::Tpetra first import add: -0->0: 4.000e+00 -1->1: 1.000e+02 - +4.000e+00 1.000e+02 IndexSet: {[0,2]} [0]: 1.000e+00 [1]: 1.000e+02 [2]: 1.000e+01 DEAL:0::Tpetra second import add: -0->0: 8.000e+00 -1->1: 2.000e+02 - +8.000e+00 2.000e+02 IndexSet: {[0,2]} [0]: 2.000e+00 @@ -37,18 +33,14 @@ IndexSet: {[0,2]} [2]: 1.000e+02 DEAL:1::Tpetra first import add: -0->2: 1.000e+01 -1->3: 1.010e+02 - +1.000e+01 1.010e+02 IndexSet: {0, [3,4]} [0]: 1.000e+00 [3]: 1.010e+02 [4]: 1.100e+01 DEAL:1::Tpetra second import add: -0->2: 3.000e+01 -1->3: 2.010e+02 - +3.000e+01 2.010e+02 IndexSet: {0, [3,4]} [0]: 2.000e+00 @@ -75,18 +67,14 @@ IndexSet: {0, [3,4]} DEAL:2::Tpetra first import add: -0->4: 1.100e+01 -1->5: 1.020e+02 - +1.100e+01 1.020e+02 IndexSet: {0, [5,6]} [0]: 1.000e+00 [5]: 1.020e+02 [6]: 1.200e+01 DEAL:2::Tpetra second import add: -0->4: 3.200e+01 -1->5: 2.020e+02 - +3.200e+01 2.020e+02 IndexSet: {0, [5,6]} [0]: 2.000e+00 @@ -113,17 +101,13 @@ IndexSet: {0, [5,6]} DEAL:3::Tpetra first import add: -0->6: 1.200e+01 -1->7: 1.030e+02 - +1.200e+01 1.030e+02 IndexSet: {0, 7} [0]: 1.000e+00 [7]: 1.030e+02 DEAL:3::Tpetra second import add: -0->6: 3.400e+01 -1->7: 2.030e+02 - +3.400e+01 2.030e+02 IndexSet: {0, 7} [0]: 2.000e+00 From 1bbf0198f12dc8e0238883ec75cf90b4592fb26c Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Fri, 14 Sep 2018 13:59:27 +0200 Subject: [PATCH 148/507] Working --- cmake/config/template-arguments.in | 15 +- cmake/configure/configure_2_trilinos.cmake | 3 +- include/deal.II/dofs/dof_accessor.templates.h | 13 +- .../fe/fe_tools_extrapolate.templates.h | 6 +- .../fe/fe_tools_interpolate.templates.h | 10 +- include/deal.II/lac/read_write_vector.h | 12 +- .../deal.II/lac/read_write_vector.templates.h | 16 +- include/deal.II/lac/trilinos_sparse_matrix.h | 8 + include/deal.II/lac/trilinos_tpetra_vector.h | 80 +++--- include/deal.II/lac/vector_element_access.h | 102 +++++-- include/deal.II/multigrid/mg_transfer.h | 4 +- source/fe/mapping_q1_eulerian.cc | 3 +- source/lac/trilinos_sparse_matrix.cc | 84 ++++-- source/lac/trilinos_tpetra_vector.cc | 267 ++++++++++-------- tests/trilinos/tpetra_vector_01.cc | 21 +- tests/trilinos/tpetra_vector_02.cc | 26 +- tests/trilinos/tpetra_vector_03.cc | 9 +- .../trilinos/tpetra_vector_03.mpirun=2.output | 59 ++++ .../trilinos/tpetra_vector_03.mpirun=4.output | 123 ++++++++ 19 files changed, 607 insertions(+), 254 deletions(-) diff --git a/cmake/config/template-arguments.in b/cmake/config/template-arguments.in index 17a9f2ba9477..8a58e905961b 100644 --- a/cmake/config/template-arguments.in +++ b/cmake/config/template-arguments.in @@ -95,7 +95,8 @@ VECTOR_TYPES := { Vector; @DEAL_II_EXPAND_TRILINOS_MPI_VECTOR@; @DEAL_II_EXPAND_EPETRA_VECTOR@; - @DEAL_II_EXPAND_TPETRA_VECTOR@; + @DEAL_II_EXPAND_TPETRA_VECTOR_DOUBLE@; + @DEAL_II_EXPAND_TPETRA_VECTOR_FLOAT@; @DEAL_II_EXPAND_PETSC_MPI_VECTOR@; @DEAL_II_EXPAND_TRILINOS_MPI_BLOCKVECTOR@; @@ -121,7 +122,8 @@ REAL_VECTOR_TYPES := { Vector; @DEAL_II_EXPAND_TRILINOS_MPI_VECTOR@; @DEAL_II_EXPAND_EPETRA_VECTOR@; - @DEAL_II_EXPAND_TPETRA_VECTOR@; + @DEAL_II_EXPAND_TPETRA_VECTOR_DOUBLE@; + @DEAL_II_EXPAND_TPETRA_VECTOR_FLOAT@; @DEAL_II_EXPAND_PETSC_MPI_VECTOR_REAL@; @DEAL_II_EXPAND_TRILINOS_MPI_BLOCKVECTOR@; @@ -140,7 +142,8 @@ REAL_NONBLOCK_VECTORS := { Vector; @DEAL_II_EXPAND_TRILINOS_MPI_VECTOR@; @DEAL_II_EXPAND_EPETRA_VECTOR@; - @DEAL_II_EXPAND_TPETRA_VECTOR@; + @DEAL_II_EXPAND_TPETRA_VECTOR_DOUBLE@; + @DEAL_II_EXPAND_TPETRA_VECTOR_FLOAT@; @DEAL_II_EXPAND_PETSC_MPI_VECTOR_REAL@; } @@ -148,7 +151,8 @@ REAL_NONBLOCK_VECTORS := { Vector; EXTERNAL_PARALLEL_VECTORS := { @DEAL_II_EXPAND_TRILINOS_MPI_VECTOR@; @DEAL_II_EXPAND_TRILINOS_MPI_BLOCKVECTOR@; @DEAL_II_EXPAND_EPETRA_VECTOR@; - @DEAL_II_EXPAND_TPETRA_VECTOR@; + @DEAL_II_EXPAND_TPETRA_VECTOR_DOUBLE@; + @DEAL_II_EXPAND_TPETRA_VECTOR_FLOAT@; @DEAL_II_EXPAND_PETSC_MPI_VECTOR@; @DEAL_II_EXPAND_PETSC_MPI_BLOCKVECTOR@ } @@ -167,7 +171,8 @@ VECTORS_WITH_MATRIX := { Vector; @DEAL_II_EXPAND_TRILINOS_MPI_VECTOR@; @DEAL_II_EXPAND_EPETRA_VECTOR@; - @DEAL_II_EXPAND_TPETRA_VECTOR@; + @DEAL_II_EXPAND_TPETRA_VECTOR_DOUBLE@; + @DEAL_II_EXPAND_TPETRA_VECTOR_FLOAT@; @DEAL_II_EXPAND_PETSC_MPI_VECTOR@; } diff --git a/cmake/configure/configure_2_trilinos.cmake b/cmake/configure/configure_2_trilinos.cmake index abe66905d82c..661c739b7c7f 100644 --- a/cmake/configure/configure_2_trilinos.cmake +++ b/cmake/configure/configure_2_trilinos.cmake @@ -227,7 +227,8 @@ MACRO(FEATURE_TRILINOS_CONFIGURE_EXTERNAL) SET(DEAL_II_EXPAND_TRILINOS_MPI_VECTOR "TrilinosWrappers::MPI::Vector") IF (TRILINOS_WITH_MPI) SET(DEAL_II_EXPAND_EPETRA_VECTOR "LinearAlgebra::EpetraWrappers::Vector") - SET(DEAL_II_EXPAND_TPETRA_VECTOR "LinearAlgebra::TpetraWrappers::Vector") + SET(DEAL_II_EXPAND_TPETRA_VECTOR_DOUBLE "LinearAlgebra::TpetraWrappers::Vector") + #SET(DEAL_II_EXPAND_TPETRA_VECTOR_FLOAT "LinearAlgebra::TpetraWrappers::Vector") ENDIF() IF(${DEAL_II_TRILINOS_WITH_SACADO}) # Note: Only CMake 3.0 and greater support line continuation with the "\" character diff --git a/include/deal.II/dofs/dof_accessor.templates.h b/include/deal.II/dofs/dof_accessor.templates.h index 73b77c07a57d..9b89e6e31f47 100644 --- a/include/deal.II/dofs/dof_accessor.templates.h +++ b/include/deal.II/dofs/dof_accessor.templates.h @@ -1534,12 +1534,13 @@ namespace internal - template + template static void - extract_subvector_to(const LinearAlgebra::TpetraWrappers::Vector &values, - const types::global_dof_index *cache_begin, - const types::global_dof_index *cache_end, - ForwardIterator local_values_begin) + extract_subvector_to( + const LinearAlgebra::TpetraWrappers::Vector &values, + const types::global_dof_index * cache_begin, + const types::global_dof_index * cache_end, + ForwardIterator local_values_begin) { std::vector sorted_indices_pos = sort_indices(cache_begin, cache_end); @@ -1551,7 +1552,7 @@ namespace internal IndexSet index_set(cache_indices.back() + 1); index_set.add_indices(cache_indices.begin(), cache_indices.end()); index_set.compress(); - LinearAlgebra::ReadWriteVector read_write_vector(index_set); + LinearAlgebra::ReadWriteVector read_write_vector(index_set); read_write_vector.import(values, VectorOperation::insert); // Copy the elements from read_write_vector and reorder them. diff --git a/include/deal.II/fe/fe_tools_extrapolate.templates.h b/include/deal.II/fe/fe_tools_extrapolate.templates.h index 850a4c6216ca..ea76059356c7 100644 --- a/include/deal.II/fe/fe_tools_extrapolate.templates.h +++ b/include/deal.II/fe/fe_tools_extrapolate.templates.h @@ -1581,10 +1581,10 @@ namespace FETools # ifdef DEAL_II_WITH_MPI - template + template void - reinit_distributed(const DoFHandler & dh, - LinearAlgebra::TpetraWrappers::Vector &vector) + reinit_distributed(const DoFHandler & dh, + LinearAlgebra::TpetraWrappers::Vector &vector) { const parallel::distributed::Triangulation *parallel_tria = dynamic_cast< diff --git a/include/deal.II/fe/fe_tools_interpolate.templates.h b/include/deal.II/fe/fe_tools_interpolate.templates.h index e2e9b417fe02..9699c0a9b43d 100644 --- a/include/deal.II/fe/fe_tools_interpolate.templates.h +++ b/include/deal.II/fe/fe_tools_interpolate.templates.h @@ -513,17 +513,17 @@ namespace FETools AssertThrow(false, ExcNotImplemented()); } - template + template void back_interpolate( const DoFHandler &, const AffineConstraints< - typename LinearAlgebra::TpetraWrappers::Vector::value_type> &, - const LinearAlgebra::TpetraWrappers::Vector &, + typename LinearAlgebra::TpetraWrappers::Vector::value_type> &, + const LinearAlgebra::TpetraWrappers::Vector &, const DoFHandler &, const AffineConstraints< - typename LinearAlgebra::TpetraWrappers::Vector::value_type> &, - LinearAlgebra::TpetraWrappers::Vector &) + typename LinearAlgebra::TpetraWrappers::Vector::value_type> &, + LinearAlgebra::TpetraWrappers::Vector &) { AssertThrow(false, ExcNotImplemented()); } diff --git a/include/deal.II/lac/read_write_vector.h b/include/deal.II/lac/read_write_vector.h index 70d89ade7a1c..0ed6f9d829d3 100644 --- a/include/deal.II/lac/read_write_vector.h +++ b/include/deal.II/lac/read_write_vector.h @@ -344,8 +344,8 @@ namespace LinearAlgebra * performance. */ void - import(const TpetraWrappers::Vector &tpetra_vec, - VectorOperation::values operation, + import(const TpetraWrappers::Vector &tpetra_vec, + VectorOperation::values operation, const std::shared_ptr &communication_pattern = std::shared_ptr()); @@ -615,10 +615,10 @@ namespace LinearAlgebra * used directly. */ void - import(const Tpetra::Vector<> &tpetra_vector, - const IndexSet & locally_owned_elements, - VectorOperation::values operation, - const MPI_Comm & mpi_comm, + import(const Tpetra::Vector &tpetra_vector, + const IndexSet & locally_owned_elements, + VectorOperation::values operation, + const MPI_Comm & mpi_comm, const std::shared_ptr &communication_pattern); diff --git a/include/deal.II/lac/read_write_vector.templates.h b/include/deal.II/lac/read_write_vector.templates.h index b4437cfd3fbf..87139aedd776 100644 --- a/include/deal.II/lac/read_write_vector.templates.h +++ b/include/deal.II/lac/read_write_vector.templates.h @@ -509,10 +509,10 @@ namespace LinearAlgebra template void ReadWriteVector::import( - const Tpetra::Vector<> &vector, - const IndexSet & source_elements, - VectorOperation::values operation, - const MPI_Comm & mpi_comm, + const Tpetra::Vector &vector, + const IndexSet & source_elements, + VectorOperation::values operation, + const MPI_Comm & mpi_comm, const std::shared_ptr &communication_pattern) { @@ -554,13 +554,13 @@ namespace LinearAlgebra Tpetra::Export<> tpetra_export(tpetra_comm_pattern->get_tpetra_export()); - Tpetra::Vector<> target_vector(tpetra_export.getSourceMap()); + Tpetra::Vector target_vector(tpetra_export.getSourceMap()); target_vector.doImport(vector, tpetra_export, Tpetra::REPLACE); const auto *new_values = target_vector.getData().get(); const auto size = target_vector.getLocalLength(); - using size_type = std::decay::type; + using size_type = typename std::decay::type; Assert(size == 0 || values != nullptr, ExcInternalError("Export failed.")); AssertDimension(size, stored_elements.n_elements()); @@ -741,8 +741,8 @@ namespace LinearAlgebra template void ReadWriteVector::import( - const LinearAlgebra::TpetraWrappers::Vector &trilinos_vec, - VectorOperation::values operation, + const LinearAlgebra::TpetraWrappers::Vector &trilinos_vec, + VectorOperation::values operation, const std::shared_ptr &communication_pattern) { diff --git a/include/deal.II/lac/trilinos_sparse_matrix.h b/include/deal.II/lac/trilinos_sparse_matrix.h index 006dc3171219..b158a224d493 100644 --- a/include/deal.II/lac/trilinos_sparse_matrix.h +++ b/include/deal.II/lac/trilinos_sparse_matrix.h @@ -1317,6 +1317,14 @@ namespace TrilinosWrappers * initialize the matrix with a sparsity pattern to fix the matrix * structure before inserting elements. */ + template + void + set(const size_type row, + const size_type n_cols, + const size_type *col_indices, + const Number * values, + const bool elide_zero_values = false); + void set(const size_type row, const size_type n_cols, diff --git a/include/deal.II/lac/trilinos_tpetra_vector.h b/include/deal.II/lac/trilinos_tpetra_vector.h index df0b0c99c581..798248703ab4 100644 --- a/include/deal.II/lac/trilinos_tpetra_vector.h +++ b/include/deal.II/lac/trilinos_tpetra_vector.h @@ -51,16 +51,20 @@ namespace LinearAlgebra /** * This class implements a wrapper to the Trilinos distributed vector * class Tpetra::Vector. This class is derived from the - * LinearAlgebra::VectorSpaceVector class. Note however that Tpetra only - * works with Number = double. + * LinearAlgebra::VectorSpaceVector class. * * @ingroup TrilinosWrappers * @ingroup Vectors * @author Daniel Arndt, 2018 */ - class Vector : public VectorSpaceVector, public Subscriptor + template + class Vector : public VectorSpaceVector, public Subscriptor { public: + using value_type = Number; + + using size_type = typename VectorSpaceVector::size_type; + /** * Constructor. Create a vector of dimension zero. */ @@ -97,7 +101,7 @@ namespace LinearAlgebra * copied. */ virtual void - reinit(const VectorSpaceVector &V, + reinit(const VectorSpaceVector &V, const bool omit_zeroing_entries = false) override; /** @@ -113,7 +117,7 @@ namespace LinearAlgebra * only allowed if @p s is equal to zero. */ virtual Vector & - operator=(const double s) override; + operator=(const Number s) override; /** * Imports all the elements present in the vector's IndexSet from the @@ -126,7 +130,7 @@ namespace LinearAlgebra */ virtual void import( - const ReadWriteVector & V, + const ReadWriteVector & V, VectorOperation::values operation, std::shared_ptr communication_pattern = std::shared_ptr()) override; @@ -135,64 +139,64 @@ namespace LinearAlgebra * Multiply the entire vector by a fixed factor. */ virtual Vector & - operator*=(const double factor) override; + operator*=(const Number factor) override; /** * Divide the entire vector by a fixed factor. */ virtual Vector & - operator/=(const double factor) override; + operator/=(const Number factor) override; /** * Add the vector @p V to the present one. */ virtual Vector & - operator+=(const VectorSpaceVector &V) override; + operator+=(const VectorSpaceVector &V) override; /** * Subtract the vector @p V from the present one. */ virtual Vector & - operator-=(const VectorSpaceVector &V) override; + operator-=(const VectorSpaceVector &V) override; /** * Return the scalar product of two vectors. The vectors need to have the * same layout. */ - virtual double - operator*(const VectorSpaceVector &V) const override; + virtual Number + operator*(const VectorSpaceVector &V) const override; /** * Add @p a to all components. Note that @p is a scalar not a vector. */ virtual void - add(const double a) override; + add(const Number a) override; /** * Simple addition of a multiple of a vector, i.e. *this += * a*V. The vectors need to have the same layout. */ virtual void - add(const double a, const VectorSpaceVector &V) override; + add(const Number a, const VectorSpaceVector &V) override; /** * Multiple addition of multiple of a vector, i.e. *this> += * a*V+b*W. The vectors need to have the same layout. */ virtual void - add(const double a, - const VectorSpaceVector &V, - const double b, - const VectorSpaceVector &W) override; + add(const Number a, + const VectorSpaceVector &V, + const Number b, + const VectorSpaceVector &W) override; /** * Scaling and simple addition of a multiple of a vector, i.e. *this * = s*(*this)+a*V. */ virtual void - sadd(const double s, - const double a, - const VectorSpaceVector &V) override; + sadd(const Number s, + const Number a, + const VectorSpaceVector &V) override; /** * Scale each element of this vector by the corresponding element in the @@ -201,13 +205,13 @@ namespace LinearAlgebra * vectors need to have the same layout. */ virtual void - scale(const VectorSpaceVector &scaling_factors) override; + scale(const VectorSpaceVector &scaling_factors) override; /** * Assignment *this = a*V. */ virtual void - equ(const double a, const VectorSpaceVector &V) override; + equ(const Number a, const VectorSpaceVector &V) override; /** * Return whether the vector contains only elements with value zero. @@ -218,28 +222,28 @@ namespace LinearAlgebra /** * Return the mean value of the element of this vector. */ - virtual double + virtual Number mean_value() const override; /** * Return the l1 norm of the vector (i.e., the sum of the * absolute values of all entries among all processors). */ - virtual double + virtual typename LinearAlgebra::VectorSpaceVector::real_type l1_norm() const override; /** * Return the l2 norm of the vector (i.e., the square root of * the sum of the square of all entries among all processors). */ - virtual double + virtual typename LinearAlgebra::VectorSpaceVector::real_type l2_norm() const override; /** * Return the maximum norm of the vector (i.e., the maximum absolute value * among all entries and among all processors). */ - virtual double + virtual typename LinearAlgebra::VectorSpaceVector::real_type linfty_norm() const override; /** @@ -264,10 +268,10 @@ namespace LinearAlgebra * implemented as * $\left=\sum_i v_i \bar{w_i}$. */ - virtual double - add_and_dot(const double a, - const VectorSpaceVector &V, - const VectorSpaceVector &W) override; + virtual Number + add_and_dot(const Number a, + const VectorSpaceVector &V, + const VectorSpaceVector &W) override; /** * This function always returns false and is present only for backward * compatibility. @@ -306,14 +310,14 @@ namespace LinearAlgebra * Return a const reference to the underlying Trilinos * Tpetra::Vector class. */ - const Tpetra::Vector<> & + const Tpetra::Vector & trilinos_vector() const; /** * Return a (modifyable) reference to the underlying Trilinos * Tpetra::Vector class. */ - Tpetra::Vector<> & + Tpetra::Vector & trilinos_vector(); /** @@ -367,7 +371,7 @@ namespace LinearAlgebra /** * Pointer to the actual Tpetra vector object. */ - std::unique_ptr> vector; + std::unique_ptr> vector; /** * IndexSet of the elements of the last imported vector. @@ -383,8 +387,9 @@ namespace LinearAlgebra }; + template inline bool - Vector::has_ghost_elements() const + Vector::has_ghost_elements() const { return false; } @@ -395,8 +400,9 @@ namespace LinearAlgebra /** * Declare dealii::LinearAlgebra::TpetraWrappers::Vector as distributed vector. */ -template <> -struct is_serial_vector : std::false_type +template +struct is_serial_vector> + : std::false_type {}; DEAL_II_NAMESPACE_CLOSE diff --git a/include/deal.II/lac/vector_element_access.h b/include/deal.II/lac/vector_element_access.h index b16826058885..22e541033c52 100644 --- a/include/deal.II/lac/vector_element_access.h +++ b/include/deal.II/lac/vector_element_access.h @@ -127,13 +127,13 @@ namespace internal template <> inline void - ElementAccess::add( - const double value, - const types::global_dof_index i, - LinearAlgebra::TpetraWrappers::Vector &V) + ElementAccess>::add( + const double value, + const types::global_dof_index i, + LinearAlgebra::TpetraWrappers::Vector &V) { // Extract local indices in the vector. - Tpetra::Vector<> vector = V.trilinos_vector(); + Tpetra::Vector vector = V.trilinos_vector(); TrilinosWrappers::types::int_type trilinos_i = vector.getMap()->getLocalElement( static_cast(i)); @@ -144,20 +144,68 @@ namespace internal // We're going to modify the data on host. vector.modify(); vector_1d(trilinos_i) += value; - vector.sync::device_type::memory_space>(); + vector.sync::device_type::memory_space>(); } template <> inline void - ElementAccess::set( - const double value, - const types::global_dof_index i, - LinearAlgebra::TpetraWrappers::Vector &V) + ElementAccess>::add( + const float value, + const types::global_dof_index i, + LinearAlgebra::TpetraWrappers::Vector &V) + { + // Extract local indices in the vector. + Tpetra::Vector vector = V.trilinos_vector(); + TrilinosWrappers::types::int_type trilinos_i = + vector.getMap()->getLocalElement( + static_cast(i)); + + vector.sync(); + auto vector_2d = vector.getLocalView(); + auto vector_1d = Kokkos::subview(vector_2d, Kokkos::ALL(), 0); + // We're going to modify the data on host. + vector.modify(); + vector_1d(trilinos_i) += value; + vector.sync::device_type::memory_space>(); + } + + + + template <> + inline void + ElementAccess>::set( + const double value, + const types::global_dof_index i, + LinearAlgebra::TpetraWrappers::Vector &V) + { + // Extract local indices in the vector. + Tpetra::Vector vector = V.trilinos_vector(); + TrilinosWrappers::types::int_type trilinos_i = + vector.getMap()->getLocalElement( + static_cast(i)); + + vector.sync(); + auto vector_2d = vector.getLocalView(); + auto vector_1d = Kokkos::subview(vector_2d, Kokkos::ALL(), 0); + // We're going to modify the data on host. + vector.modify(); + vector_1d(trilinos_i) = value; + vector.sync::device_type::memory_space>(); + } + + + + template <> + inline void + ElementAccess>::set( + const float value, + const types::global_dof_index i, + LinearAlgebra::TpetraWrappers::Vector &V) { // Extract local indices in the vector. - Tpetra::Vector<> vector = V.trilinos_vector(); + Tpetra::Vector vector = V.trilinos_vector(); TrilinosWrappers::types::int_type trilinos_i = vector.getMap()->getLocalElement( static_cast(i)); @@ -168,18 +216,40 @@ namespace internal // We're going to modify the data on host. vector.modify(); vector_1d(trilinos_i) = value; - vector.sync::device_type::memory_space>(); + vector.sync::device_type::memory_space>(); } + template <> inline double - ElementAccess::get( - const LinearAlgebra::TpetraWrappers::Vector &V, - const types::global_dof_index i) + ElementAccess>::get( + const LinearAlgebra::TpetraWrappers::Vector &V, + const types::global_dof_index i) + { + // Extract local indices in the vector. + Tpetra::Vector vector = V.trilinos_vector(); + TrilinosWrappers::types::int_type trilinos_i = + vector.getMap()->getLocalElement( + static_cast(i)); + + vector.sync(); + auto vector_2d = vector.getLocalView(); + auto vector_1d = Kokkos::subview(vector_2d, Kokkos::ALL(), 0); + // We're going to modify the data on host. + return vector_1d(trilinos_i); + } + + + + template <> + inline float + ElementAccess>::get( + const LinearAlgebra::TpetraWrappers::Vector &V, + const types::global_dof_index i) { // Extract local indices in the vector. - Tpetra::Vector<> vector = V.trilinos_vector(); + Tpetra::Vector vector = V.trilinos_vector(); TrilinosWrappers::types::int_type trilinos_i = vector.getMap()->getLocalElement( static_cast(i)); diff --git a/include/deal.II/multigrid/mg_transfer.h b/include/deal.II/multigrid/mg_transfer.h index e4b4f3db2ac9..961b0223dfc3 100644 --- a/include/deal.II/multigrid/mg_transfer.h +++ b/include/deal.II/multigrid/mg_transfer.h @@ -132,8 +132,8 @@ namespace internal }; # ifdef DEAL_II_WITH_MPI - template <> - struct MatrixSelector + template + struct MatrixSelector> { using Sparsity = ::dealii::TrilinosWrappers::SparsityPattern; using Matrix = ::dealii::TrilinosWrappers::SparseMatrix; diff --git a/source/fe/mapping_q1_eulerian.cc b/source/fe/mapping_q1_eulerian.cc index 666a7bef6e04..3c99fb8c8336 100644 --- a/source/fe/mapping_q1_eulerian.cc +++ b/source/fe/mapping_q1_eulerian.cc @@ -77,7 +77,8 @@ MappingQ1Eulerian::get_vertices( Assert(dof_cell->active() == true, ExcInactiveCell()); // now get the values of the shift vectors at the vertices - Vector mapping_values(shiftmap_dof_handler->get_fe().dofs_per_cell); + Vector mapping_values( + shiftmap_dof_handler->get_fe().dofs_per_cell); dof_cell->get_dof_values(*euler_transform_vectors, mapping_values); for (unsigned int i = 0; i < GeometryInfo::vertices_per_cell; ++i) diff --git a/source/lac/trilinos_sparse_matrix.cc b/source/lac/trilinos_sparse_matrix.cc index 350006da3cca..0996f76053ee 100644 --- a/source/lac/trilinos_sparse_matrix.cc +++ b/source/lac/trilinos_sparse_matrix.cc @@ -48,28 +48,28 @@ namespace TrilinosWrappers namespace internal { template - double * + typename VectorType::value_type * begin(VectorType &V) { return V.begin(); } template - const double * + const typename VectorType::value_type * begin(const VectorType &V) { return V.begin(); } template - double * + typename VectorType::value_type * end(VectorType &V) { return V.end(); } template - const double * + const typename VectorType::value_type * end(const VectorType &V) { return V.end(); @@ -104,31 +104,31 @@ namespace TrilinosWrappers return V.trilinos_vector()[0] + V.trilinos_vector().MyLength(); } - template <> - double * - begin(LinearAlgebra::TpetraWrappers::Vector &V) + template + Number * + begin(LinearAlgebra::TpetraWrappers::Vector &V) { return V.trilinos_vector().getDataNonConst().get(); } - template <> - const double * - begin(const LinearAlgebra::TpetraWrappers::Vector &V) + template + const Number * + begin(const LinearAlgebra::TpetraWrappers::Vector &V) { return V.trilinos_vector().getData().get(); } - template <> - double * - end(LinearAlgebra::TpetraWrappers::Vector &V) + template + Number * + end(LinearAlgebra::TpetraWrappers::Vector &V) { return V.trilinos_vector().getDataNonConst().get() + V.trilinos_vector().getLocalLength(); } - template <> - const double * - end(const LinearAlgebra::TpetraWrappers::Vector &V) + template + const Number * + end(const LinearAlgebra::TpetraWrappers::Vector &V) { return V.trilinos_vector().getData().get() + V.trilinos_vector().getLocalLength(); @@ -1540,6 +1540,22 @@ namespace TrilinosWrappers + template + void + SparseMatrix::set(const size_type row, + const size_type n_cols, + const size_type *col_indices, + const Number * values, + const bool elide_zero_values) + { + std::vector trilinos_values(n_cols); + std::copy(values, values + n_cols, trilinos_values.begin()); + this->set( + row, n_cols, col_indices, trilinos_values.data(), elide_zero_values); + } + + + void SparseMatrix::set(const size_type row, const size_type n_cols, @@ -3476,78 +3492,98 @@ namespace TrilinosWrappers template void SparseMatrix::vmult(MPI::Vector &, const MPI::Vector &) const; + template void SparseMatrix::vmult(dealii::Vector &, const dealii::Vector &) const; + template void SparseMatrix::vmult( dealii::LinearAlgebra::distributed::Vector &, const dealii::LinearAlgebra::distributed::Vector &) const; + # ifdef DEAL_II_WITH_MPI template void SparseMatrix::vmult( - dealii::LinearAlgebra::TpetraWrappers::Vector &, - const dealii::LinearAlgebra::TpetraWrappers::Vector &) const; + dealii::LinearAlgebra::TpetraWrappers::Vector &, + const dealii::LinearAlgebra::TpetraWrappers::Vector &) const; + + /*template void + SparseMatrix::vmult( + dealii::LinearAlgebra::TpetraWrappers::Vector &, + const dealii::LinearAlgebra::TpetraWrappers::Vector &) const;*/ template void SparseMatrix::vmult( dealii::LinearAlgebra::EpetraWrappers::Vector &, const dealii::LinearAlgebra::EpetraWrappers::Vector &) const; # endif + template void SparseMatrix::Tvmult(MPI::Vector &, const MPI::Vector &) const; + template void SparseMatrix::Tvmult(dealii::Vector &, const dealii::Vector &) const; + template void SparseMatrix::Tvmult( dealii::LinearAlgebra::distributed::Vector &, const dealii::LinearAlgebra::distributed::Vector &) const; + # ifdef DEAL_II_WITH_MPI template void SparseMatrix::Tvmult( - dealii::LinearAlgebra::TpetraWrappers::Vector &, - const dealii::LinearAlgebra::TpetraWrappers::Vector &) const; + dealii::LinearAlgebra::TpetraWrappers::Vector &, + const dealii::LinearAlgebra::TpetraWrappers::Vector &) const; template void SparseMatrix::Tvmult( dealii::LinearAlgebra::EpetraWrappers::Vector &, const dealii::LinearAlgebra::EpetraWrappers::Vector &) const; # endif + template void SparseMatrix::vmult_add(MPI::Vector &, const MPI::Vector &) const; + template void SparseMatrix::vmult_add(dealii::Vector &, const dealii::Vector &) const; + template void SparseMatrix::vmult_add( dealii::LinearAlgebra::distributed::Vector &, const dealii::LinearAlgebra::distributed::Vector &) const; + # ifdef DEAL_II_WITH_MPI template void SparseMatrix::vmult_add( - dealii::LinearAlgebra::TpetraWrappers::Vector &, - const dealii::LinearAlgebra::TpetraWrappers::Vector &) const; + dealii::LinearAlgebra::TpetraWrappers::Vector &, + const dealii::LinearAlgebra::TpetraWrappers::Vector &) const; template void SparseMatrix::vmult_add( dealii::LinearAlgebra::EpetraWrappers::Vector &, const dealii::LinearAlgebra::EpetraWrappers::Vector &) const; # endif + template void SparseMatrix::Tvmult_add(MPI::Vector &, const MPI::Vector &) const; + template void SparseMatrix::Tvmult_add(dealii::Vector &, const dealii::Vector &) const; + template void SparseMatrix::Tvmult_add( dealii::LinearAlgebra::distributed::Vector &, const dealii::LinearAlgebra::distributed::Vector &) const; + # ifdef DEAL_II_WITH_MPI template void SparseMatrix::Tvmult_add( - dealii::LinearAlgebra::TpetraWrappers::Vector &, - const dealii::LinearAlgebra::TpetraWrappers::Vector &) const; + dealii::LinearAlgebra::TpetraWrappers::Vector &, + const dealii::LinearAlgebra::TpetraWrappers::Vector &) const; template void SparseMatrix::Tvmult_add( diff --git a/source/lac/trilinos_tpetra_vector.cc b/source/lac/trilinos_tpetra_vector.cc index 5e3c00b53ad4..88324e6d53a7 100644 --- a/source/lac/trilinos_tpetra_vector.cc +++ b/source/lac/trilinos_tpetra_vector.cc @@ -40,37 +40,41 @@ namespace LinearAlgebra { namespace TpetraWrappers { - Vector::Vector() - : vector(new Tpetra::Vector<>(Teuchos::RCP>( + template + Vector::Vector() + : vector(new Tpetra::Vector(Teuchos::RCP>( new Tpetra::Map<>(0, 0, Utilities::Trilinos::tpetra_comm_self())))) {} - Vector::Vector(const Vector &V) + template + Vector::Vector(const Vector &V) : Subscriptor() - , vector(new Tpetra::Vector<>(V.trilinos_vector(), Teuchos::Copy)) + , vector(new Tpetra::Vector(V.trilinos_vector(), Teuchos::Copy)) {} - Vector::Vector(const IndexSet ¶llel_partitioner, - const MPI_Comm &communicator) - : vector(new Tpetra::Vector<>(Teuchos::rcp(new Tpetra::Map<>( + template + Vector::Vector(const IndexSet ¶llel_partitioner, + const MPI_Comm &communicator) + : vector(new Tpetra::Vector(Teuchos::rcp(new Tpetra::Map<>( parallel_partitioner.make_tpetra_map(communicator, false))))) {} + template void - Vector::reinit(const IndexSet ¶llel_partitioner, - const MPI_Comm &communicator, - const bool omit_zeroing_entries) + Vector::reinit(const IndexSet ¶llel_partitioner, + const MPI_Comm &communicator, + const bool omit_zeroing_entries) { Tpetra::Map<> input_map = parallel_partitioner.make_tpetra_map(communicator, false); if (vector->getMap()->isSameAs(input_map) == false) - vector = std_cxx14::make_unique>( + vector = std_cxx14::make_unique>( Teuchos::rcp(new Tpetra::Map<>(input_map))); else if (omit_zeroing_entries == false) { @@ -80,16 +84,17 @@ namespace LinearAlgebra + template void - Vector::reinit(const VectorSpaceVector &V, - const bool omit_zeroing_entries) + Vector::reinit(const VectorSpaceVector &V, + const bool omit_zeroing_entries) { // Check that casting will work. - Assert(dynamic_cast(&V) != nullptr, + Assert(dynamic_cast *>(&V) != nullptr, ExcVectorTypeNotCompatible()); // Downcast V. If fails, throws an exception. - const Vector &down_V = dynamic_cast(V); + const Vector &down_V = dynamic_cast &>(V); reinit(down_V.locally_owned_elements(), down_V.get_mpi_communicator(), @@ -98,8 +103,9 @@ namespace LinearAlgebra - Vector & - Vector::operator=(const Vector &V) + template + Vector & + Vector::operator=(const Vector &V) { // Distinguish three cases: // - First case: both vectors have the same layout. @@ -119,8 +125,8 @@ namespace LinearAlgebra Tpetra::REPLACE); } else - vector = - std_cxx14::make_unique>(V.trilinos_vector()); + vector = std_cxx14::make_unique>( + V.trilinos_vector()); } return *this; @@ -128,10 +134,12 @@ namespace LinearAlgebra - Vector & - Vector::operator=(const double s) + template + Vector & + Vector::operator=(const Number s) { - Assert(s == 0., ExcMessage("Only 0 can be assigned to a vector.")); + Assert(s == Number(0.), + ExcMessage("Only 0 can be assigned to a vector.")); vector->putScalar(s); @@ -140,9 +148,10 @@ namespace LinearAlgebra + template void - Vector::import( - const ReadWriteVector & V, + Vector::import( + const ReadWriteVector & V, VectorOperation::values operation, std::shared_ptr communication_pattern) { @@ -177,17 +186,18 @@ namespace LinearAlgebra } Tpetra::Export<> tpetra_export(tpetra_comm_pattern->get_tpetra_export()); - Tpetra::Vector<> source_vector(tpetra_export.getSourceMap()); + Tpetra::Vector source_vector(tpetra_export.getSourceMap()); - source_vector.sync(); - auto x_2d = source_vector.getLocalView(); + source_vector.template sync(); + auto x_2d = source_vector.template getLocalView(); auto x_1d = Kokkos::subview(x_2d, Kokkos::ALL(), 0); - source_vector.modify(); + source_vector.template modify(); const size_t localLength = source_vector.getLocalLength(); auto values_it = V.begin(); for (size_t k = 0; k < localLength; ++k) x_1d(k) = *values_it++; - source_vector.sync::device_type::memory_space>(); + source_vector.template sync< + typename Tpetra::Vector::device_type::memory_space>(); if (operation == VectorOperation::insert) vector->doExport(source_vector, tpetra_export, Tpetra::REPLACE); else if (operation == VectorOperation::add) @@ -198,8 +208,9 @@ namespace LinearAlgebra - Vector & - Vector::operator*=(const double factor) + template + Vector & + Vector::operator*=(const Number factor) { AssertIsFinite(factor); vector->scale(factor); @@ -209,27 +220,29 @@ namespace LinearAlgebra - Vector & - Vector::operator/=(const double factor) + template + Vector & + Vector::operator/=(const Number factor) { AssertIsFinite(factor); - Assert(factor != 0., ExcZero()); - *this *= 1. / factor; + Assert(factor != Number(0.), ExcZero()); + *this *= Number(1.) / factor; return *this; } - Vector & - Vector::operator+=(const VectorSpaceVector &V) + template + Vector & + Vector::operator+=(const VectorSpaceVector &V) { // Check that casting will work. - Assert(dynamic_cast(&V) != nullptr, + Assert(dynamic_cast *>(&V) != nullptr, ExcVectorTypeNotCompatible()); // Downcast V. If fails, throws an exception. - const Vector &down_V = dynamic_cast(V); + const Vector &down_V = dynamic_cast &>(V); // If the maps are the same we can Update right away. if (vector->getMap()->isSameAs(*(down_V.trilinos_vector().getMap()))) { @@ -247,8 +260,8 @@ namespace LinearAlgebra data_exchange, Tpetra::ADD);*/ - Tpetra::Vector<> dummy(vector->getMap(), false); - Tpetra::Import<> data_exchange(dummy.getMap(), + Tpetra::Vector dummy(vector->getMap(), false); + Tpetra::Import<> data_exchange(dummy.getMap(), down_V.trilinos_vector().getMap()); dummy.doExport(down_V.trilinos_vector(), @@ -263,8 +276,9 @@ namespace LinearAlgebra - Vector & - Vector::operator-=(const VectorSpaceVector &V) + template + Vector & + Vector::operator-=(const VectorSpaceVector &V) { this->add(-1., V); @@ -273,14 +287,15 @@ namespace LinearAlgebra - double Vector::operator*(const VectorSpaceVector &V) const + template + Number Vector::operator*(const VectorSpaceVector &V) const { // Check that casting will work. - Assert(dynamic_cast(&V) != nullptr, + Assert(dynamic_cast *>(&V) != nullptr, ExcVectorTypeNotCompatible()); // Downcast V. If fails, throws an exception. - const Vector &down_V = dynamic_cast(V); + const Vector &down_V = dynamic_cast &>(V); Assert(this->size() == down_V.size(), ExcDimensionMismatch(this->size(), down_V.size())); Assert(vector->getMap()->isSameAs(*down_V.trilinos_vector().getMap()), @@ -291,34 +306,37 @@ namespace LinearAlgebra + template void - Vector::add(const double a) + Vector::add(const Number a) { AssertIsFinite(a); - vector->sync(); - auto vector_2d = vector->getLocalView(); + vector->template sync(); + auto vector_2d = vector->template getLocalView(); auto vector_1d = Kokkos::subview(vector_2d, Kokkos::ALL(), 0); - vector->modify(); + vector->template modify(); const size_t localLength = vector->getLocalLength(); for (size_t k = 0; k < localLength; ++k) { vector_1d(k) += a; } - vector->sync::device_type::memory_space>(); + vector->template sync< + typename Tpetra::Vector::device_type::memory_space>(); } + template void - Vector::add(const double a, const VectorSpaceVector &V) + Vector::add(const Number a, const VectorSpaceVector &V) { // Check that casting will work. - Assert(dynamic_cast(&V) != nullptr, + Assert(dynamic_cast *>(&V) != nullptr, ExcVectorTypeNotCompatible()); // Downcast V. If fails, throws an exception. - const Vector &down_V = dynamic_cast(V); + const Vector &down_V = dynamic_cast &>(V); AssertIsFinite(a); Assert(vector->getMap()->isSameAs(*(down_V.trilinos_vector().getMap())), ExcDifferentParallelPartitioning()); @@ -328,23 +346,24 @@ namespace LinearAlgebra + template void - Vector::add(const double a, - const VectorSpaceVector &V, - const double b, - const VectorSpaceVector &W) + Vector::add(const Number a, + const VectorSpaceVector &V, + const Number b, + const VectorSpaceVector &W) { // Check that casting will work. - Assert(dynamic_cast(&V) != nullptr, + Assert(dynamic_cast *>(&V) != nullptr, ExcVectorTypeNotCompatible()); // Check that casting will work. - Assert(dynamic_cast(&W) != nullptr, + Assert(dynamic_cast *>(&W) != nullptr, ExcVectorTypeNotCompatible()); // Downcast V. If fails, throws an exception. - const Vector &down_V = dynamic_cast(V); + const Vector &down_V = dynamic_cast &>(V); // Downcast W. If fails, throws an exception. - const Vector &down_W = dynamic_cast(W); + const Vector &down_W = dynamic_cast &>(W); Assert(vector->getMap()->isSameAs(*(down_V.trilinos_vector().getMap())), ExcDifferentParallelPartitioning()); Assert(vector->getMap()->isSameAs(*(down_W.trilinos_vector().getMap())), @@ -358,35 +377,37 @@ namespace LinearAlgebra + template void - Vector::sadd(const double s, - const double a, - const VectorSpaceVector &V) + Vector::sadd(const Number s, + const Number a, + const VectorSpaceVector &V) { // Check that casting will work. - Assert(dynamic_cast(&V) != nullptr, + Assert(dynamic_cast *>(&V) != nullptr, ExcVectorTypeNotCompatible()); *this *= s; // Downcast V. It fails, throws an exception. - const Vector &down_V = dynamic_cast(V); - Vector tmp(down_V); + const Vector &down_V = dynamic_cast &>(V); + Vector tmp(down_V); tmp *= a; *this += tmp; } + template void - Vector::scale(const VectorSpaceVector &scaling_factors) + Vector::scale(const VectorSpaceVector &scaling_factors) { // Check that casting will work. - Assert(dynamic_cast(&scaling_factors) != nullptr, + Assert(dynamic_cast *>(&scaling_factors) != nullptr, ExcVectorTypeNotCompatible()); // Downcast scaling_factors. If fails, throws an exception. - const Vector &down_scaling_factors = - dynamic_cast(scaling_factors); + const Vector &down_scaling_factors = + dynamic_cast &>(scaling_factors); Assert(vector->getMap()->isSameAs( *(down_scaling_factors.trilinos_vector().getMap())), ExcDifferentParallelPartitioning()); @@ -399,15 +420,16 @@ namespace LinearAlgebra + template void - Vector::equ(const double a, const VectorSpaceVector &V) + Vector::equ(const Number a, const VectorSpaceVector &V) { // Check that casting will work. - Assert(dynamic_cast(&V) != nullptr, + Assert(dynamic_cast *>(&V) != nullptr, ExcVectorTypeNotCompatible()); // Downcast V. If fails, throws an exception. - const Vector &down_V = dynamic_cast(V); + const Vector &down_V = dynamic_cast &>(V); // If we don't have the same map, copy. if (vector->getMap()->isSameAs(*down_V.trilinos_vector().getMap()) == false) @@ -421,18 +443,19 @@ namespace LinearAlgebra + template bool - Vector::all_zero() const + Vector::all_zero() const { // get a representation of the vector and // loop over all the elements - double * start_ptr = vector->getDataNonConst().get(); - const double *ptr = start_ptr, + Number * start_ptr = vector->getDataNonConst().get(); + const Number *ptr = start_ptr, *eptr = start_ptr + vector->getLocalLength(); unsigned int flag = 0; while (ptr != eptr) { - if (*ptr != 0) + if (*ptr != Number(0)) { flag = 1; break; @@ -453,42 +476,47 @@ namespace LinearAlgebra - double - Vector::mean_value() const + template + Number + Vector::mean_value() const { return vector->meanValue(); } - double - Vector::l1_norm() const + template + typename LinearAlgebra::VectorSpaceVector::real_type + Vector::l1_norm() const { return vector->norm1(); } - double - Vector::l2_norm() const + template + typename LinearAlgebra::VectorSpaceVector::real_type + Vector::l2_norm() const { return vector->norm2(); } - double - Vector::linfty_norm() const + template + typename LinearAlgebra::VectorSpaceVector::real_type + Vector::linfty_norm() const { return vector->normInf(); } - double - Vector::add_and_dot(const double a, - const VectorSpaceVector &V, - const VectorSpaceVector &W) + template + Number + Vector::add_and_dot(const Number a, + const VectorSpaceVector &V, + const VectorSpaceVector &W) { this->add(a, V); @@ -497,16 +525,18 @@ namespace LinearAlgebra - Vector::size_type - Vector::size() const + template + typename Vector::size_type + Vector::size() const { return vector->getGlobalLength(); } + template MPI_Comm - Vector::get_mpi_communicator() const + Vector::get_mpi_communicator() const { const auto tpetra_comm = dynamic_cast *>( vector->getMap()->getComm().get()); @@ -516,21 +546,17 @@ namespace LinearAlgebra + template ::dealii::IndexSet - Vector::locally_owned_elements() const + Vector::locally_owned_elements() const { IndexSet is(size()); // easy case: local range is contiguous if (vector->getMap()->isContiguous()) { -# ifndef DEAL_II_WITH_64BIT_INDICES is.add_range(vector->getMap()->getMinGlobalIndex(), vector->getMap()->getMaxGlobalIndex() + 1); -# else - is.add_range(vector->getMap()->getMinGlobalIndex(), - vector->getMap()->getMaxGlobalIndex() + 1); -# endif } else if (vector->getLocalLength() > 0) { @@ -546,27 +572,30 @@ namespace LinearAlgebra - const Tpetra::Vector<> & - Vector::trilinos_vector() const + template + const Tpetra::Vector & + Vector::trilinos_vector() const { return *vector; } - Tpetra::Vector<> & - Vector::trilinos_vector() + template + Tpetra::Vector & + Vector::trilinos_vector() { return *vector; } + template void - Vector::print(std::ostream & out, - const unsigned int precision, - const bool scientific, - const bool across) const + Vector::print(std::ostream & out, + const unsigned int precision, + const bool scientific, + const bool across) const { AssertThrow(out, ExcIO()); boost::io::ios_flags_saver restore_flags(out); @@ -581,9 +610,9 @@ namespace LinearAlgebra else out.setf(std::ios::fixed, std::ios::floatfield); - vector->sync(); - auto vector_2d = vector->getLocalView(); - auto vector_1d = Kokkos::subview(vector_2d, Kokkos::ALL(), 0); + vector->template sync(); + auto vector_2d = vector->template getLocalView(); + auto vector_1d = Kokkos::subview(vector_2d, Kokkos::ALL(), 0); const size_t local_length = vector->getLocalLength(); if (across) @@ -601,25 +630,33 @@ namespace LinearAlgebra + template std::size_t - Vector::memory_consumption() const + Vector::memory_consumption() const { return sizeof(*this) + vector->getLocalLength() * - (sizeof(double) + sizeof(TrilinosWrappers::types::int_type)); + (sizeof(Number) + sizeof(TrilinosWrappers::types::int_type)); } + template void - Vector::create_tpetra_comm_pattern(const IndexSet &source_index_set, - const MPI_Comm &mpi_comm) + Vector::create_tpetra_comm_pattern(const IndexSet &source_index_set, + const MPI_Comm &mpi_comm) { source_stored_elements = source_index_set; tpetra_comm_pattern = std::make_shared( locally_owned_elements(), source_index_set, mpi_comm); } + + template class Vector; + template class Vector; + template class Vector>; + template class Vector>; + } // namespace TpetraWrappers } // namespace LinearAlgebra diff --git a/tests/trilinos/tpetra_vector_01.cc b/tests/trilinos/tpetra_vector_01.cc index c10ac87bb1e3..ba39dfa34e84 100644 --- a/tests/trilinos/tpetra_vector_01.cc +++ b/tests/trilinos/tpetra_vector_01.cc @@ -26,7 +26,7 @@ // Check LinearAlgebra::TpetraWrappers::Vector assignment and import - +template void test() { @@ -45,10 +45,10 @@ test() } parallel_partitioner_1.compress(); parallel_partitioner_2.compress(); - LinearAlgebra::TpetraWrappers::Vector a; - LinearAlgebra::TpetraWrappers::Vector b(parallel_partitioner_1, - MPI_COMM_WORLD); - LinearAlgebra::TpetraWrappers::Vector c(b); + LinearAlgebra::TpetraWrappers::Vector a; + LinearAlgebra::TpetraWrappers::Vector b(parallel_partitioner_1, + MPI_COMM_WORLD); + LinearAlgebra::TpetraWrappers::Vector c(b); AssertThrow(a.size() == 0, ExcMessage("Vector has the wrong size.")); AssertThrow(b.size() == 10, ExcMessage("Vector has the wrong size.")); @@ -69,9 +69,9 @@ test() read_write_index_set.add_range(4, 10); read_write_index_set.compress(); - LinearAlgebra::ReadWriteVector read_write_1(read_write_index_set); - LinearAlgebra::ReadWriteVector read_write_2(read_write_index_set); - LinearAlgebra::ReadWriteVector read_write_3(read_write_index_set); + LinearAlgebra::ReadWriteVector read_write_1(read_write_index_set); + LinearAlgebra::ReadWriteVector read_write_2(read_write_index_set); + LinearAlgebra::ReadWriteVector read_write_3(read_write_index_set); if (rank == 0) { for (unsigned int i = 0; i < 6; ++i) @@ -204,7 +204,7 @@ test() b.import(read_write_1, VectorOperation::insert); c.import(read_write_1, VectorOperation::insert); - const double val = b * c; + const Number val = b * c; AssertThrow(val == 285., ExcMessage("Problem in operator *.")); } @@ -217,7 +217,8 @@ main(int argc, char **argv) Utilities::MPI::MPI_InitFinalize mpi_init(argc, argv, 1); - test(); + test(); + test(); deallog << "OK" << std::endl; diff --git a/tests/trilinos/tpetra_vector_02.cc b/tests/trilinos/tpetra_vector_02.cc index 8e4875353044..a775c7ec3025 100644 --- a/tests/trilinos/tpetra_vector_02.cc +++ b/tests/trilinos/tpetra_vector_02.cc @@ -26,6 +26,7 @@ // Check LinearAlgebra::TpetraWrappers::Vector add and sadd. +template void test() { @@ -44,12 +45,12 @@ test() } parallel_partitioner_1.compress(); parallel_partitioner_2.compress(); - LinearAlgebra::TpetraWrappers::Vector a(parallel_partitioner_1, - MPI_COMM_WORLD); - LinearAlgebra::TpetraWrappers::Vector b(parallel_partitioner_1, - MPI_COMM_WORLD); - LinearAlgebra::TpetraWrappers::Vector c(parallel_partitioner_2, - MPI_COMM_WORLD); + LinearAlgebra::TpetraWrappers::Vector a(parallel_partitioner_1, + MPI_COMM_WORLD); + LinearAlgebra::TpetraWrappers::Vector b(parallel_partitioner_1, + MPI_COMM_WORLD); + LinearAlgebra::TpetraWrappers::Vector c(parallel_partitioner_2, + MPI_COMM_WORLD); IndexSet read_write_index_set(10); if (rank == 0) @@ -58,9 +59,9 @@ test() read_write_index_set.add_range(5, 10); read_write_index_set.compress(); - LinearAlgebra::ReadWriteVector read_write_1(read_write_index_set); - LinearAlgebra::ReadWriteVector read_write_2(read_write_index_set); - LinearAlgebra::ReadWriteVector read_write_3(read_write_index_set); + LinearAlgebra::ReadWriteVector read_write_1(read_write_index_set); + LinearAlgebra::ReadWriteVector read_write_2(read_write_index_set); + LinearAlgebra::ReadWriteVector read_write_3(read_write_index_set); if (rank == 0) { for (unsigned int i = 0; i < 5; ++i) @@ -188,14 +189,14 @@ test() AssertThrow(b.l1_norm() == 95., ExcMessage("Problem in l1_norm.")); - const double eps = 1e-6; + const Number eps = 1e-6; AssertThrow(std::fabs(b.l2_norm() - 31.3847096) < eps, ExcMessage("Problem in l2_norm")); AssertThrow(b.linfty_norm() == 14., ExcMessage("Problem in linfty_norm.")); a.import(read_write_1, VectorOperation::insert); - const double val = a.add_and_dot(2., a, b); + const Number val = a.add_and_dot(2., a, b); AssertThrow(val == 1530., ExcMessage("Problem in add_and_dot")); } @@ -208,7 +209,8 @@ main(int argc, char **argv) Utilities::MPI::MPI_InitFinalize mpi_init(argc, argv, 1); - test(); + test(); + test(); deallog << "OK" << std::endl; diff --git a/tests/trilinos/tpetra_vector_03.cc b/tests/trilinos/tpetra_vector_03.cc index 4927aaedb82a..650296a4913a 100644 --- a/tests/trilinos/tpetra_vector_03.cc +++ b/tests/trilinos/tpetra_vector_03.cc @@ -28,6 +28,7 @@ #include "../tests.h" +template void test() { @@ -38,7 +39,8 @@ test() locally_owned.add_range(my_id * 2, my_id * 2 + 2); locally_owned.compress(); - LinearAlgebra::TpetraWrappers::Vector v(locally_owned, MPI_COMM_WORLD); + LinearAlgebra::TpetraWrappers::Vector v(locally_owned, + MPI_COMM_WORLD); IndexSet workaround_set(n_procs * 2); unsigned int my_first_index = (my_id * 2 + 2) % (n_procs * 2); @@ -47,7 +49,7 @@ test() workaround_set.add_index(my_second_index); workaround_set.add_index(0); workaround_set.compress(); - LinearAlgebra::ReadWriteVector rw_vector(workaround_set); + LinearAlgebra::ReadWriteVector rw_vector(workaround_set); rw_vector(my_first_index) = my_id + 10; rw_vector(my_second_index) = my_id + 100; @@ -97,5 +99,6 @@ main(int argc, char **argv) argc, argv, testing_max_num_threads()); MPILogInitAll log; - test(); + test(); + test(); } diff --git a/tests/trilinos/tpetra_vector_03.mpirun=2.output b/tests/trilinos/tpetra_vector_03.mpirun=2.output index 638319c2f1c3..e94f192176bc 100644 --- a/tests/trilinos/tpetra_vector_03.mpirun=2.output +++ b/tests/trilinos/tpetra_vector_03.mpirun=2.output @@ -31,7 +31,66 @@ IndexSet: {[0,2]} [0]: 4.000e+00 [1]: 2.000e+02 [2]: 1.000e+02 +DEAL:0::Tpetra first import add: +2.000e+00 1.000e+02 +IndexSet: {[0,2]} + +[0]: 1.000e+00 +[1]: 1.000e+02 +[2]: 1.000e+01 +DEAL:0::Tpetra second import add: +4.000e+00 2.000e+02 +IndexSet: {[0,2]} + +[0]: 2.000e+00 +[1]: 2.000e+02 +[2]: 2.000e+01 +DEAL:0::ReadWrite import add: +IndexSet: {[0,2]} + +[0]: 6.000e+00 +[1]: 4.000e+02 +[2]: 5.000e+01 +DEAL:0::ReadWrite import min: +IndexSet: {[0,2]} +[0]: 4.000e+00 +[1]: 1.000e+00 +[2]: 3.000e+01 +DEAL:0::ReadWrite import max: +IndexSet: {[0,2]} + +[0]: 4.000e+00 +[1]: 2.000e+02 +[2]: 1.000e+02 + +DEAL:1::Tpetra first import add: +1.000e+01 1.010e+02 +IndexSet: {0, 3} + +[0]: 1.000e+00 +[3]: 1.010e+02 +DEAL:1::Tpetra second import add: +3.000e+01 2.010e+02 +IndexSet: {0, 3} + +[0]: 2.000e+00 +[3]: 2.010e+02 +DEAL:1::ReadWrite import add: +IndexSet: {0, 3} + +[0]: 6.000e+00 +[3]: 4.020e+02 +DEAL:1::ReadWrite import min: +IndexSet: {0, 3} + +[0]: 4.000e+00 +[3]: 1.000e+00 +DEAL:1::ReadWrite import max: +IndexSet: {0, 3} + +[0]: 4.000e+00 +[3]: 2.010e+02 DEAL:1::Tpetra first import add: 1.000e+01 1.010e+02 IndexSet: {0, 3} diff --git a/tests/trilinos/tpetra_vector_03.mpirun=4.output b/tests/trilinos/tpetra_vector_03.mpirun=4.output index f70ed13b09e8..5fbf8dea2d1f 100644 --- a/tests/trilinos/tpetra_vector_03.mpirun=4.output +++ b/tests/trilinos/tpetra_vector_03.mpirun=4.output @@ -28,6 +28,38 @@ IndexSet: {[0,2]} DEAL:0::ReadWrite import max: IndexSet: {[0,2]} +[0]: 8.000e+00 +[1]: 2.000e+02 +[2]: 1.000e+02 +DEAL:0::Tpetra first import add: +4.000e+00 1.000e+02 +IndexSet: {[0,2]} + +[0]: 1.000e+00 +[1]: 1.000e+02 +[2]: 1.000e+01 +DEAL:0::Tpetra second import add: +8.000e+00 2.000e+02 +IndexSet: {[0,2]} + +[0]: 2.000e+00 +[1]: 2.000e+02 +[2]: 2.000e+01 +DEAL:0::ReadWrite import add: +IndexSet: {[0,2]} + +[0]: 1.000e+01 +[1]: 4.000e+02 +[2]: 5.000e+01 +DEAL:0::ReadWrite import min: +IndexSet: {[0,2]} + +[0]: 4.000e+00 +[1]: 1.000e+00 +[2]: 3.000e+01 +DEAL:0::ReadWrite import max: +IndexSet: {[0,2]} + [0]: 8.000e+00 [1]: 2.000e+02 [2]: 1.000e+02 @@ -61,6 +93,38 @@ IndexSet: {0, [3,4]} DEAL:1::ReadWrite import max: IndexSet: {0, [3,4]} +[0]: 8.000e+00 +[3]: 2.010e+02 +[4]: 1.010e+02 +DEAL:1::Tpetra first import add: +1.000e+01 1.010e+02 +IndexSet: {0, [3,4]} + +[0]: 1.000e+00 +[3]: 1.010e+02 +[4]: 1.100e+01 +DEAL:1::Tpetra second import add: +3.000e+01 2.010e+02 +IndexSet: {0, [3,4]} + +[0]: 2.000e+00 +[3]: 2.010e+02 +[4]: 2.100e+01 +DEAL:1::ReadWrite import add: +IndexSet: {0, [3,4]} + +[0]: 1.000e+01 +[3]: 4.020e+02 +[4]: 5.300e+01 +DEAL:1::ReadWrite import min: +IndexSet: {0, [3,4]} + +[0]: 4.000e+00 +[3]: 1.000e+00 +[4]: 3.200e+01 +DEAL:1::ReadWrite import max: +IndexSet: {0, [3,4]} + [0]: 8.000e+00 [3]: 2.010e+02 [4]: 1.010e+02 @@ -98,8 +162,67 @@ IndexSet: {0, [5,6]} [0]: 8.000e+00 [5]: 2.020e+02 [6]: 1.020e+02 +DEAL:2::Tpetra first import add: +1.100e+01 1.020e+02 +IndexSet: {0, [5,6]} +[0]: 1.000e+00 +[5]: 1.020e+02 +[6]: 1.200e+01 +DEAL:2::Tpetra second import add: +3.200e+01 2.020e+02 +IndexSet: {0, [5,6]} +[0]: 2.000e+00 +[5]: 2.020e+02 +[6]: 2.200e+01 +DEAL:2::ReadWrite import add: +IndexSet: {0, [5,6]} + +[0]: 1.000e+01 +[5]: 4.040e+02 +[6]: 5.600e+01 +DEAL:2::ReadWrite import min: +IndexSet: {0, [5,6]} + +[0]: 4.000e+00 +[5]: 1.000e+00 +[6]: 3.400e+01 +DEAL:2::ReadWrite import max: +IndexSet: {0, [5,6]} + +[0]: 8.000e+00 +[5]: 2.020e+02 +[6]: 1.020e+02 + + +DEAL:3::Tpetra first import add: +1.200e+01 1.030e+02 +IndexSet: {0, 7} + +[0]: 1.000e+00 +[7]: 1.030e+02 +DEAL:3::Tpetra second import add: +3.400e+01 2.030e+02 +IndexSet: {0, 7} + +[0]: 2.000e+00 +[7]: 2.030e+02 +DEAL:3::ReadWrite import add: +IndexSet: {0, 7} + +[0]: 1.000e+01 +[7]: 4.060e+02 +DEAL:3::ReadWrite import min: +IndexSet: {0, 7} + +[0]: 4.000e+00 +[7]: 1.000e+00 +DEAL:3::ReadWrite import max: +IndexSet: {0, 7} + +[0]: 8.000e+00 +[7]: 2.030e+02 DEAL:3::Tpetra first import add: 1.200e+01 1.030e+02 IndexSet: {0, 7} From 36447358f536ab190b3c81d06616cdf718db17d7 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Fri, 14 Sep 2018 17:34:33 +0200 Subject: [PATCH 149/507] Also instantiate for value_type float --- cmake/configure/configure_2_trilinos.cmake | 2 +- include/deal.II/lac/trilinos_sparse_matrix.h | 56 ++++++++++++--- source/lac/trilinos_sparse_matrix.cc | 76 +++++++++++++------- 3 files changed, 97 insertions(+), 37 deletions(-) diff --git a/cmake/configure/configure_2_trilinos.cmake b/cmake/configure/configure_2_trilinos.cmake index 661c739b7c7f..c159fe255270 100644 --- a/cmake/configure/configure_2_trilinos.cmake +++ b/cmake/configure/configure_2_trilinos.cmake @@ -228,7 +228,7 @@ MACRO(FEATURE_TRILINOS_CONFIGURE_EXTERNAL) IF (TRILINOS_WITH_MPI) SET(DEAL_II_EXPAND_EPETRA_VECTOR "LinearAlgebra::EpetraWrappers::Vector") SET(DEAL_II_EXPAND_TPETRA_VECTOR_DOUBLE "LinearAlgebra::TpetraWrappers::Vector") - #SET(DEAL_II_EXPAND_TPETRA_VECTOR_FLOAT "LinearAlgebra::TpetraWrappers::Vector") + SET(DEAL_II_EXPAND_TPETRA_VECTOR_FLOAT "LinearAlgebra::TpetraWrappers::Vector") ENDIF() IF(${DEAL_II_TRILINOS_WITH_SACADO}) # Note: Only CMake 3.0 and greater support line continuation with the "\" character diff --git a/include/deal.II/lac/trilinos_sparse_matrix.h b/include/deal.II/lac/trilinos_sparse_matrix.h index b158a224d493..2ae42c5ef157 100644 --- a/include/deal.II/lac/trilinos_sparse_matrix.h +++ b/include/deal.II/lac/trilinos_sparse_matrix.h @@ -1325,13 +1325,6 @@ namespace TrilinosWrappers const Number * values, const bool elide_zero_values = false); - void - set(const size_type row, - const size_type n_cols, - const size_type * col_indices, - const TrilinosScalar *values, - const bool elide_zero_values = false); - /** * Add @p value to the element (i,j). * @@ -1588,7 +1581,13 @@ namespace TrilinosWrappers * distributed. Otherwise, an exception will be thrown. */ template - void + typename std::enable_if::value>::type + vmult(VectorType &dst, const VectorType &src) const; + + template + typename std::enable_if::value>::type vmult(VectorType &dst, const VectorType &src) const; /** @@ -1602,7 +1601,13 @@ namespace TrilinosWrappers * see the discussion about @p VectorType in vmult(). */ template - void + typename std::enable_if::value>::type + Tvmult(VectorType &dst, const VectorType &src) const; + + template + typename std::enable_if::value>::type Tvmult(VectorType &dst, const VectorType &src) const; /** @@ -2992,6 +2997,32 @@ namespace TrilinosWrappers // Inline the set() and add() functions, since they will be called // frequently, and the compiler can optimize away some unnecessary loops // when the sizes are given at compile time. + template <> + void + SparseMatrix::set(const size_type row, + const size_type n_cols, + const size_type * col_indices, + const TrilinosScalar *values, + const bool elide_zero_values); + + + + template + void + SparseMatrix::set(const size_type row, + const size_type n_cols, + const size_type *col_indices, + const Number * values, + const bool elide_zero_values) + { + std::vector trilinos_values(n_cols); + std::copy(values, values + n_cols, trilinos_values.begin()); + this->set( + row, n_cols, col_indices, trilinos_values.data(), elide_zero_values); + } + + + inline void SparseMatrix::set(const size_type i, const size_type j, @@ -3298,6 +3329,13 @@ namespace TrilinosWrappers } // namespace LinearOperatorImplementation } // namespace internal + template <> + void + SparseMatrix::set(const size_type row, + const size_type n_cols, + const size_type * col_indices, + const TrilinosScalar *values, + const bool elide_zero_values); # endif // DOXYGEN } /* namespace TrilinosWrappers */ diff --git a/source/lac/trilinos_sparse_matrix.cc b/source/lac/trilinos_sparse_matrix.cc index 0996f76053ee..250a6d051918 100644 --- a/source/lac/trilinos_sparse_matrix.cc +++ b/source/lac/trilinos_sparse_matrix.cc @@ -1540,28 +1540,13 @@ namespace TrilinosWrappers - template + template <> void - SparseMatrix::set(const size_type row, - const size_type n_cols, - const size_type *col_indices, - const Number * values, - const bool elide_zero_values) - { - std::vector trilinos_values(n_cols); - std::copy(values, values + n_cols, trilinos_values.begin()); - this->set( - row, n_cols, col_indices, trilinos_values.data(), elide_zero_values); - } - - - - void - SparseMatrix::set(const size_type row, - const size_type n_cols, - const size_type * col_indices, - const TrilinosScalar *values, - const bool elide_zero_values) + SparseMatrix::set(const size_type row, + const size_type n_cols, + const size_type * col_indices, + const TrilinosScalar *values, + const bool elide_zero_values) { AssertIndexRange(row, this->m()); @@ -2124,7 +2109,8 @@ namespace TrilinosWrappers template - void + typename std::enable_if< + std::is_same::value>::type SparseMatrix::vmult(VectorType &dst, const VectorType &src) const { Assert(&src != &dst, ExcSourceEqualsDestination()); @@ -2157,7 +2143,18 @@ namespace TrilinosWrappers template - void + typename std::enable_if< + !std::is_same::value>::type + SparseMatrix::vmult(VectorType & /*dst*/, const VectorType & /*src*/) const + { + AssertThrow(false, ExcNotImplemented()); + } + + + + template + typename std::enable_if< + std::is_same::value>::type SparseMatrix::Tvmult(VectorType &dst, const VectorType &src) const { Assert(&src != &dst, ExcSourceEqualsDestination()); @@ -2186,6 +2183,16 @@ namespace TrilinosWrappers + template + typename std::enable_if< + !std::is_same::value>::type + SparseMatrix::Tvmult(VectorType & /*dst*/, const VectorType & /*src*/) const + { + AssertThrow(false, ExcNotImplemented()); + } + + + template void SparseMatrix::vmult_add(VectorType &dst, const VectorType &src) const @@ -3508,10 +3515,10 @@ namespace TrilinosWrappers dealii::LinearAlgebra::TpetraWrappers::Vector &, const dealii::LinearAlgebra::TpetraWrappers::Vector &) const; - /*template void - SparseMatrix::vmult( - dealii::LinearAlgebra::TpetraWrappers::Vector &, - const dealii::LinearAlgebra::TpetraWrappers::Vector &) const;*/ + template void + SparseMatrix::vmult( + dealii::LinearAlgebra::TpetraWrappers::Vector &, + const dealii::LinearAlgebra::TpetraWrappers::Vector &) const; template void SparseMatrix::vmult( @@ -3537,6 +3544,11 @@ namespace TrilinosWrappers dealii::LinearAlgebra::TpetraWrappers::Vector &, const dealii::LinearAlgebra::TpetraWrappers::Vector &) const; + template void + SparseMatrix::Tvmult( + dealii::LinearAlgebra::TpetraWrappers::Vector &, + const dealii::LinearAlgebra::TpetraWrappers::Vector &) const; + template void SparseMatrix::Tvmult( dealii::LinearAlgebra::EpetraWrappers::Vector &, @@ -3561,6 +3573,11 @@ namespace TrilinosWrappers dealii::LinearAlgebra::TpetraWrappers::Vector &, const dealii::LinearAlgebra::TpetraWrappers::Vector &) const; + template void + SparseMatrix::vmult_add( + dealii::LinearAlgebra::TpetraWrappers::Vector &, + const dealii::LinearAlgebra::TpetraWrappers::Vector &) const; + template void SparseMatrix::vmult_add( dealii::LinearAlgebra::EpetraWrappers::Vector &, @@ -3585,6 +3602,11 @@ namespace TrilinosWrappers dealii::LinearAlgebra::TpetraWrappers::Vector &, const dealii::LinearAlgebra::TpetraWrappers::Vector &) const; + template void + SparseMatrix::Tvmult_add( + dealii::LinearAlgebra::TpetraWrappers::Vector &, + const dealii::LinearAlgebra::TpetraWrappers::Vector &) const; + template void SparseMatrix::Tvmult_add( dealii::LinearAlgebra::EpetraWrappers::Vector &, From 54e52a86a8ccf6c6839854db03530071bcf998cb Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Wed, 19 Sep 2018 23:54:23 +0200 Subject: [PATCH 150/507] Support older Trilinos versions --- .../lac/trilinos_tpetra_communication_pattern.h | 1 + source/base/index_set.cc | 4 ++-- source/lac/trilinos_tpetra_vector.cc | 10 +++++++--- 3 files changed, 10 insertions(+), 5 deletions(-) diff --git a/include/deal.II/lac/trilinos_tpetra_communication_pattern.h b/include/deal.II/lac/trilinos_tpetra_communication_pattern.h index 8dc7cf787472..a3a23726fecb 100644 --- a/include/deal.II/lac/trilinos_tpetra_communication_pattern.h +++ b/include/deal.II/lac/trilinos_tpetra_communication_pattern.h @@ -25,6 +25,7 @@ # include +# include # include # include diff --git a/source/base/index_set.cc b/source/base/index_set.cc index 6fe2920ffe39..143efc6dc6b4 100644 --- a/source/base/index_set.cc +++ b/source/base/index_set.cc @@ -571,9 +571,9 @@ IndexSet::make_tpetra_map(const MPI_Comm &communicator, fill_index_vector(indices); std::vector int_indices(indices.size()); std::copy(indices.begin(), indices.end(), int_indices.begin()); + const Teuchos::ArrayView arr_view(int_indices); return Tpetra::Map<>(size(), - (n_elements() > 0 ? int_indices.data() : nullptr), - n_elements(), + arr_view, 0, # ifdef DEAL_II_WITH_MPI Teuchos::rcp(new Teuchos::MpiComm(communicator)) diff --git a/source/lac/trilinos_tpetra_vector.cc b/source/lac/trilinos_tpetra_vector.cc index 88324e6d53a7..dae177f7e5c4 100644 --- a/source/lac/trilinos_tpetra_vector.cc +++ b/source/lac/trilinos_tpetra_vector.cc @@ -561,9 +561,13 @@ namespace LinearAlgebra else if (vector->getLocalLength() > 0) { const size_type n_indices = vector->getLocalLength(); - auto vector_indices = vector->getMap()->getMyGlobalIndices(); - is.add_indices((unsigned int *)&vector_indices[0], - (unsigned int *)&vector_indices[0] + n_indices); + std::vector vector_indices; + vector_indices.reserve(n_indices); + for (unsigned int i = 0; i < n_indices; ++i) + vector_indices.push_back(vector->getMap()->getGlobalElement(i)); + + is.add_indices(vector_indices.data(), + vector_indices.data() + n_indices); } is.compress(); From 633af9f85da2e17e91d29c2a9e2baedaa9b2870f Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Thu, 20 Sep 2018 16:07:40 +0200 Subject: [PATCH 151/507] Test for complex values --- tests/trilinos/tpetra_vector_01.cc | 24 +- tests/trilinos/tpetra_vector_02.cc | 34 ++- tests/trilinos/tpetra_vector_03.cc | 2 + .../trilinos/tpetra_vector_03.mpirun=2.output | 118 +++++++++ .../trilinos/tpetra_vector_03.mpirun=4.output | 246 ++++++++++++++++++ 5 files changed, 402 insertions(+), 22 deletions(-) diff --git a/tests/trilinos/tpetra_vector_01.cc b/tests/trilinos/tpetra_vector_01.cc index ba39dfa34e84..a294f785032c 100644 --- a/tests/trilinos/tpetra_vector_01.cc +++ b/tests/trilinos/tpetra_vector_01.cc @@ -147,13 +147,13 @@ test() if (rank == 0) { for (unsigned int i = 0; i < 6; ++i) - AssertThrow(2. * read_write_2[i] == read_write_3[i], + AssertThrow(Number(2.) * read_write_2[i] == read_write_3[i], ExcMessage("Problem in operator *=.")); } else { for (unsigned int i = 4; i < 10; ++i) - AssertThrow(2. * read_write_2[i] == read_write_3[i], + AssertThrow(Number(2.) * read_write_2[i] == read_write_3[i], ExcMessage("Problem in operator *=.")); } @@ -162,13 +162,13 @@ test() if (rank == 0) { for (unsigned int i = 0; i < 6; ++i) - AssertThrow(0.5 * read_write_2[i] == read_write_3[i], + AssertThrow(Number(0.5) * read_write_2[i] == read_write_3[i], ExcMessage("Problem in operator /=.")); } else { for (unsigned int i = 4; i < 10; ++i) - AssertThrow(0.5 * read_write_2[i] == read_write_3[i], + AssertThrow(Number(0.5) * read_write_2[i] == read_write_3[i], ExcMessage("Problem in operator /=.")); } @@ -177,13 +177,15 @@ test() if (rank == 0) { for (unsigned int i = 0; i < 6; ++i) - AssertThrow(2. * read_write_2[i] + read_write_1[i] == read_write_3[i], + AssertThrow(Number(2.) * read_write_2[i] + read_write_1[i] == + read_write_3[i], ExcMessage("Problem in operator +=.")); } else { for (unsigned int i = 4; i < 10; ++i) - AssertThrow(2. * read_write_2[i] + read_write_1[i] == read_write_3[i], + AssertThrow(Number(2.) * read_write_2[i] + read_write_1[i] == + read_write_3[i], ExcMessage("Problem in operator +=.")); } @@ -192,20 +194,22 @@ test() if (rank == 0) { for (unsigned int i = 0; i < 6; ++i) - AssertThrow(1.5 * read_write_2[i] + read_write_1[i] == read_write_3[i], + AssertThrow(Number(1.5) * read_write_2[i] + read_write_1[i] == + read_write_3[i], ExcMessage("Problem in operator -=.")); } else { for (unsigned int i = 4; i < 10; ++i) - AssertThrow(1.5 * read_write_2[i] + read_write_1[i] == read_write_3[i], + AssertThrow(Number(1.5) * read_write_2[i] + read_write_1[i] == + read_write_3[i], ExcMessage("Problem in operator -=.")); } b.import(read_write_1, VectorOperation::insert); c.import(read_write_1, VectorOperation::insert); const Number val = b * c; - AssertThrow(val == 285., ExcMessage("Problem in operator *.")); + AssertThrow(val == Number(285.), ExcMessage("Problem in operator *.")); } @@ -219,6 +223,8 @@ main(int argc, char **argv) test(); test(); + test>(); + test>(); deallog << "OK" << std::endl; diff --git a/tests/trilinos/tpetra_vector_02.cc b/tests/trilinos/tpetra_vector_02.cc index a775c7ec3025..41b62d9a4c33 100644 --- a/tests/trilinos/tpetra_vector_02.cc +++ b/tests/trilinos/tpetra_vector_02.cc @@ -88,13 +88,13 @@ test() if (rank == 0) { for (unsigned int i = 0; i < 5; ++i) - AssertThrow(1. + read_write_1[i] == read_write_3[i], + AssertThrow(Number(1.) + read_write_1[i] == read_write_3[i], ExcMessage("Problem in add(scalar).")); } else { for (unsigned int i = 5; i < 10; ++i) - AssertThrow(1. + read_write_1[i] == read_write_3[i], + AssertThrow(Number(1.) + read_write_1[i] == read_write_3[i], ExcMessage("Problem in add(scalar).")); } @@ -103,14 +103,16 @@ test() if (rank == 0) { for (unsigned int i = 0; i < 5; ++i) - AssertThrow(1. + read_write_1[i] + 2. * read_write_2[i] == + AssertThrow(Number(1.) + read_write_1[i] + + Number(2.) * read_write_2[i] == read_write_3[i], ExcMessage("Problem in add(scalar,Vector).")); } else { for (unsigned int i = 5; i < 10; ++i) - AssertThrow(1. + read_write_1[i] + 2. * read_write_2[i] == + AssertThrow(Number(1.) + read_write_1[i] + + Number(2.) * read_write_2[i] == read_write_3[i], ExcMessage("Problem in add(scalar,Vector).")); } @@ -122,14 +124,16 @@ test() if (rank == 0) { for (unsigned int i = 0; i < 5; ++i) - AssertThrow(4. + 4. * read_write_1[i] + 10. * read_write_2[i] == + AssertThrow(Number(4.) + Number(4.) * read_write_1[i] + + Number(10.) * read_write_2[i] == read_write_3[i], ExcMessage("Problem in add(scalar,Vector,scalar,Vector).")); } else { for (unsigned int i = 5; i < 10; ++i) - AssertThrow(4. + 4. * read_write_1[i] + 10. * read_write_2[i] == + AssertThrow(Number(4.) + Number(4.) * read_write_1[i] + + Number(10.) * read_write_2[i] == read_write_3[i], ExcMessage("Problem in add(scalar,Vector,scalar,Vector).")); } @@ -141,14 +145,16 @@ test() if (rank == 0) { for (unsigned int i = 0; i < 5; ++i) - AssertThrow(3. * read_write_1[i] + 2. * read_write_2[i] == + AssertThrow(Number(3.) * read_write_1[i] + + Number(2.) * read_write_2[i] == read_write_3[i], ExcMessage("Problem in sadd(scalar,scalar,Vector).")); } else { for (unsigned int i = 5; i < 10; ++i) - AssertThrow(3. * read_write_1[i] + 2. * read_write_2[i] == + AssertThrow(Number(3.) * read_write_1[i] + + Number(2.) * read_write_2[i] == read_write_3[i], ExcMessage("Problem in sadd(scalar,scalar,Vector).")); } @@ -176,28 +182,28 @@ test() if (rank == 0) { for (unsigned int i = 0; i < 5; ++i) - AssertThrow(2. * read_write_2[i] == read_write_3[i], + AssertThrow(Number(2.) * read_write_2[i] == read_write_3[i], ExcMessage("Problem in scale.")); } else { for (unsigned int i = 5; i < 10; ++i) - AssertThrow(2. * read_write_2[i] == read_write_3[i], + AssertThrow((Number)2. * read_write_2[i] == read_write_3[i], ExcMessage("Problem in equ.")); } AssertThrow(b.l1_norm() == 95., ExcMessage("Problem in l1_norm.")); - const Number eps = 1e-6; - AssertThrow(std::fabs(b.l2_norm() - 31.3847096) < eps, + const double eps = 1e-6; + AssertThrow(std::fabs(b.l2_norm() - Number(31.3847096)) < eps, ExcMessage("Problem in l2_norm")); AssertThrow(b.linfty_norm() == 14., ExcMessage("Problem in linfty_norm.")); a.import(read_write_1, VectorOperation::insert); const Number val = a.add_and_dot(2., a, b); - AssertThrow(val == 1530., ExcMessage("Problem in add_and_dot")); + AssertThrow(val == Number(1530.), ExcMessage("Problem in add_and_dot")); } @@ -211,6 +217,8 @@ main(int argc, char **argv) test(); test(); + test>(); + test>(); deallog << "OK" << std::endl; diff --git a/tests/trilinos/tpetra_vector_03.cc b/tests/trilinos/tpetra_vector_03.cc index 650296a4913a..d97b8ce13ad2 100644 --- a/tests/trilinos/tpetra_vector_03.cc +++ b/tests/trilinos/tpetra_vector_03.cc @@ -101,4 +101,6 @@ main(int argc, char **argv) MPILogInitAll log; test(); test(); + test>(); + test>(); } diff --git a/tests/trilinos/tpetra_vector_03.mpirun=2.output b/tests/trilinos/tpetra_vector_03.mpirun=2.output index e94f192176bc..0a598a5c3b1a 100644 --- a/tests/trilinos/tpetra_vector_03.mpirun=2.output +++ b/tests/trilinos/tpetra_vector_03.mpirun=2.output @@ -63,6 +63,70 @@ IndexSet: {[0,2]} [0]: 4.000e+00 [1]: 2.000e+02 [2]: 1.000e+02 +DEAL:0::Tpetra first import add: +(2.000e+00,0.000e+00) (1.000e+02,0.000e+00) +IndexSet: {[0,2]} + +[0]: (1.000e+00,0.000e+00) +[1]: (1.000e+02,0.000e+00) +[2]: (1.000e+01,0.000e+00) +DEAL:0::Tpetra second import add: +(4.000e+00,0.000e+00) (2.000e+02,0.000e+00) +IndexSet: {[0,2]} + +[0]: (2.000e+00,0.000e+00) +[1]: (2.000e+02,0.000e+00) +[2]: (2.000e+01,0.000e+00) +DEAL:0::ReadWrite import add: +IndexSet: {[0,2]} + +[0]: (6.000e+00,0.000e+00) +[1]: (4.000e+02,0.000e+00) +[2]: (5.000e+01,0.000e+00) +DEAL:0::ReadWrite import min: +IndexSet: {[0,2]} + +[0]: (4.000e+00,0.000e+00) +[1]: (1.000e+00,0.000e+00) +[2]: (3.000e+01,0.000e+00) +DEAL:0::ReadWrite import max: +IndexSet: {[0,2]} + +[0]: (4.000e+00,0.000e+00) +[1]: (2.000e+02,0.000e+00) +[2]: (1.000e+02,0.000e+00) +DEAL:0::Tpetra first import add: +(2.000e+00,0.000e+00) (1.000e+02,0.000e+00) +IndexSet: {[0,2]} + +[0]: (1.000e+00,0.000e+00) +[1]: (1.000e+02,0.000e+00) +[2]: (1.000e+01,0.000e+00) +DEAL:0::Tpetra second import add: +(4.000e+00,0.000e+00) (2.000e+02,0.000e+00) +IndexSet: {[0,2]} + +[0]: (2.000e+00,0.000e+00) +[1]: (2.000e+02,0.000e+00) +[2]: (2.000e+01,0.000e+00) +DEAL:0::ReadWrite import add: +IndexSet: {[0,2]} + +[0]: (6.000e+00,0.000e+00) +[1]: (4.000e+02,0.000e+00) +[2]: (5.000e+01,0.000e+00) +DEAL:0::ReadWrite import min: +IndexSet: {[0,2]} + +[0]: (4.000e+00,0.000e+00) +[1]: (1.000e+00,0.000e+00) +[2]: (3.000e+01,0.000e+00) +DEAL:0::ReadWrite import max: +IndexSet: {[0,2]} + +[0]: (4.000e+00,0.000e+00) +[1]: (2.000e+02,0.000e+00) +[2]: (1.000e+02,0.000e+00) DEAL:1::Tpetra first import add: 1.000e+01 1.010e+02 @@ -118,4 +182,58 @@ IndexSet: {0, 3} [0]: 4.000e+00 [3]: 2.010e+02 +DEAL:1::Tpetra first import add: +(1.000e+01,0.000e+00) (1.010e+02,0.000e+00) +IndexSet: {0, 3} + +[0]: (1.000e+00,0.000e+00) +[3]: (1.010e+02,0.000e+00) +DEAL:1::Tpetra second import add: +(3.000e+01,0.000e+00) (2.010e+02,0.000e+00) +IndexSet: {0, 3} + +[0]: (2.000e+00,0.000e+00) +[3]: (2.010e+02,0.000e+00) +DEAL:1::ReadWrite import add: +IndexSet: {0, 3} + +[0]: (6.000e+00,0.000e+00) +[3]: (4.020e+02,0.000e+00) +DEAL:1::ReadWrite import min: +IndexSet: {0, 3} + +[0]: (4.000e+00,0.000e+00) +[3]: (1.000e+00,0.000e+00) +DEAL:1::ReadWrite import max: +IndexSet: {0, 3} + +[0]: (4.000e+00,0.000e+00) +[3]: (2.010e+02,0.000e+00) +DEAL:1::Tpetra first import add: +(1.000e+01,0.000e+00) (1.010e+02,0.000e+00) +IndexSet: {0, 3} + +[0]: (1.000e+00,0.000e+00) +[3]: (1.010e+02,0.000e+00) +DEAL:1::Tpetra second import add: +(3.000e+01,0.000e+00) (2.010e+02,0.000e+00) +IndexSet: {0, 3} + +[0]: (2.000e+00,0.000e+00) +[3]: (2.010e+02,0.000e+00) +DEAL:1::ReadWrite import add: +IndexSet: {0, 3} + +[0]: (6.000e+00,0.000e+00) +[3]: (4.020e+02,0.000e+00) +DEAL:1::ReadWrite import min: +IndexSet: {0, 3} + +[0]: (4.000e+00,0.000e+00) +[3]: (1.000e+00,0.000e+00) +DEAL:1::ReadWrite import max: +IndexSet: {0, 3} + +[0]: (4.000e+00,0.000e+00) +[3]: (2.010e+02,0.000e+00) diff --git a/tests/trilinos/tpetra_vector_03.mpirun=4.output b/tests/trilinos/tpetra_vector_03.mpirun=4.output index 5fbf8dea2d1f..a65e3464e6e7 100644 --- a/tests/trilinos/tpetra_vector_03.mpirun=4.output +++ b/tests/trilinos/tpetra_vector_03.mpirun=4.output @@ -63,6 +63,70 @@ IndexSet: {[0,2]} [0]: 8.000e+00 [1]: 2.000e+02 [2]: 1.000e+02 +DEAL:0::Tpetra first import add: +(4.000e+00,0.000e+00) (1.000e+02,0.000e+00) +IndexSet: {[0,2]} + +[0]: (1.000e+00,0.000e+00) +[1]: (1.000e+02,0.000e+00) +[2]: (1.000e+01,0.000e+00) +DEAL:0::Tpetra second import add: +(8.000e+00,0.000e+00) (2.000e+02,0.000e+00) +IndexSet: {[0,2]} + +[0]: (2.000e+00,0.000e+00) +[1]: (2.000e+02,0.000e+00) +[2]: (2.000e+01,0.000e+00) +DEAL:0::ReadWrite import add: +IndexSet: {[0,2]} + +[0]: (1.000e+01,0.000e+00) +[1]: (4.000e+02,0.000e+00) +[2]: (5.000e+01,0.000e+00) +DEAL:0::ReadWrite import min: +IndexSet: {[0,2]} + +[0]: (4.000e+00,0.000e+00) +[1]: (1.000e+00,0.000e+00) +[2]: (3.000e+01,0.000e+00) +DEAL:0::ReadWrite import max: +IndexSet: {[0,2]} + +[0]: (8.000e+00,0.000e+00) +[1]: (2.000e+02,0.000e+00) +[2]: (1.000e+02,0.000e+00) +DEAL:0::Tpetra first import add: +(4.000e+00,0.000e+00) (1.000e+02,0.000e+00) +IndexSet: {[0,2]} + +[0]: (1.000e+00,0.000e+00) +[1]: (1.000e+02,0.000e+00) +[2]: (1.000e+01,0.000e+00) +DEAL:0::Tpetra second import add: +(8.000e+00,0.000e+00) (2.000e+02,0.000e+00) +IndexSet: {[0,2]} + +[0]: (2.000e+00,0.000e+00) +[1]: (2.000e+02,0.000e+00) +[2]: (2.000e+01,0.000e+00) +DEAL:0::ReadWrite import add: +IndexSet: {[0,2]} + +[0]: (1.000e+01,0.000e+00) +[1]: (4.000e+02,0.000e+00) +[2]: (5.000e+01,0.000e+00) +DEAL:0::ReadWrite import min: +IndexSet: {[0,2]} + +[0]: (4.000e+00,0.000e+00) +[1]: (1.000e+00,0.000e+00) +[2]: (3.000e+01,0.000e+00) +DEAL:0::ReadWrite import max: +IndexSet: {[0,2]} + +[0]: (8.000e+00,0.000e+00) +[1]: (2.000e+02,0.000e+00) +[2]: (1.000e+02,0.000e+00) DEAL:1::Tpetra first import add: 1.000e+01 1.010e+02 @@ -128,6 +192,70 @@ IndexSet: {0, [3,4]} [0]: 8.000e+00 [3]: 2.010e+02 [4]: 1.010e+02 +DEAL:1::Tpetra first import add: +(1.000e+01,0.000e+00) (1.010e+02,0.000e+00) +IndexSet: {0, [3,4]} + +[0]: (1.000e+00,0.000e+00) +[3]: (1.010e+02,0.000e+00) +[4]: (1.100e+01,0.000e+00) +DEAL:1::Tpetra second import add: +(3.000e+01,0.000e+00) (2.010e+02,0.000e+00) +IndexSet: {0, [3,4]} + +[0]: (2.000e+00,0.000e+00) +[3]: (2.010e+02,0.000e+00) +[4]: (2.100e+01,0.000e+00) +DEAL:1::ReadWrite import add: +IndexSet: {0, [3,4]} + +[0]: (1.000e+01,0.000e+00) +[3]: (4.020e+02,0.000e+00) +[4]: (5.300e+01,0.000e+00) +DEAL:1::ReadWrite import min: +IndexSet: {0, [3,4]} + +[0]: (4.000e+00,0.000e+00) +[3]: (1.000e+00,0.000e+00) +[4]: (3.200e+01,0.000e+00) +DEAL:1::ReadWrite import max: +IndexSet: {0, [3,4]} + +[0]: (8.000e+00,0.000e+00) +[3]: (2.010e+02,0.000e+00) +[4]: (1.010e+02,0.000e+00) +DEAL:1::Tpetra first import add: +(1.000e+01,0.000e+00) (1.010e+02,0.000e+00) +IndexSet: {0, [3,4]} + +[0]: (1.000e+00,0.000e+00) +[3]: (1.010e+02,0.000e+00) +[4]: (1.100e+01,0.000e+00) +DEAL:1::Tpetra second import add: +(3.000e+01,0.000e+00) (2.010e+02,0.000e+00) +IndexSet: {0, [3,4]} + +[0]: (2.000e+00,0.000e+00) +[3]: (2.010e+02,0.000e+00) +[4]: (2.100e+01,0.000e+00) +DEAL:1::ReadWrite import add: +IndexSet: {0, [3,4]} + +[0]: (1.000e+01,0.000e+00) +[3]: (4.020e+02,0.000e+00) +[4]: (5.300e+01,0.000e+00) +DEAL:1::ReadWrite import min: +IndexSet: {0, [3,4]} + +[0]: (4.000e+00,0.000e+00) +[3]: (1.000e+00,0.000e+00) +[4]: (3.200e+01,0.000e+00) +DEAL:1::ReadWrite import max: +IndexSet: {0, [3,4]} + +[0]: (8.000e+00,0.000e+00) +[3]: (2.010e+02,0.000e+00) +[4]: (1.010e+02,0.000e+00) DEAL:2::Tpetra first import add: @@ -194,6 +322,70 @@ IndexSet: {0, [5,6]} [0]: 8.000e+00 [5]: 2.020e+02 [6]: 1.020e+02 +DEAL:2::Tpetra first import add: +(1.100e+01,0.000e+00) (1.020e+02,0.000e+00) +IndexSet: {0, [5,6]} + +[0]: (1.000e+00,0.000e+00) +[5]: (1.020e+02,0.000e+00) +[6]: (1.200e+01,0.000e+00) +DEAL:2::Tpetra second import add: +(3.200e+01,0.000e+00) (2.020e+02,0.000e+00) +IndexSet: {0, [5,6]} + +[0]: (2.000e+00,0.000e+00) +[5]: (2.020e+02,0.000e+00) +[6]: (2.200e+01,0.000e+00) +DEAL:2::ReadWrite import add: +IndexSet: {0, [5,6]} + +[0]: (1.000e+01,0.000e+00) +[5]: (4.040e+02,0.000e+00) +[6]: (5.600e+01,0.000e+00) +DEAL:2::ReadWrite import min: +IndexSet: {0, [5,6]} + +[0]: (4.000e+00,0.000e+00) +[5]: (1.000e+00,0.000e+00) +[6]: (3.400e+01,0.000e+00) +DEAL:2::ReadWrite import max: +IndexSet: {0, [5,6]} + +[0]: (8.000e+00,0.000e+00) +[5]: (2.020e+02,0.000e+00) +[6]: (1.020e+02,0.000e+00) +DEAL:2::Tpetra first import add: +(1.100e+01,0.000e+00) (1.020e+02,0.000e+00) +IndexSet: {0, [5,6]} + +[0]: (1.000e+00,0.000e+00) +[5]: (1.020e+02,0.000e+00) +[6]: (1.200e+01,0.000e+00) +DEAL:2::Tpetra second import add: +(3.200e+01,0.000e+00) (2.020e+02,0.000e+00) +IndexSet: {0, [5,6]} + +[0]: (2.000e+00,0.000e+00) +[5]: (2.020e+02,0.000e+00) +[6]: (2.200e+01,0.000e+00) +DEAL:2::ReadWrite import add: +IndexSet: {0, [5,6]} + +[0]: (1.000e+01,0.000e+00) +[5]: (4.040e+02,0.000e+00) +[6]: (5.600e+01,0.000e+00) +DEAL:2::ReadWrite import min: +IndexSet: {0, [5,6]} + +[0]: (4.000e+00,0.000e+00) +[5]: (1.000e+00,0.000e+00) +[6]: (3.400e+01,0.000e+00) +DEAL:2::ReadWrite import max: +IndexSet: {0, [5,6]} + +[0]: (8.000e+00,0.000e+00) +[5]: (2.020e+02,0.000e+00) +[6]: (1.020e+02,0.000e+00) DEAL:3::Tpetra first import add: @@ -250,4 +442,58 @@ IndexSet: {0, 7} [0]: 8.000e+00 [7]: 2.030e+02 +DEAL:3::Tpetra first import add: +(1.200e+01,0.000e+00) (1.030e+02,0.000e+00) +IndexSet: {0, 7} + +[0]: (1.000e+00,0.000e+00) +[7]: (1.030e+02,0.000e+00) +DEAL:3::Tpetra second import add: +(3.400e+01,0.000e+00) (2.030e+02,0.000e+00) +IndexSet: {0, 7} + +[0]: (2.000e+00,0.000e+00) +[7]: (2.030e+02,0.000e+00) +DEAL:3::ReadWrite import add: +IndexSet: {0, 7} + +[0]: (1.000e+01,0.000e+00) +[7]: (4.060e+02,0.000e+00) +DEAL:3::ReadWrite import min: +IndexSet: {0, 7} + +[0]: (4.000e+00,0.000e+00) +[7]: (1.000e+00,0.000e+00) +DEAL:3::ReadWrite import max: +IndexSet: {0, 7} + +[0]: (8.000e+00,0.000e+00) +[7]: (2.030e+02,0.000e+00) +DEAL:3::Tpetra first import add: +(1.200e+01,0.000e+00) (1.030e+02,0.000e+00) +IndexSet: {0, 7} + +[0]: (1.000e+00,0.000e+00) +[7]: (1.030e+02,0.000e+00) +DEAL:3::Tpetra second import add: +(3.400e+01,0.000e+00) (2.030e+02,0.000e+00) +IndexSet: {0, 7} + +[0]: (2.000e+00,0.000e+00) +[7]: (2.030e+02,0.000e+00) +DEAL:3::ReadWrite import add: +IndexSet: {0, 7} + +[0]: (1.000e+01,0.000e+00) +[7]: (4.060e+02,0.000e+00) +DEAL:3::ReadWrite import min: +IndexSet: {0, 7} + +[0]: (4.000e+00,0.000e+00) +[7]: (1.000e+00,0.000e+00) +DEAL:3::ReadWrite import max: +IndexSet: {0, 7} + +[0]: (8.000e+00,0.000e+00) +[7]: (2.030e+02,0.000e+00) From 282be8824a15c0d7f07f0a7e872e81af8ab5f44e Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Thu, 20 Sep 2018 21:39:06 +0200 Subject: [PATCH 152/507] Update external Trilinos documentation --- doc/external-libs/trilinos.html | 2 ++ 1 file changed, 2 insertions(+) diff --git a/doc/external-libs/trilinos.html b/doc/external-libs/trilinos.html index d950f55b11c0..4e3a51552298 100644 --- a/doc/external-libs/trilinos.html +++ b/doc/external-libs/trilinos.html @@ -94,6 +94,8 @@
    Installing Trilinos
    -DTrilinos_ENABLE_ML=ON \ -DTrilinos_ENABLE_ROL=ON \ -DTrilinos_ENABLE_Tpetra=ON \ + -DTpetra_INST_COMPLEX_DOUBLE=ON \ + -DTpetra_INST_COMPLEX_FLOAT=ON \ -DTrilinos_ENABLE_Zoltan=ON \ -DTrilinos_VERBOSE_CONFIGURE=OFF \ -DTPL_ENABLE_MPI=ON \ From 5717ffc1dbccb0c89af777e7d2bf00e1d004d715 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Thu, 4 Oct 2018 05:26:55 +0200 Subject: [PATCH 153/507] Fix test --- tests/trilinos/tpetra_vector_02.cc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/trilinos/tpetra_vector_02.cc b/tests/trilinos/tpetra_vector_02.cc index 41b62d9a4c33..132231491b18 100644 --- a/tests/trilinos/tpetra_vector_02.cc +++ b/tests/trilinos/tpetra_vector_02.cc @@ -118,7 +118,7 @@ test() } - LinearAlgebra::TpetraWrappers::Vector d(a); + LinearAlgebra::TpetraWrappers::Vector d(a); a.add(2., b, 3., d); read_write_3.import(a, VectorOperation::insert); if (rank == 0) From 3f9e73ecf3fb88a82360a0bcb36b4d201c482411 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Fri, 5 Oct 2018 06:40:56 +0200 Subject: [PATCH 154/507] Use definition headers instead of declaration headers --- source/lac/trilinos_tpetra_vector.cc | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/source/lac/trilinos_tpetra_vector.cc b/source/lac/trilinos_tpetra_vector.cc index dae177f7e5c4..264f21da77c9 100644 --- a/source/lac/trilinos_tpetra_vector.cc +++ b/source/lac/trilinos_tpetra_vector.cc @@ -28,8 +28,8 @@ # include # include -# include -# include +# include +# include # include @@ -660,7 +660,6 @@ namespace LinearAlgebra template class Vector; template class Vector>; template class Vector>; - } // namespace TpetraWrappers } // namespace LinearAlgebra From f1f9065aa3aee80ed59e8bb1c5eb40364cac1084 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Sun, 7 Oct 2018 04:37:41 +0200 Subject: [PATCH 155/507] Adress Wolfgang's comments a.k.a add more documentation and switches --- include/deal.II/base/utilities.h | 8 ++++ .../deal.II/lac/read_write_vector.templates.h | 45 ++++++++++--------- include/deal.II/lac/trilinos_sparse_matrix.h | 16 +++++++ source/base/utilities.cc | 2 + 4 files changed, 50 insertions(+), 21 deletions(-) diff --git a/include/deal.II/base/utilities.h b/include/deal.II/base/utilities.h index 71d05faf24ea..dc7414587e54 100644 --- a/include/deal.II/base/utilities.h +++ b/include/deal.II/base/utilities.h @@ -888,6 +888,14 @@ namespace Utilities const Epetra_Comm & comm_self(); + /** + * Return a Teuchos::Comm object needed for creation of Tpetra::Maps. + * + * If deal.II has been configured to use a compiler that does not support + * MPI then the resulting communicator will be a serial one. Otherwise, + * the communicator will correspond to MPI_COMM_SELF, i.e. a communicator + * that comprises only this one processor. + */ const Teuchos::RCP> & tpetra_comm_self(); diff --git a/include/deal.II/lac/read_write_vector.templates.h b/include/deal.II/lac/read_write_vector.templates.h index 87139aedd776..9da3c32e68e0 100644 --- a/include/deal.II/lac/read_write_vector.templates.h +++ b/include/deal.II/lac/read_write_vector.templates.h @@ -565,30 +565,33 @@ namespace LinearAlgebra Assert(size == 0 || values != nullptr, ExcInternalError("Export failed.")); AssertDimension(size, stored_elements.n_elements()); - if (operation == VectorOperation::insert) - { - for (size_type i = 0; i < size; ++i) - values[i] = new_values[i]; - } - else if (operation == VectorOperation::add) - { - for (size_type i = 0; i < size; ++i) - values[i] += new_values[i]; - } - else if (operation == VectorOperation::min) + switch (operation) { - for (size_type i = 0; i < size; ++i) - if (std::real(new_values[i]) - std::real(values[i]) < 0.0) - values[i] = new_values[i]; - } - else if (operation == VectorOperation::max) - { - for (size_type i = 0; i < size; ++i) - if (std::real(new_values[i]) - std::real(values[i]) > 0.0) + case VectorOperation::insert: + for (size_type i = 0; i < size; ++i) values[i] = new_values[i]; + break; + + case VectorOperation::add: + for (size_type i = 0; i < size; ++i) + values[i] += new_values[i]; + break; + + case VectorOperation::min: + for (size_type i = 0; i < size; ++i) + if (std::real(new_values[i]) - std::real(values[i]) < 0.0) + values[i] = new_values[i]; + break; + + case VectorOperation::max: + for (size_type i = 0; i < size; ++i) + if (std::real(new_values[i]) - std::real(values[i]) > 0.0) + values[i] = new_values[i]; + break; + + default: + AssertThrow(false, ExcNotImplemented()); } - else - AssertThrow(false, ExcNotImplemented()); } diff --git a/include/deal.II/lac/trilinos_sparse_matrix.h b/include/deal.II/lac/trilinos_sparse_matrix.h index 2ae42c5ef157..368fc70a12d4 100644 --- a/include/deal.II/lac/trilinos_sparse_matrix.h +++ b/include/deal.II/lac/trilinos_sparse_matrix.h @@ -1576,6 +1576,9 @@ namespace TrilinosWrappers * initialized with the same IndexSet that was used for the column indices * of the matrix. * + * This function will be called when the underlying number type for the + * matrix object and the one one for the vector object are the same. + * * In case of a serial vector, this function will only work when * running on one processor, since the matrix object is inherently * distributed. Otherwise, an exception will be thrown. @@ -1585,6 +1588,11 @@ namespace TrilinosWrappers TrilinosScalar>::value>::type vmult(VectorType &dst, const VectorType &src) const; + /** + * Same as the function above for the case that the underlying number type + * for the matrix object and the one for the vector object do not coincide. + * This case is not implemented. Calling it will result in an runtime error. + */ template typename std::enable_if::value>::type @@ -1599,12 +1607,20 @@ namespace TrilinosWrappers * * This function can be called with several types of vector objects, * see the discussion about @p VectorType in vmult(). + * + * This function will be called when the underlying number type for the + * matrix object and the one one for the vector object are the same. */ template typename std::enable_if::value>::type Tvmult(VectorType &dst, const VectorType &src) const; + /** + * Same as the function above for the case that the underlying number type + * for the matrix object and the one for the vector object do not coincide. + * This case is not implemented. Calling it will result in an runtime error. + */ template typename std::enable_if::value>::type diff --git a/source/base/utilities.cc b/source/base/utilities.cc index ff4d0d957322..d5f120192bf6 100644 --- a/source/base/utilities.cc +++ b/source/base/utilities.cc @@ -993,6 +993,8 @@ namespace Utilities return communicator; } + + const Epetra_Comm & comm_self() { From a557e238cbe3b30ca12afb24b56bc1b8a977f6b5 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Fri, 2 Nov 2018 19:59:37 +0100 Subject: [PATCH 156/507] Use correct template parameters also for 64bit-indices --- include/deal.II/base/index_set.h | 2 +- include/deal.II/lac/read_write_vector.h | 13 +++-- .../deal.II/lac/read_write_vector.templates.h | 14 +++-- .../trilinos_tpetra_communication_pattern.h | 10 ++-- include/deal.II/lac/trilinos_tpetra_vector.h | 7 ++- include/deal.II/lac/vector_element_access.h | 30 ++++++---- source/base/index_set.cc | 28 ++++----- .../trilinos_tpetra_communication_pattern.cc | 22 +++---- source/lac/trilinos_tpetra_vector.cc | 58 ++++++++++++------- 9 files changed, 109 insertions(+), 75 deletions(-) diff --git a/include/deal.II/base/index_set.h b/include/deal.II/base/index_set.h index 2e21fab64498..afb90fe2d784 100644 --- a/include/deal.II/base/index_set.h +++ b/include/deal.II/base/index_set.h @@ -448,7 +448,7 @@ class IndexSet make_trilinos_map(const MPI_Comm &communicator = MPI_COMM_WORLD, const bool overlapping = false) const; - Tpetra::Map<> + Tpetra::Map make_tpetra_map(const MPI_Comm &communicator = MPI_COMM_WORLD, const bool overlapping = false) const; #endif diff --git a/include/deal.II/lac/read_write_vector.h b/include/deal.II/lac/read_write_vector.h index 0ed6f9d829d3..b72a95eae233 100644 --- a/include/deal.II/lac/read_write_vector.h +++ b/include/deal.II/lac/read_write_vector.h @@ -615,12 +615,13 @@ namespace LinearAlgebra * used directly. */ void - import(const Tpetra::Vector &tpetra_vector, - const IndexSet & locally_owned_elements, - VectorOperation::values operation, - const MPI_Comm & mpi_comm, - const std::shared_ptr - &communication_pattern); + import( + const Tpetra::Vector &tpetra_vector, + const IndexSet & locally_owned_elements, + VectorOperation::values operation, + const MPI_Comm & mpi_comm, + const std::shared_ptr + &communication_pattern); /** * Import all the elements present in the vector's IndexSet from the input diff --git a/include/deal.II/lac/read_write_vector.templates.h b/include/deal.II/lac/read_write_vector.templates.h index 9da3c32e68e0..572c28f1dec9 100644 --- a/include/deal.II/lac/read_write_vector.templates.h +++ b/include/deal.II/lac/read_write_vector.templates.h @@ -509,10 +509,10 @@ namespace LinearAlgebra template void ReadWriteVector::import( - const Tpetra::Vector &vector, - const IndexSet & source_elements, - VectorOperation::values operation, - const MPI_Comm & mpi_comm, + const Tpetra::Vector &vector, + const IndexSet & source_elements, + VectorOperation::values operation, + const MPI_Comm & mpi_comm, const std::shared_ptr &communication_pattern) { @@ -552,9 +552,11 @@ namespace LinearAlgebra "LinearAlgebra::TpetraWrappers::CommunicationPattern.")); } - Tpetra::Export<> tpetra_export(tpetra_comm_pattern->get_tpetra_export()); + Tpetra::Export tpetra_export( + tpetra_comm_pattern->get_tpetra_export()); - Tpetra::Vector target_vector(tpetra_export.getSourceMap()); + Tpetra::Vector target_vector( + tpetra_export.getSourceMap()); target_vector.doImport(vector, tpetra_export, Tpetra::REPLACE); const auto *new_values = target_vector.getData().get(); diff --git a/include/deal.II/lac/trilinos_tpetra_communication_pattern.h b/include/deal.II/lac/trilinos_tpetra_communication_pattern.h index a3a23726fecb..fd3e074b2aa9 100644 --- a/include/deal.II/lac/trilinos_tpetra_communication_pattern.h +++ b/include/deal.II/lac/trilinos_tpetra_communication_pattern.h @@ -70,13 +70,13 @@ namespace LinearAlgebra /** * Return the underlying Tpetra::Import object. */ - const Tpetra::Import<> & + const Tpetra::Import & get_tpetra_import() const; /** * Return the underlying Tpetra::Export object. */ - const Tpetra::Export<> & + const Tpetra::Export & get_tpetra_export() const; private: @@ -88,12 +88,14 @@ namespace LinearAlgebra /** * Shared pointer to the Tpetra::Import object used. */ - std::unique_ptr> tpetra_import; + std::unique_ptr> + tpetra_import; /** * Shared pointer to the Tpetra::Export object used. */ - std::unique_ptr> tpetra_export; + std::unique_ptr> + tpetra_export; }; } // end of namespace TpetraWrappers } // end of namespace LinearAlgebra diff --git a/include/deal.II/lac/trilinos_tpetra_vector.h b/include/deal.II/lac/trilinos_tpetra_vector.h index 798248703ab4..911863c9d99e 100644 --- a/include/deal.II/lac/trilinos_tpetra_vector.h +++ b/include/deal.II/lac/trilinos_tpetra_vector.h @@ -310,14 +310,14 @@ namespace LinearAlgebra * Return a const reference to the underlying Trilinos * Tpetra::Vector class. */ - const Tpetra::Vector & + const Tpetra::Vector & trilinos_vector() const; /** * Return a (modifyable) reference to the underlying Trilinos * Tpetra::Vector class. */ - Tpetra::Vector & + Tpetra::Vector & trilinos_vector(); /** @@ -371,7 +371,8 @@ namespace LinearAlgebra /** * Pointer to the actual Tpetra vector object. */ - std::unique_ptr> vector; + std::unique_ptr> + vector; /** * IndexSet of the elements of the last imported vector. diff --git a/include/deal.II/lac/vector_element_access.h b/include/deal.II/lac/vector_element_access.h index 22e541033c52..4a81d97fdbc1 100644 --- a/include/deal.II/lac/vector_element_access.h +++ b/include/deal.II/lac/vector_element_access.h @@ -133,7 +133,8 @@ namespace internal LinearAlgebra::TpetraWrappers::Vector &V) { // Extract local indices in the vector. - Tpetra::Vector vector = V.trilinos_vector(); + Tpetra::Vector vector = + V.trilinos_vector(); TrilinosWrappers::types::int_type trilinos_i = vector.getMap()->getLocalElement( static_cast(i)); @@ -144,7 +145,8 @@ namespace internal // We're going to modify the data on host. vector.modify(); vector_1d(trilinos_i) += value; - vector.sync::device_type::memory_space>(); + vector.sync:: + device_type::memory_space>(); } @@ -157,7 +159,8 @@ namespace internal LinearAlgebra::TpetraWrappers::Vector &V) { // Extract local indices in the vector. - Tpetra::Vector vector = V.trilinos_vector(); + Tpetra::Vector vector = + V.trilinos_vector(); TrilinosWrappers::types::int_type trilinos_i = vector.getMap()->getLocalElement( static_cast(i)); @@ -168,7 +171,8 @@ namespace internal // We're going to modify the data on host. vector.modify(); vector_1d(trilinos_i) += value; - vector.sync::device_type::memory_space>(); + vector.sync:: + device_type::memory_space>(); } @@ -181,7 +185,8 @@ namespace internal LinearAlgebra::TpetraWrappers::Vector &V) { // Extract local indices in the vector. - Tpetra::Vector vector = V.trilinos_vector(); + Tpetra::Vector vector = + V.trilinos_vector(); TrilinosWrappers::types::int_type trilinos_i = vector.getMap()->getLocalElement( static_cast(i)); @@ -192,7 +197,8 @@ namespace internal // We're going to modify the data on host. vector.modify(); vector_1d(trilinos_i) = value; - vector.sync::device_type::memory_space>(); + vector.sync:: + device_type::memory_space>(); } @@ -205,7 +211,8 @@ namespace internal LinearAlgebra::TpetraWrappers::Vector &V) { // Extract local indices in the vector. - Tpetra::Vector vector = V.trilinos_vector(); + Tpetra::Vector vector = + V.trilinos_vector(); TrilinosWrappers::types::int_type trilinos_i = vector.getMap()->getLocalElement( static_cast(i)); @@ -216,7 +223,8 @@ namespace internal // We're going to modify the data on host. vector.modify(); vector_1d(trilinos_i) = value; - vector.sync::device_type::memory_space>(); + vector.sync:: + device_type::memory_space>(); } @@ -228,7 +236,8 @@ namespace internal const types::global_dof_index i) { // Extract local indices in the vector. - Tpetra::Vector vector = V.trilinos_vector(); + Tpetra::Vector vector = + V.trilinos_vector(); TrilinosWrappers::types::int_type trilinos_i = vector.getMap()->getLocalElement( static_cast(i)); @@ -249,7 +258,8 @@ namespace internal const types::global_dof_index i) { // Extract local indices in the vector. - Tpetra::Vector vector = V.trilinos_vector(); + Tpetra::Vector vector = + V.trilinos_vector(); TrilinosWrappers::types::int_type trilinos_i = vector.getMap()->getLocalElement( static_cast(i)); diff --git a/source/base/index_set.cc b/source/base/index_set.cc index 143efc6dc6b4..d9257454852e 100644 --- a/source/base/index_set.cc +++ b/source/base/index_set.cc @@ -520,7 +520,7 @@ IndexSet::fill_index_vector(std::vector &indices) const #ifdef DEAL_II_WITH_TRILINOS -Tpetra::Map<> +Tpetra::Map IndexSet::make_tpetra_map(const MPI_Comm &communicator, const bool overlapping) const { @@ -556,29 +556,31 @@ IndexSet::make_tpetra_map(const MPI_Comm &communicator, const bool linear = overlapping ? false : is_ascending_and_one_to_one(communicator); if (linear) - return Tpetra::Map<>(size(), - n_elements(), - 0, + return Tpetra::Map( + size(), + n_elements(), + 0, # ifdef DEAL_II_WITH_MPI - Teuchos::rcp(new Teuchos::MpiComm(communicator)) + Teuchos::rcp(new Teuchos::MpiComm(communicator)) # else - Teuchos::rcp(new Teuchos::Comm()) + Teuchos::rcp(new Teuchos::Comm()) # endif ); else { std::vector indices; fill_index_vector(indices); - std::vector int_indices(indices.size()); + std::vector int_indices(indices.size()); std::copy(indices.begin(), indices.end(), int_indices.begin()); - const Teuchos::ArrayView arr_view(int_indices); - return Tpetra::Map<>(size(), - arr_view, - 0, + const Teuchos::ArrayView arr_view(int_indices); + return Tpetra::Map( + size(), + arr_view, + 0, # ifdef DEAL_II_WITH_MPI - Teuchos::rcp(new Teuchos::MpiComm(communicator)) + Teuchos::rcp(new Teuchos::MpiComm(communicator)) # else - Teuchos::rcp(new Teuchos::Comm()) + Teuchos::rcp(new Teuchos::Comm()) # endif ); } diff --git a/source/lac/trilinos_tpetra_communication_pattern.cc b/source/lac/trilinos_tpetra_communication_pattern.cc index e78dfda3d3d1..626622d49d36 100644 --- a/source/lac/trilinos_tpetra_communication_pattern.cc +++ b/source/lac/trilinos_tpetra_communication_pattern.cc @@ -55,20 +55,22 @@ namespace LinearAlgebra { comm = std::make_shared(communicator); - auto vector_space_vector_map = Teuchos::rcp(new Tpetra::Map<>( - vector_space_vector_index_set.make_tpetra_map(*comm, false))); - auto read_write_vector_map = Teuchos::rcp(new Tpetra::Map<>( - read_write_vector_index_set.make_tpetra_map(*comm, true))); + auto vector_space_vector_map = + Teuchos::rcp(new Tpetra::Map( + vector_space_vector_index_set.make_tpetra_map(*comm, false))); + auto read_write_vector_map = + Teuchos::rcp(new Tpetra::Map( + read_write_vector_index_set.make_tpetra_map(*comm, true))); // Target map is read_write_vector_map // Source map is vector_space_vector_map. This map must have uniquely // owned GID. tpetra_import = - std_cxx14::make_unique>(read_write_vector_map, - vector_space_vector_map); + std_cxx14::make_unique>( + read_write_vector_map, vector_space_vector_map); tpetra_export = - std_cxx14::make_unique>(read_write_vector_map, - vector_space_vector_map); + std_cxx14::make_unique>( + read_write_vector_map, vector_space_vector_map); } @@ -81,7 +83,7 @@ namespace LinearAlgebra - const Tpetra::Import<> & + const Tpetra::Import & CommunicationPattern::get_tpetra_import() const { return *tpetra_import; @@ -89,7 +91,7 @@ namespace LinearAlgebra - const Tpetra::Export<> & + const Tpetra::Export & CommunicationPattern::get_tpetra_export() const { return *tpetra_export; diff --git a/source/lac/trilinos_tpetra_vector.cc b/source/lac/trilinos_tpetra_vector.cc index 264f21da77c9..f4e368669728 100644 --- a/source/lac/trilinos_tpetra_vector.cc +++ b/source/lac/trilinos_tpetra_vector.cc @@ -42,8 +42,12 @@ namespace LinearAlgebra { template Vector::Vector() - : vector(new Tpetra::Vector(Teuchos::RCP>( - new Tpetra::Map<>(0, 0, Utilities::Trilinos::tpetra_comm_self())))) + : vector(new Tpetra::Vector( + Teuchos::RCP>( + new Tpetra::Map( + 0, + 0, + Utilities::Trilinos::tpetra_comm_self())))) {} @@ -51,7 +55,9 @@ namespace LinearAlgebra template Vector::Vector(const Vector &V) : Subscriptor() - , vector(new Tpetra::Vector(V.trilinos_vector(), Teuchos::Copy)) + , vector(new Tpetra::Vector( + V.trilinos_vector(), + Teuchos::Copy)) {} @@ -59,8 +65,9 @@ namespace LinearAlgebra template Vector::Vector(const IndexSet ¶llel_partitioner, const MPI_Comm &communicator) - : vector(new Tpetra::Vector(Teuchos::rcp(new Tpetra::Map<>( - parallel_partitioner.make_tpetra_map(communicator, false))))) + : vector(new Tpetra::Vector( + Teuchos::rcp(new Tpetra::Map( + parallel_partitioner.make_tpetra_map(communicator, false))))) {} @@ -71,11 +78,12 @@ namespace LinearAlgebra const MPI_Comm &communicator, const bool omit_zeroing_entries) { - Tpetra::Map<> input_map = + Tpetra::Map input_map = parallel_partitioner.make_tpetra_map(communicator, false); if (vector->getMap()->isSameAs(input_map) == false) - vector = std_cxx14::make_unique>( - Teuchos::rcp(new Tpetra::Map<>(input_map))); + vector = std_cxx14::make_unique< + Tpetra::Vector>(Teuchos::rcp( + new Tpetra::Map(input_map))); else if (omit_zeroing_entries == false) { vector->putScalar(0.); @@ -117,15 +125,16 @@ namespace LinearAlgebra { if (size() == V.size()) { - Tpetra::Import<> data_exchange(vector->getMap(), - V.trilinos_vector().getMap()); + Tpetra::Import data_exchange( + vector->getMap(), V.trilinos_vector().getMap()); vector->doImport(V.trilinos_vector(), data_exchange, Tpetra::REPLACE); } else - vector = std_cxx14::make_unique>( + vector = std_cxx14::make_unique< + Tpetra::Vector>( V.trilinos_vector()); } @@ -185,8 +194,10 @@ namespace LinearAlgebra "LinearAlgebra::TpetraWrappers::CommunicationPattern.")); } - Tpetra::Export<> tpetra_export(tpetra_comm_pattern->get_tpetra_export()); - Tpetra::Vector source_vector(tpetra_export.getSourceMap()); + Tpetra::Export tpetra_export( + tpetra_comm_pattern->get_tpetra_export()); + Tpetra::Vector source_vector( + tpetra_export.getSourceMap()); source_vector.template sync(); auto x_2d = source_vector.template getLocalView(); @@ -197,7 +208,8 @@ namespace LinearAlgebra for (size_t k = 0; k < localLength; ++k) x_1d(k) = *values_it++; source_vector.template sync< - typename Tpetra::Vector::device_type::memory_space>(); + typename Tpetra::Vector:: + device_type::memory_space>(); if (operation == VectorOperation::insert) vector->doExport(source_vector, tpetra_export, Tpetra::REPLACE); else if (operation == VectorOperation::add) @@ -254,15 +266,16 @@ namespace LinearAlgebra ExcDimensionMismatch(this->size(), down_V.size())); // TODO: The code doesn't work as expected so we use a workaround. - /*Tpetra::Export<> data_exchange(vector->getMap(), - down_V.trilinos_vector().getMap()); + /*Tpetra::Export + data_exchange(vector->getMap(), down_V.trilinos_vector().getMap()); vector->doExport(down_V.trilinos_vector(), data_exchange, Tpetra::ADD);*/ - Tpetra::Vector dummy(vector->getMap(), false); - Tpetra::Import<> data_exchange(dummy.getMap(), - down_V.trilinos_vector().getMap()); + Tpetra::Vector dummy( + vector->getMap(), false); + Tpetra::Import data_exchange( + dummy.getMap(), down_V.trilinos_vector().getMap()); dummy.doExport(down_V.trilinos_vector(), data_exchange, @@ -322,7 +335,8 @@ namespace LinearAlgebra vector_1d(k) += a; } vector->template sync< - typename Tpetra::Vector::device_type::memory_space>(); + typename Tpetra::Vector:: + device_type::memory_space>(); } @@ -577,7 +591,7 @@ namespace LinearAlgebra template - const Tpetra::Vector & + const Tpetra::Vector & Vector::trilinos_vector() const { return *vector; @@ -586,7 +600,7 @@ namespace LinearAlgebra template - Tpetra::Vector & + Tpetra::Vector & Vector::trilinos_vector() { return *vector; From 07794a069292a47a4a25567b0a702f47a2a8da4a Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Mon, 28 Jan 2019 18:09:41 +0100 Subject: [PATCH 157/507] Add include files and restrict complex values --- include/deal.II/base/utilities.h | 2 ++ source/lac/trilinos_tpetra_vector.cc | 2 ++ 2 files changed, 4 insertions(+) diff --git a/include/deal.II/base/utilities.h b/include/deal.II/base/utilities.h index dc7414587e54..ed8724b16211 100644 --- a/include/deal.II/base/utilities.h +++ b/include/deal.II/base/utilities.h @@ -30,6 +30,8 @@ #ifdef DEAL_II_WITH_TRILINOS # include # include +# include +# include # ifdef DEAL_II_WITH_MPI # include # else diff --git a/source/lac/trilinos_tpetra_vector.cc b/source/lac/trilinos_tpetra_vector.cc index f4e368669728..8f20b0682817 100644 --- a/source/lac/trilinos_tpetra_vector.cc +++ b/source/lac/trilinos_tpetra_vector.cc @@ -672,8 +672,10 @@ namespace LinearAlgebra template class Vector; template class Vector; +#ifdef DEAL_II_WITH_COMPLEX_VALUES template class Vector>; template class Vector>; +#endif } // namespace TpetraWrappers } // namespace LinearAlgebra From 1581b8987ffdadf041a5937f3ab5595c2be53c13 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Sat, 2 Feb 2019 15:53:03 +0100 Subject: [PATCH 158/507] Fix complex tests --- tests/trilinos/tpetra_vector_01.cc | 2 + tests/trilinos/tpetra_vector_02.cc | 2 + tests/trilinos/tpetra_vector_03.cc | 2 + ...03.with_complex_values=off.mpirun=2.output | 121 +++++++++ ...03.with_complex_values=off.mpirun=4.output | 253 ++++++++++++++++++ ...03.with_complex_values=on.mpirun=2.output} | 0 ...03.with_complex_values=on.mpirun=4.output} | 0 7 files changed, 380 insertions(+) create mode 100644 tests/trilinos/tpetra_vector_03.with_complex_values=off.mpirun=2.output create mode 100644 tests/trilinos/tpetra_vector_03.with_complex_values=off.mpirun=4.output rename tests/trilinos/{tpetra_vector_03.mpirun=2.output => tpetra_vector_03.with_complex_values=on.mpirun=2.output} (100%) rename tests/trilinos/{tpetra_vector_03.mpirun=4.output => tpetra_vector_03.with_complex_values=on.mpirun=4.output} (100%) diff --git a/tests/trilinos/tpetra_vector_01.cc b/tests/trilinos/tpetra_vector_01.cc index a294f785032c..90c13ee39064 100644 --- a/tests/trilinos/tpetra_vector_01.cc +++ b/tests/trilinos/tpetra_vector_01.cc @@ -223,8 +223,10 @@ main(int argc, char **argv) test(); test(); +#ifdef DEAL_II_WITH_COMPLEX_VALUES test>(); test>(); +#endif deallog << "OK" << std::endl; diff --git a/tests/trilinos/tpetra_vector_02.cc b/tests/trilinos/tpetra_vector_02.cc index 132231491b18..5f44f3a7b269 100644 --- a/tests/trilinos/tpetra_vector_02.cc +++ b/tests/trilinos/tpetra_vector_02.cc @@ -217,8 +217,10 @@ main(int argc, char **argv) test(); test(); +#ifdef DEAL_II_WITH_COMPLEX_VALUES test>(); test>(); +#endif deallog << "OK" << std::endl; diff --git a/tests/trilinos/tpetra_vector_03.cc b/tests/trilinos/tpetra_vector_03.cc index d97b8ce13ad2..e807d30462b4 100644 --- a/tests/trilinos/tpetra_vector_03.cc +++ b/tests/trilinos/tpetra_vector_03.cc @@ -101,6 +101,8 @@ main(int argc, char **argv) MPILogInitAll log; test(); test(); +#ifdef DEAL_II_WITH_COMPLEX_VALUES test>(); test>(); +#endif } diff --git a/tests/trilinos/tpetra_vector_03.with_complex_values=off.mpirun=2.output b/tests/trilinos/tpetra_vector_03.with_complex_values=off.mpirun=2.output new file mode 100644 index 000000000000..e94f192176bc --- /dev/null +++ b/tests/trilinos/tpetra_vector_03.with_complex_values=off.mpirun=2.output @@ -0,0 +1,121 @@ + +DEAL:0::Tpetra first import add: +2.000e+00 1.000e+02 +IndexSet: {[0,2]} + +[0]: 1.000e+00 +[1]: 1.000e+02 +[2]: 1.000e+01 +DEAL:0::Tpetra second import add: +4.000e+00 2.000e+02 +IndexSet: {[0,2]} + +[0]: 2.000e+00 +[1]: 2.000e+02 +[2]: 2.000e+01 +DEAL:0::ReadWrite import add: +IndexSet: {[0,2]} + +[0]: 6.000e+00 +[1]: 4.000e+02 +[2]: 5.000e+01 +DEAL:0::ReadWrite import min: +IndexSet: {[0,2]} + +[0]: 4.000e+00 +[1]: 1.000e+00 +[2]: 3.000e+01 +DEAL:0::ReadWrite import max: +IndexSet: {[0,2]} + +[0]: 4.000e+00 +[1]: 2.000e+02 +[2]: 1.000e+02 +DEAL:0::Tpetra first import add: +2.000e+00 1.000e+02 +IndexSet: {[0,2]} + +[0]: 1.000e+00 +[1]: 1.000e+02 +[2]: 1.000e+01 +DEAL:0::Tpetra second import add: +4.000e+00 2.000e+02 +IndexSet: {[0,2]} + +[0]: 2.000e+00 +[1]: 2.000e+02 +[2]: 2.000e+01 +DEAL:0::ReadWrite import add: +IndexSet: {[0,2]} + +[0]: 6.000e+00 +[1]: 4.000e+02 +[2]: 5.000e+01 +DEAL:0::ReadWrite import min: +IndexSet: {[0,2]} + +[0]: 4.000e+00 +[1]: 1.000e+00 +[2]: 3.000e+01 +DEAL:0::ReadWrite import max: +IndexSet: {[0,2]} + +[0]: 4.000e+00 +[1]: 2.000e+02 +[2]: 1.000e+02 + +DEAL:1::Tpetra first import add: +1.000e+01 1.010e+02 +IndexSet: {0, 3} + +[0]: 1.000e+00 +[3]: 1.010e+02 +DEAL:1::Tpetra second import add: +3.000e+01 2.010e+02 +IndexSet: {0, 3} + +[0]: 2.000e+00 +[3]: 2.010e+02 +DEAL:1::ReadWrite import add: +IndexSet: {0, 3} + +[0]: 6.000e+00 +[3]: 4.020e+02 +DEAL:1::ReadWrite import min: +IndexSet: {0, 3} + +[0]: 4.000e+00 +[3]: 1.000e+00 +DEAL:1::ReadWrite import max: +IndexSet: {0, 3} + +[0]: 4.000e+00 +[3]: 2.010e+02 +DEAL:1::Tpetra first import add: +1.000e+01 1.010e+02 +IndexSet: {0, 3} + +[0]: 1.000e+00 +[3]: 1.010e+02 +DEAL:1::Tpetra second import add: +3.000e+01 2.010e+02 +IndexSet: {0, 3} + +[0]: 2.000e+00 +[3]: 2.010e+02 +DEAL:1::ReadWrite import add: +IndexSet: {0, 3} + +[0]: 6.000e+00 +[3]: 4.020e+02 +DEAL:1::ReadWrite import min: +IndexSet: {0, 3} + +[0]: 4.000e+00 +[3]: 1.000e+00 +DEAL:1::ReadWrite import max: +IndexSet: {0, 3} + +[0]: 4.000e+00 +[3]: 2.010e+02 + diff --git a/tests/trilinos/tpetra_vector_03.with_complex_values=off.mpirun=4.output b/tests/trilinos/tpetra_vector_03.with_complex_values=off.mpirun=4.output new file mode 100644 index 000000000000..5fbf8dea2d1f --- /dev/null +++ b/tests/trilinos/tpetra_vector_03.with_complex_values=off.mpirun=4.output @@ -0,0 +1,253 @@ + +DEAL:0::Tpetra first import add: +4.000e+00 1.000e+02 +IndexSet: {[0,2]} + +[0]: 1.000e+00 +[1]: 1.000e+02 +[2]: 1.000e+01 +DEAL:0::Tpetra second import add: +8.000e+00 2.000e+02 +IndexSet: {[0,2]} + +[0]: 2.000e+00 +[1]: 2.000e+02 +[2]: 2.000e+01 +DEAL:0::ReadWrite import add: +IndexSet: {[0,2]} + +[0]: 1.000e+01 +[1]: 4.000e+02 +[2]: 5.000e+01 +DEAL:0::ReadWrite import min: +IndexSet: {[0,2]} + +[0]: 4.000e+00 +[1]: 1.000e+00 +[2]: 3.000e+01 +DEAL:0::ReadWrite import max: +IndexSet: {[0,2]} + +[0]: 8.000e+00 +[1]: 2.000e+02 +[2]: 1.000e+02 +DEAL:0::Tpetra first import add: +4.000e+00 1.000e+02 +IndexSet: {[0,2]} + +[0]: 1.000e+00 +[1]: 1.000e+02 +[2]: 1.000e+01 +DEAL:0::Tpetra second import add: +8.000e+00 2.000e+02 +IndexSet: {[0,2]} + +[0]: 2.000e+00 +[1]: 2.000e+02 +[2]: 2.000e+01 +DEAL:0::ReadWrite import add: +IndexSet: {[0,2]} + +[0]: 1.000e+01 +[1]: 4.000e+02 +[2]: 5.000e+01 +DEAL:0::ReadWrite import min: +IndexSet: {[0,2]} + +[0]: 4.000e+00 +[1]: 1.000e+00 +[2]: 3.000e+01 +DEAL:0::ReadWrite import max: +IndexSet: {[0,2]} + +[0]: 8.000e+00 +[1]: 2.000e+02 +[2]: 1.000e+02 + +DEAL:1::Tpetra first import add: +1.000e+01 1.010e+02 +IndexSet: {0, [3,4]} + +[0]: 1.000e+00 +[3]: 1.010e+02 +[4]: 1.100e+01 +DEAL:1::Tpetra second import add: +3.000e+01 2.010e+02 +IndexSet: {0, [3,4]} + +[0]: 2.000e+00 +[3]: 2.010e+02 +[4]: 2.100e+01 +DEAL:1::ReadWrite import add: +IndexSet: {0, [3,4]} + +[0]: 1.000e+01 +[3]: 4.020e+02 +[4]: 5.300e+01 +DEAL:1::ReadWrite import min: +IndexSet: {0, [3,4]} + +[0]: 4.000e+00 +[3]: 1.000e+00 +[4]: 3.200e+01 +DEAL:1::ReadWrite import max: +IndexSet: {0, [3,4]} + +[0]: 8.000e+00 +[3]: 2.010e+02 +[4]: 1.010e+02 +DEAL:1::Tpetra first import add: +1.000e+01 1.010e+02 +IndexSet: {0, [3,4]} + +[0]: 1.000e+00 +[3]: 1.010e+02 +[4]: 1.100e+01 +DEAL:1::Tpetra second import add: +3.000e+01 2.010e+02 +IndexSet: {0, [3,4]} + +[0]: 2.000e+00 +[3]: 2.010e+02 +[4]: 2.100e+01 +DEAL:1::ReadWrite import add: +IndexSet: {0, [3,4]} + +[0]: 1.000e+01 +[3]: 4.020e+02 +[4]: 5.300e+01 +DEAL:1::ReadWrite import min: +IndexSet: {0, [3,4]} + +[0]: 4.000e+00 +[3]: 1.000e+00 +[4]: 3.200e+01 +DEAL:1::ReadWrite import max: +IndexSet: {0, [3,4]} + +[0]: 8.000e+00 +[3]: 2.010e+02 +[4]: 1.010e+02 + + +DEAL:2::Tpetra first import add: +1.100e+01 1.020e+02 +IndexSet: {0, [5,6]} + +[0]: 1.000e+00 +[5]: 1.020e+02 +[6]: 1.200e+01 +DEAL:2::Tpetra second import add: +3.200e+01 2.020e+02 +IndexSet: {0, [5,6]} + +[0]: 2.000e+00 +[5]: 2.020e+02 +[6]: 2.200e+01 +DEAL:2::ReadWrite import add: +IndexSet: {0, [5,6]} + +[0]: 1.000e+01 +[5]: 4.040e+02 +[6]: 5.600e+01 +DEAL:2::ReadWrite import min: +IndexSet: {0, [5,6]} + +[0]: 4.000e+00 +[5]: 1.000e+00 +[6]: 3.400e+01 +DEAL:2::ReadWrite import max: +IndexSet: {0, [5,6]} + +[0]: 8.000e+00 +[5]: 2.020e+02 +[6]: 1.020e+02 +DEAL:2::Tpetra first import add: +1.100e+01 1.020e+02 +IndexSet: {0, [5,6]} + +[0]: 1.000e+00 +[5]: 1.020e+02 +[6]: 1.200e+01 +DEAL:2::Tpetra second import add: +3.200e+01 2.020e+02 +IndexSet: {0, [5,6]} + +[0]: 2.000e+00 +[5]: 2.020e+02 +[6]: 2.200e+01 +DEAL:2::ReadWrite import add: +IndexSet: {0, [5,6]} + +[0]: 1.000e+01 +[5]: 4.040e+02 +[6]: 5.600e+01 +DEAL:2::ReadWrite import min: +IndexSet: {0, [5,6]} + +[0]: 4.000e+00 +[5]: 1.000e+00 +[6]: 3.400e+01 +DEAL:2::ReadWrite import max: +IndexSet: {0, [5,6]} + +[0]: 8.000e+00 +[5]: 2.020e+02 +[6]: 1.020e+02 + + +DEAL:3::Tpetra first import add: +1.200e+01 1.030e+02 +IndexSet: {0, 7} + +[0]: 1.000e+00 +[7]: 1.030e+02 +DEAL:3::Tpetra second import add: +3.400e+01 2.030e+02 +IndexSet: {0, 7} + +[0]: 2.000e+00 +[7]: 2.030e+02 +DEAL:3::ReadWrite import add: +IndexSet: {0, 7} + +[0]: 1.000e+01 +[7]: 4.060e+02 +DEAL:3::ReadWrite import min: +IndexSet: {0, 7} + +[0]: 4.000e+00 +[7]: 1.000e+00 +DEAL:3::ReadWrite import max: +IndexSet: {0, 7} + +[0]: 8.000e+00 +[7]: 2.030e+02 +DEAL:3::Tpetra first import add: +1.200e+01 1.030e+02 +IndexSet: {0, 7} + +[0]: 1.000e+00 +[7]: 1.030e+02 +DEAL:3::Tpetra second import add: +3.400e+01 2.030e+02 +IndexSet: {0, 7} + +[0]: 2.000e+00 +[7]: 2.030e+02 +DEAL:3::ReadWrite import add: +IndexSet: {0, 7} + +[0]: 1.000e+01 +[7]: 4.060e+02 +DEAL:3::ReadWrite import min: +IndexSet: {0, 7} + +[0]: 4.000e+00 +[7]: 1.000e+00 +DEAL:3::ReadWrite import max: +IndexSet: {0, 7} + +[0]: 8.000e+00 +[7]: 2.030e+02 + diff --git a/tests/trilinos/tpetra_vector_03.mpirun=2.output b/tests/trilinos/tpetra_vector_03.with_complex_values=on.mpirun=2.output similarity index 100% rename from tests/trilinos/tpetra_vector_03.mpirun=2.output rename to tests/trilinos/tpetra_vector_03.with_complex_values=on.mpirun=2.output diff --git a/tests/trilinos/tpetra_vector_03.mpirun=4.output b/tests/trilinos/tpetra_vector_03.with_complex_values=on.mpirun=4.output similarity index 100% rename from tests/trilinos/tpetra_vector_03.mpirun=4.output rename to tests/trilinos/tpetra_vector_03.with_complex_values=on.mpirun=4.output From dd2b650e34e6f01e37ec9f7b82973fcf706fe8fb Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Sat, 2 Feb 2019 17:17:09 +0100 Subject: [PATCH 159/507] Indentation --- include/deal.II/base/utilities.h | 2 +- source/lac/trilinos_tpetra_vector.cc | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/include/deal.II/base/utilities.h b/include/deal.II/base/utilities.h index ed8724b16211..13694ea9497b 100644 --- a/include/deal.II/base/utilities.h +++ b/include/deal.II/base/utilities.h @@ -30,8 +30,8 @@ #ifdef DEAL_II_WITH_TRILINOS # include # include -# include # include +# include # ifdef DEAL_II_WITH_MPI # include # else diff --git a/source/lac/trilinos_tpetra_vector.cc b/source/lac/trilinos_tpetra_vector.cc index 8f20b0682817..6eb2b6e1f71d 100644 --- a/source/lac/trilinos_tpetra_vector.cc +++ b/source/lac/trilinos_tpetra_vector.cc @@ -672,10 +672,10 @@ namespace LinearAlgebra template class Vector; template class Vector; -#ifdef DEAL_II_WITH_COMPLEX_VALUES +# ifdef DEAL_II_WITH_COMPLEX_VALUES template class Vector>; template class Vector>; -#endif +# endif } // namespace TpetraWrappers } // namespace LinearAlgebra From c1356b3c4ad5a1e7503166467a1d5e568eb0711d Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Tue, 5 Feb 2019 21:56:33 +0100 Subject: [PATCH 160/507] Make Tpetra optional --- cmake/configure/configure_2_trilinos.cmake | 10 ++++++---- include/deal.II/base/config.h.in | 1 + include/deal.II/base/index_set.h | 6 +++++- include/deal.II/dofs/dof_accessor.templates.h | 2 ++ .../fe/fe_tools_extrapolate.templates.h | 2 ++ .../fe/fe_tools_interpolate.templates.h | 2 ++ include/deal.II/lac/read_write_vector.h | 6 ++++++ .../deal.II/lac/read_write_vector.templates.h | 7 +++++++ .../trilinos_tpetra_communication_pattern.h | 14 +++++--------- include/deal.II/lac/trilinos_tpetra_vector.h | 2 +- include/deal.II/lac/vector_element_access.h | 2 ++ include/deal.II/multigrid/mg_transfer.h | 2 ++ source/base/index_set.cc | 19 ++++++++++--------- source/lac/trilinos_sparse_matrix.cc | 10 ++++++++++ .../trilinos_tpetra_communication_pattern.cc | 2 +- source/lac/trilinos_tpetra_vector.cc | 2 +- ...run=2.with_trilinos_with_tpetra=on.output} | 0 ...run=2.with_trilinos_with_tpetra=on.output} | 0 ...n.with_complex_values=off.mpirun=2.output} | 0 ...n.with_complex_values=off.mpirun=4.output} | 0 ...on.with_complex_values=on.mpirun=2.output} | 0 ...on.with_complex_values=on.mpirun=4.output} | 0 22 files changed, 63 insertions(+), 26 deletions(-) rename tests/trilinos/{tpetra_vector_01.mpirun=2.output => tpetra_vector_01.mpirun=2.with_trilinos_with_tpetra=on.output} (100%) rename tests/trilinos/{tpetra_vector_02.mpirun=2.output => tpetra_vector_02.mpirun=2.with_trilinos_with_tpetra=on.output} (100%) rename tests/trilinos/{tpetra_vector_03.with_complex_values=off.mpirun=2.output => tpetra_vector_03.with_trilinos_with_tpetra=on.with_complex_values=off.mpirun=2.output} (100%) rename tests/trilinos/{tpetra_vector_03.with_complex_values=off.mpirun=4.output => tpetra_vector_03.with_trilinos_with_tpetra=on.with_complex_values=off.mpirun=4.output} (100%) rename tests/trilinos/{tpetra_vector_03.with_complex_values=on.mpirun=2.output => tpetra_vector_03.with_trilinos_with_tpetra=on.with_complex_values=on.mpirun=2.output} (100%) rename tests/trilinos/{tpetra_vector_03.with_complex_values=on.mpirun=4.output => tpetra_vector_03.with_trilinos_with_tpetra=on.with_complex_values=on.mpirun=4.output} (100%) diff --git a/cmake/configure/configure_2_trilinos.cmake b/cmake/configure/configure_2_trilinos.cmake index c159fe255270..eca8862a0a40 100644 --- a/cmake/configure/configure_2_trilinos.cmake +++ b/cmake/configure/configure_2_trilinos.cmake @@ -42,7 +42,7 @@ MACRO(FEATURE_TRILINOS_FIND_EXTERNAL var) ) FOREACH(_module - Amesos Epetra Ifpack AztecOO Teuchos Tpetra ML MueLu + Amesos Epetra Ifpack AztecOO Teuchos ML MueLu ) ITEM_MATCHES(_module_found ${_module} ${Trilinos_PACKAGE_LIST}) IF(_module_found) @@ -146,7 +146,7 @@ MACRO(FEATURE_TRILINOS_FIND_EXTERNAL var) CHECK_MPI_INTERFACE(TRILINOS ${var}) IF (${var}) - FOREACH(_optional_module EpetraExt ROL Sacado Zoltan) + FOREACH(_optional_module EpetraExt ROL Sacado Tpetra Zoltan) ITEM_MATCHES(_module_found ${_optional_module} ${Trilinos_PACKAGE_LIST}) IF(_module_found) MESSAGE(STATUS "Found ${_optional_module}") @@ -227,8 +227,10 @@ MACRO(FEATURE_TRILINOS_CONFIGURE_EXTERNAL) SET(DEAL_II_EXPAND_TRILINOS_MPI_VECTOR "TrilinosWrappers::MPI::Vector") IF (TRILINOS_WITH_MPI) SET(DEAL_II_EXPAND_EPETRA_VECTOR "LinearAlgebra::EpetraWrappers::Vector") - SET(DEAL_II_EXPAND_TPETRA_VECTOR_DOUBLE "LinearAlgebra::TpetraWrappers::Vector") - SET(DEAL_II_EXPAND_TPETRA_VECTOR_FLOAT "LinearAlgebra::TpetraWrappers::Vector") + IF (${DEAL_II_TRILINOS_WITH_TPETRA}) + SET(DEAL_II_EXPAND_TPETRA_VECTOR_DOUBLE "LinearAlgebra::TpetraWrappers::Vector") + SET(DEAL_II_EXPAND_TPETRA_VECTOR_FLOAT "LinearAlgebra::TpetraWrappers::Vector") + ENDIF() ENDIF() IF(${DEAL_II_TRILINOS_WITH_SACADO}) # Note: Only CMake 3.0 and greater support line continuation with the "\" character diff --git a/include/deal.II/base/config.h.in b/include/deal.II/base/config.h.in index 23690507599d..6cf6971a90f7 100644 --- a/include/deal.II/base/config.h.in +++ b/include/deal.II/base/config.h.in @@ -186,6 +186,7 @@ #cmakedefine DEAL_II_TRILINOS_WITH_EPETRAEXT #cmakedefine DEAL_II_TRILINOS_WITH_ROL #cmakedefine DEAL_II_TRILINOS_WITH_SACADO +#cmakedefine DEAL_II_TRILINOS_WITH_TPETRA #cmakedefine DEAL_II_TRILINOS_WITH_ZOLTAN diff --git a/include/deal.II/base/index_set.h b/include/deal.II/base/index_set.h index afb90fe2d784..4800633ada5d 100644 --- a/include/deal.II/base/index_set.h +++ b/include/deal.II/base/index_set.h @@ -31,7 +31,9 @@ #ifdef DEAL_II_WITH_TRILINOS # include -# include +# ifdef DEAL_II_TRILINOS_WITH_TPETRA +# include +# endif #endif #if defined(DEAL_II_WITH_MPI) || defined(DEAL_II_WITH_PETSC) @@ -448,9 +450,11 @@ class IndexSet make_trilinos_map(const MPI_Comm &communicator = MPI_COMM_WORLD, const bool overlapping = false) const; +# ifdef DEAL_II_TRILINOS_WITH_TPETRA Tpetra::Map make_tpetra_map(const MPI_Comm &communicator = MPI_COMM_WORLD, const bool overlapping = false) const; +# endif #endif diff --git a/include/deal.II/dofs/dof_accessor.templates.h b/include/deal.II/dofs/dof_accessor.templates.h index 9b89e6e31f47..d7a097f66917 100644 --- a/include/deal.II/dofs/dof_accessor.templates.h +++ b/include/deal.II/dofs/dof_accessor.templates.h @@ -1534,6 +1534,7 @@ namespace internal +# ifdef DEAL_II_TRILINOS_WITH_TPETRA template static void extract_subvector_to( @@ -1559,6 +1560,7 @@ namespace internal for (unsigned int i = 0; i < cache_size; ++i, ++local_values_begin) *local_values_begin = read_write_vector[sorted_indices_pos[i]]; } +# endif diff --git a/include/deal.II/fe/fe_tools_extrapolate.templates.h b/include/deal.II/fe/fe_tools_extrapolate.templates.h index ea76059356c7..eb210626d7c5 100644 --- a/include/deal.II/fe/fe_tools_extrapolate.templates.h +++ b/include/deal.II/fe/fe_tools_extrapolate.templates.h @@ -1581,6 +1581,7 @@ namespace FETools # ifdef DEAL_II_WITH_MPI +# ifdef DEAL_II_TRILINOS_WITH_TPETRA template void reinit_distributed(const DoFHandler & dh, @@ -1595,6 +1596,7 @@ namespace FETools const IndexSet &locally_owned_dofs = dh.locally_owned_dofs(); vector.reinit(locally_owned_dofs, parallel_tria->get_communicator()); } +# endif template void diff --git a/include/deal.II/fe/fe_tools_interpolate.templates.h b/include/deal.II/fe/fe_tools_interpolate.templates.h index 9699c0a9b43d..a453ae0572b4 100644 --- a/include/deal.II/fe/fe_tools_interpolate.templates.h +++ b/include/deal.II/fe/fe_tools_interpolate.templates.h @@ -513,6 +513,7 @@ namespace FETools AssertThrow(false, ExcNotImplemented()); } +# ifdef DEAL_II_TRILINOS_WITH_TPETRA template void back_interpolate( @@ -527,6 +528,7 @@ namespace FETools { AssertThrow(false, ExcNotImplemented()); } +# endif #endif diff --git a/include/deal.II/lac/read_write_vector.h b/include/deal.II/lac/read_write_vector.h index b72a95eae233..f752ff815aa1 100644 --- a/include/deal.II/lac/read_write_vector.h +++ b/include/deal.II/lac/read_write_vector.h @@ -335,6 +335,7 @@ namespace LinearAlgebra std::shared_ptr()); # ifdef DEAL_II_WITH_MPI +# ifdef DEAL_II_TRILINOS_WITH_TPETRA /** * Imports all the elements present in the vector's IndexSet from the input * vector @p tpetra_vec. VectorOperation::values @p operation is used to @@ -349,6 +350,7 @@ namespace LinearAlgebra const std::shared_ptr &communication_pattern = std::shared_ptr()); +# endif /** * Imports all the elements present in the vector's IndexSet from the input @@ -609,6 +611,7 @@ namespace LinearAlgebra protected: #ifdef DEAL_II_WITH_TRILINOS +# ifdef DEAL_II_TRILINOS_WITH_TPETRA /** * Import all the elements present in the vector's IndexSet from the input * vector @p tpetra_vector. This is an helper function and it should not be @@ -622,6 +625,7 @@ namespace LinearAlgebra const MPI_Comm & mpi_comm, const std::shared_ptr &communication_pattern); +# endif /** * Import all the elements present in the vector's IndexSet from the input @@ -656,6 +660,7 @@ namespace LinearAlgebra resize_val(const size_type new_allocated_size); #if defined(DEAL_II_WITH_TRILINOS) && defined(DEAL_II_WITH_MPI) +# ifdef DEAL_II_TRILINOS_WITH_TPETRA /** * Return a TpetraWrappers::CommunicationPattern and store it for future * use. @@ -663,6 +668,7 @@ namespace LinearAlgebra TpetraWrappers::CommunicationPattern create_tpetra_comm_pattern(const IndexSet &source_index_set, const MPI_Comm &mpi_comm); +# endif /** * Return a EpetraWrappers::CommunicationPattern and store it for future diff --git a/include/deal.II/lac/read_write_vector.templates.h b/include/deal.II/lac/read_write_vector.templates.h index 572c28f1dec9..1444b00856d5 100644 --- a/include/deal.II/lac/read_write_vector.templates.h +++ b/include/deal.II/lac/read_write_vector.templates.h @@ -506,6 +506,7 @@ namespace LinearAlgebra #if defined(DEAL_II_WITH_TRILINOS) && defined(DEAL_II_WITH_MPI) +# ifdef DEAL_II_TRILINOS_WITH_TPETRA template void ReadWriteVector::import( @@ -595,6 +596,7 @@ namespace LinearAlgebra AssertThrow(false, ExcNotImplemented()); } } +# endif @@ -743,6 +745,7 @@ namespace LinearAlgebra +# ifdef DEAL_II_TRILINOS_WITH_TPETRA template void ReadWriteVector::import( @@ -757,6 +760,7 @@ namespace LinearAlgebra trilinos_vec.get_mpi_communicator(), communication_pattern); } +# endif @@ -901,6 +905,7 @@ namespace LinearAlgebra #if defined(DEAL_II_WITH_TRILINOS) && defined(DEAL_II_WITH_MPI) +# ifdef DEAL_II_TRILINOS_WITH_TPETRA template TpetraWrappers::CommunicationPattern ReadWriteVector::create_tpetra_comm_pattern( @@ -915,6 +920,8 @@ namespace LinearAlgebra return epetra_comm_pattern; } +# endif + template diff --git a/include/deal.II/lac/trilinos_tpetra_communication_pattern.h b/include/deal.II/lac/trilinos_tpetra_communication_pattern.h index fd3e074b2aa9..45c6f1d34dd9 100644 --- a/include/deal.II/lac/trilinos_tpetra_communication_pattern.h +++ b/include/deal.II/lac/trilinos_tpetra_communication_pattern.h @@ -19,16 +19,14 @@ #include -#ifdef DEAL_II_WITH_TRILINOS +#if defined(DEAL_II_TRILINOS_WITH_TPETRA) && defined(DEAL_II_WITH_MPI) -# ifdef DEAL_II_WITH_MPI +# include -# include +# include +# include -# include -# include - -# include +# include DEAL_II_NAMESPACE_OPEN @@ -102,8 +100,6 @@ namespace LinearAlgebra DEAL_II_NAMESPACE_CLOSE -# endif - #endif #endif diff --git a/include/deal.II/lac/trilinos_tpetra_vector.h b/include/deal.II/lac/trilinos_tpetra_vector.h index 911863c9d99e..a91d4e4b5547 100644 --- a/include/deal.II/lac/trilinos_tpetra_vector.h +++ b/include/deal.II/lac/trilinos_tpetra_vector.h @@ -19,7 +19,7 @@ #include -#if defined(DEAL_II_WITH_TRILINOS) && defined(DEAL_II_WITH_MPI) +#if defined(DEAL_II_TRILINOS_WITH_TPETRA) && defined(DEAL_II_WITH_MPI) # include # include diff --git a/include/deal.II/lac/vector_element_access.h b/include/deal.II/lac/vector_element_access.h index 4a81d97fdbc1..236203e19840 100644 --- a/include/deal.II/lac/vector_element_access.h +++ b/include/deal.II/lac/vector_element_access.h @@ -125,6 +125,7 @@ namespace internal +# ifdef DEAL_II_TRILINOS_WITH_TPETRA template <> inline void ElementAccess>::add( @@ -270,6 +271,7 @@ namespace internal // We're going to modify the data on host. return vector_1d(trilinos_i); } +# endif #endif } // namespace internal diff --git a/include/deal.II/multigrid/mg_transfer.h b/include/deal.II/multigrid/mg_transfer.h index 961b0223dfc3..82a82150e89e 100644 --- a/include/deal.II/multigrid/mg_transfer.h +++ b/include/deal.II/multigrid/mg_transfer.h @@ -132,6 +132,7 @@ namespace internal }; # ifdef DEAL_II_WITH_MPI +# ifdef DEAL_II_TRILINOS_WITH_TPETRA template struct MatrixSelector> { @@ -163,6 +164,7 @@ namespace internal true); } }; +# endif template <> struct MatrixSelector diff --git a/source/base/index_set.cc b/source/base/index_set.cc index d9257454852e..9e5cc43c279f 100644 --- a/source/base/index_set.cc +++ b/source/base/index_set.cc @@ -519,6 +519,7 @@ IndexSet::fill_index_vector(std::vector &indices) const #ifdef DEAL_II_WITH_TRILINOS +# ifdef DEAL_II_TRILINOS_WITH_TPETRA Tpetra::Map IndexSet::make_tpetra_map(const MPI_Comm &communicator, @@ -527,7 +528,7 @@ IndexSet::make_tpetra_map(const MPI_Comm &communicator, compress(); (void)communicator; -# ifdef DEBUG +# ifdef DEBUG if (!overlapping) { const size_type n_global_elements = @@ -549,7 +550,7 @@ IndexSet::make_tpetra_map(const MPI_Comm &communicator, "by any processor, or there are indices that are " "claimed by multiple processors.")); } -# endif +# endif // Find out if the IndexSet is ascending and 1:1. This corresponds to a // linear Tpetra::Map. Overlapping IndexSets are never 1:1. @@ -560,11 +561,11 @@ IndexSet::make_tpetra_map(const MPI_Comm &communicator, size(), n_elements(), 0, -# ifdef DEAL_II_WITH_MPI +# ifdef DEAL_II_WITH_MPI Teuchos::rcp(new Teuchos::MpiComm(communicator)) -# else +# else Teuchos::rcp(new Teuchos::Comm()) -# endif +# endif ); else { @@ -577,14 +578,15 @@ IndexSet::make_tpetra_map(const MPI_Comm &communicator, size(), arr_view, 0, -# ifdef DEAL_II_WITH_MPI +# ifdef DEAL_II_WITH_MPI Teuchos::rcp(new Teuchos::MpiComm(communicator)) -# else +# else Teuchos::rcp(new Teuchos::Comm()) -# endif +# endif ); } } +# endif @@ -657,7 +659,6 @@ IndexSet::make_trilinos_map(const MPI_Comm &communicator, #endif - bool IndexSet::is_ascending_and_one_to_one(const MPI_Comm &communicator) const { diff --git a/source/lac/trilinos_sparse_matrix.cc b/source/lac/trilinos_sparse_matrix.cc index 250a6d051918..d87c7e88c18b 100644 --- a/source/lac/trilinos_sparse_matrix.cc +++ b/source/lac/trilinos_sparse_matrix.cc @@ -104,6 +104,7 @@ namespace TrilinosWrappers return V.trilinos_vector()[0] + V.trilinos_vector().MyLength(); } +# ifdef DEAL_II_TRILINOS_WITH_TPETRA template Number * begin(LinearAlgebra::TpetraWrappers::Vector &V) @@ -133,6 +134,7 @@ namespace TrilinosWrappers return V.trilinos_vector().getData().get() + V.trilinos_vector().getLocalLength(); } +# endif # endif } // namespace internal @@ -3510,6 +3512,7 @@ namespace TrilinosWrappers const dealii::LinearAlgebra::distributed::Vector &) const; # ifdef DEAL_II_WITH_MPI +# ifdef DEAL_II_TRILINOS_WITH_TPETRA template void SparseMatrix::vmult( dealii::LinearAlgebra::TpetraWrappers::Vector &, @@ -3519,6 +3522,7 @@ namespace TrilinosWrappers SparseMatrix::vmult( dealii::LinearAlgebra::TpetraWrappers::Vector &, const dealii::LinearAlgebra::TpetraWrappers::Vector &) const; +# endif template void SparseMatrix::vmult( @@ -3539,6 +3543,7 @@ namespace TrilinosWrappers const dealii::LinearAlgebra::distributed::Vector &) const; # ifdef DEAL_II_WITH_MPI +# ifdef DEAL_II_TRILINOS_WITH_TPETRA template void SparseMatrix::Tvmult( dealii::LinearAlgebra::TpetraWrappers::Vector &, @@ -3548,6 +3553,7 @@ namespace TrilinosWrappers SparseMatrix::Tvmult( dealii::LinearAlgebra::TpetraWrappers::Vector &, const dealii::LinearAlgebra::TpetraWrappers::Vector &) const; +# endif template void SparseMatrix::Tvmult( @@ -3568,6 +3574,7 @@ namespace TrilinosWrappers const dealii::LinearAlgebra::distributed::Vector &) const; # ifdef DEAL_II_WITH_MPI +# ifdef DEAL_II_TRILINOS_WITH_TPETRA template void SparseMatrix::vmult_add( dealii::LinearAlgebra::TpetraWrappers::Vector &, @@ -3577,6 +3584,7 @@ namespace TrilinosWrappers SparseMatrix::vmult_add( dealii::LinearAlgebra::TpetraWrappers::Vector &, const dealii::LinearAlgebra::TpetraWrappers::Vector &) const; +# endif template void SparseMatrix::vmult_add( @@ -3597,6 +3605,7 @@ namespace TrilinosWrappers const dealii::LinearAlgebra::distributed::Vector &) const; # ifdef DEAL_II_WITH_MPI +# ifdef DEAL_II_TRILINOS_WITH_TPETRA template void SparseMatrix::Tvmult_add( dealii::LinearAlgebra::TpetraWrappers::Vector &, @@ -3606,6 +3615,7 @@ namespace TrilinosWrappers SparseMatrix::Tvmult_add( dealii::LinearAlgebra::TpetraWrappers::Vector &, const dealii::LinearAlgebra::TpetraWrappers::Vector &) const; +# endif template void SparseMatrix::Tvmult_add( diff --git a/source/lac/trilinos_tpetra_communication_pattern.cc b/source/lac/trilinos_tpetra_communication_pattern.cc index 626622d49d36..99d3aa5f57c4 100644 --- a/source/lac/trilinos_tpetra_communication_pattern.cc +++ b/source/lac/trilinos_tpetra_communication_pattern.cc @@ -17,7 +17,7 @@ #include -#ifdef DEAL_II_WITH_TRILINOS +#ifdef DEAL_II_TRILINOS_WITH_TPETRA # ifdef DEAL_II_WITH_MPI diff --git a/source/lac/trilinos_tpetra_vector.cc b/source/lac/trilinos_tpetra_vector.cc index 6eb2b6e1f71d..428182e91614 100644 --- a/source/lac/trilinos_tpetra_vector.cc +++ b/source/lac/trilinos_tpetra_vector.cc @@ -17,7 +17,7 @@ #include -#ifdef DEAL_II_WITH_TRILINOS +#ifdef DEAL_II_TRILINOS_WITH_TPETRA # ifdef DEAL_II_WITH_MPI diff --git a/tests/trilinos/tpetra_vector_01.mpirun=2.output b/tests/trilinos/tpetra_vector_01.mpirun=2.with_trilinos_with_tpetra=on.output similarity index 100% rename from tests/trilinos/tpetra_vector_01.mpirun=2.output rename to tests/trilinos/tpetra_vector_01.mpirun=2.with_trilinos_with_tpetra=on.output diff --git a/tests/trilinos/tpetra_vector_02.mpirun=2.output b/tests/trilinos/tpetra_vector_02.mpirun=2.with_trilinos_with_tpetra=on.output similarity index 100% rename from tests/trilinos/tpetra_vector_02.mpirun=2.output rename to tests/trilinos/tpetra_vector_02.mpirun=2.with_trilinos_with_tpetra=on.output diff --git a/tests/trilinos/tpetra_vector_03.with_complex_values=off.mpirun=2.output b/tests/trilinos/tpetra_vector_03.with_trilinos_with_tpetra=on.with_complex_values=off.mpirun=2.output similarity index 100% rename from tests/trilinos/tpetra_vector_03.with_complex_values=off.mpirun=2.output rename to tests/trilinos/tpetra_vector_03.with_trilinos_with_tpetra=on.with_complex_values=off.mpirun=2.output diff --git a/tests/trilinos/tpetra_vector_03.with_complex_values=off.mpirun=4.output b/tests/trilinos/tpetra_vector_03.with_trilinos_with_tpetra=on.with_complex_values=off.mpirun=4.output similarity index 100% rename from tests/trilinos/tpetra_vector_03.with_complex_values=off.mpirun=4.output rename to tests/trilinos/tpetra_vector_03.with_trilinos_with_tpetra=on.with_complex_values=off.mpirun=4.output diff --git a/tests/trilinos/tpetra_vector_03.with_complex_values=on.mpirun=2.output b/tests/trilinos/tpetra_vector_03.with_trilinos_with_tpetra=on.with_complex_values=on.mpirun=2.output similarity index 100% rename from tests/trilinos/tpetra_vector_03.with_complex_values=on.mpirun=2.output rename to tests/trilinos/tpetra_vector_03.with_trilinos_with_tpetra=on.with_complex_values=on.mpirun=2.output diff --git a/tests/trilinos/tpetra_vector_03.with_complex_values=on.mpirun=4.output b/tests/trilinos/tpetra_vector_03.with_trilinos_with_tpetra=on.with_complex_values=on.mpirun=4.output similarity index 100% rename from tests/trilinos/tpetra_vector_03.with_complex_values=on.mpirun=4.output rename to tests/trilinos/tpetra_vector_03.with_trilinos_with_tpetra=on.with_complex_values=on.mpirun=4.output From 2fb42804a16d8ab7667f30757c9459e9cface8a2 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Sun, 10 Feb 2019 00:53:53 +0100 Subject: [PATCH 161/507] Check if Tpetra is usable --- cmake/configure/configure_2_trilinos.cmake | 35 ++++++++++++++++++++++ 1 file changed, 35 insertions(+) diff --git a/cmake/configure/configure_2_trilinos.cmake b/cmake/configure/configure_2_trilinos.cmake index eca8862a0a40..9b3c86139577 100644 --- a/cmake/configure/configure_2_trilinos.cmake +++ b/cmake/configure/configure_2_trilinos.cmake @@ -158,6 +158,41 @@ MACRO(FEATURE_TRILINOS_FIND_EXTERNAL var) ENDFOREACH() ENDIF() + IF(${DEAL_II_TRILINOS_WITH_TPETRA}) + # + # Check if Tpetra is usable in fact. + # + LIST(APPEND CMAKE_REQUIRED_INCLUDES ${Trilinos_INCLUDE_DIRS}) + ADD_FLAGS(CMAKE_REQUIRED_FLAGS "${DEAL_II_CXX_VERSION_FLAG}") + LIST(APPEND CMAKE_REQUIRED_LIBRARIES "${Trilinos_LIBRARIES}") + CHECK_CXX_SOURCE_COMPILES( + " + #include + int + main() + { + using LO = int; + using GO = unsigned int; + using Node = Kokkos::Compat::KokkosDeviceWrapperNode; + using map_type = Tpetra::Map; + Teuchos::RCP dummy_map = Teuchos::rcp(new map_type()); + Tpetra::Vector dummy_vector(dummy_map); + (void)dummy_vector; + return 0; + } + " + TRILINOS_TPETRA_IS_FUNCTIONAL + ) + RESET_CMAKE_REQUIRED() + IF(NOT TRILINOS_TPETRA_IS_FUNCTIONAL) + MESSAGE( + STATUS + "Tpetra was found but is not usable! Disabling Tpetra support." + ) + SET(DEAL_II_TRILINOS_WITH_TPETRA OFF) + ENDIF() + ENDIF() + IF(${DEAL_II_TRILINOS_WITH_SACADO}) # # Look for Sacado_config.h - we'll query it to determine C++11 support: From c4c347acd7dfe495eaed9bd1bcf04d97cdca13d9 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Mon, 18 Feb 2019 12:44:20 +0100 Subject: [PATCH 162/507] Check for imaginary parts --- .../deal.II/lac/read_write_vector.templates.h | 88 ++++++++++++++++--- 1 file changed, 76 insertions(+), 12 deletions(-) diff --git a/include/deal.II/lac/read_write_vector.templates.h b/include/deal.II/lac/read_write_vector.templates.h index 1444b00856d5..cfbbc7db890b 100644 --- a/include/deal.II/lac/read_write_vector.templates.h +++ b/include/deal.II/lac/read_write_vector.templates.h @@ -581,15 +581,39 @@ namespace LinearAlgebra break; case VectorOperation::min: + // To ensure that this code also compiles with complex + // numbers, we only compare the real part of the + // variable. Note that min/max do not make sense with complex + // numbers. for (size_type i = 0; i < size; ++i) - if (std::real(new_values[i]) - std::real(values[i]) < 0.0) - values[i] = new_values[i]; + { + Assert( + std::imag(new_values[i]) == 0., + ExcMessage( + "VectorOperation::min is not defined if there is an imaginary part!)")); + Assert( + std::imag(values[i]) == 0., + ExcMessage( + "VectorOperation::min is not defined if there is an imaginary part!)")); + if (std::real(new_values[i]) - std::real(values[i]) < 0.0) + values[i] = new_values[i]; + } break; case VectorOperation::max: for (size_type i = 0; i < size; ++i) - if (std::real(new_values[i]) - std::real(values[i]) > 0.0) - values[i] = new_values[i]; + { + Assert( + std::imag(new_values[i]) == 0., + ExcMessage( + "VectorOperation::max is not defined if there is an imaginary part!)")); + Assert( + std::imag(values[i]) == 0., + ExcMessage( + "VectorOperation::max is not defined if there is an imaginary part!)")); + if (std::real(new_values[i]) - std::real(values[i]) > 0.0) + values[i] = new_values[i]; + } break; default: @@ -697,8 +721,18 @@ namespace LinearAlgebra // variable. Note that min/max do not make sense with complex // numbers. for (int i = 0; i < size; ++i) - if (std::real(new_values[i]) - std::real(values[i]) < 0.0) - values[i] = new_values[i]; + { + Assert( + std::imag(new_values[i]) == 0., + ExcMessage( + "VectorOperation::min is not defined if there is an imaginary part!)")); + Assert( + std::imag(values[i]) == 0., + ExcMessage( + "VectorOperation::min is not defined if there is an imaginary part!)")); + if (std::real(new_values[i]) - std::real(values[i]) < 0.0) + values[i] = new_values[i]; + } } else if (operation == VectorOperation::max) { @@ -713,8 +747,18 @@ namespace LinearAlgebra ExcInternalError("Import failed.")); for (int i = 0; i < size; ++i) - if (std::real(new_values[i]) - std::real(values[i]) > 0.0) - values[i] = new_values[i]; + { + Assert( + std::imag(new_values[i]) == 0., + ExcMessage( + "VectorOperation::max is not defined if there is an imaginary part!)")); + Assert( + std::imag(values[i]) == 0., + ExcMessage( + "VectorOperation::max is not defined if there is an imaginary part!)")); + if (std::real(new_values[i]) - std::real(values[i]) > 0.0) + values[i] = new_values[i]; + } } else AssertThrow(false, ExcNotImplemented()); @@ -828,8 +872,18 @@ namespace LinearAlgebra // variable. Note that min/max do not make sense with complex // numbers. for (unsigned int i = 0; i < n_elements; ++i) - if (std::real(tmp[i]) - std::real(values[i]) < 0.0) - values[i] = tmp[i]; + { + Assert( + std::imag(new_values[i]) == 0., + ExcMessage( + "VectorOperation::min is not defined if there is an imaginary part!)")); + Assert( + std::imag(values[i]) == 0., + ExcMessage( + "VectorOperation::min is not defined if there is an imaginary part!)")); + if (std::real(tmp[i]) - std::real(values[i]) < 0.0) + values[i] = tmp[i]; + } } else if (operation == VectorOperation::max) { @@ -842,8 +896,18 @@ namespace LinearAlgebra AssertCuda(error_code); for (unsigned int i = 0; i < n_elements; ++i) - if (std::real(tmp[i]) - std::real(values[i]) > 0.0) - values[i] = tmp[i]; + { + Assert( + std::imag(new_values[i]) == 0., + ExcMessage( + "VectorOperation::max is not defined if there is an imaginary part!)")); + Assert( + std::imag(values[i]) == 0., + ExcMessage( + "VectorOperation::max is not defined if there is an imaginary part!)")); + if (std::real(tmp[i]) - std::real(values[i]) > 0.0) + values[i] = tmp[i]; + } } else AssertThrow(false, ExcNotImplemented()); From 3f17effecbffe9217219e092a6d7576b81d94ca9 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Mon, 18 Feb 2019 14:58:40 +0100 Subject: [PATCH 163/507] Copyright dates and documentation --- include/deal.II/lac/trilinos_epetra_vector.h | 12 ++++++------ include/deal.II/lac/trilinos_sparse_matrix.h | 8 ++++---- .../lac/trilinos_tpetra_communication_pattern.h | 2 +- include/deal.II/lac/trilinos_tpetra_vector.h | 14 +++++++------- source/base/index_set.cc | 1 + .../lac/trilinos_tpetra_communication_pattern.cc | 2 +- source/lac/trilinos_tpetra_vector.cc | 2 +- tests/trilinos/tpetra_vector_01.cc | 2 +- tests/trilinos/tpetra_vector_02.cc | 2 +- tests/trilinos/tpetra_vector_03.cc | 2 +- 10 files changed, 24 insertions(+), 23 deletions(-) diff --git a/include/deal.II/lac/trilinos_epetra_vector.h b/include/deal.II/lac/trilinos_epetra_vector.h index b11b63ca616d..24b21e2774ee 100644 --- a/include/deal.II/lac/trilinos_epetra_vector.h +++ b/include/deal.II/lac/trilinos_epetra_vector.h @@ -55,7 +55,8 @@ namespace LinearAlgebra * This class implements a wrapper to the Trilinos distributed vector * class Epetra_FEVector. This class is derived from the * LinearAlgebra::VectorSpaceVector class. Note however that Epetra only - * works with Number = double. + * works with Number = double. This class requires Trilinos to be compiled + * with MPI support. * * @ingroup TrilinosWrappers * @ingroup Vectors @@ -96,7 +97,7 @@ namespace LinearAlgebra const bool omit_zeroing_entries = false); /** - * Change the dimension to that of the vector V. The elements of V are not + * Change the dimension to that of the vector @p V. The elements of @p V are not * copied. */ virtual void @@ -120,8 +121,7 @@ namespace LinearAlgebra /** * Imports all the elements present in the vector's IndexSet from the - * input - * vector @p V. VectorOperation::values @p operation is used to decide if + * input vector @p V. VectorOperation::values @p operation is used to decide if * the elements in @p V should be added to the current vector or replace the * current elements. The last parameter can be used if the same * communication pattern is used multiple times. This can be used to @@ -335,8 +335,8 @@ namespace LinearAlgebra memory_consumption() const override; /** - * The vectors have different partitioning, i.e. they have use different - * IndexSet. + * The vectors have different partitioning, i.e. their IndexSet objects + * don't represent the same indices. */ DeclException0(ExcDifferentParallelPartitioning); diff --git a/include/deal.II/lac/trilinos_sparse_matrix.h b/include/deal.II/lac/trilinos_sparse_matrix.h index 368fc70a12d4..4f8e955cb869 100644 --- a/include/deal.II/lac/trilinos_sparse_matrix.h +++ b/include/deal.II/lac/trilinos_sparse_matrix.h @@ -1577,7 +1577,7 @@ namespace TrilinosWrappers * of the matrix. * * This function will be called when the underlying number type for the - * matrix object and the one one for the vector object are the same. + * matrix object and the one for the vector object are the same. * * In case of a serial vector, this function will only work when * running on one processor, since the matrix object is inherently @@ -1591,7 +1591,7 @@ namespace TrilinosWrappers /** * Same as the function above for the case that the underlying number type * for the matrix object and the one for the vector object do not coincide. - * This case is not implemented. Calling it will result in an runtime error. + * This case is not implemented. Calling it will result in a runtime error. */ template typename std::enable_if typename std::enable_if typename std::enable_if Date: Mon, 18 Feb 2019 14:59:28 +0100 Subject: [PATCH 164/507] Generalize template specialization --- include/deal.II/lac/vector_element_access.h | 147 +++++++------------- 1 file changed, 48 insertions(+), 99 deletions(-) diff --git a/include/deal.II/lac/vector_element_access.h b/include/deal.II/lac/vector_element_access.h index 236203e19840..9e00b8de5807 100644 --- a/include/deal.II/lac/vector_element_access.h +++ b/include/deal.II/lac/vector_element_access.h @@ -126,147 +126,96 @@ namespace internal # ifdef DEAL_II_TRILINOS_WITH_TPETRA - template <> - inline void - ElementAccess>::add( - const double value, - const types::global_dof_index i, - LinearAlgebra::TpetraWrappers::Vector &V) + template + struct ElementAccess> { - // Extract local indices in the vector. - Tpetra::Vector vector = - V.trilinos_vector(); - TrilinosWrappers::types::int_type trilinos_i = - vector.getMap()->getLocalElement( - static_cast(i)); - - vector.sync(); - auto vector_2d = vector.getLocalView(); - auto vector_1d = Kokkos::subview(vector_2d, Kokkos::ALL(), 0); - // We're going to modify the data on host. - vector.modify(); - vector_1d(trilinos_i) += value; - vector.sync:: - device_type::memory_space>(); - } - - + public: + using VectorType = LinearAlgebra::TpetraWrappers::Vector; + static void + add(const typename VectorType::value_type value, + const types::global_dof_index i, + VectorType & V); - template <> - inline void - ElementAccess>::add( - const float value, - const types::global_dof_index i, - LinearAlgebra::TpetraWrappers::Vector &V) - { - // Extract local indices in the vector. - Tpetra::Vector vector = - V.trilinos_vector(); - TrilinosWrappers::types::int_type trilinos_i = - vector.getMap()->getLocalElement( - static_cast(i)); + static void + set(typename VectorType::value_type value, + const types::global_dof_index i, + VectorType & V); - vector.sync(); - auto vector_2d = vector.getLocalView(); - auto vector_1d = Kokkos::subview(vector_2d, Kokkos::ALL(), 0); - // We're going to modify the data on host. - vector.modify(); - vector_1d(trilinos_i) += value; - vector.sync:: - device_type::memory_space>(); - } + static typename VectorType::value_type + get(const VectorType &V, const types::global_dof_index i); + }; - template <> + template inline void - ElementAccess>::set( - const double value, - const types::global_dof_index i, - LinearAlgebra::TpetraWrappers::Vector &V) + ElementAccess>::add( + const typename VectorType::value_type value, + const types::global_dof_index i, + LinearAlgebra::TpetraWrappers::Vector &V) { // Extract local indices in the vector. - Tpetra::Vector vector = + Tpetra::Vector vector = V.trilinos_vector(); TrilinosWrappers::types::int_type trilinos_i = vector.getMap()->getLocalElement( static_cast(i)); - vector.sync(); - auto vector_2d = vector.getLocalView(); + vector.template sync(); + auto vector_2d = vector.template getLocalView(); auto vector_1d = Kokkos::subview(vector_2d, Kokkos::ALL(), 0); // We're going to modify the data on host. - vector.modify(); - vector_1d(trilinos_i) = value; - vector.sync:: - device_type::memory_space>(); + vector.template modify(); + vector_1d(trilinos_i) += value; + vector.template sync< + typename Tpetra::Vector:: + device_type::memory_space>(); } - template <> + template inline void - ElementAccess>::set( - const float value, - const types::global_dof_index i, - LinearAlgebra::TpetraWrappers::Vector &V) + ElementAccess>::set( + const typename VectorType::value_type value, + const types::global_dof_index i, + LinearAlgebra::TpetraWrappers::Vector &V) { // Extract local indices in the vector. - Tpetra::Vector vector = + Tpetra::Vector vector = V.trilinos_vector(); TrilinosWrappers::types::int_type trilinos_i = vector.getMap()->getLocalElement( static_cast(i)); - vector.sync(); - auto vector_2d = vector.getLocalView(); + vector.template sync(); + auto vector_2d = vector.template getLocalView(); auto vector_1d = Kokkos::subview(vector_2d, Kokkos::ALL(), 0); // We're going to modify the data on host. - vector.modify(); + vector.template modify(); vector_1d(trilinos_i) = value; - vector.sync:: - device_type::memory_space>(); + vector.template sync< + typename Tpetra::Vector:: + device_type::memory_space>(); } - template <> - inline double - ElementAccess>::get( - const LinearAlgebra::TpetraWrappers::Vector &V, - const types::global_dof_index i) - { - // Extract local indices in the vector. - Tpetra::Vector vector = - V.trilinos_vector(); - TrilinosWrappers::types::int_type trilinos_i = - vector.getMap()->getLocalElement( - static_cast(i)); - - vector.sync(); - auto vector_2d = vector.getLocalView(); - auto vector_1d = Kokkos::subview(vector_2d, Kokkos::ALL(), 0); - // We're going to modify the data on host. - return vector_1d(trilinos_i); - } - - - - template <> - inline float - ElementAccess>::get( - const LinearAlgebra::TpetraWrappers::Vector &V, - const types::global_dof_index i) + template + inline typename LinearAlgebra::TpetraWrappers::Vector::value_type + ElementAccess>::get( + const LinearAlgebra::TpetraWrappers::Vector &V, + const types::global_dof_index i) { // Extract local indices in the vector. - Tpetra::Vector vector = + Tpetra::Vector vector = V.trilinos_vector(); TrilinosWrappers::types::int_type trilinos_i = vector.getMap()->getLocalElement( static_cast(i)); - vector.sync(); - auto vector_2d = vector.getLocalView(); + vector.template sync(); + auto vector_2d = vector.template getLocalView(); auto vector_1d = Kokkos::subview(vector_2d, Kokkos::ALL(), 0); // We're going to modify the data on host. return vector_1d(trilinos_i); From bc11b29a358853de1152cd9d358049a0bbee19f4 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Mon, 18 Feb 2019 15:00:10 +0100 Subject: [PATCH 165/507] Call the base class constructor explicitly --- source/lac/trilinos_epetra_vector.cc | 6 ++++-- source/lac/trilinos_tpetra_vector.cc | 6 ++++-- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/source/lac/trilinos_epetra_vector.cc b/source/lac/trilinos_epetra_vector.cc index cc1857686f9b..64f2daad3fcf 100644 --- a/source/lac/trilinos_epetra_vector.cc +++ b/source/lac/trilinos_epetra_vector.cc @@ -41,7 +41,8 @@ namespace LinearAlgebra namespace EpetraWrappers { Vector::Vector() - : vector(new Epetra_FEVector( + : Subscriptor() + , vector(new Epetra_FEVector( Epetra_Map(0, 0, 0, Utilities::Trilinos::comm_self()))) {} @@ -56,7 +57,8 @@ namespace LinearAlgebra Vector::Vector(const IndexSet ¶llel_partitioner, const MPI_Comm &communicator) - : vector(new Epetra_FEVector( + : Subscriptor() + , vector(new Epetra_FEVector( parallel_partitioner.make_trilinos_map(communicator, false))) {} diff --git a/source/lac/trilinos_tpetra_vector.cc b/source/lac/trilinos_tpetra_vector.cc index 451acc9ce3c4..7df8249fd6c0 100644 --- a/source/lac/trilinos_tpetra_vector.cc +++ b/source/lac/trilinos_tpetra_vector.cc @@ -42,7 +42,8 @@ namespace LinearAlgebra { template Vector::Vector() - : vector(new Tpetra::Vector( + : Subscriptor() + , vector(new Tpetra::Vector( Teuchos::RCP>( new Tpetra::Map( 0, @@ -65,7 +66,8 @@ namespace LinearAlgebra template Vector::Vector(const IndexSet ¶llel_partitioner, const MPI_Comm &communicator) - : vector(new Tpetra::Vector( + : Subscriptor() + , vector(new Tpetra::Vector( Teuchos::rcp(new Tpetra::Map( parallel_partitioner.make_tpetra_map(communicator, false))))) {} From ed90c83bc159d2cd4917e3d0f926f75f69a2fd27 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Mon, 18 Feb 2019 18:28:50 +0100 Subject: [PATCH 166/507] Clarify TODO for operator+= --- source/lac/trilinos_tpetra_vector.cc | 17 ++++++----------- 1 file changed, 6 insertions(+), 11 deletions(-) diff --git a/source/lac/trilinos_tpetra_vector.cc b/source/lac/trilinos_tpetra_vector.cc index 7df8249fd6c0..ea218f8309f8 100644 --- a/source/lac/trilinos_tpetra_vector.cc +++ b/source/lac/trilinos_tpetra_vector.cc @@ -257,7 +257,7 @@ namespace LinearAlgebra // Downcast V. If fails, throws an exception. const Vector &down_V = dynamic_cast &>(V); - // If the maps are the same we can Update right away. + // If the maps are the same we can update right away. if (vector->getMap()->isSameAs(*(down_V.trilinos_vector().getMap()))) { vector->update(1., down_V.trilinos_vector(), 1.); @@ -267,21 +267,16 @@ namespace LinearAlgebra Assert(this->size() == down_V.size(), ExcDimensionMismatch(this->size(), down_V.size())); - // TODO: The code doesn't work as expected so we use a workaround. - /*Tpetra::Export - data_exchange(vector->getMap(), down_V.trilinos_vector().getMap()); - vector->doExport(down_V.trilinos_vector(), - data_exchange, - Tpetra::ADD);*/ - + // TODO: Tpetra doesn't have a combine mode that also updates local + // elements, maybe there is a better workaround. Tpetra::Vector dummy( vector->getMap(), false); Tpetra::Import data_exchange( - dummy.getMap(), down_V.trilinos_vector().getMap()); + down_V.trilinos_vector().getMap(), dummy.getMap()); - dummy.doExport(down_V.trilinos_vector(), + dummy.doImport(down_V.trilinos_vector(), data_exchange, - Tpetra::REPLACE); + Tpetra::INSERT); vector->update(1.0, dummy, 1.0); } From 8fa282a2c8ca4dc339fce857d0d8d085b3cd3d93 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Mon, 18 Feb 2019 18:30:50 +0100 Subject: [PATCH 167/507] Document some return values a bit better --- include/deal.II/lac/trilinos_sparse_matrix.h | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/include/deal.II/lac/trilinos_sparse_matrix.h b/include/deal.II/lac/trilinos_sparse_matrix.h index 4f8e955cb869..183875e6bec3 100644 --- a/include/deal.II/lac/trilinos_sparse_matrix.h +++ b/include/deal.II/lac/trilinos_sparse_matrix.h @@ -1578,6 +1578,7 @@ namespace TrilinosWrappers * * This function will be called when the underlying number type for the * matrix object and the one for the vector object are the same. + * Despite looking complicated, the return type is just `void`. * * In case of a serial vector, this function will only work when * running on one processor, since the matrix object is inherently @@ -1592,6 +1593,7 @@ namespace TrilinosWrappers * Same as the function above for the case that the underlying number type * for the matrix object and the one for the vector object do not coincide. * This case is not implemented. Calling it will result in a runtime error. + * Despite looking complicated, the return type is just `void`. */ template typename std::enable_if typename std::enable_if typename std::enable_if Date: Wed, 20 Feb 2019 15:54:10 +0100 Subject: [PATCH 168/507] Avoid ambiguous function declaration/variable initialization --- include/deal.II/lac/block_linear_operator.h | 21 ++++++++-------- include/deal.II/lac/linear_operator.h | 28 ++++++++++----------- 2 files changed, 24 insertions(+), 25 deletions(-) diff --git a/include/deal.II/lac/block_linear_operator.h b/include/deal.II/lac/block_linear_operator.h index 50868de147f5..12f9aba972a9 100644 --- a/include/deal.II/lac/block_linear_operator.h +++ b/include/deal.II/lac/block_linear_operator.h @@ -623,8 +623,8 @@ block_operator(const BlockMatrixType &block_matrix) using BlockType = typename BlockLinearOperator::BlockType; - BlockLinearOperator return_op( - BlockPayload(block_matrix, block_matrix)); + BlockLinearOperator return_op{ + BlockPayload(block_matrix, block_matrix)}; return_op.n_block_rows = [&block_matrix]() -> unsigned int { return block_matrix.n_block_rows(); @@ -698,9 +698,8 @@ block_operator( using BlockType = typename BlockLinearOperator::BlockType; - BlockLinearOperator return_op( - (BlockPayload())); // TODO: Create block payload so that this can be - // initialized correctly + // TODO: Create block payload so that this can be initialized correctly + BlockLinearOperator return_op{BlockPayload()}; return_op.n_block_rows = []() -> unsigned int { return m; }; @@ -744,8 +743,8 @@ block_diagonal_operator(const BlockMatrixType &block_matrix) using BlockType = typename BlockLinearOperator::BlockType; - BlockLinearOperator return_op( - BlockPayload(block_matrix, block_matrix)); + BlockLinearOperator return_op{ + BlockPayload(block_matrix, block_matrix)}; return_op.n_block_rows = [&block_matrix]() -> unsigned int { return block_matrix.n_block_rows(); @@ -910,8 +909,8 @@ block_forward_substitution( const BlockLinearOperator &block_operator, const BlockLinearOperator &diagonal_inverse) { - LinearOperator return_op( - (typename BlockPayload::BlockType(diagonal_inverse))); + LinearOperator return_op{ + typename BlockPayload::BlockType(diagonal_inverse)}; return_op.reinit_range_vector = diagonal_inverse.reinit_range_vector; return_op.reinit_domain_vector = diagonal_inverse.reinit_domain_vector; @@ -1025,8 +1024,8 @@ block_back_substitution( const BlockLinearOperator &block_operator, const BlockLinearOperator &diagonal_inverse) { - LinearOperator return_op( - (typename BlockPayload::BlockType(diagonal_inverse))); + LinearOperator return_op{ + typename BlockPayload::BlockType(diagonal_inverse)}; return_op.reinit_range_vector = diagonal_inverse.reinit_range_vector; return_op.reinit_domain_vector = diagonal_inverse.reinit_domain_vector; diff --git a/include/deal.II/lac/linear_operator.h b/include/deal.II/lac/linear_operator.h index b8e118fe112c..00b19126e099 100644 --- a/include/deal.II/lac/linear_operator.h +++ b/include/deal.II/lac/linear_operator.h @@ -389,9 +389,9 @@ operator+(const LinearOperator &first_op, } else { - LinearOperator return_op( + LinearOperator return_op{ static_cast(first_op) + - static_cast(second_op)); + static_cast(second_op)}; return_op.reinit_range_vector = first_op.reinit_range_vector; return_op.reinit_domain_vector = first_op.reinit_domain_vector; @@ -585,9 +585,9 @@ operator*(const LinearOperator & first_op, } else { - LinearOperator return_op( + LinearOperator return_op{ static_cast(first_op) * - static_cast(second_op)); + static_cast(second_op)}; return_op.reinit_domain_vector = second_op.reinit_domain_vector; return_op.reinit_range_vector = first_op.reinit_range_vector; @@ -649,7 +649,7 @@ template LinearOperator transpose_operator(const LinearOperator &op) { - LinearOperator return_op(op.transpose_payload()); + LinearOperator return_op{op.transpose_payload()}; return_op.reinit_range_vector = op.reinit_domain_vector; return_op.reinit_domain_vector = op.reinit_range_vector; @@ -693,8 +693,8 @@ inverse_operator(const LinearOperator &op, Solver & solver, const Preconditioner & preconditioner) { - LinearOperator return_op( - op.inverse_payload(solver, preconditioner)); + LinearOperator return_op{ + op.inverse_payload(solver, preconditioner)}; return_op.reinit_range_vector = op.reinit_domain_vector; return_op.reinit_domain_vector = op.reinit_range_vector; @@ -750,8 +750,8 @@ inverse_operator(const LinearOperator &op, Solver & solver, const LinearOperator &preconditioner) { - LinearOperator return_op( - op.inverse_payload(solver, preconditioner)); + LinearOperator return_op{ + op.inverse_payload(solver, preconditioner)}; return_op.reinit_range_vector = op.reinit_domain_vector; return_op.reinit_domain_vector = op.reinit_range_vector; @@ -856,7 +856,7 @@ template < LinearOperator identity_operator(const std::function &reinit_vector) { - LinearOperator return_op((Payload())); + LinearOperator return_op{Payload()}; return_op.reinit_range_vector = reinit_vector; return_op.reinit_domain_vector = reinit_vector; @@ -909,7 +909,7 @@ template LinearOperator null_operator(const LinearOperator &op) { - LinearOperator return_op(op.null_payload()); + LinearOperator return_op{op.null_payload()}; return_op.is_null_operator = true; @@ -946,7 +946,7 @@ template < LinearOperator mean_value_filter(const std::function &reinit_vector) { - LinearOperator return_op((Payload())); + LinearOperator return_op{Payload()}; return_op.reinit_range_vector = reinit_vector; return_op.reinit_domain_vector = reinit_vector; @@ -1402,8 +1402,8 @@ linear_operator(const OperatorExemplar &operator_exemplar, const Matrix &matrix) { using namespace internal::LinearOperatorImplementation; // Initialize the payload based on the input exemplar matrix - LinearOperator return_op( - Payload(operator_exemplar, matrix)); + LinearOperator return_op{ + Payload(operator_exemplar, matrix)}; // Always store a reference to matrix and operator_exemplar in the lambda // functions. This ensures that a modification of the matrix after the From 01fbb861229284937d9a783eeb6b5bf421d4a1ab Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Wed, 20 Feb 2019 16:49:54 +0100 Subject: [PATCH 169/507] Add a few more TpetraWrappers and EpetraWrapper tests with a matrix-vector product --- include/deal.II/lac/trilinos_sparse_matrix.h | 1 + tests/trilinos/sparse_matrix_vector_12.cc | 126 ++++++++++++++++++ tests/trilinos/sparse_matrix_vector_12.output | 2 + tests/trilinos/sparse_matrix_vector_13.cc | 125 +++++++++++++++++ tests/trilinos/sparse_matrix_vector_13.output | 2 + tests/trilinos/sparse_matrix_vector_14.cc | 126 ++++++++++++++++++ tests/trilinos/sparse_matrix_vector_14.output | 2 + tests/trilinos/sparse_matrix_vector_15.cc | 125 +++++++++++++++++ tests/trilinos/sparse_matrix_vector_15.output | 2 + 9 files changed, 511 insertions(+) create mode 100644 tests/trilinos/sparse_matrix_vector_12.cc create mode 100644 tests/trilinos/sparse_matrix_vector_12.output create mode 100644 tests/trilinos/sparse_matrix_vector_13.cc create mode 100644 tests/trilinos/sparse_matrix_vector_13.output create mode 100644 tests/trilinos/sparse_matrix_vector_14.cc create mode 100644 tests/trilinos/sparse_matrix_vector_14.output create mode 100644 tests/trilinos/sparse_matrix_vector_15.cc create mode 100644 tests/trilinos/sparse_matrix_vector_15.output diff --git a/include/deal.II/lac/trilinos_sparse_matrix.h b/include/deal.II/lac/trilinos_sparse_matrix.h index 183875e6bec3..b07e06c6f3c0 100644 --- a/include/deal.II/lac/trilinos_sparse_matrix.h +++ b/include/deal.II/lac/trilinos_sparse_matrix.h @@ -1566,6 +1566,7 @@ namespace TrilinosWrappers *
      *
    • TrilinosWrappers::MPI::Vector, *
    • LinearAlgebra::EpetraWrappers::Vector, + *
    • LinearAlgebra::TpetraWrappers::Vector, *
    • Vector, *
    • LinearAlgebra::distributed::Vector. *
    diff --git a/tests/trilinos/sparse_matrix_vector_12.cc b/tests/trilinos/sparse_matrix_vector_12.cc new file mode 100644 index 000000000000..398cf9150aa5 --- /dev/null +++ b/tests/trilinos/sparse_matrix_vector_12.cc @@ -0,0 +1,126 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2013 - 2017 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + + +// check SparseMatrix::vmult, vmult_add with +// LinearAlgebra::EpetraWrappers::Vector + +#include + +#include +#include +#include + +#include +#include + +#include "../tests.h" + + +void +test(LinearAlgebra::EpetraWrappers::Vector &v, + LinearAlgebra::EpetraWrappers::Vector &w) +{ + LinearAlgebra::ReadWriteVector read_write_v(v.size()); + LinearAlgebra::ReadWriteVector read_write_w(w.size()); + + TrilinosWrappers::SparseMatrix m(w.size(), v.size(), v.size()); + for (unsigned int i = 0; i < m.m(); ++i) + for (unsigned int j = 0; j < m.n(); ++j) + m.set(i, j, i + 2 * j); + + for (unsigned int i = 0; i < v.size(); ++i) + read_write_v(i) = i; + + m.compress(VectorOperation::insert); + v.import(read_write_v, VectorOperation::insert); + + // w:=Mv + m.vmult(w, v); + + // make sure we get the expected result + read_write_w.import(w, VectorOperation::insert); + for (unsigned int i = 0; i < m.m(); ++i) + { + double result = 0; + for (unsigned int j = 0; j < m.n(); ++j) + result += (i + 2 * j) * j; + AssertThrow(read_write_w(i) == result, ExcInternalError()); + } + + m.vmult_add(w, v); + + // make sure we get the expected result + read_write_w.import(w, VectorOperation::insert); + for (unsigned int i = 0; i < m.m(); ++i) + { + double result = 0; + for (unsigned int j = 0; j < m.n(); ++j) + result += (i + 2 * j) * j; + AssertThrow(read_write_w(i) == result + result, ExcInternalError()); + } + + deallog << "OK" << std::endl; +} + + + +int +main(int argc, char **argv) +{ + initlog(); + + Utilities::MPI::MPI_InitFinalize mpi_initialization( + argc, argv, testing_max_num_threads()); + + + try + { + { + LinearAlgebra::EpetraWrappers::Vector v(complete_index_set(100), + MPI_COMM_SELF); + LinearAlgebra::EpetraWrappers::Vector w(complete_index_set(95), + MPI_COMM_SELF); + test(v, w); + } + } + catch (std::exception &exc) + { + std::cerr << std::endl + << std::endl + << "----------------------------------------------------" + << std::endl; + std::cerr << "Exception on processing: " << std::endl + << exc.what() << std::endl + << "Aborting!" << std::endl + << "----------------------------------------------------" + << std::endl; + + return 1; + } + catch (...) + { + std::cerr << std::endl + << std::endl + << "----------------------------------------------------" + << std::endl; + std::cerr << "Unknown exception!" << std::endl + << "Aborting!" << std::endl + << "----------------------------------------------------" + << std::endl; + return 1; + }; +} diff --git a/tests/trilinos/sparse_matrix_vector_12.output b/tests/trilinos/sparse_matrix_vector_12.output new file mode 100644 index 000000000000..0fd8fc12f0b4 --- /dev/null +++ b/tests/trilinos/sparse_matrix_vector_12.output @@ -0,0 +1,2 @@ + +DEAL::OK diff --git a/tests/trilinos/sparse_matrix_vector_13.cc b/tests/trilinos/sparse_matrix_vector_13.cc new file mode 100644 index 000000000000..e13c99656c5a --- /dev/null +++ b/tests/trilinos/sparse_matrix_vector_13.cc @@ -0,0 +1,125 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2013 - 2017 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + + +// check SparseMatrix::Tvmult, Tvmult_add with +// LinearAlgebra::EpetraWrappers::Vector + +#include + +#include +#include +#include + +#include +#include + +#include "../tests.h" + + +void +test(LinearAlgebra::EpetraWrappers::Vector &v, + LinearAlgebra::EpetraWrappers::Vector &w) +{ + LinearAlgebra::ReadWriteVector read_write_v(v.size()); + LinearAlgebra::ReadWriteVector read_write_w(w.size()); + + TrilinosWrappers::SparseMatrix m(v.size(), w.size(), w.size()); + for (unsigned int i = 0; i < m.m(); ++i) + for (unsigned int j = 0; j < m.n(); ++j) + m.set(i, j, i + 2 * j); + + for (unsigned int i = 0; i < v.size(); ++i) + read_write_v(i) = i; + + m.compress(VectorOperation::insert); + v.import(read_write_v, VectorOperation::insert); + + // w:=Mv + m.Tvmult(w, v); + + // make sure we get the expected result + read_write_w.import(w, VectorOperation::insert); + for (unsigned int i = 0; i < m.n(); ++i) + { + double result = 0; + for (unsigned int j = 0; j < m.m(); ++j) + result += (j + 2 * i) * j; + AssertThrow(read_write_w(i) == result, ExcInternalError()); + } + + m.Tvmult_add(w, v); + // make sure we get the expected result + read_write_w.import(w, VectorOperation::insert); + for (unsigned int i = 0; i < m.n(); ++i) + { + double result = 0; + for (unsigned int j = 0; j < m.m(); ++j) + result += (j + 2 * i) * j; + AssertThrow(read_write_w(i) == result + result, ExcInternalError()); + } + + deallog << "OK" << std::endl; +} + + + +int +main(int argc, char **argv) +{ + initlog(); + + Utilities::MPI::MPI_InitFinalize mpi_initialization( + argc, argv, testing_max_num_threads()); + + + try + { + { + LinearAlgebra::EpetraWrappers::Vector v(complete_index_set(95), + MPI_COMM_SELF); + LinearAlgebra::EpetraWrappers::Vector w(complete_index_set(100), + MPI_COMM_SELF); + test(v, w); + } + } + catch (std::exception &exc) + { + std::cerr << std::endl + << std::endl + << "----------------------------------------------------" + << std::endl; + std::cerr << "Exception on processing: " << std::endl + << exc.what() << std::endl + << "Aborting!" << std::endl + << "----------------------------------------------------" + << std::endl; + + return 1; + } + catch (...) + { + std::cerr << std::endl + << std::endl + << "----------------------------------------------------" + << std::endl; + std::cerr << "Unknown exception!" << std::endl + << "Aborting!" << std::endl + << "----------------------------------------------------" + << std::endl; + return 1; + }; +} diff --git a/tests/trilinos/sparse_matrix_vector_13.output b/tests/trilinos/sparse_matrix_vector_13.output new file mode 100644 index 000000000000..0fd8fc12f0b4 --- /dev/null +++ b/tests/trilinos/sparse_matrix_vector_13.output @@ -0,0 +1,2 @@ + +DEAL::OK diff --git a/tests/trilinos/sparse_matrix_vector_14.cc b/tests/trilinos/sparse_matrix_vector_14.cc new file mode 100644 index 000000000000..fed0ac1c8594 --- /dev/null +++ b/tests/trilinos/sparse_matrix_vector_14.cc @@ -0,0 +1,126 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2013 - 2017 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + + +// check SparseMatrix::vmult, vmult_add with +// LinearAlgebra::TpetraWrappers::Vector + +#include + +#include +#include +#include + +#include +#include + +#include "../tests.h" + + +void +test(LinearAlgebra::TpetraWrappers::Vector &v, + LinearAlgebra::TpetraWrappers::Vector &w) +{ + LinearAlgebra::ReadWriteVector read_write_v(v.size()); + LinearAlgebra::ReadWriteVector read_write_w(w.size()); + + TrilinosWrappers::SparseMatrix m(w.size(), v.size(), v.size()); + for (unsigned int i = 0; i < m.m(); ++i) + for (unsigned int j = 0; j < m.n(); ++j) + m.set(i, j, i + 2 * j); + + for (unsigned int i = 0; i < v.size(); ++i) + read_write_v(i) = i; + + m.compress(VectorOperation::insert); + v.import(read_write_v, VectorOperation::insert); + + // w:=Mv + m.vmult(w, v); + + // make sure we get the expected result + read_write_w.import(w, VectorOperation::insert); + for (unsigned int i = 0; i < m.m(); ++i) + { + double result = 0; + for (unsigned int j = 0; j < m.n(); ++j) + result += (i + 2 * j) * j; + AssertThrow(read_write_w(i) == result, ExcInternalError()); + } + + m.vmult_add(w, v); + + // make sure we get the expected result + read_write_w.import(w, VectorOperation::insert); + for (unsigned int i = 0; i < m.m(); ++i) + { + double result = 0; + for (unsigned int j = 0; j < m.n(); ++j) + result += (i + 2 * j) * j; + AssertThrow(read_write_w(i) == result + result, ExcInternalError()); + } + + deallog << "OK" << std::endl; +} + + + +int +main(int argc, char **argv) +{ + initlog(); + + Utilities::MPI::MPI_InitFinalize mpi_initialization( + argc, argv, testing_max_num_threads()); + + + try + { + { + LinearAlgebra::TpetraWrappers::Vector v(complete_index_set(100), + MPI_COMM_SELF); + LinearAlgebra::TpetraWrappers::Vector w(complete_index_set(95), + MPI_COMM_SELF); + test(v, w); + } + } + catch (std::exception &exc) + { + std::cerr << std::endl + << std::endl + << "----------------------------------------------------" + << std::endl; + std::cerr << "Exception on processing: " << std::endl + << exc.what() << std::endl + << "Aborting!" << std::endl + << "----------------------------------------------------" + << std::endl; + + return 1; + } + catch (...) + { + std::cerr << std::endl + << std::endl + << "----------------------------------------------------" + << std::endl; + std::cerr << "Unknown exception!" << std::endl + << "Aborting!" << std::endl + << "----------------------------------------------------" + << std::endl; + return 1; + }; +} diff --git a/tests/trilinos/sparse_matrix_vector_14.output b/tests/trilinos/sparse_matrix_vector_14.output new file mode 100644 index 000000000000..0fd8fc12f0b4 --- /dev/null +++ b/tests/trilinos/sparse_matrix_vector_14.output @@ -0,0 +1,2 @@ + +DEAL::OK diff --git a/tests/trilinos/sparse_matrix_vector_15.cc b/tests/trilinos/sparse_matrix_vector_15.cc new file mode 100644 index 000000000000..870712bbe8a9 --- /dev/null +++ b/tests/trilinos/sparse_matrix_vector_15.cc @@ -0,0 +1,125 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2013 - 2017 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + + +// check SparseMatrix::Tvmult, Tvmult_add with +// LinearAlgebra::TpetraWrappers::Vector + +#include + +#include +#include +#include + +#include +#include + +#include "../tests.h" + + +void +test(LinearAlgebra::TpetraWrappers::Vector &v, + LinearAlgebra::TpetraWrappers::Vector &w) +{ + LinearAlgebra::ReadWriteVector read_write_v(v.size()); + LinearAlgebra::ReadWriteVector read_write_w(w.size()); + + TrilinosWrappers::SparseMatrix m(v.size(), w.size(), w.size()); + for (unsigned int i = 0; i < m.m(); ++i) + for (unsigned int j = 0; j < m.n(); ++j) + m.set(i, j, i + 2 * j); + + for (unsigned int i = 0; i < v.size(); ++i) + read_write_v(i) = i; + + m.compress(VectorOperation::insert); + v.import(read_write_v, VectorOperation::insert); + + // w:=Mv + m.Tvmult(w, v); + + // make sure we get the expected result + read_write_w.import(w, VectorOperation::insert); + for (unsigned int i = 0; i < m.n(); ++i) + { + double result = 0; + for (unsigned int j = 0; j < m.m(); ++j) + result += (j + 2 * i) * j; + AssertThrow(read_write_w(i) == result, ExcInternalError()); + } + + m.Tvmult_add(w, v); + // make sure we get the expected result + read_write_w.import(w, VectorOperation::insert); + for (unsigned int i = 0; i < m.n(); ++i) + { + double result = 0; + for (unsigned int j = 0; j < m.m(); ++j) + result += (j + 2 * i) * j; + AssertThrow(read_write_w(i) == result + result, ExcInternalError()); + } + + deallog << "OK" << std::endl; +} + + + +int +main(int argc, char **argv) +{ + initlog(); + + Utilities::MPI::MPI_InitFinalize mpi_initialization( + argc, argv, testing_max_num_threads()); + + + try + { + { + LinearAlgebra::TpetraWrappers::Vector v(complete_index_set(95), + MPI_COMM_SELF); + LinearAlgebra::TpetraWrappers::Vector w(complete_index_set(100), + MPI_COMM_SELF); + test(v, w); + } + } + catch (std::exception &exc) + { + std::cerr << std::endl + << std::endl + << "----------------------------------------------------" + << std::endl; + std::cerr << "Exception on processing: " << std::endl + << exc.what() << std::endl + << "Aborting!" << std::endl + << "----------------------------------------------------" + << std::endl; + + return 1; + } + catch (...) + { + std::cerr << std::endl + << std::endl + << "----------------------------------------------------" + << std::endl; + std::cerr << "Unknown exception!" << std::endl + << "Aborting!" << std::endl + << "----------------------------------------------------" + << std::endl; + return 1; + }; +} diff --git a/tests/trilinos/sparse_matrix_vector_15.output b/tests/trilinos/sparse_matrix_vector_15.output new file mode 100644 index 000000000000..0fd8fc12f0b4 --- /dev/null +++ b/tests/trilinos/sparse_matrix_vector_15.output @@ -0,0 +1,2 @@ + +DEAL::OK From eab549f6c93135c761dc8e0dd772ec9542a3fd1f Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Wed, 20 Feb 2019 15:53:31 +0100 Subject: [PATCH 170/507] Fix linear operator --- include/deal.II/lac/linear_operator.h | 2 +- include/deal.II/lac/read_write_vector.templates.h | 4 ++-- source/base/utilities.cc | 1 + 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/include/deal.II/lac/linear_operator.h b/include/deal.II/lac/linear_operator.h index b8e118fe112c..2947a092d400 100644 --- a/include/deal.II/lac/linear_operator.h +++ b/include/deal.II/lac/linear_operator.h @@ -856,7 +856,7 @@ template < LinearOperator identity_operator(const std::function &reinit_vector) { - LinearOperator return_op((Payload())); + LinearOperator return_op{Payload()}; return_op.reinit_range_vector = reinit_vector; return_op.reinit_domain_vector = reinit_vector; diff --git a/include/deal.II/lac/read_write_vector.templates.h b/include/deal.II/lac/read_write_vector.templates.h index cfbbc7db890b..c2854d9af276 100644 --- a/include/deal.II/lac/read_write_vector.templates.h +++ b/include/deal.II/lac/read_write_vector.templates.h @@ -874,7 +874,7 @@ namespace LinearAlgebra for (unsigned int i = 0; i < n_elements; ++i) { Assert( - std::imag(new_values[i]) == 0., + std::imag(tmp[i]) == 0., ExcMessage( "VectorOperation::min is not defined if there is an imaginary part!)")); Assert( @@ -898,7 +898,7 @@ namespace LinearAlgebra for (unsigned int i = 0; i < n_elements; ++i) { Assert( - std::imag(new_values[i]) == 0., + std::imag(tmp[i]) == 0., ExcMessage( "VectorOperation::max is not defined if there is an imaginary part!)")); Assert( diff --git a/source/base/utilities.cc b/source/base/utilities.cc index d5f120192bf6..c09874105d4e 100644 --- a/source/base/utilities.cc +++ b/source/base/utilities.cc @@ -60,6 +60,7 @@ # include # include +# include # endif # include # include From cb435e24a1f9c72adc9759363d4e845ec0b23970 Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Fri, 15 Feb 2019 11:52:49 +0100 Subject: [PATCH 171/507] AD Helpers: Add helper for scalar functions (QP-level) --- .../changes/major/20190220Jean-PaulPelteret | 9 + .../deal.II/differentiation/ad/ad_helpers.h | 447 ++++++++++++++++++ source/differentiation/ad/ad_helpers.cc | 329 +++++++++++++ source/differentiation/ad/ad_helpers.inst1.in | 16 + source/differentiation/ad/ad_helpers.inst2.in | 28 ++ 5 files changed, 829 insertions(+) create mode 100644 doc/news/changes/major/20190220Jean-PaulPelteret diff --git a/doc/news/changes/major/20190220Jean-PaulPelteret b/doc/news/changes/major/20190220Jean-PaulPelteret new file mode 100644 index 000000000000..c9df4e7cb7ca --- /dev/null +++ b/doc/news/changes/major/20190220Jean-PaulPelteret @@ -0,0 +1,9 @@ +New: A new class Differentiation::AD::ADHelperScalarFunction has been +added to help implement point-wise scalar functions using automatic +differentiation. In particular, this class is designed to compute the +gradient and Hessian of a scalar function that is parameterized in +terms of scalar, vector, and tensor arguments. One example of its use +would be to compute the derivatives of a multi-field constitutive law +that is expressed in terms of an energy function. +
    +(Jean-Paul Pelteret, 2019/02/20) diff --git a/include/deal.II/differentiation/ad/ad_helpers.h b/include/deal.II/differentiation/ad/ad_helpers.h index 4f36c1dbfe11..f884ee469481 100644 --- a/include/deal.II/differentiation/ad/ad_helpers.h +++ b/include/deal.II/differentiation/ad/ad_helpers.h @@ -2934,6 +2934,352 @@ namespace Differentiation }; // class ADHelperPointLevelFunctionsBase + + /** + * A helper class that facilitates the evaluation of a scalar function, + * its first derivatives (gradient), and its second derivatives (Hessian). + * This class would typically be used to compute the first and second + * derivatives of a stored energy function defined at a quadrature + * point. It can also be used to compute derivatives of any other scalar + * field so long as all its dependencies on the independent variables are + * explicit (that is to say, no independent variables may have some implicit + * dependence on one another). + * + * An example of its usage in the case of a multi-field constitutive law + * might be as follows: + * @code + * // Define some extractors that will help us set independent variables + * // and later get the computed values related to the dependent + * // variables. Each of these extractors is related to the gradient of a + * // component of the solution field (in this case, displacement and + * // magnetic scalar potential). Here "C" is the right Cauchy-Green + * // tensor and "H" is the magnetic field. + * const FEValuesExtractors::SymmetricTensor<2> C_dofs (0); + * const FEValuesExtractors::Vector H_dofs + * (dealii::SymmetricTensor<2,dim>::n_independent_components); + * const unsigned int n_independent_variables = + * SymmetricTensor<2,dim>::n_independent_components + + * Tensor<1,dim>::n_independent_components; + * + * // Define the helper that we will use in the AD computations for our + * // scalar energy function. Note that we expect it to return values of + * // type double. + * ADHelperScalarFunction ad_helper (n_independent_variables); + * using ADNumberType = typename ADHelper::ad_type; + * + * // Compute the fields that provide the independent values. + * // When the tape is being replayed, these should be set to something + * // meaningful. + * const Tensor<1,dim> H = ...; + * const SymmetricTensor<2,dim> C = ...; + * + * // If using a taped AD number, then at this point we would initiate + * // taping of the expression for the material stored energy function + * // for this particular set of material parameters: + * + * // Select a tape number to record to + * const typename Types::tape_index tape_index = ...; + * + * // Indicate that we are about to start tracing the operations for + * // function evaluation on the tape. If this tape has already been + * // used (i.e., the operations are already recorded) then we + * // (optionally) load the tape and reuse this data. + * const bool is_recording + * = ad_helper.start_recording_operations(tape_index); + * + * // The steps that follow in the recording phase are required for + * // tapeless methods as well. + * if (is_recording == true) + * { + * // This is the "recording" phase of the operations. + * + * // First, we set the values for all fields. + * // These could happily be set to anything, unless the function will + * // be evaluated along a branch not otherwise traversed during later + * // use. For this reason, in this example instead of using some dummy + * // values, we'll actually map out the function at the same point + * // around which we'll later linearize it. + * ad_helper.register_independent_variable(H, H_dofs); + * ad_helper.register_independent_variable(C, C_dofs); + * + * // NOTE: We have to extract the sensitivities in the order we wish to + * // introduce them. So this means we have to do it by logical order + * // of the extractors that we've created. + * const SymmetricTensor<2,dim,ADNumberType> C_AD = + * ad_helper.get_sensitive_variables(C_dofs); const + * const Tensor<1,dim,ADNumberType> H_AD = + * ad_helper.get_sensitive_variables(H_dofs); + * + * // Here we define the material stored energy function. + * // This example is sufficiently complex to warrant the use of AD to, + * // at the very least, verify an unassisted implementation. + * const double mu_e = 10; // Shear modulus + * const double lambda_e = 15; // Lame parameter + * const double mu_0 = 4*M_PI*1e-7; // Magnetic permeability constant + * const double mu_r = 5; // Relative magnetic permeability + * + * const ADNumberType J = std::sqrt(determinant(C_AD)); + * const SymmetricTensor<2,dim,ADNumberType> C_inv_AD = invert(C_AD); + * const ADNumberType psi = + * 0.5*mu_e*(1.0+std::tanh((H_AD*H_AD)/100.0))* + * (trace(C_AD) - dim - 2*std::log(J)) + + * lambda_e*std::log(J)*std::log(J) - + * 0.5*mu_0*mu_r*J*H_AD*C_inv_AD*H_AD; + * + * // Register the definition of the total stored energy + * ad_helper.register_dependent_variable(psi_CH); + * + * // Indicate that we have completed tracing the operations onto + * // the tape. + * ad_helper.stop_recording_operations(false); // write_tapes_to_file + * } + * else + * { + * // This is the "tape reuse" phase of the operations. + * // Here we will leverage the already traced operations that reside + * // on a tape, and simply re-evaluate the tape at a different point + * // to get the function values and their derivatives. + * + * // Load the existing tape to be reused + * ad_helper.activate_recorded_tape(tape_index); + * + * // Set the new values of the independent variables where the + * // recorded dependent functions are to be evaluated (and + * // differentiated around). + * ad_helper.set_independent_variable(C, C_dofs); + * ad_helper.set_independent_variable(H, H_dofs); + * } + * + * // Play the tape and store the output function value, its gradient and + * // linearization. These are expensive to compute, so we'll do this once + * // and extract the desired values from these intermediate outputs. + * Vector Dpsi (ad_helper.n_dependent_variables()); + * FullMatrix D2psi (ad_helper.n_dependent_variables(), + * ad_helper.n_dependent_variables()); + * const double psi = ad_helper.compute_value(); + * ad_helper.compute_gradient(Dpsi); + * ad_helper.compute_hessian(D2psi); + * + * // Extract the desired components of the gradient vector and Hessian + * // matrix. In this example, we use them to compute the Piola-Kirchhoff + * // stress tensor and its associated tangent, defined by thermodynamic + * // arguments as S = 2*dpsi/dC and HH = 2*dS/dC... + * const SymmetricTensor<2,dim> S = + * 2.0*ad_helper.extract_gradient_component(Dpsi,C_dofs); + * const SymmetricTensor<4,dim> HH = + * 4.0*ad_helper.extract_hessian_component(D2psi,C_dofs,C_dofs); + * + * // ... the magnetic induction and its associated tangent defined + * // as B = -dpsi/dH and BB = dB/dH... + * const Tensor<1,dim> B = + * -ad_helper.extract_gradient_component(Dpsi,H_dofs); + * const SymmetricTensor<2,dim> BB = + * -symmetrize(ad_helper.extract_hessian_component(D2psi,H_dofs,H_dofs)); + * + * // ... and finally the magnetoelastic coupling tangent, defined + * // as PP = -dS/dH = -d/dH(2*dpsi/dC). Here the order of the extractor + * // arguments is especially important, as it dictates the order in which + * // the directional derivatives are taken. + * const Tensor<3,dim,double> PP = + * -2.0*ad_helper.extract_hessian_component(D2psi,C_dofs,H_dofs) + * @endcode + * + * @warning ADOL-C does not support the standard threading models used by + * deal.II, so this class should @b not be embedded within a multithreaded + * function when using ADOL-C number types. It is, however, suitable for use + * in both serial and MPI routines. + * + * @author Jean-Paul Pelteret, 2016, 2017, 2018 + */ + template + class ADHelperScalarFunction + : public ADHelperPointLevelFunctionsBase + { + public: + /** + * Type definition for the floating point number type that is used in, + * and results from, all computations. + */ + using scalar_type = + typename ADHelperBase::scalar_type; + + /** + * Type definition for the auto-differentiation number type that is used + * in all computations. + */ + using ad_type = + typename ADHelperBase::ad_type; + + /** + * @name Constructor / destructor + */ + //@{ + + /** + * The constructor for the class. + * + * @param[in] n_independent_variables The number of independent variables + * that will be used in the definition of the functions that it is + * desired to compute the sensitivities of. In the computation of + * $\mathbf{f}(\mathbf{X})$, this will be the number of inputs + * $\mathbf{X}$, i.e., the dimension of the domain space. + */ + ADHelperScalarFunction(const unsigned int n_independent_variables); + + /** + * Destructor. + */ + virtual ~ADHelperScalarFunction() = default; + + //@} + + /** + * @name Dependent variables + */ + //@{ + + /** + * Register the definition of the scalar field $\Psi(\mathbf{X})$. + * + * @param[in] func The recorded function that defines a dependent + * variable. + * + * @note For this class that expects only one dependent variable, this + * function must only be called once per tape. + * + * @note For taped AD numbers, this operation is only valid in recording mode. + */ + void + register_dependent_variable(const ad_type &func); + + /** + * Compute the value of the scalar field $\Psi(\mathbf{X})$ using the + * tape as opposed to executing the source code. + * + * @return A scalar object with the value for the scalar field evaluated + * at the point defined by the independent variable values. + */ + scalar_type + compute_value() const; + + /** + * Compute the gradient (first derivative) of the scalar field with + * respect to all independent variables, i.e. + * @f[ + * \frac{\partial\Psi(\mathbf{X})}{\partial\mathbf{X}} + * @f] + * + * @param[out] gradient A Vector with the values for the scalar field + * gradient (first derivatives) evaluated at the point defined by the + * independent variable values. + */ + void + compute_gradient(Vector &gradient) const; + + /** + * Compute the Hessian (second derivative) of the scalar field with + * respect to all independent variables, i.e. + * @f[ + * \frac{\partial^{2}\Psi(\mathbf{X})}{\partial\mathbf{X} \otimes + * \partial\mathbf{X}} + * @f] + * + * @param[out] hessian A FullMatrix with the values for the scalar field + * Hessian (second derivatives) evaluated at the point defined by the + * independent variable values. + */ + void + compute_hessian(FullMatrix &hessian) const; + + /** + * Extract the function gradient for a subset of independent variables + * $\mathbf{A} \subset \mathbf{X}$, i.e. + * @f[ + * \frac{\partial\Psi(\mathbf{X})}{\partial\mathbf{A}} + * @f] + * + * @param[in] gradient The gradient of the scalar function with respect to + * all independent variables, i.e. that returned by compute_gradient(). + * @param[in] extractor_row An extractor associated with the input field + * variables. This effectively defines which components of the global set + * of independent variables this field is associated with. + */ + template + typename internal::ScalarFieldGradient::type + extract_gradient_component(const Vector &gradient, + const ExtractorType_Row &extractor_row) const; + + /** + * Extract the function Hessian for a subset of independent variables + * $\mathbf{A},\mathbf{B} \subset \mathbf{X}$, i.e. + * @f[ + * \frac{}{\partial\mathbf{B}} \left[ + * \frac{\partial\Psi(\mathbf{X})}{\partial\mathbf{A}} \right] = + * \frac{\partial^{2}\Psi(\mathbf{X})}{\partial\mathbf{B} \otimes + * \partial\mathbf{A}} + * @f] + * + * @param[in] hessian The Hessian of the scalar function with respect to + * all independent variables, i.e. that returned by compute_hessian(). + * @param[in] extractor_row An extractor associated with the input field + * variables for which the first index of the Hessian is extracted. + * @param[in] extractor_col An extractor associated with the input field + * variables for which the second index of the Hessian is extracted. + */ + template + typename internal::ScalarFieldHessian::type + extract_hessian_component(const FullMatrix &hessian, + const ExtractorType_Row & extractor_row, + const ExtractorType_Col &extractor_col) const; + + /** + * Extract the function Hessian for a subset of independent variables + * $\mathbf{A},\mathbf{B} \subset \mathbf{X}$, i.e. + * @f[ + * \frac{}{\partial\mathbf{B}} \left[ + * \frac{\partial\Psi(\mathbf{X})}{\partial\mathbf{A}} \right] + * @f] + * + * This function is a specialization of the above for rank-0 tensors + * (scalars) + */ + Tensor<0, dim, scalar_type> + extract_hessian_component( + const FullMatrix & hessian, + const FEValuesExtractors::Scalar &extractor_row, + const FEValuesExtractors::Scalar &extractor_col) const; + + /** + * Extract the function Hessian for a subset of independent variables + * $\mathbf{A},\mathbf{B} \subset \mathbf{X}$, i.e. + * @f[ + * \frac{}{\partial\mathbf{B}} \left[ + * \frac{\partial\Psi(\mathbf{X})}{\partial\mathbf{A}} \right] + * @f] + * + * This function is a specialization of the above for rank-4 symmetric + * tensors + */ + SymmetricTensor<4, dim, scalar_type> + extract_hessian_component( + const FullMatrix & hessian, + const FEValuesExtractors::SymmetricTensor<2> &extractor_row, + const FEValuesExtractors::SymmetricTensor<2> &extractor_col) const; + + //@} + + }; // class ADHelperScalarFunction + + } // namespace AD } // namespace Differentiation @@ -3099,6 +3445,107 @@ namespace Differentiation } + + /* ----------------- ADHelperScalarFunction ----------------- */ + + + + template + template + typename internal::ScalarFieldGradient< + dim, + typename ADHelperScalarFunction:: + scalar_type, + ExtractorType_Row>::type + ADHelperScalarFunction:: + extract_gradient_component(const Vector &gradient, + const ExtractorType_Row & extractor_row) const + { + // NOTE: The order of components must be consistently defined throughout + // this class. + typename internal:: + ScalarFieldGradient::type out; + + // Get indexsets for the subblock from which we wish to extract the + // gradient values + const std::vector row_index_set( + internal::extract_field_component_indices(extractor_row)); + Assert(out.n_independent_components == row_index_set.size(), + ExcMessage("Not all tensor components have been extracted!")); + for (unsigned int r = 0; r < row_index_set.size(); ++r) + internal::set_tensor_entry(out, r, gradient[row_index_set[r]]); + + return out; + } + + + + template + template + typename internal::ScalarFieldHessian< + dim, + typename ADHelperScalarFunction:: + scalar_type, + ExtractorType_Row, + ExtractorType_Col>::type + ADHelperScalarFunction:: + extract_hessian_component(const FullMatrix &hessian, + const ExtractorType_Row & extractor_row, + const ExtractorType_Col &extractor_col) const + { + using InternalHessian = internal::ScalarFieldHessian; + using InternalExtractorRow = internal::Extractor; + using InternalExtractorCol = internal::Extractor; + using HessianType = typename InternalHessian::type; + + // NOTE: The order of components must be consistently defined throughout + // this class. + HessianType out; + + // Get indexsets for the subblocks from which we wish to extract the + // Hessian values + // NOTE: Here we have to do some clever accounting when the + // one extractor is a symmetric Tensor and the other is not, e.g. + // . In this scenario the return type is a + // non-symmetric Tensor<3,dim> but we have to fetch information from a + // SymmTensor row/column that has too few entries to fill the output + // tensor. So we must duplicate the relevant entries in the row/column + // indexset to fetch off-diagonal components that are Otherwise + // non-existent in a SymmTensor. + const std::vector row_index_set( + internal::extract_field_component_indices( + extractor_row, false /*ignore_symmetries*/)); + const std::vector col_index_set( + internal::extract_field_component_indices( + extractor_col, false /*ignore_symmetries*/)); + + for (unsigned int index = 0; + index < HessianType::n_independent_components; + ++index) + { + const TableIndices ti_out = + HessianType::unrolled_to_component_indices(index); + const unsigned int r = + InternalExtractorRow::local_component(ti_out, 0); + const unsigned int c = + InternalExtractorCol::local_component(ti_out, + InternalExtractorRow::rank); + + internal::set_tensor_entry( + out, index, hessian[row_index_set[r]][col_index_set[c]]); + } + + return out; + } + + } // namespace AD } // namespace Differentiation diff --git a/source/differentiation/ad/ad_helpers.cc b/source/differentiation/ad/ad_helpers.cc index 7789a475430b..a1e0809b5bfd 100644 --- a/source/differentiation/ad/ad_helpers.cc +++ b/source/differentiation/ad/ad_helpers.cc @@ -1312,6 +1312,335 @@ namespace Differentiation } + + /* -------------------- ADHelperScalarFunction -------------------- */ + + + + template + ADHelperScalarFunction:: + ADHelperScalarFunction(const unsigned int n_independent_variables) + : ADHelperPointLevelFunctionsBase( + n_independent_variables, + 1) + {} + + + + template + void + ADHelperScalarFunction:: + register_dependent_variable(const ad_type &func) + { + Assert(this->n_dependent_variables() == 1, ExcInternalError()); + ADHelperBase::register_dependent_variable( + 0, func); + } + + + + template + typename ADHelperScalarFunction:: + scalar_type + ADHelperScalarFunction::compute_value() + const + { + if ((ADNumberTraits::is_taped == true && + this->taped_driver.keep_independent_values() == false) || + ADNumberTraits::is_tapeless == true) + { + Assert( + this->n_registered_independent_variables() == + this->n_independent_variables(), + ExcMessage( + "Not all values of sensitivities have been registered or subsequently set!")); + } + Assert(this->n_registered_dependent_variables() == + this->n_dependent_variables(), + ExcMessage("Not all dependent variables have been registered.")); + + Assert( + this->n_dependent_variables() == 1, + ExcMessage( + "The ADHelperScalarFunction class expects there to be only one dependent variable.")); + + if (ADNumberTraits::is_taped == true) + { + Assert(this->active_tape_index() != + Numbers::invalid_tape_index, + ExcMessage("Invalid tape index")); + Assert(this->is_recording() == false, + ExcMessage( + "Cannot compute values while tape is being recorded.")); + Assert(this->independent_variable_values.size() == + this->n_independent_variables(), + ExcDimensionMismatch(this->independent_variable_values.size(), + this->n_independent_variables())); + + return this->taped_driver.value(this->active_tape_index(), + this->independent_variable_values); + } + else + { + Assert(ADNumberTraits::is_tapeless == true, + ExcInternalError()); + return this->tapeless_driver.value(this->dependent_variables); + } + } + + + template + void + ADHelperScalarFunction::compute_gradient( + Vector &gradient) const + { + if ((ADNumberTraits::is_taped == true && + this->taped_driver.keep_independent_values() == false) || + ADNumberTraits::is_tapeless == true) + { + Assert( + this->n_registered_independent_variables() == + this->n_independent_variables(), + ExcMessage( + "Not all values of sensitivities have been registered or subsequently set!")); + } + Assert(this->n_registered_dependent_variables() == + this->n_dependent_variables(), + ExcMessage("Not all dependent variables have been registered.")); + + Assert( + this->n_dependent_variables() == 1, + ExcMessage( + "The ADHelperScalarFunction class expects there to be only one dependent variable.")); + + // We can neglect correctly initializing the entries as + // we'll be overwriting them immediately in the succeeding call to + // Drivers::gradient(). + if (gradient.size() != this->n_independent_variables()) + gradient.reinit(this->n_independent_variables(), + true /*omit_zeroing_entries*/); + + if (ADNumberTraits::is_taped == true) + { + Assert(this->active_tape_index() != + Numbers::invalid_tape_index, + ExcMessage("Invalid tape index")); + Assert(this->is_recording() == false, + ExcMessage( + "Cannot compute gradient while tape is being recorded.")); + Assert(this->independent_variable_values.size() == + this->n_independent_variables(), + ExcDimensionMismatch(this->independent_variable_values.size(), + this->n_independent_variables())); + + this->taped_driver.gradient(this->active_tape_index(), + this->independent_variable_values, + gradient); + } + else + { + Assert(ADNumberTraits::is_tapeless == true, + ExcInternalError()); + Assert(this->independent_variables.size() == + this->n_independent_variables(), + ExcDimensionMismatch(this->independent_variables.size(), + this->n_independent_variables())); + + this->tapeless_driver.gradient(this->independent_variables, + this->dependent_variables, + gradient); + } + + // Account for symmetries of tensor components + for (unsigned int i = 0; i < this->n_independent_variables(); i++) + { + if (this->is_symmetric_independent_variable(i) == true) + gradient[i] *= 0.5; + } + } + + + + template + void + ADHelperScalarFunction::compute_hessian( + FullMatrix &hessian) const + { + Assert(AD::ADNumberTraits::n_supported_derivative_levels >= 2, + ExcMessage( + "Cannot computed function Hessian: AD number type does" + "not support the calculation of second order derivatives.")); + + if ((ADNumberTraits::is_taped == true && + this->taped_driver.keep_independent_values() == false)) + { + Assert( + this->n_registered_independent_variables() == + this->n_independent_variables(), + ExcMessage( + "Not all values of sensitivities have been registered or subsequently set!")); + } + Assert(this->n_registered_dependent_variables() == + this->n_dependent_variables(), + ExcMessage("Not all dependent variables have been registered.")); + + Assert( + this->n_dependent_variables() == 1, + ExcMessage( + "The ADHelperScalarFunction class expects there to be only one dependent variable.")); + + // We can neglect correctly initializing the entries as + // we'll be overwriting them immediately in the succeeding call to + // Drivers::hessian(). + if (hessian.m() != this->n_independent_variables() || + hessian.n() != this->n_independent_variables()) + hessian.reinit({this->n_independent_variables(), + this->n_independent_variables()}, + true /*omit_default_initialization*/); + + if (ADNumberTraits::is_taped == true) + { + Assert(this->active_tape_index() != + Numbers::invalid_tape_index, + ExcMessage("Invalid tape index")); + Assert(this->is_recording() == false, + ExcMessage( + "Cannot compute Hessian while tape is being recorded.")); + Assert(this->independent_variable_values.size() == + this->n_independent_variables(), + ExcDimensionMismatch(this->independent_variable_values.size(), + this->n_independent_variables())); + + this->taped_driver.hessian(this->active_tape_index(), + this->independent_variable_values, + hessian); + } + else + { + Assert(ADNumberTraits::is_tapeless == true, + ExcInternalError()); + Assert(this->independent_variables.size() == + this->n_independent_variables(), + ExcDimensionMismatch(this->independent_variables.size(), + this->n_independent_variables())); + + this->tapeless_driver.hessian(this->independent_variables, + this->dependent_variables, + hessian); + } + + // Account for symmetries of tensor components + for (unsigned int i = 0; i < this->n_independent_variables(); i++) + for (unsigned int j = 0; j < i + 1; j++) + { + if (this->is_symmetric_independent_variable(i) == true && + this->is_symmetric_independent_variable(j) == true) + { + hessian[i][j] *= 0.25; + if (i != j) + hessian[j][i] *= 0.25; + } + else if ((this->is_symmetric_independent_variable(i) == true && + this->is_symmetric_independent_variable(j) == false) || + (this->is_symmetric_independent_variable(j) == true && + this->is_symmetric_independent_variable(i) == false)) + { + hessian[i][j] *= 0.5; + if (i != j) + hessian[j][i] *= 0.5; + } + } + } + + + + template + Tensor<0, + dim, + typename ADHelperScalarFunction:: + scalar_type> + ADHelperScalarFunction:: + extract_hessian_component( + const FullMatrix & hessian, + const FEValuesExtractors::Scalar &extractor_row, + const FEValuesExtractors::Scalar &extractor_col) const + { + // NOTE: It is necessary to make special provision for the case when the + // HessianType is scalar. Unfortunately Tensor<0,dim> does not provide + // the function unrolled_to_component_indices! + // NOTE: The order of components must be consistently defined throughout + // this class. + Tensor<0, dim, scalar_type> out; + + // Get indexsets for the subblocks from which we wish to extract the + // matrix values + const std::vector row_index_set( + internal::extract_field_component_indices(extractor_row)); + const std::vector col_index_set( + internal::extract_field_component_indices(extractor_col)); + Assert(row_index_set.size() == 1, ExcInternalError()); + Assert(col_index_set.size() == 1, ExcInternalError()); + + internal::set_tensor_entry(out, + 0, + hessian[row_index_set[0]][col_index_set[0]]); + + return out; + } + + + + template + SymmetricTensor<4, + dim, + typename ADHelperScalarFunction::scalar_type> + ADHelperScalarFunction:: + extract_hessian_component( + const FullMatrix & hessian, + const FEValuesExtractors::SymmetricTensor<2> &extractor_row, + const FEValuesExtractors::SymmetricTensor<2> &extractor_col) const + { + // NOTE: The order of components must be consistently defined throughout + // this class. NOTE: We require a specialisation for rank-4 symmetric + // tensors because they + // do not define their rank, and setting data using TableIndices is + // somewhat specialised as well. + SymmetricTensor<4, dim, scalar_type> out; + + // Get indexsets for the subblocks from which we wish to extract the + // matrix values + const std::vector row_index_set( + internal::extract_field_component_indices(extractor_row)); + const std::vector col_index_set( + internal::extract_field_component_indices(extractor_col)); + + for (unsigned int r = 0; r < row_index_set.size(); ++r) + for (unsigned int c = 0; c < col_index_set.size(); ++c) + { + internal::set_tensor_entry( + out, r, c, hessian[row_index_set[r]][col_index_set[c]]); + } + + return out; + } + + } // namespace AD } // namespace Differentiation diff --git a/source/differentiation/ad/ad_helpers.inst1.in b/source/differentiation/ad/ad_helpers.inst1.in index ef44c9398496..a5c9b87da3bf 100644 --- a/source/differentiation/ad/ad_helpers.inst1.in +++ b/source/differentiation/ad/ad_helpers.inst1.in @@ -117,6 +117,14 @@ for (deal_II_dimension : DIMENSIONS ; number : REAL_SCALARS) template class ADHelperPointLevelFunctionsBase; + // -------------------------- ADHelperScalarFunction ---------------------- + + template + class ADHelperScalarFunction; + + template + class ADHelperScalarFunction; + \} \} } @@ -137,6 +145,14 @@ for (deal_II_dimension : DIMENSIONS) template class ADHelperPointLevelFunctionsBase::ad_type>; + // -------------------------- ADHelperScalarFunction ---------------------- + + template + class ADHelperScalarFunction::ad_type>; + + template + class ADHelperScalarFunction::ad_type>; + \} \} } diff --git a/source/differentiation/ad/ad_helpers.inst2.in b/source/differentiation/ad/ad_helpers.inst2.in index 5fa4b2511e37..e886a8575ad0 100644 --- a/source/differentiation/ad/ad_helpers.inst2.in +++ b/source/differentiation/ad/ad_helpers.inst2.in @@ -172,6 +172,20 @@ for (deal_II_dimension : DIMENSIONS ; number : REAL_SCALARS) template class ADHelperPointLevelFunctionsBase; + // -------------------------- ADHelperScalarFunction ---------------------- + + template + class ADHelperScalarFunction; + + template + class ADHelperScalarFunction; + + template + class ADHelperScalarFunction; + + template + class ADHelperScalarFunction; + \} \} } @@ -198,6 +212,20 @@ for (deal_II_dimension : DIMENSIONS) template class ADHelperPointLevelFunctionsBase::ad_type>; + // -------------------------- ADHelperScalarFunction ---------------------- + + template + class ADHelperScalarFunction::ad_type>; + + template + class ADHelperScalarFunction::ad_type>; + + template + class ADHelperScalarFunction::ad_type>; + + template + class ADHelperScalarFunction::ad_type>; + \} \} } From 5efd5ed821dac8fdb5839ae0f5008b0e8f219de4 Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Wed, 20 Feb 2019 12:22:22 +0100 Subject: [PATCH 172/507] Small grammatical fixes to documentation of ADHelpers. --- .../deal.II/differentiation/ad/ad_helpers.h | 36 +++++++++---------- 1 file changed, 18 insertions(+), 18 deletions(-) diff --git a/include/deal.II/differentiation/ad/ad_helpers.h b/include/deal.II/differentiation/ad/ad_helpers.h index f884ee469481..bc00902024cc 100644 --- a/include/deal.II/differentiation/ad/ad_helpers.h +++ b/include/deal.II/differentiation/ad/ad_helpers.h @@ -115,8 +115,8 @@ namespace Differentiation * * // Indicate that we are about to start tracing the operations for * // function evaluation on the tape. If this tape has already been used - * // (i.e. the operations are already recorded) then we (optionally) load - * // the tape and reuse this data. + * // (i.e. the operations are already recorded) then we (optionally) + * // load the tape and reuse this data. * const bool is_recording * = ad_helper.start_recording_operations(tape_index); * if (is_recording == true) @@ -198,11 +198,11 @@ namespace Differentiation * that will be used in the definition of the functions that it is * desired to compute the sensitivities of. In the computation of * $\mathbf{f}(\mathbf{X})$, this will be the number of inputs - * $\mathbf{X}$, i.e. the dimension of the domain space. + * $\mathbf{X}$, i.e., the dimension of the domain space. * @param[in] n_dependent_variables The number of scalar functions to be * defined that will have a sensitivity to the given independent * variables. In the computation of $\mathbf{f}(\mathbf{X})$, this will - * be the number of outputs $\mathbf{f}$, i.e. the dimension of the + * be the number of outputs $\mathbf{f}$, i.e., the dimension of the * image space. */ ADHelperBase(const unsigned int n_independent_variables, @@ -324,11 +324,11 @@ namespace Differentiation * that will be used in the definition of the functions that it is * desired to compute the sensitivities of. In the computation of * $\mathbf{f}(\mathbf{X})$, this will be the number of inputs - * $\mathbf{X}$, i.e. the dimension of the domain space. + * $\mathbf{X}$, i.e., the dimension of the domain space. * @param[in] n_dependent_variables The number of scalar functions to be * defined that will have a sensitivity to the given independent * variables. In the computation of $\mathbf{f}(\mathbf{X})$, this will - * be the number of outputs $\mathbf{f}$, i.e. the dimension of the + * be the number of outputs $\mathbf{f}$, i.e., the dimension of the * image space. * @param[in] clear_registered_tapes A flag that indicates the that * list of @p registered_tapes must be cleared. @@ -867,11 +867,11 @@ namespace Differentiation * that will be used in the definition of the functions that it is * desired to compute the sensitivities of. In the computation of * $\mathbf{f}(\mathbf{X})$, this will be the number of inputs - * $\mathbf{X}$, i.e. the dimension of the domain space. + * $\mathbf{X}$, i.e., the dimension of the domain space. * @param[in] n_dependent_variables The number of scalar functions to be * defined that will have a sensitivity to the given independent * variables. In the computation of $\mathbf{f}(\mathbf{X})$, this will - * be the number of outputs $\mathbf{f}$, i.e. the dimension of the + * be the number of outputs $\mathbf{f}$, i.e., the dimension of the * image space. */ ADHelperCellLevelBase(const unsigned int n_independent_variables, @@ -964,7 +964,7 @@ namespace Differentiation //@{ /** - * Set the values for the independent variables $\mathbf{X}$, i.e. the + * Set the values for the independent variables $\mathbf{X}$, i.e., the * linearization point. * * @param[in] dof_values A vector field associated with local @@ -986,7 +986,7 @@ namespace Differentiation set_dof_values(const std::vector &dof_values); /** - * Set the values for the independent variables $\mathbf{X}$, i.e. the + * Set the values for the independent variables $\mathbf{X}$, i.e., the * linearization point. * * @param[in] values A vector field from which the values of all @@ -1252,7 +1252,7 @@ namespace Differentiation * that will be used in the definition of the functions that it is * desired to compute the sensitivities of. In the computation of * $\Psi(\mathbf{X})$, this will be the number of inputs - * $\mathbf{X}$, i.e. the dimension of the domain space. + * $\mathbf{X}$, i.e., the dimension of the domain space. * * @note There is only one dependent variable associated with the total * energy attributed to the local finite element. That is to say, this @@ -1568,11 +1568,11 @@ namespace Differentiation * that will be used in the definition of the functions that it is * desired to compute the sensitivities of. In the computation of * $\mathbf{r}(\mathbf{X})$, this will be the number of inputs - * $\mathbf{X}$, i.e. the dimension of the domain space. + * $\mathbf{X}$, i.e., the dimension of the domain space. * @param[in] n_dependent_variables The number of scalar functions to be * defined that will have a sensitivity to the given independent * variables. In the computation of $\mathbf{r}(\mathbf{X})$, this will - * be the number of outputs $\mathbf{r}$, i.e. the dimension of the + * be the number of outputs $\mathbf{r}$, i.e., the dimension of the * image space. */ ADHelperResidualLinearization(const unsigned int n_independent_variables, @@ -2682,11 +2682,11 @@ namespace Differentiation * that will be used in the definition of the functions that it is * desired to compute the sensitivities of. In the computation of * $\mathbf{f}(\mathbf{X})$, this will be the number of inputs - * $\mathbf{X}$, i.e. the dimension of the domain space. + * $\mathbf{X}$, i.e., the dimension of the domain space. * @param[in] n_dependent_variables The number of scalar functions to be * defined that will have a sensitivity to the given independent * variables. In the computation of $\mathbf{f}(\mathbf{X})$, this will - * be the number of outputs $\mathbf{f}$, i.e. the dimension of the + * be the number of outputs $\mathbf{f}$, i.e., the dimension of the * image space. */ ADHelperPointLevelFunctionsBase( @@ -2982,7 +2982,7 @@ namespace Differentiation * * // Indicate that we are about to start tracing the operations for * // function evaluation on the tape. If this tape has already been - * // used (i.e., the operations are already recorded) then we + * // used (i.e. the operations are already recorded) then we * // (optionally) load the tape and reuse this data. * const bool is_recording * = ad_helper.start_recording_operations(tape_index); @@ -3203,7 +3203,7 @@ namespace Differentiation * @f] * * @param[in] gradient The gradient of the scalar function with respect to - * all independent variables, i.e. that returned by compute_gradient(). + * all independent variables, i.e., that returned by compute_gradient(). * @param[in] extractor_row An extractor associated with the input field * variables. This effectively defines which components of the global set * of independent variables this field is associated with. @@ -3226,7 +3226,7 @@ namespace Differentiation * @f] * * @param[in] hessian The Hessian of the scalar function with respect to - * all independent variables, i.e. that returned by compute_hessian(). + * all independent variables, i.e., that returned by compute_hessian(). * @param[in] extractor_row An extractor associated with the input field * variables for which the first index of the Hessian is extracted. * @param[in] extractor_col An extractor associated with the input field From ca393d5ddd463c7d716176f5b7c44ca3d70abd2b Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Wed, 20 Feb 2019 18:20:23 +0100 Subject: [PATCH 173/507] Detect Tpetra support correctly if Trilinos is compiled with CUDA support --- cmake/configure/configure_2_trilinos.cmake | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/cmake/configure/configure_2_trilinos.cmake b/cmake/configure/configure_2_trilinos.cmake index 9b3c86139577..187fed907170 100644 --- a/cmake/configure/configure_2_trilinos.cmake +++ b/cmake/configure/configure_2_trilinos.cmake @@ -163,7 +163,15 @@ MACRO(FEATURE_TRILINOS_FIND_EXTERNAL var) # Check if Tpetra is usable in fact. # LIST(APPEND CMAKE_REQUIRED_INCLUDES ${Trilinos_INCLUDE_DIRS}) + LIST(APPEND CMAKE_REQUIRED_INCLUDES ${MPI_CXX_INCLUDE_PATH}) ADD_FLAGS(CMAKE_REQUIRED_FLAGS "${DEAL_II_CXX_VERSION_FLAG}") + CHECK_SYMBOL_EXISTS( + "KOKKOS_ENABLE_CUDA_LAMBDA" + "Kokkos_Macros.hpp" + DEAL_II_KOKKOS_LAMBDA_EXISTS) + IF(${DEAL_II_KOKKOS_LAMBDA_EXISTS}) + ADD_FLAGS(CMAKE_REQUIRED_FLAGS "--expt-extended-lambda") + ENDIF() LIST(APPEND CMAKE_REQUIRED_LIBRARIES "${Trilinos_LIBRARIES}") CHECK_CXX_SOURCE_COMPILES( " From b9c22bc392a715a64bed4b69e607e093b35aa87d Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 20 Feb 2019 23:03:16 +0100 Subject: [PATCH 174/507] add type traits to be used internally with FEEValuation --- include/deal.II/matrix_free/fe_evaluation.h | 29 +++++++++++++ .../matrix_free/fe_evaluation_type_traits.cc | 43 +++++++++++++++++++ ...tion_type_traits.with_trilinos=true.output | 5 +++ 3 files changed, 77 insertions(+) create mode 100644 tests/matrix_free/fe_evaluation_type_traits.cc create mode 100644 tests/matrix_free/fe_evaluation_type_traits.with_trilinos=true.output diff --git a/include/deal.II/matrix_free/fe_evaluation.h b/include/deal.II/matrix_free/fe_evaluation.h index e0143f51f754..8c3cc1d3bd76 100644 --- a/include/deal.II/matrix_free/fe_evaluation.h +++ b/include/deal.II/matrix_free/fe_evaluation.h @@ -3409,6 +3409,35 @@ FEEvaluationBase::read_cell_data( namespace internal { + // a helper type-trait that leverage SFINAE to figure out if type T has + // ... T::local_element() const + template + struct has_local_element + { + private: + // this will work always. + // we let it be void as we know T::local_element() (if exists) should + // certainly return something + static void + detect(...); + + // this detecter will work only if we have "... T::local_element() const" + // and its return type will be the same as local_element(), + // that we expect to be T::value_type + template + static decltype(std::declval().local_element(0)) + detect(const U &); + + public: + // finally here we check if our detector has return type same as + // T::value_type. This will happen if compiler can use second detector, + // otherwise SFINAE let it work with the more general first one that is void + static constexpr bool value = + std::is_same()))>::value; + }; + + // access to generic vectors that have operator (). template inline typename VectorType::value_type & diff --git a/tests/matrix_free/fe_evaluation_type_traits.cc b/tests/matrix_free/fe_evaluation_type_traits.cc new file mode 100644 index 000000000000..68c837d5e168 --- /dev/null +++ b/tests/matrix_free/fe_evaluation_type_traits.cc @@ -0,0 +1,43 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2014 - 2018 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + + +// test internal typetraits used in FEEvaluation + +#include +#include + +#include + +#include "../tests.h" + + +int +main() +{ + initlog(); + + deallog << "has_local_element:" << std::endl + << "LinearAlgebra::distributed::Vector = " + << internal::has_local_element< + LinearAlgebra::distributed::Vector>::value + << std::endl + << "TrilinosWrappers::MPI::Vector = " + << internal::has_local_element::value + << std::endl; + + deallog << "OK" << std::endl; +} diff --git a/tests/matrix_free/fe_evaluation_type_traits.with_trilinos=true.output b/tests/matrix_free/fe_evaluation_type_traits.with_trilinos=true.output new file mode 100644 index 000000000000..b62ca9b86d2d --- /dev/null +++ b/tests/matrix_free/fe_evaluation_type_traits.with_trilinos=true.output @@ -0,0 +1,5 @@ + +DEAL::has_local_element: +DEAL::LinearAlgebra::distributed::Vector = 1 +DEAL::TrilinosWrappers::MPI::Vector = 0 +DEAL::OK From 0dafc63e077a52c40d65b8b52a99da3b307aedf8 Mon Sep 17 00:00:00 2001 From: Martin Kronbichler Date: Thu, 21 Feb 2019 12:24:21 +0100 Subject: [PATCH 175/507] Fix face orientation in FEFaceEvaluation --- include/deal.II/matrix_free/fe_evaluation.h | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/include/deal.II/matrix_free/fe_evaluation.h b/include/deal.II/matrix_free/fe_evaluation.h index e0143f51f754..ac0e9be18f9d 100644 --- a/include/deal.II/matrix_free/fe_evaluation.h +++ b/include/deal.II/matrix_free/fe_evaluation.h @@ -8562,10 +8562,10 @@ FEFaceEvaluation:: { if (integrate) for (unsigned int q = 0; q < n_q_points; ++q) - tmp_values[orientations[q]] = this->values_quad[c][q]; + tmp_values[q] = this->values_quad[c][orientations[q]]; else for (unsigned int q = 0; q < n_q_points; ++q) - tmp_values[q] = this->values_quad[c][orientations[q]]; + tmp_values[orientations[q]] = this->values_quad[c][q]; for (unsigned int q = 0; q < n_q_points; ++q) this->values_quad[c][q] = tmp_values[q]; } @@ -8574,10 +8574,10 @@ FEFaceEvaluation:: { if (integrate) for (unsigned int q = 0; q < n_q_points; ++q) - tmp_values[orientations[q]] = this->gradients_quad[c][d][q]; + tmp_values[q] = this->gradients_quad[c][d][orientations[q]]; else for (unsigned int q = 0; q < n_q_points; ++q) - tmp_values[q] = this->gradients_quad[c][d][orientations[q]]; + tmp_values[orientations[q]] = this->gradients_quad[c][d][q]; for (unsigned int q = 0; q < n_q_points; ++q) this->gradients_quad[c][d][q] = tmp_values[q]; } From a5fc6ff9cd04fd39c88217167322b46037cb9389 Mon Sep 17 00:00:00 2001 From: Martin Kronbichler Date: Thu, 21 Feb 2019 12:26:56 +0100 Subject: [PATCH 176/507] Add test case for face orientation in FEFaceEvaluation --- tests/matrix_free/matrix_vector_faces_25.cc | 109 +++++++++++++++++ .../matrix_free/matrix_vector_faces_25.output | 113 ++++++++++++++++++ 2 files changed, 222 insertions(+) create mode 100644 tests/matrix_free/matrix_vector_faces_25.cc create mode 100644 tests/matrix_free/matrix_vector_faces_25.output diff --git a/tests/matrix_free/matrix_vector_faces_25.cc b/tests/matrix_free/matrix_vector_faces_25.cc new file mode 100644 index 000000000000..ef0f427ded98 --- /dev/null +++ b/tests/matrix_free/matrix_vector_faces_25.cc @@ -0,0 +1,109 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + + +// tests matrix-free face evaluation, matrix-vector products as compared to +// the same implementation with MeshWorker. Similar to matrix_vector_faces_04 +// but using a mesh with all sorts of different orientations, using a mesh +// somewhat related to the one in tests/grid/grid_tools_06.cc but with the +// cubes patched together appropriately + +#include + +#include + +#include "../tests.h" + +std::ofstream logfile("output"); + +#include "matrix_vector_faces_common.h" + + + +void generate_grid(Triangulation<3> &triangulation, int orientation) +{ + Point<3> vertices_1[] = {Point<3>(-1., -1., -3.), + Point<3>(+1., -1., -3.), + Point<3>(-1., +1., -3.), + Point<3>(+1., +1., -3.), + Point<3>(-1., -1., -1.), + Point<3>(+1., -1., -1.), + Point<3>(-1., +1., -1.), + Point<3>(+1., +1., -1.), + Point<3>(-1., -1., +1.), + Point<3>(+1., -1., +1.), + Point<3>(-1., +1., +1.), + Point<3>(+1., +1., +1.)}; + std::vector> vertices(&vertices_1[0], &vertices_1[12]); + + std::vector> cells(2, CellData<3>()); + + /* cell 0 */ + int cell_vertices_0[GeometryInfo<3>::vertices_per_cell] = { + 0, 1, 2, 3, 4, 5, 6, 7}; + + /* cell 1 */ + int cell_vertices_1[8][GeometryInfo<3>::vertices_per_cell] = { + {4, 5, 6, 7, 8, 9, 10, 11}, + {5, 7, 4, 6, 9, 11, 8, 10}, + {7, 6, 5, 4, 11, 10, 9, 8}, + {6, 4, 7, 5, 10, 8, 11, 9}, + {9, 8, 11, 10, 5, 4, 7, 6}, + {8, 10, 9, 11, 4, 6, 5, 7}, + {10, 11, 8, 9, 6, 7, 4, 5}, + {11, 9, 10, 8, 7, 5, 6, 4}}; + + for (unsigned int j = 0; j < GeometryInfo<3>::vertices_per_cell; ++j) + { + cells[0].vertices[j] = cell_vertices_0[j]; + cells[1].vertices[j] = cell_vertices_1[orientation][j]; + } + cells[0].material_id = 0; + cells[1].material_id = 0; + + + triangulation.create_triangulation(vertices, cells, SubCellData()); +} + + + +template +void +test() +{ + if (dim == 2) + return; + + Triangulation<3> tria; + for (unsigned int orientation = 0; orientation < 8; ++orientation) + { + deallog << "Testing orientation case " << orientation << std::endl; + tria.clear(); + generate_grid(tria, orientation); + + FE_DGQ<3> fe(fe_degree); + DoFHandler<3> dof(tria); + dof.distribute_dofs(fe); + AffineConstraints constraints; + constraints.close(); + + do_test<3, fe_degree, fe_degree + 1, double>(dof, constraints, false); + + tria.refine_global(1); + dof.distribute_dofs(fe); + do_test<3, fe_degree, fe_degree + 1, double>(dof, constraints, false); + } +} diff --git a/tests/matrix_free/matrix_vector_faces_25.output b/tests/matrix_free/matrix_vector_faces_25.output new file mode 100644 index 000000000000..c44d20e8fb3b --- /dev/null +++ b/tests/matrix_free/matrix_vector_faces_25.output @@ -0,0 +1,113 @@ + +DEAL:3d::Testing orientation case 0 +DEAL:3d::Testing FE_DGQ<3>(1) +DEAL:3d::Norm of difference: 4.93e-16 +DEAL:3d:: +DEAL:3d::Testing FE_DGQ<3>(1) +DEAL:3d::Norm of difference: 8.94e-16 +DEAL:3d:: +DEAL:3d::Testing orientation case 1 +DEAL:3d::Testing FE_DGQ<3>(1) +DEAL:3d::Norm of difference: 4.85e-16 +DEAL:3d:: +DEAL:3d::Testing FE_DGQ<3>(1) +DEAL:3d::Norm of difference: 8.94e-16 +DEAL:3d:: +DEAL:3d::Testing orientation case 2 +DEAL:3d::Testing FE_DGQ<3>(1) +DEAL:3d::Norm of difference: 3.24e-16 +DEAL:3d:: +DEAL:3d::Testing FE_DGQ<3>(1) +DEAL:3d::Norm of difference: 8.94e-16 +DEAL:3d:: +DEAL:3d::Testing orientation case 3 +DEAL:3d::Testing FE_DGQ<3>(1) +DEAL:3d::Norm of difference: 3.26e-16 +DEAL:3d:: +DEAL:3d::Testing FE_DGQ<3>(1) +DEAL:3d::Norm of difference: 8.94e-16 +DEAL:3d:: +DEAL:3d::Testing orientation case 4 +DEAL:3d::Testing FE_DGQ<3>(1) +DEAL:3d::Norm of difference: 2.45e-16 +DEAL:3d:: +DEAL:3d::Testing FE_DGQ<3>(1) +DEAL:3d::Norm of difference: 8.55e-16 +DEAL:3d:: +DEAL:3d::Testing orientation case 5 +DEAL:3d::Testing FE_DGQ<3>(1) +DEAL:3d::Norm of difference: 6.52e-16 +DEAL:3d:: +DEAL:3d::Testing FE_DGQ<3>(1) +DEAL:3d::Norm of difference: 8.55e-16 +DEAL:3d:: +DEAL:3d::Testing orientation case 6 +DEAL:3d::Testing FE_DGQ<3>(1) +DEAL:3d::Norm of difference: 4.86e-16 +DEAL:3d:: +DEAL:3d::Testing FE_DGQ<3>(1) +DEAL:3d::Norm of difference: 8.55e-16 +DEAL:3d:: +DEAL:3d::Testing orientation case 7 +DEAL:3d::Testing FE_DGQ<3>(1) +DEAL:3d::Norm of difference: 4.84e-16 +DEAL:3d:: +DEAL:3d::Testing FE_DGQ<3>(1) +DEAL:3d::Norm of difference: 8.55e-16 +DEAL:3d:: +DEAL:3d::Testing orientation case 0 +DEAL:3d::Testing FE_DGQ<3>(2) +DEAL:3d::Norm of difference: 6.75e-16 +DEAL:3d:: +DEAL:3d::Testing FE_DGQ<3>(2) +DEAL:3d::Norm of difference: 4.04e-15 +DEAL:3d:: +DEAL:3d::Testing orientation case 1 +DEAL:3d::Testing FE_DGQ<3>(2) +DEAL:3d::Norm of difference: 6.75e-16 +DEAL:3d:: +DEAL:3d::Testing FE_DGQ<3>(2) +DEAL:3d::Norm of difference: 3.97e-15 +DEAL:3d:: +DEAL:3d::Testing orientation case 2 +DEAL:3d::Testing FE_DGQ<3>(2) +DEAL:3d::Norm of difference: 5.40e-16 +DEAL:3d:: +DEAL:3d::Testing FE_DGQ<3>(2) +DEAL:3d::Norm of difference: 3.98e-15 +DEAL:3d:: +DEAL:3d::Testing orientation case 3 +DEAL:3d::Testing FE_DGQ<3>(2) +DEAL:3d::Norm of difference: 6.08e-16 +DEAL:3d:: +DEAL:3d::Testing FE_DGQ<3>(2) +DEAL:3d::Norm of difference: 3.95e-15 +DEAL:3d:: +DEAL:3d::Testing orientation case 4 +DEAL:3d::Testing FE_DGQ<3>(2) +DEAL:3d::Norm of difference: 4.99e-16 +DEAL:3d:: +DEAL:3d::Testing FE_DGQ<3>(2) +DEAL:3d::Norm of difference: 3.68e-15 +DEAL:3d:: +DEAL:3d::Testing orientation case 5 +DEAL:3d::Testing FE_DGQ<3>(2) +DEAL:3d::Norm of difference: 5.32e-16 +DEAL:3d:: +DEAL:3d::Testing FE_DGQ<3>(2) +DEAL:3d::Norm of difference: 3.68e-15 +DEAL:3d:: +DEAL:3d::Testing orientation case 6 +DEAL:3d::Testing FE_DGQ<3>(2) +DEAL:3d::Norm of difference: 5.32e-16 +DEAL:3d:: +DEAL:3d::Testing FE_DGQ<3>(2) +DEAL:3d::Norm of difference: 3.68e-15 +DEAL:3d:: +DEAL:3d::Testing orientation case 7 +DEAL:3d::Testing FE_DGQ<3>(2) +DEAL:3d::Norm of difference: 5.32e-16 +DEAL:3d:: +DEAL:3d::Testing FE_DGQ<3>(2) +DEAL:3d::Norm of difference: 3.68e-15 +DEAL:3d:: From b2979f78e051bff2c6e1f0e766701551a847c126 Mon Sep 17 00:00:00 2001 From: Martin Kronbichler Date: Thu, 21 Feb 2019 12:27:09 +0100 Subject: [PATCH 177/507] Add changelog entry --- doc/news/changes/minor/20190221MartinKronbichler | 6 ++++++ 1 file changed, 6 insertions(+) create mode 100644 doc/news/changes/minor/20190221MartinKronbichler diff --git a/doc/news/changes/minor/20190221MartinKronbichler b/doc/news/changes/minor/20190221MartinKronbichler new file mode 100644 index 000000000000..e22a5b8f6b06 --- /dev/null +++ b/doc/news/changes/minor/20190221MartinKronbichler @@ -0,0 +1,6 @@ +Fixed: FEFaceEvaluation::evaluate() and FEFaceEvaluation::integrate() would +provide wrong results for faces in non-standard orientation layout, namely +with `orientation=true, face_flip={false,true}, face_rotation=true`. This is +now fixed. +
    +(Martin Kronbichler, 2019/02/21) From bf6a24cc20ed8f3cdcf276abfc7b8a6d08b68417 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Thu, 21 Feb 2019 19:09:04 +0100 Subject: [PATCH 178/507] FEEvaluation: switch between internal::vector_access() via SFINAE --- include/deal.II/matrix_free/fe_evaluation.h | 24 ++++-- .../matrix_free/fe_evaluation_type_traits.cc | 79 +++++++++++++++++++ ...tion_type_traits.with_trilinos=true.output | 5 ++ 3 files changed, 100 insertions(+), 8 deletions(-) diff --git a/include/deal.II/matrix_free/fe_evaluation.h b/include/deal.II/matrix_free/fe_evaluation.h index 8c3cc1d3bd76..dc97327d0797 100644 --- a/include/deal.II/matrix_free/fe_evaluation.h +++ b/include/deal.II/matrix_free/fe_evaluation.h @@ -3439,7 +3439,10 @@ namespace internal // access to generic vectors that have operator (). - template + // FIXME: this is wrong for Trilinos/Petsc MPI vectors + template ::value, + VectorType>::type * = nullptr> inline typename VectorType::value_type & vector_access(VectorType &vec, const unsigned int entry) { @@ -3451,19 +3454,20 @@ namespace internal // access to distributed MPI vectors that have a local_element(uint) // method to access data in local index space, which is what we use in // DoFInfo and hence in read_dof_values etc. - template - inline Number & - vector_access(LinearAlgebra::distributed::Vector &vec, - const unsigned int entry) + template ::value, + VectorType>::type * = nullptr> + inline typename VectorType::value_type & + vector_access(VectorType &vec, const unsigned int entry) { return vec.local_element(entry); } - // this is to make sure that the parallel partitioning in the - // LinearAlgebra::distributed::Vector is really the same as stored in - // MatrixFree + // this is to make sure that the parallel partitioning in VectorType + // is really the same as stored in MatrixFree + // FIXME: this is incorrect for PETSc/Trilinos MPI vectors template inline void check_vector_compatibility( @@ -3476,6 +3480,10 @@ namespace internal AssertDimension(vec.size(), dof_info.vector_partitioner->size()); } + + // this is to make sure that the parallel partitioning in the + // LinearAlgebra::distributed::Vector is really the same as stored in + // MatrixFree template inline void check_vector_compatibility( diff --git a/tests/matrix_free/fe_evaluation_type_traits.cc b/tests/matrix_free/fe_evaluation_type_traits.cc index 68c837d5e168..458a625e8ada 100644 --- a/tests/matrix_free/fe_evaluation_type_traits.cc +++ b/tests/matrix_free/fe_evaluation_type_traits.cc @@ -24,12 +24,80 @@ #include "../tests.h" +// dummy class we use to check typetraits and internal function. +// this one mimics LA::d::Vec +template +class Dummy +{ +public: + using value_type = Number; + + Number + local_element(const unsigned int) const + { + deallog << "Dummy::local_element() const" << std::endl; + return Number(); + } + + Number & + local_element(const unsigned int) + { + deallog << "Dummy::local_element()" << std::endl; + return dummy; + } + + Number + operator()(const unsigned int) const + { + deallog << "Dummy::operator() const" << std::endl; + return Number(); + } + + Number & + operator()(const unsigned int) + { + deallog << "Dummy::operator()" << std::endl; + return dummy; + } + +private: + Number dummy; +}; + + +template +class Dummy2 +{ +public: + using value_type = Number; + + Number + operator()(const unsigned int) const + { + deallog << "Dummy2::operator() const" << std::endl; + return Number(); + } + + Number & + operator()(const unsigned int) + { + deallog << "Dummy2::operator()" << std::endl; + return dummy; + } + +private: + Number dummy; +}; + int main() { initlog(); + Dummy dummy; + Dummy2 dummy2; + deallog << "has_local_element:" << std::endl << "LinearAlgebra::distributed::Vector = " << internal::has_local_element< @@ -37,7 +105,18 @@ main() << std::endl << "TrilinosWrappers::MPI::Vector = " << internal::has_local_element::value + << std::endl + << "Dummy = " << internal::has_local_element>::value + << std::endl + << "Dummy2 = " << internal::has_local_element>::value << std::endl; + // now check internal::vector_access wrapper + // we expect local_element() to be called + deallog << "internal::vector_access:" << std::endl; + internal::vector_access(dummy, 0); + internal::vector_access(dummy2, 0); + + deallog << "OK" << std::endl; } diff --git a/tests/matrix_free/fe_evaluation_type_traits.with_trilinos=true.output b/tests/matrix_free/fe_evaluation_type_traits.with_trilinos=true.output index b62ca9b86d2d..78f076543419 100644 --- a/tests/matrix_free/fe_evaluation_type_traits.with_trilinos=true.output +++ b/tests/matrix_free/fe_evaluation_type_traits.with_trilinos=true.output @@ -2,4 +2,9 @@ DEAL::has_local_element: DEAL::LinearAlgebra::distributed::Vector = 1 DEAL::TrilinosWrappers::MPI::Vector = 0 +DEAL::Dummy = 1 +DEAL::Dummy2 = 0 +DEAL::internal::vector_access: +DEAL::Dummy::local_element() +DEAL::Dummy2::operator() DEAL::OK From 071f982eddcacb5d3efcb8fa7d0b1491273e7625 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Thu, 21 Feb 2019 23:20:50 +0100 Subject: [PATCH 179/507] add internal::has_partitioners_are_compatible<> --- include/deal.II/matrix_free/fe_evaluation.h | 21 +++++++++++++++++++ .../matrix_free/fe_evaluation_type_traits.cc | 11 ++++++++++ ...tion_type_traits.with_trilinos=true.output | 3 +++ 3 files changed, 35 insertions(+) diff --git a/include/deal.II/matrix_free/fe_evaluation.h b/include/deal.II/matrix_free/fe_evaluation.h index dc97327d0797..c7c2d8b8903c 100644 --- a/include/deal.II/matrix_free/fe_evaluation.h +++ b/include/deal.II/matrix_free/fe_evaluation.h @@ -3438,6 +3438,27 @@ namespace internal }; + // same as above to check + // bool T::partitioners_are_compatible(const Utilities::MPI::Partitioner &) + // const + template + struct has_partitioners_are_compatible + { + private: + static void + detect(...); + + template + static decltype(std::declval().partitioners_are_compatible( + std::declval())) + detect(const U &); + + public: + static constexpr bool value = + std::is_same()))>::value; + }; + + // access to generic vectors that have operator (). // FIXME: this is wrong for Trilinos/Petsc MPI vectors template Date: Thu, 21 Feb 2019 23:32:31 +0100 Subject: [PATCH 180/507] use has_partitioners_are_compatible in internal::check_vector_compatibility --- include/deal.II/matrix_free/fe_evaluation.h | 30 +++++++++------------ 1 file changed, 13 insertions(+), 17 deletions(-) diff --git a/include/deal.II/matrix_free/fe_evaluation.h b/include/deal.II/matrix_free/fe_evaluation.h index c7c2d8b8903c..8da043d70bee 100644 --- a/include/deal.II/matrix_free/fe_evaluation.h +++ b/include/deal.II/matrix_free/fe_evaluation.h @@ -40,15 +40,6 @@ DEAL_II_NAMESPACE_OPEN -// forward declarations -namespace LinearAlgebra -{ - namespace distributed - { - template - class Vector; - } -} // namespace LinearAlgebra namespace internal { DeclException0(ExcAccessToUninitializedField); @@ -3487,9 +3478,13 @@ namespace internal // this is to make sure that the parallel partitioning in VectorType - // is really the same as stored in MatrixFree + // is really the same as stored in MatrixFree. + // version below is when has_partitioners_are_compatible == false // FIXME: this is incorrect for PETSc/Trilinos MPI vectors - template + template < + typename VectorType, + typename std::enable_if::value, + VectorType>::type * = nullptr> inline void check_vector_compatibility( const VectorType & vec, @@ -3502,14 +3497,15 @@ namespace internal } - // this is to make sure that the parallel partitioning in the - // LinearAlgebra::distributed::Vector is really the same as stored in - // MatrixFree - template + // same as above for has_partitioners_are_compatible == true + template < + typename VectorType, + typename std::enable_if::value, + VectorType>::type * = nullptr> inline void check_vector_compatibility( - const LinearAlgebra::distributed::Vector &vec, - const internal::MatrixFreeFunctions::DoFInfo & dof_info) + const VectorType & vec, + const internal::MatrixFreeFunctions::DoFInfo &dof_info) { (void)vec; (void)dof_info; From 891c6d8115aeb0c577661f88c1336a8c73a8cf8b Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Fri, 22 Feb 2019 14:40:23 +0100 Subject: [PATCH 181/507] Remove redundant output files --- ...> sparse_matrix_vector_14.with_trilinos_with_tpetra=on.output} | 0 ...> sparse_matrix_vector_15.with_trilinos_with_tpetra=on.output} | 0 2 files changed, 0 insertions(+), 0 deletions(-) rename tests/trilinos/{sparse_matrix_vector_14.output => sparse_matrix_vector_14.with_trilinos_with_tpetra=on.output} (100%) rename tests/trilinos/{sparse_matrix_vector_15.output => sparse_matrix_vector_15.with_trilinos_with_tpetra=on.output} (100%) diff --git a/tests/trilinos/sparse_matrix_vector_14.output b/tests/trilinos/sparse_matrix_vector_14.with_trilinos_with_tpetra=on.output similarity index 100% rename from tests/trilinos/sparse_matrix_vector_14.output rename to tests/trilinos/sparse_matrix_vector_14.with_trilinos_with_tpetra=on.output diff --git a/tests/trilinos/sparse_matrix_vector_15.output b/tests/trilinos/sparse_matrix_vector_15.with_trilinos_with_tpetra=on.output similarity index 100% rename from tests/trilinos/sparse_matrix_vector_15.output rename to tests/trilinos/sparse_matrix_vector_15.with_trilinos_with_tpetra=on.output From 40a874a6b150c863b5be5577b19da5d06af66e4c Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Fri, 22 Feb 2019 15:04:18 +0100 Subject: [PATCH 182/507] Move implementation to templates file --- .../lac/trilinos_tpetra_vector.templates.h | 681 ++++++++++++++++++ source/lac/trilinos_tpetra_vector.cc | 646 +---------------- 2 files changed, 682 insertions(+), 645 deletions(-) create mode 100644 include/deal.II/lac/trilinos_tpetra_vector.templates.h diff --git a/include/deal.II/lac/trilinos_tpetra_vector.templates.h b/include/deal.II/lac/trilinos_tpetra_vector.templates.h new file mode 100644 index 000000000000..b102775201e3 --- /dev/null +++ b/include/deal.II/lac/trilinos_tpetra_vector.templates.h @@ -0,0 +1,681 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2018 - 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + +#ifndef dealii__trilinos_tpetra_vector_templates_h +#define dealii__trilinos_tpetra_vector_templates_h + +#include + +#include + +#ifdef DEAL_II_TRILINOS_WITH_TPETRA + +# ifdef DEAL_II_WITH_MPI + +# include + +# include + +# include + +# include +# include +# include + +# include + + +DEAL_II_NAMESPACE_OPEN + +namespace LinearAlgebra +{ + namespace TpetraWrappers + { + template + Vector::Vector() + : Subscriptor() + , vector(new Tpetra::Vector( + Teuchos::RCP>( + new Tpetra::Map( + 0, + 0, + Utilities::Trilinos::tpetra_comm_self())))) + {} + + + + template + Vector::Vector(const Vector &V) + : Subscriptor() + , vector(new Tpetra::Vector( + V.trilinos_vector(), + Teuchos::Copy)) + {} + + + + template + Vector::Vector(const IndexSet ¶llel_partitioner, + const MPI_Comm &communicator) + : Subscriptor() + , vector(new Tpetra::Vector( + Teuchos::rcp(new Tpetra::Map( + parallel_partitioner.make_tpetra_map(communicator, false))))) + {} + + + + template + void + Vector::reinit(const IndexSet ¶llel_partitioner, + const MPI_Comm &communicator, + const bool omit_zeroing_entries) + { + Tpetra::Map input_map = + parallel_partitioner.make_tpetra_map(communicator, false); + if (vector->getMap()->isSameAs(input_map) == false) + vector = std_cxx14::make_unique< + Tpetra::Vector>(Teuchos::rcp( + new Tpetra::Map(input_map))); + else if (omit_zeroing_entries == false) + { + vector->putScalar(0.); + } + } + + + + template + void + Vector::reinit(const VectorSpaceVector &V, + const bool omit_zeroing_entries) + { + // Check that casting will work. + Assert(dynamic_cast *>(&V) != nullptr, + ExcVectorTypeNotCompatible()); + + // Downcast V. If fails, throws an exception. + const Vector &down_V = dynamic_cast &>(V); + + reinit(down_V.locally_owned_elements(), + down_V.get_mpi_communicator(), + omit_zeroing_entries); + } + + + + template + Vector & + Vector::operator=(const Vector &V) + { + // Distinguish three cases: + // - First case: both vectors have the same layout. + // - Second case: both vectors have the same size but different layout. + // - Third case: the vectors have different size. + if (vector->getMap()->isSameAs(*(V.trilinos_vector().getMap()))) + *vector = V.trilinos_vector(); + else + { + if (size() == V.size()) + { + Tpetra::Import data_exchange( + vector->getMap(), V.trilinos_vector().getMap()); + + vector->doImport(V.trilinos_vector(), + data_exchange, + Tpetra::REPLACE); + } + else + vector = std_cxx14::make_unique< + Tpetra::Vector>( + V.trilinos_vector()); + } + + return *this; + } + + + + template + Vector & + Vector::operator=(const Number s) + { + Assert(s == Number(0.), + ExcMessage("Only 0 can be assigned to a vector.")); + + vector->putScalar(s); + + return *this; + } + + + + template + void + Vector::import( + const ReadWriteVector & V, + VectorOperation::values operation, + std::shared_ptr communication_pattern) + { + // If no communication pattern is given, create one. Otherwsie, use the + // one given. + if (communication_pattern == nullptr) + { + // The first time import is called, a communication pattern is + // created. Check if the communication pattern already exists and if + // it can be reused. + if ((source_stored_elements.size() != + V.get_stored_elements().size()) || + (source_stored_elements != V.get_stored_elements())) + { + const Teuchos::MpiComm *mpi_comm = + dynamic_cast *>( + vector->getMap()->getComm().get()); + Assert(mpi_comm != nullptr, ExcInternalError()); + create_tpetra_comm_pattern(V.get_stored_elements(), + *(mpi_comm->getRawMpiComm())()); + } + } + else + { + tpetra_comm_pattern = std::dynamic_pointer_cast< + const TpetraWrappers::CommunicationPattern>(communication_pattern); + AssertThrow( + tpetra_comm_pattern != nullptr, + ExcMessage( + std::string("The communication pattern is not of type ") + + "LinearAlgebra::TpetraWrappers::CommunicationPattern.")); + } + + Tpetra::Export tpetra_export( + tpetra_comm_pattern->get_tpetra_export()); + Tpetra::Vector source_vector( + tpetra_export.getSourceMap()); + + source_vector.template sync(); + auto x_2d = source_vector.template getLocalView(); + auto x_1d = Kokkos::subview(x_2d, Kokkos::ALL(), 0); + source_vector.template modify(); + const size_t localLength = source_vector.getLocalLength(); + auto values_it = V.begin(); + for (size_t k = 0; k < localLength; ++k) + x_1d(k) = *values_it++; + source_vector.template sync< + typename Tpetra::Vector:: + device_type::memory_space>(); + if (operation == VectorOperation::insert) + vector->doExport(source_vector, tpetra_export, Tpetra::REPLACE); + else if (operation == VectorOperation::add) + vector->doExport(source_vector, tpetra_export, Tpetra::ADD); + else + AssertThrow(false, ExcNotImplemented()); + } + + + + template + Vector & + Vector::operator*=(const Number factor) + { + AssertIsFinite(factor); + vector->scale(factor); + + return *this; + } + + + + template + Vector & + Vector::operator/=(const Number factor) + { + AssertIsFinite(factor); + Assert(factor != Number(0.), ExcZero()); + *this *= Number(1.) / factor; + + return *this; + } + + + + template + Vector & + Vector::operator+=(const VectorSpaceVector &V) + { + // Check that casting will work. + Assert(dynamic_cast *>(&V) != nullptr, + ExcVectorTypeNotCompatible()); + + // Downcast V. If fails, throws an exception. + const Vector &down_V = dynamic_cast &>(V); + // If the maps are the same we can update right away. + if (vector->getMap()->isSameAs(*(down_V.trilinos_vector().getMap()))) + { + vector->update(1., down_V.trilinos_vector(), 1.); + } + else + { + Assert(this->size() == down_V.size(), + ExcDimensionMismatch(this->size(), down_V.size())); + + // TODO: Tpetra doesn't have a combine mode that also updates local + // elements, maybe there is a better workaround. + Tpetra::Vector dummy( + vector->getMap(), false); + Tpetra::Import data_exchange( + down_V.trilinos_vector().getMap(), dummy.getMap()); + + dummy.doImport(down_V.trilinos_vector(), + data_exchange, + Tpetra::INSERT); + + vector->update(1.0, dummy, 1.0); + } + + return *this; + } + + + + template + Vector & + Vector::operator-=(const VectorSpaceVector &V) + { + this->add(-1., V); + + return *this; + } + + + + template + Number Vector::operator*(const VectorSpaceVector &V) const + { + // Check that casting will work. + Assert(dynamic_cast *>(&V) != nullptr, + ExcVectorTypeNotCompatible()); + + // Downcast V. If fails, throws an exception. + const Vector &down_V = dynamic_cast &>(V); + Assert(this->size() == down_V.size(), + ExcDimensionMismatch(this->size(), down_V.size())); + Assert(vector->getMap()->isSameAs(*down_V.trilinos_vector().getMap()), + ExcDifferentParallelPartitioning()); + + return vector->dot(down_V.trilinos_vector()); + } + + + + template + void + Vector::add(const Number a) + { + AssertIsFinite(a); + + vector->template sync(); + auto vector_2d = vector->template getLocalView(); + auto vector_1d = Kokkos::subview(vector_2d, Kokkos::ALL(), 0); + vector->template modify(); + const size_t localLength = vector->getLocalLength(); + for (size_t k = 0; k < localLength; ++k) + { + vector_1d(k) += a; + } + vector->template sync< + typename Tpetra::Vector:: + device_type::memory_space>(); + } + + + + template + void + Vector::add(const Number a, const VectorSpaceVector &V) + { + // Check that casting will work. + Assert(dynamic_cast *>(&V) != nullptr, + ExcVectorTypeNotCompatible()); + + // Downcast V. If fails, throws an exception. + const Vector &down_V = dynamic_cast &>(V); + AssertIsFinite(a); + Assert(vector->getMap()->isSameAs(*(down_V.trilinos_vector().getMap())), + ExcDifferentParallelPartitioning()); + + vector->update(a, down_V.trilinos_vector(), 1.); + } + + + + template + void + Vector::add(const Number a, + const VectorSpaceVector &V, + const Number b, + const VectorSpaceVector &W) + { + // Check that casting will work. + Assert(dynamic_cast *>(&V) != nullptr, + ExcVectorTypeNotCompatible()); + // Check that casting will work. + Assert(dynamic_cast *>(&W) != nullptr, + ExcVectorTypeNotCompatible()); + + // Downcast V. If fails, throws an exception. + const Vector &down_V = dynamic_cast &>(V); + // Downcast W. If fails, throws an exception. + const Vector &down_W = dynamic_cast &>(W); + Assert(vector->getMap()->isSameAs(*(down_V.trilinos_vector().getMap())), + ExcDifferentParallelPartitioning()); + Assert(vector->getMap()->isSameAs(*(down_W.trilinos_vector().getMap())), + ExcDifferentParallelPartitioning()); + AssertIsFinite(a); + AssertIsFinite(b); + + vector->update( + a, down_V.trilinos_vector(), b, down_W.trilinos_vector(), 1.); + } + + + + template + void + Vector::sadd(const Number s, + const Number a, + const VectorSpaceVector &V) + { + // Check that casting will work. + Assert(dynamic_cast *>(&V) != nullptr, + ExcVectorTypeNotCompatible()); + + *this *= s; + // Downcast V. It fails, throws an exception. + const Vector &down_V = dynamic_cast &>(V); + Vector tmp(down_V); + tmp *= a; + *this += tmp; + } + + + + template + void + Vector::scale(const VectorSpaceVector &scaling_factors) + { + // Check that casting will work. + Assert(dynamic_cast *>(&scaling_factors) != nullptr, + ExcVectorTypeNotCompatible()); + + // Downcast scaling_factors. If fails, throws an exception. + const Vector &down_scaling_factors = + dynamic_cast &>(scaling_factors); + Assert(vector->getMap()->isSameAs( + *(down_scaling_factors.trilinos_vector().getMap())), + ExcDifferentParallelPartitioning()); + + vector->elementWiseMultiply(1., + *down_scaling_factors.vector, + *vector, + 0.); + } + + + + template + void + Vector::equ(const Number a, const VectorSpaceVector &V) + { + // Check that casting will work. + Assert(dynamic_cast *>(&V) != nullptr, + ExcVectorTypeNotCompatible()); + + // Downcast V. If fails, throws an exception. + const Vector &down_V = dynamic_cast &>(V); + // If we don't have the same map, copy. + if (vector->getMap()->isSameAs(*down_V.trilinos_vector().getMap()) == + false) + this->sadd(0., a, V); + else + { + // Otherwise, just update + vector->update(a, down_V.trilinos_vector(), 0.); + } + } + + + + template + bool + Vector::all_zero() const + { + // get a representation of the vector and + // loop over all the elements + Number * start_ptr = vector->getDataNonConst().get(); + const Number *ptr = start_ptr, + *eptr = start_ptr + vector->getLocalLength(); + unsigned int flag = 0; + while (ptr != eptr) + { + if (*ptr != Number(0)) + { + flag = 1; + break; + } + ++ptr; + } + + // Check that the vector is zero on _all_ processors. + const Teuchos::MpiComm *mpi_comm = + dynamic_cast *>( + vector->getMap()->getComm().get()); + Assert(mpi_comm != nullptr, ExcInternalError()); + unsigned int num_nonzero = + Utilities::MPI::sum(flag, *(mpi_comm->getRawMpiComm())()); + + return num_nonzero == 0; + } + + + + template + Number + Vector::mean_value() const + { + return vector->meanValue(); + } + + + + template + typename LinearAlgebra::VectorSpaceVector::real_type + Vector::l1_norm() const + { + return vector->norm1(); + } + + + + template + typename LinearAlgebra::VectorSpaceVector::real_type + Vector::l2_norm() const + { + return vector->norm2(); + } + + + + template + typename LinearAlgebra::VectorSpaceVector::real_type + Vector::linfty_norm() const + { + return vector->normInf(); + } + + + + template + Number + Vector::add_and_dot(const Number a, + const VectorSpaceVector &V, + const VectorSpaceVector &W) + { + this->add(a, V); + + return *this * W; + } + + + + template + typename Vector::size_type + Vector::size() const + { + return vector->getGlobalLength(); + } + + + + template + MPI_Comm + Vector::get_mpi_communicator() const + { + const auto tpetra_comm = dynamic_cast *>( + vector->getMap()->getComm().get()); + Assert(tpetra_comm != nullptr, ExcInternalError()); + return *(tpetra_comm->getRawMpiComm())(); + } + + + + template + ::dealii::IndexSet + Vector::locally_owned_elements() const + { + IndexSet is(size()); + + // easy case: local range is contiguous + if (vector->getMap()->isContiguous()) + { + is.add_range(vector->getMap()->getMinGlobalIndex(), + vector->getMap()->getMaxGlobalIndex() + 1); + } + else if (vector->getLocalLength() > 0) + { + const size_type n_indices = vector->getLocalLength(); + std::vector vector_indices; + vector_indices.reserve(n_indices); + for (unsigned int i = 0; i < n_indices; ++i) + vector_indices.push_back(vector->getMap()->getGlobalElement(i)); + + is.add_indices(vector_indices.data(), + vector_indices.data() + n_indices); + } + is.compress(); + + return is; + } + + + + template + const Tpetra::Vector & + Vector::trilinos_vector() const + { + return *vector; + } + + + + template + Tpetra::Vector & + Vector::trilinos_vector() + { + return *vector; + } + + + + template + void + Vector::print(std::ostream & out, + const unsigned int precision, + const bool scientific, + const bool across) const + { + AssertThrow(out, ExcIO()); + boost::io::ios_flags_saver restore_flags(out); + + // Get a representation of the vector and loop over all + // the elements + const auto val = vector->get1dView(); + + out.precision(precision); + if (scientific) + out.setf(std::ios::scientific, std::ios::floatfield); + else + out.setf(std::ios::fixed, std::ios::floatfield); + + vector->template sync(); + auto vector_2d = vector->template getLocalView(); + auto vector_1d = Kokkos::subview(vector_2d, Kokkos::ALL(), 0); + const size_t local_length = vector->getLocalLength(); + + if (across) + for (unsigned int i = 0; i < local_length; ++i) + out << vector_1d(i) << ' '; + else + for (unsigned int i = 0; i < local_length; ++i) + out << vector_1d(i) << std::endl; + out << std::endl; + + // restore the representation + // of the vector + AssertThrow(out, ExcIO()); + } + + + + template + std::size_t + Vector::memory_consumption() const + { + return sizeof(*this) + + vector->getLocalLength() * + (sizeof(Number) + sizeof(TrilinosWrappers::types::int_type)); + } + + + + template + void + Vector::create_tpetra_comm_pattern(const IndexSet &source_index_set, + const MPI_Comm &mpi_comm) + { + source_stored_elements = source_index_set; + tpetra_comm_pattern = + std::make_shared( + locally_owned_elements(), source_index_set, mpi_comm); + } + } // namespace TpetraWrappers +} // namespace LinearAlgebra + +DEAL_II_NAMESPACE_CLOSE + +# endif + +#endif + +#endif diff --git a/source/lac/trilinos_tpetra_vector.cc b/source/lac/trilinos_tpetra_vector.cc index ea218f8309f8..b269bdabcf88 100644 --- a/source/lac/trilinos_tpetra_vector.cc +++ b/source/lac/trilinos_tpetra_vector.cc @@ -13,660 +13,17 @@ // // --------------------------------------------------------------------- -#include - -#include +#include #ifdef DEAL_II_TRILINOS_WITH_TPETRA - # ifdef DEAL_II_WITH_MPI -# include - -# include - -# include - -# include -# include -# include - -# include - - DEAL_II_NAMESPACE_OPEN namespace LinearAlgebra { namespace TpetraWrappers { - template - Vector::Vector() - : Subscriptor() - , vector(new Tpetra::Vector( - Teuchos::RCP>( - new Tpetra::Map( - 0, - 0, - Utilities::Trilinos::tpetra_comm_self())))) - {} - - - - template - Vector::Vector(const Vector &V) - : Subscriptor() - , vector(new Tpetra::Vector( - V.trilinos_vector(), - Teuchos::Copy)) - {} - - - - template - Vector::Vector(const IndexSet ¶llel_partitioner, - const MPI_Comm &communicator) - : Subscriptor() - , vector(new Tpetra::Vector( - Teuchos::rcp(new Tpetra::Map( - parallel_partitioner.make_tpetra_map(communicator, false))))) - {} - - - - template - void - Vector::reinit(const IndexSet ¶llel_partitioner, - const MPI_Comm &communicator, - const bool omit_zeroing_entries) - { - Tpetra::Map input_map = - parallel_partitioner.make_tpetra_map(communicator, false); - if (vector->getMap()->isSameAs(input_map) == false) - vector = std_cxx14::make_unique< - Tpetra::Vector>(Teuchos::rcp( - new Tpetra::Map(input_map))); - else if (omit_zeroing_entries == false) - { - vector->putScalar(0.); - } - } - - - - template - void - Vector::reinit(const VectorSpaceVector &V, - const bool omit_zeroing_entries) - { - // Check that casting will work. - Assert(dynamic_cast *>(&V) != nullptr, - ExcVectorTypeNotCompatible()); - - // Downcast V. If fails, throws an exception. - const Vector &down_V = dynamic_cast &>(V); - - reinit(down_V.locally_owned_elements(), - down_V.get_mpi_communicator(), - omit_zeroing_entries); - } - - - - template - Vector & - Vector::operator=(const Vector &V) - { - // Distinguish three cases: - // - First case: both vectors have the same layout. - // - Second case: both vectors have the same size but different layout. - // - Third case: the vectors have different size. - if (vector->getMap()->isSameAs(*(V.trilinos_vector().getMap()))) - *vector = V.trilinos_vector(); - else - { - if (size() == V.size()) - { - Tpetra::Import data_exchange( - vector->getMap(), V.trilinos_vector().getMap()); - - vector->doImport(V.trilinos_vector(), - data_exchange, - Tpetra::REPLACE); - } - else - vector = std_cxx14::make_unique< - Tpetra::Vector>( - V.trilinos_vector()); - } - - return *this; - } - - - - template - Vector & - Vector::operator=(const Number s) - { - Assert(s == Number(0.), - ExcMessage("Only 0 can be assigned to a vector.")); - - vector->putScalar(s); - - return *this; - } - - - - template - void - Vector::import( - const ReadWriteVector & V, - VectorOperation::values operation, - std::shared_ptr communication_pattern) - { - // If no communication pattern is given, create one. Otherwsie, use the - // one given. - if (communication_pattern == nullptr) - { - // The first time import is called, a communication pattern is - // created. Check if the communication pattern already exists and if - // it can be reused. - if ((source_stored_elements.size() != - V.get_stored_elements().size()) || - (source_stored_elements != V.get_stored_elements())) - { - const Teuchos::MpiComm *mpi_comm = - dynamic_cast *>( - vector->getMap()->getComm().get()); - Assert(mpi_comm != nullptr, ExcInternalError()); - create_tpetra_comm_pattern(V.get_stored_elements(), - *(mpi_comm->getRawMpiComm())()); - } - } - else - { - tpetra_comm_pattern = std::dynamic_pointer_cast< - const TpetraWrappers::CommunicationPattern>(communication_pattern); - AssertThrow( - tpetra_comm_pattern != nullptr, - ExcMessage( - std::string("The communication pattern is not of type ") + - "LinearAlgebra::TpetraWrappers::CommunicationPattern.")); - } - - Tpetra::Export tpetra_export( - tpetra_comm_pattern->get_tpetra_export()); - Tpetra::Vector source_vector( - tpetra_export.getSourceMap()); - - source_vector.template sync(); - auto x_2d = source_vector.template getLocalView(); - auto x_1d = Kokkos::subview(x_2d, Kokkos::ALL(), 0); - source_vector.template modify(); - const size_t localLength = source_vector.getLocalLength(); - auto values_it = V.begin(); - for (size_t k = 0; k < localLength; ++k) - x_1d(k) = *values_it++; - source_vector.template sync< - typename Tpetra::Vector:: - device_type::memory_space>(); - if (operation == VectorOperation::insert) - vector->doExport(source_vector, tpetra_export, Tpetra::REPLACE); - else if (operation == VectorOperation::add) - vector->doExport(source_vector, tpetra_export, Tpetra::ADD); - else - AssertThrow(false, ExcNotImplemented()); - } - - - - template - Vector & - Vector::operator*=(const Number factor) - { - AssertIsFinite(factor); - vector->scale(factor); - - return *this; - } - - - - template - Vector & - Vector::operator/=(const Number factor) - { - AssertIsFinite(factor); - Assert(factor != Number(0.), ExcZero()); - *this *= Number(1.) / factor; - - return *this; - } - - - - template - Vector & - Vector::operator+=(const VectorSpaceVector &V) - { - // Check that casting will work. - Assert(dynamic_cast *>(&V) != nullptr, - ExcVectorTypeNotCompatible()); - - // Downcast V. If fails, throws an exception. - const Vector &down_V = dynamic_cast &>(V); - // If the maps are the same we can update right away. - if (vector->getMap()->isSameAs(*(down_V.trilinos_vector().getMap()))) - { - vector->update(1., down_V.trilinos_vector(), 1.); - } - else - { - Assert(this->size() == down_V.size(), - ExcDimensionMismatch(this->size(), down_V.size())); - - // TODO: Tpetra doesn't have a combine mode that also updates local - // elements, maybe there is a better workaround. - Tpetra::Vector dummy( - vector->getMap(), false); - Tpetra::Import data_exchange( - down_V.trilinos_vector().getMap(), dummy.getMap()); - - dummy.doImport(down_V.trilinos_vector(), - data_exchange, - Tpetra::INSERT); - - vector->update(1.0, dummy, 1.0); - } - - return *this; - } - - - - template - Vector & - Vector::operator-=(const VectorSpaceVector &V) - { - this->add(-1., V); - - return *this; - } - - - - template - Number Vector::operator*(const VectorSpaceVector &V) const - { - // Check that casting will work. - Assert(dynamic_cast *>(&V) != nullptr, - ExcVectorTypeNotCompatible()); - - // Downcast V. If fails, throws an exception. - const Vector &down_V = dynamic_cast &>(V); - Assert(this->size() == down_V.size(), - ExcDimensionMismatch(this->size(), down_V.size())); - Assert(vector->getMap()->isSameAs(*down_V.trilinos_vector().getMap()), - ExcDifferentParallelPartitioning()); - - return vector->dot(down_V.trilinos_vector()); - } - - - - template - void - Vector::add(const Number a) - { - AssertIsFinite(a); - - vector->template sync(); - auto vector_2d = vector->template getLocalView(); - auto vector_1d = Kokkos::subview(vector_2d, Kokkos::ALL(), 0); - vector->template modify(); - const size_t localLength = vector->getLocalLength(); - for (size_t k = 0; k < localLength; ++k) - { - vector_1d(k) += a; - } - vector->template sync< - typename Tpetra::Vector:: - device_type::memory_space>(); - } - - - - template - void - Vector::add(const Number a, const VectorSpaceVector &V) - { - // Check that casting will work. - Assert(dynamic_cast *>(&V) != nullptr, - ExcVectorTypeNotCompatible()); - - // Downcast V. If fails, throws an exception. - const Vector &down_V = dynamic_cast &>(V); - AssertIsFinite(a); - Assert(vector->getMap()->isSameAs(*(down_V.trilinos_vector().getMap())), - ExcDifferentParallelPartitioning()); - - vector->update(a, down_V.trilinos_vector(), 1.); - } - - - - template - void - Vector::add(const Number a, - const VectorSpaceVector &V, - const Number b, - const VectorSpaceVector &W) - { - // Check that casting will work. - Assert(dynamic_cast *>(&V) != nullptr, - ExcVectorTypeNotCompatible()); - // Check that casting will work. - Assert(dynamic_cast *>(&W) != nullptr, - ExcVectorTypeNotCompatible()); - - // Downcast V. If fails, throws an exception. - const Vector &down_V = dynamic_cast &>(V); - // Downcast W. If fails, throws an exception. - const Vector &down_W = dynamic_cast &>(W); - Assert(vector->getMap()->isSameAs(*(down_V.trilinos_vector().getMap())), - ExcDifferentParallelPartitioning()); - Assert(vector->getMap()->isSameAs(*(down_W.trilinos_vector().getMap())), - ExcDifferentParallelPartitioning()); - AssertIsFinite(a); - AssertIsFinite(b); - - vector->update( - a, down_V.trilinos_vector(), b, down_W.trilinos_vector(), 1.); - } - - - - template - void - Vector::sadd(const Number s, - const Number a, - const VectorSpaceVector &V) - { - // Check that casting will work. - Assert(dynamic_cast *>(&V) != nullptr, - ExcVectorTypeNotCompatible()); - - *this *= s; - // Downcast V. It fails, throws an exception. - const Vector &down_V = dynamic_cast &>(V); - Vector tmp(down_V); - tmp *= a; - *this += tmp; - } - - - - template - void - Vector::scale(const VectorSpaceVector &scaling_factors) - { - // Check that casting will work. - Assert(dynamic_cast *>(&scaling_factors) != nullptr, - ExcVectorTypeNotCompatible()); - - // Downcast scaling_factors. If fails, throws an exception. - const Vector &down_scaling_factors = - dynamic_cast &>(scaling_factors); - Assert(vector->getMap()->isSameAs( - *(down_scaling_factors.trilinos_vector().getMap())), - ExcDifferentParallelPartitioning()); - - vector->elementWiseMultiply(1., - *down_scaling_factors.vector, - *vector, - 0.); - } - - - - template - void - Vector::equ(const Number a, const VectorSpaceVector &V) - { - // Check that casting will work. - Assert(dynamic_cast *>(&V) != nullptr, - ExcVectorTypeNotCompatible()); - - // Downcast V. If fails, throws an exception. - const Vector &down_V = dynamic_cast &>(V); - // If we don't have the same map, copy. - if (vector->getMap()->isSameAs(*down_V.trilinos_vector().getMap()) == - false) - this->sadd(0., a, V); - else - { - // Otherwise, just update - vector->update(a, down_V.trilinos_vector(), 0.); - } - } - - - - template - bool - Vector::all_zero() const - { - // get a representation of the vector and - // loop over all the elements - Number * start_ptr = vector->getDataNonConst().get(); - const Number *ptr = start_ptr, - *eptr = start_ptr + vector->getLocalLength(); - unsigned int flag = 0; - while (ptr != eptr) - { - if (*ptr != Number(0)) - { - flag = 1; - break; - } - ++ptr; - } - - // Check that the vector is zero on _all_ processors. - const Teuchos::MpiComm *mpi_comm = - dynamic_cast *>( - vector->getMap()->getComm().get()); - Assert(mpi_comm != nullptr, ExcInternalError()); - unsigned int num_nonzero = - Utilities::MPI::sum(flag, *(mpi_comm->getRawMpiComm())()); - - return num_nonzero == 0; - } - - - - template - Number - Vector::mean_value() const - { - return vector->meanValue(); - } - - - - template - typename LinearAlgebra::VectorSpaceVector::real_type - Vector::l1_norm() const - { - return vector->norm1(); - } - - - - template - typename LinearAlgebra::VectorSpaceVector::real_type - Vector::l2_norm() const - { - return vector->norm2(); - } - - - - template - typename LinearAlgebra::VectorSpaceVector::real_type - Vector::linfty_norm() const - { - return vector->normInf(); - } - - - - template - Number - Vector::add_and_dot(const Number a, - const VectorSpaceVector &V, - const VectorSpaceVector &W) - { - this->add(a, V); - - return *this * W; - } - - - - template - typename Vector::size_type - Vector::size() const - { - return vector->getGlobalLength(); - } - - - - template - MPI_Comm - Vector::get_mpi_communicator() const - { - const auto tpetra_comm = dynamic_cast *>( - vector->getMap()->getComm().get()); - Assert(tpetra_comm != nullptr, ExcInternalError()); - return *(tpetra_comm->getRawMpiComm())(); - } - - - - template - ::dealii::IndexSet - Vector::locally_owned_elements() const - { - IndexSet is(size()); - - // easy case: local range is contiguous - if (vector->getMap()->isContiguous()) - { - is.add_range(vector->getMap()->getMinGlobalIndex(), - vector->getMap()->getMaxGlobalIndex() + 1); - } - else if (vector->getLocalLength() > 0) - { - const size_type n_indices = vector->getLocalLength(); - std::vector vector_indices; - vector_indices.reserve(n_indices); - for (unsigned int i = 0; i < n_indices; ++i) - vector_indices.push_back(vector->getMap()->getGlobalElement(i)); - - is.add_indices(vector_indices.data(), - vector_indices.data() + n_indices); - } - is.compress(); - - return is; - } - - - - template - const Tpetra::Vector & - Vector::trilinos_vector() const - { - return *vector; - } - - - - template - Tpetra::Vector & - Vector::trilinos_vector() - { - return *vector; - } - - - - template - void - Vector::print(std::ostream & out, - const unsigned int precision, - const bool scientific, - const bool across) const - { - AssertThrow(out, ExcIO()); - boost::io::ios_flags_saver restore_flags(out); - - // Get a representation of the vector and loop over all - // the elements - const auto val = vector->get1dView(); - - out.precision(precision); - if (scientific) - out.setf(std::ios::scientific, std::ios::floatfield); - else - out.setf(std::ios::fixed, std::ios::floatfield); - - vector->template sync(); - auto vector_2d = vector->template getLocalView(); - auto vector_1d = Kokkos::subview(vector_2d, Kokkos::ALL(), 0); - const size_t local_length = vector->getLocalLength(); - - if (across) - for (unsigned int i = 0; i < local_length; ++i) - out << vector_1d(i) << ' '; - else - for (unsigned int i = 0; i < local_length; ++i) - out << vector_1d(i) << std::endl; - out << std::endl; - - // restore the representation - // of the vector - AssertThrow(out, ExcIO()); - } - - - - template - std::size_t - Vector::memory_consumption() const - { - return sizeof(*this) + - vector->getLocalLength() * - (sizeof(Number) + sizeof(TrilinosWrappers::types::int_type)); - } - - - - template - void - Vector::create_tpetra_comm_pattern(const IndexSet &source_index_set, - const MPI_Comm &mpi_comm) - { - source_stored_elements = source_index_set; - tpetra_comm_pattern = - std::make_shared( - locally_owned_elements(), source_index_set, mpi_comm); - } - template class Vector; template class Vector; # ifdef DEAL_II_WITH_COMPLEX_VALUES @@ -679,5 +36,4 @@ namespace LinearAlgebra DEAL_II_NAMESPACE_CLOSE # endif - #endif From a5dc36e301666fce055f39b3c3996520f7de3eb0 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Fri, 22 Feb 2019 15:04:35 +0100 Subject: [PATCH 183/507] Mark Tpetra as optional --- doc/external-libs/trilinos.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/external-libs/trilinos.html b/doc/external-libs/trilinos.html index 4e3a51552298..09e13e35a04e 100644 --- a/doc/external-libs/trilinos.html +++ b/doc/external-libs/trilinos.html @@ -67,7 +67,7 @@
    Installing Trilinos
  • ROL (optional),
  • Sacado (optional),
  • Teuchos, -
  • Tpetra, +
  • Tpetra (optional),
  • Zoltan (optional). From 12f2084c6ce0670a7b470aa1157bab02de31c294 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sat, 23 Feb 2019 18:09:57 +0100 Subject: [PATCH 184/507] add has_begin detector --- include/deal.II/matrix_free/fe_evaluation.h | 21 +++++++++++++++++++ .../matrix_free/fe_evaluation_type_traits.cc | 9 ++++++++ ...tion_type_traits.with_trilinos=true.output | 3 +++ 3 files changed, 33 insertions(+) diff --git a/include/deal.II/matrix_free/fe_evaluation.h b/include/deal.II/matrix_free/fe_evaluation.h index 8da043d70bee..4b088f977d17 100644 --- a/include/deal.II/matrix_free/fe_evaluation.h +++ b/include/deal.II/matrix_free/fe_evaluation.h @@ -3450,6 +3450,27 @@ namespace internal }; + + // same as above to check + // T::const_iterator T::begin() const + template + struct has_begin + { + private: + static void + detect(...); + + template + static decltype(std::declval().begin()) + detect(const U &); + + public: + static constexpr bool value = + std::is_same()))>::value; + }; + + // access to generic vectors that have operator (). // FIXME: this is wrong for Trilinos/Petsc MPI vectors template ::value << std::endl; + // check has_begin(): + deallog + << "has_begin:" << std::endl + << "LinearAlgebra::distributed::Vector = " + << internal::has_begin>::value + << std::endl + << "TrilinosWrappers::MPI::Vector = " + << internal::has_begin::value << std::endl; + deallog << "OK" << std::endl; } diff --git a/tests/matrix_free/fe_evaluation_type_traits.with_trilinos=true.output b/tests/matrix_free/fe_evaluation_type_traits.with_trilinos=true.output index 4e82d5220255..71bac87207dc 100644 --- a/tests/matrix_free/fe_evaluation_type_traits.with_trilinos=true.output +++ b/tests/matrix_free/fe_evaluation_type_traits.with_trilinos=true.output @@ -10,4 +10,7 @@ DEAL::Dummy2::operator() DEAL::has_partitioners_are_compatible: DEAL::LinearAlgebra::distributed::Vector = 1 DEAL::TrilinosWrappers::MPI::Vector = 0 +DEAL::has_begin: +DEAL::LinearAlgebra::distributed::Vector = 1 +DEAL::TrilinosWrappers::MPI::Vector = 1 DEAL::OK From 271769536678200e40d90d454d7dbd9bfad55326 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sat, 23 Feb 2019 19:26:36 +0100 Subject: [PATCH 185/507] add vectorizable type trait --- include/deal.II/matrix_free/fe_evaluation.h | 16 ++++++++++++++++ tests/matrix_free/fe_evaluation_type_traits.cc | 16 +++++++++++++++- ...luation_type_traits.with_trilinos=true.output | 4 ++++ 3 files changed, 35 insertions(+), 1 deletion(-) diff --git a/include/deal.II/matrix_free/fe_evaluation.h b/include/deal.II/matrix_free/fe_evaluation.h index 4b088f977d17..3b498f167a64 100644 --- a/include/deal.II/matrix_free/fe_evaluation.h +++ b/include/deal.II/matrix_free/fe_evaluation.h @@ -3471,8 +3471,24 @@ namespace internal }; + // type trait for vector T and Number to see if + // we can do vectorized load/save. + // for VectorReader and VectorDistributorLocalToGlobal we assume that + // if both begin() and local_element() + // exist, then begin() + offset == local_element(offset) + template + struct vectorizable + { + static constexpr bool value = + has_begin::value && has_local_element::value && + std::is_same::value; + }; + + + // access to generic vectors that have operator (). // FIXME: this is wrong for Trilinos/Petsc MPI vectors + // where we should first do Partitioner::local_to_global() template ::value, VectorType>::type * = nullptr> diff --git a/tests/matrix_free/fe_evaluation_type_traits.cc b/tests/matrix_free/fe_evaluation_type_traits.cc index d3363649aa18..3655a18f2fad 100644 --- a/tests/matrix_free/fe_evaluation_type_traits.cc +++ b/tests/matrix_free/fe_evaluation_type_traits.cc @@ -129,7 +129,7 @@ main() TrilinosWrappers::MPI::Vector>::value << std::endl; - // check has_begin(): + // check has_begin: deallog << "has_begin:" << std::endl << "LinearAlgebra::distributed::Vector = " @@ -137,6 +137,20 @@ main() << std::endl << "TrilinosWrappers::MPI::Vector = " << internal::has_begin::value << std::endl; + // check vectorizable: + deallog + << "vectorizable:" << std::endl + << "LinearAlgebra::distributed::Vector && double = " + << internal::vectorizable, + double>::value + << std::endl + << "LinearAlgebra::distributed::Vector && float = " + << internal::vectorizable, + float>::value + << std::endl + << "TrilinosWrappers::MPI::Vector && double = " + << internal::vectorizable::value + << std::endl; deallog << "OK" << std::endl; } diff --git a/tests/matrix_free/fe_evaluation_type_traits.with_trilinos=true.output b/tests/matrix_free/fe_evaluation_type_traits.with_trilinos=true.output index 71bac87207dc..d514ab7eea06 100644 --- a/tests/matrix_free/fe_evaluation_type_traits.with_trilinos=true.output +++ b/tests/matrix_free/fe_evaluation_type_traits.with_trilinos=true.output @@ -13,4 +13,8 @@ DEAL::TrilinosWrappers::MPI::Vector = 0 DEAL::has_begin: DEAL::LinearAlgebra::distributed::Vector = 1 DEAL::TrilinosWrappers::MPI::Vector = 1 +DEAL::vectorizable: +DEAL::LinearAlgebra::distributed::Vector && double = 1 +DEAL::LinearAlgebra::distributed::Vector && float = 0 +DEAL::TrilinosWrappers::MPI::Vector && double = 0 DEAL::OK From 61585e1c8b826c9f2a8729e646e59fd84691145b Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sat, 23 Feb 2019 20:14:04 +0100 Subject: [PATCH 186/507] use is_vectorizable type trait in FEEvaluation classes --- include/deal.II/matrix_free/fe_evaluation.h | 44 +++++++------------ .../matrix_free/fe_evaluation_type_traits.cc | 14 +++--- ...tion_type_traits.with_trilinos=true.output | 2 +- 3 files changed, 25 insertions(+), 35 deletions(-) diff --git a/include/deal.II/matrix_free/fe_evaluation.h b/include/deal.II/matrix_free/fe_evaluation.h index 3b498f167a64..56b5a6b2b261 100644 --- a/include/deal.II/matrix_free/fe_evaluation.h +++ b/include/deal.II/matrix_free/fe_evaluation.h @@ -3477,7 +3477,7 @@ namespace internal // if both begin() and local_element() // exist, then begin() + offset == local_element(offset) template - struct vectorizable + struct is_vectorizable { static constexpr bool value = has_begin::value && has_local_element::value && @@ -4084,6 +4084,10 @@ FEEvaluationBase::read_write_operation( ExcNotImplemented("Masking currently not implemented for " "non-contiguous DoF storage")); + std::integral_constant::value> + vector_selector; + const unsigned int dofs_per_component = this->data->dofs_per_component_on_cell; if (dof_info->index_storage_variants @@ -4102,28 +4106,17 @@ FEEvaluationBase::read_write_operation( for (unsigned int i = 0; i < dofs_per_component; ++i, dof_indices += n_vectorization) for (unsigned int comp = 0; comp < n_components; ++comp) - operation.process_dof_gather( - dof_indices, - *src[comp], - 0, - values_dofs[comp][i], - std::integral_constant< - bool, - std::is_same::value>()); + operation.process_dof_gather(dof_indices, + *src[comp], + 0, + values_dofs[comp][i], + vector_selector); else for (unsigned int comp = 0; comp < n_components; ++comp) for (unsigned int i = 0; i < dofs_per_component; ++i, dof_indices += n_vectorization) operation.process_dof_gather( - dof_indices, - *src[0], - 0, - values_dofs[comp][i], - std::integral_constant< - bool, - std::is_same::value>()); + dof_indices, *src[0], 0, values_dofs[comp][i], vector_selector); return; } @@ -4498,9 +4491,8 @@ FEEvaluationBase:: // a vector and puts the data into the local data field or write local data // into the vector. Certain operations are no-ops for the given use case. - std::integral_constant< - bool, - std::is_same::value> + std::integral_constant::value> vector_selector; const internal::MatrixFreeFunctions::DoFInfo::DoFAccessIndex ind = is_face ? dof_access_index : @@ -7628,9 +7620,8 @@ FEFaceEvaluation:: temp1 = this->scratch_data; internal::VectorReader reader; - std::integral_constant< - bool, - std::is_same::value> + std::integral_constant::value> vector_selector; // case 1: contiguous and interleaved indices @@ -8188,9 +8179,8 @@ FEFaceEvaluation:: # endif internal::VectorDistributorLocalToGlobal writer; - std::integral_constant< - bool, - std::is_same::value> + std::integral_constant::value> vector_selector; // case 1: contiguous and interleaved indices diff --git a/tests/matrix_free/fe_evaluation_type_traits.cc b/tests/matrix_free/fe_evaluation_type_traits.cc index 3655a18f2fad..a57403844271 100644 --- a/tests/matrix_free/fe_evaluation_type_traits.cc +++ b/tests/matrix_free/fe_evaluation_type_traits.cc @@ -137,19 +137,19 @@ main() << std::endl << "TrilinosWrappers::MPI::Vector = " << internal::has_begin::value << std::endl; - // check vectorizable: + // check is_vectorizable: deallog - << "vectorizable:" << std::endl + << "is_vectorizable:" << std::endl << "LinearAlgebra::distributed::Vector && double = " - << internal::vectorizable, - double>::value + << internal::is_vectorizable, + double>::value << std::endl << "LinearAlgebra::distributed::Vector && float = " - << internal::vectorizable, - float>::value + << internal::is_vectorizable, + float>::value << std::endl << "TrilinosWrappers::MPI::Vector && double = " - << internal::vectorizable::value + << internal::is_vectorizable::value << std::endl; deallog << "OK" << std::endl; diff --git a/tests/matrix_free/fe_evaluation_type_traits.with_trilinos=true.output b/tests/matrix_free/fe_evaluation_type_traits.with_trilinos=true.output index d514ab7eea06..d6140df34255 100644 --- a/tests/matrix_free/fe_evaluation_type_traits.with_trilinos=true.output +++ b/tests/matrix_free/fe_evaluation_type_traits.with_trilinos=true.output @@ -13,7 +13,7 @@ DEAL::TrilinosWrappers::MPI::Vector = 0 DEAL::has_begin: DEAL::LinearAlgebra::distributed::Vector = 1 DEAL::TrilinosWrappers::MPI::Vector = 1 -DEAL::vectorizable: +DEAL::is_vectorizable: DEAL::LinearAlgebra::distributed::Vector && double = 1 DEAL::LinearAlgebra::distributed::Vector && float = 0 DEAL::TrilinosWrappers::MPI::Vector && double = 0 From 218e6b9eeb120f08bf75e77ddae8e55a0fbd8ca2 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Sun, 24 Feb 2019 16:40:19 +0100 Subject: [PATCH 187/507] Check SUNDIALS version when configuring --- cmake/configure/configure_sundials.cmake | 28 +++++++++++ cmake/modules/FindSUNDIALS.cmake | 60 ++++++++++++++++++++++-- include/deal.II/base/config.h.in | 41 ++++++++-------- 3 files changed, 104 insertions(+), 25 deletions(-) diff --git a/cmake/configure/configure_sundials.cmake b/cmake/configure/configure_sundials.cmake index 4a67fdd8bcd7..0c62c14589de 100644 --- a/cmake/configure/configure_sundials.cmake +++ b/cmake/configure/configure_sundials.cmake @@ -17,6 +17,34 @@ # Configuration for the SUNDIALS library: # +MACRO(FEATURE_SUNDIALS_FIND_EXTERNAL var) + FIND_PACKAGE(SUNDIALS) + + IF(SUNDIALS_FOUND) + SET(${var} TRUE) + + # + # We don't support version 4.0.0 or later yet. + # + SET(_first_unsupported_sundials_version 4.0.0) + IF(NOT SUNDIALS_VERSION VERSION_LESS ${_first_unsupported_sundials_version}) + MESSAGE(STATUS + "Insufficient SUNDIALS installation found: " + "version ${_first_unsupported_sundials_version} " + "or later is not yet supported, " + "but version ${SUNDIALS_VERSION} was found." + ) + SET(SUNDIALS_ADDITIONAL_ERROR_STRING + "Insufficient SUNDIALS installation found!\n" + "Version ${_first_unsupported_sundials_version} " + "or later is not yet supported, " + "but version ${SUNDIALS_VERSION} was found.\n" + ) + SET(${var} FALSE) + ENDIF() + ENDIF() +ENDMACRO() + MACRO(FEATURE_SUNDIALS_CONFIGURE_EXTERNAL) SET(DEAL_II_SUNDIALS_WITH_IDAS ${SUNDIALS_WITH_IDAS}) ENDMACRO() diff --git a/cmake/modules/FindSUNDIALS.cmake b/cmake/modules/FindSUNDIALS.cmake index a23e113e7fc6..f7bd1a76ecca 100644 --- a/cmake/modules/FindSUNDIALS.cmake +++ b/cmake/modules/FindSUNDIALS.cmake @@ -21,6 +21,10 @@ # SUNDIALS_LIBRARIES # SUNDIALS_INCLUDE_DIR # SUNDIALS_WITH_IDAS +# SUNDIALS_VERSION +# SUNDIALS_VERSION_MAJOR +# SUNDIALS_VERSION_MINOR +# SUNDIALS_VERSION_PATCH # # Note that sundials headers are typically installed in several directories, # e.g., @@ -86,16 +90,64 @@ ELSE() SET(SUNDIALS_WITH_IDAS FALSE) ENDIF() +# +# Extract SUNDIALS version. +# +DEAL_II_FIND_FILE(SUNDIALS_CONFIG_H + NAMES sundials_config.h + HINTS ${SUNDIALS_INCLUDE_DIR}/sundials + ) +IF(NOT SUNDIALS_CONFIG_H MATCHES "-NOTFOUND") + FILE(STRINGS "${SUNDIALS_CONFIG_H}" SUNDIALS_VERSION_MAJOR_STRING + REGEX "#define.*SUNDIALS_VERSION_MAJOR" + ) + STRING(REGEX REPLACE "^.*SUNDIALS_VERSION_MAJOR.*([0-9]+).*" "\\1" + SUNDIALS_VERSION_MAJOR "${SUNDIALS_VERSION_MAJOR_STRING}" + ) + FILE(STRINGS "${SUNDIALS_CONFIG_H}" SUNDIALS_VERSION_MINOR_STRING + REGEX "#define.*SUNDIALS_VERSION_MINOR" + ) + STRING(REGEX REPLACE "^.*SUNDIALS_VERSION_MINOR.*([0-9]+).*" "\\1" + SUNDIALS_VERSION_MINOR "${SUNDIALS_VERSION_MINOR_STRING}" + ) + FILE(STRINGS "${SUNDIALS_CONFIG_H}" SUNDIALS_VERSION_PATCH_STRING + REGEX "#define.*SUNDIALS_VERSION_PATCH" + ) + STRING(REGEX REPLACE "^.*SUNDIALS_VERSION_PATCH.*([0-9]+).*" "\\1" + SUNDIALS_VERSION_PATCH "${SUNDIALS_VERSION_PATCH_STRING}" + ) +ENDIF() +IF(NOT "${SUNDIALS_VERSION_MAJOR}") + SET(SUNDIALS_VERSION_MAJOR "0") +ENDIF() +IF(NOT "${SUNDIALS_VERSION_MINOR}") + SET(SUNDIALS_VERSION_MINOR "0") +ENDIF() +IF(NOT "${SUNDIALS_VERSION_PATCH}") + SET(SUNDIALS_VERSION_PATCH "0") +ENDIF() +SET(SUNDIALS_VERSION + "${SUNDIALS_VERSION_MAJOR}.${SUNDIALS_VERSION_MINOR}.${SUNDIALS_VERSION_PATCH}" + ) DEAL_II_PACKAGE_HANDLE(SUNDIALS LIBRARIES REQUIRED - ${_sundials_lib_ida} SUNDIALS_LIB_ARKODE - SUNDIALS_LIB_KINSOL SUNDIALS_LIB_SER ${_sundials_lib_par} + ${_sundials_lib_ida} + SUNDIALS_LIB_ARKODE + SUNDIALS_LIB_KINSOL + SUNDIALS_LIB_SER + ${_sundials_lib_par} INCLUDE_DIRS REQUIRED SUNDIALS_INCLUDE_DIR USER_INCLUDE_DIRS REQUIRED SUNDIALS_INCLUDE_DIR CLEAR - SUNDIALS_LIB_IDA SUNDIALS_LIB_IDAS SUNDIALS_LIB_ARKODE - SUNDIALS_LIB_KINSOL SUNDIALS_LIB_SER ${_sundials_lib_par} + SUNDIALS_LIB_IDA + SUNDIALS_LIB_IDAS + SUNDIALS_LIB_ARKODE + SUNDIALS_LIB_KINSOL + SUNDIALS_LIB_SER + ${_sundials_lib_par} + SUNDIALS_INCLUDE_DIR + SUNDIALS_CONFIG_H ) diff --git a/include/deal.II/base/config.h.in b/include/deal.II/base/config.h.in index 23690507599d..65c5efa5bc3b 100644 --- a/include/deal.II/base/config.h.in +++ b/include/deal.II/base/config.h.in @@ -245,30 +245,29 @@ (major)*1000000 + (minor)*10000 + (subminor)*100 + (patch)) #endif - /* - * SUNDIALS: - * - * Note: The following definitions will be set in sundials_config.h, - * so we don't repeat them here. - * - * SUNDIALS_VERSION_MAJOR - * SUNDIALS_VERSION_MINOR - * SUNDIALS_VERSION_PATCH - */ - - #define DEAL_II_SUNDIALS_VERSION_GTE(major,minor,subminor) \ - ((SUNDIALS_VERSION_MAJOR * 10000 + \ - SUNDIALS_VERSION_MINOR * 100 + \ - SUNDIALS_VERSION_SUBMINOR) \ +/* + * SUNDIALS: + */ + +#ifdef DEAL_II_WITH_SUNDIALS + # define DEAL_II_SUNDIALS_VERSION_MAJOR @SUNDIALS_VERSION_MAJOR@ + # define DEAL_II_SUNDIALS_VERSION_MINOR @SUNDIALS_VERSION_MINOR@ + # define DEAL_II_SUNDIALS_VERSION_PATCH @SUNDIALS_VERSION_PATCH@ + + #define DEAL_II_SUNDIALS_VERSION_GTE(major,minor,patch) \ + ((DEAL_II_SUNDIALS_VERSION_MAJOR * 10000 + \ + DEAL_II_SUNDIALS_VERSION_MINOR * 100 + \ + DEAL_II_SUNDIALS_VERSION_PATCH) \ >= \ - (major)*10000 + (minor)*100 + (subminor)) + (major)*10000 + (minor)*100 + (patch)) - #define DEAL_II_SUNDIALS_VERSION_LT(major,minor,subminor) \ - ((SUNDIALS_VERSION_MAJOR * 10000 + \ - SUNDIALS_VERSION_MINOR * 100 + \ - SUNDIALS_VERSION_SUBMINOR) \ + #define DEAL_II_SUNDIALS_VERSION_LT(major,minor,patch) \ + ((DEAL_II_SUNDIALS_VERSION_MAJOR * 10000 + \ + DEAL_II_SUNDIALS_VERSION_MINOR * 100 + \ + DEAL_II_SUNDIALS_VERSION_PATCH) \ < \ - (major)*10000 + (minor)*100 + (subminor)) + (major)*10000 + (minor)*100 + (patch)) +#endif /* * PETSc: From 7ed7ae86f90f4ffd21a575002f63980c840439e2 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Sun, 24 Feb 2019 18:06:17 +0100 Subject: [PATCH 188/507] change is_vectorizable to work with serial vectors --- include/deal.II/matrix_free/fe_evaluation.h | 3 ++- tests/matrix_free/fe_evaluation_type_traits.cc | 10 +++++++++- ...fe_evaluation_type_traits.with_trilinos=true.output | 4 ++++ 3 files changed, 15 insertions(+), 2 deletions(-) diff --git a/include/deal.II/matrix_free/fe_evaluation.h b/include/deal.II/matrix_free/fe_evaluation.h index 56b5a6b2b261..f8b4975bf9c6 100644 --- a/include/deal.II/matrix_free/fe_evaluation.h +++ b/include/deal.II/matrix_free/fe_evaluation.h @@ -3480,7 +3480,8 @@ namespace internal struct is_vectorizable { static constexpr bool value = - has_begin::value && has_local_element::value && + has_begin::value && + (has_local_element::value || is_serial_vector::value) && std::is_same::value; }; diff --git a/tests/matrix_free/fe_evaluation_type_traits.cc b/tests/matrix_free/fe_evaluation_type_traits.cc index a57403844271..762da8b50d08 100644 --- a/tests/matrix_free/fe_evaluation_type_traits.cc +++ b/tests/matrix_free/fe_evaluation_type_traits.cc @@ -109,6 +109,8 @@ main() << "Dummy = " << internal::has_local_element>::value << std::endl << "Dummy2 = " << internal::has_local_element>::value + << std::endl + << "Vector = " << internal::has_local_element>::value << std::endl; // now check internal::vector_access wrapper @@ -127,6 +129,9 @@ main() << "TrilinosWrappers::MPI::Vector = " << internal::has_partitioners_are_compatible< TrilinosWrappers::MPI::Vector>::value + << std::endl + << "Vector = " + << internal::has_partitioners_are_compatible>::value << std::endl; // check has_begin: @@ -136,7 +141,8 @@ main() << internal::has_begin>::value << std::endl << "TrilinosWrappers::MPI::Vector = " - << internal::has_begin::value << std::endl; + << internal::has_begin::value << std::endl + << "Vector = " << internal::has_begin>::value << std::endl; // check is_vectorizable: deallog << "is_vectorizable:" << std::endl @@ -150,6 +156,8 @@ main() << std::endl << "TrilinosWrappers::MPI::Vector && double = " << internal::is_vectorizable::value + << std::endl + << "Vector = " << internal::is_vectorizable, double>::value << std::endl; deallog << "OK" << std::endl; diff --git a/tests/matrix_free/fe_evaluation_type_traits.with_trilinos=true.output b/tests/matrix_free/fe_evaluation_type_traits.with_trilinos=true.output index d6140df34255..801cf4191e20 100644 --- a/tests/matrix_free/fe_evaluation_type_traits.with_trilinos=true.output +++ b/tests/matrix_free/fe_evaluation_type_traits.with_trilinos=true.output @@ -4,17 +4,21 @@ DEAL::LinearAlgebra::distributed::Vector = 1 DEAL::TrilinosWrappers::MPI::Vector = 0 DEAL::Dummy = 1 DEAL::Dummy2 = 0 +DEAL::Vector = 0 DEAL::internal::vector_access: DEAL::Dummy::local_element() DEAL::Dummy2::operator() DEAL::has_partitioners_are_compatible: DEAL::LinearAlgebra::distributed::Vector = 1 DEAL::TrilinosWrappers::MPI::Vector = 0 +DEAL::Vector = 0 DEAL::has_begin: DEAL::LinearAlgebra::distributed::Vector = 1 DEAL::TrilinosWrappers::MPI::Vector = 1 +DEAL::Vector = 1 DEAL::is_vectorizable: DEAL::LinearAlgebra::distributed::Vector && double = 1 DEAL::LinearAlgebra::distributed::Vector && float = 0 DEAL::TrilinosWrappers::MPI::Vector && double = 0 +DEAL::Vector = 1 DEAL::OK From 5c6688aff794bf38d76eb621d04b22de7eb5bd1c Mon Sep 17 00:00:00 2001 From: Giovanni Alzetta Date: Mon, 25 Feb 2019 12:40:27 +0100 Subject: [PATCH 189/507] Guess point owner uses std::move to return tuple --- source/grid/grid_tools.cc | 13 +++---------- ...t_owner_1.cc => grid_tools_guess_pt_owner_01.cc} | 0 ...1.output => grid_tools_guess_pt_owner_01.output} | 0 3 files changed, 3 insertions(+), 10 deletions(-) rename tests/grid/{grid_tools_guess_pt_owner_1.cc => grid_tools_guess_pt_owner_01.cc} (100%) rename tests/grid/{grid_tools_guess_pt_owner_1.output => grid_tools_guess_pt_owner_01.output} (100%) diff --git a/source/grid/grid_tools.cc b/source/grid/grid_tools.cc index 58d12d3a94fc..44d49753d166 100644 --- a/source/grid/grid_tools.cc +++ b/source/grid/grid_tools.cc @@ -2091,16 +2091,9 @@ namespace GridTools map_owners_guessed[pt] = owners_found; } - std::tuple>, - std::map, - std::map>> - output_tuple; - - std::get<0>(output_tuple) = point_owners; - std::get<1>(output_tuple) = map_owners_found; - std::get<2>(output_tuple) = map_owners_guessed; - - return output_tuple; + return std::make_tuple(std::move(point_owners), + std::move(map_owners_found), + std::move(map_owners_guessed)); } diff --git a/tests/grid/grid_tools_guess_pt_owner_1.cc b/tests/grid/grid_tools_guess_pt_owner_01.cc similarity index 100% rename from tests/grid/grid_tools_guess_pt_owner_1.cc rename to tests/grid/grid_tools_guess_pt_owner_01.cc diff --git a/tests/grid/grid_tools_guess_pt_owner_1.output b/tests/grid/grid_tools_guess_pt_owner_01.output similarity index 100% rename from tests/grid/grid_tools_guess_pt_owner_1.output rename to tests/grid/grid_tools_guess_pt_owner_01.output From 34ea16872f1aac75e54ad630c9d70554bab77c42 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Sun, 24 Feb 2019 00:50:41 +0100 Subject: [PATCH 190/507] Work around nvcc_wrapper std::complex problem --- include/deal.II/base/tensor.h | 31 +++++++++++++++++++++++++++++++ 1 file changed, 31 insertions(+) diff --git a/include/deal.II/base/tensor.h b/include/deal.II/base/tensor.h index b299ed09a756..7b0531ff9312 100644 --- a/include/deal.II/base/tensor.h +++ b/include/deal.II/base/tensor.h @@ -924,6 +924,35 @@ Tensor<0, dim, Number>::operator-=(const Tensor<0, dim, OtherNumber> &p) } + +#ifdef __CUDA_ARCH__ +namespace internal +{ + template + DEAL_II_CUDA_HOST_DEV void + multiply_assign_scalar(Number &tensor, const OtherNumber &s) + { + tensor *= s; + } + + template + DEAL_II_CUDA_HOST_DEV void + multiply_assign_scalar(std::complex &, const OtherNumber &) + { + printf("This function is not implemented for std::complex!\n"); + assert(false); + } +} // namespace internal + +template +template +inline DEAL_II_CUDA_HOST_DEV Tensor<0, dim, Number> & +Tensor<0, dim, Number>::operator*=(const OtherNumber &s) +{ + internal::multiply_assign_scalar(value, s); + return *this; +} +#else template template inline DEAL_II_CUDA_HOST_DEV Tensor<0, dim, Number> & @@ -932,6 +961,8 @@ Tensor<0, dim, Number>::operator*=(const OtherNumber &s) value *= s; return *this; } +#endif + template From daf8bbc987881f83d7d194224bef6077091a8fd6 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Sun, 24 Feb 2019 11:28:20 +0100 Subject: [PATCH 191/507] Fix vector_access --- include/deal.II/matrix_free/fe_evaluation.h | 17 ++++++++++++++++- 1 file changed, 16 insertions(+), 1 deletion(-) diff --git a/include/deal.II/matrix_free/fe_evaluation.h b/include/deal.II/matrix_free/fe_evaluation.h index f8b4975bf9c6..7bdd4e15a620 100644 --- a/include/deal.II/matrix_free/fe_evaluation.h +++ b/include/deal.II/matrix_free/fe_evaluation.h @@ -3471,6 +3471,7 @@ namespace internal }; + // type trait for vector T and Number to see if // we can do vectorized load/save. // for VectorReader and VectorDistributorLocalToGlobal we assume that @@ -3487,7 +3488,21 @@ namespace internal - // access to generic vectors that have operator (). + // access to generic const vectors that have operator (). + // FIXME: this is wrong for Trilinos/Petsc MPI vectors + // where we should first do Partitioner::local_to_global() + template ::value, + VectorType>::type * = nullptr> + inline typename VectorType::value_type + vector_access(const VectorType &vec, const unsigned int entry) + { + return vec(entry); + } + + + + // access to generic non-const vectors that have operator (). // FIXME: this is wrong for Trilinos/Petsc MPI vectors // where we should first do Partitioner::local_to_global() template Date: Tue, 26 Feb 2019 06:34:05 +0100 Subject: [PATCH 192/507] fix internal::has_begin type trait used in FEEvaluation --- include/deal.II/matrix_free/fe_evaluation.h | 3 +-- tests/matrix_free/fe_evaluation_type_traits.cc | 3 ++- .../fe_evaluation_type_traits.with_trilinos=true.output | 1 + 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/include/deal.II/matrix_free/fe_evaluation.h b/include/deal.II/matrix_free/fe_evaluation.h index 20b8249e0313..77e6975cff6d 100644 --- a/include/deal.II/matrix_free/fe_evaluation.h +++ b/include/deal.II/matrix_free/fe_evaluation.h @@ -3466,8 +3466,7 @@ namespace internal public: static constexpr bool value = - std::is_same()))>::value; + !std::is_same()))>::value; }; diff --git a/tests/matrix_free/fe_evaluation_type_traits.cc b/tests/matrix_free/fe_evaluation_type_traits.cc index 762da8b50d08..ffa65526980c 100644 --- a/tests/matrix_free/fe_evaluation_type_traits.cc +++ b/tests/matrix_free/fe_evaluation_type_traits.cc @@ -142,7 +142,8 @@ main() << std::endl << "TrilinosWrappers::MPI::Vector = " << internal::has_begin::value << std::endl - << "Vector = " << internal::has_begin>::value << std::endl; + << "Vector = " << internal::has_begin>::value << std::endl + << "Dummy = " << internal::has_begin>::value << std::endl; // check is_vectorizable: deallog << "is_vectorizable:" << std::endl diff --git a/tests/matrix_free/fe_evaluation_type_traits.with_trilinos=true.output b/tests/matrix_free/fe_evaluation_type_traits.with_trilinos=true.output index 801cf4191e20..b7e821fc996f 100644 --- a/tests/matrix_free/fe_evaluation_type_traits.with_trilinos=true.output +++ b/tests/matrix_free/fe_evaluation_type_traits.with_trilinos=true.output @@ -16,6 +16,7 @@ DEAL::has_begin: DEAL::LinearAlgebra::distributed::Vector = 1 DEAL::TrilinosWrappers::MPI::Vector = 1 DEAL::Vector = 1 +DEAL::Dummy = 0 DEAL::is_vectorizable: DEAL::LinearAlgebra::distributed::Vector && double = 1 DEAL::LinearAlgebra::distributed::Vector && float = 0 From 244aa95d7f04e61318825d5fa3215ad9964c485b Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Tue, 26 Feb 2019 11:29:02 +0100 Subject: [PATCH 193/507] Define GridTools::Cache::get_covering_rtree also without nanoflann support --- source/grid/grid_tools_cache.cc | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/source/grid/grid_tools_cache.cc b/source/grid/grid_tools_cache.cc index 739ea04bda38..52f664b01aec 100644 --- a/source/grid/grid_tools_cache.cc +++ b/source/grid/grid_tools_cache.cc @@ -140,6 +140,8 @@ namespace GridTools return cell_bounding_boxes_rtree; } + + #ifdef DEAL_II_WITH_NANOFLANN template const KDTree & @@ -152,6 +154,7 @@ namespace GridTools } return vertex_kdtree; } +#endif @@ -187,7 +190,6 @@ namespace GridTools return covering_rtree; } -#endif #include "grid_tools_cache.inst" From 915f1a2149255096acb297e705e32d2499b017c7 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Tue, 26 Feb 2019 11:58:15 +0100 Subject: [PATCH 194/507] Have another namespace inclosing the workaround --- include/deal.II/base/tensor.h | 43 ++++++++++++++++------------------- 1 file changed, 19 insertions(+), 24 deletions(-) diff --git a/include/deal.II/base/tensor.h b/include/deal.II/base/tensor.h index 7b0531ff9312..97fa8d608e07 100644 --- a/include/deal.II/base/tensor.h +++ b/include/deal.II/base/tensor.h @@ -925,43 +925,38 @@ Tensor<0, dim, Number>::operator-=(const Tensor<0, dim, OtherNumber> &p) -#ifdef __CUDA_ARCH__ namespace internal { - template - DEAL_II_CUDA_HOST_DEV void - multiply_assign_scalar(Number &tensor, const OtherNumber &s) + namespace ComplexWorkaround { - tensor *= s; - } + template + inline DEAL_II_CUDA_HOST_DEV void + multiply_assign_scalar(Number &val, const OtherNumber &s) + { + val *= s; + } - template - DEAL_II_CUDA_HOST_DEV void - multiply_assign_scalar(std::complex &, const OtherNumber &) - { - printf("This function is not implemented for std::complex!\n"); - assert(false); - } +#ifdef __CUDA_ARCH__ + template + inline DEAL_II_CUDA_HOST_DEV void + multiply_assign_scalar(std::complex &, const OtherNumber &) + { + printf("This function is not implemented for std::complex!\n"); + assert(false); + } +#endif + } // namespace ComplexWorkaround } // namespace internal + template template inline DEAL_II_CUDA_HOST_DEV Tensor<0, dim, Number> & Tensor<0, dim, Number>::operator*=(const OtherNumber &s) { - internal::multiply_assign_scalar(value, s); - return *this; -} -#else -template -template -inline DEAL_II_CUDA_HOST_DEV Tensor<0, dim, Number> & -Tensor<0, dim, Number>::operator*=(const OtherNumber &s) -{ - value *= s; + internal::ComplexWorkaround::multiply_assign_scalar(value, s); return *this; } -#endif From 911cedfa9169e8e9a971ea0efb4bc8e120079894 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 26 Feb 2019 17:12:21 +0100 Subject: [PATCH 195/507] consistently for non-void in internal::has_local_element --- include/deal.II/matrix_free/fe_evaluation.h | 7 +++---- 1 file changed, 3 insertions(+), 4 deletions(-) diff --git a/include/deal.II/matrix_free/fe_evaluation.h b/include/deal.II/matrix_free/fe_evaluation.h index 77e6975cff6d..ac87eea988cd 100644 --- a/include/deal.II/matrix_free/fe_evaluation.h +++ b/include/deal.II/matrix_free/fe_evaluation.h @@ -3420,12 +3420,11 @@ namespace internal detect(const U &); public: - // finally here we check if our detector has return type same as + // finally here we check if our detector has non-void return type // T::value_type. This will happen if compiler can use second detector, // otherwise SFINAE let it work with the more general first one that is void static constexpr bool value = - std::is_same()))>::value; + !std::is_same()))>::value; }; @@ -3452,7 +3451,7 @@ namespace internal // same as above to check - // T::const_iterator T::begin() const + // ... T::begin() const template struct has_begin { From cdb24ff2c120c83517b0e458b1d31aec5000d686 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 26 Feb 2019 18:32:37 +0100 Subject: [PATCH 196/507] make old compilers happy --- include/deal.II/matrix_free/fe_evaluation.h | 20 ++++++++++++++++---- 1 file changed, 16 insertions(+), 4 deletions(-) diff --git a/include/deal.II/matrix_free/fe_evaluation.h b/include/deal.II/matrix_free/fe_evaluation.h index ac87eea988cd..337846d4bd28 100644 --- a/include/deal.II/matrix_free/fe_evaluation.h +++ b/include/deal.II/matrix_free/fe_evaluation.h @@ -3423,10 +3423,13 @@ namespace internal // finally here we check if our detector has non-void return type // T::value_type. This will happen if compiler can use second detector, // otherwise SFINAE let it work with the more general first one that is void - static constexpr bool value = + static const bool value = !std::is_same()))>::value; }; + // We need to have a separate declaration for static const members + template + const bool has_local_element::value; // same as above to check // bool T::partitioners_are_compatible(const Utilities::MPI::Partitioner &) @@ -3444,10 +3447,13 @@ namespace internal detect(const U &); public: - static constexpr bool value = + static const bool value = std::is_same()))>::value; }; + // We need to have a separate declaration for static const members + template + const bool has_partitioners_are_compatible::value; // same as above to check @@ -3464,10 +3470,13 @@ namespace internal detect(const U &); public: - static constexpr bool value = + static const bool value = !std::is_same()))>::value; }; + // We need to have a separate declaration for static const members + template + const bool has_begin::value; // type trait for vector T and Number to see if @@ -3478,12 +3487,15 @@ namespace internal template struct is_vectorizable { - static constexpr bool value = + static const bool value = has_begin::value && (has_local_element::value || is_serial_vector::value) && std::is_same::value; }; + // We need to have a separate declaration for static const members + template + const bool is_vectorizable::value; // access to generic const vectors that have operator (). From 34f9c07b2d0cad24d0d355d3a9ca3e1c8dbfaebe Mon Sep 17 00:00:00 2001 From: notxor Date: Wed, 27 Feb 2019 09:11:42 +0100 Subject: [PATCH 197/507] adapt pvtu output for tensors --- .../changes/minor/20190227DanielJodlbauer | 3 + source/base/data_out_base.cc | 41 ++-- tests/data_out/data_out_13.cc | 200 ++++++++++++++++++ tests/data_out/data_out_13.output | 101 +++++++++ 4 files changed, 330 insertions(+), 15 deletions(-) create mode 100644 doc/news/changes/minor/20190227DanielJodlbauer create mode 100644 tests/data_out/data_out_13.cc create mode 100644 tests/data_out/data_out_13.output diff --git a/doc/news/changes/minor/20190227DanielJodlbauer b/doc/news/changes/minor/20190227DanielJodlbauer new file mode 100644 index 000000000000..a7afb2bcaedd --- /dev/null +++ b/doc/news/changes/minor/20190227DanielJodlbauer @@ -0,0 +1,3 @@ +Fixed: Tensor-valued pvtu output. +
    +(Daniel Jodlbauer, 2019/02/27) diff --git a/source/base/data_out_base.cc b/source/base/data_out_base.cc index 65336ef19154..939c0c905042 100644 --- a/source/base/data_out_base.cc +++ b/source/base/data_out_base.cc @@ -5990,20 +5990,30 @@ namespace DataOutBase std::vector data_set_written(n_data_sets, false); for (const auto &nonscalar_data_range : nonscalar_data_ranges) { - AssertThrow(std::get<1>(nonscalar_data_range) >= - std::get<0>(nonscalar_data_range), - ExcLowerRange(std::get<1>(nonscalar_data_range), - std::get<0>(nonscalar_data_range))); - AssertThrow(std::get<1>(nonscalar_data_range) < n_data_sets, - ExcIndexRange(std::get<1>(nonscalar_data_range), - 0, - n_data_sets)); - AssertThrow(std::get<1>(nonscalar_data_range) + 1 - - std::get<0>(nonscalar_data_range) <= - 3, - ExcMessage( - "Can't declare a vector with more than 3 components " - "in VTK")); + const auto first_component = std::get<0>(nonscalar_data_range); + const auto last_component = std::get<1>(nonscalar_data_range); + const bool is_tensor = + (std::get<3>(nonscalar_data_range) == + DataComponentInterpretation::component_is_part_of_tensor); + const unsigned int n_components = (is_tensor ? 9 : 3); + AssertThrow(last_component >= first_component, + ExcLowerRange(last_component, first_component)); + AssertThrow(last_component < n_data_sets, + ExcIndexRange(last_component, 0, n_data_sets)); + if (is_tensor) + { + AssertThrow((last_component + 1 - first_component <= 9), + ExcMessage( + "Can't declare a tensor with more than 9 components " + "in VTK")); + } + else + { + Assert((last_component + 1 - first_component <= 3), + ExcMessage( + "Can't declare a vector with more than 3 components " + "in VTK")); + } // mark these components as already written: for (unsigned int i = std::get<0>(nonscalar_data_range); @@ -6026,7 +6036,8 @@ namespace DataOutBase out << data_names[std::get<1>(nonscalar_data_range)]; } - out << "\" NumberOfComponents=\"3\" format=\"ascii\"/>\n"; + out << "\" NumberOfComponents=\"" << n_components + << "\" format=\"ascii\"/>\n"; } for (unsigned int data_set = 0; data_set < n_data_sets; ++data_set) diff --git a/tests/data_out/data_out_13.cc b/tests/data_out/data_out_13.cc new file mode 100644 index 000000000000..582285c0d218 --- /dev/null +++ b/tests/data_out/data_out_13.cc @@ -0,0 +1,200 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2018 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + +// Output tensor-valued data in pvtu + +#include + +#include +#include +#include + +#include +#include + +#include +#include +#include + +#include +#include + +#include + +#include +#include +#include + +#include "../tests.h" + + + +template +void +check() +{ + Triangulation tria; + GridGenerator::hyper_cube(tria, 0., 1.); + + FESystem fe(FE_Q(1), + dim, // vector valued + FE_Q(1), + dim * dim); // tensor valued + + DoFHandler dof_handler(tria); + dof_handler.distribute_dofs(fe); + + Vector v(dof_handler.n_dofs()); + + + // 1 cell is enough to test: + const unsigned int dofs_per_cell = v.size(); + + // take 8 tensors from tensors.vtk file inside + // http://paraview.org/Wiki/images/8/81/TensorGlyph_v_1_0_3.zip or + // http://paraview.org/Wiki/images/3/39/SuperquadricTensorGlyph_v3.zip + const std::vector>> tensors_3d = { + {{1, 0, 0}, {0, 1, 0}, {0, 0, 1}}, + {{-2, 0, 0}, {0, -2, 0}, {0, 0, 3}}, + {{1, 0, 0}, {0, 1, 0}, {0, 0, .001}}, + {{2, 1, 1}, {1, 2, 1}, {1, 1, 3}}, + {{0.247186415568, 0.490995206139, 0.131324884836}, + {0.490995206139, -0.371055707211, 0.719071682671}, + {0.131324884836, 0.719071682671, -0.156008182087}}, + {{0.280587657181, 0.467438945439, 0.934953136331}, + {0.467438945439, 0.0600321140579, -0.211376327727}, + {0.934953136331, -0.211376327727, 0.962975830149}}, + {{0.0628609549443, -0.0117908465212, -0.667617347633}, + {-0.0117908465212, -0.390601011028, -0.95780533241}, + {-0.667617347633, -0.95780533241, -0.193319773383}}, + {{0, 0, 0}, {0, 0, 0}, {0, 0, 0}}}; + + // coords: + const std::vector> coords_3d = {{0, 0, 0}, + {1, 0, 0}, + {0, 1, 0}, + {1, 1, 0}, + {0, 0, 1}, + {1, 0, 1}, + {0, 1, 1}, + {1, 1, 1}}; + + const std::vector>> tensors_2d = { + {{1, 0}, {0, 1}}, {{3, 0}, {0, 1}}, {{1, 0}, {0, 3}}, {{3, 1}, {1, 2}}}; + + // coords: + const std::vector> coords_2d = {{0, 0}, + {1, 0}, + {0, 1}, + {1, 1}}; + + const std::vector>> &tensors = + (dim == 2 ? tensors_2d : tensors_3d); + const std::vector> &coords = + (dim == 2 ? coords_2d : coords_3d); + + const Quadrature support_quadrature(fe.get_unit_support_points()); + FEValues fe_values(fe, support_quadrature, update_quadrature_points); + for (const auto cell : dof_handler.active_cell_iterators()) + { + fe_values.reinit(cell); + const auto &qp = fe_values.get_quadrature_points(); + + for (unsigned int i = 0; i < dofs_per_cell; ++i) + { + const auto & this_qp = qp[i]; + const unsigned int i_group = fe.system_to_base_index(i).first.first; + const unsigned int i_comp = fe.system_to_component_index(i).first; + if (i_group == 0) + // vector + { + if (i_comp == 0) + v(i) = 1; + else if (i_comp == 1) + v(i) = this_qp[1]; + else + v(i) = 0.; + } + else + // tensor + { + // find matching location + unsigned int p = 0; + for (const auto c : coords) + { + Point point; + for (unsigned int d = 0; d < dim; ++d) + point[d] = c[d]; + + const auto diff = point - this_qp; + if (diff.norm() < 1e-10) + break; + + ++p; + } + + const unsigned int tens_comp = i_comp - dim; + const unsigned int ii = + Tensor<2, dim>::unrolled_to_component_indices(tens_comp)[0]; + const unsigned int jj = + Tensor<2, dim>::unrolled_to_component_indices(tens_comp)[1]; + v(i) = tensors[p][ii][jj]; + } + } + } + + std::vector + data_component_interpretation( + dim + dim * dim, + DataComponentInterpretation::component_is_part_of_tensor); + std::fill(data_component_interpretation.begin(), + data_component_interpretation.begin() + dim, + DataComponentInterpretation::component_is_part_of_vector); + + std::vector component_name(dim + dim * dim, "tensor"); + std::fill(component_name.begin(), component_name.begin() + dim, "vector"); + + DataOut data_out; + data_out.attach_dof_handler(dof_handler); + data_out.add_data_vector(v, + component_name, + DataOut::type_dof_data, + data_component_interpretation); + data_out.build_patches(); + + std::vector filenames; + filenames.push_back("output_" + Utilities::int_to_string(dim) + "d.vtu"); + + /* + std::ofstream master_output("output_" + Utilities::int_to_string(dim) + + "d.pvtu"); data_out.write_pvtu_record(master_output, filenames); + + std::ofstream out(filenames[0]); + data_out.write_vtu(out); + */ + + data_out.write_vtu(deallog.get_file_stream()); + data_out.write_pvtu_record(deallog.get_file_stream(), filenames); +} + + + +int +main() +{ + initlog(); + check<2>(); + check<3>(); +} diff --git a/tests/data_out/data_out_13.output b/tests/data_out/data_out_13.output new file mode 100644 index 000000000000..f410ee99e097 --- /dev/null +++ b/tests/data_out/data_out_13.output @@ -0,0 +1,101 @@ + + + + + + + + +AQAAADAAAAAwAAAAFAAAAA==eNpjYEAGDfYMWPkgGsIGADHwAv0= + + + + + +AQAAABAAAAAQAAAAEwAAAA==eNpjYGBgYARiZiBmAmIAADwABw== + + +AQAAAAQAAAAEAAAADAAAAA==eNpjYWBgAAAAFAAF + + +AQAAAAEAAAABAAAACQAAAA==eNrjBAAACgAK + + + + +AQAAADAAAAAwAAAAFAAAAA==eNpjYGiwZ4ADdDaMj2ADAGQuBHs= + +AQAAAJAAAACQAAAAIgAAAA==eNpjYGiwZ0AB6HwQcHAgrAZdDF0PTAymDkxjqAEAycUGOw== + + + + + + + + + + + + + + + + + + + + + + + + + +AQAAAGAAAABgAAAAGgAAAA==eNpjYEAGDfYMWPkgGpscsjyyGAIDAC3jCPU= + + + + + +AQAAACAAAAAgAAAAHQAAAA==eNpjYGBgYARiZiBmAmIWIGYFYnYgZgNiAAF4AB0= + + +AQAAAAQAAAAEAAAADAAAAA==eNrjYGBgAAAAJAAJ + + +AQAAAAEAAAABAAAACQAAAA==eNrjAQAADQAN + + + + +AQAAAGAAAABgAAAAFgAAAA==eNpjYGiwZ4ADdDaMj84mXj0An0sI9Q== + +AQAAACABAAAgAQAAhAAAAA==eNpjYGiwZ0ABWPkHUMXQ+Q4ODATMyRdqtgIphIjDMDrfwaFArtZuZ/JvO44qNjDN/HvvPlFRC3sQH0TPOSC/T39lv51GyHs78ch8exBt86TUlrM4Yh+ID6KntZbZ2+9tsE3Vc9zz44XWfhB9+8/xfbuNSveD+CB63lfXfQxEAACmEDx/ + + + + + + + + + + + + + + + + + + From 87f64afa940cb2706589058daac90b3a135607c6 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Wed, 27 Feb 2019 11:45:57 +0100 Subject: [PATCH 198/507] Fix compiling with Sacado and CUDA --- include/deal.II/base/numbers.h | 52 +++++++++++++++++-- .../differentiation/ad/sacado_number_types.h | 11 ++++ source/base/tensor.cc | 1 + 3 files changed, 60 insertions(+), 4 deletions(-) diff --git a/include/deal.II/base/numbers.h b/include/deal.II/base/numbers.h index 68bf74bef411..fca6430fd267 100644 --- a/include/deal.II/base/numbers.h +++ b/include/deal.II/base/numbers.h @@ -165,6 +165,15 @@ namespace numbers */ static const double SQRT1_2 = 0.70710678118654752440; + /** + * Check whether the given type can be used in CUDA device code. + * If not, DEAL_II_CUDA_HOST_DEV needs to be disabled for functions + * that use this type. + */ + template + struct is_cuda_compatible : std::true_type + {}; + /** * Check whether a value is not a number. * @@ -361,10 +370,21 @@ namespace numbers * general template is chosen for types not equal to std::complex, this * function simply returns the square of the given number. * - * @note This function can also be used in CUDA device code. + * @note If the template type can be used in CUDA device code, the same holds true + * for this function. */ - static DEAL_II_CUDA_HOST_DEV real_type - abs_square(const number &x); + template + static DEAL_II_CUDA_HOST_DEV + typename std::enable_if::value && + is_cuda_compatible::value, + real_type>::type + abs_square(const number &x); + + template + static typename std::enable_if::value && + !is_cuda_compatible::value, + real_type>::type + abs_square(const number &x); /** * Return the absolute value of a number. @@ -423,12 +443,20 @@ namespace numbers // --------------- inline and template functions ---------------- // + template + struct is_cuda_compatible, void> : std::false_type + {}; + + + inline bool is_nan(const double x) { return std::isnan(x); } + + inline bool is_finite(const double x) { @@ -475,7 +503,23 @@ namespace numbers template - DEAL_II_CUDA_HOST_DEV typename NumberTraits::real_type + template + DEAL_II_CUDA_HOST_DEV + typename std::enable_if::value && + is_cuda_compatible::value, + typename NumberTraits::real_type>::type + NumberTraits::abs_square(const number &x) + { + return x * x; + } + + + + template + template + typename std::enable_if::value && + !is_cuda_compatible::value, + typename NumberTraits::real_type>::type NumberTraits::abs_square(const number &x) { return x * x; diff --git a/include/deal.II/differentiation/ad/sacado_number_types.h b/include/deal.II/differentiation/ad/sacado_number_types.h index 8781865c5f40..907e830e1f01 100644 --- a/include/deal.II/differentiation/ad/sacado_number_types.h +++ b/include/deal.II/differentiation/ad/sacado_number_types.h @@ -926,6 +926,17 @@ namespace Differentiation } // namespace AD } // namespace Differentiation + +namespace numbers +{ + template + struct is_cuda_compatible< + NumberType, + typename std::enable_if::value>::type> : std::false_type + {}; +} // namespace numbers + # endif // DOXYGEN diff --git a/source/base/tensor.cc b/source/base/tensor.cc index 15cb6f3b5dfe..43dabdad75c1 100644 --- a/source/base/tensor.cc +++ b/source/base/tensor.cc @@ -19,6 +19,7 @@ #include #include +#include #include DEAL_II_NAMESPACE_OPEN From 6f384148dff2b9b2f4dbae1408793821f6d00ea1 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Wed, 27 Feb 2019 23:54:21 +0100 Subject: [PATCH 199/507] Move specialization --- include/deal.II/base/numbers.h | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/include/deal.II/base/numbers.h b/include/deal.II/base/numbers.h index fca6430fd267..60396a2af539 100644 --- a/include/deal.II/base/numbers.h +++ b/include/deal.II/base/numbers.h @@ -174,6 +174,13 @@ namespace numbers struct is_cuda_compatible : std::true_type {}; + /** + * std::complex cannot be used in CUDA device code. + */ + template + struct is_cuda_compatible, void> : std::false_type + {}; + /** * Check whether a value is not a number. * @@ -443,12 +450,6 @@ namespace numbers // --------------- inline and template functions ---------------- // - template - struct is_cuda_compatible, void> : std::false_type - {}; - - - inline bool is_nan(const double x) { From cba82d94d72867fab082b8a755f8950579c5c174 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Thu, 28 Feb 2019 02:12:22 +0100 Subject: [PATCH 200/507] Detect CUDA compute capability --- .../cuda_compute_capability.cu | 30 ++++++++++++++++ cmake/configure/configure_1_cuda.cmake | 34 +++++++++++++++++++ doc/external-libs/cuda.html | 4 +-- 3 files changed, 66 insertions(+), 2 deletions(-) create mode 100644 cmake/configure/CUDAComputeCapability/cuda_compute_capability.cu diff --git a/cmake/configure/CUDAComputeCapability/cuda_compute_capability.cu b/cmake/configure/CUDAComputeCapability/cuda_compute_capability.cu new file mode 100644 index 000000000000..23225d463234 --- /dev/null +++ b/cmake/configure/CUDAComputeCapability/cuda_compute_capability.cu @@ -0,0 +1,30 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + +#include + +int main() +{ + cudaDeviceProp device_properties; + const cudaError_t error = cudaGetDeviceProperties(&device_properties, + /*device*/0); + if( error != cudaSuccess) + { + std::cout << "CUDA error: " << cudaGetErrorString(error) << '\n'; + return error; + } + std::cout << device_properties.major << device_properties.minor; + return 0; +} diff --git a/cmake/configure/configure_1_cuda.cmake b/cmake/configure/configure_1_cuda.cmake index ce01a3b95a34..9001a9416586 100644 --- a/cmake/configure/configure_1_cuda.cmake +++ b/cmake/configure/configure_1_cuda.cmake @@ -85,6 +85,40 @@ MACRO(FEATURE_CUDA_FIND_EXTERNAL var) SET(CUDA_COMPUTE_CAPABILITY "${CMAKE_MATCH_1}") ELSEIF("${DEAL_II_CUDA_FLAGS_SAVED}" MATCHES "-arch=sm_([0-9]*)") SET(CUDA_COMPUTE_CAPABILITY "${CMAKE_MATCH_1}") + ELSEIF(DEAL_II_ALLOW_PLATFORM_INTROSPECTION) + # + # Try to autodetect the CUDA Compute Capability by asking the device + # + SET(_binary_test_dir ${CMAKE_CURRENT_BINARY_DIR}/cmake/configure/CUDAComputeCapabilityWorkdir) + FILE(REMOVE_RECURSE ${_binary_test_dir}) + FILE(MAKE_DIRECTORY ${_binary_test_dir}) + + EXECUTE_PROCESS( + COMMAND ${CUDA_NVCC_EXECUTABLE} + -ccbin=${CMAKE_CXX_COMPILER} + ${CMAKE_CURRENT_SOURCE_DIR}/cmake/configure/CUDAComputeCapability/cuda_compute_capability.cu + -o cuda_compute_capability + WORKING_DIRECTORY ${_binary_test_dir} + OUTPUT_QUIET + ERROR_QUIET + ) + EXECUTE_PROCESS(COMMAND ${_binary_test_dir}/cuda_compute_capability + RESULT_VARIABLE _result + OUTPUT_VARIABLE CUDA_COMPUTE_CAPABILITY) + IF(${_result} EQUAL 0) + ADD_FLAGS(DEAL_II_CUDA_FLAGS "-arch=sm_${CUDA_COMPUTE_CAPABILITY}") + MESSAGE(STATUS "Detected CUDA Compute Capability ${CUDA_COMPUTE_CAPABILITY}") + ELSE() + MESSAGE(STATUS "Couldn't detect CUDA Compute Capability! " + "The error message was: ${CUDA_COMPUTE_CAPABILITY}") + SET(CUDA_ADDITIONAL_ERROR_STRING + ${CUDA_ADDITIONAL_ERROR_STRING} + "Couldn't detect CUDA Compute Capability! " + "The error message was: ${CUDA_COMPUTE_CAPABILITY}\n" + "Please check the return value of ${_binary_test_dir}/cuda_compute_capability." + ) + SET(${var} FALSE) + ENDIF() ELSE() # # Assume a cuda compute capability of 35 diff --git a/doc/external-libs/cuda.html b/doc/external-libs/cuda.html index 8ba33ae33a88..345865b6a903 100644 --- a/doc/external-libs/cuda.html +++ b/doc/external-libs/cuda.html @@ -39,8 +39,8 @@

    Installing deal.II with CUDA

    If you are using CUDA 9 or CUDA 10, you will need to turn off support for C++17 similarly. - By default, we assume that your GPU has compute capability 3.5 but you - can easily set your own CUDA flags: + By default, we try to detect the compute capability of your device + but you can easily set your own CUDA flags: 
     
         -DDEAL_II_CUDA_FLAGS="-arch=sm_60"

From 86732c59c78c476084642ab6686e7d0c4931de43 Mon Sep 17 00:00:00 2001
From: Lei Qiao 
Date: Thu, 28 Feb 2019 16:55:20 +0800
Subject: [PATCH 201/507] minor fix on documentation to enum
 Triangulation::MeshSmoothing

---
 include/deal.II/grid/tria.h | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/include/deal.II/grid/tria.h b/include/deal.II/grid/tria.h
index 45e90441ff56..70e06728e490 100644
--- a/include/deal.II/grid/tria.h
+++ b/include/deal.II/grid/tria.h
@@ -1327,7 +1327,7 @@ class Triangulation : public Subscriptor
      *
      * If the smoothing indicator given to the constructor contains the bit
      * for #limit_level_difference_at_vertices, situations as the above one
-     * are eliminated by also marking the lower left cell for refinement.
+     * are eliminated by also marking the upper right cell for refinement.
      *
      * In case of anisotropic refinement, the level of a cell is not linked to
      * the refinement of a cell as directly as in case of isotropic

From f9b59e0792b7fa73c93341712e3033156c57b458 Mon Sep 17 00:00:00 2001
From: Marc Fehling 
Date: Thu, 28 Feb 2019 13:24:55 +0100
Subject: [PATCH 202/507] Complete signals for distributed_save|load.

---
 include/deal.II/grid/tria.h | 15 +++++++++++++++
 source/distributed/tria.cc  |  5 +++++
 2 files changed, 20 insertions(+)

diff --git a/include/deal.II/grid/tria.h b/include/deal.II/grid/tria.h
index 45e90441ff56..b47941a4ea0d 100644
--- a/include/deal.II/grid/tria.h
+++ b/include/deal.II/grid/tria.h
@@ -2335,6 +2335,21 @@ class Triangulation : public Subscriptor
      */
     boost::signals2::signal pre_distributed_save;
 
+    /**
+     * This signal is triggered at the end of execution of the
+     * parallel::distributed::Triangulation::save()
+     * function when the triangulation has reached its final state.
+     */
+    boost::signals2::signal post_distributed_save;
+
+    /**
+     * This signal is triggered at the beginning of execution of the
+     * parallel::distributed::Triangulation::load()
+     * function. At the time this signal is triggered, the triangulation
+     * is still unchanged.
+     */
+    boost::signals2::signal pre_distributed_load;
+
     /**
      * This signal is triggered at the end of execution of the
      * parallel::distributed::Triangulation::load()
diff --git a/source/distributed/tria.cc b/source/distributed/tria.cc
index 5fe3afb1c834..9da8894cd146 100644
--- a/source/distributed/tria.cc
+++ b/source/distributed/tria.cc
@@ -2753,6 +2753,9 @@ namespace parallel
         tria->cell_attached_data.pack_callbacks_fixed.clear();
         tria->cell_attached_data.pack_callbacks_variable.clear();
       }
+
+      // signal that serialization has finished
+      this->signals.post_distributed_save();
     }
 
 
@@ -2771,6 +2774,8 @@ namespace parallel
         ExcMessage(
           "Triangulation may only contain coarse cells when calling load()."));
 
+      // signal that de-serialization is going to happen
+      this->signals.pre_distributed_load();
 
       if (parallel_ghost != nullptr)
         {

From 81a482d591b55add052681b5503aadd326a6fd94 Mon Sep 17 00:00:00 2001
From: Marc Fehling 
Date: Thu, 28 Feb 2019 13:25:13 +0100
Subject: [PATCH 203/507] hp::DoFHandler: Moved containers with temporary
 content into a dedicated structure.

---
 include/deal.II/hp/dof_handler.h |  79 ++++++++----
 source/hp/dof_handler.cc         | 204 +++++++++++++++++++++----------
 2 files changed, 195 insertions(+), 88 deletions(-)

diff --git a/include/deal.II/hp/dof_handler.h b/include/deal.II/hp/dof_handler.h
index 29a3746ec89a..fca0cac75579 100644
--- a/include/deal.II/hp/dof_handler.h
+++ b/include/deal.II/hp/dof_handler.h
@@ -1155,6 +1155,17 @@ namespace hp
     void
     post_distributed_active_fe_index_transfer();
 
+    /**
+     * A function that will be triggered through a triangulation
+     * signal just after the associated parallel::distributed::Triangulation has
+     * been saved.
+     *
+     * The function frees all memory related to the transfer of
+     * active_fe_indices.
+     */
+    void
+    post_distributed_serialization_of_active_fe_indices();
+
     /**
      * Space to store the DoF numbers for the different levels. Analogous to
      * the levels[] tree of the Triangulation objects.
@@ -1213,33 +1224,49 @@ namespace hp
     std::vector vertex_dof_offsets;
 
     /**
-     * Container to temporarily store the iterator and active FE index of
-     * cells that will be refined.
-     */
-    std::map refined_cells_fe_index;
-
-    /**
-     * Container to temporarily store the iterator and active FE index of
-     * parent cells that will remain after coarsening.
-     */
-    std::map coarsened_cells_fe_index;
-
-    /**
-     * Container to temporarily store the active_fe_index of every locally
-     * owned cell for transfer across parallel::distributed::Triangulation
-     * objects.
+     * Whenever the underlying triangulation changes by either
+     * refinement/coarsening and serialization, the active_fe_index of cells
+     * needs to be transferred. This structure stores all temporary information
+     * required during that process.
      */
-    std::vector active_fe_indices;
-
-    /**
-     * Helper object to transfer all active_fe_indices on
-     * parallel::distributed::Triangulation objects during refinement/coarsening
-     * and serialization.
-     */
-    std::unique_ptr<
-      parallel::distributed::
-        CellDataTransfer>>
-      cell_data_transfer;
+    struct ActiveFEIndexTransfer
+    {
+      /**
+       * Container to temporarily store the iterator and active FE index of
+       * cells that will be refined.
+       */
+      std::map refined_cells_fe_index;
+
+      /**
+       * Container to temporarily store the iterator and active FE index of
+       * parent cells that will remain after coarsening.
+       */
+      std::map
+        coarsened_cells_fe_index;
+
+      /**
+       * Container to temporarily store the active_fe_index of every locally
+       * owned cell for transfer across parallel::distributed::Triangulation
+       * objects.
+       */
+      std::vector active_fe_indices;
+
+      /**
+       * Helper object to transfer all active_fe_indices on
+       * parallel::distributed::Triangulation objects during
+       * refinement/coarsening and serialization.
+       */
+      std::unique_ptr<
+        parallel::distributed::
+          CellDataTransfer>>
+        cell_data_transfer;
+    };
+
+    /**
+     * We embed our data structure into a pointer to control that
+     * all transfer related data only exists during the actual transfer process.
+     */
+    std::unique_ptr active_fe_index_transfer;
 
     /**
      * A list of connections with which this object connects to the
diff --git a/source/hp/dof_handler.cc b/source/hp/dof_handler.cc
index 01900459d885..ad53874b5bd5 100644
--- a/source/hp/dof_handler.cc
+++ b/source/hp/dof_handler.cc
@@ -1523,38 +1523,29 @@ namespace hp
     // decide whether we need a sequential or a parallel shared/distributed
     // policy and attach corresponding callback functions dealing with the
     // transfer of active_fe_indices
-    if (const auto *distributed_tria = dynamic_cast<
-          const parallel::distributed::Triangulation *>(
-          &this->get_triangulation()))
+    if (dynamic_cast
+                       *>(&this->get_triangulation()))
       {
         policy = std_cxx14::make_unique<
           internal::DoFHandlerImplementation::Policy::ParallelDistributed<
             DoFHandler>>(*this);
 
-#ifdef DEAL_II_WITH_P4EST
-        cell_data_transfer = std_cxx14::make_unique<
-          parallel::distributed::
-            CellDataTransfer>>(
-          *distributed_tria,
-          /*transfer_variable_size_data=*/false,
-          ¶llel::distributed::CellDataTransfer<
-            dim,
-            spacedim,
-            std::vector>::CoarseningStrategies::check_equality);
-#endif
-
         tria_listeners.push_back(
-          distributed_tria->signals.pre_distributed_refinement.connect(
-            std::bind(
-              &DoFHandler::pre_distributed_active_fe_index_transfer,
-              std::ref(*this))));
+          this->tria->signals.pre_distributed_refinement.connect(std::bind(
+            &DoFHandler::pre_distributed_active_fe_index_transfer,
+            std::ref(*this))));
         tria_listeners.push_back(
-          distributed_tria->signals.post_distributed_refinement.connect(
-            std::bind(
-              &DoFHandler::post_distributed_active_fe_index_transfer,
-              std::ref(*this))));
+          this->tria->signals.post_distributed_refinement.connect(std::bind(
+            &DoFHandler::post_distributed_active_fe_index_transfer,
+            std::ref(*this))));
+
+        tria_listeners.push_back(
+          this->tria->signals.post_distributed_save.connect(
+            std::bind(&DoFHandler::
+                        post_distributed_serialization_of_active_fe_indices,
+                      std::ref(*this))));
       }
     else if (dynamic_cast
                             *>(&this->get_triangulation()) != nullptr)
@@ -1791,8 +1782,10 @@ namespace hp
     // distribute_dofs() first to make this functionality available.
     if (fe_collection.size() > 0)
       {
-        Assert(refined_cells_fe_index.empty(), ExcInternalError());
-        Assert(coarsened_cells_fe_index.empty(), ExcInternalError());
+        Assert(active_fe_index_transfer == nullptr, ExcInternalError());
+
+        active_fe_index_transfer =
+          std_cxx14::make_unique();
 
         // Store active_fe_index information for all cells that will be
         // affected by refinement/coarsening.
@@ -1803,7 +1796,7 @@ namespace hp
                 {
                   // Store the active_fe_index of each cell that will be refined
                   // to and distribute it later on its children.
-                  refined_cells_fe_index.insert(
+                  active_fe_index_transfer->refined_cells_fe_index.insert(
                     {cell, cell->active_fe_index()});
                 }
               else if (cell->coarsen_flag_set())
@@ -1816,8 +1809,9 @@ namespace hp
                   const auto &parent = cell->parent();
                   // Check if the active_fe_index for the current cell has been
                   // determined already.
-                  if (coarsened_cells_fe_index.find(parent) ==
-                      coarsened_cells_fe_index.end())
+                  if (active_fe_index_transfer->coarsened_cells_fe_index.find(
+                        parent) ==
+                      active_fe_index_transfer->coarsened_cells_fe_index.end())
                     {
                       std::set fe_indices_children;
                       for (unsigned int child_index = 0;
@@ -1842,7 +1836,8 @@ namespace hp
                           "that dominates all children of a cell you are trying "
                           "to coarsen!"));
 
-                      coarsened_cells_fe_index.insert({parent, fe_index});
+                      active_fe_index_transfer->coarsened_cells_fe_index.insert(
+                        {parent, fe_index});
                     }
                 }
             }
@@ -1862,6 +1857,8 @@ namespace hp
     // distribute_dofs() first to make this functionality available.
     if (fe_collection.size() > 0)
       {
+        Assert(active_fe_index_transfer == nullptr, ExcInternalError());
+
         // If the underlying shared::Tria allows artificial cells,
         // then save the current set of subdomain ids, and set
         // subdomain ids to the "true" owner of each cell. We later
@@ -1922,6 +1919,8 @@ namespace hp
     // distribute_dofs() first to make this functionality available.
     if (fe_collection.size() > 0)
       {
+        Assert(active_fe_index_transfer == nullptr, ExcInternalError());
+
         // First, do what we would do in the sequential case.
         pre_active_fe_index_transfer();
 
@@ -1932,24 +1931,37 @@ namespace hp
         // the active_fe_indices on the new mesh.
 
         // Gather all current active_fe_indices.
-        get_active_fe_indices(active_fe_indices);
+        get_active_fe_indices(active_fe_index_transfer->active_fe_indices);
 
         // Overwrite values of cells that will be coarsened with the
         // active_fe_index determined beforehand for their parent.
-        for (const auto &pair : coarsened_cells_fe_index)
+        for (const auto &pair :
+             active_fe_index_transfer->coarsened_cells_fe_index)
           for (unsigned int child_index = 0;
                child_index < pair.first->n_children();
                ++child_index)
-            active_fe_indices[pair.first->child(child_index)
-                                ->active_cell_index()] = pair.second;
+            active_fe_index_transfer
+              ->active_fe_indices[pair.first->child(child_index)
+                                    ->active_cell_index()] = pair.second;
 
-        // Attach to transfer object.
-        cell_data_transfer->prepare_for_coarsening_and_refinement(
-          active_fe_indices);
+        // Create transfer object and attach to it.
+        const auto *distributed_tria = dynamic_cast<
+          const parallel::distributed::Triangulation *>(
+          &this->get_triangulation());
+
+        active_fe_index_transfer->cell_data_transfer = std_cxx14::make_unique<
+          parallel::distributed::
+            CellDataTransfer>>(
+          *distributed_tria,
+          /*transfer_variable_size_data=*/false,
+          ¶llel::distributed::CellDataTransfer<
+            dim,
+            spacedim,
+            std::vector>::CoarseningStrategies::check_equality);
 
-        // Free some memory.
-        refined_cells_fe_index.clear();
-        coarsened_cells_fe_index.clear();
+        active_fe_index_transfer->cell_data_transfer
+          ->prepare_for_coarsening_and_refinement(
+            active_fe_index_transfer->active_fe_indices);
       }
 #endif
   }
@@ -1964,6 +1976,8 @@ namespace hp
     // distribute_dofs() first to make this functionality available.
     if (fe_collection.size() > 0)
       {
+        Assert(active_fe_index_transfer != nullptr, ExcInternalError());
+
         // For Triangulation and p::s::Triangulation, the old cell iterators
         // are still valid. There is no need to transfer data in this case,
         // and we can re-use our previously gathered information from the
@@ -1971,7 +1985,8 @@ namespace hp
 
         // Distribute active_fe_indices from all refined cells on their
         // respective children.
-        for (const auto &pair : refined_cells_fe_index)
+        for (const auto &pair :
+             active_fe_index_transfer->refined_cells_fe_index)
           {
             const cell_iterator &parent = pair.first;
 
@@ -1991,7 +2006,8 @@ namespace hp
 
         // Set active_fe_indices on coarsened cells that have been determined
         // before the actual coarsening happened.
-        for (const auto &pair : coarsened_cells_fe_index)
+        for (const auto &pair :
+             active_fe_index_transfer->coarsened_cells_fe_index)
           {
             const cell_iterator &cell = pair.first;
 
@@ -2002,9 +2018,8 @@ namespace hp
               }
           }
 
-        // Clear stored active_fe_indices.
-        refined_cells_fe_index.clear();
-        coarsened_cells_fe_index.clear();
+        // Free memory.
+        active_fe_index_transfer.reset();
       }
   }
 
@@ -2021,6 +2036,8 @@ namespace hp
     // distribute_dofs() first to make this functionality available.
     if (fe_collection.size() > 0)
       {
+        Assert(active_fe_index_transfer != nullptr, ExcInternalError());
+
         // Do what we normally do in the sequential case.
         post_active_fe_index_transfer();
 
@@ -2046,17 +2063,19 @@ namespace hp
     // distribute_dofs() first to make this functionality available.
     if (fe_collection.size() > 0)
       {
+        Assert(active_fe_index_transfer != nullptr, ExcInternalError());
+
         // Unpack active_fe_indices.
-        active_fe_indices.resize(tria->n_active_cells(),
-                                 numbers::invalid_unsigned_int);
-        cell_data_transfer->unpack(active_fe_indices);
+        active_fe_index_transfer->active_fe_indices.resize(
+          tria->n_active_cells(), numbers::invalid_unsigned_int);
+        active_fe_index_transfer->cell_data_transfer->unpack(
+          active_fe_index_transfer->active_fe_indices);
 
         // Update all locally owned active_fe_indices.
-        set_active_fe_indices(active_fe_indices);
+        set_active_fe_indices(active_fe_index_transfer->active_fe_indices);
 
-        // Free some memory.
-        active_fe_indices.clear();
-        active_fe_indices.shrink_to_fit();
+        // Free memory.
+        active_fe_index_transfer.reset();
       }
 #endif
   }
@@ -2084,19 +2103,60 @@ namespace hp
     // distribute_dofs() first to make this functionality available.
     if (fe_collection.size() > 0)
       {
+        Assert(active_fe_index_transfer == nullptr, ExcInternalError());
+
+        active_fe_index_transfer =
+          std_cxx14::make_unique();
+
+        // Create transfer object and attach to it.
+        const auto *distributed_tria = dynamic_cast<
+          const parallel::distributed::Triangulation *>(
+          &this->get_triangulation());
+
+        active_fe_index_transfer->cell_data_transfer = std_cxx14::make_unique<
+          parallel::distributed::
+            CellDataTransfer>>(
+          *distributed_tria,
+          /*transfer_variable_size_data=*/false,
+          ¶llel::distributed::CellDataTransfer<
+            dim,
+            spacedim,
+            std::vector>::CoarseningStrategies::check_equality);
+
         // If we work on a p::d::Triangulation, we have to transfer all
         // active fe indices since ownership of cells may change.
 
         // Gather all current active_fe_indices
-        get_active_fe_indices(active_fe_indices);
+        get_active_fe_indices(active_fe_index_transfer->active_fe_indices);
 
         // Attach to transfer object
-        cell_data_transfer->prepare_for_serialization(active_fe_indices);
+        active_fe_index_transfer->cell_data_transfer->prepare_for_serialization(
+          active_fe_index_transfer->active_fe_indices);
       }
 #endif
   }
 
 
+  template 
+  void
+  DoFHandler::post_distributed_serialization_of_active_fe_indices()
+  {
+#ifndef DEAL_II_WITH_P4EST
+    Assert(false,
+           ExcMessage(
+             "You are attempting to use a functionality that is only available "
+             "if deal.II was configured to use p4est, but cmake did not find a "
+             "valid p4est library."));
+#else
+    Assert(active_fe_index_transfer != nullptr, ExcInternalError());
+
+    // Free memory.
+    active_fe_index_transfer.reset();
+#endif
+  }
+
+
 
   template 
   void
@@ -2119,17 +2179,37 @@ namespace hp
     // distribute_dofs() first to make this functionality available.
     if (fe_collection.size() > 0)
       {
+        Assert(active_fe_index_transfer == nullptr, ExcInternalError());
+
+        active_fe_index_transfer =
+          std_cxx14::make_unique();
+
+        // Create transfer object and attach to it.
+        const auto *distributed_tria = dynamic_cast<
+          const parallel::distributed::Triangulation *>(
+          &this->get_triangulation());
+
+        active_fe_index_transfer->cell_data_transfer = std_cxx14::make_unique<
+          parallel::distributed::
+            CellDataTransfer>>(
+          *distributed_tria,
+          /*transfer_variable_size_data=*/false,
+          ¶llel::distributed::CellDataTransfer<
+            dim,
+            spacedim,
+            std::vector>::CoarseningStrategies::check_equality);
+
         // Unpack active_fe_indices.
-        active_fe_indices.resize(tria->n_active_cells(),
-                                 numbers::invalid_unsigned_int);
-        cell_data_transfer->deserialize(active_fe_indices);
+        active_fe_index_transfer->active_fe_indices.resize(
+          tria->n_active_cells(), numbers::invalid_unsigned_int);
+        active_fe_index_transfer->cell_data_transfer->deserialize(
+          active_fe_index_transfer->active_fe_indices);
 
         // Update all locally owned active_fe_indices.
-        set_active_fe_indices(active_fe_indices);
+        set_active_fe_indices(active_fe_index_transfer->active_fe_indices);
 
-        // Free some memory.
-        active_fe_indices.clear();
-        active_fe_indices.shrink_to_fit();
+        // Free memory.
+        active_fe_index_transfer.reset();
       }
 #endif
   }

From 052b9b1b3cbd27520a63daf7b085b2bd84fecc2a Mon Sep 17 00:00:00 2001
From: Marc Fehling 
Date: Sun, 3 Feb 2019 01:24:43 +0100
Subject: [PATCH 204/507] Added 'set_fe' functionality to DoFHandlers.

---
 doc/news/changes/minor/20190210MarcFehling    |  6 ++
 .../deal.II/distributed/solution_transfer.h   |  2 +-
 include/deal.II/dofs/dof_handler.h            | 32 ++++++---
 include/deal.II/hp/dof_handler.h              | 13 ++++
 source/dofs/dof_handler.cc                    | 18 +++--
 source/hp/dof_handler.cc                      | 71 +++++++++----------
 tests/mpi/hp_active_fe_indices_transfer_01.cc |  3 +-
 tests/mpi/hp_active_fe_indices_transfer_02.cc |  8 +--
 tests/mpi/hp_cell_weights_01.cc               | 11 ++-
 tests/mpi/hp_cell_weights_02.cc               | 11 ++-
 tests/mpi/hp_cell_weights_03.cc               | 11 ++-
 tests/mpi/p4est_save_06.cc                    |  2 +-
 12 files changed, 107 insertions(+), 81 deletions(-)
 create mode 100644 doc/news/changes/minor/20190210MarcFehling

diff --git a/doc/news/changes/minor/20190210MarcFehling b/doc/news/changes/minor/20190210MarcFehling
new file mode 100644
index 000000000000..9a3e1e9f4751
--- /dev/null
+++ b/doc/news/changes/minor/20190210MarcFehling
@@ -0,0 +1,6 @@
+New: Member functions DoFHandler::set_fe() and hp::DoFHandler::set_fe()
+that will register a finite element object without enumerating all
+degrees of freedom. In the hp case, the active_fe_indices will be
+initialized and communicated amongst all processors, additionally.
+
    
+(2019/02/10, Marc Fehling)
diff --git a/include/deal.II/distributed/solution_transfer.h b/include/deal.II/distributed/solution_transfer.h
index 558ebeed2966..9d61878b2770 100644
--- a/include/deal.II/distributed/solution_transfer.h
+++ b/include/deal.II/distributed/solution_transfer.h
@@ -203,7 +203,7 @@ namespace parallel
      * hp::DoFHandler hp_dof_handler(triangulation);
      * // We need to introduce our dof_handler to the fe_collection
      * // before setting all active_fe_indices.
-     * hp_dof_handler.distribute_dofs(fe_collection);
+     * hp_dof_handler.set_fe(fe_collection);
      * hp_dof_handler.deserialize_active_fe_indices();
      * hp_dof_handler.distribute_dofs(fe_collection);
      *
diff --git a/include/deal.II/dofs/dof_handler.h b/include/deal.II/dofs/dof_handler.h
index 638e98b535ee..1da5931739ac 100644
--- a/include/deal.II/dofs/dof_handler.h
+++ b/include/deal.II/dofs/dof_handler.h
@@ -472,6 +472,25 @@ class DoFHandler : public Subscriptor
   initialize(const Triangulation &tria,
              const FiniteElement &fe);
 
+  /**
+   * Assign a FiniteElement @p fe to this object.
+   *
+   * @note This function makes a copy of the finite element given as
+   * argument, and stores it as a member variable. Consequently, it is
+   * possible to write code such as
+   * @code
+   *   dof_handler.set_fe(FE_Q(2));
+   * @endcode
+   * You can then access the finite element later on by calling
+   * DoFHandler::get_fe(). However, it is often more convenient to
+   * keep a named finite element object as a member variable in your
+   * main class and refer to it directly whenever you need to access
+   * properties of the finite element (such as
+   * FiniteElementData::dofs_per_cell). This is what all tutorial programs do.
+   */
+  virtual void
+  set_fe(const FiniteElement &fe);
+
   /**
    * Go through the triangulation and "distribute" the degrees of
    * freedom needed for the given finite element. "Distributing"
@@ -498,17 +517,8 @@ class DoFHandler : public Subscriptor
    * step-2 tutorial program.
    *
    * @note This function makes a copy of the finite element given as
-   * argument, and stores it as a member variable. Consequently, it is
-   * possible to write code such as
-   * @code
-   *   dof_handler.distribute_dofs (FE_Q(2));
-   * @endcode
-   * You can then access the finite element later on by calling
-   * DoFHandler::get_fe().  However, it is often more convenient to
-   * keep a named finite element object as a member variable in your
-   * main class and refer to it directly whenever you need to access
-   * properties of the finite element (such as FiniteElement::dofs_per_cell).
-   * This is what all tutorial programs do.
+   * argument, and stores it as a member variable, similarly to the above
+   * function set_fe().
    */
   virtual void
   distribute_dofs(const FiniteElement &fe);
diff --git a/include/deal.II/hp/dof_handler.h b/include/deal.II/hp/dof_handler.h
index 29a3746ec89a..3b73789941c6 100644
--- a/include/deal.II/hp/dof_handler.h
+++ b/include/deal.II/hp/dof_handler.h
@@ -417,6 +417,19 @@ namespace hp
     initialize(const Triangulation &   tria,
                const hp::FECollection &fe);
 
+    /**
+     * Assign a hp::FECollection @p fe to this object.
+     *
+     * In case a parallel::Triangulation is assigned to this object,
+     * the active_fe_indices will be exchanged between processors so that
+     * each one knows the indices on its own cells and all ghost cells.
+     *
+     * @note In accordance with dealii::DoFHandler::set_fe(),
+     * this function also makes a copy of the object given as argument.
+     */
+    virtual void
+    set_fe(const hp::FECollection &fe);
+
     /**
      * Go through the triangulation and "distribute" the degrees of
      * freedom needed for the given finite element. "Distributing"
diff --git a/source/dofs/dof_handler.cc b/source/dofs/dof_handler.cc
index 03603ee5a05e..f5b0a0fd2064 100644
--- a/source/dofs/dof_handler.cc
+++ b/source/dofs/dof_handler.cc
@@ -1197,6 +1197,18 @@ DoFHandler::memory_consumption() const
 
 
 
+template 
+void
+DoFHandler::set_fe(const FiniteElement &ff)
+{
+  // Only recreate the FECollection if we don't already store
+  // the exact same FiniteElement object.
+  if (fe_collection.size() == 0 || fe_collection[0] != ff)
+    fe_collection = hp::FECollection(ff);
+}
+
+
+
 template 
 void
 DoFHandler::distribute_dofs(
@@ -1210,10 +1222,8 @@ DoFHandler::distribute_dofs(
   Assert(tria->n_levels() > 0,
          ExcMessage("The Triangulation you are using is empty!"));
 
-  // Only recreate the FECollection if we don't already store
-  // the exact same FiniteElement object.
-  if (fe_collection.size() == 0 || fe_collection[0] != ff)
-    fe_collection = hp::FECollection(ff);
+  // first, assign the finite_element
+  set_fe(ff);
 
   // delete all levels and set them
   // up newly. note that we still
diff --git a/source/hp/dof_handler.cc b/source/hp/dof_handler.cc
index 01900459d885..35e4a1766649 100644
--- a/source/hp/dof_handler.cc
+++ b/source/hp/dof_handler.cc
@@ -1390,6 +1390,33 @@ namespace hp
 
 
 
+  template 
+  void
+  DoFHandler::set_fe(const hp::FECollection &ff)
+  {
+    // don't create a new object if the one we have is already appropriate
+    if (fe_collection != ff)
+      fe_collection = hp::FECollection(ff);
+
+    // ensure that the active_fe_indices vectors are initialized correctly
+    create_active_fe_table();
+
+    // make sure every processor knows the active_fe_indices
+    // on both its own cells and all ghost cells
+    dealii::internal::hp::DoFHandlerImplementation::Implementation::
+      communicate_active_fe_indices(*this);
+
+    // make sure that the fe collection is large enough to
+    // cover all fe indices presently in use on the mesh
+    for (const auto &cell : active_cell_iterators())
+      if (cell->is_locally_owned())
+        Assert(cell->active_fe_index() < fe_collection.size(),
+               ExcInvalidFEIndex(cell->active_fe_index(),
+                                 fe_collection.size()));
+  }
+
+
+
   template 
   void
   DoFHandler::distribute_dofs(
@@ -1404,14 +1431,8 @@ namespace hp
            ExcMessage("The Triangulation you are using is empty!"));
     Assert(ff.size() > 0, ExcMessage("The hp::FECollection given is empty!"));
 
-    // don't create a new object if the one we have is already appropriate
-    if (fe_collection != ff)
-      fe_collection = hp::FECollection(ff);
-
-    // at the beginning, make sure every processor knows the
-    // active_fe_indices on both its own cells and all ghost cells
-    dealii::internal::hp::DoFHandlerImplementation::Implementation::
-      communicate_active_fe_indices(*this);
+    // first, assign the fe_collection
+    set_fe(ff);
 
     // If an underlying shared::Tria allows artificial cells,
     // then save the current set of subdomain ids, and set
@@ -1425,51 +1446,29 @@ namespace hp
         {
           saved_subdomain_ids.resize(shared_tria->n_active_cells());
 
-          typename parallel::shared::Triangulation::
-            active_cell_iterator cell = get_triangulation().begin_active(),
-                                 endc = get_triangulation().end();
-
           const std::vector &true_subdomain_ids =
             shared_tria->get_true_subdomain_ids_of_cells();
 
-          for (unsigned int index = 0; cell != endc; ++cell, ++index)
+          for (const auto &cell : shared_tria->active_cell_iterators())
             {
+              const unsigned int index   = cell->active_cell_index();
               saved_subdomain_ids[index] = cell->subdomain_id();
               cell->set_subdomain_id(true_subdomain_ids[index]);
             }
         }
 
-    // ensure that the active_fe_indices vectors are
-    // initialized correctly.
-    create_active_fe_table();
-
-    // up front make sure that the fe collection is large enough to
-    // cover all fe indices presently in use on the mesh
-    for (active_cell_iterator cell = begin_active(); cell != end(); ++cell)
-      if (cell->is_locally_owned())
-        Assert(cell->active_fe_index() < fe_collection.size(),
-               ExcInvalidFEIndex(cell->active_fe_index(),
-                                 fe_collection.size()));
-
-
-    // then allocate space for all the other tables
+    // then allocate space for all tables
     dealii::internal::hp::DoFHandlerImplementation::Implementation::
       reserve_space(*this);
 
-
     // now undo the subdomain modification
     if (const parallel::shared::Triangulation *shared_tria =
           (dynamic_cast *>(
             &get_triangulation())))
       if (shared_tria->with_artificial_cells())
-        {
-          typename parallel::shared::Triangulation::
-            active_cell_iterator cell = get_triangulation().begin_active(),
-                                 endc = get_triangulation().end();
-
-          for (unsigned int index = 0; cell != endc; ++cell, ++index)
-            cell->set_subdomain_id(saved_subdomain_ids[index]);
-        }
+        for (const auto &cell : shared_tria->active_cell_iterators())
+          cell->set_subdomain_id(
+            saved_subdomain_ids[cell->active_cell_index()]);
 
 
     // Clear user flags because we will need them. But first we save
diff --git a/tests/mpi/hp_active_fe_indices_transfer_01.cc b/tests/mpi/hp_active_fe_indices_transfer_01.cc
index 2d5cb00ab231..5fd0cc5108dc 100644
--- a/tests/mpi/hp_active_fe_indices_transfer_01.cc
+++ b/tests/mpi/hp_active_fe_indices_transfer_01.cc
@@ -50,9 +50,8 @@ test()
   for (unsigned int i = 0; i < max_degree; ++i)
     fe_collection.push_back(FE_Q(max_degree - i));
 
-  // this distribute_dofs() call is necessary
   // we need to introduce dof_handler to its fe_collection first
-  dh.distribute_dofs(fe_collection);
+  dh.set_fe(fe_collection);
 
   unsigned int i = 0;
   for (auto &cell : dh.active_cell_iterators())
diff --git a/tests/mpi/hp_active_fe_indices_transfer_02.cc b/tests/mpi/hp_active_fe_indices_transfer_02.cc
index 65393457401e..e40dc29a2b67 100644
--- a/tests/mpi/hp_active_fe_indices_transfer_02.cc
+++ b/tests/mpi/hp_active_fe_indices_transfer_02.cc
@@ -48,10 +48,9 @@ test()
     GridGenerator::subdivided_hyper_cube(tria, 2);
     tria.refine_global(1);
 
-    // this distribute_dofs() call is necessary
-    // we need to introduce dof_handler to its fe_collection first
     hp::DoFHandler dh(tria);
-    dh.distribute_dofs(fe_collection);
+    // we need to introduce dof_handler to its fe_collection first
+    dh.set_fe(fe_collection);
 
     unsigned int i = 0;
     for (auto &cell : dh.active_cell_iterators())
@@ -85,10 +84,9 @@ test()
     GridGenerator::subdivided_hyper_cube(tria, 2);
     // triangulation has to be initialized with correct coarse cells
 
-    // this distribute_dofs() call is necessary
     // we need to introduce dof_handler to its fe_collection first
     hp::DoFHandler dh(tria);
-    dh.distribute_dofs(fe_collection);
+    dh.set_fe(fe_collection);
 
     // ----- transfer -----
     tria.load("file");
diff --git a/tests/mpi/hp_cell_weights_01.cc b/tests/mpi/hp_cell_weights_01.cc
index 6d15d5841b32..6edf11841294 100644
--- a/tests/mpi/hp_cell_weights_01.cc
+++ b/tests/mpi/hp_cell_weights_01.cc
@@ -57,17 +57,12 @@ test()
   fe_collection.push_back(FE_Q(5));
 
   hp::DoFHandler dh(tria);
+  dh.set_fe(fe_collection);
   // default: active_fe_index = 0
   for (auto &cell : dh.active_cell_iterators())
     if (cell->is_locally_owned())
       if (cell->id().to_string() == "0_2:00")
         cell->set_active_fe_index(1);
-  dh.distribute_dofs(fe_collection);
-
-
-  parallel::CellWeights cell_weights(dh);
-  cell_weights.register_ndofs_weighting(100000);
-
 
   deallog << "Number of cells before repartitioning: "
           << tria.n_locally_owned_active_cells() << std::endl;
@@ -80,8 +75,10 @@ test()
   }
 
 
+  parallel::CellWeights cell_weights(dh);
+  cell_weights.register_ndofs_weighting(100000);
+
   tria.repartition();
-  dh.distribute_dofs(fe_collection);
 
 
   deallog << "Number of cells after repartitioning: "
diff --git a/tests/mpi/hp_cell_weights_02.cc b/tests/mpi/hp_cell_weights_02.cc
index 5d13dff77469..e116925d70de 100644
--- a/tests/mpi/hp_cell_weights_02.cc
+++ b/tests/mpi/hp_cell_weights_02.cc
@@ -63,17 +63,12 @@ test()
   fe_collection.push_back(FE_Q(7));
 
   hp::DoFHandler dh(tria);
+  dh.set_fe(fe_collection);
   // default: active_fe_index = 0
   for (auto &cell : dh.active_cell_iterators())
     if (cell->is_locally_owned())
       if (cell->id().to_string() == "0_3:000")
         cell->set_active_fe_index(1);
-  dh.distribute_dofs(fe_collection);
-
-
-  parallel::CellWeights cell_weights(dh);
-  cell_weights.register_ndofs_weighting(100000);
-
 
   deallog << "Number of cells before repartitioning: "
           << tria.n_locally_owned_active_cells() << std::endl;
@@ -86,8 +81,10 @@ test()
   }
 
 
+  parallel::CellWeights cell_weights(dh);
+  cell_weights.register_ndofs_weighting(100000);
+
   tria.repartition();
-  dh.distribute_dofs(fe_collection);
 
 
   deallog << "Number of cells after repartitioning: "
diff --git a/tests/mpi/hp_cell_weights_03.cc b/tests/mpi/hp_cell_weights_03.cc
index c2eccc249f98..afe9d5be68d9 100644
--- a/tests/mpi/hp_cell_weights_03.cc
+++ b/tests/mpi/hp_cell_weights_03.cc
@@ -63,17 +63,12 @@ test()
   fe_collection.push_back(FE_Q(5));
 
   hp::DoFHandler dh(tria);
+  dh.set_fe(fe_collection);
   // default: active_fe_index = 0
   for (auto &cell : dh.active_cell_iterators())
     if (cell->is_locally_owned())
       if (cell->id().to_string() == "0_2:00")
         cell->set_active_fe_index(1);
-  dh.distribute_dofs(fe_collection);
-
-
-  parallel::CellWeights cell_weights(dh);
-  cell_weights.register_ndofs_weighting(100000);
-
 
   deallog << "Number of cells before repartitioning: "
           << tria.n_locally_owned_active_cells() << std::endl;
@@ -86,9 +81,11 @@ test()
   }
 
 
+  parallel::CellWeights cell_weights(dh);
+  cell_weights.register_ndofs_weighting(100000);
+
   // we didn't mark any cells, but we want to repartition our domain
   tria.execute_coarsening_and_refinement();
-  dh.distribute_dofs(fe_collection);
 
 
   deallog << "Number of cells after repartitioning: "
diff --git a/tests/mpi/p4est_save_06.cc b/tests/mpi/p4est_save_06.cc
index 5af46a86964b..453ed583896d 100644
--- a/tests/mpi/p4est_save_06.cc
+++ b/tests/mpi/p4est_save_06.cc
@@ -134,7 +134,7 @@ test()
     for (unsigned int i = 0; i < max_degree; ++i)
       fe_collection.push_back(FE_Q(max_degree - i));
 
-    dh.distribute_dofs(fe_collection);
+    dh.set_fe(fe_collection);
     dh.deserialize_active_fe_indices();
     dh.distribute_dofs(fe_collection);
 

From 2be46094200872ffa8cc9f63d20d20926cb392eb Mon Sep 17 00:00:00 2001
From: Marc Fehling 
Date: Mon, 11 Feb 2019 18:02:27 +0100
Subject: [PATCH 205/507] Add warning to set_fe.

---
 include/deal.II/dofs/dof_handler.h | 5 +++++
 include/deal.II/hp/dof_handler.h   | 6 ++++++
 2 files changed, 11 insertions(+)

diff --git a/include/deal.II/dofs/dof_handler.h b/include/deal.II/dofs/dof_handler.h
index 1da5931739ac..d07ecf0738dd 100644
--- a/include/deal.II/dofs/dof_handler.h
+++ b/include/deal.II/dofs/dof_handler.h
@@ -487,6 +487,11 @@ class DoFHandler : public Subscriptor
    * main class and refer to it directly whenever you need to access
    * properties of the finite element (such as
    * FiniteElementData::dofs_per_cell). This is what all tutorial programs do.
+   *
+   * @warning This function only sets a FiniteElement. Degrees of freedom have
+   * either not been distributed yet, or are distributed using a previously set
+   * element. In both cases, accessing degrees of freedom will lead to invalid
+   * results. To restore consistency, call distribute_dofs().
    */
   virtual void
   set_fe(const FiniteElement &fe);
diff --git a/include/deal.II/hp/dof_handler.h b/include/deal.II/hp/dof_handler.h
index 3b73789941c6..e16a52495283 100644
--- a/include/deal.II/hp/dof_handler.h
+++ b/include/deal.II/hp/dof_handler.h
@@ -426,6 +426,12 @@ namespace hp
      *
      * @note In accordance with dealii::DoFHandler::set_fe(),
      * this function also makes a copy of the object given as argument.
+     *
+     * @warning This function only sets a hp::FECollection. Degrees of freedom
+     * have either not been distributed yet, or are distributed using a
+     * previously set collection. In both cases, accessing degrees of freedom
+     * will lead to invalid results. To restore consistency, call
+     * distribute_dofs().
      */
     virtual void
     set_fe(const hp::FECollection &fe);

From a501894dc24a677998ba57fb6392547cb7d0fc71 Mon Sep 17 00:00:00 2001
From: Marc Fehling 
Date: Thu, 28 Feb 2019 13:57:06 +0100
Subject: [PATCH 206/507] hp::distribute_dofs: Move 'set_fe' call to the place
 where active_fe_indices are initialized.

---
 source/hp/dof_handler.cc | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/source/hp/dof_handler.cc b/source/hp/dof_handler.cc
index 35e4a1766649..f2cfe2686dbc 100644
--- a/source/hp/dof_handler.cc
+++ b/source/hp/dof_handler.cc
@@ -1431,9 +1431,6 @@ namespace hp
            ExcMessage("The Triangulation you are using is empty!"));
     Assert(ff.size() > 0, ExcMessage("The hp::FECollection given is empty!"));
 
-    // first, assign the fe_collection
-    set_fe(ff);
-
     // If an underlying shared::Tria allows artificial cells,
     // then save the current set of subdomain ids, and set
     // subdomain ids to the "true" owner of each cell. we later
@@ -1457,7 +1454,10 @@ namespace hp
             }
         }
 
-    // then allocate space for all tables
+    // assign the fe_collection and initialize all active_fe_indices
+    set_fe(ff);
+
+    // then allocate space for all the other tables
     dealii::internal::hp::DoFHandlerImplementation::Implementation::
       reserve_space(*this);
 

From 15b4cfaac6b2aba3036d05ac155ec31db62ef6c6 Mon Sep 17 00:00:00 2001
From: tcclevenger 
Date: Fri, 8 Feb 2019 15:42:12 -0700
Subject: [PATCH 207/507] add no normal flux to MGConstrainedDoFs (box mesh)

---
 .../changes/minor/20190211ConradClevenger     |  6 ++
 .../deal.II/multigrid/mg_constrained_dofs.h   | 75 +++++++++++++++++++
 tests/multigrid/constrained_dofs_06.cc        | 75 +++++++++++++++++++
 tests/multigrid/constrained_dofs_06.output    | 14 ++++
 4 files changed, 170 insertions(+)
 create mode 100644 doc/news/changes/minor/20190211ConradClevenger
 create mode 100644 tests/multigrid/constrained_dofs_06.cc
 create mode 100644 tests/multigrid/constrained_dofs_06.output

diff --git a/doc/news/changes/minor/20190211ConradClevenger b/doc/news/changes/minor/20190211ConradClevenger
new file mode 100644
index 000000000000..da07b583e6eb
--- /dev/null
+++ b/doc/news/changes/minor/20190211ConradClevenger
@@ -0,0 +1,6 @@
+New: Function MGConstrainedDoFs::make_no_normal_flux_constraints which adds 
+functionality for no normal flux constraints during geometric mutigrid computations. 
+Currently, this function is limited to meshes with no normal flux boundaries 
+normal to the x-, y-, or z-axis.
+
    
+(Conrad Clevenger, 2019/02/11)
diff --git a/include/deal.II/multigrid/mg_constrained_dofs.h b/include/deal.II/multigrid/mg_constrained_dofs.h
index 40f2cd7c0d1c..452563eb3b11 100644
--- a/include/deal.II/multigrid/mg_constrained_dofs.h
+++ b/include/deal.II/multigrid/mg_constrained_dofs.h
@@ -100,6 +100,26 @@ class MGConstrainedDoFs : public Subscriptor
     const std::set &boundary_ids,
     const ComponentMask &               component_mask = ComponentMask());
 
+  /**
+   * Fill the internal data structures with information
+   * about no normal flux boundary dofs.
+   *
+   * This function is limited to meshes whose no normal flux boundaries
+   * have faces which are normal to the x-, y-, or z-axis. Also, for a
+   * specific boundary id, all faces must be facing in the same direction,
+   * i.e., a boundary normal to the x-axis must have a different boundary
+   * id than a boundary normal to the y- or z-axis and so on. If the mesh
+   * was produced, for example, using the GridGenerator::hyper_cube()
+   * function, setting colorize=true during mesh generation and calling
+   * make_no_normal_flux_constraints() for each no normal flux boundary is
+   * sufficient.
+   */
+  template 
+  void
+  make_no_normal_flux_constraints(const DoFHandler &dof,
+                                  const types::boundary_id         bid,
+                                  const unsigned int first_vector_component);
+
   /**
    * Reset the data structures.
    */
@@ -321,6 +341,61 @@ MGConstrainedDoFs::make_zero_boundary_constraints(
 }
 
 
+template 
+inline void
+MGConstrainedDoFs::make_no_normal_flux_constraints(
+  const DoFHandler &dof,
+  const types::boundary_id         bid,
+  const unsigned int               first_vector_component)
+{
+  // For a given boundary id, find which vector component is on the boundary
+  // and set a zero boundary constraint for those degrees of freedom.
+  const unsigned int n_components = DoFTools::n_components(dof);
+  Assert(first_vector_component + dim <= n_components,
+         ExcIndexRange(first_vector_component, 0, n_components - dim + 1));
+
+  ComponentMask comp_mask(n_components, false);
+
+
+  typename Triangulation::face_iterator
+    face = dof.get_triangulation().begin_face(),
+    endf = dof.get_triangulation().end_face();
+  for (; face != endf; ++face)
+    if (face->at_boundary() && face->boundary_id() == bid)
+      for (unsigned int d = 0; d < dim; ++d)
+        {
+          Tensor<1, dim, double> unit_vec;
+          unit_vec[d] = 1.0;
+
+          const Tensor<1, dim> normal_vec =
+            face->get_manifold().normal_vector(face, face->center());
+
+          if (std::abs(std::abs(unit_vec * normal_vec) - 1.0) < 1e-10)
+            comp_mask.set(d + first_vector_component, true);
+          else
+            Assert(
+              std::abs(unit_vec * normal_vec) < 1e-10,
+              ExcMessage(
+                "We can currently only support no normal flux conditions "
+                "for a specific boundary id if all faces are normal to the "
+                "x, y, or z axis."));
+        }
+
+  Assert(comp_mask.n_selected_components() == 1,
+         ExcMessage(
+           "We can currently only support no normal flux conditions "
+           "for a specific boundary id if all faces are facing in the "
+           "same direction, i.e., a boundary normal to the x-axis must "
+           "have a different boundary id than a boundary normal to the "
+           "y- or z-axis and so on. If the mesh here was produced using "
+           "GridGenerator::..., setting colorize=true during mesh generation "
+           "and calling make_no_normal_flux_constraints() for each no normal "
+           "flux boundary will fulfill the condition."));
+
+  this->make_zero_boundary_constraints(dof, {bid}, comp_mask);
+}
+
+
 inline void
 MGConstrainedDoFs::clear()
 {
diff --git a/tests/multigrid/constrained_dofs_06.cc b/tests/multigrid/constrained_dofs_06.cc
new file mode 100644
index 000000000000..cc0101f5995c
--- /dev/null
+++ b/tests/multigrid/constrained_dofs_06.cc
@@ -0,0 +1,75 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2018 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+// Check make_no_normal_flux_constraints function for a box mesh
+
+#include 
+
+#include 
+
+#include 
+#include 
+
+#include 
+#include 
+#include 
+
+#include 
+
+#include 
+
+#include "../tests.h"
+
+
+template 
+void
+test()
+{
+  Triangulation triangulation(
+    Triangulation::limit_level_difference_at_vertices);
+  GridGenerator::hyper_cube(triangulation, 0., 1., true);
+  triangulation.refine_global(4 - dim);
+
+  DoFHandler dof_handler(triangulation);
+  dof_handler.distribute_dofs(FESystem(FE_Q(1), dim));
+  dof_handler.distribute_mg_dofs();
+
+  std::set no_flux_boundary = {0, 1, 2};
+
+  MGConstrainedDoFs mg_constrained_dofs;
+  mg_constrained_dofs.initialize(dof_handler);
+  for (auto bid : no_flux_boundary)
+    mg_constrained_dofs.make_no_normal_flux_constraints(dof_handler, bid, 0);
+
+  for (unsigned int level = 0; level < triangulation.n_levels(); ++level)
+    {
+      deallog << "Level " << level << ": " << std::flush;
+      mg_constrained_dofs.get_boundary_indices(level).print(
+        deallog.get_file_stream());
+      deallog << std::endl;
+    }
+}
+
+int
+main()
+{
+  initlog();
+
+  deallog << "2D" << std::endl;
+  test<2>();
+  deallog << std::endl << "3D" << std::endl;
+  test<3>();
+  return 0;
+}
diff --git a/tests/multigrid/constrained_dofs_06.output b/tests/multigrid/constrained_dofs_06.output
new file mode 100644
index 000000000000..8f3fffee1a76
--- /dev/null
+++ b/tests/multigrid/constrained_dofs_06.output
@@ -0,0 +1,14 @@
+
+DEAL::2D
+DEAL::Level 0: {[0,4], 6}
+
+DEAL::Level 1: {[0,1], [3,4], [8,10], 12, 16}
+
+DEAL::Level 2: {[0,1], [3,4], 9, 12, 19, [22,24], 28, 30, 36, 44, 48}
+
+DEAL::
+DEAL::3D
+DEAL::Level 0: {[0,1], [3,4], 6, 9, [12,13], [15,16], 18, 21}
+
+DEAL::Level 1: {[0,1], 4, 6, [12,13], 16, 18, [24,25], 27, [30,31], 33, 36, 42, 48, 51, [54,55], 58, 60, [66,67], 69, 72, 78}
+

From 2b541384f0210bbf8140d7442ede9039fee4a831 Mon Sep 17 00:00:00 2001
From: Matthias Maier 
Date: Thu, 28 Feb 2019 14:23:12 -0600
Subject: [PATCH 208/507] SparsityPattern::Iterator  - add a constructor for
 initalizing an iterator from an accessor

When trying to increment a sparsity pattern iterator:

  auto iterator = sparsity_pattern.begin();
  iterator++;

The corresponding function in LinearIndexIterator:

  template 
  inline DerivedIterator
  LinearIndexIterator::operator++(int)
  {
    const DerivedIterator copy(this->accessor);
    operator+=(1);
    return copy;
  }

creates a copy that is initialized by the accessor. Thus, we need a
constructor that can create an interator from an accessor.
---
 include/deal.II/lac/sparsity_pattern.h | 13 +++++++++++++
 1 file changed, 13 insertions(+)

diff --git a/include/deal.II/lac/sparsity_pattern.h b/include/deal.II/lac/sparsity_pattern.h
index 89c507a31e16..573c6c29475b 100644
--- a/include/deal.II/lac/sparsity_pattern.h
+++ b/include/deal.II/lac/sparsity_pattern.h
@@ -298,6 +298,12 @@ namespace SparsityPatternIterators
      * the zeroth row).
      */
     Iterator(const SparsityPattern *sp, const std::size_t linear_index);
+
+    /**
+     * Constructor. Create an iterator into the sparsity pattern @p sp for
+     * a given accessor.
+     */
+    Iterator(const Accessor &accessor);
   };
 } // namespace SparsityPatternIterators
 
@@ -1272,6 +1278,13 @@ namespace SparsityPatternIterators
                             const std::size_t      linear_index)
     : LinearIndexIterator(Accessor(sp, linear_index))
   {}
+
+
+  inline Iterator::Iterator(const Accessor &accessor)
+    : LinearIndexIterator(accessor)
+  {}
+
+
 } // namespace SparsityPatternIterators
 
 

From e9c20e609eb6f7ff6ba75bf0377466b98dfbcc62 Mon Sep 17 00:00:00 2001
From: Matthias Maier 
Date: Thu, 28 Feb 2019 14:34:24 -0600
Subject: [PATCH 209/507] add a test

---
 .../sparsity/sparsity_pattern_iterator_09.cc  | 51 +++++++++++++++++++
 .../sparsity_pattern_iterator_09.output       |  2 +
 2 files changed, 53 insertions(+)
 create mode 100644 tests/sparsity/sparsity_pattern_iterator_09.cc
 create mode 100644 tests/sparsity/sparsity_pattern_iterator_09.output

diff --git a/tests/sparsity/sparsity_pattern_iterator_09.cc b/tests/sparsity/sparsity_pattern_iterator_09.cc
new file mode 100644
index 000000000000..17493bd5123a
--- /dev/null
+++ b/tests/sparsity/sparsity_pattern_iterator_09.cc
@@ -0,0 +1,51 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2004 - 2017 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+
+
+// test that i++ and i+n operations work with SparsityPattern::iterator.
+
+#include 
+
+#include "../tests.h"
+
+void
+test()
+{
+  SparsityPattern sp(5, 5, 3);
+  for (unsigned int i = 0; i < 5; ++i)
+    for (unsigned int j = 0; j < 5; ++j)
+      if ((i + 2 * j + 1) % 3 == 0)
+        sp.add(i, j);
+  sp.compress();
+
+  SparsityPattern::const_iterator i = sp.begin();
+
+  ++i;
+  i++;
+  i + 2;
+
+  deallog << "OK" << std::endl;
+}
+
+
+
+int
+main()
+{
+  initlog();
+
+  test();
+}
diff --git a/tests/sparsity/sparsity_pattern_iterator_09.output b/tests/sparsity/sparsity_pattern_iterator_09.output
new file mode 100644
index 000000000000..0fd8fc12f0b4
--- /dev/null
+++ b/tests/sparsity/sparsity_pattern_iterator_09.output
@@ -0,0 +1,2 @@
+
+DEAL::OK

From b9057152a4868e66dc828e27ba7258c211ac5f79 Mon Sep 17 00:00:00 2001
From: Daniel Arndt 
Date: Fri, 22 Feb 2019 15:36:31 +0100
Subject: [PATCH 210/507] Also instantiate for complex scalar types

---
 cmake/config/template-arguments.in         | 6 ++++++
 cmake/configure/configure_2_trilinos.cmake | 4 ++++
 2 files changed, 10 insertions(+)

diff --git a/cmake/config/template-arguments.in b/cmake/config/template-arguments.in
index 8a58e905961b..2e1a69bd7618 100644
--- a/cmake/config/template-arguments.in
+++ b/cmake/config/template-arguments.in
@@ -97,6 +97,8 @@ VECTOR_TYPES := {   Vector;
                     @DEAL_II_EXPAND_EPETRA_VECTOR@;
                     @DEAL_II_EXPAND_TPETRA_VECTOR_DOUBLE@;
                     @DEAL_II_EXPAND_TPETRA_VECTOR_FLOAT@;
+                    @DEAL_II_EXPAND_TPETRA_VECTOR_COMPLEX_DOUBLE@;
+                    @DEAL_II_EXPAND_TPETRA_VECTOR_COMPLEX_FLOAT@;
                     @DEAL_II_EXPAND_PETSC_MPI_VECTOR@;
 
                     @DEAL_II_EXPAND_TRILINOS_MPI_BLOCKVECTOR@;
@@ -153,6 +155,8 @@ EXTERNAL_PARALLEL_VECTORS := { @DEAL_II_EXPAND_TRILINOS_MPI_VECTOR@;
                                @DEAL_II_EXPAND_EPETRA_VECTOR@;
                                @DEAL_II_EXPAND_TPETRA_VECTOR_DOUBLE@;
                                @DEAL_II_EXPAND_TPETRA_VECTOR_FLOAT@;
+                               @DEAL_II_EXPAND_TPETRA_VECTOR_COMPLEX_DOUBLE@;
+                               @DEAL_II_EXPAND_TPETRA_VECTOR_COMPLEX_FLOAT@;
                                @DEAL_II_EXPAND_PETSC_MPI_VECTOR@;
                                @DEAL_II_EXPAND_PETSC_MPI_BLOCKVECTOR@
                              }
@@ -173,6 +177,8 @@ VECTORS_WITH_MATRIX := { Vector;
                          @DEAL_II_EXPAND_EPETRA_VECTOR@;
                          @DEAL_II_EXPAND_TPETRA_VECTOR_DOUBLE@;
                          @DEAL_II_EXPAND_TPETRA_VECTOR_FLOAT@;
+                         @DEAL_II_EXPAND_TPETRA_VECTOR_COMPLEX_DOUBLE@;
+                         @DEAL_II_EXPAND_TPETRA_VECTOR_COMPLEX_FLOAT@;
                          @DEAL_II_EXPAND_PETSC_MPI_VECTOR@;
                        }
 
diff --git a/cmake/configure/configure_2_trilinos.cmake b/cmake/configure/configure_2_trilinos.cmake
index 187fed907170..7a1f32cc5cc0 100644
--- a/cmake/configure/configure_2_trilinos.cmake
+++ b/cmake/configure/configure_2_trilinos.cmake
@@ -273,6 +273,10 @@ MACRO(FEATURE_TRILINOS_CONFIGURE_EXTERNAL)
     IF (${DEAL_II_TRILINOS_WITH_TPETRA})
       SET(DEAL_II_EXPAND_TPETRA_VECTOR_DOUBLE "LinearAlgebra::TpetraWrappers::Vector")
       SET(DEAL_II_EXPAND_TPETRA_VECTOR_FLOAT "LinearAlgebra::TpetraWrappers::Vector")
+      IF (${DEAL_II_WITH_COMPLEX_NUMBERS})
+        SET(DEAL_II_EXPAND_TPETRA_VECTOR_COMPLEX_DOUBLE "LinearAlgebra::TpetraWrappers::Vector>")
+        SET(DEAL_II_EXPAND_TPETRA_VECTOR_COMPLEX_FLOAT "LinearAlgebra::TpetraWrappers::Vector>")
+      ENDIF()
     ENDIF()
   ENDIF()
   IF(${DEAL_II_TRILINOS_WITH_SACADO})

From a49023961e854d2629a6a289f1b0edc5b6bf2337 Mon Sep 17 00:00:00 2001
From: Daniel Arndt 
Date: Fri, 1 Mar 2019 01:06:17 +0100
Subject: [PATCH 211/507] Enhance error message

---
 cmake/configure/configure_1_cuda.cmake | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/cmake/configure/configure_1_cuda.cmake b/cmake/configure/configure_1_cuda.cmake
index 9001a9416586..94c34940db70 100644
--- a/cmake/configure/configure_1_cuda.cmake
+++ b/cmake/configure/configure_1_cuda.cmake
@@ -115,7 +115,8 @@ MACRO(FEATURE_CUDA_FIND_EXTERNAL var)
           ${CUDA_ADDITIONAL_ERROR_STRING}
           "Couldn't detect CUDA Compute Capability! "
           "The error message was: ${CUDA_COMPUTE_CAPABILITY}\n"
-          "Please check the return value of ${_binary_test_dir}/cuda_compute_capability."
+          "Please check the return value of ${_binary_test_dir}/cuda_compute_capability.\n"
+          "If you want to disable the autodetection, set the compute capability to be used manually."
           )
         SET(${var} FALSE)
       ENDIF()

From 4f6a313d8eb6adc884951680bd860a81878b43e8 Mon Sep 17 00:00:00 2001
From: Daniel Arndt 
Date: Fri, 1 Mar 2019 01:22:29 +0100
Subject: [PATCH 212/507] Add description of memory and exceution space for
 CUDA support

---
 include/deal.II/lac/trilinos_tpetra_vector.h | 8 +++++++-
 1 file changed, 7 insertions(+), 1 deletion(-)

diff --git a/include/deal.II/lac/trilinos_tpetra_vector.h b/include/deal.II/lac/trilinos_tpetra_vector.h
index e883b24a00a8..35e31cc92eb1 100644
--- a/include/deal.II/lac/trilinos_tpetra_vector.h
+++ b/include/deal.II/lac/trilinos_tpetra_vector.h
@@ -54,9 +54,15 @@ namespace LinearAlgebra
      * LinearAlgebra::VectorSpaceVector class and requires Trilinos to be
      * compiled with MPI support.
      *
+     * Tpetra uses Kokkos for thread-parallelism. In case Trilinos was
+     * configured with CUDA support, this class stores the values in unified
+     * virtual memory space and performs its action on the GPU. In particular,
+     * there is no need for manually synchronizing memory between host and
+     * device.
+     *
      * @ingroup TrilinosWrappers
      * @ingroup Vectors
-     * @author Daniel Arndt, 2018
+     * @author Daniel Arndt, 2019
      */
     template 
     class Vector : public VectorSpaceVector, public Subscriptor

From 2e5bd57206d8ee0c6f156aad67b0725010630979 Mon Sep 17 00:00:00 2001
From: Reza Rastak 
Date: Thu, 28 Feb 2019 16:55:00 -0800
Subject: [PATCH 213/507] Out of date description of quadrature_point_data test
 fixed

---
 tests/base/quadrature_point_data.cc    | 2 +-
 tests/base/quadrature_point_data_02.cc | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/base/quadrature_point_data.cc b/tests/base/quadrature_point_data.cc
index 45aaefe99ad1..2963250bc09a 100644
--- a/tests/base/quadrature_point_data.cc
+++ b/tests/base/quadrature_point_data.cc
@@ -15,7 +15,7 @@
 
 
 
-// Check that QuadraturePointManager class. To that end first evaluate some
+// Check CellDataStorage class. To that end first evaluate some
 // quadratic function at quadrature points. Then refine cells and project using
 // FE_Q(2). Finally check that the values at quadrature points are still
 // consistent with the original function.
diff --git a/tests/base/quadrature_point_data_02.cc b/tests/base/quadrature_point_data_02.cc
index 546c0a437d29..16d9f4df671d 100644
--- a/tests/base/quadrature_point_data_02.cc
+++ b/tests/base/quadrature_point_data_02.cc
@@ -15,7 +15,7 @@
 
 
 
-// Check that QuadraturePointManager class. To that end first evaluate some
+// Check CellDataStorage class. To that end first evaluate some
 // quadratic function at quadrature points. Then refine cells and project using
 // FE_Q(2). Finally check that the values at quadrature points are still
 // consistent with the original function. Same as quadrature_point_data.cc, but

From 98145fce9e71a0a14acb24197c0e839dcccaa58d Mon Sep 17 00:00:00 2001
From: Wolfgang Bangerth 
Date: Fri, 1 Mar 2019 00:10:36 -0700
Subject: [PATCH 214/507] Convert a few explicit loops to range-based for
 loops.

---
 source/grid/tria.cc | 29 +++++++++--------------------
 1 file changed, 9 insertions(+), 20 deletions(-)

diff --git a/source/grid/tria.cc b/source/grid/tria.cc
index b3c515621858..2e7fce823fe5 100644
--- a/source/grid/tria.cc
+++ b/source/grid/tria.cc
@@ -14119,9 +14119,7 @@ Triangulation::prepare_coarsening_and_refinement()
   if (((smooth_grid & coarsest_level_1) || (smooth_grid & patch_level_1)) &&
       n_levels() >= 2)
     {
-      active_cell_iterator cell = begin_active(1), endc = end_active(1);
-
-      for (; cell != endc; ++cell)
+      for (const auto &cell : active_cell_iterators_on_level(1))
         cell->clear_coarsen_flag();
     }
 
@@ -14137,10 +14135,7 @@ Triangulation::prepare_coarsening_and_refinement()
       if (smooth_grid & do_not_produce_unrefined_islands &&
           !(smooth_grid & patch_level_1))
         {
-          cell_iterator       cell;
-          const cell_iterator endc = end();
-
-          for (cell = begin(); cell != endc; ++cell)
+          for (const auto &cell : cell_iterators())
             {
               // only do something if this
               // cell will be coarsened
@@ -14173,10 +14168,7 @@ Triangulation::prepare_coarsening_and_refinement()
                          eliminate_refined_boundary_islands) &&
           !(smooth_grid & patch_level_1))
         {
-          cell_iterator       cell;
-          const cell_iterator endc = end();
-
-          for (cell = begin(); cell != endc; ++cell)
+          for (const auto &cell : cell_iterators())
             if (!cell->active() || (cell->active() && cell->refine_flag_set() &&
                                     cell->is_locally_owned()))
               {
@@ -14271,9 +14263,8 @@ Triangulation::prepare_coarsening_and_refinement()
 
           // store highest level one of the cells adjacent to a vertex
           // belongs to
-          std::vector     vertex_level(vertices.size(), 0);
-          active_cell_iterator cell = begin_active(), endc = end();
-          for (; cell != endc; ++cell)
+          std::vector vertex_level(vertices.size(), 0);
+          for (const auto &cell : active_cell_iterators())
             {
               if (cell->refine_flag_set())
                 for (unsigned int vertex = 0;
@@ -14315,7 +14306,7 @@ Triangulation::prepare_coarsening_and_refinement()
           // refinement flags, but we will also have to remove
           // coarsening flags on cells adjacent to vertices that will
           // see refinement
-          for (cell = last_active(); cell != endc; --cell)
+          for (active_cell_iterator cell = last_active(); cell != end(); --cell)
             if (cell->refine_flag_set() == false)
               {
                 for (unsigned int vertex = 0;
@@ -14363,9 +14354,7 @@ Triangulation::prepare_coarsening_and_refinement()
       //    may trigger more cells further down below
       if (smooth_grid & eliminate_unrefined_islands)
         {
-          active_cell_iterator cell = last_active(), endc = end();
-
-          for (; cell != endc; --cell)
+          for (active_cell_iterator cell = last_active(); cell != end(); --cell)
             // only do something if cell is not already flagged for
             // (isotropic) refinement
             if (cell->refine_flag_set() !=
@@ -14409,7 +14398,7 @@ Triangulation::prepare_coarsening_and_refinement()
           // active).  If the refine flag of at least one of the
           // children is set then set_refine_flag and
           // clear_coarsen_flag of all children.
-          for (cell_iterator cell = begin(); cell != end(); ++cell)
+          for (const auto &cell : cell_iterators())
             if (!cell->active())
               {
                 // ensure the invariant. we can then check whether all
@@ -14445,7 +14434,7 @@ Triangulation::prepare_coarsening_and_refinement()
           //
           // for a case where this is a bit tricky, take a look at the
           // mesh_smoothing_0[12] testcases
-          for (cell_iterator cell = begin(); cell != end(); ++cell)
+          for (const auto &cell : cell_iterators())
             {
               // check if this cell has active grandchildren. note
               // that we know that it is patch_level_1, i.e. if one of

From 59a3884d61e5257e003135b719d93abb97b649f9 Mon Sep 17 00:00:00 2001
From: Timo Heister 
Date: Fri, 1 Mar 2019 10:00:40 -0700
Subject: [PATCH 215/507] work around gcc 4.8.5 behavior in GridTools::Cache

fixes #7771
---
 source/grid/grid_tools_cache.cc | 11 +++++++++--
 1 file changed, 9 insertions(+), 2 deletions(-)

diff --git a/source/grid/grid_tools_cache.cc b/source/grid/grid_tools_cache.cc
index 52f664b01aec..d1098c69862d 100644
--- a/source/grid/grid_tools_cache.cc
+++ b/source/grid/grid_tools_cache.cc
@@ -167,9 +167,16 @@ namespace GridTools
         // TO DO: the locally owned portion of the domain
         // might consists of more separate pieces: a single
         // bounding box might not always be the best choice.
+
+        // Note: we create the local variable ptr here, because gcc 4.8.5
+        // fails to compile if we pass the variable directly.
         IteratorFilters::LocallyOwnedCell locally_owned_cell_predicate;
-        const BoundingBox       bbox =
-          GridTools::compute_bounding_box(*tria, locally_owned_cell_predicate);
+        std::function::active_cell_iterator &)>
+          ptr(locally_owned_cell_predicate);
+
+        const BoundingBox bbox =
+          GridTools::compute_bounding_box(get_triangulation(), ptr);
 
 
         std::vector> bbox_v(1, bbox);

From 15dbfa671881458b13f56aafe9dc19d62d1cde63 Mon Sep 17 00:00:00 2001
From: Marc Fehling 
Date: Fri, 1 Mar 2019 19:17:29 +0100
Subject: [PATCH 216/507] hp::DoFHandler::ActiveFEIndicesTransfer: Separate
 work from memory management.

---
 source/hp/dof_handler.cc | 235 ++++++++++++++++++++++++---------------
 1 file changed, 144 insertions(+), 91 deletions(-)

diff --git a/source/hp/dof_handler.cc b/source/hp/dof_handler.cc
index ad53874b5bd5..891b1ef72351 100644
--- a/source/hp/dof_handler.cc
+++ b/source/hp/dof_handler.cc
@@ -1036,6 +1036,131 @@ namespace internal
                 ExcInternalError());
             }
         }
+
+
+
+        /**
+         * Collect all finite element indices on cells that will be affected by
+         * future refinement and coarsening. Further, prepare those indices to
+         * be distributed on on the updated triangulation later.
+         *
+         * On cells to be refined, the active_fe_index will be inherited to
+         * their childrean and thus will be stored as such.
+         *
+         * On cells to be coarsened, the active_fe_index on parent cells will be
+         * determined by the least dominating finite element of its children. We
+         * will thus assign the corresponding fe_index to the parent cell. See
+         * documentation of
+         * FECollection::find_least_dominating_fe_in_collection() for further
+         * information.
+         */
+        template 
+        static void
+        collect_fe_indices_on_cells_to_be_refined(
+          dealii::hp::DoFHandler &dof_handler)
+        {
+          const auto &fe_transfer = dof_handler.active_fe_index_transfer;
+
+          for (const auto &cell : dof_handler.active_cell_iterators())
+            if (cell->is_locally_owned())
+              {
+                if (cell->refine_flag_set())
+                  {
+                    // Store the active_fe_index of each cell that will be
+                    // refined to and distribute it later on its children.
+                    fe_transfer->refined_cells_fe_index.insert(
+                      {cell, cell->active_fe_index()});
+                  }
+                else if (cell->coarsen_flag_set())
+                  {
+                    // From all cells that will be coarsened, determine their
+                    // parent and calculate its proper active_fe_index, so that
+                    // it can be set after refinement. But first, check if that
+                    // particular cell has a parent at all.
+                    Assert(cell->level() > 0, ExcInternalError());
+                    const auto &parent = cell->parent();
+                    // Check if the active_fe_index for the current cell has
+                    // been determined already.
+                    if (fe_transfer->coarsened_cells_fe_index.find(parent) ==
+                        fe_transfer->coarsened_cells_fe_index.end())
+                      {
+                        std::set fe_indices_children;
+                        for (unsigned int child_index = 0;
+                             child_index < parent->n_children();
+                             ++child_index)
+                          {
+                            Assert(parent->child(child_index)->active(),
+                                   ExcInternalError());
+
+                            fe_indices_children.insert(
+                              parent->child(child_index)->active_fe_index());
+                          }
+
+                        const unsigned int fe_index =
+                          dof_handler.fe_collection
+                            .find_least_dominating_fe_in_collection(
+                              fe_indices_children, /*codim=*/0);
+
+                        Assert(
+                          fe_index != numbers::invalid_unsigned_int,
+                          ExcMessage(
+                            "No FiniteElement has been found in your FECollection "
+                            "that dominates all children of a cell you are trying "
+                            "to coarsen!"));
+
+                        fe_transfer->coarsened_cells_fe_index.insert(
+                          {parent, fe_index});
+                      }
+                  }
+              }
+        }
+
+
+
+        /**
+         * Distribute active finite element indices that have been previously
+         * prepared in collect_fe_indices_on_cells_to_be_refined().
+         */
+        template 
+        static void
+        distribute_fe_indices_on_refined_cells(
+          dealii::hp::DoFHandler &dof_handler)
+        {
+          const auto &fe_transfer = dof_handler.active_fe_index_transfer;
+
+          // Distribute active_fe_indices from all refined cells on their
+          // respective children.
+          for (const auto &pair : fe_transfer->refined_cells_fe_index)
+            {
+              const auto &parent = pair.first;
+
+              for (unsigned int child_index = 0;
+                   child_index < parent->n_children();
+                   ++child_index)
+                {
+                  const auto &child = parent->child(child_index);
+
+                  if (child->is_locally_owned())
+                    {
+                      Assert(child->active(), ExcInternalError());
+                      child->set_active_fe_index(pair.second);
+                    }
+                }
+            }
+
+          // Set active_fe_indices on coarsened cells that have been determined
+          // before the actual coarsening happened.
+          for (const auto &pair : fe_transfer->coarsened_cells_fe_index)
+            {
+              const auto &cell = pair.first;
+
+              if (cell->is_locally_owned())
+                {
+                  Assert(cell->active(), ExcInternalError());
+                  cell->set_active_fe_index(pair.second);
+                }
+            }
+        }
       };
     } // namespace DoFHandlerImplementation
   }   // namespace hp
@@ -1787,60 +1912,8 @@ namespace hp
         active_fe_index_transfer =
           std_cxx14::make_unique();
 
-        // Store active_fe_index information for all cells that will be
-        // affected by refinement/coarsening.
-        for (const auto &cell : active_cell_iterators())
-          if (cell->is_locally_owned())
-            {
-              if (cell->refine_flag_set())
-                {
-                  // Store the active_fe_index of each cell that will be refined
-                  // to and distribute it later on its children.
-                  active_fe_index_transfer->refined_cells_fe_index.insert(
-                    {cell, cell->active_fe_index()});
-                }
-              else if (cell->coarsen_flag_set())
-                {
-                  // From all cells that will be coarsened, determine their
-                  // parent and calculate its proper active_fe_index, so that it
-                  // can be set after refinement. But first, check if that
-                  // particular cell has a parent at all.
-                  Assert(cell->level() > 0, ExcInternalError());
-                  const auto &parent = cell->parent();
-                  // Check if the active_fe_index for the current cell has been
-                  // determined already.
-                  if (active_fe_index_transfer->coarsened_cells_fe_index.find(
-                        parent) ==
-                      active_fe_index_transfer->coarsened_cells_fe_index.end())
-                    {
-                      std::set fe_indices_children;
-                      for (unsigned int child_index = 0;
-                           child_index < parent->n_children();
-                           ++child_index)
-                        {
-                          Assert(parent->child(child_index)->active(),
-                                 ExcInternalError());
-
-                          fe_indices_children.insert(
-                            parent->child(child_index)->active_fe_index());
-                        }
-
-                      const unsigned int fe_index =
-                        fe_collection.find_least_dominating_fe_in_collection(
-                          fe_indices_children, /*codim=*/0);
-
-                      Assert(
-                        fe_index != numbers::invalid_unsigned_int,
-                        ExcMessage(
-                          "No FiniteElement has been found in your FECollection "
-                          "that dominates all children of a cell you are trying "
-                          "to coarsen!"));
-
-                      active_fe_index_transfer->coarsened_cells_fe_index.insert(
-                        {parent, fe_index});
-                    }
-                }
-            }
+        dealii::internal::hp::DoFHandlerImplementation::Implementation::
+          collect_fe_indices_on_cells_to_be_refined(*this);
       }
   }
 
@@ -1859,6 +1932,9 @@ namespace hp
       {
         Assert(active_fe_index_transfer == nullptr, ExcInternalError());
 
+        active_fe_index_transfer =
+          std_cxx14::make_unique();
+
         // If the underlying shared::Tria allows artificial cells,
         // then save the current set of subdomain ids, and set
         // subdomain ids to the "true" owner of each cell. We later
@@ -1890,7 +1966,8 @@ namespace hp
           }
 
         // Now do what we would do in the sequential case.
-        pre_active_fe_index_transfer();
+        dealii::internal::hp::DoFHandlerImplementation::Implementation::
+          collect_fe_indices_on_cells_to_be_refined(*this);
 
         // Finally, restore current subdomain_ids.
         if (shared_tria->with_artificial_cells())
@@ -1921,8 +1998,12 @@ namespace hp
       {
         Assert(active_fe_index_transfer == nullptr, ExcInternalError());
 
+        active_fe_index_transfer =
+          std_cxx14::make_unique();
+
         // First, do what we would do in the sequential case.
-        pre_active_fe_index_transfer();
+        dealii::internal::hp::DoFHandlerImplementation::Implementation::
+          collect_fe_indices_on_cells_to_be_refined(*this);
 
         // If we work on a p::d::Triangulation, we have to transfer all
         // active_fe_indices since ownership of cells may change. We will
@@ -1983,40 +2064,8 @@ namespace hp
         // and we can re-use our previously gathered information from the
         // container.
 
-        // Distribute active_fe_indices from all refined cells on their
-        // respective children.
-        for (const auto &pair :
-             active_fe_index_transfer->refined_cells_fe_index)
-          {
-            const cell_iterator &parent = pair.first;
-
-            for (unsigned int child_index = 0;
-                 child_index < parent->n_children();
-                 ++child_index)
-              {
-                const cell_iterator child = parent->child(child_index);
-
-                if (child->is_locally_owned())
-                  {
-                    Assert(child->active(), ExcInternalError());
-                    child->set_active_fe_index(pair.second);
-                  }
-              }
-          }
-
-        // Set active_fe_indices on coarsened cells that have been determined
-        // before the actual coarsening happened.
-        for (const auto &pair :
-             active_fe_index_transfer->coarsened_cells_fe_index)
-          {
-            const cell_iterator &cell = pair.first;
-
-            if (cell->is_locally_owned())
-              {
-                Assert(cell->active(), ExcInternalError());
-                cell->set_active_fe_index(pair.second);
-              }
-          }
+        dealii::internal::hp::DoFHandlerImplementation::Implementation::
+          distribute_fe_indices_on_refined_cells(*this);
 
         // Free memory.
         active_fe_index_transfer.reset();
@@ -2039,13 +2088,17 @@ namespace hp
         Assert(active_fe_index_transfer != nullptr, ExcInternalError());
 
         // Do what we normally do in the sequential case.
-        post_active_fe_index_transfer();
+        dealii::internal::hp::DoFHandlerImplementation::Implementation::
+          distribute_fe_indices_on_refined_cells(*this);
 
         // We have to distribute the information about active_fe_indices
         // on all processors, if a parallel::shared::Triangulation
         // has been used.
         dealii::internal::hp::DoFHandlerImplementation::Implementation::
           communicate_active_fe_indices(*this);
+
+        // Free memory.
+        active_fe_index_transfer.reset();
       }
 #endif
   }

From 92951fa7959b8a6b53d40b61516b304068023bcc Mon Sep 17 00:00:00 2001
From: Daniel Arndt 
Date: Sat, 2 Mar 2019 17:16:12 +0100
Subject: [PATCH 217/507] Document the execution space some more

---
 include/deal.II/lac/trilinos_tpetra_vector.h | 17 ++++++++++++-----
 1 file changed, 12 insertions(+), 5 deletions(-)

diff --git a/include/deal.II/lac/trilinos_tpetra_vector.h b/include/deal.II/lac/trilinos_tpetra_vector.h
index 35e31cc92eb1..69303e228403 100644
--- a/include/deal.II/lac/trilinos_tpetra_vector.h
+++ b/include/deal.II/lac/trilinos_tpetra_vector.h
@@ -54,11 +54,18 @@ namespace LinearAlgebra
      * LinearAlgebra::VectorSpaceVector class and requires Trilinos to be
      * compiled with MPI support.
      *
-     * Tpetra uses Kokkos for thread-parallelism. In case Trilinos was
-     * configured with CUDA support, this class stores the values in unified
-     * virtual memory space and performs its action on the GPU. In particular,
-     * there is no need for manually synchronizing memory between host and
-     * device.
+     * Tpetra uses Kokkos for thread-parallelism and chooses the execution and
+     * memory space automatically depending on Kokkos configuration. The
+     * priority is ranked from highest to lowest:
+     * - Kokkos::Cuda
+     * - Kokkos::OpenMP
+     * - Kokkos::Threads
+     * - Kokkos::Serial
+     *
+     * In case Kokkos was configured with CUDA support, this class stores the
+     * values in unified virtual memory space and performs its action on the
+     * GPU. In particular, there is no need for manually synchronizing memory
+     * between host and device.
      *
      * @ingroup TrilinosWrappers
      * @ingroup Vectors

From 4d60dc9831cc1f6be761e077d4cdaafd8a3d9051 Mon Sep 17 00:00:00 2001
From: Daniel Arndt 
Date: Sat, 2 Mar 2019 21:10:24 +0100
Subject: [PATCH 218/507] Fix inteference if material_id with the manifold
 object in the codimension case

---
 doc/news/changes/minor/20190302ArndtStark     |  4 ++
 source/grid/tria.cc                           | 48 +----------------
 tests/codim_one/mesh_bug_02.cc                | 53 +++++++++++++++++++
 tests/codim_one/mesh_bug_02.output            | 48 +++++++++++++++++
 tests/opencascade/circle_normal_projection.cc |  3 +-
 .../circle_normal_projection.output           | 32 +++++------
 .../interpolation_curve_boundary.cc           |  3 +-
 .../interpolation_curve_boundary.output       | 32 +++++------
 tests/serialization/triangulation_01.output   |  4 +-
 tests/serialization/triangulation_02.output   |  4 +-
 10 files changed, 147 insertions(+), 84 deletions(-)
 create mode 100644 doc/news/changes/minor/20190302ArndtStark
 create mode 100644 tests/codim_one/mesh_bug_02.cc
 create mode 100644 tests/codim_one/mesh_bug_02.output

diff --git a/doc/news/changes/minor/20190302ArndtStark b/doc/news/changes/minor/20190302ArndtStark
new file mode 100644
index 000000000000..5b720d590c1b
--- /dev/null
+++ b/doc/news/changes/minor/20190302ArndtStark
@@ -0,0 +1,4 @@
+Fixed: CellAccessor::material_id interfered with the manifold object
+for refining the mesh in case its dimension was less than the space dimension.
+
    
+(Daniel Arndt, Sebastian Stark, 2019/03/02)
diff --git a/source/grid/tria.cc b/source/grid/tria.cc
index b3c515621858..40d171cf074d 100644
--- a/source/grid/tria.cc
+++ b/source/grid/tria.cc
@@ -4984,29 +4984,7 @@ namespace internal
                           typename Triangulation::line_iterator
                             line = cell->line(line_no);
                           if (line->has_children() == false)
-                            {
-                              line->set_user_flag();
-                              // TODO[WB]: we overwrite the user_index here
-                              // because we later on need
-                              // to find out which boundary object we have to
-                              // ask to refine this line. we can't use the
-                              // boundary_id field because that can only be used
-                              // for lines at the boundary of the domain, but we
-                              // also need a domain description for interior
-                              // lines in the codim-1 case
-                              if (spacedim > dim)
-                                {
-                                  if (line->at_boundary())
-                                    // if possible honor boundary
-                                    // indicator
-                                    line->set_user_index(line->boundary_id());
-                                  else
-                                    // otherwise take manifold
-                                    // description from the adjacent
-                                    // cell
-                                    line->set_user_index(cell->material_id());
-                                }
-                            }
+                            line->set_user_flag();
                         }
                     }
                 }
@@ -5098,29 +5076,7 @@ namespace internal
                     "Internal error: During refinement, the triangulation wants to access an element of the 'vertices' array but it turns out that the array is not large enough."));
                 triangulation.vertices_used[next_unused_vertex] = true;
 
-                if (spacedim == dim)
-                  {
-                    // for the case of a domain in an
-                    // equal-dimensional space we only have to treat
-                    // boundary lines differently; for interior
-                    // lines we can compute the midpoint as the mean
-                    // of the two vertices: if (line->at_boundary())
-                    triangulation.vertices[next_unused_vertex] =
-                      line->center(true);
-                  }
-                else
-                  // however, if spacedim>dim, we always have to ask
-                  // the boundary object for its answer. We use the
-                  // same object of the cell (which was stored in
-                  // line->user_index() before) unless a manifold_id
-                  // has been set on this very line.
-                  if (line->manifold_id() == numbers::flat_manifold_id)
-                  triangulation.vertices[next_unused_vertex] =
-                    triangulation.get_manifold(line->user_index())
-                      .get_new_point_on_line(line);
-                else
-                  triangulation.vertices[next_unused_vertex] =
-                    line->center(true);
+                triangulation.vertices[next_unused_vertex] = line->center(true);
 
                 // now that we created the right point, make up the
                 // two child lines.  To this end, find a pair of
diff --git a/tests/codim_one/mesh_bug_02.cc b/tests/codim_one/mesh_bug_02.cc
new file mode 100644
index 000000000000..c723f44ad7ac
--- /dev/null
+++ b/tests/codim_one/mesh_bug_02.cc
@@ -0,0 +1,53 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2019 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+
+// Test that material_id and manifold_id don't interfere with each other.
+
+#include 
+#include 
+#include 
+
+#include "../tests.h"
+
+
+int
+main()
+{
+  initlog();
+
+  // triangulation is a single 2d square element embedded into 3d space
+  Triangulation<2, 3>   plane;
+  Point<3>              p1(1., 0., 0.);
+  Point<3>              p2(1., 1., 0.);
+  Point<3>              p3(1., 0., 1.);
+  Point<3>              p4(1., 1., 1.);
+  std::vector> vertices = {p1, p2, p3, p4};
+  GridGenerator::general_cell(plane, vertices);
+
+  // set the material id of the cell to 1
+  plane.begin_active()->set_material_id(1);
+
+  // now associate a spherical manifold object with manifold_id 1
+  //(this object isn't used in this minimal example, but there could
+  // in principle be other cells to which the manifold_id 1 is assigned)
+  SphericalManifold<2, 3> spherical_manifold;
+  plane.set_manifold(1, spherical_manifold);
+
+  plane.refine_global(2);
+
+  GridOut gridout;
+  gridout.write_msh(plane, deallog.get_file_stream());
+}
diff --git a/tests/codim_one/mesh_bug_02.output b/tests/codim_one/mesh_bug_02.output
new file mode 100644
index 000000000000..7cbab8ea52ca
--- /dev/null
+++ b/tests/codim_one/mesh_bug_02.output
@@ -0,0 +1,48 @@
+
+$NOD
+25
+1  1.00000 0.00000 0.00000
+2  1.00000 1.00000 0.00000
+3  1.00000 0.00000 1.00000
+4  1.00000 1.00000 1.00000
+5  1.00000 0.500000 0.00000
+6  1.00000 0.00000 0.500000
+7  1.00000 1.00000 0.500000
+8  1.00000 0.500000 1.00000
+9  1.00000 0.500000 0.500000
+10  1.00000 0.250000 0.00000
+11  1.00000 0.750000 0.00000
+12  1.00000 0.00000 0.250000
+13  1.00000 0.00000 0.750000
+14  1.00000 1.00000 0.250000
+15  1.00000 1.00000 0.750000
+16  1.00000 0.250000 1.00000
+17  1.00000 0.750000 1.00000
+18  1.00000 0.500000 0.250000
+19  1.00000 0.500000 0.750000
+20  1.00000 0.250000 0.500000
+21  1.00000 0.750000 0.500000
+22  1.00000 0.250000 0.250000
+23  1.00000 0.750000 0.250000
+24  1.00000 0.250000 0.750000
+25  1.00000 0.750000 0.750000
+$ENDNOD
+$ELM
+16
+1 3 1 0 4 1 10 22 12 
+2 3 1 0 4 10 5 18 22 
+3 3 1 0 4 12 22 20 6 
+4 3 1 0 4 22 18 9 20 
+5 3 1 0 4 5 11 23 18 
+6 3 1 0 4 11 2 14 23 
+7 3 1 0 4 18 23 21 9 
+8 3 1 0 4 23 14 7 21 
+9 3 1 0 4 6 20 24 13 
+10 3 1 0 4 20 9 19 24 
+11 3 1 0 4 13 24 16 3 
+12 3 1 0 4 24 19 8 16 
+13 3 1 0 4 9 21 25 19 
+14 3 1 0 4 21 7 15 25 
+15 3 1 0 4 19 25 17 8 
+16 3 1 0 4 25 15 4 17 
+$ENDELM
diff --git a/tests/opencascade/circle_normal_projection.cc b/tests/opencascade/circle_normal_projection.cc
index 1df8c677ccc3..77a2559403af 100644
--- a/tests/opencascade/circle_normal_projection.cc
+++ b/tests/opencascade/circle_normal_projection.cc
@@ -73,12 +73,13 @@ main()
   GridGenerator::hyper_cube(tria);
 
   // Set the exterior boundary
+  tria.set_all_manifold_ids(0);
   tria.set_manifold(0, boundary_line);
 
   // This is here to ignore the
   // points created in the interior
   // of the face.
-  tria.begin()->set_material_id(1);
+  tria.begin()->set_manifold_id(1);
 
   // We refine twice, and expect the
   // outer points to end up on the
diff --git a/tests/opencascade/circle_normal_projection.output b/tests/opencascade/circle_normal_projection.output
index 3291307f5a02..7b05605db020 100644
--- a/tests/opencascade/circle_normal_projection.output
+++ b/tests/opencascade/circle_normal_projection.output
@@ -25,19 +25,19 @@
 23  0.810567 0.189433 0.00000
 24  0.189433 0.810567 0.00000
 25  0.810567 0.810567 0.00000
-1 1 quad    1 10 22 12 
-2 1 quad    10 5 18 22 
-3 1 quad    12 22 20 6 
-4 1 quad    22 18 9 20 
-5 1 quad    5 11 23 18 
-6 1 quad    11 2 14 23 
-7 1 quad    18 23 21 9 
-8 1 quad    23 14 7 21 
-9 1 quad    6 20 24 13 
-10 1 quad    20 9 19 24 
-11 1 quad    13 24 16 3 
-12 1 quad    24 19 8 16 
-13 1 quad    9 21 25 19 
-14 1 quad    21 7 15 25 
-15 1 quad    19 25 17 8 
-16 1 quad    25 15 4 17 
+1 0 quad    1 10 22 12 
+2 0 quad    10 5 18 22 
+3 0 quad    12 22 20 6 
+4 0 quad    22 18 9 20 
+5 0 quad    5 11 23 18 
+6 0 quad    11 2 14 23 
+7 0 quad    18 23 21 9 
+8 0 quad    23 14 7 21 
+9 0 quad    6 20 24 13 
+10 0 quad    20 9 19 24 
+11 0 quad    13 24 16 3 
+12 0 quad    24 19 8 16 
+13 0 quad    9 21 25 19 
+14 0 quad    21 7 15 25 
+15 0 quad    19 25 17 8 
+16 0 quad    25 15 4 17 
diff --git a/tests/opencascade/interpolation_curve_boundary.cc b/tests/opencascade/interpolation_curve_boundary.cc
index bbdaf50e46bf..55e4ec1c7d46 100644
--- a/tests/opencascade/interpolation_curve_boundary.cc
+++ b/tests/opencascade/interpolation_curve_boundary.cc
@@ -63,11 +63,12 @@ main()
   GridGenerator::hyper_cube(tria);
 
   // Set the exterior boundary
+  tria.set_all_manifold_ids(0);
   tria.set_manifold(0, boundary_line);
 
   // This is here to ignore the points created in the interior of the
   // face.
-  tria.begin()->set_material_id(1);
+  tria.begin()->set_manifold_id(1);
 
   // We refine twice, and expect the outer points to end up on a
   // smooth curve interpolating the square vertices.
diff --git a/tests/opencascade/interpolation_curve_boundary.output b/tests/opencascade/interpolation_curve_boundary.output
index 894bc2686080..f2609d8f092d 100644
--- a/tests/opencascade/interpolation_curve_boundary.output
+++ b/tests/opencascade/interpolation_curve_boundary.output
@@ -29,20 +29,20 @@ $NOD
 $ENDNOD
 $ELM
 16
-1 3 1 0 4 1 10 22 12 
-2 3 1 0 4 10 5 18 22 
-3 3 1 0 4 12 22 20 6 
-4 3 1 0 4 22 18 9 20 
-5 3 1 0 4 5 11 23 18 
-6 3 1 0 4 11 2 14 23 
-7 3 1 0 4 18 23 21 9 
-8 3 1 0 4 23 14 7 21 
-9 3 1 0 4 6 20 24 13 
-10 3 1 0 4 20 9 19 24 
-11 3 1 0 4 13 24 16 3 
-12 3 1 0 4 24 19 8 16 
-13 3 1 0 4 9 21 25 19 
-14 3 1 0 4 21 7 15 25 
-15 3 1 0 4 19 25 17 8 
-16 3 1 0 4 25 15 4 17 
+1 3 0 0 4 1 10 22 12 
+2 3 0 0 4 10 5 18 22 
+3 3 0 0 4 12 22 20 6 
+4 3 0 0 4 22 18 9 20 
+5 3 0 0 4 5 11 23 18 
+6 3 0 0 4 11 2 14 23 
+7 3 0 0 4 18 23 21 9 
+8 3 0 0 4 23 14 7 21 
+9 3 0 0 4 6 20 24 13 
+10 3 0 0 4 20 9 19 24 
+11 3 0 0 4 13 24 16 3 
+12 3 0 0 4 24 19 8 16 
+13 3 0 0 4 9 21 25 19 
+14 3 0 0 4 21 7 15 25 
+15 3 0 0 4 19 25 17 8 
+16 3 0 0 4 25 15 4 17 
 $ENDELM
diff --git a/tests/serialization/triangulation_01.output b/tests/serialization/triangulation_01.output
index 9808705bb2c7..7a0fb80a1518 100644
--- a/tests/serialization/triangulation_01.output
+++ b/tests/serialization/triangulation_01.output
@@ -23,12 +23,12 @@ DEAL::0 0 0 3 0 0 2 1 0
 0 1 0 0 1 0 0 0 4 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 1 0 0 1 0 0 1 0 -1 1 1 0 0 0 0 1 0 0 0 4 1 2 0 3 2 0 0 2 0 0 1 0 0 0 3 1 1 1 0 0 0 1 0 0 0 0 1 0 4294967295 0 0 1 0 0 1 0 0 0 0 0 2
 1 4 0 0 0 0 0 4 0 0 0 0 16 0 -1 -1 1 1 -1 -1 1 2 1 0 -1 -1 -1 -1 1 3 -1 -1 1 3 1 0 -1 -1 1 2 -1 -1 1 1 -1 -1 4 0 0 0 0 0 4 0 0 0 0 0 2 0 0 0 4 1 1 1 1 4 0 4 6 12 4 14 4 12 8 5 15 4 7 13 14 10 4 13 9 15 11 8 0 0 2 4 6 8 10 12 14 4 0 3 3 3 3 4 1 1 1 1 4 0 0 0 0 4 0 0 0 0 0 4 0 4294967295 4294967295 4294967295 4294967295 3 0 1 4 0 0 0 0 0 0 2
 2 16 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 64 0 -1 -1 2 1 -1 -1 2 2 2 0 2 4 -1 -1 2 3 -1 -1 2 3 2 0 2 8 2 2 2 6 2 1 2 9 2 1 2 5 -1 -1 2 6 2 4 -1 -1 -1 -1 2 7 2 3 2 7 2 4 2 12 2 6 -1 -1 2 5 2 13 -1 -1 2 9 2 2 2 10 2 8 2 12 2 3 2 11 -1 -1 2 11 2 8 -1 -1 2 10 2 14 2 9 -1 -1 2 9 2 13 2 6 2 14 2 12 -1 -1 2 7 2 15 2 11 2 15 2 12 -1 -1 2 14 -1 -1 2 13 -1 -1 16 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 0 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 8 0 0 0 1 1 2 2 3 3 16 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 0 4 20 40 16 42 4 40 32 17 43 4 21 41 42 36 4 41 33 43 37 4 32 44 18 46 4 44 24 19 47 4 33 45 46 38 4 45 25 47 39 4 22 48 36 50 4 48 34 37 51 4 23 49 50 28 4 49 35 51 29 4 34 52 38 54 4 52 26 39 55 4 35 53 54 30 4 53 27 55 31 32 0 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 16 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 0 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 15 0 1 16 0 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 0 19 1 0
-3 0 0 0 0 56 0 0 0 2 0 1 2 0 2 2 1 3 2 2 3 2 0 4 2 4 1 2 0 5 2 5 2 2 1 6 2 6 3 2 2 7 2 7 3 2 4 8 2 8 7 2 5 8 2 8 6 2 0 9 2 9 4 2 4 10 2 10 1 2 0 11 2 11 5 2 5 12 2 12 2 2 1 13 2 13 6 2 6 14 2 14 3 2 2 15 2 15 7 2 7 16 2 16 3 2 4 17 2 17 8 2 8 18 2 18 7 2 5 19 2 19 8 2 8 20 2 20 6 2 9 21 2 21 19 2 11 21 2 21 17 2 10 22 2 22 20 2 17 22 2 22 13 2 19 23 2 23 15 2 12 23 2 23 18 2 20 24 2 24 16 2 18 24 2 24 14 56 0 4 6 8 10 16 18 20 22 24 26 28 30 32 34 36 38 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 56 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 56 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 56 0 0 0 42 42 42 42 42 42 42 42 42 42 42 42 4294967295 4294967295 4294967295 4294967295 42 42 42 42 42 42 42 42 42 42 42 42 42 42 42 42 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 56 0 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 55 0 1 0 0 56 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 25 0 0 0 0 0 3 0 0 0.00000000000000000e+00 0.00000000000000000e+00 0.00000000000000000e+00 3 1.00000000000000000e+00 0.00000000000000000e+00 0.00000000000000000e+00 3 0.00000000000000000e+00 1.00000000000000000e+00 0.00000000000000000e+00 3 1.00000000000000000e+00 1.00000000000000000e+00 0.00000000000000000e+00 3 5.00000000000000000e-01 0.00000000000000000e+00 0.00000000000000000e+00 3 0.00000000000000000e+00 5.00000000000000000e-01 0.00000000000000000e+00 3 1.00000000000000000e+00 5.00000000000000000e-01 0.00000000000000000e+00 3 5.00000000000000000e-01 1.00000000000000000e+00 0.00000000000000000e+00 3 5.00000000000000000e-01 5.00000000000000000e-01 0.00000000000000000e+00 3 2.50000000000000000e-01 0.00000000000000000e+00 0.00000000000000000e+00 3 7.50000000000000000e-01 0.00000000000000000e+00 0.00000000000000000e+00 3 0.00000000000000000e+00 2.50000000000000000e-01 0.00000000000000000e+00 3 0.00000000000000000e+00 7.50000000000000000e-01 0.00000000000000000e+00 3 1.00000000000000000e+00 2.50000000000000000e-01 0.00000000000000000e+00 3 1.00000000000000000e+00 7.50000000000000000e-01 0.00000000000000000e+00 3 2.50000000000000000e-01 1.00000000000000000e+00 0.00000000000000000e+00 3 7.50000000000000000e-01 1.00000000000000000e+00 0.00000000000000000e+00 3 5.00000000000000000e-01 2.50000000000000000e-01 0.00000000000000000e+00 3 5.00000000000000000e-01 7.50000000000000000e-01 0.00000000000000000e+00 3 2.50000000000000000e-01 5.00000000000000000e-01 0.00000000000000000e+00 3 7.50000000000000000e-01 5.00000000000000000e-01 0.00000000000000000e+00 3 2.50000000000000000e-01 2.50000000000000000e-01 0.00000000000000000e+00 3 7.50000000000000000e-01 2.50000000000000000e-01 0.00000000000000000e+00 3 2.50000000000000000e-01 7.50000000000000000e-01 0.00000000000000000e+00 3 7.50000000000000000e-01 7.50000000000000000e-01 0.00000000000000000e+00 25 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 3 56 0 0 40 0 0 21 3 0 1 4 16 16 3 0 0 0 16 0
+3 0 0 0 0 56 0 0 0 2 0 1 2 0 2 2 1 3 2 2 3 2 0 4 2 4 1 2 0 5 2 5 2 2 1 6 2 6 3 2 2 7 2 7 3 2 4 8 2 8 7 2 5 8 2 8 6 2 0 9 2 9 4 2 4 10 2 10 1 2 0 11 2 11 5 2 5 12 2 12 2 2 1 13 2 13 6 2 6 14 2 14 3 2 2 15 2 15 7 2 7 16 2 16 3 2 4 17 2 17 8 2 8 18 2 18 7 2 5 19 2 19 8 2 8 20 2 20 6 2 9 21 2 21 19 2 11 21 2 21 17 2 10 22 2 22 20 2 17 22 2 22 13 2 19 23 2 23 15 2 12 23 2 23 18 2 20 24 2 24 16 2 18 24 2 24 14 56 0 4 6 8 10 16 18 20 22 24 26 28 30 32 34 36 38 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 0 0 0 0 56 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 56 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 56 0 0 0 42 42 42 42 42 42 42 42 42 42 42 42 4294967295 4294967295 4294967295 4294967295 42 42 42 42 42 42 42 42 42 42 42 42 42 42 42 42 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 56 0 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 55 0 1 0 0 56 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 25 0 0 0 0 0 3 0 0 0.00000000000000000e+00 0.00000000000000000e+00 0.00000000000000000e+00 3 1.00000000000000000e+00 0.00000000000000000e+00 0.00000000000000000e+00 3 0.00000000000000000e+00 1.00000000000000000e+00 0.00000000000000000e+00 3 1.00000000000000000e+00 1.00000000000000000e+00 0.00000000000000000e+00 3 5.00000000000000000e-01 0.00000000000000000e+00 0.00000000000000000e+00 3 0.00000000000000000e+00 5.00000000000000000e-01 0.00000000000000000e+00 3 1.00000000000000000e+00 5.00000000000000000e-01 0.00000000000000000e+00 3 5.00000000000000000e-01 1.00000000000000000e+00 0.00000000000000000e+00 3 5.00000000000000000e-01 5.00000000000000000e-01 0.00000000000000000e+00 3 2.50000000000000000e-01 0.00000000000000000e+00 0.00000000000000000e+00 3 7.50000000000000000e-01 0.00000000000000000e+00 0.00000000000000000e+00 3 0.00000000000000000e+00 2.50000000000000000e-01 0.00000000000000000e+00 3 0.00000000000000000e+00 7.50000000000000000e-01 0.00000000000000000e+00 3 1.00000000000000000e+00 2.50000000000000000e-01 0.00000000000000000e+00 3 1.00000000000000000e+00 7.50000000000000000e-01 0.00000000000000000e+00 3 2.50000000000000000e-01 1.00000000000000000e+00 0.00000000000000000e+00 3 7.50000000000000000e-01 1.00000000000000000e+00 0.00000000000000000e+00 3 5.00000000000000000e-01 2.50000000000000000e-01 0.00000000000000000e+00 3 5.00000000000000000e-01 7.50000000000000000e-01 0.00000000000000000e+00 3 2.50000000000000000e-01 5.00000000000000000e-01 0.00000000000000000e+00 3 7.50000000000000000e-01 5.00000000000000000e-01 0.00000000000000000e+00 3 2.50000000000000000e-01 2.50000000000000000e-01 0.00000000000000000e+00 3 7.50000000000000000e-01 2.50000000000000000e-01 0.00000000000000000e+00 3 2.50000000000000000e-01 7.50000000000000000e-01 0.00000000000000000e+00 3 7.50000000000000000e-01 7.50000000000000000e-01 0.00000000000000000e+00 25 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 3 56 0 0 40 0 0 21 3 0 1 4 16 16 3 0 0 0 16 0
 
 DEAL::0 0 0 3 0 0 2 1 0
 0 1 0 0 1 0 0 0 6 0 0 0 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 -1 1 0 0 1 0 0 1 0 -1 0 0 0 0 0 1 0 0 0 6 2 3 0 4 1 5 4 0 0 2 4 6 0 0 1 0 0 0 7 1 1 1 0 0 0 1 0 0 0 0 1 0 4294967295 0 0 0 0 0 1 0 0 0 0 0 6 1 1 1 1 1 1 6 0 0 0 0 0 0 6 0 0 0 0 0 0 2
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 DEAL::OK
diff --git a/tests/serialization/triangulation_02.output b/tests/serialization/triangulation_02.output
index 4b31b19f3592..a88c705ebd68 100644
--- a/tests/serialization/triangulation_02.output
+++ b/tests/serialization/triangulation_02.output
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0.00000000000000000e+00 0.00000000000000000e+00 2.50000000000000000e-01 3 2.50000000000000000e-01 0.00000000000000000e+00 5.00000000000000000e-01 3 5.00000000000000000e-01 0.00000000000000000e+00 2.50000000000000000e-01 3 5.00000000000000000e-01 2.50000000000000000e-01 0.00000000000000000e+00 3 2.50000000000000000e-01 5.00000000000000000e-01 0.00000000000000000e+00 3 0.00000000000000000e+00 5.00000000000000000e-01 2.50000000000000000e-01 3 0.00000000000000000e+00 2.50000000000000000e-01 5.00000000000000000e-01 3 5.00000000000000000e-01 5.00000000000000000e-01 2.50000000000000000e-01 3 2.50000000000000000e-01 5.00000000000000000e-01 5.00000000000000000e-01 3 5.00000000000000000e-01 2.50000000000000000e-01 5.00000000000000000e-01 3 2.50000000000000000e-01 0.00000000000000000e+00 2.50000000000000000e-01 3 2.50000000000000000e-01 2.50000000000000000e-01 0.00000000000000000e+00 3 0.00000000000000000e+00 2.50000000000000000e-01 2.50000000000000000e-01 3 2.50000000000000000e-01 2.50000000000000000e-01 5.00000000000000000e-01 3 2.50000000000000000e-01 5.00000000000000000e-01 2.50000000000000000e-01 3 5.00000000000000000e-01 2.50000000000000000e-01 2.50000000000000000e-01 3 2.50000000000000000e-01 2.50000000000000000e-01 2.50000000000000000e-01 3 0.00000000000000000e+00 7.50000000000000000e-01 1.00000000000000000e+00 3 1.00000000000000000e+00 2.50000000000000000e-01 1.00000000000000000e+00 3 1.00000000000000000e+00 7.50000000000000000e-01 1.00000000000000000e+00 3 2.50000000000000000e-01 1.00000000000000000e+00 1.00000000000000000e+00 3 7.50000000000000000e-01 1.00000000000000000e+00 1.00000000000000000e+00 3 2.50000000000000000e-01 0.00000000000000000e+00 5.00000000000000000e-01 3 7.50000000000000000e-01 0.00000000000000000e+00 5.00000000000000000e-01 3 5.00000000000000000e-01 0.00000000000000000e+00 2.50000000000000000e-01 3 5.00000000000000000e-01 0.00000000000000000e+00 7.50000000000000000e-01 3 5.00000000000000000e-01 2.50000000000000000e-01 0.00000000000000000e+00 3 5.00000000000000000e-01 7.50000000000000000e-01 0.00000000000000000e+00 3 2.50000000000000000e-01 5.00000000000000000e-01 0.00000000000000000e+00 3 7.50000000000000000e-01 5.00000000000000000e-01 0.00000000000000000e+00 3 0.00000000000000000e+00 5.00000000000000000e-01 2.50000000000000000e-01 3 0.00000000000000000e+00 5.00000000000000000e-01 7.50000000000000000e-01 3 0.00000000000000000e+00 2.50000000000000000e-01 5.00000000000000000e-01 3 0.00000000000000000e+00 7.50000000000000000e-01 5.00000000000000000e-01 3 1.00000000000000000e+00 5.00000000000000000e-01 2.50000000000000000e-01 3 1.00000000000000000e+00 5.00000000000000000e-01 7.50000000000000000e-01 3 1.00000000000000000e+00 2.50000000000000000e-01 5.00000000000000000e-01 3 1.00000000000000000e+00 7.50000000000000000e-01 5.00000000000000000e-01 3 2.50000000000000000e-01 1.00000000000000000e+00 5.00000000000000000e-01 3 7.50000000000000000e-01 1.00000000000000000e+00 5.00000000000000000e-01 3 5.00000000000000000e-01 1.00000000000000000e+00 2.50000000000000000e-01 3 5.00000000000000000e-01 1.00000000000000000e+00 7.50000000000000000e-01 3 5.00000000000000000e-01 2.50000000000000000e-01 1.00000000000000000e+00 3 5.00000000000000000e-01 7.50000000000000000e-01 1.00000000000000000e+00 3 2.50000000000000000e-01 5.00000000000000000e-01 1.00000000000000000e+00 3 7.50000000000000000e-01 5.00000000000000000e-01 1.00000000000000000e+00 3 5.00000000000000000e-01 5.00000000000000000e-01 7.50000000000000000e-01 3 5.00000000000000000e-01 5.00000000000000000e-01 2.50000000000000000e-01 3 7.50000000000000000e-01 5.00000000000000000e-01 5.00000000000000000e-01 3 2.50000000000000000e-01 5.00000000000000000e-01 5.00000000000000000e-01 3 5.00000000000000000e-01 7.50000000000000000e-01 5.00000000000000000e-01 3 5.00000000000000000e-01 2.50000000000000000e-01 5.00000000000000000e-01 3 2.50000000000000000e-01 0.00000000000000000e+00 2.50000000000000000e-01 3 2.50000000000000000e-01 0.00000000000000000e+00 7.50000000000000000e-01 3 7.50000000000000000e-01 0.00000000000000000e+00 2.50000000000000000e-01 3 7.50000000000000000e-01 0.00000000000000000e+00 7.50000000000000000e-01 3 2.50000000000000000e-01 2.50000000000000000e-01 0.00000000000000000e+00 3 7.50000000000000000e-01 2.50000000000000000e-01 0.00000000000000000e+00 3 2.50000000000000000e-01 7.50000000000000000e-01 0.00000000000000000e+00 3 7.50000000000000000e-01 7.50000000000000000e-01 0.00000000000000000e+00 3 0.00000000000000000e+00 2.50000000000000000e-01 2.50000000000000000e-01 3 0.00000000000000000e+00 7.50000000000000000e-01 2.50000000000000000e-01 3 0.00000000000000000e+00 2.50000000000000000e-01 7.50000000000000000e-01 3 0.00000000000000000e+00 7.50000000000000000e-01 7.50000000000000000e-01 3 1.00000000000000000e+00 2.50000000000000000e-01 2.50000000000000000e-01 3 1.00000000000000000e+00 7.50000000000000000e-01 2.50000000000000000e-01 3 1.00000000000000000e+00 2.50000000000000000e-01 7.50000000000000000e-01 3 1.00000000000000000e+00 7.50000000000000000e-01 7.50000000000000000e-01 3 2.50000000000000000e-01 1.00000000000000000e+00 2.50000000000000000e-01 3 2.50000000000000000e-01 1.00000000000000000e+00 7.50000000000000000e-01 3 7.50000000000000000e-01 1.00000000000000000e+00 2.50000000000000000e-01 3 7.50000000000000000e-01 1.00000000000000000e+00 7.50000000000000000e-01 3 2.50000000000000000e-01 2.50000000000000000e-01 1.00000000000000000e+00 3 7.50000000000000000e-01 2.50000000000000000e-01 1.00000000000000000e+00 3 2.50000000000000000e-01 7.50000000000000000e-01 1.00000000000000000e+00 3 7.50000000000000000e-01 7.50000000000000000e-01 1.00000000000000000e+00 3 7.50000000000000000e-01 7.50000000000000000e-01 5.00000000000000000e-01 3 2.50000000000000000e-01 7.50000000000000000e-01 5.00000000000000000e-01 3 7.50000000000000000e-01 2.50000000000000000e-01 5.00000000000000000e-01 3 2.50000000000000000e-01 2.50000000000000000e-01 5.00000000000000000e-01 3 7.50000000000000000e-01 5.00000000000000000e-01 7.50000000000000000e-01 3 7.50000000000000000e-01 5.00000000000000000e-01 2.50000000000000000e-01 3 2.50000000000000000e-01 5.00000000000000000e-01 7.50000000000000000e-01 3 2.50000000000000000e-01 5.00000000000000000e-01 2.50000000000000000e-01 3 5.00000000000000000e-01 7.50000000000000000e-01 7.50000000000000000e-01 3 5.00000000000000000e-01 2.50000000000000000e-01 7.50000000000000000e-01 3 5.00000000000000000e-01 7.50000000000000000e-01 2.50000000000000000e-01 3 5.00000000000000000e-01 2.50000000000000000e-01 2.50000000000000000e-01 3 2.50000000000000000e-01 2.50000000000000000e-01 2.50000000000000000e-01 3 7.50000000000000000e-01 2.50000000000000000e-01 2.50000000000000000e-01 3 2.50000000000000000e-01 7.50000000000000000e-01 2.50000000000000000e-01 3 7.50000000000000000e-01 7.50000000000000000e-01 2.50000000000000000e-01 3 2.50000000000000000e-01 2.50000000000000000e-01 7.50000000000000000e-01 3 7.50000000000000000e-01 2.50000000000000000e-01 7.50000000000000000e-01 3 2.50000000000000000e-01 7.50000000000000000e-01 7.50000000000000000e-01 3 7.50000000000000000e-01 7.50000000000000000e-01 7.50000000000000000e-01 125 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 3 120 0 0 96 0 0 78 0 0 66 0 0 17 3 0 1 8 8 15 3 0 0 7 8 0
 
 DEAL::OK

From aa24d0d936d79aae2c32ed419442206c68f0e686 Mon Sep 17 00:00:00 2001
From: Daniel Arndt 
Date: Sun, 3 Mar 2019 14:42:25 +0100
Subject: [PATCH 219/507] Move the TODO

---
 source/grid/tria.cc | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/source/grid/tria.cc b/source/grid/tria.cc
index 40d171cf074d..8493ae39df86 100644
--- a/source/grid/tria.cc
+++ b/source/grid/tria.cc
@@ -4907,8 +4907,7 @@ namespace internal
                 }
         }
 
-
-        // first clear user flags and pointers of lines; we're going
+        // TODO[WB]: we clear user flags and pointers of lines; we're going
         // to use them to flag which lines need refinement
         for (typename Triangulation::line_iterator line =
                triangulation.begin_line();

From be4fcc0a2569e74269124835fdff6e14c3464d1f Mon Sep 17 00:00:00 2001
From: Marc Fehling 
Date: Tue, 26 Feb 2019 16:34:09 +0100
Subject: [PATCH 220/507] Added hierarchy to hp::FECollection.

---
 doc/doxygen/headers/hp.h               |  15 ++++
 doc/news/changes/minor/20190228Fehling |   7 ++
 include/deal.II/hp/fe_collection.h     | 118 ++++++++++++++++++++++++-
 source/hp/fe_collection.cc             |  68 ++++++++++++++
 tests/hp/fe_hierarchy.cc               |  61 +++++++++++++
 tests/hp/fe_hierarchy.output           |  11 +++
 6 files changed, 277 insertions(+), 3 deletions(-)
 create mode 100644 doc/news/changes/minor/20190228Fehling
 create mode 100644 tests/hp/fe_hierarchy.cc
 create mode 100644 tests/hp/fe_hierarchy.output

diff --git a/doc/doxygen/headers/hp.h b/doc/doxygen/headers/hp.h
index 5fceed9e248c..b9c69531681f 100644
--- a/doc/doxygen/headers/hp.h
+++ b/doc/doxygen/headers/hp.h
@@ -89,6 +89,21 @@
  * collection of mappings is used, the same holds for hp::MappingCollection
  * objects as well.
  *
+ * Whenever p adaptivity is considered in an hp finite element program,
+ * a hierarchy of finite elements needs to be established to determine
+ * succeeding finite elements for refinement and preceding ones for coarsening.
+ * Typically, this hierarchy considers how finite element spaces are nested:
+ * for example, a $Q_1$ element describes a sub-space of a $Q_2$ element,
+ * and so doing $p$ refinement usually means using a larger (more accurate)
+ * finite element space. In other words, the hierarchy of finite elements is built
+ * by considering whether some elements of the collection are sub- or
+ * super-spaces of others.
+ *
+ * By default, we assume that finite elements are stored in an ascending order
+ * based on their polynomial degree. If the order of elements differs,
+ * a corresponding hierarchy needs to be supplied to the collection via the
+ * hp::FECollection::set_hierarchy() member function.
+ *
  * @ingroup hp
  */
 
diff --git a/doc/news/changes/minor/20190228Fehling b/doc/news/changes/minor/20190228Fehling
new file mode 100644
index 000000000000..85c0089d88c7
--- /dev/null
+++ b/doc/news/changes/minor/20190228Fehling
@@ -0,0 +1,7 @@
+New: Hierarchy of finite elements in hp::FECollection objects. Get succeeding
+and preceding indices via hp::FECollection::next_in_hierarchy() and
+hp::FECollection::prev_in_hierarchy(). By default, a hierarchy corresponding
+to indices is established. Hierarchy can be overridden via
+hp::FECollection::set_hierarchy().
+
    
+(Marc Fehling, 2019/02/28)
diff --git a/include/deal.II/hp/fe_collection.h b/include/deal.II/hp/fe_collection.h
index a58bef7ea2dc..c4668b89dcc5 100644
--- a/include/deal.II/hp/fe_collection.h
+++ b/include/deal.II/hp/fe_collection.h
@@ -54,11 +54,53 @@ namespace hp
   class FECollection : public Subscriptor
   {
   public:
+    /**
+     * Whenever p adaptivity is considered in an hp finite element program,
+     * a hierarchy of finite elements needs to be established to determine
+     * succeeding finite elements for refinement and preceding ones for
+     * coarsening.
+     *
+     * In this struct, we supply a hierachy that is imposed on all FECollection
+     * objects by default.
+     */
+    struct DefaultHierarchy
+    {
+      /**
+       * Return the index succeeding @p fe_index in the @p fe_collection.
+       *
+       * Once the last element of the @p fe_collection is reached, there is no element on a higher level in
+       * the hierarchy and thus we return the last value.
+       */
+      static unsigned int
+      next_index(const typename hp::FECollection &fe_collection,
+                 const unsigned int                              fe_index)
+      {
+        return ((fe_index + 1) < fe_collection.size()) ? fe_index + 1 :
+                                                         fe_index;
+      }
+
+      /**
+       * Return the index preceding @p fe_index in the @p fe_collection.
+       *
+       * Once the first element of the @p fe_collection is reached, there is no element on a lower level in
+       * the hierarchy and thus we return the first value.
+       */
+      static unsigned int
+      previous_index(
+        const typename hp::FECollection &fe_collection,
+        const unsigned int                              fe_index)
+      {
+        (void)fe_collection;
+        return (fe_index > 0) ? fe_index - 1 : fe_index;
+      }
+    };
+
     /**
      * Default constructor. Leads to an empty collection that can later be
-     * filled using push_back().
+     * filled using push_back(). Establishes a hierarchy of finite elements
+     * corresponding to their index in the collection.
      */
-    FECollection() = default;
+    FECollection();
 
     /**
      * Conversion constructor. This constructor creates a FECollection from a
@@ -94,7 +136,7 @@ namespace hp
     /**
      * Move constructor.
      */
-    FECollection(FECollection &&) noexcept = default;
+    FECollection(FECollection &&) = default;
 
     /**
      * Move assignment operator.
@@ -371,6 +413,60 @@ namespace hp
     find_dominating_fe_in_subset(const std::set &fes,
                                  const unsigned int            codim = 0) const;
 
+    /**
+     * Set functions determining the hierarchy of finite elements, i.e. a
+     * function @p next that returns the index of the finite element following
+     * the given one, and a function @p prev returning the preceding one.
+     *
+     * Both functions expect an hp::FECollection to be passed along with a
+     * finite element index, on whose basis the new index will be found and
+     * returned.
+     *
+     * @note Both passed and returned indices have to be valid within the index
+     * range of this collection, i.e. within [0, size()).
+     */
+    void
+    set_hierarchy(const std::function &,
+                    const unsigned int)> &next,
+                  const std::function &,
+                    const unsigned int)> &prev);
+
+    /**
+     * Set the default hierarchy corresponding to the index of each finite
+     * element in the collection.
+     *
+     * This default hierarchy is established with functions
+     * DefaultHierarchy::next_index() and DefaultHierarchy::previous_index().
+     */
+    void
+    set_default_hierarchy();
+
+    /**
+     * Function returning the index of the finite element following the given
+     * @p fe_index in hierarchy.
+     *
+     * By default, the index succeeding @p fe_index will be returned. If @p fe_index
+     * already corresponds to the last index, the last index will be returned.
+     * A custom hierarchy can be supplied via the member function
+     * set_hierachy().
+     */
+    unsigned int
+    next_in_hierarchy(const unsigned int fe_index) const;
+
+    /**
+     * Function returning the index of the finite element preceding the given
+     * @p fe_index in hierarchy.
+     *
+     * By default, the index preceding @p fe_index will be returned. If @p fe_index
+     * already corresponds to the first index, the first index will be returned.
+     * A custom hierarchy can be supplied via the member function
+     * set_hierachy().
+     */
+    unsigned int
+    previous_in_hierarchy(const unsigned int fe_index) const;
+
     /**
      * Return a component mask with as many elements as this object has vector
      * components and of which exactly the one component is true that
@@ -576,6 +672,22 @@ namespace hp
      */
     std::vector>>
       finite_elements;
+
+    /**
+     * Function returning the index of the finite element following the given
+     * one in hierarchy.
+     */
+    std::function &,
+                               const unsigned int)>
+      hierarchy_next;
+
+    /**
+     * Function returning the index of the finite element preceding the given
+     * one in hierarchy.
+     */
+    std::function &,
+                               const unsigned int)>
+      hierarchy_prev;
   };
 
 
diff --git a/source/hp/fe_collection.cc b/source/hp/fe_collection.cc
index 616359767d63..cc3c26634a84 100644
--- a/source/hp/fe_collection.cc
+++ b/source/hp/fe_collection.cc
@@ -160,9 +160,18 @@ namespace hp
 
 
 
+  template 
+  FECollection::FECollection()
+  {
+    set_default_hierarchy();
+  }
+
+
+
   template 
   FECollection::FECollection(
     const FiniteElement &fe)
+    : FECollection()
   {
     push_back(fe);
   }
@@ -172,6 +181,7 @@ namespace hp
   template 
   FECollection::FECollection(
     const std::vector *> &fes)
+    : FECollection()
   {
     Assert(fes.size() > 0,
            ExcMessage("Need to pass at least one finite element."));
@@ -202,6 +212,64 @@ namespace hp
 
 
 
+  template 
+  void
+  FECollection::set_hierarchy(
+    const std::function<
+      unsigned int(const typename hp::FECollection &,
+                   const unsigned int)> &next,
+    const std::function<
+      unsigned int(const typename hp::FECollection &,
+                   const unsigned int)> &prev)
+  {
+    // copy hierarchy functions
+    hierarchy_next = next;
+    hierarchy_prev = prev;
+  }
+
+
+
+  template 
+  void
+  FECollection::set_default_hierarchy()
+  {
+    // establish hierarchy corresponding to order of indices
+    set_hierarchy(&DefaultHierarchy::next_index,
+                  &DefaultHierarchy::previous_index);
+  }
+
+
+
+  template 
+  unsigned int
+  FECollection::next_in_hierarchy(
+    const unsigned int fe_index) const
+  {
+    Assert(fe_index < size(), ExcIndexRange(fe_index, 0, size()));
+
+    const unsigned int new_fe_index = hierarchy_next(*this, fe_index);
+    Assert(new_fe_index < size(), ExcIndexRange(new_fe_index, 0, size()));
+
+    return new_fe_index;
+  }
+
+
+
+  template 
+  unsigned int
+  FECollection::previous_in_hierarchy(
+    const unsigned int fe_index) const
+  {
+    Assert(fe_index < size(), ExcIndexRange(fe_index, 0, size()));
+
+    const unsigned int new_fe_index = hierarchy_prev(*this, fe_index);
+    Assert(new_fe_index < size(), ExcIndexRange(new_fe_index, 0, size()));
+
+    return new_fe_index;
+  }
+
+
+
   template 
   ComponentMask
   FECollection::component_mask(
diff --git a/tests/hp/fe_hierarchy.cc b/tests/hp/fe_hierarchy.cc
new file mode 100644
index 000000000000..185421afa4ec
--- /dev/null
+++ b/tests/hp/fe_hierarchy.cc
@@ -0,0 +1,61 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2005 - 2019 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+
+
+// Test default hierarchy of any hp::FECollection object.
+// In the default implementation, the new indices are either the
+// succeeding or preceding indices until limits are reached.
+
+
+#include 
+
+#include 
+
+#include "../tests.h"
+
+
+template 
+void
+test()
+{
+  hp::FECollection fe_collection;
+
+  while (fe_collection.size() < 3)
+    {
+      // add dummy fe to collection
+      fe_collection.push_back(FE_Q(1));
+      deallog << "size:" << fe_collection.size() << std::endl;
+
+      for (unsigned int fe_index = 0; fe_index < fe_collection.size();
+           ++fe_index)
+        deallog << " idx:" << fe_index
+                << " next:" << fe_collection.next_in_hierarchy(fe_index)
+                << " prev:" << fe_collection.previous_in_hierarchy(fe_index)
+                << std::endl;
+    }
+}
+
+
+
+int
+main()
+{
+  initlog();
+
+  test<1>();
+
+  deallog << "OK" << std::endl;
+}
diff --git a/tests/hp/fe_hierarchy.output b/tests/hp/fe_hierarchy.output
new file mode 100644
index 000000000000..64e52b61e739
--- /dev/null
+++ b/tests/hp/fe_hierarchy.output
@@ -0,0 +1,11 @@
+
+DEAL::size:1
+DEAL:: idx:0 next:0 prev:0
+DEAL::size:2
+DEAL:: idx:0 next:1 prev:0
+DEAL:: idx:1 next:1 prev:0
+DEAL::size:3
+DEAL:: idx:0 next:1 prev:0
+DEAL:: idx:1 next:2 prev:0
+DEAL:: idx:2 next:2 prev:1
+DEAL::OK

From 20094c005d082401ab4a43a68e48f5567eb2c3d1 Mon Sep 17 00:00:00 2001
From: Marc Fehling 
Date: Fri, 8 Feb 2019 00:59:12 +0100
Subject: [PATCH 221/507] Added 'repartition' signals. Attached
 'active_fe_transfer' functions to them.

---
 doc/news/changes/minor/20190303Fehling        |   5 +
 include/deal.II/grid/tria.h                   |  19 ++
 source/distributed/tria.cc                    |   9 +
 source/hp/dof_handler.cc                      |  11 +
 tests/mpi/hp_active_fe_indices_transfer_03.cc | 104 ++++++++
 ...ransfer_03.with_p4est=true.mpirun=2.output | 175 ++++++++++++++
 ...ransfer_03.with_p4est=true.mpirun=8.output | 223 ++++++++++++++++++
 7 files changed, 546 insertions(+)
 create mode 100644 doc/news/changes/minor/20190303Fehling
 create mode 100644 tests/mpi/hp_active_fe_indices_transfer_03.cc
 create mode 100644 tests/mpi/hp_active_fe_indices_transfer_03.with_p4est=true.mpirun=2.output
 create mode 100644 tests/mpi/hp_active_fe_indices_transfer_03.with_p4est=true.mpirun=8.output

diff --git a/doc/news/changes/minor/20190303Fehling b/doc/news/changes/minor/20190303Fehling
new file mode 100644
index 000000000000..5bcb949a02ff
--- /dev/null
+++ b/doc/news/changes/minor/20190303Fehling
@@ -0,0 +1,5 @@
+New: Signals Triangulation::pre_distributed_repartition and
+Triangulation::post_distributed_repartition which will be triggered in
+parallel::distributed::Triangulation::repartition().
+
    
+(Marc Fehling, 2019/03/03)
diff --git a/include/deal.II/grid/tria.h b/include/deal.II/grid/tria.h
index 6976f51fb1f0..baf3beefda60 100644
--- a/include/deal.II/grid/tria.h
+++ b/include/deal.II/grid/tria.h
@@ -2327,6 +2327,25 @@ class Triangulation : public Subscriptor
      */
     boost::signals2::signal post_distributed_refinement;
 
+    /**
+     * This signal is triggered at the beginning of execution of the
+     * parallel::distributed::Triangulation::repartition() function. At the time
+     * this signal is triggered, the triangulation is still unchanged.
+     *
+     * @note The parallel::distributed::Triangulation::repartition() function is
+     * also called by parallel::distributed::Triangulation::load(). Thus, the
+     * pre_distributed_repartition signal will be triggered after the
+     * pre_distributed_load one.
+     */
+    boost::signals2::signal pre_distributed_repartition;
+
+    /**
+     * This signal is triggered at the end of execution of the
+     * parallel::distributed::Triangulation::repartition()
+     * function when the triangulation has reached its final state.
+     */
+    boost::signals2::signal post_distributed_repartition;
+
     /**
      * This signal is triggered at the beginning of execution of the
      * parallel::distributed::Triangulation::save()
diff --git a/source/distributed/tria.cc b/source/distributed/tria.cc
index 9da8894cd146..7541203735c6 100644
--- a/source/distributed/tria.cc
+++ b/source/distributed/tria.cc
@@ -4085,6 +4085,9 @@ namespace parallel
               "Error: There shouldn't be any cells flagged for coarsening/refinement when calling repartition()."));
 #  endif
 
+      // signal that repartitioning is going to happen
+      this->signals.pre_distributed_repartition();
+
       // before repartitioning the mesh let others attach mesh related info
       // (such as SolutionTransfer data) to the p4est
       std::vector::gloidx>
@@ -4160,6 +4163,12 @@ namespace parallel
 
       // update how many cells, edges, etc, we store locally
       this->update_number_cache();
+
+      // signal that repartitioning is finished,
+      // this is triggered before update_periodic_face_map
+      // to be consistent with the serial triangulation class
+      this->signals.post_distributed_repartition();
+
       this->update_periodic_face_map();
     }
 
diff --git a/source/hp/dof_handler.cc b/source/hp/dof_handler.cc
index 8e9dc7e65a9d..fb3742c33e38 100644
--- a/source/hp/dof_handler.cc
+++ b/source/hp/dof_handler.cc
@@ -1654,6 +1654,17 @@ namespace hp
           internal::DoFHandlerImplementation::Policy::ParallelDistributed<
             DoFHandler>>(*this);
 
+        tria_listeners.push_back(
+          this->tria->signals.pre_distributed_repartition.connect(std::bind(
+            &DoFHandler::pre_distributed_active_fe_index_transfer,
+            std::ref(*this))));
+        tria_listeners.push_back(
+          this->tria->signals.post_distributed_repartition.connect(std::bind(
+            &DoFHandler::post_distributed_active_fe_index_transfer,
+            std::ref(*this))));
+
         tria_listeners.push_back(
           this->tria->signals.pre_distributed_refinement.connect(std::bind(
             &DoFHandler
+#include 
+
+#include 
+
+#include 
+
+#include 
+
+#include "../tests.h"
+
+
+template 
+void
+test()
+{
+  const unsigned int myid = Utilities::MPI::this_mpi_process(MPI_COMM_WORLD);
+
+  // ------ setup ------
+  parallel::distributed::Triangulation tria(MPI_COMM_WORLD);
+
+  GridGenerator::subdivided_hyper_cube(tria, 2);
+  tria.refine_global(1);
+  deallog << "cells before: " << tria.n_global_active_cells() << std::endl;
+
+  // prepare FECollection with arbitrary number of entries
+  hp::FECollection fe_collection;
+  for (unsigned int i = 0; i < Utilities::MPI::n_mpi_processes(MPI_COMM_WORLD);
+       ++i)
+    fe_collection.push_back(FE_Q(i + 1));
+
+  // we need to introduce dof_handler to its fe_collection first
+  hp::DoFHandler dh(tria);
+  dh.set_fe(fe_collection);
+
+  for (auto &cell : dh.active_cell_iterators())
+    if (cell->is_locally_owned())
+      {
+        // set active fe index
+        if (!(cell->is_artificial()))
+          cell->set_active_fe_index(myid);
+
+        deallog << "myid=" << myid << " cellid=" << cell->id()
+                << " fe_index=" << cell->active_fe_index() << std::endl;
+      }
+
+  // ----- transfer -----
+  parallel::CellWeights cell_weights(dh);
+  cell_weights.register_ndofs_weighting(100000);
+
+  tria.repartition();
+
+  deallog << "cells after: " << tria.n_global_active_cells() << std::endl;
+
+  // ------ verify ------
+  // check if all children adopted the correct id
+  for (auto &cell : dh.active_cell_iterators())
+    if (cell->is_locally_owned())
+      deallog << "myid=" << myid << " cellid=" << cell->id()
+              << " fe_index=" << cell->active_fe_index() << std::endl;
+
+  // for further calculations, distribute dofs, i.e.
+  // dh.distribute_dofs(fe_collection);
+
+  // make sure no processor is hanging
+  MPI_Barrier(MPI_COMM_WORLD);
+
+  deallog << "OK" << std::endl;
+}
+
+
+int
+main(int argc, char *argv[])
+{
+  Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1);
+  MPILogInitAll                    log;
+
+  deallog.push("2d");
+  test<2>();
+  deallog.pop();
+  deallog.push("3d");
+  test<3>();
+  deallog.pop();
+}
diff --git a/tests/mpi/hp_active_fe_indices_transfer_03.with_p4est=true.mpirun=2.output b/tests/mpi/hp_active_fe_indices_transfer_03.with_p4est=true.mpirun=2.output
new file mode 100644
index 000000000000..7db8f630504a
--- /dev/null
+++ b/tests/mpi/hp_active_fe_indices_transfer_03.with_p4est=true.mpirun=2.output
@@ -0,0 +1,175 @@
+
+DEAL:0:2d::cells before: 16
+DEAL:0:2d::myid=0 cellid=0_1:0 fe_index=0
+DEAL:0:2d::myid=0 cellid=0_1:1 fe_index=0
+DEAL:0:2d::myid=0 cellid=0_1:2 fe_index=0
+DEAL:0:2d::myid=0 cellid=0_1:3 fe_index=0
+DEAL:0:2d::myid=0 cellid=1_1:0 fe_index=0
+DEAL:0:2d::myid=0 cellid=1_1:1 fe_index=0
+DEAL:0:2d::myid=0 cellid=1_1:2 fe_index=0
+DEAL:0:2d::myid=0 cellid=1_1:3 fe_index=0
+DEAL:0:2d::cells after: 16
+DEAL:0:2d::myid=0 cellid=0_1:0 fe_index=0
+DEAL:0:2d::myid=0 cellid=0_1:1 fe_index=0
+DEAL:0:2d::myid=0 cellid=0_1:2 fe_index=0
+DEAL:0:2d::myid=0 cellid=0_1:3 fe_index=0
+DEAL:0:2d::myid=0 cellid=1_1:0 fe_index=0
+DEAL:0:2d::myid=0 cellid=1_1:1 fe_index=0
+DEAL:0:2d::myid=0 cellid=1_1:2 fe_index=0
+DEAL:0:2d::myid=0 cellid=1_1:3 fe_index=0
+DEAL:0:2d::myid=0 cellid=2_1:0 fe_index=1
+DEAL:0:2d::myid=0 cellid=2_1:1 fe_index=1
+DEAL:0:2d::myid=0 cellid=2_1:2 fe_index=1
+DEAL:0:2d::myid=0 cellid=2_1:3 fe_index=1
+DEAL:0:2d::OK
+DEAL:0:3d::cells before: 64
+DEAL:0:3d::myid=0 cellid=0_1:0 fe_index=0
+DEAL:0:3d::myid=0 cellid=0_1:1 fe_index=0
+DEAL:0:3d::myid=0 cellid=0_1:2 fe_index=0
+DEAL:0:3d::myid=0 cellid=0_1:3 fe_index=0
+DEAL:0:3d::myid=0 cellid=0_1:4 fe_index=0
+DEAL:0:3d::myid=0 cellid=0_1:5 fe_index=0
+DEAL:0:3d::myid=0 cellid=0_1:6 fe_index=0
+DEAL:0:3d::myid=0 cellid=0_1:7 fe_index=0
+DEAL:0:3d::myid=0 cellid=1_1:0 fe_index=0
+DEAL:0:3d::myid=0 cellid=1_1:1 fe_index=0
+DEAL:0:3d::myid=0 cellid=1_1:2 fe_index=0
+DEAL:0:3d::myid=0 cellid=1_1:3 fe_index=0
+DEAL:0:3d::myid=0 cellid=1_1:4 fe_index=0
+DEAL:0:3d::myid=0 cellid=1_1:5 fe_index=0
+DEAL:0:3d::myid=0 cellid=1_1:6 fe_index=0
+DEAL:0:3d::myid=0 cellid=1_1:7 fe_index=0
+DEAL:0:3d::myid=0 cellid=2_1:0 fe_index=0
+DEAL:0:3d::myid=0 cellid=2_1:1 fe_index=0
+DEAL:0:3d::myid=0 cellid=2_1:2 fe_index=0
+DEAL:0:3d::myid=0 cellid=2_1:3 fe_index=0
+DEAL:0:3d::myid=0 cellid=2_1:4 fe_index=0
+DEAL:0:3d::myid=0 cellid=2_1:5 fe_index=0
+DEAL:0:3d::myid=0 cellid=2_1:6 fe_index=0
+DEAL:0:3d::myid=0 cellid=2_1:7 fe_index=0
+DEAL:0:3d::myid=0 cellid=3_1:0 fe_index=0
+DEAL:0:3d::myid=0 cellid=3_1:1 fe_index=0
+DEAL:0:3d::myid=0 cellid=3_1:2 fe_index=0
+DEAL:0:3d::myid=0 cellid=3_1:3 fe_index=0
+DEAL:0:3d::myid=0 cellid=3_1:4 fe_index=0
+DEAL:0:3d::myid=0 cellid=3_1:5 fe_index=0
+DEAL:0:3d::myid=0 cellid=3_1:6 fe_index=0
+DEAL:0:3d::myid=0 cellid=3_1:7 fe_index=0
+DEAL:0:3d::cells after: 64
+DEAL:0:3d::myid=0 cellid=0_1:0 fe_index=0
+DEAL:0:3d::myid=0 cellid=0_1:1 fe_index=0
+DEAL:0:3d::myid=0 cellid=0_1:2 fe_index=0
+DEAL:0:3d::myid=0 cellid=0_1:3 fe_index=0
+DEAL:0:3d::myid=0 cellid=0_1:4 fe_index=0
+DEAL:0:3d::myid=0 cellid=0_1:5 fe_index=0
+DEAL:0:3d::myid=0 cellid=0_1:6 fe_index=0
+DEAL:0:3d::myid=0 cellid=0_1:7 fe_index=0
+DEAL:0:3d::myid=0 cellid=1_1:0 fe_index=0
+DEAL:0:3d::myid=0 cellid=1_1:1 fe_index=0
+DEAL:0:3d::myid=0 cellid=1_1:2 fe_index=0
+DEAL:0:3d::myid=0 cellid=1_1:3 fe_index=0
+DEAL:0:3d::myid=0 cellid=1_1:4 fe_index=0
+DEAL:0:3d::myid=0 cellid=1_1:5 fe_index=0
+DEAL:0:3d::myid=0 cellid=1_1:6 fe_index=0
+DEAL:0:3d::myid=0 cellid=1_1:7 fe_index=0
+DEAL:0:3d::myid=0 cellid=2_1:0 fe_index=0
+DEAL:0:3d::myid=0 cellid=2_1:1 fe_index=0
+DEAL:0:3d::myid=0 cellid=2_1:2 fe_index=0
+DEAL:0:3d::myid=0 cellid=2_1:3 fe_index=0
+DEAL:0:3d::myid=0 cellid=2_1:4 fe_index=0
+DEAL:0:3d::myid=0 cellid=2_1:5 fe_index=0
+DEAL:0:3d::myid=0 cellid=2_1:6 fe_index=0
+DEAL:0:3d::myid=0 cellid=2_1:7 fe_index=0
+DEAL:0:3d::myid=0 cellid=3_1:0 fe_index=0
+DEAL:0:3d::myid=0 cellid=3_1:1 fe_index=0
+DEAL:0:3d::myid=0 cellid=3_1:2 fe_index=0
+DEAL:0:3d::myid=0 cellid=3_1:3 fe_index=0
+DEAL:0:3d::myid=0 cellid=3_1:4 fe_index=0
+DEAL:0:3d::myid=0 cellid=3_1:5 fe_index=0
+DEAL:0:3d::myid=0 cellid=3_1:6 fe_index=0
+DEAL:0:3d::myid=0 cellid=3_1:7 fe_index=0
+DEAL:0:3d::myid=0 cellid=4_1:0 fe_index=1
+DEAL:0:3d::myid=0 cellid=4_1:1 fe_index=1
+DEAL:0:3d::myid=0 cellid=4_1:2 fe_index=1
+DEAL:0:3d::myid=0 cellid=4_1:3 fe_index=1
+DEAL:0:3d::myid=0 cellid=4_1:4 fe_index=1
+DEAL:0:3d::myid=0 cellid=4_1:5 fe_index=1
+DEAL:0:3d::myid=0 cellid=4_1:6 fe_index=1
+DEAL:0:3d::myid=0 cellid=4_1:7 fe_index=1
+DEAL:0:3d::myid=0 cellid=5_1:0 fe_index=1
+DEAL:0:3d::myid=0 cellid=5_1:1 fe_index=1
+DEAL:0:3d::myid=0 cellid=5_1:2 fe_index=1
+DEAL:0:3d::myid=0 cellid=5_1:3 fe_index=1
+DEAL:0:3d::myid=0 cellid=5_1:4 fe_index=1
+DEAL:0:3d::myid=0 cellid=5_1:5 fe_index=1
+DEAL:0:3d::myid=0 cellid=5_1:6 fe_index=1
+DEAL:0:3d::myid=0 cellid=5_1:7 fe_index=1
+DEAL:0:3d::OK
+
+DEAL:1:2d::cells before: 16
+DEAL:1:2d::myid=1 cellid=2_1:0 fe_index=1
+DEAL:1:2d::myid=1 cellid=2_1:1 fe_index=1
+DEAL:1:2d::myid=1 cellid=2_1:2 fe_index=1
+DEAL:1:2d::myid=1 cellid=2_1:3 fe_index=1
+DEAL:1:2d::myid=1 cellid=3_1:0 fe_index=1
+DEAL:1:2d::myid=1 cellid=3_1:1 fe_index=1
+DEAL:1:2d::myid=1 cellid=3_1:2 fe_index=1
+DEAL:1:2d::myid=1 cellid=3_1:3 fe_index=1
+DEAL:1:2d::cells after: 16
+DEAL:1:2d::myid=1 cellid=3_1:0 fe_index=1
+DEAL:1:2d::myid=1 cellid=3_1:1 fe_index=1
+DEAL:1:2d::myid=1 cellid=3_1:2 fe_index=1
+DEAL:1:2d::myid=1 cellid=3_1:3 fe_index=1
+DEAL:1:2d::OK
+DEAL:1:3d::cells before: 64
+DEAL:1:3d::myid=1 cellid=4_1:0 fe_index=1
+DEAL:1:3d::myid=1 cellid=4_1:1 fe_index=1
+DEAL:1:3d::myid=1 cellid=4_1:2 fe_index=1
+DEAL:1:3d::myid=1 cellid=4_1:3 fe_index=1
+DEAL:1:3d::myid=1 cellid=4_1:4 fe_index=1
+DEAL:1:3d::myid=1 cellid=4_1:5 fe_index=1
+DEAL:1:3d::myid=1 cellid=4_1:6 fe_index=1
+DEAL:1:3d::myid=1 cellid=4_1:7 fe_index=1
+DEAL:1:3d::myid=1 cellid=5_1:0 fe_index=1
+DEAL:1:3d::myid=1 cellid=5_1:1 fe_index=1
+DEAL:1:3d::myid=1 cellid=5_1:2 fe_index=1
+DEAL:1:3d::myid=1 cellid=5_1:3 fe_index=1
+DEAL:1:3d::myid=1 cellid=5_1:4 fe_index=1
+DEAL:1:3d::myid=1 cellid=5_1:5 fe_index=1
+DEAL:1:3d::myid=1 cellid=5_1:6 fe_index=1
+DEAL:1:3d::myid=1 cellid=5_1:7 fe_index=1
+DEAL:1:3d::myid=1 cellid=6_1:0 fe_index=1
+DEAL:1:3d::myid=1 cellid=6_1:1 fe_index=1
+DEAL:1:3d::myid=1 cellid=6_1:2 fe_index=1
+DEAL:1:3d::myid=1 cellid=6_1:3 fe_index=1
+DEAL:1:3d::myid=1 cellid=6_1:4 fe_index=1
+DEAL:1:3d::myid=1 cellid=6_1:5 fe_index=1
+DEAL:1:3d::myid=1 cellid=6_1:6 fe_index=1
+DEAL:1:3d::myid=1 cellid=6_1:7 fe_index=1
+DEAL:1:3d::myid=1 cellid=7_1:0 fe_index=1
+DEAL:1:3d::myid=1 cellid=7_1:1 fe_index=1
+DEAL:1:3d::myid=1 cellid=7_1:2 fe_index=1
+DEAL:1:3d::myid=1 cellid=7_1:3 fe_index=1
+DEAL:1:3d::myid=1 cellid=7_1:4 fe_index=1
+DEAL:1:3d::myid=1 cellid=7_1:5 fe_index=1
+DEAL:1:3d::myid=1 cellid=7_1:6 fe_index=1
+DEAL:1:3d::myid=1 cellid=7_1:7 fe_index=1
+DEAL:1:3d::cells after: 64
+DEAL:1:3d::myid=1 cellid=6_1:0 fe_index=1
+DEAL:1:3d::myid=1 cellid=6_1:1 fe_index=1
+DEAL:1:3d::myid=1 cellid=6_1:2 fe_index=1
+DEAL:1:3d::myid=1 cellid=6_1:3 fe_index=1
+DEAL:1:3d::myid=1 cellid=6_1:4 fe_index=1
+DEAL:1:3d::myid=1 cellid=6_1:5 fe_index=1
+DEAL:1:3d::myid=1 cellid=6_1:6 fe_index=1
+DEAL:1:3d::myid=1 cellid=6_1:7 fe_index=1
+DEAL:1:3d::myid=1 cellid=7_1:0 fe_index=1
+DEAL:1:3d::myid=1 cellid=7_1:1 fe_index=1
+DEAL:1:3d::myid=1 cellid=7_1:2 fe_index=1
+DEAL:1:3d::myid=1 cellid=7_1:3 fe_index=1
+DEAL:1:3d::myid=1 cellid=7_1:4 fe_index=1
+DEAL:1:3d::myid=1 cellid=7_1:5 fe_index=1
+DEAL:1:3d::myid=1 cellid=7_1:6 fe_index=1
+DEAL:1:3d::myid=1 cellid=7_1:7 fe_index=1
+DEAL:1:3d::OK
+
diff --git a/tests/mpi/hp_active_fe_indices_transfer_03.with_p4est=true.mpirun=8.output b/tests/mpi/hp_active_fe_indices_transfer_03.with_p4est=true.mpirun=8.output
new file mode 100644
index 000000000000..167a31a6fe41
--- /dev/null
+++ b/tests/mpi/hp_active_fe_indices_transfer_03.with_p4est=true.mpirun=8.output
@@ -0,0 +1,223 @@
+
+DEAL:0:2d::cells before: 16
+DEAL:0:2d::myid=0 cellid=0_1:0 fe_index=0
+DEAL:0:2d::myid=0 cellid=0_1:1 fe_index=0
+DEAL:0:2d::myid=0 cellid=0_1:2 fe_index=0
+DEAL:0:2d::myid=0 cellid=0_1:3 fe_index=0
+DEAL:0:2d::cells after: 16
+DEAL:0:2d::myid=0 cellid=0_1:0 fe_index=0
+DEAL:0:2d::myid=0 cellid=0_1:1 fe_index=0
+DEAL:0:2d::myid=0 cellid=0_1:2 fe_index=0
+DEAL:0:2d::myid=0 cellid=0_1:3 fe_index=0
+DEAL:0:2d::myid=0 cellid=1_1:0 fe_index=2
+DEAL:0:2d::myid=0 cellid=1_1:1 fe_index=2
+DEAL:0:2d::myid=0 cellid=1_1:2 fe_index=2
+DEAL:0:2d::myid=0 cellid=1_1:3 fe_index=2
+DEAL:0:2d::OK
+DEAL:0:3d::cells before: 64
+DEAL:0:3d::myid=0 cellid=0_1:0 fe_index=0
+DEAL:0:3d::myid=0 cellid=0_1:1 fe_index=0
+DEAL:0:3d::myid=0 cellid=0_1:2 fe_index=0
+DEAL:0:3d::myid=0 cellid=0_1:3 fe_index=0
+DEAL:0:3d::myid=0 cellid=0_1:4 fe_index=0
+DEAL:0:3d::myid=0 cellid=0_1:5 fe_index=0
+DEAL:0:3d::myid=0 cellid=0_1:6 fe_index=0
+DEAL:0:3d::myid=0 cellid=0_1:7 fe_index=0
+DEAL:0:3d::cells after: 64
+DEAL:0:3d::myid=0 cellid=0_1:0 fe_index=0
+DEAL:0:3d::myid=0 cellid=0_1:1 fe_index=0
+DEAL:0:3d::myid=0 cellid=0_1:2 fe_index=0
+DEAL:0:3d::myid=0 cellid=0_1:3 fe_index=0
+DEAL:0:3d::myid=0 cellid=0_1:4 fe_index=0
+DEAL:0:3d::myid=0 cellid=0_1:5 fe_index=0
+DEAL:0:3d::myid=0 cellid=0_1:6 fe_index=0
+DEAL:0:3d::myid=0 cellid=0_1:7 fe_index=0
+DEAL:0:3d::myid=0 cellid=1_1:0 fe_index=1
+DEAL:0:3d::myid=0 cellid=1_1:1 fe_index=1
+DEAL:0:3d::myid=0 cellid=1_1:2 fe_index=1
+DEAL:0:3d::myid=0 cellid=1_1:3 fe_index=1
+DEAL:0:3d::myid=0 cellid=1_1:4 fe_index=1
+DEAL:0:3d::myid=0 cellid=1_1:5 fe_index=1
+DEAL:0:3d::myid=0 cellid=1_1:6 fe_index=1
+DEAL:0:3d::myid=0 cellid=1_1:7 fe_index=1
+DEAL:0:3d::myid=0 cellid=2_1:0 fe_index=2
+DEAL:0:3d::myid=0 cellid=2_1:1 fe_index=2
+DEAL:0:3d::myid=0 cellid=2_1:2 fe_index=2
+DEAL:0:3d::myid=0 cellid=2_1:3 fe_index=2
+DEAL:0:3d::myid=0 cellid=2_1:4 fe_index=2
+DEAL:0:3d::myid=0 cellid=2_1:5 fe_index=2
+DEAL:0:3d::myid=0 cellid=2_1:6 fe_index=2
+DEAL:0:3d::myid=0 cellid=2_1:7 fe_index=2
+DEAL:0:3d::myid=0 cellid=3_1:0 fe_index=3
+DEAL:0:3d::myid=0 cellid=3_1:1 fe_index=3
+DEAL:0:3d::myid=0 cellid=3_1:2 fe_index=3
+DEAL:0:3d::myid=0 cellid=3_1:3 fe_index=3
+DEAL:0:3d::myid=0 cellid=3_1:4 fe_index=3
+DEAL:0:3d::myid=0 cellid=3_1:5 fe_index=3
+DEAL:0:3d::myid=0 cellid=3_1:6 fe_index=3
+DEAL:0:3d::myid=0 cellid=3_1:7 fe_index=3
+DEAL:0:3d::OK
+
+DEAL:1:2d::cells before: 16
+DEAL:1:2d::cells after: 16
+DEAL:1:2d::myid=1 cellid=2_1:0 fe_index=4
+DEAL:1:2d::myid=1 cellid=2_1:1 fe_index=4
+DEAL:1:2d::myid=1 cellid=2_1:2 fe_index=4
+DEAL:1:2d::myid=1 cellid=2_1:3 fe_index=4
+DEAL:1:2d::OK
+DEAL:1:3d::cells before: 64
+DEAL:1:3d::myid=1 cellid=1_1:0 fe_index=1
+DEAL:1:3d::myid=1 cellid=1_1:1 fe_index=1
+DEAL:1:3d::myid=1 cellid=1_1:2 fe_index=1
+DEAL:1:3d::myid=1 cellid=1_1:3 fe_index=1
+DEAL:1:3d::myid=1 cellid=1_1:4 fe_index=1
+DEAL:1:3d::myid=1 cellid=1_1:5 fe_index=1
+DEAL:1:3d::myid=1 cellid=1_1:6 fe_index=1
+DEAL:1:3d::myid=1 cellid=1_1:7 fe_index=1
+DEAL:1:3d::cells after: 64
+DEAL:1:3d::myid=1 cellid=4_1:0 fe_index=4
+DEAL:1:3d::myid=1 cellid=4_1:1 fe_index=4
+DEAL:1:3d::myid=1 cellid=4_1:2 fe_index=4
+DEAL:1:3d::myid=1 cellid=4_1:3 fe_index=4
+DEAL:1:3d::myid=1 cellid=4_1:4 fe_index=4
+DEAL:1:3d::myid=1 cellid=4_1:5 fe_index=4
+DEAL:1:3d::myid=1 cellid=4_1:6 fe_index=4
+DEAL:1:3d::myid=1 cellid=4_1:7 fe_index=4
+DEAL:1:3d::OK
+
+
+DEAL:2:2d::cells before: 16
+DEAL:2:2d::myid=2 cellid=1_1:0 fe_index=2
+DEAL:2:2d::myid=2 cellid=1_1:1 fe_index=2
+DEAL:2:2d::myid=2 cellid=1_1:2 fe_index=2
+DEAL:2:2d::myid=2 cellid=1_1:3 fe_index=2
+DEAL:2:2d::cells after: 16
+DEAL:2:2d::OK
+DEAL:2:3d::cells before: 64
+DEAL:2:3d::myid=2 cellid=2_1:0 fe_index=2
+DEAL:2:3d::myid=2 cellid=2_1:1 fe_index=2
+DEAL:2:3d::myid=2 cellid=2_1:2 fe_index=2
+DEAL:2:3d::myid=2 cellid=2_1:3 fe_index=2
+DEAL:2:3d::myid=2 cellid=2_1:4 fe_index=2
+DEAL:2:3d::myid=2 cellid=2_1:5 fe_index=2
+DEAL:2:3d::myid=2 cellid=2_1:6 fe_index=2
+DEAL:2:3d::myid=2 cellid=2_1:7 fe_index=2
+DEAL:2:3d::cells after: 64
+DEAL:2:3d::myid=2 cellid=5_1:0 fe_index=5
+DEAL:2:3d::myid=2 cellid=5_1:1 fe_index=5
+DEAL:2:3d::myid=2 cellid=5_1:2 fe_index=5
+DEAL:2:3d::myid=2 cellid=5_1:3 fe_index=5
+DEAL:2:3d::myid=2 cellid=5_1:4 fe_index=5
+DEAL:2:3d::myid=2 cellid=5_1:5 fe_index=5
+DEAL:2:3d::myid=2 cellid=5_1:6 fe_index=5
+DEAL:2:3d::myid=2 cellid=5_1:7 fe_index=5
+DEAL:2:3d::OK
+
+
+DEAL:3:2d::cells before: 16
+DEAL:3:2d::cells after: 16
+DEAL:3:2d::myid=3 cellid=3_1:0 fe_index=6
+DEAL:3:2d::myid=3 cellid=3_1:1 fe_index=6
+DEAL:3:2d::myid=3 cellid=3_1:2 fe_index=6
+DEAL:3:2d::myid=3 cellid=3_1:3 fe_index=6
+DEAL:3:2d::OK
+DEAL:3:3d::cells before: 64
+DEAL:3:3d::myid=3 cellid=3_1:0 fe_index=3
+DEAL:3:3d::myid=3 cellid=3_1:1 fe_index=3
+DEAL:3:3d::myid=3 cellid=3_1:2 fe_index=3
+DEAL:3:3d::myid=3 cellid=3_1:3 fe_index=3
+DEAL:3:3d::myid=3 cellid=3_1:4 fe_index=3
+DEAL:3:3d::myid=3 cellid=3_1:5 fe_index=3
+DEAL:3:3d::myid=3 cellid=3_1:6 fe_index=3
+DEAL:3:3d::myid=3 cellid=3_1:7 fe_index=3
+DEAL:3:3d::cells after: 64
+DEAL:3:3d::myid=3 cellid=6_1:0 fe_index=6
+DEAL:3:3d::myid=3 cellid=6_1:1 fe_index=6
+DEAL:3:3d::myid=3 cellid=6_1:2 fe_index=6
+DEAL:3:3d::myid=3 cellid=6_1:3 fe_index=6
+DEAL:3:3d::myid=3 cellid=6_1:4 fe_index=6
+DEAL:3:3d::myid=3 cellid=6_1:5 fe_index=6
+DEAL:3:3d::myid=3 cellid=6_1:6 fe_index=6
+DEAL:3:3d::myid=3 cellid=6_1:7 fe_index=6
+DEAL:3:3d::OK
+
+
+DEAL:4:2d::cells before: 16
+DEAL:4:2d::myid=4 cellid=2_1:0 fe_index=4
+DEAL:4:2d::myid=4 cellid=2_1:1 fe_index=4
+DEAL:4:2d::myid=4 cellid=2_1:2 fe_index=4
+DEAL:4:2d::myid=4 cellid=2_1:3 fe_index=4
+DEAL:4:2d::cells after: 16
+DEAL:4:2d::OK
+DEAL:4:3d::cells before: 64
+DEAL:4:3d::myid=4 cellid=4_1:0 fe_index=4
+DEAL:4:3d::myid=4 cellid=4_1:1 fe_index=4
+DEAL:4:3d::myid=4 cellid=4_1:2 fe_index=4
+DEAL:4:3d::myid=4 cellid=4_1:3 fe_index=4
+DEAL:4:3d::myid=4 cellid=4_1:4 fe_index=4
+DEAL:4:3d::myid=4 cellid=4_1:5 fe_index=4
+DEAL:4:3d::myid=4 cellid=4_1:6 fe_index=4
+DEAL:4:3d::myid=4 cellid=4_1:7 fe_index=4
+DEAL:4:3d::cells after: 64
+DEAL:4:3d::OK
+
+
+DEAL:5:2d::cells before: 16
+DEAL:5:2d::cells after: 16
+DEAL:5:2d::OK
+DEAL:5:3d::cells before: 64
+DEAL:5:3d::myid=5 cellid=5_1:0 fe_index=5
+DEAL:5:3d::myid=5 cellid=5_1:1 fe_index=5
+DEAL:5:3d::myid=5 cellid=5_1:2 fe_index=5
+DEAL:5:3d::myid=5 cellid=5_1:3 fe_index=5
+DEAL:5:3d::myid=5 cellid=5_1:4 fe_index=5
+DEAL:5:3d::myid=5 cellid=5_1:5 fe_index=5
+DEAL:5:3d::myid=5 cellid=5_1:6 fe_index=5
+DEAL:5:3d::myid=5 cellid=5_1:7 fe_index=5
+DEAL:5:3d::cells after: 64
+DEAL:5:3d::myid=5 cellid=7_1:0 fe_index=7
+DEAL:5:3d::myid=5 cellid=7_1:1 fe_index=7
+DEAL:5:3d::myid=5 cellid=7_1:2 fe_index=7
+DEAL:5:3d::myid=5 cellid=7_1:3 fe_index=7
+DEAL:5:3d::myid=5 cellid=7_1:4 fe_index=7
+DEAL:5:3d::myid=5 cellid=7_1:5 fe_index=7
+DEAL:5:3d::myid=5 cellid=7_1:6 fe_index=7
+DEAL:5:3d::myid=5 cellid=7_1:7 fe_index=7
+DEAL:5:3d::OK
+
+
+DEAL:6:2d::cells before: 16
+DEAL:6:2d::myid=6 cellid=3_1:0 fe_index=6
+DEAL:6:2d::myid=6 cellid=3_1:1 fe_index=6
+DEAL:6:2d::myid=6 cellid=3_1:2 fe_index=6
+DEAL:6:2d::myid=6 cellid=3_1:3 fe_index=6
+DEAL:6:2d::cells after: 16
+DEAL:6:2d::OK
+DEAL:6:3d::cells before: 64
+DEAL:6:3d::myid=6 cellid=6_1:0 fe_index=6
+DEAL:6:3d::myid=6 cellid=6_1:1 fe_index=6
+DEAL:6:3d::myid=6 cellid=6_1:2 fe_index=6
+DEAL:6:3d::myid=6 cellid=6_1:3 fe_index=6
+DEAL:6:3d::myid=6 cellid=6_1:4 fe_index=6
+DEAL:6:3d::myid=6 cellid=6_1:5 fe_index=6
+DEAL:6:3d::myid=6 cellid=6_1:6 fe_index=6
+DEAL:6:3d::myid=6 cellid=6_1:7 fe_index=6
+DEAL:6:3d::cells after: 64
+DEAL:6:3d::OK
+
+
+DEAL:7:2d::cells before: 16
+DEAL:7:2d::cells after: 16
+DEAL:7:2d::OK
+DEAL:7:3d::cells before: 64
+DEAL:7:3d::myid=7 cellid=7_1:0 fe_index=7
+DEAL:7:3d::myid=7 cellid=7_1:1 fe_index=7
+DEAL:7:3d::myid=7 cellid=7_1:2 fe_index=7
+DEAL:7:3d::myid=7 cellid=7_1:3 fe_index=7
+DEAL:7:3d::myid=7 cellid=7_1:4 fe_index=7
+DEAL:7:3d::myid=7 cellid=7_1:5 fe_index=7
+DEAL:7:3d::myid=7 cellid=7_1:6 fe_index=7
+DEAL:7:3d::myid=7 cellid=7_1:7 fe_index=7
+DEAL:7:3d::cells after: 64
+DEAL:7:3d::OK
+

From 514aff2d48c675ca4e0aa10eeb796414207b5e51 Mon Sep 17 00:00:00 2001
From: Marc Fehling 
Date: Mon, 4 Mar 2019 22:39:52 +0100
Subject: [PATCH 222/507] Call post_distributed signals in the end of
 'execute_coarsening_and_refinement' and 'repartition'.

---
 source/distributed/tria.cc | 16 ++++++----------
 1 file changed, 6 insertions(+), 10 deletions(-)

diff --git a/source/distributed/tria.cc b/source/distributed/tria.cc
index 7541203735c6..f814270c31a8 100644
--- a/source/distributed/tria.cc
+++ b/source/distributed/tria.cc
@@ -4059,12 +4059,10 @@ namespace parallel
 
       this->update_number_cache();
 
-      // signal that refinement is finished,
-      // this is triggered before update_periodic_face_map
-      // to be consistent with the serial triangulation class
-      this->signals.post_distributed_refinement();
-
       this->update_periodic_face_map();
+
+      // signal that refinement is finished
+      this->signals.post_distributed_refinement();
     }
 
 
@@ -4164,12 +4162,10 @@ namespace parallel
       // update how many cells, edges, etc, we store locally
       this->update_number_cache();
 
-      // signal that repartitioning is finished,
-      // this is triggered before update_periodic_face_map
-      // to be consistent with the serial triangulation class
-      this->signals.post_distributed_repartition();
-
       this->update_periodic_face_map();
+
+      // signal that repartitioning is finished
+      this->signals.post_distributed_repartition();
     }
 
 

From 48954cca022288b739fb598b2be76cf15c5d28be Mon Sep 17 00:00:00 2001
From: Marc Fehling 
Date: Tue, 5 Mar 2019 00:05:15 +0100
Subject: [PATCH 223/507] Explicitly set noexcept specifier for move
 constructor.

---
 include/deal.II/hp/fe_collection.h | 15 +++++++++++++--
 1 file changed, 13 insertions(+), 2 deletions(-)

diff --git a/include/deal.II/hp/fe_collection.h b/include/deal.II/hp/fe_collection.h
index c4668b89dcc5..4368627dff7d 100644
--- a/include/deal.II/hp/fe_collection.h
+++ b/include/deal.II/hp/fe_collection.h
@@ -135,8 +135,19 @@ namespace hp
 
     /**
      * Move constructor.
-     */
-    FECollection(FECollection &&) = default;
+     *
+     * @note The implementation of standard datatypes may change with different
+     * libraries, so their move members may or may not be flagged non-throwing.
+     * We need to explicitly set the noexcept specifier according to its
+     * member variables to still get the performance benefits (and to satisfy
+     * clang-tidy).
+     */
+    FECollection(FECollection &&) noexcept(
+      std::is_nothrow_move_constructible<
+        std::vector>>>::value
+        &&std::is_nothrow_move_constructible &,
+                       const unsigned int)>>::value) = default;
 
     /**
      * Move assignment operator.

From a0f02dedcde22b485d0a2ed24f700894785d2e2c Mon Sep 17 00:00:00 2001
From: Martin Kronbichler 
Date: Tue, 5 Mar 2019 18:39:31 +0100
Subject: [PATCH 224/507] Fix documentation of cylindrical manifold

---
 include/deal.II/grid/manifold_lib.h | 16 +++++++++-------
 1 file changed, 9 insertions(+), 7 deletions(-)

diff --git a/include/deal.II/grid/manifold_lib.h b/include/deal.II/grid/manifold_lib.h
index 6eb5d7e32878..a550c26613fa 100644
--- a/include/deal.II/grid/manifold_lib.h
+++ b/include/deal.II/grid/manifold_lib.h
@@ -406,17 +406,19 @@ class CylindricalManifold : public ChartManifold
   clone() const override;
 
   /**
-   * Compute the Cartesian coordinates for a point given in cylindrical
-   * coordinates.
+   * Compute the cylindrical coordinates $(r, \phi, \lambda)$ for the given
+   * space point where $r$ denotes the distance from the axis,
+   * $\phi$ the angle between the given point and the computed normal
+   * direction, and $\lambda$ the axial position.
    */
   virtual Point<3>
   pull_back(const Point &space_point) const override;
 
   /**
-   * Compute the cylindrical coordinates $(r, \phi, \lambda)$ for the given
-   * point where $r$ denotes the distance from the axis,
-   * $\phi$ the angle between the given point and the computed normal
-   * direction and $\lambda$ the axial position.
+   * Compute the Cartesian coordinates for a chart point given in cylindrical
+   * coordinates $(r, \phi, \lambda)$, where $r$ denotes the distance from the
+   * axis, $\phi$ the angle between the given point and the computed normal
+   * direction, and $\lambda$ the axial position.
    */
   virtual Point
   push_forward(const Point<3> &chart_point) const override;
@@ -425,7 +427,7 @@ class CylindricalManifold : public ChartManifold
    * Compute the derivatives of the mapping from cylindrical coordinates
    * $(r, \phi, \lambda)$ to cartesian coordinates where $r$ denotes the
    * distance from the axis, $\phi$ the angle between the given point and the
-   * computed normal direction and $\lambda$ the axial position.
+   * computed normal direction, and $\lambda$ the axial position.
    */
   virtual DerivativeForm<1, 3, spacedim>
   push_forward_gradient(const Point<3> &chart_point) const override;

From dc21bf441614471a2a330a28eb1aab455c3180eb Mon Sep 17 00:00:00 2001
From: Martin Kronbichler 
Date: Tue, 5 Mar 2019 18:40:11 +0100
Subject: [PATCH 225/507] Fix EllipticalManifold::push_forward_gradient

---
 source/grid/manifold_lib.cc | 27 ++++++++++++---------------
 1 file changed, 12 insertions(+), 15 deletions(-)

diff --git a/source/grid/manifold_lib.cc b/source/grid/manifold_lib.cc
index 4dd1c9a31d05..c08bff2f32e5 100644
--- a/source/grid/manifold_lib.cc
+++ b/source/grid/manifold_lib.cc
@@ -1091,11 +1091,7 @@ CylindricalManifold::push_forward(
   Assert(spacedim == 3,
          ExcMessage("CylindricalManifold can only be used for spacedim==3!"));
 
-  // Rotate the orthogonal direction by the given angle.
-  // Formula from Section 5.2 in
-  // http://inside.mines.edu/fs_home/gmurray/ArbitraryAxisRotation/
-  // simplified assuming normal_direction and direction are orthogonal
-  // and unit vectors.
+  // Rotate the orthogonal direction by the given angle
   const double sine_r           = std::sin(chart_point(1)) * chart_point(0);
   const double cosine_r         = std::cos(chart_point(1)) * chart_point(0);
   const Tensor<1, spacedim> dxn = cross_product_3d(direction, normal_direction);
@@ -1118,11 +1114,7 @@ CylindricalManifold::push_forward_gradient(
 
   Tensor<2, 3> derivatives;
 
-  // Rotate the orthogonal direction by the given angle.
-  // Formula from Section 5.2 in
-  // http://inside.mines.edu/fs_home/gmurray/ArbitraryAxisRotation/
-  // simplified assuming normal_direction and direction are orthogonal
-  // and unit vectors.
+  // Rotate the orthogonal direction by the given angle
   const double              sine   = std::sin(chart_point(1));
   const double              cosine = std::cos(chart_point(1));
   const Tensor<1, spacedim> dxn = cross_product_3d(direction, normal_direction);
@@ -1289,14 +1281,19 @@ DerivativeForm<1, 2, 2>
 EllipticalManifold<2, 2>::push_forward_gradient(
   const Point<2> &chart_point) const
 {
-  const double            cs = std::cos(chart_point[1]);
-  const double            sn = std::sin(chart_point[1]);
-  DerivativeForm<1, 2, 2> dX;
+  const double cs = std::cos(chart_point[1]);
+  const double sn = std::sin(chart_point[1]);
+  Tensor<2, 2> dX;
   dX[0][0] = cosh_u * cs;
   dX[0][1] = -chart_point[0] * cosh_u * sn;
   dX[1][0] = sinh_u * sn;
-  dX[1][1] = chart_point[1] * sinh_u * cs;
-  return dX;
+  dX[1][1] = chart_point[0] * sinh_u * cs;
+
+  // rotate according to the major axis direction
+  Tensor<2, 2, double> rot{
+    {{+direction[0], -direction[1]}, {direction[1], direction[0]}}};
+
+  return rot * dX;
 }
 
 

From 8537d3b27290f665b31276c6c2b5515770ee2e98 Mon Sep 17 00:00:00 2001
From: Martin Kronbichler 
Date: Tue, 5 Mar 2019 18:41:11 +0100
Subject: [PATCH 226/507] Fix CylindricalManifold::get_new_point

---
 source/grid/manifold_lib.cc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/source/grid/manifold_lib.cc b/source/grid/manifold_lib.cc
index c08bff2f32e5..eb0be274ff17 100644
--- a/source/grid/manifold_lib.cc
+++ b/source/grid/manifold_lib.cc
@@ -1049,7 +1049,7 @@ CylindricalManifold::get_new_point(
   const double lambda = middle * direction;
 
   if ((middle - direction * lambda).square() < tolerance * average_length)
-    return Point() + direction * lambda;
+    return point_on_axis + direction * lambda;
   else // If not, using the ChartManifold should yield valid results.
     return ChartManifold::get_new_point(surrounding_points,
                                                           weights);

From 38d757306e87fc15e8819be1370d96e68668f278 Mon Sep 17 00:00:00 2001
From: Martin Kronbichler 
Date: Tue, 5 Mar 2019 18:41:39 +0100
Subject: [PATCH 227/507] Add test for cylindrical manifold

---
 tests/manifold/cylindrical_manifold_03.cc     | 75 +++++++++++++++++++
 tests/manifold/cylindrical_manifold_03.output |  4 +
 2 files changed, 79 insertions(+)
 create mode 100644 tests/manifold/cylindrical_manifold_03.cc
 create mode 100644 tests/manifold/cylindrical_manifold_03.output

diff --git a/tests/manifold/cylindrical_manifold_03.cc b/tests/manifold/cylindrical_manifold_03.cc
new file mode 100644
index 000000000000..ec2994904b68
--- /dev/null
+++ b/tests/manifold/cylindrical_manifold_03.cc
@@ -0,0 +1,75 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2019 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+// Test cylindrical manifold for the mid point axis of a cylinder
+
+#include "../tests.h"
+
+
+// all include files you need here
+#include 
+
+
+
+int
+main()
+{
+  initlog();
+  deallog << std::setprecision(10);
+
+  Tensor<1, 3>   axis({0.0, 0.0, 1.0});
+  const Point<3> origin(1.0, 2.0, 3.0);
+
+  // the larger the tolerance value, the more likely we identify the mid point
+  const double tolerance = 1e-6;
+
+  const CylindricalManifold<3> cylinder(axis, origin, tolerance);
+
+  // take two points symmetric about cylinder axis
+  const double          offset = 1.0;
+  std::vector> surrounding_points_vector(
+    {Point<3>(origin[0] + offset, origin[1], origin[2]),
+     Point<3>(origin[0] - offset, origin[1], origin[2])});
+  const ArrayView> surrounding_points =
+    make_array_view(surrounding_points_vector);
+  const std::vector     weights_vector({0.5, 0.5});
+  const ArrayView weights = make_array_view(weights_vector);
+
+  deallog << "New point is at "
+          << cylinder.get_new_point(surrounding_points, weights)
+          << " and it should be " << origin << std::endl;
+
+  surrounding_points_vector[0][2] = -1;
+  surrounding_points_vector[1][2] = -1;
+
+  deallog << "New point is at "
+          << cylinder.get_new_point(surrounding_points, weights)
+          << " and it should be " << Point<3>(origin[0], origin[1], -1.0)
+          << std::endl;
+
+  axis[0] = 0.3;
+  axis[1] = 0.6;
+  axis[2] = 0.8;
+
+  surrounding_points_vector[0][2] = origin[2];
+  surrounding_points_vector[1][2] = origin[2];
+
+  const CylindricalManifold<3> second_cylinder(axis, origin, tolerance);
+  deallog << "New point is at "
+          << second_cylinder.get_new_point(surrounding_points, weights)
+          << " and it should be " << origin << std::endl;
+
+  return 0;
+}
diff --git a/tests/manifold/cylindrical_manifold_03.output b/tests/manifold/cylindrical_manifold_03.output
new file mode 100644
index 000000000000..87c17c1da545
--- /dev/null
+++ b/tests/manifold/cylindrical_manifold_03.output
@@ -0,0 +1,4 @@
+
+DEAL::New point is at 1.000000000 2.000000000 3.000000000 and it should be 1.000000000 2.000000000 3.000000000
+DEAL::New point is at 1.000000000 2.000000000 -1.000000000 and it should be 1.000000000 2.000000000 -1.000000000
+DEAL::New point is at 1.000000000 2.000000000 3.000000000 and it should be 1.000000000 2.000000000 3.000000000

From b65307e98f613676fad3935851ee89743d6a7d37 Mon Sep 17 00:00:00 2001
From: Martin Kronbichler 
Date: Tue, 5 Mar 2019 18:41:56 +0100
Subject: [PATCH 228/507] Add test for
 EllipticalManifold::push_forward_gradient

---
 tests/manifold/elliptical_manifold_03.cc     | 78 ++++++++++++++++++++
 tests/manifold/elliptical_manifold_03.output |  3 +
 2 files changed, 81 insertions(+)
 create mode 100644 tests/manifold/elliptical_manifold_03.cc
 create mode 100644 tests/manifold/elliptical_manifold_03.output

diff --git a/tests/manifold/elliptical_manifold_03.cc b/tests/manifold/elliptical_manifold_03.cc
new file mode 100644
index 000000000000..ad72999421e3
--- /dev/null
+++ b/tests/manifold/elliptical_manifold_03.cc
@@ -0,0 +1,78 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2019 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+
+// Check gradient of elliptical manifold
+
+#include "../tests.h"
+
+
+// all include files you need here
+#include 
+#include 
+
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+
+#include 
+
+
+
+int
+main()
+{
+  initlog();
+
+  deallog << std::setprecision(10);
+
+  // setup elliptical manifold
+  const Tensor<1, 2> major_axis({2.0, 1.0});
+  const Point<2>     center(7.0, 6.0);
+  const double       eccentricity = 0.1;
+
+  const EllipticalManifold<2> ellipse(center, major_axis, eccentricity);
+
+  // reference point for computing gradient
+  const Point<2> chart_point(1.0, 0.25 * numbers::PI);
+
+  // compute gradient by central finite differences
+  const double   h = 1e-6;
+  const Point<2> chart_point_plusc(chart_point[0] + h, chart_point[1]);
+  const Point<2> chart_point_minusc(chart_point[0] - h, chart_point[1]);
+  const Point<2> chart_point_plusphi(chart_point[0], chart_point[1] + h);
+  const Point<2> chart_point_minusphi(chart_point[0], chart_point[1] - h);
+
+  const Point<2> space_point_plusc  = ellipse.push_forward(chart_point_plusc);
+  const Point<2> space_point_minusc = ellipse.push_forward(chart_point_minusc);
+  const Point<2> space_point_plusphi =
+    ellipse.push_forward(chart_point_plusphi);
+  const Point<2> space_point_minusphi =
+    ellipse.push_forward(chart_point_minusphi);
+
+  deallog << "Gradient by finite differences: "
+          << (space_point_plusc - space_point_minusc) / (2.0 * h) << " "
+          << (space_point_plusphi - space_point_minusphi) / (2.0 * h)
+          << std::endl;
+  deallog << "Analytic gradient:              "
+          << transpose(Tensor<2, 2>(ellipse.push_forward_gradient(chart_point)))
+          << std::endl;
+
+  return 0;
+}
diff --git a/tests/manifold/elliptical_manifold_03.output b/tests/manifold/elliptical_manifold_03.output
new file mode 100644
index 000000000000..602c91bbc8b7
--- /dev/null
+++ b/tests/manifold/elliptical_manifold_03.output
@@ -0,0 +1,3 @@
+
+DEAL::Gradient by finite differences: 3.178128775 9.455130749 -9.470981865 3.130575430
+DEAL::Analytic gradient:              3.178128776 9.455130749 -9.470981865 3.130575429

From 3c544115ac47a81d59c947f982e86e86d31bd387 Mon Sep 17 00:00:00 2001
From: Martin Kronbichler 
Date: Tue, 5 Mar 2019 18:47:19 +0100
Subject: [PATCH 229/507] Add changelogs

---
 .../changes/minor/20190305DanielAppelMartinKronbichler-1     | 5 +++++
 .../changes/minor/20190305DanielAppelMartinKronbichler-2     | 4 ++++
 2 files changed, 9 insertions(+)
 create mode 100644 doc/news/changes/minor/20190305DanielAppelMartinKronbichler-1
 create mode 100644 doc/news/changes/minor/20190305DanielAppelMartinKronbichler-2

diff --git a/doc/news/changes/minor/20190305DanielAppelMartinKronbichler-1 b/doc/news/changes/minor/20190305DanielAppelMartinKronbichler-1
new file mode 100644
index 000000000000..e9604fb6dccd
--- /dev/null
+++ b/doc/news/changes/minor/20190305DanielAppelMartinKronbichler-1
@@ -0,0 +1,5 @@
+Fixed: CylindricalManifold::get_new_point would previously return wrong
+results if the resulting point is on the axis, and the cylinder axis does not
+pass through the origin.
+
    
+(Daniel Appel, Martin Kronbichler, 2019/03/05)
diff --git a/doc/news/changes/minor/20190305DanielAppelMartinKronbichler-2 b/doc/news/changes/minor/20190305DanielAppelMartinKronbichler-2
new file mode 100644
index 000000000000..2396b24c9e28
--- /dev/null
+++ b/doc/news/changes/minor/20190305DanielAppelMartinKronbichler-2
@@ -0,0 +1,4 @@
+Fixed: EllipiticalManifold::push_forward_gradient did previously not take the
+rotation into account. This is now fixed.
+
    
+(Daniel Appel, Martin Kronbichler, 2019/03/05)

From 41e0507737bebcaae9d8a6859cef9c2d1c6ef189 Mon Sep 17 00:00:00 2001
From: Denis Davydov 
Date: Tue, 5 Mar 2019 15:13:53 +0100
Subject: [PATCH 230/507] add two more type traits to FEEvaluation

---
 include/deal.II/matrix_free/fe_evaluation.h   |  52 ++++++++
 .../fe_evaluation_type_traits_02.cc           | 120 ++++++++++++++++++
 .../fe_evaluation_type_traits_02.output       |   8 ++
 3 files changed, 180 insertions(+)
 create mode 100644 tests/matrix_free/fe_evaluation_type_traits_02.cc
 create mode 100644 tests/matrix_free/fe_evaluation_type_traits_02.output

diff --git a/include/deal.II/matrix_free/fe_evaluation.h b/include/deal.II/matrix_free/fe_evaluation.h
index 337846d4bd28..5d3b0f41288e 100644
--- a/include/deal.II/matrix_free/fe_evaluation.h
+++ b/include/deal.II/matrix_free/fe_evaluation.h
@@ -3431,6 +3431,58 @@ namespace internal
   template 
   const bool has_local_element::value;
 
+
+
+  // a helper type-trait that leverage SFINAE to figure out if type T has
+  // void T::add_local_element(const uint, const typename T::value_type)
+  template 
+  struct has_add_local_element
+  {
+  private:
+    static int
+    detect(...);
+
+    template 
+    static decltype(
+      std::declval().add_local_element(0, typename T::value_type()))
+    detect(const U &);
+
+  public:
+    static const bool value =
+      !std::is_same()))>::value;
+  };
+
+  // We need to have a separate declaration for static const members
+  template 
+  const bool has_add_local_element::value;
+
+
+
+  // a helper type-trait that leverage SFINAE to figure out if type T has
+  // void T::set_local_element(const uint, const typename T::value_type)
+  template 
+  struct has_set_local_element
+  {
+  private:
+    static int
+    detect(...);
+
+    template 
+    static decltype(
+      std::declval().set_local_element(0, typename T::value_type()))
+    detect(const U &);
+
+  public:
+    static const bool value =
+      !std::is_same()))>::value;
+  };
+
+  // We need to have a separate declaration for static const members
+  template 
+  const bool has_set_local_element::value;
+
+
+
   // same as above to check
   // bool T::partitioners_are_compatible(const Utilities::MPI::Partitioner &)
   // const
diff --git a/tests/matrix_free/fe_evaluation_type_traits_02.cc b/tests/matrix_free/fe_evaluation_type_traits_02.cc
new file mode 100644
index 000000000000..f87bf95c1b00
--- /dev/null
+++ b/tests/matrix_free/fe_evaluation_type_traits_02.cc
@@ -0,0 +1,120 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2019 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+
+
+// test internal typetraits used in FEEvaluation
+
+#include 
+
+#include "../tests.h"
+
+// dummy class we use to check typetraits and internal function.
+// this one mimics LA::d::Vec
+template 
+class Dummy
+{
+public:
+  using value_type = Number;
+
+  Number
+  local_element(const unsigned int) const
+  {
+    deallog << "Dummy::local_element() const" << std::endl;
+    return Number();
+  }
+
+  void
+  set_local_element(const unsigned int, const Number)
+  {
+    deallog << "Dummy::set_local_element()" << std::endl;
+  }
+
+  void
+  add_local_element(const unsigned int, const Number)
+  {
+    deallog << "Dummy::add_local_element()" << std::endl;
+  }
+
+  Number
+  operator()(const unsigned int) const
+  {
+    deallog << "Dummy::operator() const" << std::endl;
+    return Number();
+  }
+};
+
+
+template 
+class Dummy2
+{
+public:
+  using value_type = Number;
+
+  Number
+  local_element(const unsigned int) const
+  {
+    deallog << "Dummy2::local_element() const" << std::endl;
+    return Number();
+  }
+
+  Number &
+  local_element(const unsigned int)
+  {
+    deallog << "Dummy2::local_element()" << std::endl;
+    return dummy;
+  }
+
+  Number
+  operator()(const unsigned int) const
+  {
+    deallog << "Dummy2::operator() const" << std::endl;
+    return Number();
+  }
+
+  Number &
+  operator()(const unsigned int)
+  {
+    deallog << "Dummy2::operator()" << std::endl;
+    return dummy;
+  }
+
+private:
+  Number dummy;
+};
+
+
+int
+main()
+{
+  initlog();
+
+  Dummy  dummy;
+  Dummy2 dummy2;
+
+  deallog << "has_add_local_element:" << std::endl
+          << "Dummy = " << internal::has_add_local_element>::value
+          << std::endl
+          << "Dummy2 = "
+          << internal::has_add_local_element>::value << std::endl
+          << "has_set_local_element:" << std::endl
+          << "Dummy = " << internal::has_set_local_element>::value
+          << std::endl
+          << "Dummy2 = "
+          << internal::has_set_local_element>::value
+          << std::endl;
+
+  deallog << "OK" << std::endl;
+}
diff --git a/tests/matrix_free/fe_evaluation_type_traits_02.output b/tests/matrix_free/fe_evaluation_type_traits_02.output
new file mode 100644
index 000000000000..d6fcec824872
--- /dev/null
+++ b/tests/matrix_free/fe_evaluation_type_traits_02.output
@@ -0,0 +1,8 @@
+
+DEAL::has_add_local_element:
+DEAL::Dummy = 1
+DEAL::Dummy2 = 0
+DEAL::has_set_local_element:
+DEAL::Dummy = 1
+DEAL::Dummy2 = 0
+DEAL::OK

From e217995d6f04b92a285f79263e8b43078e14583e Mon Sep 17 00:00:00 2001
From: Martin Kronbichler 
Date: Wed, 6 Mar 2019 12:09:06 +0100
Subject: [PATCH 231/507] Fix file name date in two changelog entries

---
 .../minor/{20190401ArndtTurcksin => 20190104ArndtTurcksin}        | 0
 .../changes/minor/{20191301VishalBoddu => 20190113VishalBoddu}    | 0
 2 files changed, 0 insertions(+), 0 deletions(-)
 rename doc/news/changes/minor/{20190401ArndtTurcksin => 20190104ArndtTurcksin} (100%)
 rename doc/news/changes/minor/{20191301VishalBoddu => 20190113VishalBoddu} (100%)

diff --git a/doc/news/changes/minor/20190401ArndtTurcksin b/doc/news/changes/minor/20190104ArndtTurcksin
similarity index 100%
rename from doc/news/changes/minor/20190401ArndtTurcksin
rename to doc/news/changes/minor/20190104ArndtTurcksin
diff --git a/doc/news/changes/minor/20191301VishalBoddu b/doc/news/changes/minor/20190113VishalBoddu
similarity index 100%
rename from doc/news/changes/minor/20191301VishalBoddu
rename to doc/news/changes/minor/20190113VishalBoddu

From aa7ee309719ddccef14056091b39594051189768 Mon Sep 17 00:00:00 2001
From: Martin Kronbichler 
Date: Wed, 6 Mar 2019 12:20:30 +0100
Subject: [PATCH 232/507] Fix date markup for changelog.

---
 doc/news/changes/major/20180524MatthiasMaierDanielArndt      | 2 +-
 doc/news/changes/major/20180531MatthiasMaier                 | 2 +-
 doc/news/changes/major/20180709Harper                        | 2 +-
 doc/news/changes/major/20180811DavidWells                    | 2 +-
 doc/news/changes/major/20190208MatthiasMaier                 | 2 +-
 doc/news/changes/minor/20180524MartinKronbichlerDenisDavydov | 2 +-
 doc/news/changes/minor/20180529DenisDavydov                  | 2 +-
 doc/news/changes/minor/20180529DenisDavydov_b                | 2 +-
 doc/news/changes/minor/20180606SambitDas                     | 2 +-
 doc/news/changes/minor/20180611MatthiasMaier                 | 2 +-
 doc/news/changes/minor/20180612DenisDavydov                  | 2 +-
 doc/news/changes/minor/20180614PiYuehChuang                  | 2 +-
 doc/news/changes/minor/20180614UweKoecher                    | 2 +-
 doc/news/changes/minor/20180621DenisDavydov                  | 2 +-
 doc/news/changes/minor/20180621DenisDavydov_b                | 3 ++-
 doc/news/changes/minor/20180706DenisDavydov                  | 2 +-
 doc/news/changes/minor/20180726DenisDavydov                  | 2 +-
 doc/news/changes/minor/20180802DenisDavydov                  | 2 +-
 doc/news/changes/minor/20180810BenjaminBrands                | 2 +-
 doc/news/changes/minor/20180813AlexanderKnieps               | 2 +-
 doc/news/changes/minor/20180821SvenjaSchoeder                | 1 +
 doc/news/changes/minor/20180913DenisDavydov                  | 2 +-
 doc/news/changes/minor/20180919DenisDavydov                  | 2 +-
 doc/news/changes/minor/20180920DenisDavydov                  | 2 +-
 doc/news/changes/minor/20181005DenisDavydov                  | 2 +-
 doc/news/changes/minor/20190210MarcFehling                   | 2 +-
 doc/news/changes/minor/20190213MatthiasMaier                 | 2 +-
 27 files changed, 28 insertions(+), 26 deletions(-)

diff --git a/doc/news/changes/major/20180524MatthiasMaierDanielArndt b/doc/news/changes/major/20180524MatthiasMaierDanielArndt
index 3144a172b929..f76fada44e8e 100644
--- a/doc/news/changes/major/20180524MatthiasMaierDanielArndt
+++ b/doc/news/changes/major/20180524MatthiasMaierDanielArndt
@@ -1,3 +1,3 @@
 Changed: clang-format replaces astyle as source code formatting tool.
 
    
-(2018/05/24, Matthias Maier, Daniel Arndt)
+(Matthias Maier, Daniel Arndt, 2018/05/24)
diff --git a/doc/news/changes/major/20180531MatthiasMaier b/doc/news/changes/major/20180531MatthiasMaier
index 32f6875ac019..05476ca921b8 100644
--- a/doc/news/changes/major/20180531MatthiasMaier
+++ b/doc/news/changes/major/20180531MatthiasMaier
@@ -4,4 +4,4 @@ storage type. This in particular enables the definition of complex-valued
 constraints (for example, complex-valued Dirichlet boundary conditions, or
 periodic boundary conditions with an additional phase shift).
 
    
-(2018/05/31, Matthias Maier, Daniel Arndt, David Wells)
+(Matthias Maier, Daniel Arndt, David Wells, 2018/05/31)
diff --git a/doc/news/changes/major/20180709Harper b/doc/news/changes/major/20180709Harper
index 43baeb009cb7..380ed6877c88 100644
--- a/doc/news/changes/major/20180709Harper
+++ b/doc/news/changes/major/20180709Harper
@@ -5,4 +5,4 @@ bubble functions. The original description is for simplicial meshes, but this im
 for quadrilateral and hexahedral meshes. The BR1-P0 pair is LBB stable for Stokes problems. Due
 to the edge-based bubble functions, features such as hanging nodes are not supported.
 
    
-(Graham Harper 07/09/2018)
+(Graham Harper, 07/09/2018)
diff --git a/doc/news/changes/major/20180811DavidWells b/doc/news/changes/major/20180811DavidWells
index 7a7ca6ed3d83..c6ec70b3af96 100644
--- a/doc/news/changes/major/20180811DavidWells
+++ b/doc/news/changes/major/20180811DavidWells
@@ -1,4 +1,4 @@
 Improved: GridGenerator::extrude_triangulation can now optionally extrude manifold
 ids.
 
    
-(2018/08/11, David Wells)
+(David Wells, 2018/08/11)
diff --git a/doc/news/changes/major/20190208MatthiasMaier b/doc/news/changes/major/20190208MatthiasMaier
index b1cd3de01f22..2131b88f999b 100644
--- a/doc/news/changes/major/20190208MatthiasMaier
+++ b/doc/news/changes/major/20190208MatthiasMaier
@@ -1,4 +1,4 @@
 Improved: The preconditioner and solver setup in step-20 has been rewritten
 to highlight the new LinearOperator and PackagedOperation classes.
 
    
-(2019/02/08, Matthias Maier)
+(Matthias Maier, 2019/02/08)
diff --git a/doc/news/changes/minor/20180524MartinKronbichlerDenisDavydov b/doc/news/changes/minor/20180524MartinKronbichlerDenisDavydov
index 7ceb99438d25..23b1c066746c 100644
--- a/doc/news/changes/minor/20180524MartinKronbichlerDenisDavydov
+++ b/doc/news/changes/minor/20180524MartinKronbichlerDenisDavydov
@@ -5,4 +5,4 @@ with many blocks, rather than splitting each method into two parts for
 overlapping communication and computation. The latter is inefficient as soon
 as too many MPI requests are in flight.
 
    
-(Martin Kronbichler, Denis Davydov 2018/05/24)
+(Martin Kronbichler, Denis Davydov, 2018/05/24)
diff --git a/doc/news/changes/minor/20180529DenisDavydov b/doc/news/changes/minor/20180529DenisDavydov
index c2a26fb7ec37..942cac916f41 100644
--- a/doc/news/changes/minor/20180529DenisDavydov
+++ b/doc/news/changes/minor/20180529DenisDavydov
@@ -1,3 +1,3 @@
 Improved: TimerOutput now dynamically adjust to the the width of Section column.
 
    
-(Denis Davydov 2018/05/29)
+(Denis Davydov, 2018/05/29)
diff --git a/doc/news/changes/minor/20180529DenisDavydov_b b/doc/news/changes/minor/20180529DenisDavydov_b
index aed99f61361c..231c323f136a 100644
--- a/doc/news/changes/minor/20180529DenisDavydov_b
+++ b/doc/news/changes/minor/20180529DenisDavydov_b
@@ -1,4 +1,4 @@
 New: TimerOutput::cpu_and_wall_times_grouped will print CPU and
 wallclock time in a single table.
 
    
-(Denis Davydov 2018/05/29)
+(Denis Davydov, 2018/05/29)
diff --git a/doc/news/changes/minor/20180606SambitDas b/doc/news/changes/minor/20180606SambitDas
index ac62bd989571..cc39f0cf671a 100644
--- a/doc/news/changes/minor/20180606SambitDas
+++ b/doc/news/changes/minor/20180606SambitDas
@@ -1,3 +1,3 @@
 Improved: Extend ScaLAPACKMatrix::invert() to use pXtrtri for inversion of triangular matrices.
 
    
-(Sambit Das 2018/06/06)
+(Sambit Das, 2018/06/06)
diff --git a/doc/news/changes/minor/20180611MatthiasMaier b/doc/news/changes/minor/20180611MatthiasMaier
index 982f29806d83..1e0bf2ca2390 100644
--- a/doc/news/changes/minor/20180611MatthiasMaier
+++ b/doc/news/changes/minor/20180611MatthiasMaier
@@ -1,4 +1,4 @@
 Fixed: CMake now supports again in-source builds (This functionality was
 accidentally broken in the previous release).
 
    
-(Matthias Maier 2018/06/11)
+(Matthias Maier, 2018/06/11)
diff --git a/doc/news/changes/minor/20180612DenisDavydov b/doc/news/changes/minor/20180612DenisDavydov
index e9adf8101555..cf260cba941a 100644
--- a/doc/news/changes/minor/20180612DenisDavydov
+++ b/doc/news/changes/minor/20180612DenisDavydov
@@ -2,4 +2,4 @@ Bugfix: Fixed a bug where VectorDataExchange::ghosts_were_set was
 not set inside MatrixFree::cell_loop() for block vectors
 with many blocks.
 
    
-(Denis Davydov 2018/06/12)
+(Denis Davydov, 2018/06/12)
diff --git a/doc/news/changes/minor/20180614PiYuehChuang b/doc/news/changes/minor/20180614PiYuehChuang
index 62dd7e40c2f3..44bda16aa164 100644
--- a/doc/news/changes/minor/20180614PiYuehChuang
+++ b/doc/news/changes/minor/20180614PiYuehChuang
@@ -1,4 +1,4 @@
 Fixed: Mismatched numbers of components between the exact solution and 
 underlying FE in Step-51.
 
    
-(Pi-Yueh Chuang 2018/06/14)
+(Pi-Yueh Chuang, 2018/06/14)
diff --git a/doc/news/changes/minor/20180614UweKoecher b/doc/news/changes/minor/20180614UweKoecher
index 3d855ebc2e56..e12782b921f8 100644
--- a/doc/news/changes/minor/20180614UweKoecher
+++ b/doc/news/changes/minor/20180614UweKoecher
@@ -2,4 +2,4 @@ Bugfix: Fixed bugs for TrilinosWrapper::SparseMatrix::add(factor, other_matrix)
 and TrilinosWrapper::SparseMatrix::copy_from(other_matrix) for the case of
 non-contiguous rows.
 
    
-(Uwe Koecher 2018/06/14)
+(Uwe Koecher, 2018/06/14)
diff --git a/doc/news/changes/minor/20180621DenisDavydov b/doc/news/changes/minor/20180621DenisDavydov
index e996dfe6922d..28e18a78c00b 100644
--- a/doc/news/changes/minor/20180621DenisDavydov
+++ b/doc/news/changes/minor/20180621DenisDavydov
@@ -2,4 +2,4 @@ New: Extend get_vector_data_ranges() to return extra element in
 the tuple to represent DataComponentInterpretation. The functions
 were renamed to get_nonscalar_data_ranges().
 
    
-(Denis Davydov 2018/06/21)
+(Denis Davydov, 2018/06/21)
diff --git a/doc/news/changes/minor/20180621DenisDavydov_b b/doc/news/changes/minor/20180621DenisDavydov_b
index cd9ef39ad6d6..8b52b7dc6975 100644
--- a/doc/news/changes/minor/20180621DenisDavydov_b
+++ b/doc/news/changes/minor/20180621DenisDavydov_b
@@ -1,3 +1,4 @@
 New: Add support for output of tensor-valued data in
 DataOut::write_vtu().
-(Denis Davydov 2018/06/21)
+
    
+(Denis Davydov, 2018/06/21)
diff --git a/doc/news/changes/minor/20180706DenisDavydov b/doc/news/changes/minor/20180706DenisDavydov
index 0df86818f5e4..2a80d652b014 100644
--- a/doc/news/changes/minor/20180706DenisDavydov
+++ b/doc/news/changes/minor/20180706DenisDavydov
@@ -1,4 +1,4 @@
 New: Add GridGenerator::plate_with_a_hole() that generates a
 rectangular plate with an (offset) cylindrical hole.
 
    
-(Denis Davydov 2018/06/21)
+(Denis Davydov, 2018/06/21)
diff --git a/doc/news/changes/minor/20180726DenisDavydov b/doc/news/changes/minor/20180726DenisDavydov
index e279c877e59e..f19d6b7d91e8 100644
--- a/doc/news/changes/minor/20180726DenisDavydov
+++ b/doc/news/changes/minor/20180726DenisDavydov
@@ -1,3 +1,3 @@
 New: Add FiniteSizeHistory class to store a finite-size history of objects.
 
    
-(Denis Davydov 2018/07/26)
+(Denis Davydov, 2018/07/26)
diff --git a/doc/news/changes/minor/20180802DenisDavydov b/doc/news/changes/minor/20180802DenisDavydov
index 543dc6cd9775..c3b00e3a8331 100644
--- a/doc/news/changes/minor/20180802DenisDavydov
+++ b/doc/news/changes/minor/20180802DenisDavydov
@@ -1,4 +1,4 @@
 Fixed: Minor issues when using matrix-free cell categorization
 with multi-grid operators.
 
    
-(Denis Davydov 2018/08/02)
+(Denis Davydov, 2018/08/02)
diff --git a/doc/news/changes/minor/20180810BenjaminBrands b/doc/news/changes/minor/20180810BenjaminBrands
index 963c26bb6a20..44d7d40ce9d3 100644
--- a/doc/news/changes/minor/20180810BenjaminBrands
+++ b/doc/news/changes/minor/20180810BenjaminBrands
@@ -1,3 +1,3 @@
 Fixed: Bug using ScaLAPACKMatrix::save() and load() for configurations with pHDF5 in combination with serial HDF5 matrices from user code.
 
    
-(Benjamin Brands 2018/08/10)
+(Benjamin Brands, 2018/08/10)
diff --git a/doc/news/changes/minor/20180813AlexanderKnieps b/doc/news/changes/minor/20180813AlexanderKnieps
index 7a324b2f42bd..aada74e48131 100644
--- a/doc/news/changes/minor/20180813AlexanderKnieps
+++ b/doc/news/changes/minor/20180813AlexanderKnieps
@@ -1,3 +1,3 @@
 Fixed: MGConstrainedDofs::initialize(...) now handles refinement edges across periodic boundaries correctly.
 
    
-(Alexander Knieps 2018/08/13)
+(Alexander Knieps, 2018/08/13)
diff --git a/doc/news/changes/minor/20180821SvenjaSchoeder b/doc/news/changes/minor/20180821SvenjaSchoeder
index f8a03c2cf6ff..1e91757b2e95 100644
--- a/doc/news/changes/minor/20180821SvenjaSchoeder
+++ b/doc/news/changes/minor/20180821SvenjaSchoeder
@@ -2,4 +2,5 @@ New: Add a mask argument to filter out some vector lanes in FEEvaluationBase
 This is required for local time stepping using the MatrixFree framework,
 because some cells of batches must be excluded from read/write operations
 when operating on different time steps compared to their neighbor cells.
+
    
 (Svenja Schoeder, 2018/08/21)
diff --git a/doc/news/changes/minor/20180913DenisDavydov b/doc/news/changes/minor/20180913DenisDavydov
index 31324ece9746..3d6b6b3d4e97 100644
--- a/doc/news/changes/minor/20180913DenisDavydov
+++ b/doc/news/changes/minor/20180913DenisDavydov
@@ -1,3 +1,3 @@
 New: Add line minimization functions.
 
    
-(Denis Davydov 2018/09/13)
+(Denis Davydov, 2018/09/13)
diff --git a/doc/news/changes/minor/20180919DenisDavydov b/doc/news/changes/minor/20180919DenisDavydov
index 2c7ed701efcb..3588933927df 100644
--- a/doc/news/changes/minor/20180919DenisDavydov
+++ b/doc/news/changes/minor/20180919DenisDavydov
@@ -1,4 +1,4 @@
 New: extend Patterns::Tools::Convert to work with ComponentMask
 and std::unique_ptr.
 
    
-(Denis Davydov 2018/09/19)
+(Denis Davydov, 2018/09/19)
diff --git a/doc/news/changes/minor/20180920DenisDavydov b/doc/news/changes/minor/20180920DenisDavydov
index 38f78916f180..a1767d7433fd 100644
--- a/doc/news/changes/minor/20180920DenisDavydov
+++ b/doc/news/changes/minor/20180920DenisDavydov
@@ -1,4 +1,4 @@
 New: Add optional flag to ParameterHandler to skip undefined
 sections and parameters.
 
    
-(Denis Davydov 2018/09/20)
+(Denis Davydov, 2018/09/20)
diff --git a/doc/news/changes/minor/20181005DenisDavydov b/doc/news/changes/minor/20181005DenisDavydov
index d8e1aa30c94a..10e6241a5662 100644
--- a/doc/news/changes/minor/20181005DenisDavydov
+++ b/doc/news/changes/minor/20181005DenisDavydov
@@ -1,4 +1,4 @@
 New: Add inverse_Hilbert_space_filling_curve() to map points in dim-dimensional
 space to line index of the Hilbert space filling curve.
 
    
-(Denis Davydov 2018/10/05)
+(Denis Davydov, 2018/10/05)
diff --git a/doc/news/changes/minor/20190210MarcFehling b/doc/news/changes/minor/20190210MarcFehling
index 9a3e1e9f4751..ab3127585a65 100644
--- a/doc/news/changes/minor/20190210MarcFehling
+++ b/doc/news/changes/minor/20190210MarcFehling
@@ -3,4 +3,4 @@ that will register a finite element object without enumerating all
 degrees of freedom. In the hp case, the active_fe_indices will be
 initialized and communicated amongst all processors, additionally.
 
    
-(2019/02/10, Marc Fehling)
+(Marc Fehling, 2019/02/10)
diff --git a/doc/news/changes/minor/20190213MatthiasMaier b/doc/news/changes/minor/20190213MatthiasMaier
index 6d3a30db0f87..4307beeed445 100644
--- a/doc/news/changes/minor/20190213MatthiasMaier
+++ b/doc/news/changes/minor/20190213MatthiasMaier
@@ -2,4 +2,4 @@ Fixed: inverse_operator() now handles a (composite) LinearOperator, the
 temporary PreconditionIdentity(), or no argument as preconditioner argument
 correctly.
 
    
-(Matthias Maier 2018/06/11)
+(Matthias Maier, 2019/02/13)

From 45cf863d2d1dacca033ad79b313d8cec2460dd98 Mon Sep 17 00:00:00 2001
From: Denis Davydov 
Date: Tue, 5 Mar 2019 19:24:58 +0100
Subject: [PATCH 233/507] add more vector_access_XYZ internal function in
 FEEvaluation and improve const-correctness of reader class

---
 include/deal.II/matrix_free/fe_evaluation.h   | 209 ++++++++++++++++--
 .../fe_evaluation_type_traits_02.cc           |   9 +
 .../fe_evaluation_type_traits_02.output       |   6 +
 3 files changed, 205 insertions(+), 19 deletions(-)

diff --git a/include/deal.II/matrix_free/fe_evaluation.h b/include/deal.II/matrix_free/fe_evaluation.h
index 5d3b0f41288e..5ae7b1905cd0 100644
--- a/include/deal.II/matrix_free/fe_evaluation.h
+++ b/include/deal.II/matrix_free/fe_evaluation.h
@@ -36,6 +36,7 @@
 #include 
 #include 
 
+
 DEAL_II_NAMESPACE_OPEN
 
 
@@ -3592,6 +3593,96 @@ namespace internal
 
 
 
+  // same for const access
+  template ::value,
+                                    VectorType>::type * = nullptr>
+  inline typename VectorType::value_type
+  vector_access(const VectorType &vec, const unsigned int entry)
+  {
+    return vec.local_element(entry);
+  }
+
+
+
+  template ::value,
+                                    VectorType>::type * = nullptr>
+  inline void
+  vector_access_add(VectorType &                           vec,
+                    const unsigned int                     entry,
+                    const typename VectorType::value_type &val)
+  {
+    vec.add_local_element(entry, val);
+  }
+
+
+
+  template ::value,
+                                    VectorType>::type * = nullptr>
+  inline void
+  vector_access_add(VectorType &                           vec,
+                    const unsigned int                     entry,
+                    const typename VectorType::value_type &val)
+  {
+    vector_access(vec, entry) += val;
+  }
+
+
+
+  template ::value,
+                                    VectorType>::type * = nullptr>
+  inline void
+  vector_access_add_global(VectorType &                           vec,
+                           const types::global_dof_index          entry,
+                           const typename VectorType::value_type &val)
+  {
+    vec.add(entry, val);
+  }
+
+
+
+  template ::value,
+                                    VectorType>::type * = nullptr>
+  inline void
+  vector_access_add_global(VectorType &                           vec,
+                           const types::global_dof_index          entry,
+                           const typename VectorType::value_type &val)
+  {
+    vec(entry) += val;
+  }
+
+
+
+  template ::value,
+                                    VectorType>::type * = nullptr>
+  inline void
+  vector_access_set(VectorType &                           vec,
+                    const unsigned int                     entry,
+                    const typename VectorType::value_type &val)
+  {
+    vec.set_local_element(entry, val);
+  }
+
+
+
+  template ::value,
+                                    VectorType>::type * = nullptr>
+  inline void
+  vector_access_set(VectorType &                           vec,
+                    const unsigned int                     entry,
+                    const typename VectorType::value_type &val)
+  {
+    vector_access(vec, entry) = val;
+  }
+
+
+
   // this is to make sure that the parallel partitioning in VectorType
   // is really the same as stored in MatrixFree.
   // version below is when has_partitioners_are_compatible == false
@@ -3612,6 +3703,7 @@ namespace internal
   }
 
 
+
   // same as above for has_partitioners_are_compatible == true
   template <
     typename VectorType,
@@ -3632,17 +3724,28 @@ namespace internal
              "compatible vector."));
   }
 
-  // A class to use the same code to read from and write to vector
+
+
+  // Below, three classes (VectorReader, VectorSetter,
+  // VectorDistributorLocalToGlobal) implement the same interface and can be
+  // used to to read from vector, set elements of a vector and add to elements
+  // of the vector.
+
+  // 1. A class to read data from vector
   template 
   struct VectorReader
   {
     template 
     void
-    process_dof(const unsigned int index, VectorType &vec, Number &res) const
+    process_dof(const unsigned int index,
+                const VectorType & vec,
+                Number &           res) const
     {
       res = vector_access(vec, index);
     }
 
+
+
     template 
     void
     process_dofs_vectorized(const unsigned int       dofs_per_cell,
@@ -3658,11 +3761,12 @@ namespace internal
     }
 
 
+
     template 
     void
     process_dofs_vectorized(const unsigned int       dofs_per_cell,
                             const unsigned int       dof_index,
-                            VectorType &             vec,
+                            const VectorType &       vec,
                             VectorizedArray *dof_values,
                             std::integral_constant) const
     {
@@ -3673,6 +3777,8 @@ namespace internal
             vec, dof_index + v + i * VectorizedArray::n_array_elements);
     }
 
+
+
     template 
     void
     process_dofs_vectorized_transpose(const unsigned int       dofs_per_cell,
@@ -3688,11 +3794,12 @@ namespace internal
     }
 
 
+
     template 
     void
     process_dofs_vectorized_transpose(const unsigned int       dofs_per_cell,
                                       const unsigned int *     dof_indices,
-                                      VectorType &             vec,
+                                      const VectorType &       vec,
                                       VectorizedArray *dof_values,
                                       std::integral_constant) const
     {
@@ -3702,6 +3809,8 @@ namespace internal
           dof_values[d][v] = vector_access(vec, dof_indices[v] + d);
     }
 
+
+
     // variant where VectorType::value_type is the same as Number -> can call
     // gather
     template 
@@ -3715,12 +3824,14 @@ namespace internal
       res.gather(vec.begin() + constant_offset, indices);
     }
 
+
+
     // variant where VectorType::value_type is not the same as Number -> must
     // manually load the data
     template 
     void
     process_dof_gather(const unsigned int *     indices,
-                       VectorType &             vec,
+                       const VectorType &       vec,
                        const unsigned int       constant_offset,
                        VectorizedArray &res,
                        std::integral_constant) const
@@ -3730,37 +3841,47 @@ namespace internal
         res[v] = vector_access(vec, indices[v] + constant_offset);
     }
 
+
+
     template 
     void
     process_dof_global(const types::global_dof_index index,
-                       VectorType &                  vec,
+                       const VectorType &            vec,
                        Number &                      res) const
     {
-      res = const_cast(vec)(index);
+      res = vec(index);
     }
 
+
+
     void
     pre_constraints(const Number &, Number &res) const
     {
       res = Number();
     }
 
+
+
     template 
     void
     process_constraint(const unsigned int index,
                        const Number       weight,
-                       VectorType &       vec,
+                       const VectorType & vec,
                        Number &           res) const
     {
       res += weight * vector_access(vec, index);
     }
 
+
+
     void
     post_constraints(const Number &sum, Number &write_pos) const
     {
       write_pos = sum;
     }
 
+
+
     void
     process_empty(VectorizedArray &res) const
     {
@@ -3768,7 +3889,10 @@ namespace internal
     }
   };
 
-  // A class to use the same code to read from and write to vector
+
+
+  // 2. A class to add values to the vector during
+  // FEEvaluation::distribute_local_to_global() call
   template 
   struct VectorDistributorLocalToGlobal
   {
@@ -3776,9 +3900,11 @@ namespace internal
     void
     process_dof(const unsigned int index, VectorType &vec, Number &res) const
     {
-      vector_access(vec, index) += res;
+      vector_access_add(vec, index, res);
     }
 
+
+
     template 
     void
     process_dofs_vectorized(const unsigned int       dofs_per_cell,
@@ -3798,6 +3924,8 @@ namespace internal
         }
     }
 
+
+
     template 
     void
     process_dofs_vectorized(const unsigned int       dofs_per_cell,
@@ -3809,12 +3937,14 @@ namespace internal
       for (unsigned int i = 0; i < dofs_per_cell; ++i)
         for (unsigned int v = 0; v < VectorizedArray::n_array_elements;
              ++v)
-          vector_access(vec,
-                        dof_index + v +
-                          i * VectorizedArray::n_array_elements) +=
-            dof_values[i][v];
+          vector_access_add(vec,
+                            dof_index + v +
+                              i * VectorizedArray::n_array_elements,
+                            dof_values[i][v]);
     }
 
+
+
     template 
     void
     process_dofs_vectorized_transpose(const unsigned int       dofs_per_cell,
@@ -3827,6 +3957,8 @@ namespace internal
         true, dofs_per_cell, dof_values, dof_indices, vec.begin());
     }
 
+
+
     template 
     void
     process_dofs_vectorized_transpose(const unsigned int       dofs_per_cell,
@@ -3838,9 +3970,11 @@ namespace internal
       for (unsigned int d = 0; d < dofs_per_cell; ++d)
         for (unsigned int v = 0; v < VectorizedArray::n_array_elements;
              ++v)
-          vector_access(vec, dof_indices[v] + d) += dof_values[d][v];
+          vector_access_add(vec, dof_indices[v] + d, dof_values[d][v]);
     }
 
+
+
     // variant where VectorType::value_type is the same as Number -> can call
     // scatter
     template 
@@ -3864,6 +3998,8 @@ namespace internal
 #  endif
     }
 
+
+
     // variant where VectorType::value_type is not the same as Number -> must
     // manually append all data
     template 
@@ -3876,24 +4012,30 @@ namespace internal
     {
       for (unsigned int v = 0; v < VectorizedArray::n_array_elements;
            ++v)
-        vector_access(vec, indices[v] + constant_offset) += res[v];
+        vector_access_add(vec, indices[v] + constant_offset, res[v]);
     }
 
+
+
     template 
     void
     process_dof_global(const types::global_dof_index index,
                        VectorType &                  vec,
                        Number &                      res) const
     {
-      vec(index) += res;
+      vector_access_add_global(vec, index, res);
     }
 
+
+
     void
     pre_constraints(const Number &input, Number &res) const
     {
       res = input;
     }
 
+
+
     template 
     void
     process_constraint(const unsigned int index,
@@ -3901,20 +4043,25 @@ namespace internal
                        VectorType &       vec,
                        Number &           res) const
     {
-      vector_access(vec, index) += weight * res;
+      vector_access_add(vec, index, weight * res);
     }
 
+
+
     void
     post_constraints(const Number &, Number &) const
     {}
 
+
+
     void
     process_empty(VectorizedArray &) const
     {}
   };
 
 
-  // A class to use the same code to read from and write to vector
+
+  // 3. A class to set elements of the vector
   template 
   struct VectorSetter
   {
@@ -3925,6 +4072,8 @@ namespace internal
       vector_access(vec, index) = res;
     }
 
+
+
     template 
     void
     process_dofs_vectorized(const unsigned int       dofs_per_cell,
@@ -3939,6 +4088,8 @@ namespace internal
         dof_values[i].store(vec_ptr);
     }
 
+
+
     template 
     void
     process_dofs_vectorized(const unsigned int       dofs_per_cell,
@@ -3956,6 +4107,8 @@ namespace internal
             dof_values[i][v];
     }
 
+
+
     template 
     void
     process_dofs_vectorized_transpose(const unsigned int       dofs_per_cell,
@@ -3968,6 +4121,8 @@ namespace internal
         false, dofs_per_cell, dof_values, dof_indices, vec.begin());
     }
 
+
+
     template 
     void
     process_dofs_vectorized_transpose(const unsigned int       dofs_per_cell,
@@ -3982,6 +4137,8 @@ namespace internal
           vector_access(vec, dof_indices[v] + i) = dof_values[i][v];
     }
 
+
+
     template 
     void
     process_dof_gather(const unsigned int *     indices,
@@ -3993,6 +4150,8 @@ namespace internal
       res.scatter(indices, vec.begin() + constant_offset);
     }
 
+
+
     template 
     void
     process_dof_gather(const unsigned int *     indices,
@@ -4006,6 +4165,8 @@ namespace internal
         vector_access(vec, indices[v] + constant_offset) = res[v];
     }
 
+
+
     template 
     void
     process_dof_global(const types::global_dof_index index,
@@ -4015,10 +4176,14 @@ namespace internal
       vec(index) = res;
     }
 
+
+
     void
     pre_constraints(const Number &, Number &) const
     {}
 
+
+
     template 
     void
     process_constraint(const unsigned int,
@@ -4027,15 +4192,21 @@ namespace internal
                        Number &) const
     {}
 
+
+
     void
     post_constraints(const Number &, Number &) const
     {}
 
+
+
     void
     process_empty(VectorizedArray &) const
     {}
   };
 
+
+
   // allows to select between block vectors and non-block vectors, which
   // allows to use a unified interface for extracting blocks on block vectors
   // and doing nothing on usual vectors
diff --git a/tests/matrix_free/fe_evaluation_type_traits_02.cc b/tests/matrix_free/fe_evaluation_type_traits_02.cc
index f87bf95c1b00..6f57b2aab2d7 100644
--- a/tests/matrix_free/fe_evaluation_type_traits_02.cc
+++ b/tests/matrix_free/fe_evaluation_type_traits_02.cc
@@ -116,5 +116,14 @@ main()
           << internal::has_set_local_element>::value
           << std::endl;
 
+  // now check internal::vector_access_[set|add] wrappers
+  deallog << "internal::vector_access_set:" << std::endl;
+  internal::vector_access_set(dummy, 0, 0);
+  internal::vector_access_set(dummy2, 0, 0);
+
+  deallog << "internal::vector_access_add:" << std::endl;
+  internal::vector_access_add(dummy, 0, 0);
+  internal::vector_access_add(dummy2, 0, 0);
+
   deallog << "OK" << std::endl;
 }
diff --git a/tests/matrix_free/fe_evaluation_type_traits_02.output b/tests/matrix_free/fe_evaluation_type_traits_02.output
index d6fcec824872..8413d1fad52e 100644
--- a/tests/matrix_free/fe_evaluation_type_traits_02.output
+++ b/tests/matrix_free/fe_evaluation_type_traits_02.output
@@ -5,4 +5,10 @@ DEAL::Dummy2 = 0
 DEAL::has_set_local_element:
 DEAL::Dummy = 1
 DEAL::Dummy2 = 0
+DEAL::internal::vector_access_set:
+DEAL::Dummy::set_local_element()
+DEAL::Dummy2::local_element()
+DEAL::internal::vector_access_add:
+DEAL::Dummy::add_local_element()
+DEAL::Dummy2::local_element()
 DEAL::OK

From 74685cc3082336d0aff9560c43ba01dd6337a7ab Mon Sep 17 00:00:00 2001
From: Denis Davydov 
Date: Wed, 6 Mar 2019 13:43:08 +0100
Subject: [PATCH 234/507] add LA::d::Vector::set_ghost_state() and use it in
 VectorDataExchange::update_ghost_values_finish() to allow reading from ghosts
 in LA::d::Vector::local_element() const

---
 include/deal.II/lac/la_parallel_vector.h  | 16 ++++++++++++++++
 include/deal.II/matrix_free/matrix_free.h |  7 +++++++
 2 files changed, 23 insertions(+)

diff --git a/include/deal.II/lac/la_parallel_vector.h b/include/deal.II/lac/la_parallel_vector.h
index 840a5ca03116..8b7cbb9119ff 100644
--- a/include/deal.II/lac/la_parallel_vector.h
+++ b/include/deal.II/lac/la_parallel_vector.h
@@ -1192,6 +1192,13 @@ namespace LinearAlgebra
       bool
       partitioners_are_globally_compatible(
         const Utilities::MPI::Partitioner &part) const;
+
+      /**
+       * Change the ghost state of this vector to @p ghosted.
+       */
+      void
+      set_ghost_state(const bool ghosted) const;
+
       //@}
 
       /**
@@ -1812,6 +1819,15 @@ namespace LinearAlgebra
       return partitioner;
     }
 
+
+
+    template 
+    inline void
+    Vector::set_ghost_state(const bool ghosted) const
+    {
+      vector_is_ghosted = ghosted;
+    }
+
 #endif
 
   } // namespace distributed
diff --git a/include/deal.II/matrix_free/matrix_free.h b/include/deal.II/matrix_free/matrix_free.h
index a0134ebfe76d..e1d18fc083a7 100644
--- a/include/deal.II/matrix_free/matrix_free.h
+++ b/include/deal.II/matrix_free/matrix_free.h
@@ -2805,6 +2805,10 @@ namespace internal
           matrix_free.release_scratch_data_non_threadsafe(
             tmp_data[component_in_block_vector]);
           tmp_data[component_in_block_vector] = nullptr;
+
+          // let vector know that ghosts are being updated and we can read from
+          // them
+          vec.set_ghost_state(true);
 #  endif
         }
     }
@@ -2938,6 +2942,9 @@ namespace internal
                       .local_element(j + part.local_size()) = 0.;
                   }
             }
+
+          // let vector know that it's not ghosted anymore
+          vec.set_ghost_state(false);
 #  endif
         }
     }

From 2b4c20d6f4d9fe96e5d278b46eccdba079211967 Mon Sep 17 00:00:00 2001
From: Luca Heltai 
Date: Thu, 7 Mar 2019 15:51:44 +0100
Subject: [PATCH 235/507] Type to string.

---
 doc/news/changes/minor/20190307LucaHeltai |  4 +++
 include/deal.II/base/utilities.h          | 23 +++++++++++++++
 tests/base/utilities_15.cc                | 35 +++++++++++++++++++++++
 tests/base/utilities_15.output            |  4 +++
 4 files changed, 66 insertions(+)
 create mode 100644 doc/news/changes/minor/20190307LucaHeltai
 create mode 100644 tests/base/utilities_15.cc
 create mode 100644 tests/base/utilities_15.output

diff --git a/doc/news/changes/minor/20190307LucaHeltai b/doc/news/changes/minor/20190307LucaHeltai
new file mode 100644
index 000000000000..3dc9cf177e56
--- /dev/null
+++ b/doc/news/changes/minor/20190307LucaHeltai
@@ -0,0 +1,4 @@
+New: Added a new function Utilities::type_to_string() to demangle type names.
+
    
+(Luca Heltai, 2019/03/07)
+
diff --git a/include/deal.II/base/utilities.h b/include/deal.II/base/utilities.h
index f49c3021321b..9e3c8c278fc4 100644
--- a/include/deal.II/base/utilities.h
+++ b/include/deal.II/base/utilities.h
@@ -24,6 +24,7 @@
 #include 
 #include 
 #include 
+#include 
 #include 
 #include 
 
@@ -39,6 +40,7 @@
 
 #include 
 #include 
+#include 
 #include 
 #include 
 #include 
@@ -340,6 +342,18 @@ namespace Utilities
   double
   generate_normal_random_number(const double a, const double sigma);
 
+  /**
+   * Return a string description of the type of the variable @p t.
+   *
+   * In general, C++ uses mangled names to identify types. This function
+   * uses boost::core::demangle to return a human readable string describing
+   * the type of the variable passed as argument.
+   *
+   * @author Luca Heltai, 2019.
+   */
+  template 
+  std::string
+  type_to_string(const T &t);
 
   /**
    * Calculate a fixed power, provided as a template argument, of a number.
@@ -1019,6 +1033,15 @@ namespace Utilities
 
 
 
+  template 
+  inline std::string
+  type_to_string(const T &t)
+  {
+    return boost::core::demangle(typeid(t).name());
+  }
+
+
+
   template 
   inline Iterator
   lower_bound(Iterator first, Iterator last, const T &val)
diff --git a/tests/base/utilities_15.cc b/tests/base/utilities_15.cc
new file mode 100644
index 000000000000..e4054b9d2781
--- /dev/null
+++ b/tests/base/utilities_15.cc
@@ -0,0 +1,35 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2019 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+
+// test Utilities::type_to_string()
+
+#include 
+
+#include "../tests.h"
+
+int
+main()
+{
+  initlog();
+
+  double   a = 1.0;
+  int      b = 3;
+  Point<2> c;
+
+  deallog << Utilities::type_to_string(a) << std::endl
+          << Utilities::type_to_string(b) << std::endl
+          << Utilities::type_to_string(c) << std::endl;
+}
diff --git a/tests/base/utilities_15.output b/tests/base/utilities_15.output
new file mode 100644
index 000000000000..3e6cc9b262ef
--- /dev/null
+++ b/tests/base/utilities_15.output
@@ -0,0 +1,4 @@
+
+DEAL::double
+DEAL::int
+DEAL::dealii::Point<2, double>

From fa5b5beb0d66e21b114f3b4467115d4a4de0e757 Mon Sep 17 00:00:00 2001
From: Timo Heister 
Date: Thu, 7 Mar 2019 13:25:00 -0700
Subject: [PATCH 236/507] fix uninitialized reads

valgrind warns about uninitialized reads in the following two MPI
functions. The totals are only available on rank 0. Note that the value
doesn't matter as the results will be thrown away for rank !=0.
---
 source/distributed/grid_refinement.cc | 10 ++++++----
 1 file changed, 6 insertions(+), 4 deletions(-)

diff --git a/source/distributed/grid_refinement.cc b/source/distributed/grid_refinement.cc
index 6de9b6a6b8a5..ccd69d2c55b3 100644
--- a/source/distributed/grid_refinement.cc
+++ b/source/distributed/grid_refinement.cc
@@ -260,7 +260,8 @@ namespace
                             return c > test_threshold;
                           });
 
-          unsigned int total_count;
+          unsigned int total_count = 0;
+
           ierr = MPI_Reduce(&my_count,
                             &total_count,
                             1,
@@ -270,7 +271,7 @@ namespace
                             mpi_communicator);
           AssertThrowMPI(ierr);
 
-          // now adjust the range. if we have to many cells, we take the upper
+          // now adjust the range. if we have too many cells, we take the upper
           // half of the previous range, otherwise the lower half. if we have
           // hit the right number, then set the range to the exact value.
           // slave nodes also update their own interesting_range, however their
@@ -369,7 +370,8 @@ namespace
             if (criteria(i) > test_threshold)
               my_error += criteria(i);
 
-          double total_error;
+          double total_error = 0.;
+
           ierr = MPI_Reduce(&my_error,
                             &total_error,
                             1,
@@ -379,7 +381,7 @@ namespace
                             mpi_communicator);
           AssertThrowMPI(ierr);
 
-          // now adjust the range. if we have to many cells, we take the upper
+          // now adjust the range. if we have too many cells, we take the upper
           // half of the previous range, otherwise the lower half. if we have
           // hit the right number, then set the range to the exact value.
           // slave nodes also update their own interesting_range, however their

From cf869efca396e8f53d9a2ec727c6f37d0b6be1dc Mon Sep 17 00:00:00 2001
From: Bruno Turcksin 
Date: Wed, 6 Mar 2019 22:48:18 +0000
Subject: [PATCH 237/507] Fix a bug where add_and_dot was giving the wrong
 results if the vector size was greater than 4096

---
 doc/news/changes/minor/20190306BrunoTurcksin |  4 ++
 include/deal.II/lac/cuda_kernels.templates.h |  2 +-
 tests/cuda/cuda_vector_05.cu                 | 71 ++++++++++++++++++++
 tests/cuda/cuda_vector_05.output             |  2 +
 4 files changed, 78 insertions(+), 1 deletion(-)
 create mode 100644 doc/news/changes/minor/20190306BrunoTurcksin
 create mode 100644 tests/cuda/cuda_vector_05.cu
 create mode 100644 tests/cuda/cuda_vector_05.output

diff --git a/doc/news/changes/minor/20190306BrunoTurcksin b/doc/news/changes/minor/20190306BrunoTurcksin
new file mode 100644
index 000000000000..5bbf2b57151d
--- /dev/null
+++ b/doc/news/changes/minor/20190306BrunoTurcksin
@@ -0,0 +1,4 @@
+Fixed: LinearAlgebra::CUDAWrappers::Vector::add_and_dot was giving a wrong result
+if the size of vector was greater than 4096.
+
    
+(Bruno Turcksin, 2018/03/06)
diff --git a/include/deal.II/lac/cuda_kernels.templates.h b/include/deal.II/lac/cuda_kernels.templates.h
index cadeb4d11a39..d42e469329e1 100644
--- a/include/deal.II/lac/cuda_kernels.templates.h
+++ b/include/deal.II/lac/cuda_kernels.templates.h
@@ -517,7 +517,7 @@ namespace LinearAlgebra
         else
           res_buf[local_idx] = 0.;
 
-        for (unsigned int i = 1; i < block_size; ++i)
+        for (unsigned int i = 1; i < chunk_size; ++i)
           {
             const unsigned int idx = global_idx + i * block_size;
             if (idx < N)
diff --git a/tests/cuda/cuda_vector_05.cu b/tests/cuda/cuda_vector_05.cu
new file mode 100644
index 000000000000..d11c59877478
--- /dev/null
+++ b/tests/cuda/cuda_vector_05.cu
@@ -0,0 +1,71 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2019 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+
+#include 
+
+#include 
+#include 
+
+#include 
+#include 
+#include 
+
+#include "../tests.h"
+
+// There was a bug where add_and_dot would give the wrong result if the size of
+// the vectors was greater than BLOCK_SIZE*CHUNK_SIZE.
+
+void
+test()
+{
+  const unsigned int                          size = 4100;
+  LinearAlgebra::CUDAWrappers::Vector a(size);
+  LinearAlgebra::CUDAWrappers::Vector b(size);
+  Vector                              a_host(size);
+  Vector                              b_host(size);
+
+  LinearAlgebra::ReadWriteVector read_write_1(size);
+  LinearAlgebra::ReadWriteVector read_write_2(size);
+
+  for (unsigned int i = 0; i < size; ++i)
+    {
+      read_write_1[i] = i;
+      read_write_2[i] = 5. + i;
+      a_host[i]       = i;
+      b_host[i]       = 5. + i;
+    }
+
+  a.import(read_write_1, VectorOperation::insert);
+  b.import(read_write_2, VectorOperation::insert);
+  AssertThrow(a.add_and_dot(2., a, b) == a_host.add_and_dot(2., a_host, b_host),
+              ExcMessage("Problem in add_and_dot"));
+}
+
+
+int
+main(int argc, char **argv)
+{
+  initlog();
+  deallog.depth_console(0);
+
+  init_cuda();
+
+  test();
+
+  deallog << "OK" << std::endl;
+
+  return 0;
+}
diff --git a/tests/cuda/cuda_vector_05.output b/tests/cuda/cuda_vector_05.output
new file mode 100644
index 000000000000..0fd8fc12f0b4
--- /dev/null
+++ b/tests/cuda/cuda_vector_05.output
@@ -0,0 +1,2 @@
+
+DEAL::OK

From e68d75d19c94cd100b1b312669641b1f6a8bc90a Mon Sep 17 00:00:00 2001
From: Martin Kronbichler 
Date: Fri, 8 Mar 2019 19:13:06 +0100
Subject: [PATCH 238/507] Fix renumbering of mg dofs for FE_Q

---
 source/dofs/dof_handler_policy.cc             |  59 +++--
 tests/multigrid/renumbering_08.cc             | 130 ++++++++++
 ...mbering_08.with_p4est=true.mpirun=2.output | 227 ++++++++++++++++++
 3 files changed, 392 insertions(+), 24 deletions(-)
 create mode 100644 tests/multigrid/renumbering_08.cc
 create mode 100644 tests/multigrid/renumbering_08.with_p4est=true.mpirun=2.output

diff --git a/source/dofs/dof_handler_policy.cc b/source/dofs/dof_handler_policy.cc
index aa9b53c70372..a2f2eca38fe4 100644
--- a/source/dofs/dof_handler_policy.cc
+++ b/source/dofs/dof_handler_policy.cc
@@ -3097,6 +3097,7 @@ namespace internal
           const unsigned int         level,
           const bool                 check_validity)
         {
+          (void)check_validity;
           Assert(level < dof_handler.get_triangulation().n_levels(),
                  ExcInternalError());
 
@@ -3116,18 +3117,21 @@ namespace internal
                                  d,
                                  dof_handler.get_fe().dofs_per_vertex);
 
-                  if (check_validity)
-                    Assert(idx != numbers::invalid_dof_index,
-                           ExcInternalError());
-
                   if (idx != numbers::invalid_dof_index)
-                    i->set_index(level,
-                                 d,
-                                 dof_handler.get_fe().dofs_per_vertex,
-                                 (indices_we_care_about.size() == 0) ?
-                                   (new_numbers[idx]) :
-                                   (new_numbers[indices_we_care_about
-                                                  .index_within_set(idx)]));
+                    {
+                      Assert(check_validity == false ||
+                               (indices_we_care_about.size() > 0 ?
+                                  indices_we_care_about.is_element(idx) :
+                                  (idx < new_numbers.size())),
+                             ExcInternalError());
+                      i->set_index(level,
+                                   d,
+                                   dof_handler.get_fe().dofs_per_vertex,
+                                   (indices_we_care_about.size() == 0) ?
+                                     (new_numbers[idx]) :
+                                     (new_numbers[indices_we_care_about
+                                                    .index_within_set(idx)]));
+                    }
                 }
         }
 
@@ -3215,10 +3219,12 @@ namespace internal
               typename DoFHandler<2, spacedim>::level_cell_iterator cell,
                 endc = dof_handler.end(level);
               for (cell = dof_handler.begin(level); cell != endc; ++cell)
-                for (unsigned int line = 0;
-                     line < GeometryInfo<2>::faces_per_cell;
-                     ++line)
-                  cell->face(line)->set_user_flag();
+                if (cell->level_subdomain_id() !=
+                    numbers::artificial_subdomain_id)
+                  for (unsigned int line = 0;
+                       line < GeometryInfo<2>::faces_per_cell;
+                       ++line)
+                    cell->face(line)->set_user_flag();
 
               for (typename DoFHandler<2, spacedim>::cell_iterator cell =
                      dof_handler.begin();
@@ -3283,10 +3289,12 @@ namespace internal
               typename DoFHandler<3, spacedim>::level_cell_iterator cell,
                 endc = dof_handler.end(level);
               for (cell = dof_handler.begin(level); cell != endc; ++cell)
-                for (unsigned int line = 0;
-                     line < GeometryInfo<3>::lines_per_cell;
-                     ++line)
-                  cell->line(line)->set_user_flag();
+                if (cell->level_subdomain_id() !=
+                    numbers::artificial_subdomain_id)
+                  for (unsigned int line = 0;
+                       line < GeometryInfo<3>::lines_per_cell;
+                       ++line)
+                    cell->line(line)->set_user_flag();
 
               for (typename DoFHandler<3, spacedim>::cell_iterator cell =
                      dof_handler.begin();
@@ -3322,10 +3330,12 @@ namespace internal
               // those quads logically belong to the same level as the cell,
               // at least for isotropic refinement
               for (cell = dof_handler.begin(level); cell != endc; ++cell)
-                for (unsigned int quad = 0;
-                     quad < GeometryInfo<3>::quads_per_cell;
-                     ++quad)
-                  cell->quad(quad)->set_user_flag();
+                if (cell->level_subdomain_id() !=
+                    numbers::artificial_subdomain_id)
+                  for (unsigned int quad = 0;
+                       quad < GeometryInfo<3>::quads_per_cell;
+                       ++quad)
+                    cell->quad(quad)->set_user_flag();
 
               for (typename DoFHandler<3, spacedim>::cell_iterator cell =
                      dof_handler.begin();
@@ -5898,7 +5908,8 @@ namespace internal
 
         // in case we do not own any of the given level (but only some remote
         // processor), we do not need to call the renumbering
-        if (level < this->dof_handler->get_triangulation().n_levels())
+        if (level < this->dof_handler->get_triangulation().n_levels() &&
+            relevant_dofs.n_elements() > 0)
           Implementation::renumber_mg_dofs(
             ghosted_new_numbers, relevant_dofs, *dof_handler, level, true);
 #else
diff --git a/tests/multigrid/renumbering_08.cc b/tests/multigrid/renumbering_08.cc
new file mode 100644
index 000000000000..64d388beb44d
--- /dev/null
+++ b/tests/multigrid/renumbering_08.cc
@@ -0,0 +1,130 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2019 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+
+// check renumbering the degrees of freedom on the multigrid levels in
+// parallel for FE_Q, otherwise similar to renumbering_05
+
+#include 
+
+#include 
+
+#include 
+
+#include 
+#include 
+
+#include 
+
+#include "../tests.h"
+
+using namespace std;
+
+
+template 
+void
+print_dof_numbers(const DoFHandler &dof)
+{
+  std::vector dof_indices(dof.get_fe().dofs_per_cell);
+  deallog << "DoF numbers on active cells" << std::endl;
+  for (auto cell : dof.active_cell_iterators())
+    if (!cell->is_artificial())
+      {
+        cell->get_dof_indices(dof_indices);
+        deallog << "cell " << cell->id() << ": ";
+        for (types::global_dof_index i : dof_indices)
+          deallog << i << " ";
+        deallog << std::endl;
+      }
+  for (unsigned int l = 0; l < dof.get_triangulation().n_global_levels(); ++l)
+    {
+      deallog << "DoF numbers on level " << l << std::endl;
+      for (auto cell : dof.cell_iterators_on_level(l))
+        if (cell->level_subdomain_id() != numbers::artificial_subdomain_id)
+          {
+            cell->get_mg_dof_indices(dof_indices);
+            deallog << "cell " << cell->id() << ": ";
+            for (types::global_dof_index i : dof_indices)
+              deallog << i << " ";
+            deallog << std::endl;
+          }
+    }
+}
+
+template 
+void
+check()
+{
+  FE_Q fe(2);
+
+  parallel::distributed::Triangulation tr(
+    MPI_COMM_WORLD,
+    Triangulation::limit_level_difference_at_vertices,
+    parallel::distributed::Triangulation::construct_multigrid_hierarchy);
+  for (unsigned int cycle = 0; cycle < 5; ++cycle)
+    {
+      tr.clear();
+      const unsigned int n_refine  = cycle / 3;
+      const unsigned int remainder = cycle % 3;
+      Point         p1;
+      for (unsigned int d = 0; d < dim; ++d)
+        p1[d] = -1;
+      Point p2;
+      for (unsigned int d = 0; d < remainder; ++d)
+        p2[d] = 2.8;
+      for (unsigned int d = remainder; d < dim; ++d)
+        p2[d] = 1;
+      std::vector subdivisions(dim, 1);
+      for (unsigned int d = 0; d < remainder; ++d)
+        subdivisions[d] = 2;
+      GridGenerator::subdivided_hyper_rectangle(tr, subdivisions, p1, p2);
+
+      DoFHandler mgdof(tr);
+      mgdof.distribute_dofs(fe);
+      mgdof.distribute_mg_dofs();
+
+      print_dof_numbers(mgdof);
+
+      // compute a renumbering on the level degrees of freedom by simply
+      // flipping the local numbers
+      for (unsigned int l = 0; l < tr.n_global_levels(); ++l)
+        {
+          std::vector new_indices;
+          if (mgdof.locally_owned_mg_dofs(l).n_elements() > 0)
+            {
+              const types::global_dof_index first =
+                mgdof.locally_owned_mg_dofs(l).nth_index_in_set(0);
+              const types::global_dof_index last =
+                first + mgdof.locally_owned_mg_dofs(l).n_elements();
+              for (unsigned int i = 0; i < last - first; ++i)
+                new_indices.push_back(last - 1 - i);
+            }
+          mgdof.renumber_dofs(l, new_indices);
+        }
+
+      print_dof_numbers(mgdof);
+    }
+}
+
+
+int
+main(int argc, char **argv)
+{
+  Utilities::MPI::MPI_InitFinalize mpi(argc, argv);
+  MPILogInitAll                    log;
+
+  check<2>();
+  check<3>();
+}
diff --git a/tests/multigrid/renumbering_08.with_p4est=true.mpirun=2.output b/tests/multigrid/renumbering_08.with_p4est=true.mpirun=2.output
new file mode 100644
index 000000000000..9f389f39c949
--- /dev/null
+++ b/tests/multigrid/renumbering_08.with_p4est=true.mpirun=2.output
@@ -0,0 +1,227 @@
+
+DEAL:0::DoF numbers on active cells
+DEAL:0::DoF numbers on level 0
+DEAL:0::DoF numbers on active cells
+DEAL:0::DoF numbers on level 0
+DEAL:0::DoF numbers on active cells
+DEAL:0::cell 0_0:: 0 1 2 3 4 5 6 7 8 
+DEAL:0::cell 1_0:: 1 9 3 10 5 11 12 13 14 
+DEAL:0::DoF numbers on level 0
+DEAL:0::cell 0_0:: 0 1 2 3 4 5 6 7 8 
+DEAL:0::cell 1_0:: 1 9 3 10 5 11 12 13 14 
+DEAL:0::DoF numbers on active cells
+DEAL:0::cell 0_0:: 0 1 2 3 4 5 6 7 8 
+DEAL:0::cell 1_0:: 1 9 3 10 5 11 12 13 14 
+DEAL:0::DoF numbers on level 0
+DEAL:0::cell 0_0:: 8 7 6 5 4 3 2 1 0 
+DEAL:0::cell 1_0:: 7 14 5 13 3 12 11 10 9 
+DEAL:0::DoF numbers on active cells
+DEAL:0::cell 0_0:: 0 1 2 3 4 5 6 7 8 
+DEAL:0::cell 1_0:: 1 9 3 10 5 11 12 13 14 
+DEAL:0::cell 2_0:: 2 3 15 16 17 18 7 19 20 
+DEAL:0::cell 3_0:: 3 10 16 21 18 22 13 23 24 
+DEAL:0::DoF numbers on level 0
+DEAL:0::cell 0_0:: 0 1 2 3 4 5 6 7 8 
+DEAL:0::cell 1_0:: 1 9 3 10 5 11 12 13 14 
+DEAL:0::cell 2_0:: 2 3 15 16 17 18 7 19 20 
+DEAL:0::cell 3_0:: 3 10 16 21 18 22 13 23 24 
+DEAL:0::DoF numbers on active cells
+DEAL:0::cell 0_0:: 0 1 2 3 4 5 6 7 8 
+DEAL:0::cell 1_0:: 1 9 3 10 5 11 12 13 14 
+DEAL:0::cell 2_0:: 2 3 15 16 17 18 7 19 20 
+DEAL:0::cell 3_0:: 3 10 16 21 18 22 13 23 24 
+DEAL:0::DoF numbers on level 0
+DEAL:0::cell 0_0:: 14 13 12 11 10 9 8 7 6 
+DEAL:0::cell 1_0:: 13 5 11 4 9 3 2 1 0 
+DEAL:0::cell 2_0:: 12 11 24 23 22 21 7 20 19 
+DEAL:0::cell 3_0:: 11 4 23 18 21 17 1 16 15 
+DEAL:0::DoF numbers on active cells
+DEAL:0::DoF numbers on level 0
+DEAL:0::DoF numbers on active cells
+DEAL:0::DoF numbers on level 0
+DEAL:0::DoF numbers on active cells
+DEAL:0::cell 0_0:: 0 1 2 3 4 5 6 7 8 
+DEAL:0::cell 1_0:: 1 9 3 10 5 11 12 13 14 
+DEAL:0::DoF numbers on level 0
+DEAL:0::cell 0_0:: 0 1 2 3 4 5 6 7 8 
+DEAL:0::cell 1_0:: 1 9 3 10 5 11 12 13 14 
+DEAL:0::DoF numbers on active cells
+DEAL:0::cell 0_0:: 0 1 2 3 4 5 6 7 8 
+DEAL:0::cell 1_0:: 1 9 3 10 5 11 12 13 14 
+DEAL:0::DoF numbers on level 0
+DEAL:0::cell 0_0:: 8 7 6 5 4 3 2 1 0 
+DEAL:0::cell 1_0:: 7 14 5 13 3 12 11 10 9 
+DEAL:0::DoF numbers on active cells
+DEAL:0::DoF numbers on level 0
+DEAL:0::DoF numbers on active cells
+DEAL:0::DoF numbers on level 0
+DEAL:0::DoF numbers on active cells
+DEAL:0::cell 0_0:: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 
+DEAL:0::cell 1_0:: 1 27 3 28 5 29 7 30 9 31 32 33 13 34 35 36 17 37 19 38 21 39 40 41 42 43 44 
+DEAL:0::DoF numbers on level 0
+DEAL:0::cell 0_0:: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 
+DEAL:0::cell 1_0:: 1 27 3 28 5 29 7 30 9 31 32 33 13 34 35 36 17 37 19 38 21 39 40 41 42 43 44 
+DEAL:0::DoF numbers on active cells
+DEAL:0::cell 0_0:: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 
+DEAL:0::cell 1_0:: 1 27 3 28 5 29 7 30 9 31 32 33 13 34 35 36 17 37 19 38 21 39 40 41 42 43 44 
+DEAL:0::DoF numbers on level 0
+DEAL:0::cell 0_0:: 26 25 24 23 22 21 20 19 18 17 16 15 14 13 12 11 10 9 8 7 6 5 4 3 2 1 0 
+DEAL:0::cell 1_0:: 25 44 23 43 21 42 19 41 17 40 39 38 13 37 36 35 9 34 7 33 5 32 31 30 29 28 27 
+DEAL:0::DoF numbers on active cells
+DEAL:0::cell 0_0:: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 
+DEAL:0::cell 1_0:: 1 27 3 28 5 29 7 30 9 31 32 33 13 34 35 36 17 37 19 38 21 39 40 41 42 43 44 
+DEAL:0::cell 2_0:: 2 3 45 46 6 7 47 48 49 50 11 51 52 53 15 54 18 19 55 56 57 58 23 59 60 61 62 
+DEAL:0::cell 3_0:: 3 28 46 63 7 30 48 64 50 65 33 66 53 67 36 68 19 38 56 69 58 70 41 71 72 73 74 
+DEAL:0::DoF numbers on level 0
+DEAL:0::cell 0_0:: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 
+DEAL:0::cell 1_0:: 1 27 3 28 5 29 7 30 9 31 32 33 13 34 35 36 17 37 19 38 21 39 40 41 42 43 44 
+DEAL:0::cell 2_0:: 2 3 45 46 6 7 47 48 49 50 11 51 52 53 15 54 18 19 55 56 57 58 23 59 60 61 62 
+DEAL:0::cell 3_0:: 3 28 46 63 7 30 48 64 50 65 33 66 53 67 36 68 19 38 56 69 58 70 41 71 72 73 74 
+DEAL:0::DoF numbers on active cells
+DEAL:0::cell 0_0:: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 
+DEAL:0::cell 1_0:: 1 27 3 28 5 29 7 30 9 31 32 33 13 34 35 36 17 37 19 38 21 39 40 41 42 43 44 
+DEAL:0::cell 2_0:: 2 3 45 46 6 7 47 48 49 50 11 51 52 53 15 54 18 19 55 56 57 58 23 59 60 61 62 
+DEAL:0::cell 3_0:: 3 28 46 63 7 30 48 64 50 65 33 66 53 67 36 68 19 38 56 69 58 70 41 71 72 73 74 
+DEAL:0::DoF numbers on level 0
+DEAL:0::cell 0_0:: 44 43 42 41 40 39 38 37 36 35 34 33 32 31 30 29 28 27 26 25 24 23 22 21 20 19 18 
+DEAL:0::cell 1_0:: 43 17 41 16 39 15 37 14 35 13 12 11 31 10 9 8 27 7 25 6 23 5 4 3 2 1 0 
+DEAL:0::cell 2_0:: 42 41 74 73 38 37 72 71 70 69 33 68 67 66 29 65 26 25 64 63 62 61 21 60 59 58 57 
+DEAL:0::cell 3_0:: 41 16 73 56 37 14 71 55 69 54 11 53 66 52 8 51 25 6 63 50 61 49 3 48 47 46 45 
+DEAL:0::DoF numbers on active cells
+DEAL:0::DoF numbers on level 0
+DEAL:0::DoF numbers on active cells
+DEAL:0::DoF numbers on level 0
+DEAL:0::DoF numbers on active cells
+DEAL:0::cell 0_0:: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 
+DEAL:0::cell 1_0:: 1 27 3 28 5 29 7 30 9 31 32 33 13 34 35 36 17 37 19 38 21 39 40 41 42 43 44 
+DEAL:0::DoF numbers on level 0
+DEAL:0::cell 0_0:: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 
+DEAL:0::cell 1_0:: 1 27 3 28 5 29 7 30 9 31 32 33 13 34 35 36 17 37 19 38 21 39 40 41 42 43 44 
+DEAL:0::DoF numbers on active cells
+DEAL:0::cell 0_0:: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 
+DEAL:0::cell 1_0:: 1 27 3 28 5 29 7 30 9 31 32 33 13 34 35 36 17 37 19 38 21 39 40 41 42 43 44 
+DEAL:0::DoF numbers on level 0
+DEAL:0::cell 0_0:: 26 25 24 23 22 21 20 19 18 17 16 15 14 13 12 11 10 9 8 7 6 5 4 3 2 1 0 
+DEAL:0::cell 1_0:: 25 44 23 43 21 42 19 41 17 40 39 38 13 37 36 35 9 34 7 33 5 32 31 30 29 28 27 
+
+DEAL:1::DoF numbers on active cells
+DEAL:1::cell 0_0:: 0 1 2 3 4 5 6 7 8 
+DEAL:1::DoF numbers on level 0
+DEAL:1::cell 0_0:: 0 1 2 3 4 5 6 7 8 
+DEAL:1::DoF numbers on active cells
+DEAL:1::cell 0_0:: 0 1 2 3 4 5 6 7 8 
+DEAL:1::DoF numbers on level 0
+DEAL:1::cell 0_0:: 8 7 6 5 4 3 2 1 0 
+DEAL:1::DoF numbers on active cells
+DEAL:1::cell 0_0:: 0 1 2 3 4 5 6 7 8 
+DEAL:1::cell 1_0:: 1 9 3 10 5 11 12 13 14 
+DEAL:1::DoF numbers on level 0
+DEAL:1::cell 0_0:: 0 1 2 3 4 5 6 7 8 
+DEAL:1::cell 1_0:: 1 9 3 10 5 11 12 13 14 
+DEAL:1::DoF numbers on active cells
+DEAL:1::cell 0_0:: 0 1 2 3 4 5 6 7 8 
+DEAL:1::cell 1_0:: 1 9 3 10 5 11 12 13 14 
+DEAL:1::DoF numbers on level 0
+DEAL:1::cell 0_0:: 8 7 6 5 4 3 2 1 0 
+DEAL:1::cell 1_0:: 7 14 5 13 3 12 11 10 9 
+DEAL:1::DoF numbers on active cells
+DEAL:1::cell 0_0:: 0 1 2 3 4 5 6 7 8 
+DEAL:1::cell 1_0:: 1 9 3 10 5 11 12 13 14 
+DEAL:1::cell 2_0:: 2 3 15 16 17 18 7 19 20 
+DEAL:1::cell 3_0:: 3 10 16 21 18 22 13 23 24 
+DEAL:1::DoF numbers on level 0
+DEAL:1::cell 0_0:: 0 1 2 3 4 5 6 7 8 
+DEAL:1::cell 1_0:: 1 9 3 10 5 11 12 13 14 
+DEAL:1::cell 2_0:: 2 3 15 16 17 18 7 19 20 
+DEAL:1::cell 3_0:: 3 10 16 21 18 22 13 23 24 
+DEAL:1::DoF numbers on active cells
+DEAL:1::cell 0_0:: 0 1 2 3 4 5 6 7 8 
+DEAL:1::cell 1_0:: 1 9 3 10 5 11 12 13 14 
+DEAL:1::cell 2_0:: 2 3 15 16 17 18 7 19 20 
+DEAL:1::cell 3_0:: 3 10 16 21 18 22 13 23 24 
+DEAL:1::DoF numbers on level 0
+DEAL:1::cell 0_0:: 14 13 12 11 10 9 8 7 6 
+DEAL:1::cell 1_0:: 13 5 11 4 9 3 2 1 0 
+DEAL:1::cell 2_0:: 12 11 24 23 22 21 7 20 19 
+DEAL:1::cell 3_0:: 11 4 23 18 21 17 1 16 15 
+DEAL:1::DoF numbers on active cells
+DEAL:1::cell 0_0:: 0 1 2 3 4 5 6 7 8 
+DEAL:1::DoF numbers on level 0
+DEAL:1::cell 0_0:: 0 1 2 3 4 5 6 7 8 
+DEAL:1::DoF numbers on active cells
+DEAL:1::cell 0_0:: 0 1 2 3 4 5 6 7 8 
+DEAL:1::DoF numbers on level 0
+DEAL:1::cell 0_0:: 8 7 6 5 4 3 2 1 0 
+DEAL:1::DoF numbers on active cells
+DEAL:1::cell 0_0:: 0 1 2 3 4 5 6 7 8 
+DEAL:1::cell 1_0:: 1 9 3 10 5 11 12 13 14 
+DEAL:1::DoF numbers on level 0
+DEAL:1::cell 0_0:: 0 1 2 3 4 5 6 7 8 
+DEAL:1::cell 1_0:: 1 9 3 10 5 11 12 13 14 
+DEAL:1::DoF numbers on active cells
+DEAL:1::cell 0_0:: 0 1 2 3 4 5 6 7 8 
+DEAL:1::cell 1_0:: 1 9 3 10 5 11 12 13 14 
+DEAL:1::DoF numbers on level 0
+DEAL:1::cell 0_0:: 8 7 6 5 4 3 2 1 0 
+DEAL:1::cell 1_0:: 7 14 5 13 3 12 11 10 9 
+DEAL:1::DoF numbers on active cells
+DEAL:1::cell 0_0:: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 
+DEAL:1::DoF numbers on level 0
+DEAL:1::cell 0_0:: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 
+DEAL:1::DoF numbers on active cells
+DEAL:1::cell 0_0:: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 
+DEAL:1::DoF numbers on level 0
+DEAL:1::cell 0_0:: 26 25 24 23 22 21 20 19 18 17 16 15 14 13 12 11 10 9 8 7 6 5 4 3 2 1 0 
+DEAL:1::DoF numbers on active cells
+DEAL:1::cell 0_0:: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 
+DEAL:1::cell 1_0:: 1 27 3 28 5 29 7 30 9 31 32 33 13 34 35 36 17 37 19 38 21 39 40 41 42 43 44 
+DEAL:1::DoF numbers on level 0
+DEAL:1::cell 0_0:: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 
+DEAL:1::cell 1_0:: 1 27 3 28 5 29 7 30 9 31 32 33 13 34 35 36 17 37 19 38 21 39 40 41 42 43 44 
+DEAL:1::DoF numbers on active cells
+DEAL:1::cell 0_0:: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 
+DEAL:1::cell 1_0:: 1 27 3 28 5 29 7 30 9 31 32 33 13 34 35 36 17 37 19 38 21 39 40 41 42 43 44 
+DEAL:1::DoF numbers on level 0
+DEAL:1::cell 0_0:: 26 25 24 23 22 21 20 19 18 17 16 15 14 13 12 11 10 9 8 7 6 5 4 3 2 1 0 
+DEAL:1::cell 1_0:: 25 44 23 43 21 42 19 41 17 40 39 38 13 37 36 35 9 34 7 33 5 32 31 30 29 28 27 
+DEAL:1::DoF numbers on active cells
+DEAL:1::cell 0_0:: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 
+DEAL:1::cell 1_0:: 1 27 3 28 5 29 7 30 9 31 32 33 13 34 35 36 17 37 19 38 21 39 40 41 42 43 44 
+DEAL:1::cell 2_0:: 2 3 45 46 6 7 47 48 49 50 11 51 52 53 15 54 18 19 55 56 57 58 23 59 60 61 62 
+DEAL:1::cell 3_0:: 3 28 46 63 7 30 48 64 50 65 33 66 53 67 36 68 19 38 56 69 58 70 41 71 72 73 74 
+DEAL:1::DoF numbers on level 0
+DEAL:1::cell 0_0:: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 
+DEAL:1::cell 1_0:: 1 27 3 28 5 29 7 30 9 31 32 33 13 34 35 36 17 37 19 38 21 39 40 41 42 43 44 
+DEAL:1::cell 2_0:: 2 3 45 46 6 7 47 48 49 50 11 51 52 53 15 54 18 19 55 56 57 58 23 59 60 61 62 
+DEAL:1::cell 3_0:: 3 28 46 63 7 30 48 64 50 65 33 66 53 67 36 68 19 38 56 69 58 70 41 71 72 73 74 
+DEAL:1::DoF numbers on active cells
+DEAL:1::cell 0_0:: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 
+DEAL:1::cell 1_0:: 1 27 3 28 5 29 7 30 9 31 32 33 13 34 35 36 17 37 19 38 21 39 40 41 42 43 44 
+DEAL:1::cell 2_0:: 2 3 45 46 6 7 47 48 49 50 11 51 52 53 15 54 18 19 55 56 57 58 23 59 60 61 62 
+DEAL:1::cell 3_0:: 3 28 46 63 7 30 48 64 50 65 33 66 53 67 36 68 19 38 56 69 58 70 41 71 72 73 74 
+DEAL:1::DoF numbers on level 0
+DEAL:1::cell 0_0:: 44 43 42 41 40 39 38 37 36 35 34 33 32 31 30 29 28 27 26 25 24 23 22 21 20 19 18 
+DEAL:1::cell 1_0:: 43 17 41 16 39 15 37 14 35 13 12 11 31 10 9 8 27 7 25 6 23 5 4 3 2 1 0 
+DEAL:1::cell 2_0:: 42 41 74 73 38 37 72 71 70 69 33 68 67 66 29 65 26 25 64 63 62 61 21 60 59 58 57 
+DEAL:1::cell 3_0:: 41 16 73 56 37 14 71 55 69 54 11 53 66 52 8 51 25 6 63 50 61 49 3 48 47 46 45 
+DEAL:1::DoF numbers on active cells
+DEAL:1::cell 0_0:: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 
+DEAL:1::DoF numbers on level 0
+DEAL:1::cell 0_0:: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 
+DEAL:1::DoF numbers on active cells
+DEAL:1::cell 0_0:: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 
+DEAL:1::DoF numbers on level 0
+DEAL:1::cell 0_0:: 26 25 24 23 22 21 20 19 18 17 16 15 14 13 12 11 10 9 8 7 6 5 4 3 2 1 0 
+DEAL:1::DoF numbers on active cells
+DEAL:1::cell 0_0:: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 
+DEAL:1::cell 1_0:: 1 27 3 28 5 29 7 30 9 31 32 33 13 34 35 36 17 37 19 38 21 39 40 41 42 43 44 
+DEAL:1::DoF numbers on level 0
+DEAL:1::cell 0_0:: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 
+DEAL:1::cell 1_0:: 1 27 3 28 5 29 7 30 9 31 32 33 13 34 35 36 17 37 19 38 21 39 40 41 42 43 44 
+DEAL:1::DoF numbers on active cells
+DEAL:1::cell 0_0:: 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 
+DEAL:1::cell 1_0:: 1 27 3 28 5 29 7 30 9 31 32 33 13 34 35 36 17 37 19 38 21 39 40 41 42 43 44 
+DEAL:1::DoF numbers on level 0
+DEAL:1::cell 0_0:: 26 25 24 23 22 21 20 19 18 17 16 15 14 13 12 11 10 9 8 7 6 5 4 3 2 1 0 
+DEAL:1::cell 1_0:: 25 44 23 43 21 42 19 41 17 40 39 38 13 37 36 35 9 34 7 33 5 32 31 30 29 28 27 
+

From 0f870e05318229d0edf00e05f3c93739fc7e4f73 Mon Sep 17 00:00:00 2001
From: Martin Kronbichler 
Date: Fri, 8 Mar 2019 19:13:14 +0100
Subject: [PATCH 239/507] Add changelog

---
 doc/news/changes/minor/20190308MartinKronbichler | 5 +++++
 1 file changed, 5 insertions(+)
 create mode 100644 doc/news/changes/minor/20190308MartinKronbichler

diff --git a/doc/news/changes/minor/20190308MartinKronbichler b/doc/news/changes/minor/20190308MartinKronbichler
new file mode 100644
index 000000000000..714316a34d7b
--- /dev/null
+++ b/doc/news/changes/minor/20190308MartinKronbichler
@@ -0,0 +1,5 @@
+Fixed: DoFHandler::renumber_dofs() called on levels would previously run into
+an assertion on distributed triangulation when used with continuous
+elements. This is now fixed.
+
    
+(Martin Kronbichler, 2019/03/08)

From c58e98040508b2581a6ed3a59cce9d0a9a94ab22 Mon Sep 17 00:00:00 2001
From: Denis Davydov 
Date: Wed, 6 Mar 2019 17:52:18 +0100
Subject: [PATCH 240/507] add internal type-traits to be used with
 VectorDataExchange of matrix-free framework

---
 include/deal.II/matrix_free/fe_evaluation.h   | 151 +-------
 include/deal.II/matrix_free/matrix_free.h     |   1 +
 include/deal.II/matrix_free/type_traits.h     | 328 ++++++++++++++++++
 tests/matrix_free/matrix_free_type_traits.cc  |  94 +++++
 ...free_type_traits.with_trilinos=true.output |  22 ++
 5 files changed, 447 insertions(+), 149 deletions(-)
 create mode 100644 include/deal.II/matrix_free/type_traits.h
 create mode 100644 tests/matrix_free/matrix_free_type_traits.cc
 create mode 100644 tests/matrix_free/matrix_free_type_traits.with_trilinos=true.output

diff --git a/include/deal.II/matrix_free/fe_evaluation.h b/include/deal.II/matrix_free/fe_evaluation.h
index 5ae7b1905cd0..0a8e2c29e259 100644
--- a/include/deal.II/matrix_free/fe_evaluation.h
+++ b/include/deal.II/matrix_free/fe_evaluation.h
@@ -35,6 +35,7 @@
 #include 
 #include 
 #include 
+#include 
 
 
 DEAL_II_NAMESPACE_OPEN
@@ -3401,155 +3402,7 @@ FEEvaluationBase::read_cell_data(
 
 namespace internal
 {
-  // a helper type-trait that leverage SFINAE to figure out if type T has
-  // ... T::local_element() const
-  template 
-  struct has_local_element
-  {
-  private:
-    // this will work always.
-    // we let it be void as we know T::local_element() (if exists) should
-    // certainly return something
-    static void
-    detect(...);
-
-    // this detecter will work only if we have "... T::local_element() const"
-    // and its return type will be the same as local_element(),
-    // that we expect to be T::value_type
-    template 
-    static decltype(std::declval().local_element(0))
-    detect(const U &);
-
-  public:
-    // finally here we check if our detector has non-void return type
-    // T::value_type. This will happen if compiler can use second detector,
-    // otherwise SFINAE let it work with the more general first one that is void
-    static const bool value =
-      !std::is_same()))>::value;
-  };
-
-  // We need to have a separate declaration for static const members
-  template 
-  const bool has_local_element::value;
-
-
-
-  // a helper type-trait that leverage SFINAE to figure out if type T has
-  // void T::add_local_element(const uint, const typename T::value_type)
-  template 
-  struct has_add_local_element
-  {
-  private:
-    static int
-    detect(...);
-
-    template 
-    static decltype(
-      std::declval().add_local_element(0, typename T::value_type()))
-    detect(const U &);
-
-  public:
-    static const bool value =
-      !std::is_same()))>::value;
-  };
-
-  // We need to have a separate declaration for static const members
-  template 
-  const bool has_add_local_element::value;
-
-
-
-  // a helper type-trait that leverage SFINAE to figure out if type T has
-  // void T::set_local_element(const uint, const typename T::value_type)
-  template 
-  struct has_set_local_element
-  {
-  private:
-    static int
-    detect(...);
-
-    template 
-    static decltype(
-      std::declval().set_local_element(0, typename T::value_type()))
-    detect(const U &);
-
-  public:
-    static const bool value =
-      !std::is_same()))>::value;
-  };
-
-  // We need to have a separate declaration for static const members
-  template 
-  const bool has_set_local_element::value;
-
-
-
-  // same as above to check
-  // bool T::partitioners_are_compatible(const Utilities::MPI::Partitioner &)
-  // const
-  template 
-  struct has_partitioners_are_compatible
-  {
-  private:
-    static void
-    detect(...);
-
-    template 
-    static decltype(std::declval().partitioners_are_compatible(
-      std::declval()))
-    detect(const U &);
-
-  public:
-    static const bool value =
-      std::is_same()))>::value;
-  };
-
-  // We need to have a separate declaration for static const members
-  template 
-  const bool has_partitioners_are_compatible::value;
-
-
-  // same as above to check
-  // ... T::begin() const
-  template 
-  struct has_begin
-  {
-  private:
-    static void
-    detect(...);
-
-    template 
-    static decltype(std::declval().begin())
-    detect(const U &);
-
-  public:
-    static const bool value =
-      !std::is_same()))>::value;
-  };
-
-  // We need to have a separate declaration for static const members
-  template 
-  const bool has_begin::value;
-
-
-  // type trait for vector T and Number to see if
-  // we can do vectorized load/save.
-  // for VectorReader and VectorDistributorLocalToGlobal we assume that
-  // if both begin() and local_element()
-  // exist, then begin() + offset == local_element(offset)
-  template 
-  struct is_vectorizable
-  {
-    static const bool value =
-      has_begin::value &&
-      (has_local_element::value || is_serial_vector::value) &&
-      std::is_same::value;
-  };
-
-  // We need to have a separate declaration for static const members
-  template 
-  const bool is_vectorizable::value;
-
+  // below we use type-traits from matrix-free/type_traits.h
 
   // access to generic const vectors that have operator ().
   // FIXME: this is wrong for Trilinos/Petsc MPI vectors
diff --git a/include/deal.II/matrix_free/matrix_free.h b/include/deal.II/matrix_free/matrix_free.h
index e1d18fc083a7..6397dec747d8 100644
--- a/include/deal.II/matrix_free/matrix_free.h
+++ b/include/deal.II/matrix_free/matrix_free.h
@@ -44,6 +44,7 @@
 #include 
 #include 
 #include 
+#include 
 
 #include 
 #include 
diff --git a/include/deal.II/matrix_free/type_traits.h b/include/deal.II/matrix_free/type_traits.h
new file mode 100644
index 000000000000..70d784d954d2
--- /dev/null
+++ b/include/deal.II/matrix_free/type_traits.h
@@ -0,0 +1,328 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2019 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+
+#ifndef dealii_matrix_free_type_traits_h
+#define dealii_matrix_free_type_traits_h
+
+// various type-traits used exclusively within the matrix-free framework
+
+#include 
+
+#include 
+
+#include 
+
+
+DEAL_II_NAMESPACE_OPEN
+
+
+namespace internal
+{
+  //
+  // type traits for FEEvaluation
+  //
+
+  // a helper type-trait that leverage SFINAE to figure out if type T has
+  // ... T::local_element() const
+  template 
+  struct has_local_element
+  {
+  private:
+    // this will work always.
+    // we let it be void as we know T::local_element() (if exists) should
+    // certainly return something
+    static void
+    detect(...);
+
+    // this detecter will work only if we have "... T::local_element() const"
+    // and its return type will be the same as local_element(),
+    // that we expect to be T::value_type
+    template 
+    static decltype(std::declval().local_element(0))
+    detect(const U &);
+
+  public:
+    // finally here we check if our detector has non-void return type
+    // T::value_type. This will happen if compiler can use second detector,
+    // otherwise SFINAE let it work with the more general first one that is void
+    static const bool value =
+      !std::is_same()))>::value;
+  };
+
+  // We need to have a separate declaration for static const members
+  template 
+  const bool has_local_element::value;
+
+
+
+  // a helper type-trait that leverage SFINAE to figure out if type T has
+  // void T::add_local_element(const uint, const typename T::value_type)
+  template 
+  struct has_add_local_element
+  {
+  private:
+    static int
+    detect(...);
+
+    template 
+    static decltype(
+      std::declval().add_local_element(0, typename T::value_type()))
+    detect(const U &);
+
+  public:
+    static const bool value =
+      !std::is_same()))>::value;
+  };
+
+  // We need to have a separate declaration for static const members
+  template 
+  const bool has_add_local_element::value;
+
+
+
+  // a helper type-trait that leverage SFINAE to figure out if type T has
+  // void T::set_local_element(const uint, const typename T::value_type)
+  template 
+  struct has_set_local_element
+  {
+  private:
+    static int
+    detect(...);
+
+    template 
+    static decltype(
+      std::declval().set_local_element(0, typename T::value_type()))
+    detect(const U &);
+
+  public:
+    static const bool value =
+      !std::is_same()))>::value;
+  };
+
+  // We need to have a separate declaration for static const members
+  template 
+  const bool has_set_local_element::value;
+
+
+
+  // same as above to check
+  // bool T::partitioners_are_compatible(const Utilities::MPI::Partitioner &)
+  // const
+  template 
+  struct has_partitioners_are_compatible
+  {
+  private:
+    static void
+    detect(...);
+
+    template 
+    static decltype(std::declval().partitioners_are_compatible(
+      std::declval()))
+    detect(const U &);
+
+  public:
+    static const bool value =
+      std::is_same()))>::value;
+  };
+
+  // We need to have a separate declaration for static const members
+  template 
+  const bool has_partitioners_are_compatible::value;
+
+
+  // same as above to check
+  // ... T::begin() const
+  template 
+  struct has_begin
+  {
+  private:
+    static void
+    detect(...);
+
+    template 
+    static decltype(std::declval().begin())
+    detect(const U &);
+
+  public:
+    static const bool value =
+      !std::is_same()))>::value;
+  };
+
+  // We need to have a separate declaration for static const members
+  template 
+  const bool has_begin::value;
+
+
+  // type trait for vector T and Number to see if
+  // we can do vectorized load/save.
+  // for VectorReader and VectorDistributorLocalToGlobal we assume that
+  // if both begin() and local_element()
+  // exist, then begin() + offset == local_element(offset)
+  template 
+  struct is_vectorizable
+  {
+    static const bool value =
+      has_begin::value &&
+      (has_local_element::value || is_serial_vector::value) &&
+      std::is_same::value;
+  };
+
+  // We need to have a separate declaration for static const members
+  template 
+  const bool is_vectorizable::value;
+
+
+  //
+  // type-traits for Matrix-Free
+  //
+  // similar to type traits in FEEvaluation, below we add type-traits
+  // to distinguish between vectors that provide different interface for
+  // operations like update_ghost_values(), compress(), etc.
+  // see internal::has_local_element in fe_evaluation.h that documents
+  // how those type traits work.
+
+  // a helper type-trait that leverage SFINAE to figure out if type T has
+  // void T::update_ghost_values_start(const uint) const
+  template 
+  struct has_update_ghost_values_start
+  {
+  private:
+    static bool
+    detect(...);
+
+    template 
+    static decltype(std::declval().update_ghost_values_start(0))
+    detect(const U &);
+
+  public:
+    static const bool value =
+      !std::is_same()))>::value;
+  };
+
+  // We need to have a separate declaration for static const members
+  template 
+  const bool has_update_ghost_values_start::value;
+
+
+
+  // a helper type-trait that leverage SFINAE to figure out if type T has
+  // void T::	compress_start(const uint, VectorOperation::values)
+  template 
+  struct has_compress_start
+  {
+  private:
+    static bool
+    detect(...);
+
+    template 
+    static decltype(std::declval().compress_start(0, VectorOperation::add))
+    detect(const U &);
+
+  public:
+    static const bool value =
+      !std::is_same()))>::value;
+  };
+
+  // We need to have a separate declaration for static const members
+  template 
+  const bool has_compress_start::value;
+
+
+
+  // type trait for vector T to see if
+  // we do a custom data exchange route.
+  // We assume that if both begin() and local_element()
+  // exist, then begin() + offset == local_element(offset)
+  template 
+  struct has_exchange_on_subset
+  {
+    static const bool value =
+      has_begin::value && has_local_element::value;
+  };
+
+  // We need to have a separate declaration for static const members
+  template 
+  const bool has_exchange_on_subset::value;
+
+
+
+  // a helper type-trait that leverage SFINAE to figure out if type T has
+  // T::communication_block_size
+  template 
+  struct has_communication_block_size
+  {
+  private:
+    static void
+    detect(...);
+
+    template 
+    static decltype(U::communication_block_size)
+    detect(const U &);
+
+  public:
+    static const bool value =
+      !std::is_same()))>::value;
+  };
+
+  // We need to have a separate declaration for static const members
+  template 
+  const bool has_communication_block_size::value;
+
+
+
+  // type trait for vector T to see if
+  // we need to do any data exchange for this vector type at all.
+  // is_serial_vector<> would have been enough, but in some circumstances
+  // (like calculation of diagonals for matrix-free operators)
+  // a dummy InVector == unsigned int is provided.
+  // Thus we have to treat this case as well.
+  template 
+  struct is_serial_or_dummy
+  {
+  private:
+    // catches all cases including unsigned int
+    static void
+    detect(...);
+
+    // catches serial vectors
+    template <
+      typename U,
+      typename std::enable_if::value, U>::type * = nullptr>
+    static void
+    detect(const U &);
+
+    // catches parallel vectors
+    template <
+      typename U,
+      typename std::enable_if::value, U>::type * = nullptr>
+    static bool
+    detect(const U &);
+
+  public:
+    static const bool value =
+      std::is_same()))>::value;
+  };
+
+  // We need to have a separate declaration for static const members
+  template 
+  const bool is_serial_or_dummy::value;
+
+
+} // namespace internal
+
+DEAL_II_NAMESPACE_CLOSE
+
+#endif
diff --git a/tests/matrix_free/matrix_free_type_traits.cc b/tests/matrix_free/matrix_free_type_traits.cc
new file mode 100644
index 000000000000..fb0f597c0c64
--- /dev/null
+++ b/tests/matrix_free/matrix_free_type_traits.cc
@@ -0,0 +1,94 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2019 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+
+
+// test internal typetraits used in matrix_free.h
+
+#include 
+#include 
+#include 
+
+#include 
+
+#include "../tests.h"
+
+int
+main()
+{
+  initlog();
+
+  deallog << "has_update_ghost_values_start:" << std::endl
+          << "LinearAlgebra::distributed::Vector = "
+          << internal::has_update_ghost_values_start<
+               LinearAlgebra::distributed::Vector>::value
+          << std::endl
+          << "TrilinosWrappers::MPI::Vector = "
+          << internal::has_update_ghost_values_start<
+               TrilinosWrappers::MPI::Vector>::value
+          << std::endl
+          << "Vector = "
+          << internal::has_update_ghost_values_start>::value
+          << std::endl;
+
+  deallog << "has_compress_start:" << std::endl
+          << "LinearAlgebra::distributed::Vector = "
+          << internal::has_compress_start<
+               LinearAlgebra::distributed::Vector>::value
+          << std::endl
+          << "TrilinosWrappers::MPI::Vector = "
+          << internal::has_compress_start::value
+          << std::endl
+          << "Vector = " << internal::has_compress_start>::value
+          << std::endl;
+
+  deallog
+    << "has_exchange_on_subset:" << std::endl
+    << "LinearAlgebra::distributed::Vector = "
+    << internal::has_exchange_on_subset<
+         LinearAlgebra::distributed::Vector>::value
+    << std::endl
+    << "TrilinosWrappers::MPI::Vector = "
+    << internal::has_exchange_on_subset::value
+    << std::endl
+    << "Vector = " << internal::has_exchange_on_subset>::value
+    << std::endl;
+
+
+  deallog << "has_communication_block_size:" << std::endl
+          << "LinearAlgebra::distributed::Vector = "
+          << internal::has_communication_block_size<
+               LinearAlgebra::distributed::Vector>::value
+          << std::endl
+          << "LinearAlgebra::distributed::BlockVector = "
+          << internal::has_communication_block_size<
+               LinearAlgebra::distributed::BlockVector>::value
+          << std::endl;
+
+  deallog << "is_serial_or_dummy:" << std::endl
+          << "LinearAlgebra::distributed::Vector = "
+          << internal::is_serial_or_dummy<
+               LinearAlgebra::distributed::Vector>::value
+          << std::endl
+          << "TrilinosWrappers::MPI::Vector = "
+          << internal::is_serial_or_dummy::value
+          << std::endl
+          << "Vector = " << internal::is_serial_or_dummy>::value
+          << std::endl
+          << "unsigned int = "
+          << internal::is_serial_or_dummy::value << std::endl;
+
+  deallog << "OK" << std::endl;
+}
diff --git a/tests/matrix_free/matrix_free_type_traits.with_trilinos=true.output b/tests/matrix_free/matrix_free_type_traits.with_trilinos=true.output
new file mode 100644
index 000000000000..0382073a9358
--- /dev/null
+++ b/tests/matrix_free/matrix_free_type_traits.with_trilinos=true.output
@@ -0,0 +1,22 @@
+
+DEAL::has_update_ghost_values_start:
+DEAL::LinearAlgebra::distributed::Vector = 1
+DEAL::TrilinosWrappers::MPI::Vector = 0
+DEAL::Vector = 0
+DEAL::has_compress_start:
+DEAL::LinearAlgebra::distributed::Vector = 1
+DEAL::TrilinosWrappers::MPI::Vector = 0
+DEAL::Vector = 0
+DEAL::has_exchange_on_subset:
+DEAL::LinearAlgebra::distributed::Vector = 1
+DEAL::TrilinosWrappers::MPI::Vector = 0
+DEAL::Vector = 0
+DEAL::has_communication_block_size:
+DEAL::LinearAlgebra::distributed::Vector = 0
+DEAL::LinearAlgebra::distributed::BlockVector = 1
+DEAL::is_serial_or_dummy:
+DEAL::LinearAlgebra::distributed::Vector = 0
+DEAL::TrilinosWrappers::MPI::Vector = 0
+DEAL::Vector = 1
+DEAL::unsigned int = 1
+DEAL::OK

From 9f980e3688eb7ebd3ec15e2b05191bbf300ed088 Mon Sep 17 00:00:00 2001
From: Denis Davydov 
Date: Thu, 7 Mar 2019 09:29:28 +0100
Subject: [PATCH 241/507] use type-traits to generalize VectorDataExchange

---
 include/deal.II/matrix_free/matrix_free.h | 382 +++++++++++++++++++++-
 1 file changed, 367 insertions(+), 15 deletions(-)

diff --git a/include/deal.II/matrix_free/matrix_free.h b/include/deal.II/matrix_free/matrix_free.h
index 6397dec747d8..19edab9683f6 100644
--- a/include/deal.II/matrix_free/matrix_free.h
+++ b/include/deal.II/matrix_free/matrix_free.h
@@ -2642,6 +2642,12 @@ namespace internal
     // set up
     static constexpr unsigned int channel_shift = 103;
 
+
+
+    /**
+     * Constructor. Takes MF data, flag for face access in DG and
+     * number of components.
+     */
     VectorDataExchange(
       const dealii::MatrixFree &matrix_free,
       const typename dealii::MatrixFree::DataAccessOnFaces
@@ -2667,6 +2673,11 @@ namespace internal
             3);
     }
 
+
+
+    /**
+     * Destructor.
+     */
     ~VectorDataExchange() // NOLINT
     {
 #  ifdef DEAL_II_WITH_MPI
@@ -2676,9 +2687,16 @@ namespace internal
 #  endif
     }
 
+
+
+    /**
+     * Go through all components in MF object and choose the one
+     * whose partitioner is compatible with the Partitioner in this component.
+     */
+    template 
     unsigned int
-    find_vector_in_mf(const LinearAlgebra::distributed::Vector &vec,
-                      const bool check_global_compatibility = true) const
+    find_vector_in_mf(const VectorType &vec,
+                      const bool        check_global_compatibility = true) const
     {
       unsigned int mf_component = numbers::invalid_unsigned_int;
       (void)check_global_compatibility;
@@ -2698,6 +2716,12 @@ namespace internal
       return mf_component;
     }
 
+
+
+    /**
+     * Get partitioner for the given @p mf_component taking into
+     * account vector_face_access set in constructor.
+     */
     const Utilities::MPI::Partitioner &
     get_partitioner(const unsigned int mf_component) const
     {
@@ -2717,13 +2741,87 @@ namespace internal
                   .vector_partitioner_face_variants[2];
     }
 
+
+
+    /**
+     * Start update_ghost_value for serial vectors
+     */
+    template ::value,
+                                      VectorType>::type * = nullptr>
     void
-    update_ghost_values_start(
-      const unsigned int component_in_block_vector,
-      const LinearAlgebra::distributed::Vector &vec)
+    update_ghost_values_start(const unsigned int /*component_in_block_vector*/,
+                              const VectorType & /*vec*/)
+    {}
+
+
+    /**
+     * Start update_ghost_value for vectors that do not support
+     * the split into _start() and finish() stages
+     */
+    template ::value &&
+                  !is_serial_or_dummy::value,
+                VectorType>::type * = nullptr>
+    void
+    update_ghost_values_start(const unsigned int component_in_block_vector,
+                              const VectorType & vec)
     {
       (void)component_in_block_vector;
       bool ghosts_set = vec.has_ghost_elements();
+      if (ghosts_set)
+        ghosts_were_set = true;
+
+      vec.update_ghost_values();
+    }
+
+
+
+    /**
+     * Start update_ghost_value for vectors that _do_ support
+     * the split into _start() and finish() stages, but don't support
+     * exchange on a subset of DoFs
+     */
+    template ::value &&
+                  !has_exchange_on_subset::value,
+                VectorType>::type * = nullptr>
+    void
+    update_ghost_values_start(const unsigned int component_in_block_vector,
+                              const VectorType & vec)
+    {
+      (void)component_in_block_vector;
+      bool ghosts_set = vec.has_ghost_elements();
+      if (ghosts_set)
+        ghosts_were_set = true;
+
+      vec.update_ghost_values_start(component_in_block_vector + channel_shift);
+    }
+
+
+
+    /**
+     * Finally, start update_ghost_value for vectors that _do_ support
+     * the split into _start() and finish() stages and also support
+     * exchange on a subset of DoFs,
+     * i.e. LinearAlgebra::distributed::Vector
+     */
+    template ::value &&
+                  has_exchange_on_subset::value,
+                VectorType>::type * = nullptr>
+    void
+    update_ghost_values_start(const unsigned int component_in_block_vector,
+                              const VectorType & vec)
+    {
+      static_assert(
+        std::is_same::value,
+        "Type mismatch between VectorType and VectorDataExchange");
+      (void)component_in_block_vector;
+      bool ghosts_set = vec.has_ghost_elements();
       if (ghosts_set)
         ghosts_were_set = true;
       if (vector_face_access ==
@@ -2767,11 +2865,67 @@ namespace internal
         }
     }
 
+
+
+    /**
+     * Finish update_ghost_value for vectors that do not support
+     * the split into _start() and finish() stages and serial vectors
+     */
+    template <
+      typename VectorType,
+      typename std::enable_if::value,
+                              VectorType>::type * = nullptr>
+    void
+    update_ghost_values_finish(const unsigned int /*component_in_block_vector*/,
+                               const VectorType & /*vec*/)
+    {}
+
+
+
+    /**
+     * Finish update_ghost_value for vectors that _do_ support
+     * the split into _start() and finish() stages, but don't support
+     * exchange on a subset of DoFs
+     */
+    template ::value &&
+                  !has_exchange_on_subset::value,
+                VectorType>::type * = nullptr>
+    void
+    update_ghost_values_finish(const unsigned int component_in_block_vector,
+                               const VectorType & vec)
+    {
+      (void)component_in_block_vector;
+      Assert(
+        (vector_face_access ==
+           dealii::MatrixFree::DataAccessOnFaces::unspecified ||
+         vec.size() == 0),
+        ExcNotImplemented());
+
+      vec.update_ghost_values_finish();
+    }
+
+
+
+    /**
+     * Finish update_ghost_value for vectors that _do_ support
+     * the split into _start() and finish() stages and also support
+     * exchange on a subset of DoFs,
+     * i.e. LinearAlgebra::distributed::Vector
+     */
+    template ::value &&
+                  has_exchange_on_subset::value,
+                VectorType>::type * = nullptr>
     void
-    update_ghost_values_finish(
-      const unsigned int component_in_block_vector,
-      const LinearAlgebra::distributed::Vector &vec)
+    update_ghost_values_finish(const unsigned int component_in_block_vector,
+                               const VectorType & vec)
     {
+      static_assert(
+        std::is_same::value,
+        "Type mismatch between VectorType and VectorDataExchange");
       (void)component_in_block_vector;
       if (vector_face_access ==
             dealii::MatrixFree::DataAccessOnFaces::unspecified ||
@@ -2814,12 +2968,81 @@ namespace internal
         }
     }
 
+
+
+    /**
+     * Start compress for serial vectors
+     */
+    template ::value,
+                                      VectorType>::type * = nullptr>
+    void
+    compress_start(const unsigned int /*component_in_block_vector*/,
+                   VectorType & /*vec*/)
+    {}
+
+
+
+    /**
+     * Start compress for vectors that do not support
+     * the split into _start() and finish() stages
+     */
+    template ::value &&
+                                        !is_serial_or_dummy::value,
+                                      VectorType>::type * = nullptr>
     void
     compress_start(const unsigned int component_in_block_vector,
-                   LinearAlgebra::distributed::Vector &vec)
+                   VectorType &       vec)
     {
       (void)component_in_block_vector;
       Assert(vec.has_ghost_elements() == false, ExcNotImplemented());
+      vec.compress(dealii::VectorOperation::add);
+    }
+
+
+
+    /**
+     * Start compress for vectors that _do_ support
+     * the split into _start() and finish() stages, but don't support
+     * exchange on a subset of DoFs
+     */
+    template <
+      typename VectorType,
+      typename std::enable_if::value &&
+                                !has_exchange_on_subset::value,
+                              VectorType>::type * = nullptr>
+    void
+    compress_start(const unsigned int component_in_block_vector,
+                   VectorType &       vec)
+    {
+      (void)component_in_block_vector;
+      Assert(vec.has_ghost_elements() == false, ExcNotImplemented());
+      vec.compress_start(component_in_block_vector + channel_shift);
+    }
+
+
+
+    /**
+     * Start compress for vectors that _do_ support
+     * the split into _start() and finish() stages and also support
+     * exchange on a subset of DoFs,
+     * i.e. LinearAlgebra::distributed::Vector
+     */
+    template <
+      typename VectorType,
+      typename std::enable_if::value &&
+                                has_exchange_on_subset::value,
+                              VectorType>::type * = nullptr>
+    void
+    compress_start(const unsigned int component_in_block_vector,
+                   VectorType &       vec)
+    {
+      static_assert(
+        std::is_same::value,
+        "Type mismatch between VectorType and VectorDataExchange");
+      (void)component_in_block_vector;
+      Assert(vec.has_ghost_elements() == false, ExcNotImplemented());
       if (vector_face_access ==
             dealii::MatrixFree::DataAccessOnFaces::unspecified ||
           vec.size() == 0)
@@ -2859,10 +3082,60 @@ namespace internal
         }
     }
 
+
+
+    /**
+     * Finish compress for vectors that do not support
+     * the split into _start() and finish() stages and serial vectors
+     */
+    template ::value,
+                                      VectorType>::type * = nullptr>
+    void
+    compress_finish(const unsigned int /*component_in_block_vector*/,
+                    VectorType & /*vec*/)
+    {}
+
+
+
+    /**
+     * Finish compress for vectors that _do_ support
+     * the split into _start() and finish() stages, but don't support
+     * exchange on a subset of DoFs
+     */
+    template <
+      typename VectorType,
+      typename std::enable_if::value &&
+                                !has_exchange_on_subset::value,
+                              VectorType>::type * = nullptr>
+    void
+    compress_finish(const unsigned int component_in_block_vector,
+                    VectorType &       vec)
+    {
+      (void)component_in_block_vector;
+      vec.compress_finish(dealii::VectorOperation::add);
+    }
+
+
+
+    /**
+     * Start compress for vectors that _do_ support
+     * the split into _start() and finish() stages and also support
+     * exchange on a subset of DoFs,
+     * i.e. LinearAlgebra::distributed::Vector
+     */
+    template <
+      typename VectorType,
+      typename std::enable_if::value &&
+                                has_exchange_on_subset::value,
+                              VectorType>::type * = nullptr>
     void
     compress_finish(const unsigned int component_in_block_vector,
-                    LinearAlgebra::distributed::Vector &vec)
+                    VectorType &       vec)
     {
+      static_assert(
+        std::is_same::value,
+        "Type mismatch between VectorType and VectorDataExchange");
       (void)component_in_block_vector;
       if (vector_face_access ==
             dealii::MatrixFree::DataAccessOnFaces::unspecified ||
@@ -2905,10 +3178,54 @@ namespace internal
         }
     }
 
+
+
+    /**
+     * Reset all ghost values for serial vectors
+     */
+    template ::value,
+                                      VectorType>::type * = nullptr>
+    void
+    reset_ghost_values(const VectorType & /*vec*/) const
+    {}
+
+
+
+    /**
+     * Reset all ghost values for vector that don't support
+     * exchange on a subset of DoFs
+     */
+    template <
+      typename VectorType,
+      typename std::enable_if::value &&
+                                !is_serial_or_dummy::value,
+                              VectorType>::type * = nullptr>
+    void
+    reset_ghost_values(const VectorType &vec) const
+    {
+      if (ghosts_were_set == true)
+        return;
+
+      vec.zero_out_ghosts();
+    }
+
+
+
+    /**
+     * Reset all ghost values for vector that _do_ support
+     * exchange on a subset of DoFs, i.e.
+     * LinearAlgebra::distributed::Vector
+     */
+    template ::value,
+                                      VectorType>::type * = nullptr>
     void
-    reset_ghost_values(
-      const LinearAlgebra::distributed::Vector &vec) const
+    reset_ghost_values(const VectorType &vec) const
     {
+      static_assert(
+        std::is_same::value,
+        "Type mismatch between VectorType and VectorDataExchange");
       if (ghosts_were_set == true)
         return;
 
@@ -2950,10 +3267,22 @@ namespace internal
         }
     }
 
+
+
+    /**
+     * Zero out vector region for vector that _do_ support
+     * exchange on a subset of DoFs <==> begin() + ind == local_element(ind),
+     * i.e. LinearAlgebra::distributed::Vector
+     */
+    template ::value,
+                                      VectorType>::type * = nullptr>
     void
-    zero_vector_region(const unsigned int                          range_index,
-                       LinearAlgebra::distributed::Vector &vec) const
+    zero_vector_region(const unsigned int range_index, VectorType &vec) const
     {
+      static_assert(
+        std::is_same::value,
+        "Type mismatch between VectorType and VectorDataExchange");
       if (range_index == numbers::invalid_unsigned_int)
         vec = Number();
       else
@@ -2989,6 +3318,29 @@ namespace internal
         }
     }
 
+
+
+    /**
+     * Zero out vector region for vector that do _not_ support
+     * exchange on a subset of DoFs <==> begin() + ind == local_element(ind)
+     */
+    template <
+      typename VectorType,
+      typename std::enable_if::value,
+                              VectorType>::type * = nullptr>
+    void
+    zero_vector_region(const unsigned int range_index, VectorType &vec) const
+    {
+      if (range_index == numbers::invalid_unsigned_int)
+        vec = typename VectorType::value_type();
+      else
+        {
+          Assert(false, ExcNotImplemented());
+        }
+    }
+
+
+
     const dealii::MatrixFree &matrix_free;
     const typename dealii::MatrixFree::DataAccessOnFaces
          vector_face_access;
@@ -2997,7 +3349,7 @@ namespace internal
     std::vector *>  tmp_data;
     std::vector> requests;
 #  endif
-  };
+  }; // VectorDataExchange
 
   template 
   unsigned int

From 75c9fd3d9ede2fef51846b7314ff4a27da267304 Mon Sep 17 00:00:00 2001
From: Denis Davydov 
Date: Thu, 7 Mar 2019 09:33:00 +0100
Subject: [PATCH 242/507] streamline treatment of block and non-block vectors
 in MatrixFree using updated VectorDataExchange

---
 include/deal.II/matrix_free/matrix_free.h | 509 +++++++++-------------
 1 file changed, 218 insertions(+), 291 deletions(-)

diff --git a/include/deal.II/matrix_free/matrix_free.h b/include/deal.II/matrix_free/matrix_free.h
index 19edab9683f6..4877be670b78 100644
--- a/include/deal.II/matrix_free/matrix_free.h
+++ b/include/deal.II/matrix_free/matrix_free.h
@@ -3405,166 +3405,17 @@ namespace internal
     return components;
   }
 
-  template 
-  void
-  update_ghost_values_start_block(const VectorStruct &vec,
-                                  const unsigned int  channel,
-                                  std::integral_constant,
-                                  VectorDataExchange &exchanger);
-  template 
-  void
-  reset_ghost_values_block(const VectorStruct &vec,
-                           std::integral_constant,
-                           VectorDataExchange &exchanger);
-  template 
-  void
-  update_ghost_values_finish_block(const VectorStruct &vec,
-                                   const unsigned int  channel,
-                                   std::integral_constant,
-                                   VectorDataExchange &exchanger);
-  template 
-  void
-  compress_start_block(const VectorStruct &vec,
-                       const unsigned int  channel,
-                       std::integral_constant,
-                       VectorDataExchange &exchanger);
-  template 
-  void
-  compress_finish_block(const VectorStruct &vec,
-                        const unsigned int  channel,
-                        std::integral_constant,
-                        VectorDataExchange &exchanger);
-  template 
-  void
-  zero_vector_region_block(const unsigned int range_index,
-                           VectorStruct &,
-                           std::integral_constant,
-                           VectorDataExchange &);
-
-  template 
-  void
-  update_ghost_values_start_block(const VectorStruct &,
-                                  const unsigned int,
-                                  std::integral_constant,
-                                  VectorDataExchange &)
-  {}
-  template 
-  void
-  reset_ghost_values_block(const VectorStruct &,
-                           std::integral_constant,
-                           VectorDataExchange &)
-  {}
-  template 
-  void
-  update_ghost_values_finish_block(const VectorStruct &,
-                                   const unsigned int,
-                                   std::integral_constant,
-                                   VectorDataExchange &)
-  {}
-  template 
-  void
-  compress_start_block(const VectorStruct &,
-                       const unsigned int,
-                       std::integral_constant,
-                       VectorDataExchange &)
-  {}
-  template 
-  void
-  compress_finish_block(const VectorStruct &,
-                        const unsigned int,
-                        std::integral_constant,
-                        VectorDataExchange &)
-  {}
-  template 
-  void
-  zero_vector_region_block(const unsigned int range_index,
-                           VectorStruct &     vec,
-                           std::integral_constant,
-                           VectorDataExchange &)
-  {
-    if (range_index == 0 || range_index == numbers::invalid_unsigned_int)
-      vec = 0;
-  }
-
-
-
-  // if the input vector did not have ghosts imported, clear them here again
-  // in order to avoid subsequent operations e.g. in linear solvers to work
-  // with ghosts all the time
-  template 
-  inline void
-  reset_ghost_values(const VectorStruct &             vec,
-                     VectorDataExchange &exchanger)
-  {
-    reset_ghost_values_block(
-      vec,
-      std::integral_constant::value>(),
-      exchanger);
-  }
-
-
-
-  template 
-  inline void
-  reset_ghost_values(const LinearAlgebra::distributed::Vector &vec,
-                     VectorDataExchange &exchanger)
-  {
-    exchanger.reset_ghost_values(vec);
-  }
-
-
-
-  template 
-  inline void
-  reset_ghost_values(const std::vector &vec,
-                     VectorDataExchange &exchanger)
-  {
-    // return immediately if there is nothing to do.
-    if (exchanger.ghosts_were_set == true)
-      return;
-
-    for (unsigned int comp = 0; comp < vec.size(); comp++)
-      reset_ghost_values(vec[comp], exchanger);
-  }
-
-
-
-  template 
-  inline void
-  reset_ghost_values(const std::vector &vec,
-                     VectorDataExchange &  exchanger)
-  {
-    // return immediately if there is nothing to do.
-    if (exchanger.ghosts_were_set == true)
-      return;
-
-    for (unsigned int comp = 0; comp < vec.size(); comp++)
-      reset_ghost_values(*vec[comp], exchanger);
-  }
-
-
-
-  template 
-  inline void
-  reset_ghost_values_block(const VectorStruct &vec,
-                           std::integral_constant,
-                           VectorDataExchange &exchanger)
-  {
-    // return immediately if there is nothing to do.
-    if (exchanger.ghosts_were_set == true)
-      return;
-
-    for (unsigned int i = 0; i < vec.n_blocks(); ++i)
-      reset_ghost_values(vec.block(i), exchanger);
-  }
-
 
 
   // A helper function to identify block vectors with many components where we
   // should not try to overlap computations and communication because there
-  // would be too many outstanding communication requests. This is the base case
-  // for generic vectors
-  template 
+  // would be too many outstanding communication requests.
+
+  // default value for vectors that do not have communication_block_size
+  template <
+    typename VectorStruct,
+    typename std::enable_if::value,
+                            VectorStruct>::type * = nullptr>
   constexpr unsigned int
   get_communication_block_size(const VectorStruct &)
   {
@@ -3573,46 +3424,70 @@ namespace internal
 
 
 
-  // Specialized case for the block vector which as the additional member
-  // variable
-  template 
+  template <
+    typename VectorStruct,
+    typename std::enable_if::value,
+                            VectorStruct>::type * = nullptr>
   constexpr unsigned int
-  get_communication_block_size(
-    const LinearAlgebra::distributed::BlockVector &)
+  get_communication_block_size(const VectorStruct &)
   {
-    return LinearAlgebra::distributed::BlockVector<
-      Number>::communication_block_size;
+    return VectorStruct::communication_block_size;
   }
 
 
 
-  template 
-  inline void
+  // --------------------------------------------------------------------------
+  // below we have wrappers to distinguish between block and non-block vectors.
+  // --------------------------------------------------------------------------
+
+  //
+  // update_ghost_values_start
+  //
+
+  // update_ghost_values for block vectors
+  template ::value,
+                                    VectorStruct>::type * = nullptr>
+  void
   update_ghost_values_start(const VectorStruct &             vec,
                             VectorDataExchange &exchanger,
                             const unsigned int               channel = 0)
   {
-    update_ghost_values_start_block(
-      vec,
-      channel,
-      std::integral_constant::value>(),
-      exchanger);
+    if (get_communication_block_size(vec) < vec.n_blocks())
+      {
+        // don't forget to set ghosts_were_set, that otherwise happens
+        // inside VectorDataExchange::update_ghost_values_start()
+        exchanger.ghosts_were_set = vec.has_ghost_elements();
+        vec.update_ghost_values();
+      }
+    else
+      {
+        for (unsigned int i = 0; i < vec.n_blocks(); ++i)
+          update_ghost_values_start(vec.block(i), exchanger, channel + i);
+      }
   }
 
 
 
-  template 
-  inline void
-  update_ghost_values_start(
-    const LinearAlgebra::distributed::Vector &vec,
-    VectorDataExchange &                exchanger,
-    const unsigned int                                channel = 0)
+  // update_ghost_values for non-block vectors
+  template ::value,
+                                    VectorStruct>::type * = nullptr>
+  void
+  update_ghost_values_start(const VectorStruct &             vec,
+                            VectorDataExchange &exchanger,
+                            const unsigned int               channel = 0)
   {
     exchanger.update_ghost_values_start(channel, vec);
   }
 
 
 
+  // update_ghost_values_start() for vector of vectors
   template 
   inline void
   update_ghost_values_start(const std::vector &vec,
@@ -3628,6 +3503,7 @@ namespace internal
 
 
 
+  // update_ghost_values_start() for vector of pointers to vectors
   template 
   inline void
   update_ghost_values_start(const std::vector &vec,
@@ -3643,56 +3519,50 @@ namespace internal
 
 
 
-  template 
-  inline void
-  update_ghost_values_start_block(const VectorStruct &vec,
-                                  const unsigned int  channel,
-                                  std::integral_constant,
-                                  VectorDataExchange &exchanger)
+  //
+  // update_ghost_values_finish
+  //
+
+  // for block vectors
+  template ::value,
+                                    VectorStruct>::type * = nullptr>
+  void
+  update_ghost_values_finish(const VectorStruct &             vec,
+                             VectorDataExchange &exchanger,
+                             const unsigned int               channel = 0)
   {
     if (get_communication_block_size(vec) < vec.n_blocks())
       {
-        // don't forget to set ghosts_were_set, that otherwise happens
-        // inside VectorDataExchange::update_ghost_values_start()
-        exchanger.ghosts_were_set = vec.has_ghost_elements();
-        vec.update_ghost_values();
+        // do nothing, everything has already been completed in the _start()
+        // call
       }
     else
-      {
-        for (unsigned int i = 0; i < vec.n_blocks(); ++i)
-          update_ghost_values_start(vec.block(i), exchanger, channel + i);
-      }
+      for (unsigned int i = 0; i < vec.n_blocks(); ++i)
+        update_ghost_values_finish(vec.block(i), exchanger, channel + i);
   }
 
 
 
-  template 
-  inline void
+  // for non-block vectors
+  template ::value,
+                                    VectorStruct>::type * = nullptr>
+  void
   update_ghost_values_finish(const VectorStruct &             vec,
                              VectorDataExchange &exchanger,
                              const unsigned int               channel = 0)
-  {
-    update_ghost_values_finish_block(
-      vec,
-      channel,
-      std::integral_constant::value>(),
-      exchanger);
-  }
-
-
-
-  template 
-  inline void
-  update_ghost_values_finish(
-    const LinearAlgebra::distributed::Vector &vec,
-    VectorDataExchange &                exchanger,
-    const unsigned int                                channel = 0)
   {
     exchanger.update_ghost_values_finish(channel, vec);
   }
 
 
 
+  // for vector of vectors
   template 
   inline void
   update_ghost_values_finish(const std::vector &vec,
@@ -3708,6 +3578,7 @@ namespace internal
 
 
 
+  // for vector of pointers to vectors
   template 
   inline void
   update_ghost_values_finish(const std::vector &vec,
@@ -3723,51 +3594,47 @@ namespace internal
 
 
 
-  template 
+  //
+  // compress_start
+  //
+
+  // for block vectors
+  template ::value,
+                                    VectorStruct>::type * = nullptr>
   inline void
-  update_ghost_values_finish_block(const VectorStruct &vec,
-                                   const unsigned int  channel,
-                                   std::integral_constant,
-                                   VectorDataExchange &exchanger)
+  compress_start(VectorStruct &                   vec,
+                 VectorDataExchange &exchanger,
+                 const unsigned int               channel = 0)
   {
     if (get_communication_block_size(vec) < vec.n_blocks())
-      {
-        // do nothing, everything has already been completed in the _start()
-        // call
-      }
+      vec.compress(dealii::VectorOperation::add);
     else
       for (unsigned int i = 0; i < vec.n_blocks(); ++i)
-        update_ghost_values_finish(vec.block(i), exchanger, channel + i);
+        compress_start(vec.block(i), exchanger, channel + i);
   }
 
 
 
-  template 
+  // for non-block vectors
+  template ::value,
+                                    VectorStruct>::type * = nullptr>
   inline void
   compress_start(VectorStruct &                   vec,
                  VectorDataExchange &exchanger,
                  const unsigned int               channel = 0)
-  {
-    compress_start_block(
-      vec,
-      channel,
-      std::integral_constant::value>(),
-      exchanger);
-  }
-
-
-
-  template 
-  inline void
-  compress_start(LinearAlgebra::distributed::Vector &vec,
-                 VectorDataExchange &          exchanger,
-                 const unsigned int                          channel = 0)
   {
     exchanger.compress_start(channel, vec);
   }
 
 
 
+  // for std::vector of vectors
   template 
   inline void
   compress_start(std::vector &      vec,
@@ -3783,6 +3650,7 @@ namespace internal
 
 
 
+  // for std::vector of pointer to vectors
   template 
   inline void
   compress_start(std::vector &    vec,
@@ -3798,48 +3666,50 @@ namespace internal
 
 
 
-  template 
+  //
+  // compress_finish
+  //
+
+  // for block vectors
+  template ::value,
+                                    VectorStruct>::type * = nullptr>
   inline void
-  compress_start_block(VectorStruct &     vec,
-                       const unsigned int channel,
-                       std::integral_constant,
-                       VectorDataExchange &exchanger)
+  compress_finish(VectorStruct &                   vec,
+                  VectorDataExchange &exchanger,
+                  const unsigned int               channel = 0)
   {
     if (get_communication_block_size(vec) < vec.n_blocks())
-      vec.compress(dealii::VectorOperation::add);
+      {
+        // do nothing, everything has already been completed in the _start()
+        // call
+      }
     else
       for (unsigned int i = 0; i < vec.n_blocks(); ++i)
-        compress_start(vec.block(i), exchanger, channel + i);
+        compress_finish(vec.block(i), exchanger, channel + i);
   }
 
 
 
-  template 
+  // for non-block vectors
+  template ::value,
+                                    VectorStruct>::type * = nullptr>
   inline void
   compress_finish(VectorStruct &                   vec,
                   VectorDataExchange &exchanger,
                   const unsigned int               channel = 0)
-  {
-    compress_finish_block(
-      vec,
-      channel,
-      std::integral_constant::value>(),
-      exchanger);
-  }
-
-
-
-  template 
-  inline void
-  compress_finish(LinearAlgebra::distributed::Vector &vec,
-                  VectorDataExchange &          exchanger,
-                  const unsigned int                          channel = 0)
   {
     exchanger.compress_finish(channel, vec);
   }
 
 
 
+  // for std::vector of vectors
   template 
   inline void
   compress_finish(std::vector &      vec,
@@ -3855,6 +3725,7 @@ namespace internal
 
 
 
+  // for std::vector of pointer to vectors
   template 
   inline void
   compress_finish(std::vector &    vec,
@@ -3870,51 +3741,119 @@ namespace internal
 
 
 
+  //
+  // reset_ghost_values:
+  //
+  // if the input vector did not have ghosts imported, clear them here again
+  // in order to avoid subsequent operations e.g. in linear solvers to work
+  // with ghosts all the time
+  //
+
+  // for block vectors
+  template ::value,
+                                    VectorStruct>::type * = nullptr>
+  inline void
+  reset_ghost_values(const VectorStruct &             vec,
+                     VectorDataExchange &exchanger)
+  {
+    // return immediately if there is nothing to do.
+    if (exchanger.ghosts_were_set == true)
+      return;
+
+    for (unsigned int i = 0; i < vec.n_blocks(); ++i)
+      reset_ghost_values(vec.block(i), exchanger);
+  }
+
+
+
+  // for non-block vectors
+  template ::value,
+                                    VectorStruct>::type * = nullptr>
+  inline void
+  reset_ghost_values(const VectorStruct &             vec,
+                     VectorDataExchange &exchanger)
+  {
+    exchanger.reset_ghost_values(vec);
+  }
+
+
+
+  // for std::vector of vectors
   template 
   inline void
-  compress_finish_block(VectorStruct &     vec,
-                        const unsigned int channel,
-                        std::integral_constant,
-                        VectorDataExchange &exchanger)
+  reset_ghost_values(const std::vector &vec,
+                     VectorDataExchange &exchanger)
   {
-    if (get_communication_block_size(vec) < vec.n_blocks())
-      {
-        // do nothing, everything has already been completed in the _start()
-        // call
-      }
-    else
-      for (unsigned int i = 0; i < vec.n_blocks(); ++i)
-        compress_finish(vec.block(i), exchanger, channel + i);
+    // return immediately if there is nothing to do.
+    if (exchanger.ghosts_were_set == true)
+      return;
+
+    for (unsigned int comp = 0; comp < vec.size(); comp++)
+      reset_ghost_values(vec[comp], exchanger);
   }
 
 
 
+  // for std::vector of pointer to vectors
   template 
   inline void
+  reset_ghost_values(const std::vector &vec,
+                     VectorDataExchange &  exchanger)
+  {
+    // return immediately if there is nothing to do.
+    if (exchanger.ghosts_were_set == true)
+      return;
+
+    for (unsigned int comp = 0; comp < vec.size(); comp++)
+      reset_ghost_values(*vec[comp], exchanger);
+  }
+
+
+
+  //
+  // zero_vector_region
+  //
+
+  // for block vectors
+  template ::value,
+                                    VectorStruct>::type * = nullptr>
+  inline void
   zero_vector_region(const unsigned int               range_index,
                      VectorStruct &                   vec,
                      VectorDataExchange &exchanger)
   {
-    zero_vector_region_block(
-      range_index,
-      vec,
-      std::integral_constant::value>(),
-      exchanger);
+    for (unsigned int i = 0; i < vec.n_blocks(); ++i)
+      exchanger.zero_vector_region(range_index, vec.block(i));
   }
 
 
 
-  template 
+  // for non-block vectors
+  template ::value,
+                                    VectorStruct>::type * = nullptr>
   inline void
-  zero_vector_region(const unsigned int                          range_index,
-                     LinearAlgebra::distributed::Vector &vec,
-                     VectorDataExchange &          exchanger)
+  zero_vector_region(const unsigned int               range_index,
+                     VectorStruct &                   vec,
+                     VectorDataExchange &exchanger)
   {
     exchanger.zero_vector_region(range_index, vec);
   }
 
 
 
+  // for std::vector of vectors
   template 
   inline void
   zero_vector_region(const unsigned int               range_index,
@@ -3927,6 +3866,7 @@ namespace internal
 
 
 
+  // for std::vector of pointers to vectors
   template 
   inline void
   zero_vector_region(const unsigned int               range_index,
@@ -3939,19 +3879,6 @@ namespace internal
 
 
 
-  template 
-  inline void
-  zero_vector_region_block(const unsigned int range_index,
-                           VectorStruct &     vec,
-                           std::integral_constant,
-                           VectorDataExchange &exchanger)
-  {
-    for (unsigned int i = 0; i < vec.n_blocks(); ++i)
-      zero_vector_region(range_index, vec.block(i), exchanger);
-  }
-
-
-
   namespace MatrixFreeFunctions
   {
     // struct to select between a const interface and a non-const interface

From 2052911df8eb516594cf6bd2e27d200e0716c07b Mon Sep 17 00:00:00 2001
From: David Wells 
Date: Sat, 9 Mar 2019 10:26:53 -0500
Subject: [PATCH 243/507] Fix link targets in frames.

The first link is currently unclickable and it should have
'target="body"' anyway since it should not be framed.

The second link works but it should not be framed.
---
 doc/documentation.html | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/doc/documentation.html b/doc/documentation.html
index ee8bee879069..9977691eb5fc 100644
--- a/doc/documentation.html
+++ b/doc/documentation.html
@@ -36,7 +36,7 @@
           
  • Code gallery
    • 
           
  • Manual
    • 
           
  • Wolfgang's lectures
    • 
-          
  • Technical reports
    • 
+          
  • Technical reports
    • 
           
  • Publications
    • 
         
       
@@ -52,7 +52,7 @@
           
  • CMake internals
    • 
           
  • Writing documentation
    • 
           
  • Porting
    • 
-          
  • Coding conventions
    • 
+          
  • Coding conventions
    • 
           
  • Testsuite
    • 
         
       

From f6539ceb99759acae824c6286d1f238e6554b6d6 Mon Sep 17 00:00:00 2001
From: Marc Fehling 
Date: Thu, 21 Feb 2019 08:12:36 +0100
Subject: [PATCH 244/507] Introduced p-refinement and p-coarsening flags.

---
 doc/news/changes/minor/20190224MarcFehling    |   7 +
 include/deal.II/dofs/dof_accessor.h           |  78 ++++
 include/deal.II/dofs/dof_accessor.templates.h | 338 ++++++++++++++++++
 include/deal.II/hp/dof_handler.h              |  16 +-
 include/deal.II/hp/dof_level.h                |  16 +
 source/hp/dof_handler.cc                      |  66 +++-
 source/hp/dof_level.cc                        |   4 +-
 tests/hp/refine_and_coarsen_flags.cc          |  92 +++++
 tests/hp/refine_and_coarsen_flags.output      |  16 +
 tests/serialization/hp_dof_handler_01.cc      |  19 +
 ...f_handler_01.with_64bit_indices=off.output |  28 +-
 ...of_handler_01.with_64bit_indices=on.output |  28 +-
 12 files changed, 670 insertions(+), 38 deletions(-)
 create mode 100644 doc/news/changes/minor/20190224MarcFehling
 create mode 100644 tests/hp/refine_and_coarsen_flags.cc
 create mode 100644 tests/hp/refine_and_coarsen_flags.output

diff --git a/doc/news/changes/minor/20190224MarcFehling b/doc/news/changes/minor/20190224MarcFehling
new file mode 100644
index 000000000000..a1bf46b6ff45
--- /dev/null
+++ b/doc/news/changes/minor/20190224MarcFehling
@@ -0,0 +1,7 @@
+New: Introduced flags for p-refinement and p-coarsening that can be
+accessed and changed via member functions of the DoFCellAccessor class,
+namely DoFCellAccessor::p_refine_flag_set, DoFCellAccessor::set_p_refine_flag,
+DoFCellAccessor::clear_p_refine_flag, and DoFCellAccessor::p_coarsen_flag_set,
+DoFCellAccessor::set_p_coarsen_flag, DoFCellAccessor::clear_p_coarsen_flag.
+
    
+(Marc Fehling, 2019/02/24)
diff --git a/include/deal.II/dofs/dof_accessor.h b/include/deal.II/dofs/dof_accessor.h
index ae1826087776..98280ee71017 100644
--- a/include/deal.II/dofs/dof_accessor.h
+++ b/include/deal.II/dofs/dof_accessor.h
@@ -596,6 +596,23 @@ class DoFAccessor
   DeclExceptionMsg(ExcInvalidObject,
                    "This accessor object has not been "
                    "associated with any DoFHandler object.");
+  /**
+   * Exception
+   *
+   * @ingroup Exceptions
+   */
+  DeclExceptionMsg(ExcRefinementNotSupported,
+                   "DoFHandler is not of type hp::DoFHandler and "
+                   "does not support p-refinement.");
+  /**
+   * Exception
+   *
+   * @ingroup Exceptions
+   */
+  DeclExceptionMsg(ExcCoarseningNotSupported,
+                   "DoFHandler is not of type hp::DoFHandler and "
+                   "does not support p-coarsening.");
+
   /**
    * Exception
    *
@@ -1945,6 +1962,67 @@ class DoFCellAccessor : public DoFAccessor
+      static bool
+      p_refine_flag_set(const DoFCellAccessor,
+                                              level_dof_access> &accessor)
+      {
+        (void)accessor;
+        // ::DoFHandler does not support p-refinement
+        Assert(false,
+               (typename std::decay::type::ExcRefinementNotSupported()));
+        return false;
+      }
+
+
+
+      template 
+      static bool
+      p_refine_flag_set(
+        const DoFCellAccessor,
+                              level_dof_access> &accessor)
+      {
+        Assert(
+          accessor.dof_handler != nullptr,
+          (typename std::decay::type::ExcInvalidObject()));
+        Assert(static_cast(accessor.level()) <
+                 accessor.dof_handler->levels.size(),
+               ExcMessage("DoFHandler not initialized"));
+
+        const auto &p_refine_flags =
+          accessor.dof_handler->levels[accessor.level()]->p_refine_flags;
+        Assert(static_cast(accessor.present_index) <
+                 p_refine_flags.size(),
+               ExcIndexRange(accessor.present_index, 0, p_refine_flags.size()));
+
+        return p_refine_flags[accessor.present_index];
+      }
+
+
+
+      template 
+      static void
+      set_p_refine_flag(const DoFCellAccessor,
+                                              level_dof_access> &accessor)
+      {
+        (void)accessor;
+        // ::DoFHandler does not support p-refinement
+        Assert(false,
+               (typename std::decay::type::ExcRefinementNotSupported()));
+      }
+
+
+
+      template 
+      static void
+      set_p_refine_flag(
+        const DoFCellAccessor,
+                              level_dof_access> &accessor)
+      {
+        Assert(
+          accessor.dof_handler != nullptr,
+          (typename std::decay::type::ExcInvalidObject()));
+        Assert(static_cast(accessor.level()) <
+                 accessor.dof_handler->levels.size(),
+               ExcMessage("DoFHandler not initialized"));
+
+        auto &p_refine_flags =
+          accessor.dof_handler->levels[accessor.level()]->p_refine_flags;
+        Assert(static_cast(accessor.present_index) <
+                 p_refine_flags.size(),
+               ExcIndexRange(accessor.present_index, 0, p_refine_flags.size()));
+
+        p_refine_flags[accessor.present_index] = true;
+      }
+
+
+
+      template 
+      static void
+      clear_p_refine_flag(const DoFCellAccessor,
+                                                level_dof_access> &accessor)
+      {
+        (void)accessor;
+        // ::DoFHandler does not support p-refinement
+        Assert(false,
+               (typename std::decay::type::ExcRefinementNotSupported()));
+      }
+
+
+
+      template 
+      static void
+      clear_p_refine_flag(
+        const DoFCellAccessor,
+                              level_dof_access> &accessor)
+      {
+        Assert(
+          accessor.dof_handler != nullptr,
+          (typename std::decay::type::ExcInvalidObject()));
+        Assert(static_cast(accessor.level()) <
+                 accessor.dof_handler->levels.size(),
+               ExcMessage("DoFHandler not initialized"));
+
+        auto &p_refine_flags =
+          accessor.dof_handler->levels[accessor.level()]->p_refine_flags;
+        Assert(static_cast(accessor.present_index) <
+                 p_refine_flags.size(),
+               ExcIndexRange(accessor.present_index, 0, p_refine_flags.size()));
+
+        p_refine_flags[accessor.present_index] = false;
+      }
+
+
+
+      template 
+      static bool
+      p_coarsen_flag_set(const DoFCellAccessor,
+                                               level_dof_access> &accessor)
+      {
+        (void)accessor;
+        // ::DoFHandler does not support p-coarsening
+        Assert(false,
+               (typename std::decay::type::ExcCoarseningNotSupported()));
+        return false;
+      }
+
+
+
+      template 
+      static bool
+      p_coarsen_flag_set(
+        const DoFCellAccessor,
+                              level_dof_access> &accessor)
+      {
+        Assert(
+          accessor.dof_handler != nullptr,
+          (typename std::decay::type::ExcInvalidObject()));
+        Assert(static_cast(accessor.level()) <
+                 accessor.dof_handler->levels.size(),
+               ExcMessage("DoFHandler not initialized"));
+
+        const auto &p_coarsen_flags =
+          accessor.dof_handler->levels[accessor.level()]->p_coarsen_flags;
+        Assert(static_cast(accessor.present_index) <
+                 p_coarsen_flags.size(),
+               ExcIndexRange(accessor.present_index,
+                             0,
+                             p_coarsen_flags.size()));
+
+        return p_coarsen_flags[accessor.present_index];
+      }
+
+
+
+      template 
+      static void
+      set_p_coarsen_flag(const DoFCellAccessor,
+                                               level_dof_access> &accessor)
+      {
+        (void)accessor;
+        // ::DoFHandler does not support p-coarsening
+        Assert(false,
+               (typename std::decay::type::ExcCoarseningNotSupported()));
+      }
+
+
+
+      template 
+      static void
+      set_p_coarsen_flag(
+        const DoFCellAccessor,
+                              level_dof_access> &accessor)
+      {
+        Assert(
+          accessor.dof_handler != nullptr,
+          (typename std::decay::type::ExcInvalidObject()));
+        Assert(static_cast(accessor.level()) <
+                 accessor.dof_handler->levels.size(),
+               ExcMessage("DoFHandler not initialized"));
+
+        auto &p_coarsen_flags =
+          accessor.dof_handler->levels[accessor.level()]->p_coarsen_flags;
+        Assert(static_cast(accessor.present_index) <
+                 p_coarsen_flags.size(),
+               ExcIndexRange(accessor.present_index,
+                             0,
+                             p_coarsen_flags.size()));
+
+        p_coarsen_flags[accessor.present_index] = true;
+      }
+
+
+
+      template 
+      static void
+      clear_p_coarsen_flag(const DoFCellAccessor,
+                                                 level_dof_access> &accessor)
+      {
+        (void)accessor;
+        // ::DoFHandler does not support p-coarsening
+        Assert(false,
+               (typename std::decay::type::ExcCoarseningNotSupported()));
+      }
+
+
+
+      template 
+      static void
+      clear_p_coarsen_flag(
+        const DoFCellAccessor,
+                              level_dof_access> &accessor)
+      {
+        Assert(
+          accessor.dof_handler != nullptr,
+          (typename std::decay::type::ExcInvalidObject()));
+        Assert(static_cast(accessor.level()) <
+                 accessor.dof_handler->levels.size(),
+               ExcMessage("DoFHandler not initialized"));
+
+        auto &p_coarsen_flags =
+          accessor.dof_handler->levels[accessor.level()]->p_coarsen_flags;
+        Assert(static_cast(accessor.present_index) <
+                 p_coarsen_flags.size(),
+               ExcIndexRange(accessor.present_index,
+                             0,
+                             p_coarsen_flags.size()));
+
+        p_coarsen_flags[accessor.present_index] = false;
+      }
+
+
+
       template ::distribute_local_to_global(
 }
 
 
+
+template 
+inline bool
+DoFCellAccessor::p_refine_flag_set() const
+{
+  Assert(this->used(), TriaAccessorExceptions::ExcCellNotUsed());
+  // cells flagged for refinement must be active
+  // (the @p set_p_refine_flag function checks this,
+  // but activity may change when refinement is
+  // executed and for some reason the refine
+  // flag is not cleared).
+  Assert(this->active() || !dealii::internal::DoFCellAccessorImplementation::
+                             Implementation::p_refine_flag_set(*this),
+         (typename CellAccessor::ExcRefineCellNotActive()));
+
+  return dealii::internal::DoFCellAccessorImplementation::Implementation::
+    p_refine_flag_set(*this);
+}
+
+
+
+template 
+inline void
+DoFCellAccessor::set_p_refine_flag() const
+{
+  Assert(this->used(), TriaAccessorExceptions::ExcCellNotUsed());
+  Assert(this->active(),
+         (typename CellAccessor::ExcRefineCellNotActive()));
+  Assert(!dealii::internal::DoFCellAccessorImplementation::Implementation::
+           p_coarsen_flag_set(*this),
+         (typename CellAccessor::ExcCellFlaggedForCoarsening()));
+
+  dealii::internal::DoFCellAccessorImplementation::Implementation::
+    set_p_refine_flag(*this);
+}
+
+
+
+template 
+inline void
+DoFCellAccessor::clear_p_refine_flag() const
+{
+  Assert(this->used(), TriaAccessorExceptions::ExcCellNotUsed());
+  Assert(this->active(),
+         (typename CellAccessor::ExcRefineCellNotActive()));
+
+  dealii::internal::DoFCellAccessorImplementation::Implementation::
+    clear_p_refine_flag(*this);
+}
+
+
+
+template 
+inline bool
+DoFCellAccessor::p_coarsen_flag_set() const
+{
+  Assert(this->used(), TriaAccessorExceptions::ExcCellNotUsed());
+  // cells flagged for coarsening must be active
+  // (the @p set_refine_flag function checks this,
+  // but activity may change when refinement is
+  // executed and for some reason the refine
+  // flag is not cleared).
+  Assert(this->active() || !dealii::internal::DoFCellAccessorImplementation::
+                             Implementation::p_coarsen_flag_set(*this),
+         (typename CellAccessor::ExcRefineCellNotActive()));
+
+  return dealii::internal::DoFCellAccessorImplementation::Implementation::
+    p_coarsen_flag_set(*this);
+}
+
+
+
+template 
+inline void
+DoFCellAccessor::set_p_coarsen_flag() const
+{
+  Assert(this->used(), TriaAccessorExceptions::ExcCellNotUsed());
+  Assert(this->active(),
+         (typename CellAccessor::ExcRefineCellNotActive()));
+  Assert(!dealii::internal::DoFCellAccessorImplementation::Implementation::
+           p_refine_flag_set(*this),
+         (typename CellAccessor::ExcCellFlaggedForRefinement()));
+
+  dealii::internal::DoFCellAccessorImplementation::Implementation::
+    set_p_coarsen_flag(*this);
+}
+
+
+
+template 
+inline void
+DoFCellAccessor::clear_p_coarsen_flag() const
+{
+  Assert(this->used(), TriaAccessorExceptions::ExcCellNotUsed());
+  Assert(this->active(),
+         (typename CellAccessor::ExcRefineCellNotActive()));
+
+  dealii::internal::DoFCellAccessorImplementation::Implementation::
+    clear_p_coarsen_flag(*this);
+}
+
+
 DEAL_II_NAMESPACE_CLOSE
 
 #endif
diff --git a/include/deal.II/hp/dof_handler.h b/include/deal.II/hp/dof_handler.h
index a218d8b2a3e2..a35a1f115f21 100644
--- a/include/deal.II/hp/dof_handler.h
+++ b/include/deal.II/hp/dof_handler.h
@@ -1080,13 +1080,23 @@ namespace hp
     /**
      * Create default tables for the active_fe_indices in the
      * dealii::internal::hp::DoFLevel. They are initialized with a zero
-     * indicator, meaning that fe[0] is going to be used by default.  This
-     * method is called before refinement and before distribute_dofs is
-     * called. It ensures each cell has a valid active_fe_index.
+     * indicator, meaning that fe[0] is going to be used by default. This
+     * method is called before refinement and while setting the finite elements
+     * via set_fe(). It ensures each cell has a valid active_fe_index.
      */
     void
     create_active_fe_table();
 
+    /**
+     * Create default tables for the p_refine_flags and p_coarsen_flags in the
+     * dealii::internal::hp::DoFLevel. All of them are initialized with a false
+     * boolean, meaning that no cell is initially flagged for p-refinement or
+     * p-coarsening. This method is called while setting the finite elements via
+     * set_fe().
+     */
+    void
+    create_p_adaptation_flags();
+
     /**
      * A function that will be triggered through a triangulation
      * signal just before the triangulation is modified.
diff --git a/include/deal.II/hp/dof_level.h b/include/deal.II/hp/dof_level.h
index 3af1013c4b33..aa70ce9dea34 100644
--- a/include/deal.II/hp/dof_level.h
+++ b/include/deal.II/hp/dof_level.h
@@ -184,6 +184,20 @@ namespace internal
        */
       std::vector cell_dof_indices_cache;
 
+      /**
+       * Indicators for p-refinement for different cells on the current level.
+       * The vector stores one flag per cell, specifying whether the cell is
+       * scheduled for future p-refinement.
+       */
+      std::vector p_refine_flags;
+
+      /**
+       * Indicators for p-coarsening for different cells on the current level.
+       * The vector stores one flag per cell, specifying whether the cell is
+       * scheduled for future p-coarssening.
+       */
+      std::vector p_coarsen_flags;
+
     public:
       /**
        * Set the global index of the @p local_index-th degree of freedom
@@ -491,6 +505,8 @@ namespace internal
       ar & this->cell_dof_indices_cache;
       ar & this->dof_indices;
       ar & this->dof_offsets;
+      ar & this->p_refine_flags;
+      ar & this->p_coarsen_flags;
     }
   } // namespace hp
 
diff --git a/source/hp/dof_handler.cc b/source/hp/dof_handler.cc
index 8e9dc7e65a9d..073cbe580438 100644
--- a/source/hp/dof_handler.cc
+++ b/source/hp/dof_handler.cc
@@ -90,15 +90,25 @@ namespace internal
         static void
         reserve_space_release_space(DoFHandler &dof_handler)
         {
-          // Release all space except the active_fe_indices field
-          // which we have to back up before
+          // Release all space except the fields for active_fe_indices and
+          // refinement flags which we have to back up before
           {
             std::vector>
-              active_fe_backup(dof_handler.levels.size());
+                                           active_fe_backup(dof_handler.levels.size());
+            std::vector> p_refine_flags_backup(
+              dof_handler.levels.size());
+            std::vector> p_coarsen_flags_backup(
+              dof_handler.levels.size());
             for (unsigned int level = 0; level < dof_handler.levels.size();
                  ++level)
-              active_fe_backup[level] =
-                std::move(dof_handler.levels[level]->active_fe_indices);
+              {
+                active_fe_backup[level] =
+                  std::move(dof_handler.levels[level]->active_fe_indices);
+                p_refine_flags_backup[level] =
+                  std::move(dof_handler.levels[level]->p_refine_flags);
+                p_coarsen_flags_backup[level] =
+                  std::move(dof_handler.levels[level]->p_coarsen_flags);
+              }
 
             // delete all levels and set them up newly, since vectors
             // are troublesome if you want to change their size
@@ -108,8 +118,13 @@ namespace internal
                  ++level)
               {
                 dof_handler.levels.emplace_back(new internal::hp::DoFLevel);
+                // recover backups
                 dof_handler.levels[level]->active_fe_indices =
                   std::move(active_fe_backup[level]);
+                dof_handler.levels[level]->p_refine_flags =
+                  std::move(p_refine_flags_backup[level]);
+                dof_handler.levels[level]->p_coarsen_flags =
+                  std::move(p_coarsen_flags_backup[level]);
               }
 
             if (dim > 1)
@@ -1538,6 +1553,9 @@ namespace hp
         Assert(cell->active_fe_index() < fe_collection.size(),
                ExcInvalidFEIndex(cell->active_fe_index(),
                                  fe_collection.size()));
+
+    // initialize all p-refinement and p-coarsening flags
+    create_p_adaptation_flags();
   }
 
 
@@ -1864,6 +1882,38 @@ namespace hp
 
 
 
+  template 
+  void
+  DoFHandler::create_p_adaptation_flags()
+  {
+    Assert(fe_collection.size() > 0, ExcNoFESelected());
+    Assert(tria->n_levels() > 0,
+           ExcMessage("The current Triangulation must not be empty."));
+    Assert(tria->n_levels() == levels.size(), ExcInternalError());
+
+    for (unsigned int level = 0; level < tria->n_levels(); ++level)
+      if (levels[level]->p_refine_flags.size() == 0 &&
+          levels[level]->p_coarsen_flags.size() == 0)
+        {
+          levels[level]->p_refine_flags.resize(tria->n_raw_cells(level), false);
+          levels[level]->p_coarsen_flags.resize(tria->n_raw_cells(level),
+                                                false);
+        }
+      else
+        {
+          // Either the p_refine_flags and p_coarsen_flags have size zero
+          // because they were just created, or the correct size. Other sizes
+          // indicate that something went wrong.
+          Assert(levels[level]->p_refine_flags.size() ==
+                     tria->n_raw_cells(level) &&
+                   levels[level]->p_coarsen_flags.size() ==
+                     tria->n_raw_cells(level),
+                 ExcInternalError());
+        }
+  }
+
+
+
   template 
   void
   DoFHandler::pre_refinement_action()
@@ -1893,7 +1943,11 @@ namespace hp
 
     // Resize active_fe_indices vectors. use zero indicator to extend
     for (unsigned int i = 0; i < levels.size(); ++i)
-      levels[i]->active_fe_indices.resize(tria->n_raw_cells(i), 0);
+      {
+        levels[i]->active_fe_indices.resize(tria->n_raw_cells(i), 0);
+        levels[i]->p_refine_flags.resize(tria->n_raw_cells(i), false);
+        levels[i]->p_coarsen_flags.resize(tria->n_raw_cells(i), false);
+      }
   }
 
 
diff --git a/source/hp/dof_level.cc b/source/hp/dof_level.cc
index 94982880f5a3..2f2c653a7a21 100644
--- a/source/hp/dof_level.cc
+++ b/source/hp/dof_level.cc
@@ -248,7 +248,9 @@ namespace internal
               MemoryConsumption::memory_consumption(dof_indices) +
               MemoryConsumption::memory_consumption(dof_offsets) +
               MemoryConsumption::memory_consumption(cell_cache_offsets) +
-              MemoryConsumption::memory_consumption(cell_dof_indices_cache));
+              MemoryConsumption::memory_consumption(cell_dof_indices_cache) +
+              MemoryConsumption::memory_consumption(p_refine_flags) +
+              MemoryConsumption::memory_consumption(p_coarsen_flags));
     }
 
 
diff --git a/tests/hp/refine_and_coarsen_flags.cc b/tests/hp/refine_and_coarsen_flags.cc
new file mode 100644
index 000000000000..716107f91105
--- /dev/null
+++ b/tests/hp/refine_and_coarsen_flags.cc
@@ -0,0 +1,92 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2006 - 2019 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+
+
+// check if p-adaptive flags will be set correctly
+
+
+#include 
+
+#include 
+#include 
+
+#include 
+#include 
+
+#include "../tests.h"
+
+
+template 
+void
+test()
+{
+  Triangulation tria;
+  GridGenerator::hyper_cube(tria);
+  tria.refine_global(1);
+
+  hp::FECollection fe_collection;
+  fe_collection.push_back(FE_Q(1));
+
+  hp::DoFHandler dh(tria);
+  dh.distribute_dofs(fe_collection);
+
+  // check if flags are initialized correctly
+  for (const auto &cell : dh.active_cell_iterators())
+    Assert(!cell->p_refine_flag_set() && !cell->p_coarsen_flag_set(),
+           ExcInternalError());
+
+  // set flags at least once
+  auto cell = dh.begin_active();
+  cell->set_p_refine_flag();
+  (++cell)->set_p_coarsen_flag();
+
+  // verify flags
+  for (const auto &cell : dh.active_cell_iterators())
+    deallog << "cell:" << cell->id().to_string()
+            << ", refine:" << cell->p_refine_flag_set()
+            << ", coarsen:" << cell->p_coarsen_flag_set() << std::endl;
+
+  // clear all flags and check if all were cleared
+  for (const auto &cell : dh.active_cell_iterators())
+    {
+      cell->clear_p_refine_flag();
+      Assert(!cell->p_refine_flag_set(), ExcInternalError());
+
+      cell->clear_p_coarsen_flag();
+      Assert(!cell->p_coarsen_flag_set(), ExcInternalError());
+    }
+}
+
+
+int
+main()
+{
+  initlog();
+
+  deallog.push("1D");
+  test<1>();
+  deallog.pop();
+
+  deallog.push("2D");
+  test<2>();
+  deallog.pop();
+
+  deallog.push("3D");
+  test<3>();
+  deallog.pop();
+
+  deallog << "OK" << std::endl;
+}
diff --git a/tests/hp/refine_and_coarsen_flags.output b/tests/hp/refine_and_coarsen_flags.output
new file mode 100644
index 000000000000..df5baf06f4cf
--- /dev/null
+++ b/tests/hp/refine_and_coarsen_flags.output
@@ -0,0 +1,16 @@
+
+DEAL:1D::cell:0_1:0, refine:1, coarsen:0
+DEAL:1D::cell:0_1:1, refine:0, coarsen:1
+DEAL:2D::cell:0_1:0, refine:1, coarsen:0
+DEAL:2D::cell:0_1:1, refine:0, coarsen:1
+DEAL:2D::cell:0_1:2, refine:0, coarsen:0
+DEAL:2D::cell:0_1:3, refine:0, coarsen:0
+DEAL:3D::cell:0_1:0, refine:1, coarsen:0
+DEAL:3D::cell:0_1:1, refine:0, coarsen:1
+DEAL:3D::cell:0_1:2, refine:0, coarsen:0
+DEAL:3D::cell:0_1:3, refine:0, coarsen:0
+DEAL:3D::cell:0_1:4, refine:0, coarsen:0
+DEAL:3D::cell:0_1:5, refine:0, coarsen:0
+DEAL:3D::cell:0_1:6, refine:0, coarsen:0
+DEAL:3D::cell:0_1:7, refine:0, coarsen:0
+DEAL::OK
diff --git a/tests/serialization/hp_dof_handler_01.cc b/tests/serialization/hp_dof_handler_01.cc
index fb997c9a6328..500a4c83630e 100644
--- a/tests/serialization/hp_dof_handler_01.cc
+++ b/tests/serialization/hp_dof_handler_01.cc
@@ -92,6 +92,14 @@ namespace dealii
             c1->active_fe_index() != c2->active_fe_index())
           return false;
 
+        if (c1->active() && c2->active() &&
+            c1->p_refine_flag_set() != c2->p_refine_flag_set())
+          return false;
+
+        if (c1->active() && c2->active() &&
+            c1->p_coarsen_flag_set() != c2->p_coarsen_flag_set())
+          return false;
+
         // compare dofs on this cell and then on the faces
         if (c1->has_children() == false)
           {
@@ -174,13 +182,24 @@ test()
   hp::FECollection fe_collection;
   fe_collection.push_back(FESystem(
     FE_Q(2), dim, FE_Q(1), 1));
+  fe_collection.push_back(FESystem(
+    FE_Q(3), dim, FE_Q(2), 1));
 
   hp::DoFHandler dof_1(tria);
   hp::DoFHandler dof_2(tria);
 
+  dof_1.begin_active()->set_active_fe_index(1);
+  dof_2.begin_active()->set_active_fe_index(1);
+
   dof_1.distribute_dofs(fe_collection);
   dof_2.distribute_dofs(fe_collection);
 
+  dof_1.begin_active()->set_p_refine_flag();
+  dof_2.begin_active()->set_p_refine_flag();
+
+  (++dof_1.begin_active())->set_p_coarsen_flag();
+  (++dof_2.begin_active())->set_p_coarsen_flag();
+
   // right now, both hp::DoFHandlers are the same. Renumber one of them
   DoFRenumbering::random(dof_1);
 
diff --git a/tests/serialization/hp_dof_handler_01.with_64bit_indices=off.output b/tests/serialization/hp_dof_handler_01.with_64bit_indices=off.output
index 0792fffde608..0f3297458035 100644
--- a/tests/serialization/hp_dof_handler_01.with_64bit_indices=off.output
+++ b/tests/serialization/hp_dof_handler_01.with_64bit_indices=off.output
@@ -1,19 +1,19 @@
 
-DEAL::0 0 20 0 0 5 11 4294967295 0 8 7 4294967295 0 2 9 4294967295 0 0 13 4294967295 0 1 6 4294967295 5 0 0 4 8 12 16 0 0 14 14 0 0 0 0 1 0 0 0 0 14 0 1 14 0 1 0 14 0 0 1 0 1 0 0 14 0 1 14 0 0 0 0 0 3 0 0 9 1 0
-0 1 0 0 1 0 4294967295 0 0 0 0 1 0 4294967295 9
-1 2 0 0 0 2 0 4294967295 4294967295 0 0 0 0 2 0 4294967295 4294967295 9
-2 4 0 65535 65535 65535 65535 4 0 0 5 10 15 20 0 5 11 0 13 4 0 13 2 9 12 2 9 1 6 3 1 6 8 7 10 4 0 4 12 3 10 4 0 0 1 2 3 1 7 23 Policy::Sequential<1,1>
+DEAL::0 0 23 0 1 5 11 4294967295 0 10 0 4294967295 0 12 15 4294967295 0 2 9 1 2 9 4294967295 0 3 8 4294967295 5 0 0 4 8 12 19 0 0 16 16 0 0 0 0 1 0 0 0 0 16 0 1 16 0 1 0 16 0 0 1 0 1 0 0 16 0 1 16 0 0 0 0 0 3 0 0 9 1 0
+0 1 0 0 1 0 4294967295 0 0 0 0 1 0 4294967295 1 0 1 0 9
+1 2 0 0 0 2 0 4294967295 4294967295 0 0 0 0 2 0 4294967295 4294967295 2 0 0 2 0 0 9
+2 4 0 1 65535 65535 65535 4 0 0 7 12 17 22 0 5 11 2 9 14 13 4 2 9 12 15 6 12 15 3 8 7 3 8 10 0 1 6 0 14 13 4 6 7 1 4 0 0 3 4 5 4 1 0 0 0 4 0 1 0 0 1 7 23 Policy::Sequential<1,1>
 
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1241 52 201 1916 1880 1013 417 1221 887 2025 1586 132 2073 2245 2253 1864 738 1082 374 104 13 1182 659 1496 1573 426 1773 842 1222 1300 1322 2033 1485 756 2125 700 1202 2164 2192 1730 1521 604 571 956 592 612 1582 1660 279 549 169 2233 1512 197 605 54 2126 1051 1802 1261 783 716 679 747 1243 1813 53 1817 1130 111 1697 1267 1091 1469 901 1768 1975 995 1860 1247 960 1655 967 254 1255 1241 52 201 1837 316 313 1314 373 1639 1016 635 2012 2090 75 230 270 2056 6 966 1333 73 1736 2142 1053 1457 1907 2283 2208 1211 453 1702 498 841 1781 1542 399 1751 2102 2164 2192 1730 105 862 294 2189 1128 1884 1157 1125 1793 473 2060 1020 1558 2085 735 1376 438 1989 1960 1581 1563 775 1886 335 940 391 1927 1130 111 1697 1267 562 1401 338 202 1975 995 1860 1247 1173 764 1473 952 1255 1241 52 201 1916 1880 1013 417 373 1639 1016 635 1156 28 1538 1552 230 270 2056 1673 2161 2277 738 1082 374 1508 520 1890 2283 2208 1211 164 2294 984 1222 1300 1322 1536 227 1201 2164 2192 1730 1521 604 571 2189 1128 1884 1132 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4294967295 0 2449 585 405 4294967295 0 906 826 185 4294967295 0 1174 388 2083 4294967295 0 1052 917 427 4294967295 0 93 2146 1123 4294967295 0 2028 404 692 4294967295 0 623 1072 179 4294967295 0 1952 2207 1135 4294967295 0 1034 799 685 4294967295 0 510 911 1424 4294967295 0 1061 1723 1027 4294967295 0 1516 2261 1375 4294967295 0 2056 73 1736 4294967295 0 2371 2177 303 4294967295 0 2199 1438 1102 4294967295 0 1146 474 2474 4294967295 0 1160 1296 1999 4294967295 0 2338 418 450 4294967295 0 1179 1081 1056 4294967295 0 579 304 825 4294967295 0 2153 183 2231 4294967295 0 833 936 182 4294967295 0 851 1110 224 4294967295 0 1425 349 737 4294967295 0 2297 344 832 4294967295 0 1436 49 365 4294967295 0 2114 1987 481 4294967295 0 1972 360 1057 4294967295 0 1829 927 296 4294967295 0 1660 279 1512 4294967295 0 343 1390 534 4294967295 0 1300 1322 1521 4294967295 0 137 1931 1764 4294967295 0 1441 1100 162 4294967295 0 2426 1017 1405 4294967295 0 1350 2200 281 4294967295 0 2021 2451 1554 4294967295 0 1157 1783 1106 4294967295 0 1727 2461 1197 4294967295 0 1044 918 1522 4294967295 0 944 980 1294 4294967295 0 2049 1386 699 4294967295 0 2345 1260 2115 4294967295 0 1142 2457 460 4294967295 0 1377 2116 1514 4294967295 0 1408 533 1986 4294967295 0 937 2383 151 4294967295 0 1094 2324 2118 4294967295 0 1835 2209 2020 4294967295 0 656 1688 2092 4294967295 0 1492 2318 1862 4294967295 0 1097 517 1381 4294967295 0 719 456 1324 4294967295 0 1413 2235 2287 4294967295 0 2444 1674 1815 4294967295 0 2464 785 633 4294967295 0 864 2112 2313 4294967295 0 1295 2203 392 4294967295 0 33 1302 1183 4294967295 0 2359 2306 463 4294967295 0 1961 1410 1024 4294967295 0 524 1344 55 4294967295 0 2358 23 1111 4294967295 0 309 504 2370 4294967295 0 666 1869 257 4294967295 0 1724 1238 1641 4294967295 0 614 1562 1580 4294967295 0 41 1632 2247 4294967295 0 2317 13 1182 4294967295 0 604 571 1582 4294967295 0 1241 52 2394 4294967295 0 940 391 1927 4294967295 0 967 254 1255 4294967295 0 1280 1849 562 4294967295 0 808 320 1440 4294967295 0 667 1672 1049 4294967295 0 682 1850 319 4294967295 0 315 986 408 4294967295 0 2378 152 654 4294967295 0 2074 753 1775 4294967295 0 941 369 1451 1 1591 447 1120 1418 1510 1363 1290 4294967295 0 2046 43 1303 4294967295 0 636 1882 2348 1 637 1068 1305 817 846 848 879 4294967295 0 1705 974 1009 4294967295 0 375 1759 223 1 1941 2034 1285 1383 607 2063 1863 4294967295 366 0 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 0 9 14 19 24 33 38 43 48 57 62 67 72 77 82 87 92 97 102 107 112 117 122 127 132 137 142 147 152 157 162 167 172 177 182 187 192 197 202 207 212 217 222 227 232 237 242 247 252 257 262 267 272 277 282 287 292 297 302 307 312 317 322 327 332 337 342 347 352 357 362 367 372 377 382 387 392 397 402 407 412 417 422 427 432 437 442 447 452 457 462 467 472 477 482 487 492 497 502 507 512 517 522 527 532 537 542 547 552 565 570 583 588 593 598 603 608 613 618 623 628 633 638 643 648 661 666 679 684 689 694 699 704 709 714 719 724 729 734 739 744 757 762 775 780 785 790 795 800 805 810 815 820 825 830 835 840 845 850 855 860 865 870 875 880 885 890 895 900 905 910 915 920 925 930 935 940 945 950 955 960 965 970 975 980 985 990 995 1000 1005 1010 1015 1020 1025 1030 1035 1040 1045 1050 1055 1060 1065 1070 1075 1080 1085 1090 1095 1100 1105 1110 1115 1120 1125 1130 1135 1140 1145 1150 1155 1160 1165 1170 1175 1180 1185 1190 1195 1200 1205 1210 1215 1220 1225 1230 1235 1240 1245 1250 1255 1260 1265 1270 1275 1280 1285 1290 1295 1300 1305 1310 1315 1320 1325 1330 1335 1340 1345 1350 1355 1360 1365 1370 1375 1380 1385 1390 1395 1400 1405 1410 1415 1420 1425 1430 1435 1440 1445 1450 1455 1460 1465 1470 1475 1480 1485 1490 1495 1500 1505 1510 1515 1520 1525 1530 1535 1548 1553 1566 1571 0 0 1272 0 1 2127 2120 751 715 2066 1511 2213 724 1567 165 1178 2255 285 4294967295 0 401 651 1896 1 122 2413 860 1249 1878 2154 500 976 1035 1343 641 2373 2416 4294967295 1 1406 1200 2465 2110 497 1997 1140 1904 1266 1525 2279 284 1965 4294967295 0 1096 653 396 1 713 797 1680 849 1416 1642 2124 1368 1940 1748 441 1787 1497 4294967295 1 2103 1595 1647 1694 1439 240 187 1059 340 156 298 570 1630 4294967295 0 435 642 11 1 1675 1774 634 536 548 776 1297 1741 1187 1083 1321 219 1577 4294967295 0 1944 1456 932 4294967295 0 1093 1007 1299 4294967295 0 1279 886 1004 4294967295 0 2128 947 655 4294967295 0 1654 2195 1339 4294967295 0 793 1236 1651 4294967295 0 660 1646 1616 4294967295 0 1767 2 899 4294967295 0 513 1937 1228 4294967295 0 576 1638 573 4294967295 0 1690 1045 302 4294967295 0 426 1773 842 4294967295 0 2125 700 1202 4294967295 0 798 1066 857 4294967295 0 861 68 1509 4294967295 0 1963 2007 1877 4294967295 0 2336 188 1707 4294967295 0 2250 2041 2417 4294967295 0 1499 2123 1391 4294967295 0 1682 1685 171 4294967295 0 703 312 2162 4294967295 0 149 457 2221 4294967295 0 1220 1507 1936 4294967295 0 1326 606 1613 4294967295 0 496 752 1834 4294967295 0 367 1338 218 4294967295 0 1432 1360 823 4294967295 0 1696 1337 1108 4294967295 0 2108 1771 1932 4294967295 0 1795 809 2439 4294967295 0 508 625 1588 4294967295 0 351 794 999 4294967295 0 2150 1366 566 4294967295 0 1275 1843 1246 4294967295 0 1565 100 1576 4294967295 0 1644 1084 1980 4294967295 0 2054 370 2385 4294967295 0 61 930 1203 4294967295 0 45 624 467 4294967295 0 2197 1715 1677 4294967295 0 2396 2342 1894 4294967295 0 676 2003 327 4294967295 0 483 2055 696 4294967295 0 305 1807 915 4294967295 0 582 1274 1168 4294967295 0 1221 2323 2025 4294967295 0 6 966 1333 4294967295 0 1010 1447 749 4294967295 0 1401 338 202 4294967295 0 806 1922 1857 4294967295 0 436 2059 2305 4294967295 0 1586 132 2073 4294967295 0 618 813 485 4294967295 0 1091 1469 901 4294967295 0 1768 2375 995 4294967295 0 1860 1247 632 4294967295 0 2142 2407 236 4294967295 0 1474 235 2453 4294967295 0 1335 669 1650 4294967295 0 1042 2425 1891 4294967295 0 2204 2397 764 4294967295 0 1473 952 256 4294967295 0 453 1702 498 4294967295 0 399 1751 2102 4294967295 0 2164 2192 1730 4294967295 0 2130 781 1854 4294967295 0 956 592 612 4294967295 0 197 2339 1802 4294967295 0 1261 783 716 4294967295 0 679 747 1837 4294967295 0 316 313 1314 4294967295 0 1201 1132 883 4294967295 0 1031 1822 1055 4294967295 0 890 1163 1374 4294967295 0 295 1738 1547 4294967295 0 358 2184 1915 4294967295 0 2227 272 1659 4294967295 0 796 1820 1872 4294967295 0 416 638 822 4294967295 0 419 2377 687 4294967295 0 1550 2079 77 4294967295 0 1962 1826 1150 4294967295 0 691 2326 2138 4294967295 0 1968 274 2289 4294967295 0 2113 19 1328 4294967295 0 414 2078 895 4294967295 0 1030 647 232 4294967295 0 384 1602 742 4294967295 0 1589 1575 26 4294967295 0 558 1230 69 4294967295 0 17 1050 1365 4294967295 0 951 1033 350 4294967295 0 2077 701 2169 4294967295 0 1186 1403 1621 4294967295 0 875 588 398 4294967295 0 425 465 1196 4294967295 0 1394 1584 58 4294967295 0 733 1259 509 4294967295 0 2167 1991 2171 4294967295 0 1903 1226 118 4294967295 0 472 1945 1649 4294967295 0 1914 1597 1640 4294967295 0 1917 2163 471 4294967295 0 90 1726 1117 4294967295 0 1678 2047 2009 4294967295 0 838 586 2131 4294967295 0 2158 1909 559 4294967295 0 157 1832 2096 4294967295 0 761 2473 2086 4294967295 0 664 1490 1734 4294967295 0 1306 1133 433 4294967295 0 2302 1750 92 4294967295 0 1317 1361 46 4294967295 0 1298 1883 1312 4294967295 0 601 263 2369 4294967295 0 1676 1251 1885 4294967295 0 38 2421 110 4294967295 0 492 1620 2303 4294967295 0 2151 125 1718 4294967295 0 331 2333 1948 4294967295 0 1105 1396 324 4294967295 0 2143 997 95 4294967295 0 2286 729 2225 4294967295 0 1505 710 241 4294967295 0 681 1463 1206 4294967295 0 253 2427 1158 4294967295 0 1599 922 1967 4294967295 0 1443 1378 1618 4294967295 0 359 1480 176 4294967295 0 2069 1080 458 4294967295 0 1792 216 1336 4294967295 0 51 505 1624 4294967295 0 609 969 1627 4294967295 0 2472 1340 1423 4294967295 0 975 220 1148 4294967295 0 1232 1008 1327 4294967295 0 800 2242 36 4294967295 0 342 880 269 4294967295 0 2111 1151 153 4294967295 0 244 2004 246 4294967295 0 831 726 873 4294967295 0 1225 1192 665 4294967295 0 1533 1486 328 4294967295 0 1021 1263 1786 4294967295 0 2475 1720 62 4294967295 0 348 2381 1905 4294967295 0 2211 2027 777 4294967295 0 928 79 812 4294967295 0 407 2351 2319 4294967295 0 515 1634 1523 4294967295 0 758 2174 2387 4294967295 0 1358 1411 1976 4294967295 0 383 1504 1958 4294967295 0 2337 1079 1681 4294967295 0 1951 950 1257 4294967295 0 490 488 1852 4294967295 0 2470 1631 577 4294967295 0 2038 1844 1078 4294967295 0 1362 1388 1532 4294967295 0 1866 2230 326 4294967295 0 1555 1729 959 4294967295 0 717 2238 1710 4294967295 0 722 1349 2134 4294967295 0 1219 1704 1137 4294967295 0 2168 2226 646 4294967295 0 2404 834 1036 4294967295 0 301 1180 556 4294967295 0 2356 2136 1993 4294967295 0 2064 1762 1252 4294967295 0 268 2222 142 4294967295 0 2315 2462 1838 4294967295 0 1769 181 769 4294967295 0 451 2450 1559 4294967295 0 2471 2188 102 4294967295 0 2198 2349 136 4294967295 0 1501 2429 1784 4294967295 0 958 964 1791 4294967295 0 1022 1152 2030 4294967295 0 912 172 658 4294967295 0 1370 663 31 4294967295 0 2251 1628 2234 4294967295 0 2068 466 661 4294967295 0 1464 2291 619 4294967295 0 1867 163 9 4294967295 0 292 541 830 4294967295 0 1003 2271 439 4294967295 0 1625 1830 2101 4294967295 0 1038 97 523 4294967295 0 2214 158 1926 4294967295 0 287 1955 1437 4294967295 0 1301 538 978 4294967295 0 409 1481 2145 4294967295 0 2183 683 522 4294967295 0 963 1912 1780 4294967295 0 805 1006 626 4294967295 0 1692 1345 954 4294967295 0 2045 429 1985 4294967295 0 770 1973 1939 4294967295 0 1876 1430 780 4294967295 0 1853 2135 1043 4294967295 0 1282 2137 1269 4294967295 0 1744 866 290 4294967295 0 1453 489 1978 4294967295 0 865 1782 1839 4294967295 0 493 754 114 4294967295 0 1873 1757 2353 4294967295 0 1841 786 205 4294967295 0 2206 1171 2180 4294967295 0 2194 454 732 4294967295 0 1956 1814 1765 4294967295 0 346 1098 233 4294967295 0 1687 728 127 4294967295 0 620 1385 507 4294967295 0 480 104 1943 4294967295 0 1193 2152 2187 4294967295 0 40 887 2411 4294967295 0 0 1281 1346 4294967295 0 299 1777 526 4294967295 0 394 174 385 4294967295 0 616 1415 2139 4294967295 0 1145 1175 1600 4294967295 0 1517 856 2435 4294967295 0 564 993 1670 4294967295 0 201 845 1116 4294967295 0 1173 1165 1352 4294967295 0 1037 170 2232 4294967295 0 1330 1569 957 4294967295 0 1356 885 1789 4294967295 0 1907 2011 1797 4294967295 0 1452 1315 2350 4294967295 0 1181 528 1051 4294967295 0 1816 230 1359 4294967295 0 1691 1245 971 4294967295 0 1129 1369 2256 4294967295 282 0 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 34 182 107 202 722 802 742 822 257 347 282 367 877 947 897 967 68 117 142 162 267 292 312 332 427 447 472 492 582 602 622 642 0 127 172 217 412 457 502 537 712 757 792 837 1012 1047 1082 1117 277 322 362 397 592 632 667 697 892 927 962 997 1167 1197 1227 1257 467 547 487 562 1057 1127 1072 1142 617 687 637 702 1187 1247 1202 1262 812 832 852 867 957 977 992 1007 1097 1112 1132 1147 1222 1237 1252 1267 662 677 692 707 517 532 552 567 357 377 392 407 192 212 232 247 917 987 932 1002 307 387 327 402 767 847 782 862 137 227 157 242 1032 1067 1102 1137 737 777 817 857 437 482 522 557 102 152 197 237 1207 1192 1177 1162 1232 1172 1217 1157 1242 1212 1182 1152 1077 1062 1042 1027 1107 1037 1092 1022 1122 1087 1052 1017 937 922 907 887 972 902 952 882 982 942 912 872 787 772 752 732 827 747 807 727 842 797 762 717 647 627 607 587 672 597 657 577 682 652 612 572 497 477 452 432 527 442 512 422 542 507 462 417 337 317 297 272 372 287 352 262 382 342 302 252 167 147 122 83 207 112 187 49 222 177 132 15 73 23 Policy::Sequential<3,3>
 
 DEAL::OK
diff --git a/tests/serialization/hp_dof_handler_01.with_64bit_indices=on.output b/tests/serialization/hp_dof_handler_01.with_64bit_indices=on.output
index 0c1e987c5a53..f189f05a4d12 100644
--- a/tests/serialization/hp_dof_handler_01.with_64bit_indices=on.output
+++ b/tests/serialization/hp_dof_handler_01.with_64bit_indices=on.output
@@ -1,19 +1,19 @@
 
-DEAL::0 0 20 0 0 5 11 18446744073709551615 0 8 7 18446744073709551615 0 2 9 18446744073709551615 0 0 13 18446744073709551615 0 1 6 18446744073709551615 5 0 0 4 8 12 16 0 0 14 14 0 0 0 0 1 0 0 0 0 14 0 1 14 0 1 0 14 0 0 1 0 1 0 0 14 0 1 14 0 0 0 0 0 3 0 0 10 1 0
-0 1 0 0 1 0 4294967295 0 0 0 0 1 0 4294967295 10
-1 2 0 0 0 2 0 4294967295 4294967295 0 0 0 0 2 0 4294967295 4294967295 10
-2 4 0 65535 65535 65535 65535 4 0 0 5 10 15 20 0 5 11 0 13 4 0 13 2 9 12 2 9 1 6 3 1 6 8 7 10 4 0 4 12 3 10 4 0 0 1 2 3 1 7 23 Policy::Sequential<1,1>
+DEAL::0 0 23 0 1 5 11 18446744073709551615 0 10 0 18446744073709551615 0 12 15 18446744073709551615 0 2 9 1 2 9 18446744073709551615 0 3 8 18446744073709551615 5 0 0 4 8 12 19 0 0 16 16 0 0 0 0 1 0 0 0 0 16 0 1 16 0 1 0 16 0 0 1 0 1 0 0 16 0 1 16 0 0 0 0 0 3 0 0 10 1 0
+0 1 0 0 1 0 4294967295 0 0 0 0 1 0 4294967295 1 0 1 0 10
+1 2 0 0 0 2 0 4294967295 4294967295 0 0 0 0 2 0 4294967295 4294967295 2 0 0 2 0 0 10
+2 4 0 1 65535 65535 65535 4 0 0 7 12 17 22 0 5 11 2 9 14 13 4 2 9 12 15 6 12 15 3 8 7 3 8 10 0 1 6 0 14 13 4 6 7 1 4 0 0 3 4 5 4 1 0 0 0 4 0 1 0 0 1 7 23 Policy::Sequential<1,1>
 
-DEAL::0 0 125 0 0 104 43 148 18446744073709551615 0 182 77 159 18446744073709551615 0 80 52 164 18446744073709551615 0 90 124 40 18446744073709551615 0 16 36 75 18446744073709551615 0 147 178 78 18446744073709551615 0 118 165 185 18446744073709551615 0 126 139 0 18446744073709551615 0 110 73 51 18446744073709551615 0 88 86 2 18446744073709551615 0 72 18 11 18446744073709551615 0 69 12 15 18446744073709551615 0 97 66 84 18446744073709551615 0 106 132 57 18446744073709551615 0 4 29 8 18446744073709551615 0 173 175 45 18446744073709551615 0 115 145 48 18446744073709551615 0 24 119 41 18446744073709551615 0 141 79 98 18446744073709551615 0 155 53 93 18446744073709551615 0 112 67 127 18446744073709551615 0 183 82 162 18446744073709551615 0 95 125 50 18446744073709551615 0 103 113 186 18446744073709551615 0 128 123 37 18446744073709551615 25 0 0 5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80 85 90 95 100 105 110 115 120 0 0 187 187 0 0 0 0 1 0 0 0 0 187 0 1 187 0 1 0 187 0 0 1 0 1 0 0 187 0 1 187 0 0 0 0 0 3 0 0 10 1 0
-0 1 0 0 1 0 4294967295 0 0 0 0 1 0 4294967295 10
-1 4 0 0 0 0 0 4 0 4294967295 4294967295 4294967295 4294967295 0 0 0 0 4 0 4294967295 4294967295 4294967295 4294967295 10
-2 16 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 16 0 0 22 44 66 88 110 132 154 176 198 220 242 264 286 308 330 352 0 104 43 148 88 86 2 69 12 15 183 82 162 7 181 33 1 89 107 135 19 137 134 88 86 2 16 36 75 183 82 162 24 119 41 33 1 101 25 153 138 150 49 42 81 69 12 15 183 82 162 147 178 78 155 53 93 92 61 146 91 135 19 94 22 144 171 183 82 162 24 119 41 155 53 93 110 73 51 146 91 151 14 150 49 130 161 39 76 16 36 75 72 18 11 24 119 41 95 125 50 101 25 184 3 177 174 117 108 58 102 72 18 11 182 77 159 95 125 50 106 132 57 184 3 63 20 100 68 35 17 60 31 24 119 41 95 125 50 110 73 51 112 67 127 151 14 6 121 117 108 167 10 30 180 95 125 50 106 132 57 112 67 127 118 165 185 6 121 176 5 35 17 122 179 70 136 147 178 78 155 53 93 97 66 84 103 113 186 13 9 27 140 94 22 129 71 172 170 155 53 93 110 73 51 103 113 186 141 79 98 27 140 23 168 130 161 116 26 131 44 97 66 84 103 113 186 80 52 164 173 175 45 55 65 163 64 129 71 152 149 85 142 103 113 186 141 79 98 173 175 45 126 139 0 163 64 46 47 116 26 143 120 156 83 110 73 51 112 67 127 141 79 98 128 123 37 23 168 54 169 167 10 28 87 160 99 112 67 127 118 165 185 128 123 37 4 29 8 54 169 32 111 122 179 157 56 38 158 141 79 98 128 123 37 126 139 0 115 145 48 46 47 105 154 28 87 59 96 166 34 128 123 37 4 29 8 115 145 48 90 124 40 105 154 109 133 157 56 74 114 21 62 32 0 137 134 42 81 144 171 39 76 58 102 60 31 30 180 70 136 172 170 131 44 85 142 156 83 160 99 38 158 166 34 21 62 16 0 0 2 4 6 8 10 12 14 16 18 20 22 24 26 28 30 0 0 0 13 1 0
-3 0 0 160 0 0 7 181 18446744073709551615 0 33 1 18446744073709551615 0 89 107 18446744073709551615 0 135 19 18446744073709551615 0 101 25 18446744073709551615 0 153 138 18446744073709551615 0 150 49 18446744073709551615 0 92 61 18446744073709551615 0 146 91 18446744073709551615 0 94 22 18446744073709551615 0 151 14 18446744073709551615 0 130 161 18446744073709551615 0 184 3 18446744073709551615 0 177 174 18446744073709551615 0 117 108 18446744073709551615 0 63 20 18446744073709551615 0 100 68 18446744073709551615 0 35 17 18446744073709551615 0 6 121 18446744073709551615 0 167 10 18446744073709551615 0 176 5 18446744073709551615 0 122 179 18446744073709551615 0 13 9 18446744073709551615 0 27 140 18446744073709551615 0 129 71 18446744073709551615 0 23 168 18446744073709551615 0 116 26 18446744073709551615 0 55 65 18446744073709551615 0 163 64 18446744073709551615 0 152 149 18446744073709551615 0 46 47 18446744073709551615 0 143 120 18446744073709551615 0 54 169 18446744073709551615 0 28 87 18446744073709551615 0 32 111 18446744073709551615 0 157 56 18446744073709551615 0 105 154 18446744073709551615 0 59 96 18446744073709551615 0 109 133 18446744073709551615 0 74 114 18446744073709551615 56 0 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 8 20 52 64 0 28 88 108 60 80 136 152 116 124 148 156 16 40 100 120 36 44 76 84 4 32 12 24 48 72 56 68 92 112 96 104 128 144 132 140 21 23 Policy::Sequential<2,2>
+DEAL::0 0 137 0 1 104 43 197 18446744073709551615 0 118 165 185 18446744073709551615 0 128 123 37 18446744073709551615 0 150 177 8 18446744073709551615 0 81 147 178 18446744073709551615 0 39 76 72 18446744073709551615 0 141 79 98 18446744073709551615 0 157 56 38 18446744073709551615 0 182 77 159 18446744073709551615 0 201 49 209 1 201 49 209 18446744073709551615 0 68 35 17 18446744073709551615 0 14 130 161 1 14 130 161 18446744073709551615 0 80 208 164 18446744073709551615 0 176 5 122 18446744073709551615 0 74 190 21 18446744073709551615 0 54 169 28 18446744073709551615 0 25 186 132 18446744073709551615 0 93 92 61 18446744073709551615 0 126 139 198 18446744073709551615 0 18 11 95 18446744073709551615 0 193 13 9 18446744073709551615 0 78 155 53 1 78 155 53 18446744073709551615 0 60 31 112 18446744073709551615 0 173 175 45 18446744073709551615 0 59 96 166 18446744073709551615 25 0 0 5 10 15 20 25 30 35 40 45 54 59 68 73 78 83 88 93 98 103 108 113 122 127 132 0 0 210 210 0 0 0 0 1 0 0 0 0 210 0 1 210 0 1 0 210 0 0 1 0 1 0 0 210 0 1 210 0 0 0 0 0 3 0 0 10 1 0
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4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 4294967295 34 182 107 202 722 802 742 822 257 347 282 367 877 947 897 967 68 117 142 162 267 292 312 332 427 447 472 492 582 602 622 642 0 127 172 217 412 457 502 537 712 757 792 837 1012 1047 1082 1117 277 322 362 397 592 632 667 697 892 927 962 997 1167 1197 1227 1257 467 547 487 562 1057 1127 1072 1142 617 687 637 702 1187 1247 1202 1262 812 832 852 867 957 977 992 1007 1097 1112 1132 1147 1222 1237 1252 1267 662 677 692 707 517 532 552 567 357 377 392 407 192 212 232 247 917 987 932 1002 307 387 327 402 767 847 782 862 137 227 157 242 1032 1067 1102 1137 737 777 817 857 437 482 522 557 102 152 197 237 1207 1192 1177 1162 1232 1172 1217 1157 1242 1212 1182 1152 1077 1062 1042 1027 1107 1037 1092 1022 1122 1087 1052 1017 937 922 907 887 972 902 952 882 982 942 912 872 787 772 752 732 827 747 807 727 842 797 762 717 647 627 607 587 672 597 657 577 682 652 612 572 497 477 452 432 527 442 512 422 542 507 462 417 337 317 297 272 372 287 352 262 382 342 302 252 167 147 122 83 207 112 187 49 222 177 132 15 73 23 Policy::Sequential<3,3>
 
 DEAL::OK

From 950cfca3abb5ba36505ed286f4ab2424bb2cb8f9 Mon Sep 17 00:00:00 2001
From: Timo Heister 
Date: Mon, 11 Mar 2019 09:48:48 -0400
Subject: [PATCH 245/507] enable lld linker if available

---
 cmake/checks/check_02_compiler_features.cmake | 28 +++++++++++++++----
 doc/news/changes/minor/20190411TimoHeister    |  3 ++
 2 files changed, 25 insertions(+), 6 deletions(-)
 create mode 100644 doc/news/changes/minor/20190411TimoHeister

diff --git a/cmake/checks/check_02_compiler_features.cmake b/cmake/checks/check_02_compiler_features.cmake
index 7ac38fe19f3c..d108cc47672f 100644
--- a/cmake/checks/check_02_compiler_features.cmake
+++ b/cmake/checks/check_02_compiler_features.cmake
@@ -420,19 +420,33 @@ RESET_CMAKE_REQUIRED()
 
 
 #
-# Use the 'gold' linker if possible, given that it's substantially faster.
+# Use 'lld' or the 'gold' linker if possible, given that either of them is
+# substantially faster.
 #
-# We have to try to link a full executable with -fuse-ld=gold to check
-# whether "ld.gold" is actually available.
+# We have to try to link a full executable with -fuse-ld=lld or -fuse-ld=gold
+# to check whether "ld.lld" or "ld.gold" is actually available.
 #
-# Clang always reports "argument unused during compilation"
-# if "-fuse-ld=" is used, but fails at link time for an unsupported linker.
+# Clang always reports "argument unused during compilation", but fails at link
+# time for an unsupported linker.
 #
 # ICC also emits a warning but passes for unsupported linkers
 # unless we turn diagnostic warnings into errors.
 #
 # Wolfgang Bangerth, Matthias Maier, Daniel Arndt, 2015, 2018
 #
+IF(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
+  ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-Wno-unused-command-line-argument")
+ELSEIF(CMAKE_CXX_COMPILER_ID MATCHES "Intel")
+  ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-diag-error warn")
+ENDIF()
+ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-Werror -fuse-ld=lld")
+CHECK_CXX_SOURCE_COMPILES(
+  "
+  int main() { return 0; }
+  "
+  DEAL_II_COMPILER_HAS_FUSE_LD_LLD)
+RESET_CMAKE_REQUIRED()
+
 IF(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
   ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-Wno-unused-command-line-argument")
 ELSEIF(CMAKE_CXX_COMPILER_ID MATCHES "Intel")
@@ -446,7 +460,9 @@ CHECK_CXX_SOURCE_COMPILES(
   DEAL_II_COMPILER_HAS_FUSE_LD_GOLD)
 RESET_CMAKE_REQUIRED()
 
-IF(DEAL_II_COMPILER_HAS_FUSE_LD_GOLD)
+IF(DEAL_II_COMPILER_HAS_FUSE_LD_LLD)
+  ADD_FLAGS(DEAL_II_LINKER_FLAGS "-fuse-ld=lld")
+ELSEIF(DEAL_II_COMPILER_HAS_FUSE_LD_GOLD)
   ADD_FLAGS(DEAL_II_LINKER_FLAGS "-fuse-ld=gold")
 ENDIF()
 
diff --git a/doc/news/changes/minor/20190411TimoHeister b/doc/news/changes/minor/20190411TimoHeister
new file mode 100644
index 000000000000..db6c9bdafb94
--- /dev/null
+++ b/doc/news/changes/minor/20190411TimoHeister
@@ -0,0 +1,3 @@
+New: If present, we will detect the LLD linker ld.lld at configuration time.
+
    
+(Timo Heister, 2019/03/11)

From ee9245435d37cdc5887f33c8656abe9ea24e33ef Mon Sep 17 00:00:00 2001
From: Daniel Arndt 
Date: Mon, 11 Mar 2019 18:56:31 +0100
Subject: [PATCH 246/507] Fix warnings in Convert::to_pattern()

---
 include/deal.II/base/patterns.h | 46 ++++++++++++++++++++++-----------
 1 file changed, 31 insertions(+), 15 deletions(-)

diff --git a/include/deal.II/base/patterns.h b/include/deal.II/base/patterns.h
index 3a8617fc91e0..bbb5b50adf6c 100644
--- a/include/deal.II/base/patterns.h
+++ b/include/deal.II/base/patterns.h
@@ -1493,22 +1493,38 @@ namespace Patterns
     struct Convert::value>::type>
     {
-      static std::unique_ptr
-      to_pattern()
+      template 
+      static
+        typename std::enable_if::value &&
+                                  std::is_same::value,
+                                std::unique_ptr>::type
+        to_pattern()
       {
-        if (std::is_same::value)
-          return std_cxx14::make_unique();
-        else if (std::is_integral::value)
-          return std_cxx14::make_unique(
-            static_cast(std::numeric_limits::lowest()),
-            static_cast(std::numeric_limits::max()));
-        else if (std::is_floating_point::value)
-          return std_cxx14::make_unique(
-            std::numeric_limits::lowest(), std::numeric_limits::max());
-
-        Assert(false, ExcNotImplemented());
-        // the following line should never be invoked
-        return nullptr;
+        return std_cxx14::make_unique();
+      }
+
+      template 
+      static
+        typename std::enable_if::value &&
+                                  !std::is_same::value &&
+                                  std::is_integral::value,
+                                std::unique_ptr>::type
+        to_pattern()
+      {
+        return std_cxx14::make_unique(
+          std::numeric_limits::lowest(), std::numeric_limits::max());
+      }
+
+      template 
+      static
+        typename std::enable_if::value &&
+                                  !std::is_same::value &&
+                                  std::is_floating_point::value,
+                                std::unique_ptr>::type
+        to_pattern()
+      {
+        return std_cxx14::make_unique(
+          std::numeric_limits::lowest(), std::numeric_limits::max());
       }
 
       static std::string

From d21b2a9064356332ad81f905ae54d42f84b51ce6 Mon Sep 17 00:00:00 2001
From: David Wells 
Date: Mon, 11 Mar 2019 15:32:21 -0400
Subject: [PATCH 247/507] Excise remaining calls to VectorSlice.

---
 .../meshworker/vector_selector.templates.h    | 49 +++++++++----------
 source/lac/chunk_sparsity_pattern.cc          |  2 +-
 source/lac/sparsity_pattern.cc                |  2 +-
 3 files changed, 24 insertions(+), 29 deletions(-)

diff --git a/include/deal.II/meshworker/vector_selector.templates.h b/include/deal.II/meshworker/vector_selector.templates.h
index 1efeaa4852ea..acf92bac61b4 100644
--- a/include/deal.II/meshworker/vector_selector.templates.h
+++ b/include/deal.II/meshworker/vector_selector.templates.h
@@ -132,21 +132,21 @@ namespace MeshWorker
     for (unsigned int i = 0; i < this->n_values(); ++i)
       {
         const VectorType *src = data.read_ptr(this->value_index(i));
-        VectorSlice>>
-          dst(values[i], component, n_comp);
-        fe.get_function_values(*src, make_slice(index, start, size), dst, true);
+        fe.get_function_values(*src,
+                               make_array_view(index, start, size),
+                               make_array_view(values[i], component, n_comp),
+                               true);
       }
 
     for (unsigned int i = 0; i < this->n_gradients(); ++i)
       {
         const VectorType *src =
           data.read_ptr(this->gradient_index(i));
-        VectorSlice>>>
-          dst(gradients[i], component, n_comp);
         fe.get_function_gradients(*src,
-                                  make_slice(index, start, size),
-                                  dst,
+                                  make_array_view(index, start, size),
+                                  make_array_view(gradients[i],
+                                                  component,
+                                                  n_comp),
                                   true);
       }
 
@@ -154,12 +154,11 @@ namespace MeshWorker
       {
         const VectorType *src =
           data.read_ptr(this->hessian_index(i));
-        VectorSlice>>>
-          dst(hessians[i], component, n_comp);
         fe.get_function_hessians(*src,
-                                 make_slice(index, start, size),
-                                 dst,
+                                 make_array_view(index, start, size),
+                                 make_array_view(hessians[i],
+                                                 component,
+                                                 n_comp),
                                  true);
       }
   }
@@ -233,11 +232,9 @@ namespace MeshWorker
       {
         const MGLevelObject *src =
           data.read_ptr>(this->value_index(i));
-        VectorSlice>>
-          dst(values[i], component, n_comp);
         fe.get_function_values((*src)[level],
-                               make_slice(index, start, size),
-                               dst,
+                               make_array_view(index, start, size),
+                               make_array_view(values[i], component, n_comp),
                                true);
       }
 
@@ -245,12 +242,11 @@ namespace MeshWorker
       {
         const MGLevelObject *src =
           data.read_ptr>(this->value_index(i));
-        VectorSlice>>>
-          dst(gradients[i], component, n_comp);
         fe.get_function_gradients((*src)[level],
-                                  make_slice(index, start, size),
-                                  dst,
+                                  make_array_view(index, start, size),
+                                  make_array_view(gradients[i],
+                                                  component,
+                                                  n_comp),
                                   true);
       }
 
@@ -258,12 +254,11 @@ namespace MeshWorker
       {
         const MGLevelObject *src =
           data.read_ptr>(this->value_index(i));
-        VectorSlice>>>
-          dst(hessians[i], component, n_comp);
         fe.get_function_hessians((*src)[level],
-                                 make_slice(index, start, size),
-                                 dst,
+                                 make_array_view(index, start, size),
+                                 make_array_view(hessians[i],
+                                                 component,
+                                                 n_comp),
                                  true);
       }
   }
diff --git a/source/lac/chunk_sparsity_pattern.cc b/source/lac/chunk_sparsity_pattern.cc
index db9cc4bbe47b..836c5077e393 100644
--- a/source/lac/chunk_sparsity_pattern.cc
+++ b/source/lac/chunk_sparsity_pattern.cc
@@ -264,7 +264,7 @@ ChunkSparsityPattern::reinit(const size_type               m,
 {
   Assert(chunk_size > 0, ExcInvalidNumber(chunk_size));
 
-  reinit(m, n, make_slice(row_lengths), chunk_size);
+  reinit(m, n, make_array_view(row_lengths), chunk_size);
 }
 
 
diff --git a/source/lac/sparsity_pattern.cc b/source/lac/sparsity_pattern.cc
index 2eb565a4542d..0e747a27c1a0 100644
--- a/source/lac/sparsity_pattern.cc
+++ b/source/lac/sparsity_pattern.cc
@@ -605,7 +605,7 @@ SparsityPattern::reinit(const size_type                  m,
                         const size_type                  n,
                         const std::vector &row_lengths)
 {
-  reinit(m, n, make_slice(row_lengths));
+  reinit(m, n, make_array_view(row_lengths));
 }
 
 

From 9853a35a8f31afeba27858cde01a20f104bfeafd Mon Sep 17 00:00:00 2001
From: Jean-Paul Pelteret 
Date: Sun, 10 Mar 2019 22:07:44 +0100
Subject: [PATCH 248/507] Rename a test

---
 .../{precondition_amg_dgp.cc => precondition_amg_dgp_01.cc}       | 0
 ...tput => precondition_amg_dgp_01.with_64bit_indices=off.output} | 0
 2 files changed, 0 insertions(+), 0 deletions(-)
 rename tests/trilinos/{precondition_amg_dgp.cc => precondition_amg_dgp_01.cc} (100%)
 rename tests/trilinos/{precondition_amg_dgp.with_64bit_indices=off.output => precondition_amg_dgp_01.with_64bit_indices=off.output} (100%)

diff --git a/tests/trilinos/precondition_amg_dgp.cc b/tests/trilinos/precondition_amg_dgp_01.cc
similarity index 100%
rename from tests/trilinos/precondition_amg_dgp.cc
rename to tests/trilinos/precondition_amg_dgp_01.cc
diff --git a/tests/trilinos/precondition_amg_dgp.with_64bit_indices=off.output b/tests/trilinos/precondition_amg_dgp_01.with_64bit_indices=off.output
similarity index 100%
rename from tests/trilinos/precondition_amg_dgp.with_64bit_indices=off.output
rename to tests/trilinos/precondition_amg_dgp_01.with_64bit_indices=off.output

From 0f0f6ee19b351e1a943e52b5020ad6d338a67a2d Mon Sep 17 00:00:00 2001
From: Jean-Paul Pelteret 
Date: Tue, 12 Mar 2019 09:35:07 +0100
Subject: [PATCH 249/507] Add useful methods to
 TrilinosWrappers::PreconditionAMG::AdditionalData.

These include:
- the initialization of a parameter list, which can be later modified by
the
user, and
- the initialisation of the null space settings in an existing parameter
list.
---
 .../changes/minor/20190310Jean-PaulPelteret-1 |   6 +
 include/deal.II/lac/trilinos_precondition.h   |  72 +++++++++
 source/lac/trilinos_precondition_ml.cc        | 151 ++++++++++++------
 3 files changed, 180 insertions(+), 49 deletions(-)
 create mode 100644 doc/news/changes/minor/20190310Jean-PaulPelteret-1

diff --git a/doc/news/changes/minor/20190310Jean-PaulPelteret-1 b/doc/news/changes/minor/20190310Jean-PaulPelteret-1
new file mode 100644
index 000000000000..6030de9655c3
--- /dev/null
+++ b/doc/news/changes/minor/20190310Jean-PaulPelteret-1
@@ -0,0 +1,6 @@
+Changed: The TrilinosWrappers::PreconditionAMG::AdditionalData data structure
+is now able to return a parameter list, which can be adjusted and fine-tuned by 
+the user and later used to initialize the AMG preconditioner. It can also
+initialize the null space settings of an existing parameter list.
+
    
+(Jean-Paul Pelteret, 2019/03/10)
diff --git a/include/deal.II/lac/trilinos_precondition.h b/include/deal.II/lac/trilinos_precondition.h
index cb6d2ee11b62..aba329ce8a6e 100644
--- a/include/deal.II/lac/trilinos_precondition.h
+++ b/include/deal.II/lac/trilinos_precondition.h
@@ -34,6 +34,7 @@
 #      include 
 #    endif
 #    include 
+#    include 
 #    include 
 #    include 
 #    include 
@@ -1382,6 +1383,77 @@ namespace TrilinosWrappers
                      const char *       smoother_type    = "Chebyshev",
                      const char *       coarse_type      = "Amesos-KLU");
 
+      /**
+       * Fill in a @p parameter_list that can be used to initialize the
+       * AMG preconditioner.
+       *
+       * The @p matrix is used in conjunction with the @p constant_modes to
+       * configure the null space settings for the preconditioner.
+       * The @p distributed_constant_modes are initialized by this function, and
+       * must remain in scope until PreconditionAMG::initialize() has been
+       * called.
+       *
+       * @note The set parameters reflect the current settings in this
+       * object, with various options being set both directly though the state
+       * of the member variables (e.g. the "smoother: type") as well as
+       * indirectly (e.g. the "aggregation: type"). If you wish to have
+       * fine-grained control over the configuration of the AMG preconditioner,
+       * then you can create the parameter list using this function (which
+       * conveniently sets the null space of the operator), change the relevant
+       * settings, and use the amended parameters list as an argument to
+       * PreconditionAMG::initialize(), instead of the AdditionalData object
+       * itself.
+       *
+       * See the documentation for the
+       * 
+       * Trilinos ML package for details on what options are available for
+       * modification.
+       *
+       * @note Any user-defined parameters that are not in conflict with those
+       * set by this data structure will be retained.
+       */
+      void
+      set_parameters(
+        Teuchos::ParameterList &             parameter_list,
+        std::unique_ptr &distributed_constant_modes,
+        const Epetra_RowMatrix &             matrix) const;
+
+      /**
+       * Fill in a parameter list that can be used to initialize the
+       * AMG preconditioner.
+       *
+       * @note Any user-defined parameters that are not in conflict with those
+       * set by this data structure will be retained.
+       */
+      void
+      set_parameters(
+        Teuchos::ParameterList &             parameter_list,
+        std::unique_ptr &distributed_constant_modes,
+        const SparseMatrix &                 matrix) const;
+
+      /**
+       * Configure the null space setting in the @p parameter_list for
+       * the input @p matrix based on the state of the @p constant_modes
+       * variable.
+       */
+      void
+      set_operator_null_space(
+        Teuchos::ParameterList &             parameter_list,
+        std::unique_ptr &distributed_constant_modes,
+        const Epetra_RowMatrix &             matrix) const;
+
+      /**
+       * Configure the null space setting in the @p parameter_list for
+       * the input @p matrix based on the state of the @p constant_modes
+       * variable.
+       */
+      void
+      set_operator_null_space(
+        Teuchos::ParameterList &             parameter_list,
+        std::unique_ptr &distributed_constant_modes,
+        const SparseMatrix &                 matrix) const;
+
       /**
        * Determines whether the AMG preconditioner should be optimized for
        * elliptic problems (ML option smoothed aggregation SA, using a
diff --git a/source/lac/trilinos_precondition_ml.cc b/source/lac/trilinos_precondition_ml.cc
index 0375697c3920..848315efaa74 100644
--- a/source/lac/trilinos_precondition_ml.cc
+++ b/source/lac/trilinos_precondition_ml.cc
@@ -63,31 +63,14 @@ namespace TrilinosWrappers
   {}
 
 
-  PreconditionAMG::~PreconditionAMG()
-  {
-    preconditioner.reset();
-    trilinos_matrix.reset();
-  }
-
-
 
   void
-  PreconditionAMG::initialize(const SparseMatrix &  matrix,
-                              const AdditionalData &additional_data)
-  {
-    initialize(matrix.trilinos_matrix(), additional_data);
-  }
-
-
-
-  void
-  PreconditionAMG::initialize(const Epetra_RowMatrix &matrix,
-                              const AdditionalData &  additional_data)
+  PreconditionAMG::AdditionalData::set_parameters(
+    Teuchos::ParameterList &             parameter_list,
+    std::unique_ptr &distributed_constant_modes,
+    const Epetra_RowMatrix &             matrix) const
   {
-    // Build the AMG preconditioner.
-    Teuchos::ParameterList parameter_list;
-
-    if (additional_data.elliptic == true)
+    if (elliptic == true)
       {
         ML_Epetra::SetDefaults("SA", parameter_list);
 
@@ -99,7 +82,7 @@ namespace TrilinosWrappers
         // standard choice uncoupled. if higher order, right now we also just
         // use Uncoupled, but we should be aware that maybe MIS might be
         // needed
-        if (additional_data.higher_order_elements)
+        if (higher_order_elements)
           parameter_list.set("aggregation: type", "Uncoupled");
       }
     else
@@ -109,8 +92,8 @@ namespace TrilinosWrappers
         parameter_list.set("aggregation: block scaling", true);
       }
 
-    parameter_list.set("smoother: type", additional_data.smoother_type);
-    parameter_list.set("coarse: type", additional_data.coarse_type);
+    parameter_list.set("smoother: type", smoother_type);
+    parameter_list.set("coarse: type", coarse_type);
 
     // Force re-initialization of the random seed to make ML deterministic
     // (only supported in trilinos >12.2):
@@ -118,34 +101,43 @@ namespace TrilinosWrappers
     parameter_list.set("initialize random seed", true);
 #  endif
 
-    parameter_list.set("smoother: sweeps",
-                       static_cast(additional_data.smoother_sweeps));
-    parameter_list.set("cycle applications",
-                       static_cast(additional_data.n_cycles));
-    if (additional_data.w_cycle == true)
+    parameter_list.set("smoother: sweeps", static_cast(smoother_sweeps));
+    parameter_list.set("cycle applications", static_cast(n_cycles));
+    if (w_cycle == true)
       parameter_list.set("prec type", "MGW");
     else
       parameter_list.set("prec type", "MGV");
 
     parameter_list.set("smoother: Chebyshev alpha", 10.);
     parameter_list.set("smoother: ifpack overlap",
-                       static_cast(additional_data.smoother_overlap));
-    parameter_list.set("aggregation: threshold",
-                       additional_data.aggregation_threshold);
+                       static_cast(smoother_overlap));
+    parameter_list.set("aggregation: threshold", aggregation_threshold);
     parameter_list.set("coarse: max size", 2000);
 
-    if (additional_data.output_details)
+    if (output_details)
       parameter_list.set("ML output", 10);
     else
       parameter_list.set("ML output", 0);
 
+    set_operator_null_space(parameter_list, distributed_constant_modes, matrix);
+  }
+
+
+
+  void
+  PreconditionAMG::AdditionalData::set_operator_null_space(
+    Teuchos::ParameterList &             parameter_list,
+    std::unique_ptr &ptr_distributed_constant_modes,
+    const Epetra_RowMatrix &             matrix) const
+  {
     const Epetra_Map &domain_map = matrix.OperatorDomainMap();
 
-    const size_type constant_modes_dimension =
-      additional_data.constant_modes.size();
-    Epetra_MultiVector distributed_constant_modes(
-      domain_map, constant_modes_dimension > 0 ? constant_modes_dimension : 1);
-    std::vector dummy(constant_modes_dimension);
+    const size_type constant_modes_dimension = constant_modes.size();
+    ptr_distributed_constant_modes.reset(new Epetra_MultiVector(
+      domain_map, constant_modes_dimension > 0 ? constant_modes_dimension : 1));
+    Assert(ptr_distributed_constant_modes, ExcNotInitialized());
+    Epetra_MultiVector &distributed_constant_modes =
+      *ptr_distributed_constant_modes;
 
     if (constant_modes_dimension > 0)
       {
@@ -159,7 +151,7 @@ namespace TrilinosWrappers
                                     TrilinosWrappers::global_length(
                                       distributed_constant_modes)));
         const bool constant_modes_are_global =
-          additional_data.constant_modes[0].size() == global_size;
+          constant_modes[0].size() == global_size;
         const size_type my_size = domain_map.NumMyElements();
 
         // Reshape null space as a contiguous vector of doubles so that
@@ -168,10 +160,9 @@ namespace TrilinosWrappers
           constant_modes_are_global ? global_size : my_size;
         for (size_type d = 0; d < constant_modes_dimension; ++d)
           {
-            Assert(
-              additional_data.constant_modes[d].size() == expected_mode_size,
-              ExcDimensionMismatch(additional_data.constant_modes[d].size(),
-                                   expected_mode_size));
+            Assert(constant_modes[d].size() == expected_mode_size,
+                   ExcDimensionMismatch(constant_modes[d].size(),
+                                        expected_mode_size));
             for (size_type row = 0; row < my_size; ++row)
               {
                 const TrilinosWrappers::types::int_type mode_index =
@@ -179,7 +170,7 @@ namespace TrilinosWrappers
                     TrilinosWrappers::global_index(domain_map, row) :
                     row;
                 distributed_constant_modes[d][row] =
-                  additional_data.constant_modes[d][mode_index];
+                  constant_modes[d][mode_index];
               }
           }
         (void)expected_mode_size;
@@ -190,13 +181,75 @@ namespace TrilinosWrappers
         if (my_size > 0)
           parameter_list.set("null space: vectors",
                              distributed_constant_modes.Values());
-        // We need to set a valid pointer to data even if there is no data on
-        // the current processor. Therefore, pass a dummy in that case
         else
-          parameter_list.set("null space: vectors", dummy.data());
+          {
+            // We need to set a valid pointer to data even if there is no data
+            // on the current processor. Therefore, pass a dummy in that case
+            static std::vector dummy;
+            if (dummy.size() != constant_modes_dimension)
+              dummy.resize(constant_modes_dimension);
+            parameter_list.set("null space: vectors", dummy.data());
+          }
       }
+  }
+
+
+
+  void
+  PreconditionAMG::AdditionalData::set_parameters(
+    Teuchos::ParameterList &             parameter_list,
+    std::unique_ptr &distributed_constant_modes,
+    const SparseMatrix &                 matrix) const
+  {
+    return set_parameters(parameter_list,
+                          distributed_constant_modes,
+                          matrix.trilinos_matrix());
+  }
+
+
+
+  void
+  PreconditionAMG::AdditionalData::set_operator_null_space(
+    Teuchos::ParameterList &             parameter_list,
+    std::unique_ptr &distributed_constant_modes,
+    const SparseMatrix &                 matrix) const
+  {
+    return set_operator_null_space(parameter_list,
+                                   distributed_constant_modes,
+                                   matrix.trilinos_matrix());
+  }
+
+
+
+  PreconditionAMG::~PreconditionAMG()
+  {
+    preconditioner.reset();
+    trilinos_matrix.reset();
+  }
+
+
+
+  void
+  PreconditionAMG::initialize(const SparseMatrix &  matrix,
+                              const AdditionalData &additional_data)
+  {
+    initialize(matrix.trilinos_matrix(), additional_data);
+  }
+
+
+
+  void
+  PreconditionAMG::initialize(const Epetra_RowMatrix &matrix,
+                              const AdditionalData &  additional_data)
+  {
+    // Build the AMG preconditioner.
+    Teuchos::ParameterList              ml_parameters;
+    std::unique_ptr distributed_constant_modes;
+    additional_data.set_parameters(ml_parameters,
+                                   distributed_constant_modes,
+                                   matrix);
 
-    initialize(matrix, parameter_list);
+    initialize(matrix, ml_parameters);
 
     if (additional_data.output_details)
       {

From df6e953a83aae7b3a3d5ba30b6771486312797a9 Mon Sep 17 00:00:00 2001
From: David Wells 
Date: Mon, 11 Mar 2019 15:35:27 -0400
Subject: [PATCH 250/507] Excise remaining inclusions of vector_slice.h.

---
 include/deal.II/fe/fe_values.h                         | 1 -
 include/deal.II/lac/chunk_sparsity_pattern.h           | 1 -
 include/deal.II/meshworker/vector_selector.templates.h | 2 --
 source/lac/block_sparsity_pattern.cc                   | 1 -
 source/lac/sparsity_pattern.cc                         | 1 -
 tests/integrators/advection_01.cc                      | 1 +
 tests/integrators/divergence_01.cc                     | 1 +
 tests/integrators/elasticity_01.cc                     | 1 +
 tests/integrators/elasticity_02.cc                     | 1 +
 tests/integrators/grad_div_01.cc                       | 1 +
 tests/integrators/laplacian_01.cc                      | 1 +
 11 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/include/deal.II/fe/fe_values.h b/include/deal.II/fe/fe_values.h
index 3e03139485d1..713f1c64adad 100644
--- a/include/deal.II/fe/fe_values.h
+++ b/include/deal.II/fe/fe_values.h
@@ -25,7 +25,6 @@
 #include 
 #include 
 #include 
-#include 
 
 #include 
 #include 
diff --git a/include/deal.II/lac/chunk_sparsity_pattern.h b/include/deal.II/lac/chunk_sparsity_pattern.h
index e958ecd89a54..a5e14d6de72d 100644
--- a/include/deal.II/lac/chunk_sparsity_pattern.h
+++ b/include/deal.II/lac/chunk_sparsity_pattern.h
@@ -21,7 +21,6 @@
 
 #include 
 #include 
-#include 
 
 #include 
 
diff --git a/include/deal.II/meshworker/vector_selector.templates.h b/include/deal.II/meshworker/vector_selector.templates.h
index acf92bac61b4..283edd873bc0 100644
--- a/include/deal.II/meshworker/vector_selector.templates.h
+++ b/include/deal.II/meshworker/vector_selector.templates.h
@@ -17,8 +17,6 @@
 #define dealii_vector_selector_templates_h
 
 
-#include 
-
 #include 
 
 #include 
diff --git a/source/lac/block_sparsity_pattern.cc b/source/lac/block_sparsity_pattern.cc
index de077a77a494..7cec15500db0 100644
--- a/source/lac/block_sparsity_pattern.cc
+++ b/source/lac/block_sparsity_pattern.cc
@@ -15,7 +15,6 @@
 
 
 #include 
-#include 
 
 #include 
 
diff --git a/source/lac/sparsity_pattern.cc b/source/lac/sparsity_pattern.cc
index 0e747a27c1a0..6b4bb1a1f476 100644
--- a/source/lac/sparsity_pattern.cc
+++ b/source/lac/sparsity_pattern.cc
@@ -16,7 +16,6 @@
 
 #include 
 #include 
-#include 
 
 #include 
 #include 
diff --git a/tests/integrators/advection_01.cc b/tests/integrators/advection_01.cc
index 44d11ab050ec..06e81f156156 100644
--- a/tests/integrators/advection_01.cc
+++ b/tests/integrators/advection_01.cc
@@ -16,6 +16,7 @@
 
 // Test the functions in integrators/laplace.h
 // Output matrices and assert consistency of residuals
+#include 
 
 #include 
 #include 
diff --git a/tests/integrators/divergence_01.cc b/tests/integrators/divergence_01.cc
index 5df9cd73f716..8fec5dbb1442 100644
--- a/tests/integrators/divergence_01.cc
+++ b/tests/integrators/divergence_01.cc
@@ -16,6 +16,7 @@
 
 // Test the functions in integrators/divergence.h
 // Output matrices and assert consistency of residuals
+#include 
 
 #include 
 #include 
diff --git a/tests/integrators/elasticity_01.cc b/tests/integrators/elasticity_01.cc
index 20cfaa40bf48..8e548adec15b 100644
--- a/tests/integrators/elasticity_01.cc
+++ b/tests/integrators/elasticity_01.cc
@@ -16,6 +16,7 @@
 
 // Test the functions in integrators/elasticity.h
 // Output matrices and assert consistency of residuals
+#include 
 
 #include 
 #include 
diff --git a/tests/integrators/elasticity_02.cc b/tests/integrators/elasticity_02.cc
index 656f336d581d..723e15ecdd25 100644
--- a/tests/integrators/elasticity_02.cc
+++ b/tests/integrators/elasticity_02.cc
@@ -16,6 +16,7 @@
 
 // Test nitsche_tangential in Elasticity
 // Output matrices and assert consistency of residuals
+#include 
 
 #include 
 #include 
diff --git a/tests/integrators/grad_div_01.cc b/tests/integrators/grad_div_01.cc
index 645294228716..8953f9ec92f8 100644
--- a/tests/integrators/grad_div_01.cc
+++ b/tests/integrators/grad_div_01.cc
@@ -16,6 +16,7 @@
 
 // Test the functions in integrators/grad_div.h
 // Output matrices and assert consistency of residuals
+#include 
 
 #include 
 #include 
diff --git a/tests/integrators/laplacian_01.cc b/tests/integrators/laplacian_01.cc
index 2eb8a8cd534f..2e0dd1550640 100644
--- a/tests/integrators/laplacian_01.cc
+++ b/tests/integrators/laplacian_01.cc
@@ -16,6 +16,7 @@
 
 // Test the functions in integrators/laplace.h
 // Output matrices and assert consistency of residuals
+#include 
 
 #include 
 #include 

From d16e5bcfbd81ac9f1303b3cfda95b67374a1ce71 Mon Sep 17 00:00:00 2001
From: Wolfgang Bangerth 
Date: Mon, 11 Mar 2019 22:59:07 -0600
Subject: [PATCH 251/507] Update documentation of class Vector.

---
 include/deal.II/lac/vector.h | 25 ++++++++++++++++---------
 1 file changed, 16 insertions(+), 9 deletions(-)

diff --git a/include/deal.II/lac/vector.h b/include/deal.II/lac/vector.h
index b413f686b129..5ba965853180 100644
--- a/include/deal.II/lac/vector.h
+++ b/include/deal.II/lac/vector.h
@@ -78,15 +78,22 @@ namespace parallel
  */
 
 /**
- * Numerical vector of data.  For this class there are different types of
- * functions available. The first type of function initializes the vector,
- * changes its size, or computes the norm of the vector in order to measure
- * its length in a suitable norm. The second type helps us to manipulate the
- * components of the vector. The third type defines the algebraic operations
- * for vectors, while the last type defines a few input and output functions.
- * As opposed to the array of the C++ standard library called @p vector (with
- * a lowercase "v"), this class implements an element of a vector space
- * suitable for numerical computations.
+ * A class that represents a vector of numerical elements. As for the
+ * other classes, in the @ref Vectors group, this class has a substantial
+ * number of member functions. These include:
+ * - functions that initialize the vector or change its size;
+ * - functions that compute properties of the vector, such as a variety of
+ *   norms;
+ * - functions that allow reading from or writing to individual elements of the
+ *   vector;
+ * - functions that implement algebraic operations for vectors, such as
+ *   addition of vectors; and
+ * - functions that allow inputting and outputting the data stored by vectors.
+ *
+ * In contrast to the C++ standard library class `std::vector`, this class
+ * intends to implement not simply an array that allows access to its elements,
+ * but indeed a vector that is a member of the mathematical concept of a
+ * "vector space" suitable for numerical computations.
  *
  * @note Instantiations for this template are provided for @,
  * @, @@>, @@>;

From cf5d11dcc2e5cfdf6194be9c25e4edf27897224f Mon Sep 17 00:00:00 2001
From: Daniel Arndt 
Date: Tue, 12 Mar 2019 17:02:16 +0100
Subject: [PATCH 252/507] Update allowed MSVC version in bundled boost

---
 .../boost-1.62.0/include/boost/config/compiler/visualc.hpp    | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/bundled/boost-1.62.0/include/boost/config/compiler/visualc.hpp b/bundled/boost-1.62.0/include/boost/config/compiler/visualc.hpp
index 200d39df5e13..3a68c4d6bd9f 100644
--- a/bundled/boost-1.62.0/include/boost/config/compiler/visualc.hpp
+++ b/bundled/boost-1.62.0/include/boost/config/compiler/visualc.hpp
@@ -294,10 +294,10 @@
 #endif
 
 //
-// masterleinad: upgrade supported MSVC version to 19.16 (last checked 19.16.27024.1)
+// masterleinad: upgrade supported MSVC version to 19.20 (last checked 19.20.27404)
 // Boost repo has only 19.10:
 // last known and checked version is 19.10.24629 (VC++ 2017 RC):
-#if (_MSC_VER > 1916)
+#if (_MSC_VER > 1920)
 #  if defined(BOOST_ASSERT_CONFIG)
 #     error "Unknown compiler version - please run the configure tests and report the results"
 #  else

From 2f9053427795e0c23bbc54a1d8fd003a3d251197 Mon Sep 17 00:00:00 2001
From: Daniel Arndt 
Date: Tue, 12 Mar 2019 21:35:11 +0100
Subject: [PATCH 253/507] Allow CXX14/17 autodetection for MSVC

---
 cmake/checks/check_01_cxx_features.cmake      | 32 +++++++++++++++----
 cmake/checks/check_02_compiler_features.cmake | 26 ++++++++++++---
 cmake/configure/configure_2_boost.cmake       |  6 +++-
 3 files changed, 53 insertions(+), 11 deletions(-)

diff --git a/cmake/checks/check_01_cxx_features.cmake b/cmake/checks/check_01_cxx_features.cmake
index bf1aedec3bee..1f71219af41f 100644
--- a/cmake/checks/check_01_cxx_features.cmake
+++ b/cmake/checks/check_01_cxx_features.cmake
@@ -99,10 +99,17 @@ ENDIF()
 
 MACRO(_check_cxx_flag _suffix)
   IF("${DEAL_II_CXX_VERSION_FLAG}" STREQUAL "")
-    CHECK_CXX_COMPILER_FLAG("-std=c++${_suffix}" DEAL_II_HAVE_FLAG_stdcxx${_suffix})
-    IF(DEAL_II_HAVE_FLAG_stdcxx${_suffix})
-      SET(DEAL_II_CXX_VERSION_FLAG "-std=c++${_suffix}")
-    ENDIF()
+    IF(CMAKE_CXX_COMPILER_ID MATCHES "MSVC")
+      CHECK_CXX_COMPILER_FLAG("/std:c++${_suffix}" DEAL_II_HAVE_FLAG_stdcxx${_suffix})
+      IF(DEAL_II_HAVE_FLAG_stdcxx${_suffix})
+        SET(DEAL_II_CXX_VERSION_FLAG "/std:c++${_suffix}")
+      ENDIF()
+	ELSE()
+      CHECK_CXX_COMPILER_FLAG("-std=c++${_suffix}" DEAL_II_HAVE_FLAG_stdcxx${_suffix})
+      IF(DEAL_II_HAVE_FLAG_stdcxx${_suffix})
+        SET(DEAL_II_CXX_VERSION_FLAG "-std=c++${_suffix}")
+      ENDIF()
+	ENDIF()
   ENDIF()
 ENDMACRO()
 
@@ -126,7 +133,12 @@ IF(NOT DEFINED DEAL_II_WITH_CXX17 OR DEAL_II_WITH_CXX17)
   IF(NOT "${DEAL_II_CXX_VERSION_FLAG}" STREQUAL "")
     # Set CMAKE_REQUIRED_FLAGS for the unit tests
     MESSAGE(STATUS "Using C++ version flag \"${DEAL_II_CXX_VERSION_FLAG}\"")
-    ADD_FLAGS(CMAKE_REQUIRED_FLAGS "${DEAL_II_CXX_VERSION_FLAG} -Werror")
+    IF(CMAKE_CXX_COMPILER_ID MATCHES "MSVC")
+      ADD_FLAGS(CMAKE_REQUIRED_FLAGS "/WX /EHsc")
+    ELSE()
+      ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-Werror")
+    ENDIF()
+    ADD_FLAGS(CMAKE_REQUIRED_FLAGS "${DEAL_II_CXX_VERSION_FLAG}")
 
     UNSET_IF_CHANGED(CHECK_CXX_FEATURES_FLAGS_CXX17_SAVED
       "${CMAKE_REQUIRED_FLAGS}${DEAL_II_CXX_VERSION_FLAG}"
@@ -512,6 +524,9 @@ _bailout("17" "1z")
 # try to avoid adding an extra flag by doing one last test:
 #
 RESET_CMAKE_REQUIRED()
+IF(CMAKE_CXX_COMPILER_ID MATCHES "MSVC")
+  ADD_FLAGS(CMAKE_REQUIRED_FLAGS "/Zc:__cplusplus")
+ENDIF()
 CHECK_CXX_SOURCE_COMPILES(
   "
   #include 
@@ -527,6 +542,7 @@ CHECK_CXX_SOURCE_COMPILES(
   }
   "
   DEAL_II_COMPILER_DEFAULTS_TO_CXX11_OR_NEWER)
+  RESET_CMAKE_REQUIRED()
 
 IF(_user_provided_cxx_version_flag OR
     NOT DEAL_II_COMPILER_DEFAULTS_TO_CXX11_OR_NEWER OR
@@ -570,7 +586,11 @@ UNSET_IF_CHANGED(CHECK_CXX_FEATURES_FLAGS_SAVED
 # possibilities here.
 #
 ADD_FLAGS(CMAKE_REQUIRED_FLAGS "${DEAL_II_CXX_FLAGS}")
-ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-Werror -Wno-unused-command-line-argument")
+IF(CMAKE_CXX_COMPILER_ID MATCHES "MSVC")
+  ADD_FLAGS(CMAKE_REQUIRED_FLAGS "/WX")
+ELSE()
+  ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-Werror -Wno-unused-command-line-argument")
+ENDIF()
 #
 # first try the attribute [[fallthrough]]
 #
diff --git a/cmake/checks/check_02_compiler_features.cmake b/cmake/checks/check_02_compiler_features.cmake
index d108cc47672f..d7d7c8321893 100644
--- a/cmake/checks/check_02_compiler_features.cmake
+++ b/cmake/checks/check_02_compiler_features.cmake
@@ -298,7 +298,11 @@ ENDIF()
 # "warning #1292: unknown attribute "deprecated"" (icc)
 # Hence, we treat warnings as errors:
 ADD_FLAGS(CMAKE_REQUIRED_FLAGS "${DEAL_II_CXX_FLAGS}")
-ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-Werror -Wno-unused-command-line-argument")
+IF(CMAKE_CXX_COMPILER_ID MATCHES "MSVC")
+  ADD_FLAGS(CMAKE_REQUIRED_FLAGS "/WX")
+ELSE()
+  ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-Werror -Wno-unused-command-line-argument")
+ENDIF()
 
 # first see if the compiler accepts the attribute
 CHECK_CXX_SOURCE_COMPILES(
@@ -405,7 +409,11 @@ ENDIF()
 #
 # - Matthias Maier, 2015
 #
-ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-Werror")
+IF(CMAKE_CXX_COMPILER_ID MATCHES "MSVC")
+  ADD_FLAGS(CMAKE_REQUIRED_FLAGS "/WX")
+ELSE()
+  ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-Werror")
+ENDIF()
 CHECK_CXX_SOURCE_COMPILES(
   "
   _Pragma(\"GCC diagnostic push\")
@@ -439,7 +447,12 @@ IF(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
 ELSEIF(CMAKE_CXX_COMPILER_ID MATCHES "Intel")
   ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-diag-error warn")
 ENDIF()
-ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-Werror -fuse-ld=lld")
+IF(CMAKE_CXX_COMPILER_ID MATCHES "MSVC")
+  ADD_FLAGS(CMAKE_REQUIRED_FLAGS "/WX")
+ELSE()
+  ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-Werror")
+ENDIF()
+ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-fuse-ld=lld")
 CHECK_CXX_SOURCE_COMPILES(
   "
   int main() { return 0; }
@@ -452,7 +465,12 @@ IF(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
 ELSEIF(CMAKE_CXX_COMPILER_ID MATCHES "Intel")
   ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-diag-error warn")
 ENDIF()
-ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-Werror -fuse-ld=gold")
+IF(CMAKE_CXX_COMPILER_ID MATCHES "MSVC")
+  ADD_FLAGS(CMAKE_REQUIRED_FLAGS "/WX")
+ELSE()
+  ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-Werror")
+ENDIF()
+ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-fuse-ld=gold")
 CHECK_CXX_SOURCE_COMPILES(
   "
   int main() { return 0; }
diff --git a/cmake/configure/configure_2_boost.cmake b/cmake/configure/configure_2_boost.cmake
index 5c6f9c35a806..1b5988fc8f36 100644
--- a/cmake/configure/configure_2_boost.cmake
+++ b/cmake/configure/configure_2_boost.cmake
@@ -58,7 +58,11 @@ MACRO(FEATURE_BOOST_CONFIGURE_COMMON)
   # Older boost versions can't know about this but provide a possibility to
   # circumvent the issue. Hence, we just check ourselves.
   ADD_FLAGS(CMAKE_REQUIRED_FLAGS "${DEAL_II_CXX_VERSION_FLAG}")
-  ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-Werror")
+  IF(CMAKE_CXX_COMPILER_ID MATCHES "MSVC")
+    ADD_FLAGS(CMAKE_REQUIRED_FLAGS "/WX")
+  ELSE()
+    ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-Werror")
+  ENDIF()
 
   CHECK_CXX_SOURCE_COMPILES(
     "

From 2876a2686c53ae96e215226c7f8104e413e628cb Mon Sep 17 00:00:00 2001
From: Daniel Arndt 
Date: Wed, 13 Mar 2019 09:56:12 +0100
Subject: [PATCH 254/507] Avoid tabs and don't test for alternative linker with
 MSVC

---
 cmake/checks/check_01_cxx_features.cmake      |  6 +-
 cmake/checks/check_02_compiler_features.cmake | 67 +++++++++----------
 cmake/configure/configure_2_boost.cmake       |  2 +-
 3 files changed, 34 insertions(+), 41 deletions(-)

diff --git a/cmake/checks/check_01_cxx_features.cmake b/cmake/checks/check_01_cxx_features.cmake
index 1f71219af41f..2f5cf61e7efc 100644
--- a/cmake/checks/check_01_cxx_features.cmake
+++ b/cmake/checks/check_01_cxx_features.cmake
@@ -104,12 +104,12 @@ MACRO(_check_cxx_flag _suffix)
       IF(DEAL_II_HAVE_FLAG_stdcxx${_suffix})
         SET(DEAL_II_CXX_VERSION_FLAG "/std:c++${_suffix}")
       ENDIF()
-	ELSE()
+    ELSE()
       CHECK_CXX_COMPILER_FLAG("-std=c++${_suffix}" DEAL_II_HAVE_FLAG_stdcxx${_suffix})
       IF(DEAL_II_HAVE_FLAG_stdcxx${_suffix})
         SET(DEAL_II_CXX_VERSION_FLAG "-std=c++${_suffix}")
       ENDIF()
-	ENDIF()
+    ENDIF()
   ENDIF()
 ENDMACRO()
 
@@ -542,7 +542,7 @@ CHECK_CXX_SOURCE_COMPILES(
   }
   "
   DEAL_II_COMPILER_DEFAULTS_TO_CXX11_OR_NEWER)
-  RESET_CMAKE_REQUIRED()
+RESET_CMAKE_REQUIRED()
 
 IF(_user_provided_cxx_version_flag OR
     NOT DEAL_II_COMPILER_DEFAULTS_TO_CXX11_OR_NEWER OR
diff --git a/cmake/checks/check_02_compiler_features.cmake b/cmake/checks/check_02_compiler_features.cmake
index d7d7c8321893..e844e7d904dc 100644
--- a/cmake/checks/check_02_compiler_features.cmake
+++ b/cmake/checks/check_02_compiler_features.cmake
@@ -442,45 +442,38 @@ RESET_CMAKE_REQUIRED()
 #
 # Wolfgang Bangerth, Matthias Maier, Daniel Arndt, 2015, 2018
 #
-IF(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
-  ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-Wno-unused-command-line-argument")
-ELSEIF(CMAKE_CXX_COMPILER_ID MATCHES "Intel")
-  ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-diag-error warn")
-ENDIF()
-IF(CMAKE_CXX_COMPILER_ID MATCHES "MSVC")
-  ADD_FLAGS(CMAKE_REQUIRED_FLAGS "/WX")
-ELSE()
+IF(NOT CMAKE_CXX_COMPILER_ID MATCHES "MSVC")
+  IF(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
+    ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-Wno-unused-command-line-argument")
+  ELSEIF(CMAKE_CXX_COMPILER_ID MATCHES "Intel")
+    ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-diag-error warn")
+  ENDIF()
   ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-Werror")
-ENDIF()
-ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-fuse-ld=lld")
-CHECK_CXX_SOURCE_COMPILES(
-  "
-  int main() { return 0; }
-  "
-  DEAL_II_COMPILER_HAS_FUSE_LD_LLD)
-RESET_CMAKE_REQUIRED()
+  ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-fuse-ld=lld")
+  CHECK_CXX_SOURCE_COMPILES(
+    "
+    int main() { return 0; }
+    "
+    DEAL_II_COMPILER_HAS_FUSE_LD_LLD)
+  RESET_CMAKE_REQUIRED()
 
-IF(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
-  ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-Wno-unused-command-line-argument")
-ELSEIF(CMAKE_CXX_COMPILER_ID MATCHES "Intel")
-  ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-diag-error warn")
-ENDIF()
-IF(CMAKE_CXX_COMPILER_ID MATCHES "MSVC")
-  ADD_FLAGS(CMAKE_REQUIRED_FLAGS "/WX")
-ELSE()
+  IF(CMAKE_CXX_COMPILER_ID MATCHES "Clang")
+    ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-Wno-unused-command-line-argument")
+  ELSEIF(CMAKE_CXX_COMPILER_ID MATCHES "Intel")
+    ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-diag-error warn")
+  ENDIF()
   ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-Werror")
-ENDIF()
-ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-fuse-ld=gold")
-CHECK_CXX_SOURCE_COMPILES(
-  "
-  int main() { return 0; }
-  "
-  DEAL_II_COMPILER_HAS_FUSE_LD_GOLD)
-RESET_CMAKE_REQUIRED()
+  ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-fuse-ld=gold")
+  CHECK_CXX_SOURCE_COMPILES(
+    "
+    int main() { return 0; }
+    "
+    DEAL_II_COMPILER_HAS_FUSE_LD_GOLD)
+  RESET_CMAKE_REQUIRED()
 
-IF(DEAL_II_COMPILER_HAS_FUSE_LD_LLD)
-  ADD_FLAGS(DEAL_II_LINKER_FLAGS "-fuse-ld=lld")
-ELSEIF(DEAL_II_COMPILER_HAS_FUSE_LD_GOLD)
-  ADD_FLAGS(DEAL_II_LINKER_FLAGS "-fuse-ld=gold")
+  IF(DEAL_II_COMPILER_HAS_FUSE_LD_LLD)
+    ADD_FLAGS(DEAL_II_LINKER_FLAGS "-fuse-ld=lld")
+  ELSEIF(DEAL_II_COMPILER_HAS_FUSE_LD_GOLD)
+    ADD_FLAGS(DEAL_II_LINKER_FLAGS "-fuse-ld=gold")
+  ENDIF()
 ENDIF()
-
diff --git a/cmake/configure/configure_2_boost.cmake b/cmake/configure/configure_2_boost.cmake
index 1b5988fc8f36..1637b16695c8 100644
--- a/cmake/configure/configure_2_boost.cmake
+++ b/cmake/configure/configure_2_boost.cmake
@@ -59,7 +59,7 @@ MACRO(FEATURE_BOOST_CONFIGURE_COMMON)
   # circumvent the issue. Hence, we just check ourselves.
   ADD_FLAGS(CMAKE_REQUIRED_FLAGS "${DEAL_II_CXX_VERSION_FLAG}")
   IF(CMAKE_CXX_COMPILER_ID MATCHES "MSVC")
-    ADD_FLAGS(CMAKE_REQUIRED_FLAGS "/WX")
+    ADD_FLAGS(CMAKE_REQUIRED_FLAGS "/WX /EHsc")
   ELSE()
     ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-Werror")
   ENDIF()

From 632294e2abf0c86b550e8c5f8875edd1aa0c7407 Mon Sep 17 00:00:00 2001
From: Daniel Arndt 
Date: Wed, 13 Mar 2019 10:28:23 +0100
Subject: [PATCH 255/507] Replace '-Werror' by a _werror_flag variable

---
 cmake/checks/check_01_cxx_features.cmake      | 25 +++++++++++--------
 cmake/checks/check_02_compiler_features.cmake | 22 +++++++++-------
 2 files changed, 28 insertions(+), 19 deletions(-)

diff --git a/cmake/checks/check_01_cxx_features.cmake b/cmake/checks/check_01_cxx_features.cmake
index 2f5cf61e7efc..d1ec609daaf0 100644
--- a/cmake/checks/check_01_cxx_features.cmake
+++ b/cmake/checks/check_01_cxx_features.cmake
@@ -32,6 +32,17 @@
 #
 
 
+#
+# MSVC needs different compiler flags to turn warnings into errors
+# additionally a suitable exception handling model is required
+#
+IF(CMAKE_CXX_COMPILER_ID MATCHES "MSVC")
+  SET(_werror_flag "/WX /EHsc")
+ELSE()
+  SET(_werror_flag "-Werror")
+ENDIF()
+
+
 ########################################################################
 #                                                                      #
 #                         C++ Version Support:                         #
@@ -133,12 +144,7 @@ IF(NOT DEFINED DEAL_II_WITH_CXX17 OR DEAL_II_WITH_CXX17)
   IF(NOT "${DEAL_II_CXX_VERSION_FLAG}" STREQUAL "")
     # Set CMAKE_REQUIRED_FLAGS for the unit tests
     MESSAGE(STATUS "Using C++ version flag \"${DEAL_II_CXX_VERSION_FLAG}\"")
-    IF(CMAKE_CXX_COMPILER_ID MATCHES "MSVC")
-      ADD_FLAGS(CMAKE_REQUIRED_FLAGS "/WX /EHsc")
-    ELSE()
-      ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-Werror")
-    ENDIF()
-    ADD_FLAGS(CMAKE_REQUIRED_FLAGS "${DEAL_II_CXX_VERSION_FLAG}")
+    ADD_FLAGS(CMAKE_REQUIRED_FLAGS "${DEAL_II_CXX_VERSION_FLAG} ${_werror_flag}")
 
     UNSET_IF_CHANGED(CHECK_CXX_FEATURES_FLAGS_CXX17_SAVED
       "${CMAKE_REQUIRED_FLAGS}${DEAL_II_CXX_VERSION_FLAG}"
@@ -586,10 +592,9 @@ UNSET_IF_CHANGED(CHECK_CXX_FEATURES_FLAGS_SAVED
 # possibilities here.
 #
 ADD_FLAGS(CMAKE_REQUIRED_FLAGS "${DEAL_II_CXX_FLAGS}")
-IF(CMAKE_CXX_COMPILER_ID MATCHES "MSVC")
-  ADD_FLAGS(CMAKE_REQUIRED_FLAGS "/WX")
-ELSE()
-  ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-Werror -Wno-unused-command-line-argument")
+ADD_FLAGS(CMAKE_REQUIRED_FLAGS "${_werror_flag}")
+IF(NOT CMAKE_CXX_COMPILER_ID MATCHES "MSVC")
+  ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-Wno-unused-command-line-argument")
 ENDIF()
 #
 # first try the attribute [[fallthrough]]
diff --git a/cmake/checks/check_02_compiler_features.cmake b/cmake/checks/check_02_compiler_features.cmake
index e844e7d904dc..32019e2d331c 100644
--- a/cmake/checks/check_02_compiler_features.cmake
+++ b/cmake/checks/check_02_compiler_features.cmake
@@ -48,6 +48,15 @@ UNSET_IF_CHANGED(CHECK_CXX_FEATURES_FLAGS_SAVED
   DEAL_II_COMPILER_HAS_ATTRIBUTE_DEPRECATED
   )
 
+#
+# MSVC needs different compiler flags to turn warnings into errors
+# additionally a suitable exception handling model is required
+#
+IF(CMAKE_CXX_COMPILER_ID MATCHES "MSVC")
+  SET(_werror_flag "/WX /EHsc")
+ELSE()
+  SET(_werror_flag "-Werror")
+ENDIF()
 
 #
 # Check whether the compiler allows to use arithmetic operations
@@ -298,10 +307,9 @@ ENDIF()
 # "warning #1292: unknown attribute "deprecated"" (icc)
 # Hence, we treat warnings as errors:
 ADD_FLAGS(CMAKE_REQUIRED_FLAGS "${DEAL_II_CXX_FLAGS}")
-IF(CMAKE_CXX_COMPILER_ID MATCHES "MSVC")
-  ADD_FLAGS(CMAKE_REQUIRED_FLAGS "/WX")
-ELSE()
-  ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-Werror -Wno-unused-command-line-argument")
+ADD_FLAGS(CMAKE_REQUIRED_FLAGS "${_werror_flag}")
+IF(NOT CMAKE_CXX_COMPILER_ID MATCHES "MSVC")
+  ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-Wno-unused-command-line-argument")
 ENDIF()
 
 # first see if the compiler accepts the attribute
@@ -409,11 +417,7 @@ ENDIF()
 #
 # - Matthias Maier, 2015
 #
-IF(CMAKE_CXX_COMPILER_ID MATCHES "MSVC")
-  ADD_FLAGS(CMAKE_REQUIRED_FLAGS "/WX")
-ELSE()
-  ADD_FLAGS(CMAKE_REQUIRED_FLAGS "-Werror")
-ENDIF()
+ADD_FLAGS(CMAKE_REQUIRED_FLAGS "${_werror_flag}")
 CHECK_CXX_SOURCE_COMPILES(
   "
   _Pragma(\"GCC diagnostic push\")

From 6225139ff3ef6273575d57656bad05827d62df62 Mon Sep 17 00:00:00 2001
From: Martin Kronbichler 
Date: Wed, 13 Mar 2019 17:16:04 +0100
Subject: [PATCH 256/507] Fix MatrixFree::loop() for the case where VectorType
 is not a vector

---
 include/deal.II/matrix_free/matrix_free.h    | 23 ++++++++++++++++----
 source/matrix_free/task_info.cc              |  1 +
 tests/matrix_free/matrix_free_type_traits.cc | 11 ++++++++++
 3 files changed, 31 insertions(+), 4 deletions(-)

diff --git a/include/deal.II/matrix_free/matrix_free.h b/include/deal.II/matrix_free/matrix_free.h
index 4877be670b78..65a2f533f5f8 100644
--- a/include/deal.II/matrix_free/matrix_free.h
+++ b/include/deal.II/matrix_free/matrix_free.h
@@ -1436,7 +1436,6 @@ class MatrixFree : public Subscriptor
    * Queries whether or not the geometry-related information for the cells has
    * been set.
    */
-
   bool
   mapping_initialized() const;
 
@@ -3321,13 +3320,15 @@ namespace internal
 
 
     /**
-     * Zero out vector region for vector that do _not_ support
-     * exchange on a subset of DoFs <==> begin() + ind == local_element(ind)
+     * Zero out vector region for vector that do _not_ support exchange on a
+     * subset of DoFs <==> begin() + ind == local_element(ind) but are still a
+     * vector type
      */
     template <
       typename VectorType,
       typename std::enable_if::value,
-                              VectorType>::type * = nullptr>
+                              VectorType>::type * = nullptr,
+      typename VectorType::value_type *           = nullptr>
     void
     zero_vector_region(const unsigned int range_index, VectorType &vec) const
     {
@@ -3341,6 +3342,20 @@ namespace internal
 
 
 
+    /**
+     * Zero out vector region for non-vector types, i.e., classes that do not
+     * have VectorType::value_type
+     */
+    void
+    zero_vector_region(const unsigned int, ...) const
+    {
+      Assert(false,
+             ExcNotImplemented("Zeroing is only implemented for vector types "
+                               "which provide VectorType::value_type"));
+    }
+
+
+
     const dealii::MatrixFree &matrix_free;
     const typename dealii::MatrixFree::DataAccessOnFaces
          vector_face_access;
diff --git a/source/matrix_free/task_info.cc b/source/matrix_free/task_info.cc
index d60db786c86b..203fcad6ea72 100644
--- a/source/matrix_free/task_info.cc
+++ b/source/matrix_free/task_info.cc
@@ -631,6 +631,7 @@ namespace internal
       n_blocks             = 0;
       scheme               = none;
       partition_row_index.clear();
+      partition_row_index.resize(2);
       cell_partition_data.clear();
       face_partition_data.clear();
       boundary_partition_data.clear();
diff --git a/tests/matrix_free/matrix_free_type_traits.cc b/tests/matrix_free/matrix_free_type_traits.cc
index fb0f597c0c64..4ea0771d0bd2 100644
--- a/tests/matrix_free/matrix_free_type_traits.cc
+++ b/tests/matrix_free/matrix_free_type_traits.cc
@@ -90,5 +90,16 @@ main()
           << "unsigned int = "
           << internal::is_serial_or_dummy::value << std::endl;
 
+  // check that MatrixFree::cell_loop can run for non-vector types
+  MatrixFree<2> matrix_free;
+  int           dummy = 0;
+  matrix_free.cell_loop(
+    std::function &,
+                       int &,
+                       const int &,
+                       const std::pair &)>(),
+    dummy,
+    dummy);
+
   deallog << "OK" << std::endl;
 }

From 266a351d3a4ce16bfeb2b0ad9f7d302d2877dea9 Mon Sep 17 00:00:00 2001
From: Denis Davydov 
Date: Wed, 13 Mar 2019 15:39:56 +0100
Subject: [PATCH 257/507] remove unneeded assert in
 internal::update_ghost_values_finish()

---
 include/deal.II/matrix_free/matrix_free.h | 6 ------
 1 file changed, 6 deletions(-)

diff --git a/include/deal.II/matrix_free/matrix_free.h b/include/deal.II/matrix_free/matrix_free.h
index 4877be670b78..ed477fd6cfa7 100644
--- a/include/deal.II/matrix_free/matrix_free.h
+++ b/include/deal.II/matrix_free/matrix_free.h
@@ -2897,12 +2897,6 @@ namespace internal
                                const VectorType & vec)
     {
       (void)component_in_block_vector;
-      Assert(
-        (vector_face_access ==
-           dealii::MatrixFree::DataAccessOnFaces::unspecified ||
-         vec.size() == 0),
-        ExcNotImplemented());
-
       vec.update_ghost_values_finish();
     }
 

From 6bda43589a278cb5e2a20ce0698744341c9ab394 Mon Sep 17 00:00:00 2001
From: Wolfgang Bangerth 
Date: Wed, 13 Mar 2019 12:26:27 -0600
Subject: [PATCH 258/507] Improve the error text of an assertion.

---
 include/deal.II/numerics/vector_tools.templates.h | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/include/deal.II/numerics/vector_tools.templates.h b/include/deal.II/numerics/vector_tools.templates.h
index aebdafb33768..5e024874eb18 100644
--- a/include/deal.II/numerics/vector_tools.templates.h
+++ b/include/deal.II/numerics/vector_tools.templates.h
@@ -2947,7 +2947,12 @@ namespace VectorTools
                             ExcMessage(
                               "This function can only deal with requested boundary "
                               "values that correspond to primitive (scalar) base "
-                              "elements"));
+                              "elements. You may want to look up in the deal.II "
+                              "glossary what the term 'primitive' means."
+                              "\n\n"
+                              "There are alternative boundary value interpolation "
+                              "functions in namespace 'VectorTools' that you can "
+                              "use for non-primitive finite elements."));
                     }
 
                   const typename DoFHandlerType::face_iterator

From 1d929dd41a003e0131d24040d659e30315c5cf88 Mon Sep 17 00:00:00 2001
From: Daniel Arndt 
Date: Wed, 13 Mar 2019 17:25:57 +0100
Subject: [PATCH 259/507] Fix compiling bundled boost with MSVC and C++17

---
 .../include/boost/algorithm/cxx14/equal.hpp   |  3 +-
 .../algorithm/string/detail/case_conv.hpp     |  8 ++-
 .../boost/algorithm/string/detail/util.hpp    |  5 +-
 .../boost/config/stdlib/dinkumware.hpp        |  2 +-
 .../boost/function/function_template.hpp      | 11 ----
 .../boost-1.62.0/include/boost/functional.hpp | 58 ++++++++++++++-----
 .../boost/functional/hash/extensions.hpp      |  9 ++-
 .../include/boost/functional/hash/hash.hpp    | 12 ++--
 .../include/boost/graph/astar_search.hpp      |  5 +-
 .../include/boost/graph/detail/geodesic.hpp   | 12 ++--
 .../crauser_et_al_shortest_paths.hpp          | 10 +++-
 .../boost/graph/parallel/algorithm.hpp        | 15 ++++-
 .../boost/graph/transitive_closure.hpp        |  3 +-
 .../include/boost/iostreams/chain.hpp         |  5 +-
 .../numeric/conversion/detail/converter.hpp   | 15 +----
 .../boost/signals2/detail/signal_template.hpp |  1 -
 .../signals2/detail/signals_common_macros.hpp |  6 +-
 .../boost/signals2/detail/slot_template.hpp   |  2 +-
 .../signals2/detail/variadic_arg_type.hpp     | 19 +++---
 .../include/boost/smart_ptr/owner_less.hpp    | 49 +++++-----------
 .../include/boost/typeof/std/functional.hpp   |  2 +
 .../boost/utility/compare_pointees.hpp        | 13 ++++-
 22 files changed, 147 insertions(+), 118 deletions(-)

diff --git a/bundled/boost-1.62.0/include/boost/algorithm/cxx14/equal.hpp b/bundled/boost-1.62.0/include/boost/algorithm/cxx14/equal.hpp
index f1539f885cee..9f97be1d626d 100644
--- a/bundled/boost-1.62.0/include/boost/algorithm/cxx14/equal.hpp
+++ b/bundled/boost-1.62.0/include/boost/algorithm/cxx14/equal.hpp
@@ -13,7 +13,6 @@
 #define BOOST_ALGORITHM_EQUAL_HPP
 
 #include     // for std::equal
-#include    // for std::binary_function
 #include 
 
 namespace boost { namespace algorithm {
@@ -21,7 +20,7 @@ namespace boost { namespace algorithm {
 namespace detail {
 
     template 
-    struct eq : public std::binary_function {
+    struct eq {
         bool operator () ( const T1& v1, const T2& v2 ) const { return v1 == v2 ;}
         };
     
diff --git a/bundled/boost-1.62.0/include/boost/algorithm/string/detail/case_conv.hpp b/bundled/boost-1.62.0/include/boost/algorithm/string/detail/case_conv.hpp
index 42621c74f06e..233912ca0f20 100644
--- a/bundled/boost-1.62.0/include/boost/algorithm/string/detail/case_conv.hpp
+++ b/bundled/boost-1.62.0/include/boost/algorithm/string/detail/case_conv.hpp
@@ -30,8 +30,10 @@ namespace boost {
 
             // a tolower functor
             template
-            struct to_lowerF : public std::unary_function
+            struct to_lowerF
             {
+                typedef CharT argument_type;
+                typedef CharT result_type;
                 // Constructor
                 to_lowerF( const std::locale& Loc ) : m_Loc( &Loc ) {}
 
@@ -50,8 +52,10 @@ namespace boost {
 
             // a toupper functor
             template
-            struct to_upperF : public std::unary_function
+            struct to_upperF
             {
+                typedef CharT argument_type;
+                typedef CharT result_type;
                 // Constructor
                 to_upperF( const std::locale& Loc ) : m_Loc( &Loc ) {}
 
diff --git a/bundled/boost-1.62.0/include/boost/algorithm/string/detail/util.hpp b/bundled/boost-1.62.0/include/boost/algorithm/string/detail/util.hpp
index cf4a8b1c8cd4..7844b6723cc6 100644
--- a/bundled/boost-1.62.0/include/boost/algorithm/string/detail/util.hpp
+++ b/bundled/boost-1.62.0/include/boost/algorithm/string/detail/util.hpp
@@ -89,9 +89,10 @@ namespace boost {
             template< 
                 typename SeqT, 
                 typename IteratorT=BOOST_STRING_TYPENAME SeqT::const_iterator >
-            struct copy_iterator_rangeF : 
-                public std::unary_function< iterator_range, SeqT >
+            struct copy_iterator_rangeF
             {
+                typedef iterator_range argument_type;
+                typedef SeqT result_type;
                 SeqT operator()( const iterator_range& Range ) const
                 {
                     return copy_range(Range);
diff --git a/bundled/boost-1.62.0/include/boost/config/stdlib/dinkumware.hpp b/bundled/boost-1.62.0/include/boost/config/stdlib/dinkumware.hpp
index af8ddda528da..293a17675f5c 100644
--- a/bundled/boost-1.62.0/include/boost/config/stdlib/dinkumware.hpp
+++ b/bundled/boost-1.62.0/include/boost/config/stdlib/dinkumware.hpp
@@ -180,7 +180,7 @@
 // If _HAS_AUTO_PTR_ETC is defined to 0, std::auto_ptr is not available.
 // See https://www.visualstudio.com/en-us/news/vs2015-vs.aspx#C++
 // and http://blogs.msdn.com/b/vcblog/archive/2015/06/19/c-11-14-17-features-in-vs-2015-rtm.aspx
-#  if defined(_HAS_AUTO_PTR_ETC) && (_HAS_AUTO_PTR_ETC == 0)
+#  if defined(_HAS_AUTO_PTR_ETC) && (_HAS_AUTO_PTR_ETC == 0) && !defined BOOST_NO_AUTO_PTR
 #    define BOOST_NO_AUTO_PTR
 #  endif
 #endif
diff --git a/bundled/boost-1.62.0/include/boost/function/function_template.hpp b/bundled/boost-1.62.0/include/boost/function/function_template.hpp
index 82c81d769733..7984c8323fed 100644
--- a/bundled/boost-1.62.0/include/boost/function/function_template.hpp
+++ b/bundled/boost-1.62.0/include/boost/function/function_template.hpp
@@ -656,17 +656,6 @@ namespace boost {
     BOOST_FUNCTION_TEMPLATE_PARMS
   >
   class BOOST_FUNCTION_FUNCTION : public function_base
-
-#if BOOST_FUNCTION_NUM_ARGS == 1
-
-    , public std::unary_function
-
-#elif BOOST_FUNCTION_NUM_ARGS == 2
-
-    , public std::binary_function
-
-#endif
-
   {
   public:
 #ifndef BOOST_NO_VOID_RETURNS
diff --git a/bundled/boost-1.62.0/include/boost/functional.hpp b/bundled/boost-1.62.0/include/boost/functional.hpp
index b618485c102e..731e4e1f1c97 100644
--- a/bundled/boost-1.62.0/include/boost/functional.hpp
+++ b/bundled/boost-1.62.0/include/boost/functional.hpp
@@ -18,6 +18,36 @@
 
 namespace boost
 {
+  namespace functional
+    {
+        namespace detail {
+#if defined(_HAS_AUTO_PTR_ETC) && !_HAS_AUTO_PTR_ETC
+            // std::unary_function and std::binary_function were both removed
+            // in C++17.
+
+            template 
+            struct unary_function
+            {
+                typedef Arg1 argument_type;
+                typedef Result result_type;
+            };
+
+            template 
+            struct binary_function
+            {
+                typedef Arg1 first_argument_type;
+                typedef Arg2 second_argument_type;
+                typedef Result result_type;
+            };
+#else
+            // Use the standard objects when we have them.
+
+            using std::unary_function;
+            using std::binary_function;
+#endif
+        }
+    }
+
 #ifndef BOOST_NO_TEMPLATE_PARTIAL_SPECIALIZATION
     // --------------------------------------------------------------------------
     // The following traits classes allow us to avoid the need for ptr_fun
@@ -147,7 +177,7 @@ namespace boost
     // --------------------------------------------------------------------------
     template 
     class unary_negate
-        : public std::unary_function::argument_type,bool>
+        : public boost::functional::detail::unary_function::argument_type,bool>
     {
       public:
         explicit unary_negate(typename unary_traits::param_type x)
@@ -181,7 +211,7 @@ namespace boost
     // --------------------------------------------------------------------------
     template 
     class binary_negate
-        : public std::binary_function::first_argument_type,
+        : public boost::functional::detail::binary_function::first_argument_type,
                                       typename binary_traits::second_argument_type,
                                       bool>
     {
@@ -218,7 +248,7 @@ namespace boost
     // --------------------------------------------------------------------------
     template 
     class binder1st
-        : public std::unary_function::second_argument_type,
+        : public boost::functional::detail::unary_function::second_argument_type,
                                      typename binary_traits::result_type>
     {       
       public:
@@ -264,7 +294,7 @@ namespace boost
     // --------------------------------------------------------------------------
     template 
     class binder2nd
-        : public std::unary_function::first_argument_type,
+        : public boost::functional::detail::unary_function::first_argument_type,
                                      typename binary_traits::result_type>
     {
       public:
@@ -309,7 +339,7 @@ namespace boost
     // mem_fun, etc
     // --------------------------------------------------------------------------
     template 
-    class mem_fun_t : public std::unary_function
+    class mem_fun_t : public boost::functional::detail::unary_function
     {
       public:
         explicit mem_fun_t(S (T::*p)())
@@ -325,7 +355,7 @@ namespace boost
     };
 
     template 
-    class mem_fun1_t : public std::binary_function
+    class mem_fun1_t : public boost::functional::detail::binary_function
     {
       public:   
         explicit mem_fun1_t(S (T::*p)(A))
@@ -341,7 +371,7 @@ namespace boost
     };
 
     template 
-    class const_mem_fun_t : public std::unary_function
+    class const_mem_fun_t : public boost::functional::detail::unary_function
     {
       public:
         explicit const_mem_fun_t(S (T::*p)() const)
@@ -357,7 +387,7 @@ namespace boost
     };
 
     template 
-    class const_mem_fun1_t : public std::binary_function
+    class const_mem_fun1_t : public boost::functional::detail::binary_function
     {
       public:
         explicit const_mem_fun1_t(S (T::*p)(A) const)
@@ -402,7 +432,7 @@ namespace boost
     // mem_fun_ref, etc
     // --------------------------------------------------------------------------
     template 
-    class mem_fun_ref_t : public std::unary_function
+    class mem_fun_ref_t : public boost::functional::detail::unary_function
     {
       public:
         explicit mem_fun_ref_t(S (T::*p)())
@@ -418,7 +448,7 @@ namespace boost
     };
 
     template 
-    class mem_fun1_ref_t : public std::binary_function
+    class mem_fun1_ref_t : public boost::functional::detail::binary_function
     {
       public:
         explicit mem_fun1_ref_t(S (T::*p)(A))
@@ -434,7 +464,7 @@ namespace boost
     };
     
     template 
-    class const_mem_fun_ref_t : public std::unary_function
+    class const_mem_fun_ref_t : public boost::functional::detail::unary_function
     {
       public:
         explicit const_mem_fun_ref_t(S (T::*p)() const)
@@ -451,7 +481,7 @@ namespace boost
     };
 
     template 
-    class const_mem_fun1_ref_t : public std::binary_function
+    class const_mem_fun1_ref_t : public boost::functional::detail::binary_function
     {
       public:
         explicit const_mem_fun1_ref_t(S (T::*p)(A) const)
@@ -497,7 +527,7 @@ namespace boost
     // ptr_fun
     // --------------------------------------------------------------------------
     template 
-    class pointer_to_unary_function : public std::unary_function
+    class pointer_to_unary_function : public boost::functional::detail::unary_function
     {
       public:
         explicit pointer_to_unary_function(Result (*f)(Arg))
@@ -521,7 +551,7 @@ namespace boost
     }
 
     template 
-    class pointer_to_binary_function : public std::binary_function
+    class pointer_to_binary_function : public boost::functional::detail::binary_function
     {
       public:
         explicit pointer_to_binary_function(Result (*f)(Arg1, Arg2))
diff --git a/bundled/boost-1.62.0/include/boost/functional/hash/extensions.hpp b/bundled/boost-1.62.0/include/boost/functional/hash/extensions.hpp
index eafaefe85dce..9f8fe4d65da1 100644
--- a/bundled/boost-1.62.0/include/boost/functional/hash/extensions.hpp
+++ b/bundled/boost-1.62.0/include/boost/functional/hash/extensions.hpp
@@ -254,8 +254,9 @@ namespace boost
 #if !defined(BOOST_NO_TEMPLATE_PARTIAL_SPECIALIZATION)
 
     template  struct hash
-        : std::unary_function
     {
+        typedef T argument_type;
+        typedef std::size_t result_type;
 #if !defined(BOOST_NO_FUNCTION_TEMPLATE_ORDERING)
         std::size_t operator()(T const& val) const
         {
@@ -271,8 +272,9 @@ namespace boost
 
 #if BOOST_WORKAROUND(__DMC__, <= 0x848)
     template  struct hash
-        : std::unary_function
     {
+        typedef T[n] argument_type;
+        typedef std::size_t result_type;
         std::size_t operator()(const T* val) const
         {
             return boost::hash_range(val, val+n);
@@ -296,8 +298,9 @@ namespace boost
         {
             template 
             struct inner
-                : std::unary_function
             {
+                typedef T argument_type;
+                typedef std::size_t result_type;
 #if !defined(BOOST_NO_FUNCTION_TEMPLATE_ORDERING)
                 std::size_t operator()(T const& val) const
                 {
diff --git a/bundled/boost-1.62.0/include/boost/functional/hash/hash.hpp b/bundled/boost-1.62.0/include/boost/functional/hash/hash.hpp
index 0a8ceeb4742e..56941c964116 100644
--- a/bundled/boost-1.62.0/include/boost/functional/hash/hash.hpp
+++ b/bundled/boost-1.62.0/include/boost/functional/hash/hash.hpp
@@ -419,8 +419,9 @@ namespace boost
 
 #define BOOST_HASH_SPECIALIZE(type) \
     template <> struct hash \
-         : public std::unary_function \
     { \
+        typedef type argument_type; \
+        typedef std::size_t result_type; \
         std::size_t operator()(type v) const \
         { \
             return boost::hash_value(v); \
@@ -429,8 +430,9 @@ namespace boost
 
 #define BOOST_HASH_SPECIALIZE_REF(type) \
     template <> struct hash \
-         : public std::unary_function \
     { \
+        typedef type argument_type; \
+        typedef std::size_t result_type; \
         std::size_t operator()(type const& v) const \
         { \
             return boost::hash_value(v); \
@@ -483,8 +485,9 @@ namespace boost
 
     template 
     struct hash
-        : public std::unary_function
     {
+        typedef T* argument_type;
+        typedef std::size_t result_type;
         std::size_t operator()(T* v) const
         {
 #if !BOOST_WORKAROUND(__SUNPRO_CC, <= 0x590)
@@ -516,8 +519,9 @@ namespace boost
         {
             template 
             struct inner
-                : public std::unary_function
             {
+                typedef T argument_type;
+                typedef std::size_t result_type;
                 std::size_t operator()(T val) const
                 {
 #if !BOOST_WORKAROUND(__SUNPRO_CC, <= 590)
diff --git a/bundled/boost-1.62.0/include/boost/graph/astar_search.hpp b/bundled/boost-1.62.0/include/boost/graph/astar_search.hpp
index 435ccf03b53a..95795f27c2d3 100644
--- a/bundled/boost-1.62.0/include/boost/graph/astar_search.hpp
+++ b/bundled/boost-1.62.0/include/boost/graph/astar_search.hpp
@@ -46,11 +46,12 @@ namespace boost {
 
 
   template 
-  class astar_heuristic : public std::unary_function<
-    typename graph_traits::vertex_descriptor, CostType>
+  class astar_heuristic
   {
   public:
     typedef typename graph_traits::vertex_descriptor Vertex;
+    typedef Vertex argument_type;
+    typedef CostType result_type;
     astar_heuristic() {}
     CostType operator()(Vertex u) { return static_cast(0); }
   };
diff --git a/bundled/boost-1.62.0/include/boost/graph/detail/geodesic.hpp b/bundled/boost-1.62.0/include/boost/graph/detail/geodesic.hpp
index adcb17f0ae64..0f2f2024fa2a 100644
--- a/bundled/boost-1.62.0/include/boost/graph/detail/geodesic.hpp
+++ b/bundled/boost-1.62.0/include/boost/graph/detail/geodesic.hpp
@@ -82,8 +82,11 @@ namespace detail {
     // Similar to std::plus, but maximizes parameters
     // rather than adding them.
     template 
-    struct maximize : public std::binary_function
+    struct maximize
     {
+        typedef T result_type;
+        typedef T first_argument_type;
+        typedef T second_argument_type;
         T operator ()(T x, T y) const
         { BOOST_USING_STD_MAX(); return max BOOST_PREVENT_MACRO_SUBSTITUTION (x, y); }
     };
@@ -93,11 +96,10 @@ namespace detail {
     // types, but should be specialized for those types that have
     // discrete notions of reciprocals.
     template 
-    struct reciprocal : public std::unary_function
+    struct reciprocal
     {
-        typedef std::unary_function function_type;
-        typedef typename function_type::result_type result_type;
-        typedef typename function_type::argument_type argument_type;
+        typedef T result_type;
+        typedef T first_argument_type;
         T operator ()(T t)
         { return T(1) / t; }
     };
diff --git a/bundled/boost-1.62.0/include/boost/graph/distributed/crauser_et_al_shortest_paths.hpp b/bundled/boost-1.62.0/include/boost/graph/distributed/crauser_et_al_shortest_paths.hpp
index 060cbf9cabe9..70090ce4cfbe 100644
--- a/bundled/boost-1.62.0/include/boost/graph/distributed/crauser_et_al_shortest_paths.hpp
+++ b/bundled/boost-1.62.0/include/boost/graph/distributed/crauser_et_al_shortest_paths.hpp
@@ -95,8 +95,10 @@ namespace detail {
   template
   struct min_in_distance_compare
-    : std::binary_function
   {
+    typedef Vertex first_argument_type;
+    typedef Vertex second_argument_type;
+    typedef bool result_type;
     min_in_distance_compare(DistanceMap d, MinInWeightMap m,
                             Combine combine, Compare compare)
       : distance_map(d), min_in_weight(m), combine(combine),
@@ -119,9 +121,11 @@ namespace detail {
 
   template
-  struct min_out_distance_compare
-    : std::binary_function
+  struct min_out_distance_compares
   {
+    typedef Vertex first_argument_type;
+    typedef Vertex second_argument_type;
+    typedef bool result_type;
     min_out_distance_compare(DistanceMap d, MinOutWeightMap m,
                              Combine combine, Compare compare)
       : distance_map(d), min_out_weight(m), combine(combine),
diff --git a/bundled/boost-1.62.0/include/boost/graph/parallel/algorithm.hpp b/bundled/boost-1.62.0/include/boost/graph/parallel/algorithm.hpp
index eed9bf8769a0..21ad7cc29588 100644
--- a/bundled/boost-1.62.0/include/boost/graph/parallel/algorithm.hpp
+++ b/bundled/boost-1.62.0/include/boost/graph/parallel/algorithm.hpp
@@ -26,20 +26,29 @@ namespace boost { namespace parallel {
   };
 
   template
-  struct minimum : std::binary_function
+  struct minimum
   {
+    typedef T first_argument_type;
+    typedef T second_argument_type;
+    typedef T result_type;
     const T& operator()(const T& x, const T& y) const { return x < y? x : y; }
   };
 
   template
-  struct maximum : std::binary_function
+  struct maximum
   {
+    typedef T first_argument_type;
+    typedef T second_argument_type;
+    typedef T result_type;
     const T& operator()(const T& x, const T& y) const { return x < y? y : x; }
   };
 
   template
-  struct sum : std::binary_function
+  struct sum
   {
+    typedef T first_argument_type;
+    typedef T second_argument_type;
+    typedef T result_type;
     const T operator()(const T& x, const T& y) const { return x + y; }
   };
 
diff --git a/bundled/boost-1.62.0/include/boost/graph/transitive_closure.hpp b/bundled/boost-1.62.0/include/boost/graph/transitive_closure.hpp
index 4f81349bf2e1..c8c1629f455a 100644
--- a/bundled/boost-1.62.0/include/boost/graph/transitive_closure.hpp
+++ b/bundled/boost-1.62.0/include/boost/graph/transitive_closure.hpp
@@ -41,8 +41,9 @@ namespace boost
   {
     template < typename TheContainer, typename ST = std::size_t,
       typename VT = typename TheContainer::value_type >
-      struct subscript_t:public std::unary_function < ST, VT >
+    struct subscript_t
     {
+      typedef ST& argument_type;
       typedef VT& result_type;
 
       subscript_t(TheContainer & c):container(&c)
diff --git a/bundled/boost-1.62.0/include/boost/iostreams/chain.hpp b/bundled/boost-1.62.0/include/boost/iostreams/chain.hpp
index bc0fab58ea12..78434f393aed 100644
--- a/bundled/boost-1.62.0/include/boost/iostreams/chain.hpp
+++ b/bundled/boost-1.62.0/include/boost/iostreams/chain.hpp
@@ -14,7 +14,6 @@
 
 #include 
 #include 
-#include                            // unary_function.
 #include                              // advance.
 #include 
 #include                                // allocator, auto_ptr.
@@ -286,7 +285,9 @@ class chain_base {
     static void set_auto_close(streambuf_type* b, bool close)
     { b->set_auto_close(close); }
 
-    struct closer  : public std::unary_function  {
+    struct closer {
+        typedef streambuf_type* argument_type;
+        typedef void result_type;
         closer(BOOST_IOS::openmode m) : mode_(m) { }
         void operator() (streambuf_type* b)
         {
diff --git a/bundled/boost-1.62.0/include/boost/numeric/conversion/detail/converter.hpp b/bundled/boost-1.62.0/include/boost/numeric/conversion/detail/converter.hpp
index 10550f8daaed..2884e84e8d8a 100644
--- a/bundled/boost-1.62.0/include/boost/numeric/conversion/detail/converter.hpp
+++ b/bundled/boost-1.62.0/include/boost/numeric/conversion/detail/converter.hpp
@@ -450,10 +450,7 @@ namespace boost { namespace numeric { namespace convdetail
   // Trivial Converter : used when (cv-unqualified) T == (cv-unqualified)  S
   //
   template
-  struct trivial_converter_impl : public std::unary_function<  BOOST_DEDUCED_TYPENAME Traits::argument_type
-                                                              ,BOOST_DEDUCED_TYPENAME Traits::result_type
-                                                            >
-                                 ,public dummy_range_checker
+  struct trivial_converter_impl : public dummy_range_checker
   {
     typedef Traits traits ;
 
@@ -471,10 +468,7 @@ namespace boost { namespace numeric { namespace convdetail
   // Rounding Converter : used for float to integral conversions.
   //
   template
-  struct rounding_converter : public std::unary_function<  BOOST_DEDUCED_TYPENAME Traits::argument_type
-                                                          ,BOOST_DEDUCED_TYPENAME Traits::result_type
-                                                        >
-                             ,public RangeChecker
+  struct rounding_converter : public RangeChecker
                              ,public Float2IntRounder
                              ,public RawConverter
   {
@@ -501,10 +495,7 @@ namespace boost { namespace numeric { namespace convdetail
   // Non-Rounding Converter : used for all other conversions.
   //
   template
-  struct non_rounding_converter : public std::unary_function< BOOST_DEDUCED_TYPENAME Traits::argument_type
-                                                             ,BOOST_DEDUCED_TYPENAME Traits::result_type
-                                                           >
-                                 ,public RangeChecker
+  struct non_rounding_converter : public RangeChecker
                                  ,public RawConverter
   {
     typedef RangeChecker RangeCheckerBase ;
diff --git a/bundled/boost-1.62.0/include/boost/signals2/detail/signal_template.hpp b/bundled/boost-1.62.0/include/boost/signals2/detail/signal_template.hpp
index fb7591bbc14c..fa19499d871e 100644
--- a/bundled/boost-1.62.0/include/boost/signals2/detail/signal_template.hpp
+++ b/bundled/boost-1.62.0/include/boost/signals2/detail/signal_template.hpp
@@ -599,7 +599,6 @@ namespace boost
     class BOOST_SIGNALS2_SIGNAL_CLASS_NAME(BOOST_SIGNALS2_NUM_ARGS)
       BOOST_SIGNALS2_SIGNAL_TEMPLATE_SPECIALIZATION: public signal_base,
       public detail::BOOST_SIGNALS2_STD_FUNCTIONAL_BASE
-        (typename detail::result_type_wrapper::type)
     {
       typedef detail::BOOST_SIGNALS2_SIGNAL_IMPL_CLASS_NAME(BOOST_SIGNALS2_NUM_ARGS)
          impl_class;
diff --git a/bundled/boost-1.62.0/include/boost/signals2/detail/signals_common_macros.hpp b/bundled/boost-1.62.0/include/boost/signals2/detail/signals_common_macros.hpp
index 4ca440382750..acc09362814d 100644
--- a/bundled/boost-1.62.0/include/boost/signals2/detail/signals_common_macros.hpp
+++ b/bundled/boost-1.62.0/include/boost/signals2/detail/signals_common_macros.hpp
@@ -137,7 +137,7 @@
 #define BOOST_SIGNALS2_SIGNAL_TEMPLATE_SPECIALIZATION_DECL(arity) BOOST_SIGNALS2_SIGNAL_TEMPLATE_DECL(arity)
 #define BOOST_SIGNALS2_SIGNAL_TEMPLATE_SPECIALIZATION
 
-#define BOOST_SIGNALS2_STD_FUNCTIONAL_BASE(result_type) std_functional_base
+#define BOOST_SIGNALS2_STD_FUNCTIONAL_BASE std_functional_base
 
 #define BOOST_SIGNALS2_PP_COMMA_IF(arity) BOOST_PP_COMMA_IF(arity)
 
@@ -205,8 +205,8 @@
   ExtendedSlotFunction, \
   Mutex>
 
-#define BOOST_SIGNALS2_STD_FUNCTIONAL_BASE(result_type) \
-  std_functional_base
+#define BOOST_SIGNALS2_STD_FUNCTIONAL_BASE \
+  std_functional_base
 
 #define BOOST_SIGNALS2_PP_COMMA_IF(arity) ,
 
diff --git a/bundled/boost-1.62.0/include/boost/signals2/detail/slot_template.hpp b/bundled/boost-1.62.0/include/boost/signals2/detail/slot_template.hpp
index fc19f5139cc4..1c17c5b76aff 100644
--- a/bundled/boost-1.62.0/include/boost/signals2/detail/slot_template.hpp
+++ b/bundled/boost-1.62.0/include/boost/signals2/detail/slot_template.hpp
@@ -35,7 +35,7 @@ namespace boost
 
     template
       class BOOST_SIGNALS2_SLOT_CLASS_NAME(BOOST_SIGNALS2_NUM_ARGS) BOOST_SIGNALS2_SLOT_TEMPLATE_SPECIALIZATION
-      : public slot_base, public detail::BOOST_SIGNALS2_STD_FUNCTIONAL_BASE(R)
+      : public slot_base, public detail::BOOST_SIGNALS2_STD_FUNCTIONAL_BASE
 
     {
     public:
diff --git a/bundled/boost-1.62.0/include/boost/signals2/detail/variadic_arg_type.hpp b/bundled/boost-1.62.0/include/boost/signals2/detail/variadic_arg_type.hpp
index 14d54b2e3ed2..db9e81c2f3d6 100644
--- a/bundled/boost-1.62.0/include/boost/signals2/detail/variadic_arg_type.hpp
+++ b/bundled/boost-1.62.0/include/boost/signals2/detail/variadic_arg_type.hpp
@@ -32,15 +32,20 @@ namespace boost
         typedef typename variadic_arg_type::type type;
       };
 
-      template 
+      template 
         struct std_functional_base
       {};
-      template 
-        struct std_functional_base: public std::unary_function
-      {};
-      template 
-        struct std_functional_base: public std::binary_function
-      {};
+      template 
+	    struct std_functional_base
+      {
+        typedef T1 argument_type;
+      };
+      template 
+        struct std_functional_base
+      {
+        typedef T1 first_argument_type;
+        typedef T2 second_argument_type;
+      };
     } // namespace detail
   } // namespace signals2
 } // namespace boost
diff --git a/bundled/boost-1.62.0/include/boost/smart_ptr/owner_less.hpp b/bundled/boost-1.62.0/include/boost/smart_ptr/owner_less.hpp
index 6899325bd61e..88c3c226d0b9 100644
--- a/bundled/boost-1.62.0/include/boost/smart_ptr/owner_less.hpp
+++ b/bundled/boost-1.62.0/include/boost/smart_ptr/owner_less.hpp
@@ -5,53 +5,30 @@
 //  owner_less.hpp
 //
 //  Copyright (c) 2008 Frank Mori Hess
+//  Copyright (c) 2016 Peter Dimov
 //
 //  Distributed under the Boost Software License, Version 1.0. (See
 //  accompanying file LICENSE_1_0.txt or copy at
 //  http://www.boost.org/LICENSE_1_0.txt)
 //
-//  See http://www.boost.org/libs/smart_ptr/smart_ptr.htm for documentation.
+//  See http://www.boost.org/libs/smart_ptr/ for documentation.
 //
 
-#include 
-
 namespace boost
 {
-  template class shared_ptr;
-  template class weak_ptr;
-
-  namespace detail
-  {
-    template
-      struct generic_owner_less : public std::binary_function
-    {
-      bool operator()(const T &lhs, const T &rhs) const
-      {
-        return lhs.owner_before(rhs);
-      }
-      bool operator()(const T &lhs, const U &rhs) const
-      {
-        return lhs.owner_before(rhs);
-      }
-      bool operator()(const U &lhs, const T &rhs) const
-      {
-        return lhs.owner_before(rhs);
-      }
-    };
-  } // namespace detail
 
-  template struct owner_less;
-
-  template
-    struct owner_less >:
-    public detail::generic_owner_less, weak_ptr >
-  {};
+template struct owner_less
+{
+    typedef bool result_type;
+    typedef T first_argument_type;
+    typedef T second_argument_type;
 
-  template
-    struct owner_less >:
-    public detail::generic_owner_less, shared_ptr >
-  {};
+    template bool operator()( U const & u, V const & v ) const
+    {
+        return u.owner_before( v );
+    }
+};
 
 } // namespace boost
 
-#endif  // #ifndef BOOST_SMART_PTR_OWNER_LESS_HPP_INCLUDED
+#endif  // #ifndef BOOST_SMART_PTR_OWNER_LESS_HPP_INCLUDED
\ No newline at end of file
diff --git a/bundled/boost-1.62.0/include/boost/typeof/std/functional.hpp b/bundled/boost-1.62.0/include/boost/typeof/std/functional.hpp
index f1b157764e4e..043a2ba27a08 100644
--- a/bundled/boost-1.62.0/include/boost/typeof/std/functional.hpp
+++ b/bundled/boost-1.62.0/include/boost/typeof/std/functional.hpp
@@ -10,8 +10,10 @@
 
 #include BOOST_TYPEOF_INCREMENT_REGISTRATION_GROUP()
 
+#ifndef BOOST_NO_CXX98_FUNCTION_BASE
 BOOST_TYPEOF_REGISTER_TEMPLATE(std::unary_function, 2)
 BOOST_TYPEOF_REGISTER_TEMPLATE(std::binary_function, 3)
+#endif//BOOST_NO_CXX98_FUNCTION_BASE
 BOOST_TYPEOF_REGISTER_TEMPLATE(std::plus, 1)
 BOOST_TYPEOF_REGISTER_TEMPLATE(std::minus, 1)
 BOOST_TYPEOF_REGISTER_TEMPLATE(std::multiplies, 1)
diff --git a/bundled/boost-1.62.0/include/boost/utility/compare_pointees.hpp b/bundled/boost-1.62.0/include/boost/utility/compare_pointees.hpp
index 7e2515c6eea2..7914370f1fad 100644
--- a/bundled/boost-1.62.0/include/boost/utility/compare_pointees.hpp
+++ b/bundled/boost-1.62.0/include/boost/utility/compare_pointees.hpp
@@ -33,14 +33,17 @@ bool equal_pointees ( OptionalPointee const& x, OptionalPointee const& y )
 }
 
 template
-struct equal_pointees_t : std::binary_function
+struct equal_pointees_t
 {
+  typedef bool result_type;
+  typedef OptionalPointee first_argument_type;
+  typedef OptionalPointee second_argument_type;
+
   bool operator() ( OptionalPointee const& x, OptionalPointee const& y ) const
     { return equal_pointees(x,y) ; }
 } ;
 
 // template bool less_pointees(OP const& x, OP const& y);
-// template struct less_pointees_t;
 //
 // Being OP a model of OptionalPointee (either a pointer or an optional):
 //
@@ -56,8 +59,12 @@ bool less_pointees ( OptionalPointee const& x, OptionalPointee const& y )
 }
 
 template
-struct less_pointees_t : std::binary_function
+struct less_pointees_t
 {
+  typedef bool result_type;
+  typedef OptionalPointee first_argument_type;
+  typedef OptionalPointee second_argument_type;
+
   bool operator() ( OptionalPointee const& x, OptionalPointee const& y ) const
     { return less_pointees(x,y) ; }
 } ;

From 95f6e6068ff5675aba5f814942550fcaff23fdec Mon Sep 17 00:00:00 2001
From: Jean-Paul Pelteret 
Date: Thu, 14 Mar 2019 09:54:01 +0100
Subject: [PATCH 260/507] Add CMake module and configuration files for
 SymEngine

---
 cmake/configure/configure_symengine.cmake |  41 +++++++
 cmake/modules/FindSYMENGINE.cmake         | 129 ++++++++++++++++++++++
 2 files changed, 170 insertions(+)
 create mode 100644 cmake/configure/configure_symengine.cmake
 create mode 100644 cmake/modules/FindSYMENGINE.cmake

diff --git a/cmake/configure/configure_symengine.cmake b/cmake/configure/configure_symengine.cmake
new file mode 100644
index 000000000000..4867772178fe
--- /dev/null
+++ b/cmake/configure/configure_symengine.cmake
@@ -0,0 +1,41 @@
+## ---------------------------------------------------------------------
+##
+## Copyright (C) 2019 by the deal.II authors
+##
+## This file is part of the deal.II library.
+##
+## The deal.II library is free software; you can use it, redistribute
+## it, and/or modify it under the terms of the GNU Lesser General
+## Public License as published by the Free Software Foundation; either
+## version 2.1 of the License, or (at your option) any later version.
+## The full text of the license can be found in the file LICENSE at
+## the top level of the deal.II distribution.
+##
+## ---------------------------------------------------------------------
+
+#
+# Configuration for the SymEngine library:
+#
+
+#
+# We require at least version 0.3 of the symengine library:
+#
+SET(SYMENGINE_MINIMUM_REQUIRED_VERSION "0.3")
+
+
+MACRO(FEATURE_SYMENGINE_CONFIGURE_EXTERNAL)
+  SET(DEAL_II_SYMENGINE_WITH_LLVM ${SYMENGINE_WITH_LLVM})
+
+  IF(DEAL_II_SYMENGINE_WITH_LLVM)
+    MESSAGE(STATUS "Configured with SymEngine LLVM capabilities.")
+  ENDIF()
+
+  #
+  # Overwrite the compiler flags imported from SymEngine
+  #
+  SET(SYMENGINE_CXX_FLAGS_DEBUG)
+  SET(SYMENGINE_CXX_FLAGS_RELEASE)
+ENDMACRO()
+
+
+CONFIGURE_FEATURE(SYMENGINE)
diff --git a/cmake/modules/FindSYMENGINE.cmake b/cmake/modules/FindSYMENGINE.cmake
new file mode 100644
index 000000000000..4b7468f9eca8
--- /dev/null
+++ b/cmake/modules/FindSYMENGINE.cmake
@@ -0,0 +1,129 @@
+## ---------------------------------------------------------------------
+##
+## Copyright (C) 2019 by the deal.II authors
+##
+## This file is part of the deal.II library.
+##
+## The deal.II library is free software; you can use it, redistribute
+## it, and/or modify it under the terms of the GNU Lesser General
+## Public License as published by the Free Software Foundation; either
+## version 2.1 of the License, or (at your option) any later version.
+## The full text of the license can be found in the file LICENSE at
+## the top level of the deal.II distribution.
+##
+## ---------------------------------------------------------------------
+
+#
+# - Try to find SymEngine
+#
+# This module exports
+#
+#   SYMENGINE_INCLUDE_DIR
+#   SYMENGINE_LIBRARY
+#   SYMENGINE_WITH_LLVM
+#
+
+SET(SYMENGINE_DIR "" CACHE PATH "An optional hint to a SymEngine installation")
+SET_IF_EMPTY(SYMENGINE_DIR "$ENV{SYMENGINE_DIR}")
+
+#
+# SymEngine overwrites the CMake module path, so we save
+# and restore it after this library is found and configured.
+#
+SET (DEAL_II_CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH})
+
+#
+# Include the SymEngine:
+#
+FIND_PACKAGE(SymEngine ${SYMENGINE_MINIMUM_REQUIRED_VERSION}
+  CONFIG QUIET
+  HINTS ${SYMENGINE_DIR}
+  PATH_SUFFIXES lib/cmake/symengine
+  NO_SYSTEM_ENVIRONMENT_PATH
+  )
+
+#
+# Reset the CMake module path
+#
+SET (CMAKE_MODULE_PATH ${DEAL_II_CMAKE_MODULE_PATH})
+
+
+#
+# Look for symengine_config.h - we'll query it to determine supported features:
+#
+IF(SymEngine_FOUND)
+  DEAL_II_FIND_FILE(SYMENGINE_SETTINGS_H symengine_config.h
+    HINTS ${SYMENGINE_INCLUDE_DIRS}
+    PATH_SUFFIXES symengine
+    NO_DEFAULT_PATH
+    NO_CMAKE_ENVIRONMENT_PATH
+    NO_CMAKE_PATH
+    NO_SYSTEM_ENVIRONMENT_PATH
+    NO_CMAKE_SYSTEM_PATH
+    NO_CMAKE_FIND_ROOT_PATH
+    )
+ENDIF()
+
+#
+# Version check
+#
+IF(EXISTS ${SYMENGINE_SETTINGS_H})
+
+  FILE(STRINGS "${SYMENGINE_SETTINGS_H}" SYMENGINE_VERSION_MAJOR_STRING
+    REGEX "#define.*SYMENGINE_MAJOR_VERSION")
+  STRING(REGEX REPLACE "^.*SYMENGINE_MAJOR_VERSION.*([0-9]+).*" "\\1"
+    SYMENGINE_VERSION_MAJOR "${SYMENGINE_VERSION_MAJOR_STRING}"
+    )
+  FILE(STRINGS "${SYMENGINE_SETTINGS_H}" SYMENGINE_VERSION_MINOR_STRING
+    REGEX "#define.*SYMENGINE_MINOR_VERSION")
+  STRING(REGEX REPLACE "^.*SYMENGINE_MINOR_VERSION.*([0-9]+).*" "\\1"
+    SYMENGINE_VERSION_MINOR "${SYMENGINE_VERSION_MINOR_STRING}"
+    )
+  FILE(STRINGS "${SYMENGINE_SETTINGS_H}" SYMENGINE_VERSION_PATCH_STRING
+    REGEX "#define.*SYMENGINE_PATCH_VERSION")
+  STRING(REGEX REPLACE "^.*SYMENGINE_PATCH_VERSION.*([0-9]+).*" "\\1"
+    SYMENGINE_VERSION_PATCH "${SYMENGINE_VERSION_PATCH_STRING}"
+    )
+  SET(SYMENGINE_VERSION
+    "${SYMENGINE_VERSION_MAJOR}.${SYMENGINE_VERSION_MINOR}.${SYMENGINE_VERSION_PATCH}"
+    )
+ENDIF()
+
+#
+# Feature checks
+#
+
+MACRO(_symengine_feature_check _var _regex)
+  IF(EXISTS ${SYMENGINE_SETTINGS_H})
+    FILE(STRINGS "${SYMENGINE_SETTINGS_H}" SYMENGINE_${_var}_STRING
+      REGEX "${_regex}")
+    IF("${SYMENGINE_${_var}_STRING}" STREQUAL "")
+      SET(SYMENGINE_WITH_${_var} FALSE)
+    ELSE()
+      SET(SYMENGINE_WITH_${_var} TRUE)
+    ENDIF()
+  ENDIF()
+ENDMACRO()
+
+# Other possible features of interest: BOOST, GMP
+_symengine_feature_check(LLVM "#define.*HAVE_SYMENGINE_LLVM")
+
+#
+# Sanitize include dirs:
+#
+
+STRING(REGEX REPLACE
+  "(lib64|lib)\\/cmake\\/symengine\\/\\.\\.\\/\\.\\.\\/\\.\\.\\/" ""
+  _symengine_include_dirs "${SYMENGINE_INCLUDE_DIRS}"
+  )
+REMOVE_DUPLICATES(_symengine_include_dirs)
+
+SET(_symengine_libraries ${SYMENGINE_LIBRARIES})
+
+
+DEAL_II_PACKAGE_HANDLE(SYMENGINE
+  LIBRARIES REQUIRED _symengine_libraries
+  INCLUDE_DIRS REQUIRED _symengine_include_dirs
+  USER_INCLUDE_DIRS REQUIRED  _symengine_include_dirs
+  CLEAR SYMENGINE_SETTINGS_H SYMENGINE_SKIP_DEPENDENCIES SymEngine_DIR
+)

From e3a394d4e47307036dddd0cc3db5bedc8424019c Mon Sep 17 00:00:00 2001
From: Daniel Arndt 
Date: Thu, 14 Mar 2019 19:06:29 +0100
Subject: [PATCH 261/507] Fix 'test' target for MSVC

---
 tests/quick_tests/CMakeLists.txt | 6 +++---
 tests/quick_tests/run.cmake      | 1 +
 2 files changed, 4 insertions(+), 3 deletions(-)

diff --git a/tests/quick_tests/CMakeLists.txt b/tests/quick_tests/CMakeLists.txt
index f76cfc008b7a..8393f3ed1c38 100644
--- a/tests/quick_tests/CMakeLists.txt
+++ b/tests/quick_tests/CMakeLists.txt
@@ -44,9 +44,9 @@ MACRO(make_quicktest test_basename build_name mpi_run)
   DEAL_II_INSOURCE_SETUP_TARGET(${_target} ${build_name})
 
   IF("${mpi_run}" STREQUAL "")
-    SET(_command ./${_target})
+    SET(_command ${_target})
   ELSE()
-    SET(_command ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${mpi_run} ${MPIEXEC_PREFLAGS} ./${_target})
+    SET(_command ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${mpi_run} ${MPIEXEC_PREFLAGS} ${_target})
   ENDIF()
   ADD_CUSTOM_TARGET(${_target}.run
     DEPENDS ${_target}
@@ -195,7 +195,7 @@ ENDIF()
 
 # A custom test target:
 ADD_CUSTOM_TARGET(test
-  COMMAND ${CMAKE_COMMAND} -D ALL_TESTS="${ALL_TESTS}" -P ${CMAKE_CURRENT_SOURCE_DIR}/run.cmake
+  COMMAND ${CMAKE_COMMAND} -D ALL_TESTS="${ALL_TESTS}" -DCMAKE_BUILD_TYPE=${_mybuild} -P ${CMAKE_CURRENT_SOURCE_DIR}/run.cmake
   WORKING_DIRECTORY ${CMAKE_CURRENT_BINARY_DIR}
   COMMENT "Running quicktests..."
   )
diff --git a/tests/quick_tests/run.cmake b/tests/quick_tests/run.cmake
index 4e4c21299836..ab6e7fc80626 100644
--- a/tests/quick_tests/run.cmake
+++ b/tests/quick_tests/run.cmake
@@ -25,6 +25,7 @@ ENDIF()
 SEPARATE_ARGUMENTS(ALL_TESTS)
 
 EXECUTE_PROCESS(COMMAND ${CMAKE_CTEST_COMMAND} -j${_n_processors}
+  -C ${CMAKE_BUILD_TYPE}
   --force-new-ctest-process
   --output-on-failure
   -O quicktests.log

From 9f73b559112557765bb53f9b288158040cae697e Mon Sep 17 00:00:00 2001
From: Bruno Turcksin 
Date: Tue, 12 Mar 2019 09:32:28 -0400
Subject: [PATCH 262/507] Encapsulate the calls to tbb::parallel_for

---
 include/deal.II/base/parallel.h               | 75 +++++++++++++------
 include/deal.II/base/work_stream.h            |  9 +--
 .../deal.II/lac/vector_operations_internal.h  | 12 +--
 3 files changed, 61 insertions(+), 35 deletions(-)

diff --git a/include/deal.II/base/parallel.h b/include/deal.II/base/parallel.h
index 9f82c1175025..d9db08f5acd5 100644
--- a/include/deal.II/base/parallel.h
+++ b/include/deal.II/base/parallel.h
@@ -131,6 +131,7 @@ namespace parallel
     };
 
 
+
     /**
      * Take a function object and create a Body object from it. We do this in
      * this helper function since alternatively we would have to specify the
@@ -143,6 +144,41 @@ namespace parallel
     {
       return Body(f);
     }
+
+
+
+    /**
+     * Encapsulate tbb::parallel_for.
+     */
+    template 
+    void
+    parallel_for(Iterator           x_begin,
+                 Iterator           x_end,
+                 const Functor &    functor,
+                 const unsigned int grainsize)
+    {
+      tbb::parallel_for(tbb::blocked_range(x_begin, x_end, grainsize),
+                        functor,
+                        tbb::auto_partitioner());
+    }
+
+
+
+    /**
+     * Encapsulate tbb::parallel_for when an affinite_partitioner is provided.
+     */
+    template 
+    void
+    parallel_for(Iterator                                          x_begin,
+                 Iterator                                          x_end,
+                 const Functor &                                   functor,
+                 const unsigned int                                grainsize,
+                 const std::shared_ptr &partitioner)
+    {
+      tbb::parallel_for(tbb::blocked_range(x_begin, x_end, grainsize),
+                        functor,
+                        *partitioner);
+    }
   } // namespace internal
 
   /**
@@ -188,11 +224,10 @@ namespace parallel
     using SyncIterators = SynchronousIterators;
     Iterators x_begin(begin_in, out);
     Iterators x_end(end_in, OutputIterator());
-    tbb::parallel_for(tbb::blocked_range(x_begin,
-                                                        x_end,
-                                                        grainsize),
-                      internal::make_body(predicate),
-                      tbb::auto_partitioner());
+    internal::parallel_for(SyncIterators(x_begin),
+                           SyncIterators(x_end),
+                           internal::make_body(predicate),
+                           grainsize);
 #endif
   }
 
@@ -246,11 +281,10 @@ namespace parallel
     using SyncIterators = SynchronousIterators;
     Iterators x_begin(begin_in1, in2, out);
     Iterators x_end(end_in1, InputIterator2(), OutputIterator());
-    tbb::parallel_for(tbb::blocked_range(x_begin,
-                                                        x_end,
-                                                        grainsize),
-                      internal::make_body(predicate),
-                      tbb::auto_partitioner());
+    internal::parallel_for(SyncIterators(x_begin),
+                           SyncIterators(x_end),
+                           internal::make_body(predicate),
+                           grainsize);
 #endif
   }
 
@@ -309,11 +343,10 @@ namespace parallel
                     InputIterator2(),
                     InputIterator3(),
                     OutputIterator());
-    tbb::parallel_for(tbb::blocked_range(x_begin,
-                                                        x_end,
-                                                        grainsize),
-                      internal::make_body(predicate),
-                      tbb::auto_partitioner());
+    internal::parallel_for(SyncIterators(x_begin),
+                           SyncIterators(x_end),
+                           internal::make_body(predicate),
+                           grainsize);
 #endif
   }
 
@@ -428,12 +461,13 @@ namespace parallel
     ff(begin, end);
 #  endif
 #else
-    tbb::parallel_for(
-      tbb::blocked_range(begin, end, grainsize),
+    internal::parallel_for(
+      begin,
+      end,
       std::bind(&internal::apply_to_subranges,
                 std::placeholders::_1,
                 std::cref(f)),
-      tbb::auto_partitioner());
+      grainsize);
 #endif
   }
 
@@ -826,10 +860,7 @@ namespace parallel
     apply_to_subrange(begin, end);
 #else
     internal::ParallelForWrapper worker(*this);
-    tbb::parallel_for(
-      tbb::blocked_range(begin, end, minimum_parallel_grain_size),
-      worker,
-      tbb::auto_partitioner());
+    internal::parallel_for(begin, end, worker, minimum_parallel_grain_size);
 #endif
   }
 
diff --git a/include/deal.II/base/work_stream.h b/include/deal.II/base/work_stream.h
index b09c2d1fdfb4..555c35c98da7 100644
--- a/include/deal.II/base/work_stream.h
+++ b/include/deal.II/base/work_stream.h
@@ -1154,14 +1154,13 @@ namespace WorkStream
                                                 sample_scratch_data,
                                                 sample_copy_data);
 
-              tbb::parallel_for(
-                tbb::blocked_range(colored_iterators[color].begin(),
-                                              colored_iterators[color].end(),
-                                              /*grain_size=*/chunk_size),
+              parallel::internal::parallel_for(
+                colored_iterators[color].begin(),
+                colored_iterators[color].end(),
                 std::bind(&WorkerAndCopier::operator(),
                           std::ref(worker_and_copier),
                           std::placeholders::_1),
-                tbb::auto_partitioner());
+                chunk_size);
             }
       }
 #  endif
diff --git a/include/deal.II/lac/vector_operations_internal.h b/include/deal.II/lac/vector_operations_internal.h
index 5d98e3f23a6b..bd13406faac5 100644
--- a/include/deal.II/lac/vector_operations_internal.h
+++ b/include/deal.II/lac/vector_operations_internal.h
@@ -188,10 +188,8 @@ namespace internal
             partitioner->acquire_one_partitioner();
 
           TBBForFunctor generic_functor(functor, start, end);
-          tbb::parallel_for(
-            tbb::blocked_range(0, generic_functor.n_chunks, 1),
-            generic_functor,
-            *tbb_partitioner);
+          parallel::internal::parallel_for(
+            0U, generic_functor.n_chunks, generic_functor, 1, tbb_partitioner);
           partitioner->release_one_partitioner(tbb_partitioner);
         }
       else if (vec_size > 0)
@@ -1389,10 +1387,8 @@ namespace internal
           TBBReduceFunctor generic_functor(op,
                                                                   start,
                                                                   end);
-          tbb::parallel_for(
-            tbb::blocked_range(0, generic_functor.n_chunks, 1),
-            generic_functor,
-            *tbb_partitioner);
+          parallel::internal::parallel_for(
+            0U, generic_functor.n_chunks, generic_functor, 1, tbb_partitioner);
           partitioner->release_one_partitioner(tbb_partitioner);
           result = generic_functor.do_sum();
         }

From e74a4ba7c6051960e28c278a6cb8ce9d5a95c555 Mon Sep 17 00:00:00 2001
From: Bruno Turcksin 
Date: Thu, 14 Mar 2019 17:58:31 -0400
Subject: [PATCH 263/507] Make clear that the predicate must be const

---
 include/deal.II/base/parallel.h | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/include/deal.II/base/parallel.h b/include/deal.II/base/parallel.h
index d9db08f5acd5..8b9d5cc49159 100644
--- a/include/deal.II/base/parallel.h
+++ b/include/deal.II/base/parallel.h
@@ -209,7 +209,7 @@ namespace parallel
   transform(const InputIterator &begin_in,
             const InputIterator &end_in,
             OutputIterator       out,
-            Predicate &          predicate,
+            const Predicate &    predicate,
             const unsigned int   grainsize)
   {
 #ifndef DEAL_II_WITH_THREADS
@@ -265,7 +265,7 @@ namespace parallel
             const InputIterator1 &end_in1,
             InputIterator2        in2,
             OutputIterator        out,
-            Predicate &           predicate,
+            const Predicate &     predicate,
             const unsigned int    grainsize)
   {
 #ifndef DEAL_II_WITH_THREADS
@@ -324,7 +324,7 @@ namespace parallel
             InputIterator2        in2,
             InputIterator3        in3,
             OutputIterator        out,
-            Predicate &           predicate,
+            const Predicate &     predicate,
             const unsigned int    grainsize)
   {
 #ifndef DEAL_II_WITH_THREADS

From de5ff7d6fe6443960b41cf58a9019062ca2d4178 Mon Sep 17 00:00:00 2001
From: Bruno Turcksin 
Date: Thu, 14 Mar 2019 18:00:30 -0400
Subject: [PATCH 264/507] Use std::lambda instead of boost::lambda

---
 tests/base/parallel_transform_01.cc | 4 +---
 tests/base/parallel_transform_02.cc | 4 +---
 tests/base/parallel_transform_03.cc | 5 +----
 3 files changed, 3 insertions(+), 10 deletions(-)

diff --git a/tests/base/parallel_transform_01.cc b/tests/base/parallel_transform_01.cc
index 78939f85eff9..9bf1faf5a966 100644
--- a/tests/base/parallel_transform_01.cc
+++ b/tests/base/parallel_transform_01.cc
@@ -20,8 +20,6 @@
 
 #include 
 
-#include 
-
 #include "../tests.h"
 
 
@@ -39,7 +37,7 @@ main()
 
   // set y=2*x
   parallel::transform(
-    x.begin(), x.end(), y.begin(), (2 * boost::lambda::_1), 10);
+    x.begin(), x.end(), y.begin(), [](double i) { return 2. * i; }, 10);
 
   // compute y=0 from the previous result
   y -= x;
diff --git a/tests/base/parallel_transform_02.cc b/tests/base/parallel_transform_02.cc
index f3cfdd4eca9a..764746bab152 100644
--- a/tests/base/parallel_transform_02.cc
+++ b/tests/base/parallel_transform_02.cc
@@ -20,8 +20,6 @@
 
 #include 
 
-#include 
-
 #include "../tests.h"
 
 
@@ -45,7 +43,7 @@ main()
                       x.end(),
                       y.begin(),
                       z.begin(),
-                      (boost::lambda::_1 + 2 * boost::lambda::_2),
+                      [](double i, double j) { return i + 2 * j; },
                       10);
 
   Assert(z.l2_norm() == 0, ExcInternalError());
diff --git a/tests/base/parallel_transform_03.cc b/tests/base/parallel_transform_03.cc
index 741f3eac8124..2931c4dbe87d 100644
--- a/tests/base/parallel_transform_03.cc
+++ b/tests/base/parallel_transform_03.cc
@@ -20,8 +20,6 @@
 
 #include 
 
-#include 
-
 #include "../tests.h"
 
 
@@ -48,8 +46,7 @@ main()
                       y.begin(),
                       z.begin(),
                       a.begin(),
-                      (boost::lambda::_1 + boost::lambda::_2 -
-                       boost::lambda::_3),
+                      [](double i, double j, double k) { return i + j - k; },
                       10);
 
   AssertThrow(a.l2_norm() == 0, ExcInternalError());

From 91b02361986948ffd0bc82daebd17ef7fe8576d7 Mon Sep 17 00:00:00 2001
From: Jean-Paul Pelteret 
Date: Fri, 15 Mar 2019 09:40:03 +0100
Subject: [PATCH 265/507] Remove dummy vector when initializing AMG constant
 modes

---
 source/lac/trilinos_precondition_ml.cc        |  14 +-
 tests/trilinos/precondition_amg_dgp_03.cc     | 273 ++++++++++++++++++
 ...n_amg_dgp_03.with_64bit_indices=off.output |   5 +
 3 files changed, 280 insertions(+), 12 deletions(-)
 create mode 100644 tests/trilinos/precondition_amg_dgp_03.cc
 create mode 100644 tests/trilinos/precondition_amg_dgp_03.with_64bit_indices=off.output

diff --git a/source/lac/trilinos_precondition_ml.cc b/source/lac/trilinos_precondition_ml.cc
index 848315efaa74..1e65a430e9b4 100644
--- a/source/lac/trilinos_precondition_ml.cc
+++ b/source/lac/trilinos_precondition_ml.cc
@@ -178,18 +178,8 @@ namespace TrilinosWrappers
         parameter_list.set("null space: type", "pre-computed");
         parameter_list.set("null space: dimension",
                            distributed_constant_modes.NumVectors());
-        if (my_size > 0)
-          parameter_list.set("null space: vectors",
-                             distributed_constant_modes.Values());
-        else
-          {
-            // We need to set a valid pointer to data even if there is no data
-            // on the current processor. Therefore, pass a dummy in that case
-            static std::vector dummy;
-            if (dummy.size() != constant_modes_dimension)
-              dummy.resize(constant_modes_dimension);
-            parameter_list.set("null space: vectors", dummy.data());
-          }
+        parameter_list.set("null space: vectors",
+                           distributed_constant_modes.Values());
       }
   }
 
diff --git a/tests/trilinos/precondition_amg_dgp_03.cc b/tests/trilinos/precondition_amg_dgp_03.cc
new file mode 100644
index 000000000000..1fcf871403be
--- /dev/null
+++ b/tests/trilinos/precondition_amg_dgp_03.cc
@@ -0,0 +1,273 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2013 - 2019 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+
+
+// solves a 2D Poisson equation for linear FE_DGP elements (SIP
+// discretization) with AMG preconditioner.
+//
+// This variant of the test trilinos/precondition_amg_dgp_01 does not initialize
+// the constant modes vector passes to the AMG preconditioner.
+
+#include 
+
+#include 
+#include 
+
+#include 
+
+#include 
+#include 
+
+#include 
+
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+
+#include 
+#include 
+#include 
+#include 
+
+#include 
+
+#include "../tests.h"
+
+
+
+template 
+class MatrixIntegrator : public MeshWorker::LocalIntegrator
+{
+public:
+  void
+  cell(MeshWorker::DoFInfo &                 dinfo,
+       typename MeshWorker::IntegrationInfo &info) const;
+  void
+  boundary(MeshWorker::DoFInfo &                 dinfo,
+           typename MeshWorker::IntegrationInfo &info) const;
+  void
+  face(MeshWorker::DoFInfo &                 dinfo1,
+       MeshWorker::DoFInfo &                 dinfo2,
+       typename MeshWorker::IntegrationInfo &info1,
+       typename MeshWorker::IntegrationInfo &info2) const;
+};
+
+template 
+void
+MatrixIntegrator::cell(
+  MeshWorker::DoFInfo &                 dinfo,
+  typename MeshWorker::IntegrationInfo &info) const
+{
+  LocalIntegrators::Laplace::cell_matrix(dinfo.matrix(0, false).matrix,
+                                         info.fe_values());
+}
+
+template 
+void
+MatrixIntegrator::boundary(
+  MeshWorker::DoFInfo &                 dinfo,
+  typename MeshWorker::IntegrationInfo &info) const
+{
+  const unsigned int deg = info.fe_values(0).get_fe().degree;
+  LocalIntegrators::Laplace ::nitsche_matrix(
+    dinfo.matrix(0, false).matrix,
+    info.fe_values(0),
+    LocalIntegrators::Laplace::compute_penalty(dinfo, dinfo, deg, deg));
+}
+
+template 
+void
+MatrixIntegrator::face(
+  MeshWorker::DoFInfo &                 dinfo1,
+  MeshWorker::DoFInfo &                 dinfo2,
+  typename MeshWorker::IntegrationInfo &info1,
+  typename MeshWorker::IntegrationInfo &info2) const
+{
+  const unsigned int deg = info1.fe_values(0).get_fe().degree;
+  LocalIntegrators::Laplace ::ip_matrix(
+    dinfo1.matrix(0, false).matrix,
+    dinfo1.matrix(0, true).matrix,
+    dinfo2.matrix(0, true).matrix,
+    dinfo2.matrix(0, false).matrix,
+    info1.fe_values(0),
+    info2.fe_values(0),
+    LocalIntegrators::Laplace::compute_penalty(dinfo1, dinfo2, deg, deg));
+}
+
+
+template 
+class Step4
+{
+public:
+  Step4();
+  void
+  run();
+
+private:
+  void
+  make_grid();
+  void
+  setup_system();
+  void
+  solve();
+
+  Triangulation triangulation;
+  FE_DGP        fe;
+  DoFHandler    dof_handler;
+
+  TrilinosWrappers::SparseMatrix system_matrix;
+
+  Vector solution;
+  Vector system_rhs;
+};
+
+
+
+template 
+Step4::Step4()
+  : fe(1)
+  , dof_handler(triangulation)
+{}
+
+
+template 
+void
+Step4::make_grid()
+{
+  GridGenerator::hyper_cube(triangulation, -1, 1);
+  triangulation.refine_global(6);
+}
+
+
+
+template 
+void
+Step4::setup_system()
+{
+  dof_handler.distribute_dofs(fe);
+
+  DynamicSparsityPattern c_sparsity(dof_handler.n_dofs());
+  DoFTools::make_flux_sparsity_pattern(dof_handler, c_sparsity);
+  system_matrix.reinit(c_sparsity);
+
+  solution.reinit(dof_handler.n_dofs());
+  system_rhs.reinit(dof_handler.n_dofs());
+
+  MappingQGeneric                mapping(1);
+  MeshWorker::IntegrationInfoBox info_box;
+  UpdateFlags update_flags = update_values | update_gradients;
+  info_box.add_update_flags_all(update_flags);
+  info_box.initialize(fe, mapping);
+
+  MeshWorker::DoFInfo dof_info(dof_handler);
+  MeshWorker::Assembler::MatrixSimple assembler;
+  assembler.initialize(system_matrix);
+  MatrixIntegrator integrator;
+  MeshWorker::integration_loop(dof_handler.begin_active(),
+                                         dof_handler.end(),
+                                         dof_info,
+                                         info_box,
+                                         integrator,
+                                         assembler);
+
+  system_matrix.compress(VectorOperation::add);
+
+  for (unsigned int i = 0; i < system_rhs.size(); ++i)
+    system_rhs(i) = 0.01 * i - 0.000001 * i * i;
+}
+
+
+
+template 
+void
+Step4::solve()
+{
+  deallog.push(Utilities::int_to_string(dof_handler.n_dofs(), 5));
+  TrilinosWrappers::PreconditionAMG                 preconditioner;
+  TrilinosWrappers::PreconditionAMG::AdditionalData data;
+  data.smoother_sweeps = 2;
+  {
+    solution = 0;
+    SolverControl solver_control(1000, 1e-10);
+    SolverCG<>    solver(solver_control);
+    preconditioner.initialize(system_matrix, data);
+    solver.solve(system_matrix, solution, system_rhs, preconditioner);
+  }
+  deallog.pop();
+}
+
+
+
+template 
+void
+Step4::run()
+{
+  for (unsigned int cycle = 0; cycle < 2; ++cycle)
+    {
+      if (cycle == 0)
+        make_grid();
+      else
+        triangulation.refine_global(1);
+
+      setup_system();
+      solve();
+    }
+}
+
+
+int
+main(int argc, char **argv)
+{
+  initlog();
+
+  Utilities::MPI::MPI_InitFinalize mpi_initialization(
+    argc, argv, testing_max_num_threads());
+
+  try
+    {
+      Step4<2> test;
+      test.run();
+    }
+  catch (std::exception &exc)
+    {
+      deallog << std::endl
+              << std::endl
+              << "----------------------------------------------------"
+              << std::endl;
+      deallog << "Exception on processing: " << std::endl
+              << exc.what() << std::endl
+              << "Aborting!" << std::endl
+              << "----------------------------------------------------"
+              << std::endl;
+
+      return 1;
+    }
+  catch (...)
+    {
+      deallog << std::endl
+              << std::endl
+              << "----------------------------------------------------"
+              << std::endl;
+      deallog << "Unknown exception!" << std::endl
+              << "Aborting!" << std::endl
+              << "----------------------------------------------------"
+              << std::endl;
+      return 1;
+    };
+}
diff --git a/tests/trilinos/precondition_amg_dgp_03.with_64bit_indices=off.output b/tests/trilinos/precondition_amg_dgp_03.with_64bit_indices=off.output
new file mode 100644
index 000000000000..5399b9277c21
--- /dev/null
+++ b/tests/trilinos/precondition_amg_dgp_03.with_64bit_indices=off.output
@@ -0,0 +1,5 @@
+
+DEAL:12288:cg::Starting value 1970.22
+DEAL:12288:cg::Convergence step 121 value 0
+DEAL:49152:cg::Starting value 179304.
+DEAL:49152:cg::Convergence step 271 value 0

From 7ca10c52d89ec0e201320acaa9b34822d47779df Mon Sep 17 00:00:00 2001
From: Jean-Paul Pelteret 
Date: Fri, 15 Mar 2019 10:05:20 +0100
Subject: [PATCH 266/507] Only permit use of ld.lld linker when the Clang
 compiler is used.

Fixes #7811
---
 cmake/checks/check_02_compiler_features.cmake | 6 +++++-
 1 file changed, 5 insertions(+), 1 deletion(-)

diff --git a/cmake/checks/check_02_compiler_features.cmake b/cmake/checks/check_02_compiler_features.cmake
index d108cc47672f..fae50833f9e4 100644
--- a/cmake/checks/check_02_compiler_features.cmake
+++ b/cmake/checks/check_02_compiler_features.cmake
@@ -460,7 +460,11 @@ CHECK_CXX_SOURCE_COMPILES(
   DEAL_II_COMPILER_HAS_FUSE_LD_GOLD)
 RESET_CMAKE_REQUIRED()
 
-IF(DEAL_II_COMPILER_HAS_FUSE_LD_LLD)
+#
+# The ld.lld linker is not compatible with GCC. So we only enable it when
+# the Clang compiler is used. See https://github.com/dealii/dealii/issues/7811
+#
+IF(DEAL_II_COMPILER_HAS_FUSE_LD_LLD AND CMAKE_CXX_COMPILER_ID MATCHES "Clang")
   ADD_FLAGS(DEAL_II_LINKER_FLAGS "-fuse-ld=lld")
 ELSEIF(DEAL_II_COMPILER_HAS_FUSE_LD_GOLD)
   ADD_FLAGS(DEAL_II_LINKER_FLAGS "-fuse-ld=gold")

From 234b815f4df093d4210a8b2efef6732493b7aa0e Mon Sep 17 00:00:00 2001
From: Jean-Paul Pelteret 
Date: Fri, 15 Mar 2019 11:03:46 +0100
Subject: [PATCH 267/507] Fix SymEngine CMake module.

---
 cmake/modules/FindSYMENGINE.cmake | 14 +++++++++++++-
 1 file changed, 13 insertions(+), 1 deletion(-)

diff --git a/cmake/modules/FindSYMENGINE.cmake b/cmake/modules/FindSYMENGINE.cmake
index 4b7468f9eca8..b318dd5992fd 100644
--- a/cmake/modules/FindSYMENGINE.cmake
+++ b/cmake/modules/FindSYMENGINE.cmake
@@ -118,7 +118,19 @@ STRING(REGEX REPLACE
   )
 REMOVE_DUPLICATES(_symengine_include_dirs)
 
-SET(_symengine_libraries ${SYMENGINE_LIBRARIES})
+#
+# The SYMENGINE_LIBRARIES variable configured by SymEngine only lists the
+# libraries, but does not set their paths. So we configure this outselves.
+# 
+FOREACH(SYMENGINE_LIBRARY_NAME ${SYMENGINE_LIBRARIES})
+  DEAL_II_FIND_LIBRARY(SYMENGINE_LIBRARY
+    NAMES ${SYMENGINE_LIBRARY_NAME}
+    HINTS ${SYMENGINE_DIR}
+    PATH_SUFFIXES lib${LIB_SUFFIX} lib64 lib
+  )
+
+  SET(_symengine_libraries ${_symengine_libraries} ${SYMENGINE_LIBRARY})
+ENDFOREACH()
 
 
 DEAL_II_PACKAGE_HANDLE(SYMENGINE

From 8f713e8f0f889cea3269404fb65742ddefd17d3a Mon Sep 17 00:00:00 2001
From: Jean-Paul Pelteret 
Date: Thu, 14 Mar 2019 18:27:51 +0100
Subject: [PATCH 268/507] Add some initial tests for SymEngine

---
 tests/symengine/CMakeLists.txt                |   6 +
 tests/symengine/basic_01.cc                   | 134 +++++++++++
 tests/symengine/basic_01.output               |  35 +++
 tests/symengine/basic_02.cc                   | 152 +++++++++++++
 tests/symengine/basic_02.output               |  35 +++
 tests/symengine/basic_03.cc                   | 211 ++++++++++++++++++
 tests/symengine/basic_03.output               |  62 +++++
 tests/symengine/basic_04.cc                   | 170 ++++++++++++++
 ...c_04.with_symengine_with_llvm=false.output |   4 +
 ...ic_04.with_symengine_with_llvm=true.output |   5 +
 tests/symengine/basic_05.cc                   | 190 ++++++++++++++++
 ...c_05.with_symengine_with_llvm=false.output |   4 +
 ...ic_05.with_symengine_with_llvm=true.output |   5 +
 tests/symengine/basic_06.cc                   | 115 ++++++++++
 tests/symengine/basic_06.output               |  12 +
 tests/symengine/basic_07.cc                   | 123 ++++++++++
 tests/symengine/basic_07.output               |  12 +
 17 files changed, 1275 insertions(+)
 create mode 100644 tests/symengine/CMakeLists.txt
 create mode 100644 tests/symengine/basic_01.cc
 create mode 100644 tests/symengine/basic_01.output
 create mode 100644 tests/symengine/basic_02.cc
 create mode 100644 tests/symengine/basic_02.output
 create mode 100644 tests/symengine/basic_03.cc
 create mode 100644 tests/symengine/basic_03.output
 create mode 100644 tests/symengine/basic_04.cc
 create mode 100644 tests/symengine/basic_04.with_symengine_with_llvm=false.output
 create mode 100644 tests/symengine/basic_04.with_symengine_with_llvm=true.output
 create mode 100644 tests/symengine/basic_05.cc
 create mode 100644 tests/symengine/basic_05.with_symengine_with_llvm=false.output
 create mode 100644 tests/symengine/basic_05.with_symengine_with_llvm=true.output
 create mode 100644 tests/symengine/basic_06.cc
 create mode 100644 tests/symengine/basic_06.output
 create mode 100644 tests/symengine/basic_07.cc
 create mode 100644 tests/symengine/basic_07.output

diff --git a/tests/symengine/CMakeLists.txt b/tests/symengine/CMakeLists.txt
new file mode 100644
index 000000000000..46145a04668f
--- /dev/null
+++ b/tests/symengine/CMakeLists.txt
@@ -0,0 +1,6 @@
+CMAKE_MINIMUM_REQUIRED(VERSION 2.8.9)
+INCLUDE(../setup_testsubproject.cmake)
+PROJECT(testsuite CXX)
+IF(DEAL_II_WITH_SYMENGINE AND DEAL_II_WITH_CXX11)
+  DEAL_II_PICKUP_TESTS()
+ENDIF()
diff --git a/tests/symengine/basic_01.cc b/tests/symengine/basic_01.cc
new file mode 100644
index 000000000000..1022f6aa9eb5
--- /dev/null
+++ b/tests/symengine/basic_01.cc
@@ -0,0 +1,134 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2016 - 2018 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE at
+// the top level of the deal.II distribution.
+//
+// ---------------------------------------------------------------------
+
+
+// Check that all fundamental operations with primitive SymEngine number
+// types work as expected
+
+// References:
+// https://github.com/symengine/symengine/blob/master/symengine/tests/basic/test_basic.cpp
+// https://github.com/symengine/symengine/blob/master/symengine/tests/basic/test_number.cpp
+
+#include "../tests.h"
+
+#pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wextra-semi"
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#pragma clang diagnostic pop
+
+#include 
+#include 
+
+using namespace dealii;
+namespace SE = SymEngine;
+
+SE::RCP
+make_symengine_rcp(const int &val)
+{
+  return SE::integer(val);
+}
+
+SE::RCP
+make_symengine_rcp(const float &val)
+{
+  return SE::real_double(val);
+}
+
+SE::RCP
+make_symengine_rcp(const double &val)
+{
+  return SE::real_double(val);
+}
+
+template 
+SE::RCP
+make_symengine_rcp(const std::complex &val)
+{
+  // Build complex from two SymEngine numbers
+  return SE::Complex::from_two_nums(*make_symengine_rcp(val.real()),
+                                    *make_symengine_rcp(val.imag()));
+}
+
+template 
+void
+test_number()
+{
+  SE::RCP a = make_symengine_rcp(NumberType(4.2));
+  deallog << "a: " << *a << std::endl;
+
+  SE::RCP b(make_symengine_rcp(NumberType(2.1)));
+  deallog << "b: " << *b << std::endl;
+
+  SE::RCP c;
+  // deallog << "c (no constructor): " << *c << std::endl; // Fails
+
+  c = SE::add(a, b);
+  deallog << "c = a+b: " << *c << std::endl;
+
+  c = SE::sub(a, b);
+  deallog << "c = a-b: " << *c << std::endl;
+
+  c = SE::mul(a, b);
+  deallog << "c = a*b: " << *c << std::endl;
+
+  c = SE::div(a, b);
+  deallog << "c = a/b: " << *c << std::endl;
+
+  c = a;
+  deallog << "c = a: " << *c << std::endl;
+
+  c = SE::add(c, a);
+  deallog << "c += a: " << *c << std::endl;
+
+  c = SE::sub(c, a);
+  deallog << "c -= a: " << *c << std::endl;
+
+  c = SE::mul(c, a);
+  deallog << "c *= a: " << *c << std::endl;
+
+  c = SE::div(c, a);
+  deallog << "c /= a: " << *c << std::endl;
+}
+
+int
+main()
+{
+  initlog();
+
+  deallog.push("Integer");
+  test_number();
+  deallog.pop();
+
+  deallog.push("Float");
+  test_number();
+  deallog.pop();
+
+  deallog.push("Double");
+  test_number();
+  deallog.pop();
+
+  // Not available yet
+  // SymEngine::SymEngineException: Invalid Format: Expected Integer or Rational
+  // deallog << "Complex double" << std::endl;
+  // test_number>();
+  // deallog.pop();
+
+  deallog << "OK" << std::endl;
+}
diff --git a/tests/symengine/basic_01.output b/tests/symengine/basic_01.output
new file mode 100644
index 000000000000..f6307bc99a8c
--- /dev/null
+++ b/tests/symengine/basic_01.output
@@ -0,0 +1,35 @@
+
+DEAL:Integer::a: 4
+DEAL:Integer::b: 2
+DEAL:Integer::c = a+b: 6
+DEAL:Integer::c = a-b: 2
+DEAL:Integer::c = a*b: 8
+DEAL:Integer::c = a/b: 2
+DEAL:Integer::c = a: 4
+DEAL:Integer::c += a: 8
+DEAL:Integer::c -= a: 4
+DEAL:Integer::c *= a: 16
+DEAL:Integer::c /= a: 4
+DEAL:Float::a: 4.19999980926514
+DEAL:Float::b: 2.09999990463257
+DEAL:Float::c = a+b: 6.29999971389771
+DEAL:Float::c = a-b: 2.09999990463257
+DEAL:Float::c = a*b: 8.81999919891359
+DEAL:Float::c = a/b: 2.
+DEAL:Float::c = a: 4.19999980926514
+DEAL:Float::c += a: 8.39999961853027
+DEAL:Float::c -= a: 4.19999980926514
+DEAL:Float::c *= a: 17.6399983978272
+DEAL:Float::c /= a: 4.19999980926514
+DEAL:Double::a: 4.2
+DEAL:Double::b: 2.1
+DEAL:Double::c = a+b: 6.3
+DEAL:Double::c = a-b: 2.1
+DEAL:Double::c = a*b: 8.82
+DEAL:Double::c = a/b: 2.
+DEAL:Double::c = a: 4.2
+DEAL:Double::c += a: 8.4
+DEAL:Double::c -= a: 4.2
+DEAL:Double::c *= a: 17.64
+DEAL:Double::c /= a: 4.2
+DEAL::OK
diff --git a/tests/symengine/basic_02.cc b/tests/symengine/basic_02.cc
new file mode 100644
index 000000000000..7284e26f9c67
--- /dev/null
+++ b/tests/symengine/basic_02.cc
@@ -0,0 +1,152 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2016 - 2018 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE at
+// the top level of the deal.II distribution.
+//
+// ---------------------------------------------------------------------
+
+
+// Check that SymEngine can perform symbolic differentiation correctly
+
+// References:
+// https://github.com/symengine/symengine/blob/master/symengine/tests/basic/test_basic.cpp
+// https://github.com/symengine/symengine/blob/master/symengine/tests/basic/test_number.cpp
+// https://github.com/symengine/symengine/blob/master/symengine/tests/basic/test_subs.cpp
+// https://github.com/symengine/symengine/blob/master/symengine/symengine_casts.h
+// https://github.com/symengine/symengine/blob/master/symengine/symengine_rcp.h
+// https://github.com/symengine/symengine/blob/master/symengine/derivative.h
+// https://github.com/symengine/symengine/blob/master/symengine/subs.h
+
+#include "../tests.h"
+
+#pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wextra-semi"
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#pragma clang diagnostic pop
+
+#include 
+#include 
+
+using namespace dealii;
+namespace SE = SymEngine;
+
+SE::RCP
+make_symengine_rcp(const int &val)
+{
+  return SE::integer(val);
+}
+
+SE::RCP
+make_symengine_rcp(const float &val)
+{
+  return SE::real_double(val);
+}
+
+SE::RCP
+make_symengine_rcp(const double &val)
+{
+  return SE::real_double(val);
+}
+
+template 
+SE::RCP
+make_symengine_rcp(const std::complex &val)
+{
+  // Build complex from two SymEngine numbers
+  return SE::Complex::from_two_nums(*make_symengine_rcp(val.real()),
+                                    *make_symengine_rcp(val.imag()));
+}
+
+SE::RCP
+make_symengine_rcp(const std::string &name)
+{
+  return SE::symbol(name);
+}
+
+template 
+void
+test_number()
+{
+  SE::RCP a = make_symengine_rcp(NumberType(3.1));
+  SE::RCP  b = make_symengine_rcp(NumberType(7.5));
+  deallog << "a: " << *a << std::endl;
+  deallog << "b: " << *b << std::endl;
+
+  SE::RCP x(make_symengine_rcp("x"));
+  SE::RCP  y(make_symengine_rcp("y"));
+  deallog << "x: " << *x << std::endl;
+  deallog << "y: " << *y << std::endl;
+
+  SE::RCP c;
+  // deallog << "c (no constructor): " << *c << std::endl; // Fails
+
+  // Construction of symbolic function
+  c = SE::mul(y, SE::mul(SE::sub(y, b), SE::add(a, x)));
+  deallog << "c = y*(y-b)*(a+x): " << *c << std::endl;
+
+  // Perform symbolic differentiation
+  SE::RCP dc_dx = c->diff(x);
+  // SE::RCP dc_dy = diff(c,SE::implicit_cast &>(y));
+  SE::RCP dc_dy =
+    diff(c, SE::rcp_static_cast(y));
+  SE::RCP dc_dy_2 = sdiff(c, y);
+
+  deallog << "dc_dx = a*y*(y-b): " << *dc_dx << std::endl;
+  deallog << "dc_dy = 2*y*(a+x): " << *dc_dy << std::endl;
+  deallog << "dc_dy = 2*y*(a+x): " << *dc_dy_2 << std::endl;
+
+  // Substitute values
+  SE::map_basic_basic sub_vals;
+  sub_vals[x] = make_symengine_rcp(NumberType(1));
+  sub_vals[y] = make_symengine_rcp(NumberType(2.2));
+  deallog << "dc_dx(x=1,y=2.2): " << *(dc_dx->subs(sub_vals)) << std::endl;
+
+  sub_vals[x] = make_symengine_rcp(NumberType(0.75));
+  sub_vals[y] = make_symengine_rcp(NumberType(-2.08));
+  deallog << "dc_dy(x=0.75,y=-1.08): " << *(dc_dy->subs(sub_vals)) << std::endl;
+
+  deallog << std::endl;
+}
+
+int
+main()
+{
+  initlog();
+
+  deallog.push("Integer");
+  test_number();
+  deallog.pop();
+
+  deallog.push("Float");
+  test_number();
+  deallog.pop();
+
+  deallog.push("Double");
+  test_number();
+  deallog.pop();
+
+  // Not available yet
+  // SymEngine::SymEngineException: Invalid Format: Expected Integer or Rational
+  // deallog << "Complex double" << std::endl;
+  // test_number>();
+  // deallog.pop();
+
+  deallog << "OK" << std::endl;
+}
diff --git a/tests/symengine/basic_02.output b/tests/symengine/basic_02.output
new file mode 100644
index 000000000000..a023eec9d8d3
--- /dev/null
+++ b/tests/symengine/basic_02.output
@@ -0,0 +1,35 @@
+
+DEAL:Integer::a: 3
+DEAL:Integer::b: 7
+DEAL:Integer::x: x
+DEAL:Integer::y: y
+DEAL:Integer::c = y*(y-b)*(a+x): y*(-7 + y)*(3 + x)
+DEAL:Integer::dc_dx = a*y*(y-b): y*(-7 + y)
+DEAL:Integer::dc_dy = 2*y*(a+x): y*(3 + x) + (-7 + y)*(3 + x)
+DEAL:Integer::dc_dy = 2*y*(a+x): y*(3 + x) + (-7 + y)*(3 + x)
+DEAL:Integer::dc_dx(x=1,y=2.2): -10
+DEAL:Integer::dc_dy(x=0.75,y=-1.08): -33
+DEAL:Integer::
+DEAL:Float::a: 3.09999990463257
+DEAL:Float::b: 7.5
+DEAL:Float::x: x
+DEAL:Float::y: y
+DEAL:Float::c = y*(y-b)*(a+x): y*(3.09999990463257 + x)*(-7.5 + y)
+DEAL:Float::dc_dx = a*y*(y-b): y*(-7.5 + y)
+DEAL:Float::dc_dy = 2*y*(a+x): y*(3.09999990463257 + x) + (3.09999990463257 + x)*(-7.5 + y)
+DEAL:Float::dc_dy = 2*y*(a+x): y*(3.09999990463257 + x) + (3.09999990463257 + x)*(-7.5 + y)
+DEAL:Float::dc_dx(x=1,y=2.2): -11.6600001478195
+DEAL:Float::dc_dy(x=0.75,y=-1.08): -44.8909983005524
+DEAL:Float::
+DEAL:Double::a: 3.1
+DEAL:Double::b: 7.5
+DEAL:Double::x: x
+DEAL:Double::y: y
+DEAL:Double::c = y*(y-b)*(a+x): y*(3.1 + x)*(-7.5 + y)
+DEAL:Double::dc_dx = a*y*(y-b): y*(-7.5 + y)
+DEAL:Double::dc_dy = 2*y*(a+x): y*(3.1 + x) + (3.1 + x)*(-7.5 + y)
+DEAL:Double::dc_dy = 2*y*(a+x): y*(3.1 + x) + (3.1 + x)*(-7.5 + y)
+DEAL:Double::dc_dx(x=1,y=2.2): -11.66
+DEAL:Double::dc_dy(x=0.75,y=-1.08): -44.891
+DEAL:Double::
+DEAL::OK
diff --git a/tests/symengine/basic_03.cc b/tests/symengine/basic_03.cc
new file mode 100644
index 000000000000..3a11eb2be9fc
--- /dev/null
+++ b/tests/symengine/basic_03.cc
@@ -0,0 +1,211 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2016 - 2018 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE at
+// the top level of the deal.II distribution.
+//
+// ---------------------------------------------------------------------
+
+
+// Check that SymEngine can perform symbolic differentiation using function
+// symbols correctly
+
+// References:
+// https://github.com/symengine/symengine/blob/master/symengine/tests/basic/test_functions.cpp
+// https://github.com/symengine/symengine/blob/master/symengine/function.h
+// https://github.com/symengine/symengine/blob/master/symengine/tests/basic/test_basic.cpp
+// https://github.com/symengine/symengine/blob/master/symengine/tests/basic/test_number.cpp
+// https://github.com/symengine/symengine/blob/master/symengine/tests/basic/test_subs.cpp
+// https://github.com/symengine/symengine/blob/master/symengine/symengine_casts.h
+// https://github.com/symengine/symengine/blob/master/symengine/symengine_rcp.h
+// https://github.com/symengine/symengine/blob/master/symengine/derivative.h
+// https://github.com/symengine/symengine/blob/master/symengine/subs.h
+
+#include "../tests.h"
+
+#pragma clang diagnostic push
+#pragma clang diagnostic ignored "-Wextra-semi"
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#pragma clang diagnostic pop
+
+#include 
+#include 
+
+using namespace dealii;
+namespace SE = SymEngine;
+
+SE::RCP
+make_symengine_rcp(const int &val)
+{
+  return SE::integer(val);
+}
+
+SE::RCP
+make_symengine_rcp(const float &val)
+{
+  return SE::real_double(val);
+}
+
+SE::RCP
+make_symengine_rcp(const double &val)
+{
+  return SE::real_double(val);
+}
+
+template 
+SE::RCP
+make_symengine_rcp(const std::complex &val)
+{
+  // Build complex from two SymEngine numbers
+  return SE::Complex::from_two_nums(*make_symengine_rcp(val.real()),
+                                    *make_symengine_rcp(val.imag()));
+}
+
+SE::RCP
+make_symengine_rcp(const std::string &name)
+{
+  return SE::symbol(name);
+}
+
+SE::RCP
+make_symengine_rcp(const std::string &                          name,
+                   const std::vector> &args)
+{
+  return SE::function_symbol(name, args);
+}
+
+SE::RCP
+make_symengine_rcp(const std::string &name, const SE::RCP &arg)
+{
+  return SE::function_symbol(name, arg);
+}
+
+template 
+void
+test_number()
+{
+  // Modified snippet from SymEngine test
+  // {
+  //   SE::RCP x = SE::symbol("x");
+  //   SE::RCP _xi_1 = SE::symbol("_xi_1");
+  //   SE::RCP f = SE::function_symbol("f", x);
+  //   SE::RCP r1, r2;
+  //
+  //   f = function_symbol("f", SE::pow(x, SE::integer(2)));
+  //   deallog << "f: " << *f << std::endl;
+  //   r1 = f->diff(x);
+  //   deallog << "r1: " << *r1 << std::endl;
+  //   r2 = SE::Derivative::create(SE::function_symbol("f", _xi_1), {_xi_1});
+  //   deallog << "r2: " << *r2 << std::endl;
+  //   r2 = SE::Subs::create(r2, {{_xi_1, SE::pow(x, SE::integer(2))}});
+  //   deallog << "r2: " << *r2 << std::endl;
+  // }
+
+  // Normal symbols
+  SE::RCP x(make_symengine_rcp("x"));
+  SE::RCP  y(make_symengine_rcp("y"));
+  deallog << "x: " << *x << std::endl;
+  deallog << "y: " << *y << std::endl;
+
+  // Function symbols
+  SE::RCP f(make_symengine_rcp("f", x));
+  SE::RCP g(make_symengine_rcp("g", {x, y}));
+  SE::RCP h(
+    make_symengine_rcp("h", {SE::add(x, y), SE::mul(x, y)}));
+  deallog << "f: " << *f << std::endl;
+  deallog << "g: " << *g << std::endl;
+  deallog << "h: " << *h << std::endl;
+
+  // Perform symbolic differentiation
+  SE::RCP df_dx = f->diff(x);
+  SE::RCP dg_dx = g->diff(x);
+  SE::RCP dh_dx = h->diff(x);
+  deallog << "df_dx: " << *df_dx << std::endl;
+  deallog << "dg_dx: " << *dg_dx << std::endl;
+  deallog << "dh_dx: " << *dh_dx << std::endl;
+  SE::RCP df_dy =
+    f->diff(SE::rcp_static_cast(y));
+  SE::RCP dg_dy =
+    g->diff(SE::rcp_static_cast(y));
+  SE::RCP dh_dy =
+    h->diff(SE::rcp_static_cast(y));
+  deallog << "df_dy: " << *df_dy << std::endl;
+  deallog << "dg_dy: " << *dg_dy << std::endl;
+  deallog << "dh_dy: " << *dh_dy << std::endl;
+
+  // Substitute values
+  SE::map_basic_basic sub_vals;
+  sub_vals[x] = make_symengine_rcp(NumberType(1));
+  sub_vals[y] = make_symengine_rcp(NumberType(2.2));
+  sub_vals[f] = SE::pow(x, SE::integer(2));
+  sub_vals[g] = SE::add(x, y);
+  sub_vals[h] = SE::sub(x, y);
+
+  deallog << "f(x=1,y=2.2): " << *(f->subs(sub_vals))
+          << std::endl; // ->subs(sub_vals)
+  deallog << "g(x=1,y=2.2): " << *(g->subs(sub_vals))
+          << std::endl; // ->subs(sub_vals)
+  deallog << "h(x=1,y=2.2): " << *(h->subs(sub_vals))
+          << std::endl; // ->subs(sub_vals)
+  deallog << "Eval: f(x=1,y=2.2): "
+          << eval_double(*(f->subs(sub_vals)->subs(sub_vals))) << std::endl;
+  deallog << "Eval: g(x=1,y=2.2): "
+          << eval_double(*(g->subs(sub_vals)->subs(sub_vals))) << std::endl;
+  deallog << "Eval: h(x=1,y=2.2): "
+          << eval_double(*(h->subs(sub_vals)->subs(sub_vals))) << std::endl;
+
+  // Not yet implemented
+  deallog << "df_dx(x=1,y=2.2): " << *(df_dx->subs(sub_vals))
+          << std::endl; // ->subs(sub_vals)
+  deallog << "dg_dx(x=1,y=2.2): " << *(dg_dx->subs(sub_vals))
+          << std::endl; // ->subs(sub_vals)
+  deallog << "dh_dx(x=1,y=2.2): " << *(dh_dx->subs(sub_vals))
+          << std::endl; // ->subs(sub_vals)
+  // deallog << "Eval: df_dx(x=1,y=2.2): " <<
+  // eval_double(*(df_dx->subs(sub_vals)->subs(sub_vals))) << std::endl; deallog
+  // << "Eval: dg_dx(x=1,y=2.2): " <<
+  // eval_double(*(dg_dx->subs(sub_vals)->subs(sub_vals))) << std::endl; deallog
+  // << "Eval: dh_dx(x=1,y=2.2): " <<
+  // eval_double(*(dh_dx->subs(sub_vals)->subs(sub_vals))) << std::endl;
+}
+
+int
+main()
+{
+  initlog();
+
+  deallog.push("Integer");
+  test_number();
+  deallog.pop();
+
+  deallog.push("Float");
+  test_number();
+  deallog.pop();
+
+  deallog.push("Double");
+  test_number();
+  deallog.pop();
+
+  // Not available yet
+  // SymEngine::SymEngineException: Invalid Format: Expected Integer or Rational
+  // deallog << "Complex double" << std::endl;
+  // test_number>();
+  // deallog.pop();
+
+  deallog << "OK" << std::endl;
+}
diff --git a/tests/symengine/basic_03.output b/tests/symengine/basic_03.output
new file mode 100644
index 000000000000..d65a0e705c37
--- /dev/null
+++ b/tests/symengine/basic_03.output
@@ -0,0 +1,62 @@
+
+DEAL:Integer::x: x
+DEAL:Integer::y: y
+DEAL:Integer::f: f(x)
+DEAL:Integer::g: g(x, y)
+DEAL:Integer::h: h(x + y, x*y)
+DEAL:Integer::df_dx: Derivative(f(x), x)
+DEAL:Integer::dg_dx: Derivative(g(x, y), x)
+DEAL:Integer::dh_dx: y*Subs(Derivative(h(x + y, _xi_2), _xi_2), (_xi_2), (x*y)) + Subs(Derivative(h(_xi_1, x*y), _xi_1), (_xi_1), (x + y))
+DEAL:Integer::df_dy: 0
+DEAL:Integer::dg_dy: Derivative(g(x, y), y)
+DEAL:Integer::dh_dy: x*Subs(Derivative(h(x + y, _xi_2), _xi_2), (_xi_2), (x*y)) + Subs(Derivative(h(_xi_1, x*y), _xi_1), (_xi_1), (x + y))
+DEAL:Integer::f(x=1,y=2.2): x**2
+DEAL:Integer::g(x=1,y=2.2): x + y
+DEAL:Integer::h(x=1,y=2.2): x - y
+DEAL:Integer::Eval: f(x=1,y=2.2): 1.00
+DEAL:Integer::Eval: g(x=1,y=2.2): 3.00
+DEAL:Integer::Eval: h(x=1,y=2.2): -1.00
+DEAL:Integer::df_dx(x=1,y=2.2): 2*x
+DEAL:Integer::dg_dx(x=1,y=2.2): 1
+DEAL:Integer::dh_dx(x=1,y=2.2): 2*Subs(Derivative(h(3, _xi_2), _xi_2), (_xi_2), (2)) + Subs(Derivative(h(_xi_1, 2), _xi_1), (_xi_1), (3))
+DEAL:Float::x: x
+DEAL:Float::y: y
+DEAL:Float::f: f(x)
+DEAL:Float::g: g(x, y)
+DEAL:Float::h: h(x + y, x*y)
+DEAL:Float::df_dx: Derivative(f(x), x)
+DEAL:Float::dg_dx: Derivative(g(x, y), x)
+DEAL:Float::dh_dx: y*Subs(Derivative(h(x + y, _xi_2), _xi_2), (_xi_2), (x*y)) + Subs(Derivative(h(_xi_1, x*y), _xi_1), (_xi_1), (x + y))
+DEAL:Float::df_dy: 0
+DEAL:Float::dg_dy: Derivative(g(x, y), y)
+DEAL:Float::dh_dy: x*Subs(Derivative(h(x + y, _xi_2), _xi_2), (_xi_2), (x*y)) + Subs(Derivative(h(_xi_1, x*y), _xi_1), (_xi_1), (x + y))
+DEAL:Float::f(x=1,y=2.2): x**2
+DEAL:Float::g(x=1,y=2.2): x + y
+DEAL:Float::h(x=1,y=2.2): x - y
+DEAL:Float::Eval: f(x=1,y=2.2): 1.00
+DEAL:Float::Eval: g(x=1,y=2.2): 3.20
+DEAL:Float::Eval: h(x=1,y=2.2): -1.20
+DEAL:Float::df_dx(x=1,y=2.2): 2*x
+DEAL:Float::dg_dx(x=1,y=2.2): 1
+DEAL:Float::dh_dx(x=1,y=2.2): 2.20000004768372*Subs(Derivative(h(3.20000004768372, _xi_2), _xi_2), (_xi_2), (2.20000004768372)) + Subs(Derivative(h(_xi_1, 2.20000004768372), _xi_1), (_xi_1), (3.20000004768372))
+DEAL:Double::x: x
+DEAL:Double::y: y
+DEAL:Double::f: f(x)
+DEAL:Double::g: g(x, y)
+DEAL:Double::h: h(x + y, x*y)
+DEAL:Double::df_dx: Derivative(f(x), x)
+DEAL:Double::dg_dx: Derivative(g(x, y), x)
+DEAL:Double::dh_dx: y*Subs(Derivative(h(x + y, _xi_2), _xi_2), (_xi_2), (x*y)) + Subs(Derivative(h(_xi_1, x*y), _xi_1), (_xi_1), (x + y))
+DEAL:Double::df_dy: 0
+DEAL:Double::dg_dy: Derivative(g(x, y), y)
+DEAL:Double::dh_dy: x*Subs(Derivative(h(x + y, _xi_2), _xi_2), (_xi_2), (x*y)) + Subs(Derivative(h(_xi_1, x*y), _xi_1), (_xi_1), (x + y))
+DEAL:Double::f(x=1,y=2.2): x**2
+DEAL:Double::g(x=1,y=2.2): x + y
+DEAL:Double::h(x=1,y=2.2): x - y
+DEAL:Double::Eval: f(x=1,y=2.2): 1.00
+DEAL:Double::Eval: g(x=1,y=2.2): 3.20
+DEAL:Double::Eval: h(x=1,y=2.2): -1.20
+DEAL:Double::df_dx(x=1,y=2.2): 2*x
+DEAL:Double::dg_dx(x=1,y=2.2): 1
+DEAL:Double::dh_dx(x=1,y=2.2): 2.2*Subs(Derivative(h(3.2, _xi_2), _xi_2), (_xi_2), (2.2)) + Subs(Derivative(h(_xi_1, 2.2), _xi_1), (_xi_1), (3.2))
+DEAL::OK
diff --git a/tests/symengine/basic_04.cc b/tests/symengine/basic_04.cc
new file mode 100644
index 000000000000..9ffad422cf48
--- /dev/null
+++ b/tests/symengine/basic_04.cc
@@ -0,0 +1,170 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2016 - 2018 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE at
+// the top level of the deal.II distribution.
+//
+// ---------------------------------------------------------------------
+
+
+// Check that SymEngine can do some optimsation using lambda functions
+
+// References:
+// https://github.com/symengine/symengine/blob/master/symengine/tests/eval/test_lambda_double.cpp
+
+#include "../tests.h"
+
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wextra-semi"
+
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+
+#pragma GCC diagnostic pop
+
+#include 
+#include 
+#include 
+
+using namespace dealii;
+namespace SE = SymEngine;
+
+int
+main(int argc, char *argv[])
+{
+  initlog();
+
+  const unsigned int n_runs = 1000;
+
+  SE::RCP t_11 = SE::symbol("t_11");
+  SE::RCP t_12 = SE::symbol("t_12");
+  SE::RCP s    = SE::symbol("s");
+  SE::RCP t_02 = SE::symbol("t_02");
+  SE::RCP v_0  = SE::symbol("v_0");
+  SE::RCP v_1  = SE::symbol("v_1");
+  SE::RCP v_2  = SE::symbol("v_2");
+  SE::RCP t_10 = SE::symbol("t_10");
+  SE::RCP t_00 = SE::symbol("t_00");
+  SE::RCP t_01 = SE::symbol("t_01");
+  SE::RCP t_20 = SE::symbol("t_20");
+  SE::RCP t_21 = SE::symbol("t_21");
+  SE::RCP t_22 = SE::symbol("t_22");
+
+  SE::vec_basic v = {
+    t_11, t_12, s, t_02, v_0, v_1, v_2, t_10, t_00, t_01, t_20, t_21, t_22};
+
+  SE::RCP h =
+    SE::parse("2.*s**2.2*(v_0**2 + v_1**2 + v_2**2)**3*"
+              "(-1.*t_20*(1.*t_01*t_12 - 1.*t_02*t_11) "
+              "+ 1.*t_21*(1.*t_00*t_12 - 1.*t_02*t_10) "
+              "- 1.*t_22*(1.*t_00*t_11 - 1.*t_01*t_10))"
+              "*(1.*t_21*t_12 - 1.*t_22*t_11)");
+
+  SE::map_basic_basic dict;
+  std::vector vals(v.size());
+  for (unsigned i = 0; i < v.size(); i++)
+    {
+      dict[v[i]] = SE::real_double(i);
+      vals[i]    = i;
+    }
+
+  double res = 0.0, res1 = 0.0, res2 = 0.0;
+
+
+  // Standard substitution
+
+  auto t1 = std::chrono::high_resolution_clock::now();
+  for (unsigned j = 0; j < n_runs; j++)
+    {
+      res += static_cast(*h->subs(dict)).i;
+    }
+  auto         t2 = std::chrono::high_resolution_clock::now();
+  const double diff_symm_subs =
+    std::chrono::duration_cast(t2 - t1).count();
+  std::cout
+    << "Subs " << n_runs << " calls                  :"
+    << std::chrono::duration_cast(t2 - t1).count()
+    << " us" << std::endl;
+
+  deallog << "Value (subs): " << res << std::endl;
+
+  // Optimisation via lambda functions
+
+  t1 = std::chrono::high_resolution_clock::now();
+  SE::LambdaRealDoubleVisitor l;
+  l.init(v, *h);
+  t2 = std::chrono::high_resolution_clock::now();
+  const double diff_lambda_real_double_setup =
+    std::chrono::duration_cast(t2 - t1).count();
+  std::cout
+    << "LambdaDoubleVisitor setup-time   :"
+    << std::chrono::duration_cast(t2 - t1).count()
+    << " us" << std::endl;
+
+  t1 = std::chrono::high_resolution_clock::now();
+  for (unsigned j = 0; j < n_runs; j++)
+    {
+      res1 += l.call(vals);
+    }
+  t2 = std::chrono::high_resolution_clock::now();
+  const double diff_lambda_real_double_call =
+    std::chrono::duration_cast(t2 - t1).count();
+  std::cout
+    << "LambdaDoubleVisitor run-time     :"
+    << std::chrono::duration_cast(t2 - t1).count()
+    << " us" << std::endl;
+
+  deallog << "Value (lambda): " << res1 << std::endl;
+
+  std::cout << "Timing ratio (subs/lambda_double): "
+            << (diff_symm_subs) /
+                 (diff_lambda_real_double_setup + diff_lambda_real_double_call)
+            << std::endl;
+
+#ifdef HAVE_SYMENGINE_LLVM
+  // Optimisation via LLVM JIT optimiser
+
+  t1 = std::chrono::high_resolution_clock::now();
+  SE::LLVMDoubleVisitor l2;
+  l2.init(v, *h);
+  t2 = std::chrono::high_resolution_clock::now();
+  std::cout
+    << "LLVMDoubleVisitor setup-time     :"
+    << std::chrono::duration_cast(t2 - t1).count()
+    << " us" << std::endl;
+
+  t1 = std::chrono::high_resolution_clock::now();
+  for (unsigned j = 0; j < n_runs; j++)
+    {
+      res2 += l2.call(vals);
+    }
+  t2 = std::chrono::high_resolution_clock::now();
+  std::cout
+    << "LLVMDoubleVisitor run-time       :"
+    << std::chrono::duration_cast(t2 - t1).count()
+    << " us : Value: " << res2 << std::endl;
+
+  deallog << "Value (llvm): " << res2 << std::endl;
+#endif
+
+  deallog << "OK" << std::endl;
+
+  return 0;
+}
diff --git a/tests/symengine/basic_04.with_symengine_with_llvm=false.output b/tests/symengine/basic_04.with_symengine_with_llvm=false.output
new file mode 100644
index 000000000000..7eb32c0d555c
--- /dev/null
+++ b/tests/symengine/basic_04.with_symengine_with_llvm=false.output
@@ -0,0 +1,4 @@
+
+DEAL::Value (subs): 2.41358e+13
+DEAL::Value (lambda): 2.41358e+13
+DEAL::OK
diff --git a/tests/symengine/basic_04.with_symengine_with_llvm=true.output b/tests/symengine/basic_04.with_symengine_with_llvm=true.output
new file mode 100644
index 000000000000..e230bb2c3478
--- /dev/null
+++ b/tests/symengine/basic_04.with_symengine_with_llvm=true.output
@@ -0,0 +1,5 @@
+
+DEAL::Value (subs): 2.41358e+13
+DEAL::Value (lambda): 2.41358e+13
+DEAL::Value (llvm): 2.41358e+13
+DEAL::OK
diff --git a/tests/symengine/basic_05.cc b/tests/symengine/basic_05.cc
new file mode 100644
index 000000000000..41d59d174d84
--- /dev/null
+++ b/tests/symengine/basic_05.cc
@@ -0,0 +1,190 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2016 - 2018 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE at
+// the top level of the deal.II distribution.
+//
+// ---------------------------------------------------------------------
+
+// Check that SymEngine can do some optimsation on diffentiated expressions
+// using lambda functions
+// This is an extension of basic_04.cc
+
+// References:
+// https://github.com/symengine/symengine/blob/master/symengine/tests/eval/test_lambda_double.cpp
+
+#include "../tests.h"
+
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wextra-semi"
+
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+
+#pragma GCC diagnostic pop
+
+#include 
+#include 
+#include 
+
+using namespace dealii;
+namespace SE = SymEngine;
+
+int
+main(int argc, char *argv[])
+{
+  initlog();
+
+  const unsigned int n_runs = 1000;
+
+  SE::RCP t_11 = SE::symbol("t_11");
+  SE::RCP t_12 = SE::symbol("t_12");
+  SE::RCP s    = SE::symbol("s");
+  SE::RCP t_02 = SE::symbol("t_02");
+  SE::RCP v_0  = SE::symbol("v_0");
+  SE::RCP v_1  = SE::symbol("v_1");
+  SE::RCP v_2  = SE::symbol("v_2");
+  SE::RCP t_10 = SE::symbol("t_10");
+  SE::RCP t_00 = SE::symbol("t_00");
+  SE::RCP t_01 = SE::symbol("t_01");
+  SE::RCP t_20 = SE::symbol("t_20");
+  SE::RCP t_21 = SE::symbol("t_21");
+  SE::RCP t_22 = SE::symbol("t_22");
+
+  SE::vec_basic v = {
+    t_11, t_12, s, t_02, v_0, v_1, v_2, t_10, t_00, t_01, t_20, t_21, t_22};
+
+  SE::RCP h =
+    SE::parse("2.*s**2.2*(v_0**2 + v_1**2 + v_2**2)**3*"
+              "(-1.*t_20*(1.*t_01*t_12 - 1.*t_02*t_11) "
+              "+ 1.*t_21*(1.*t_00*t_12 - 1.*t_02*t_10) "
+              "- 1.*t_22*(1.*t_00*t_11 - 1.*t_01*t_10))"
+              "*(1.*t_21*t_12 - 1.*t_22*t_11)");
+
+  SE::vec_basic diffs = {h->diff(t_20),
+                         h->diff(t_21),
+                         h->diff(t_22),
+                         h->diff(t_10),
+                         h->diff(t_11),
+                         h->diff(t_12),
+                         h->diff(t_00),
+                         h->diff(t_01),
+                         h->diff(t_02),
+                         h->diff(s)};
+
+  std::cout << *h << std::endl;
+
+  SE::map_basic_basic dict;
+  std::vector vals(v.size());
+  for (unsigned i = 0; i < v.size(); i++)
+    {
+      dict[v[i]] = SE::real_double(i);
+      vals[i]    = i;
+    }
+
+  double res[10] = {}, res1[10] = {}, res2[10] = {};
+  double r = 0.0, r2 = 0.0, r3 = 0.0;
+
+  // Standard substitution
+
+  auto t1 = std::chrono::high_resolution_clock::now();
+  for (unsigned j = 0; j < n_runs; j++)
+    {
+      for (unsigned k = 0; k < diffs.size(); k++)
+        {
+          res[k] = static_cast(*diffs[k]->subs(dict)).i;
+          r += res[k];
+        }
+    }
+  auto         t2 = std::chrono::high_resolution_clock::now();
+  const double diff_symm_subs =
+    std::chrono::duration_cast(t2 - t1).count();
+  std::cout
+    << "Subs " << n_runs << " calls                  :"
+    << std::chrono::duration_cast(t2 - t1).count()
+    << " us" << std::endl;
+
+  deallog << "Value (subs): " << r << std::endl;
+
+  // Optimisation via lambda functions
+
+  t1 = std::chrono::high_resolution_clock::now();
+  SE::LambdaRealDoubleVisitor l;
+  l.init(v, diffs);
+  t2 = std::chrono::high_resolution_clock::now();
+  const double diff_lambda_real_double_setup =
+    std::chrono::duration_cast(t2 - t1).count();
+  std::cout
+    << "LambdaDoubleVisitor setup-time   :"
+    << std::chrono::duration_cast(t2 - t1).count()
+    << " us" << std::endl;
+
+  t1 = std::chrono::high_resolution_clock::now();
+  for (unsigned j = 0; j < n_runs; j++)
+    {
+      l.call(res1, vals.data());
+      for (unsigned k = 0; k < diffs.size(); k++)
+        {
+          r2 += res1[k];
+        }
+    }
+  t2 = std::chrono::high_resolution_clock::now();
+  const double diff_lambda_real_double_call =
+    std::chrono::duration_cast(t2 - t1).count();
+  std::cout
+    << "LambdaDoubleVisitor run-time     :"
+    << std::chrono::duration_cast(t2 - t1).count()
+    << " us" << std::endl;
+
+  deallog << "Value (lambda): " << r2 << std::endl;
+
+#ifdef HAVE_SYMENGINE_LLVM
+  // Optimisation via LLVM JIT optimiser
+
+  t1 = std::chrono::high_resolution_clock::now();
+  SE::LLVMDoubleVisitor l2;
+  l2.init(v, diffs);
+  t2 = std::chrono::high_resolution_clock::now();
+  std::cout
+    << "LLVMDoubleVisitor setup-time     :"
+    << std::chrono::duration_cast(t2 - t1).count()
+    << " us" << std::endl;
+
+  t1 = std::chrono::high_resolution_clock::now();
+  for (unsigned j = 0; j < 1000; j++)
+    {
+      l2.call(res2, vals.data());
+      for (unsigned k = 0; k < diffs.size(); k++)
+        {
+          r3 += res2[k];
+        }
+    }
+  t2 = std::chrono::high_resolution_clock::now();
+  std::cout
+    << "LLVMDoubleVisitor run-time       :"
+    << std::chrono::duration_cast(t2 - t1).count()
+    << " us : Value: " << r3 << std::endl;
+
+  deallog << "Value (llvm): " << r3 << std::endl;
+#endif
+
+  deallog << "OK" << std::endl;
+
+  return 0;
+}
diff --git a/tests/symengine/basic_05.with_symengine_with_llvm=false.output b/tests/symengine/basic_05.with_symengine_with_llvm=false.output
new file mode 100644
index 000000000000..b68d7bd3b6c4
--- /dev/null
+++ b/tests/symengine/basic_05.with_symengine_with_llvm=false.output
@@ -0,0 +1,4 @@
+
+DEAL::Value (subs): 2.91338e+13
+DEAL::Value (lambda): 2.91338e+13
+DEAL::OK
diff --git a/tests/symengine/basic_05.with_symengine_with_llvm=true.output b/tests/symengine/basic_05.with_symengine_with_llvm=true.output
new file mode 100644
index 000000000000..14de91cc39e6
--- /dev/null
+++ b/tests/symengine/basic_05.with_symengine_with_llvm=true.output
@@ -0,0 +1,5 @@
+
+DEAL::Value (subs): 2.91338e+13
+DEAL::Value (lambda): 2.91338e+13
+DEAL::Value (llvm): 2.91338e+13
+DEAL::OK
diff --git a/tests/symengine/basic_06.cc b/tests/symengine/basic_06.cc
new file mode 100644
index 000000000000..a664af2b46f7
--- /dev/null
+++ b/tests/symengine/basic_06.cc
@@ -0,0 +1,115 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2016 - 2018 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE at
+// the top level of the deal.II distribution.
+//
+// ---------------------------------------------------------------------
+
+// Check that SymEngine can do delayed substitution of explicitly dependent
+// symbolic functions and evaluate their derivatives as well.
+// This is inline with what is required to implement some material laws that
+// have internal variables
+
+#include "../tests.h"
+
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wextra-semi"
+
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+
+#pragma GCC diagnostic pop
+
+#include 
+#include 
+
+using namespace dealii;
+namespace SE = SymEngine;
+
+int
+main(int argc, char *argv[])
+{
+  initlog();
+
+  // 0. Define some independent variables
+  // Here we have two definitions of Q: One it is treated as a completely
+  // indepdent variable, and the other where its dependence on C is
+  // explicitly defined
+  SE::RCP C  = SE::symbol("C");  // Primary variable
+  SE::RCP Qi = SE::symbol("Qi"); // Some internal variable
+  SE::RCP  Q =
+    SE::function_symbol("Q", C); // This sets up the dependence of Q on C
+
+  deallog << *C << ",  " << *Qi << ",  " << *Q << std::endl;
+
+  // 1. Define a function with Q being independent of C
+  SE::RCP f_CQ_symb =
+    SE::mul(SE::real_double(0.5), SE::mul(Qi, SE::pow(C, SE::integer(2))));
+
+  deallog << "f_CQ_symb: " << *f_CQ_symb << std::endl;
+
+  // 2. Compute the partial derivative of f wrt C. This is a "partial
+  // derivative" as Q != Q(C).
+  SE::RCP df_CQ_dC_symb = f_CQ_symb->diff(C);
+
+  deallog << "df_CQ_dC_symb: " << *df_CQ_dC_symb << std::endl;
+
+  // 3. Substitute Qi -> Q=Q(C) to now make SymEngine aware of Q's dependence
+  // on C.
+  SE::map_basic_basic int_var_dict;
+  int_var_dict[Qi] = Q;
+  SE::RCP df_CQ_dC_symb_subs =
+    df_CQ_dC_symb->subs(int_var_dict);
+
+  deallog << "df_CQ_dC_symb_subs: " << *df_CQ_dC_symb_subs << std::endl;
+
+  // 4. Compute total derivative of df_dC wrt C.
+  SE::RCP D2f_CQ_DC_dC_symb = df_CQ_dC_symb_subs->diff(C);
+
+  deallog << "D2f_CQ_DC_dC_symb: " << *D2f_CQ_DC_dC_symb << std::endl;
+
+  // 5. Perform some numerical substitutions
+  SE::map_basic_basic all_var_dict;
+  all_var_dict[C]  = SE::real_double(5);
+  all_var_dict[Qi] = SE::real_double(3);
+  all_var_dict[Q] =
+    SE::mul(SE::real_double(0.6),
+            C); // This explicitly defines the relationship between Q and C
+
+  SE::RCP f_CQ_subs = f_CQ_symb->subs(all_var_dict);
+  deallog << "f_CQ_subs: " << *f_CQ_subs << std::endl;
+
+  SE::RCP df_CQ_dC_subs = df_CQ_dC_symb->subs(all_var_dict);
+  deallog << "df_CQ_dC: subs: " << *df_CQ_dC_subs << std::endl
+          << "df_CQ_dC: eval: " << SE::eval_double(*df_CQ_dC_subs) << std::endl;
+
+  // This first substitution should presumably convert Q(C)->0.6C and thus
+  // dQ(C)_dC into 0.6
+  SE::RCP D2f_CQ_DC_dC_subs_1 =
+    D2f_CQ_DC_dC_symb->subs(all_var_dict);
+  // This second substitution should fill out the remaining entries for C
+  SE::RCP D2f_CQ_DC_dC_subs =
+    D2f_CQ_DC_dC_subs_1->subs(all_var_dict);
+  deallog << "D2f_CQ_DC_dC: subs 1: " << *D2f_CQ_DC_dC_subs_1 << std::endl
+          << "D2f_CQ_DC_dC: subs 2: " << *D2f_CQ_DC_dC_subs << std::endl
+          << "D2f_CQ_DC_dC: eval: " << SE::eval_double(*D2f_CQ_DC_dC_subs)
+          << std::endl;
+
+  return 0;
+}
diff --git a/tests/symengine/basic_06.output b/tests/symengine/basic_06.output
new file mode 100644
index 000000000000..ad5bc7ba117a
--- /dev/null
+++ b/tests/symengine/basic_06.output
@@ -0,0 +1,12 @@
+
+DEAL::C,  Qi,  Q(C)
+DEAL::f_CQ_symb: 0.5*C**2*Qi
+DEAL::df_CQ_dC_symb: 1.0*C*Qi
+DEAL::df_CQ_dC_symb_subs: 1.0*C*Q(C)
+DEAL::D2f_CQ_DC_dC_symb: 1.0*C*Derivative(Q(C), C) + 1.0*Q(C)
+DEAL::f_CQ_subs: 37.5
+DEAL::df_CQ_dC: subs: 15.
+DEAL::df_CQ_dC: eval: 15.0000
+DEAL::D2f_CQ_DC_dC: subs 1: 3.0 + 0.6*C
+DEAL::D2f_CQ_DC_dC: subs 2: 6.0
+DEAL::D2f_CQ_DC_dC: eval: 6.00000
diff --git a/tests/symengine/basic_07.cc b/tests/symengine/basic_07.cc
new file mode 100644
index 000000000000..2963db1902a9
--- /dev/null
+++ b/tests/symengine/basic_07.cc
@@ -0,0 +1,123 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2016 - 2018 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE at
+// the top level of the deal.II distribution.
+//
+// ---------------------------------------------------------------------
+
+// Check that SymEngine can do delayed substitution of implicitly dependent
+// symbolic functions and evaluate their derivatives as well.
+// This is inline with what is required to implement some material laws that
+// have internal variables
+
+#include "../tests.h"
+
+#pragma GCC diagnostic push
+#pragma GCC diagnostic ignored "-Wextra-semi"
+
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+
+#pragma GCC diagnostic pop
+
+#include 
+#include 
+
+using namespace dealii;
+namespace SE = SymEngine;
+
+int
+main(int argc, char *argv[])
+{
+  initlog();
+
+  // 0. Define some independent variables
+  // Here we have two definitions of Q: One it is treated as a completely
+  // independent variable, and the other where its dependence on C is
+  // implicitly defined
+  // That is to say, we'd have to compute Q=Q(C) using a nonlinear solution
+  // scheme, as might be the case for a viscoelastic material with a
+  // nonlinear evolution law.
+  SE::RCP C  = SE::symbol("C");  // Primary variable
+  SE::RCP Qi = SE::symbol("Qi"); // Some internal variable
+  SE::RCP  Q =
+    SE::function_symbol("Q", C); // This sets up the dependence of Q on C
+
+  deallog << *C << ",  " << *Qi << ",  " << *Q << std::endl;
+
+  // 1. Define a function with Q being independent of C
+  SE::RCP f_CQ_symb =
+    SE::mul(SE::real_double(0.5), SE::mul(Qi, SE::pow(C, SE::integer(2))));
+
+  deallog << "f_CQ_symb: " << *f_CQ_symb << std::endl;
+
+  // 2. Compute the partial derivative of f wrt C. This is a "partial
+  // derivative" as Q != Q(C).
+  SE::RCP df_CQ_dC_symb = f_CQ_symb->diff(C);
+
+  deallog << "df_CQ_dC_symb: " << *df_CQ_dC_symb << std::endl;
+
+  // 3. Substitute Qi -> Q=Q(C) to now make SymEngine aware of Q's dependence
+  // on C.
+  SE::map_basic_basic int_var_dict;
+  int_var_dict[Qi] = Q;
+  SE::RCP df_CQ_dC_symb_subs =
+    df_CQ_dC_symb->subs(int_var_dict);
+
+  deallog << "df_CQ_dC_symb_subs: " << *df_CQ_dC_symb_subs << std::endl;
+
+  // 4. Compute total derivative of df_dC wrt C.
+  SE::RCP D2f_CQ_DC_dC_symb = df_CQ_dC_symb_subs->diff(C);
+
+  deallog << "D2f_CQ_DC_dC_symb: " << *D2f_CQ_DC_dC_symb << std::endl;
+
+  // 5. Perform some numerical substitutions
+  // Lets assume Q = 0.6*C*C
+  // Then dQ_dC = 1.2*C
+  SE::map_basic_basic all_var_dict;
+  all_var_dict[C] = SE::real_double(5);
+  all_var_dict[Qi] =
+    SE::real_double(0.6 * 5 * 5); // This would be the numerical end result of
+                                  // an internal nonlinear solver for Q
+  all_var_dict[Q] = Qi;           // These are numerically the same thing
+  all_var_dict[Q->diff(C)] =
+    SE::mul(SE::real_double(1.2),
+            C); // This resolves the implicit relationship between Q and C
+
+  SE::RCP f_CQ_subs = f_CQ_symb->subs(all_var_dict);
+  deallog << "f_CQ_subs: " << *f_CQ_subs << std::endl;
+
+  SE::RCP df_CQ_dC_subs = df_CQ_dC_symb->subs(all_var_dict);
+  deallog << "df_CQ_dC: subs: " << *df_CQ_dC_subs << std::endl
+          << "df_CQ_dC: eval: " << SE::eval_double(*df_CQ_dC_subs) << std::endl;
+
+  // This first substitution should presumably convert Q(C)->0.6C and thus
+  // dQ(C)_dC into 0.6
+  SE::RCP D2f_CQ_DC_dC_subs_1 =
+    D2f_CQ_DC_dC_symb->subs(all_var_dict);
+  // This second substitution should fill out the remaining entries for C
+  SE::RCP D2f_CQ_DC_dC_subs =
+    D2f_CQ_DC_dC_subs_1->subs(all_var_dict);
+  deallog << "D2f_CQ_DC_dC: subs 1: " << *D2f_CQ_DC_dC_subs_1 << std::endl
+          << "D2f_CQ_DC_dC: subs 2: " << *D2f_CQ_DC_dC_subs << std::endl
+          << "D2f_CQ_DC_dC: eval: " << SE::eval_double(*D2f_CQ_DC_dC_subs)
+          << std::endl;
+
+  return 0;
+}
diff --git a/tests/symengine/basic_07.output b/tests/symengine/basic_07.output
new file mode 100644
index 000000000000..6b1e0b525cd5
--- /dev/null
+++ b/tests/symengine/basic_07.output
@@ -0,0 +1,12 @@
+
+DEAL::C,  Qi,  Q(C)
+DEAL::f_CQ_symb: 0.5*C**2*Qi
+DEAL::df_CQ_dC_symb: 1.0*C*Qi
+DEAL::df_CQ_dC_symb_subs: 1.0*C*Q(C)
+DEAL::D2f_CQ_DC_dC_symb: 1.0*C*Derivative(Q(C), C) + 1.0*Q(C)
+DEAL::f_CQ_subs: 187.5
+DEAL::df_CQ_dC: subs: 75.
+DEAL::df_CQ_dC: eval: 75.0000
+DEAL::D2f_CQ_DC_dC: subs 1: 6.0*C + 1.0*Qi
+DEAL::D2f_CQ_DC_dC: subs 2: 45.0
+DEAL::D2f_CQ_DC_dC: eval: 45.0000

From ae76d46602dee986943538700a1b4f1b0a69a723 Mon Sep 17 00:00:00 2001
From: Denis Davydov 
Date: Fri, 15 Mar 2019 21:48:39 +0100
Subject: [PATCH 269/507] extend DoFRenumbering::cell_wise to
 parallel::Triangulation

---
 source/dofs/dof_renumbering.cc | 80 +++++++++++++++++-----------------
 1 file changed, 41 insertions(+), 39 deletions(-)

diff --git a/source/dofs/dof_renumbering.cc b/source/dofs/dof_renumbering.cc
index adc401e0f70d..087479b3dd25 100644
--- a/source/dofs/dof_renumbering.cc
+++ b/source/dofs/dof_renumbering.cc
@@ -1592,8 +1592,9 @@ namespace DoFRenumbering
     DoFHandlerType &                                                  dof,
     const std::vector &cells)
   {
-    std::vector renumbering(dof.n_dofs());
-    std::vector reverse(dof.n_dofs());
+    std::vector renumbering(
+      dof.n_locally_owned_dofs());
+    std::vector reverse(dof.n_locally_owned_dofs());
     compute_cell_wise(renumbering, reverse, dof, cells);
 
     dof.renumber_dofs(renumbering);
@@ -1609,69 +1610,70 @@ namespace DoFRenumbering
     const typename std::vector
       &cells)
   {
-    Assert(cells.size() == dof.get_triangulation().n_active_cells(),
-           ExcDimensionMismatch(cells.size(),
-                                dof.get_triangulation().n_active_cells()));
+    if (const parallel::Triangulation *p =
+          dynamic_cast<
+            const parallel::Triangulation *>(
+            &dof.get_triangulation()))
+      {
+        AssertDimension(cells.size(), p->n_locally_owned_active_cells());
+      }
+    else
+      {
+        AssertDimension(cells.size(), dof.get_triangulation().n_active_cells());
+      }
 
-    types::global_dof_index n_global_dofs = dof.n_dofs();
+    const auto n_owned_dofs = dof.n_locally_owned_dofs();
 
-    // Actually, we compute the
-    // inverse of the reordering
-    // vector, called reverse here.
-    // Later, irs inverse is computed
-    // into new_indices, which is the
+    // Actually, we compute the inverse of the reordering vector, called reverse
+    // here. Later, its inverse is computed into new_indices, which is the
     // return argument.
 
-    Assert(new_indices.size() == n_global_dofs,
-           ExcDimensionMismatch(new_indices.size(), n_global_dofs));
-    Assert(reverse.size() == n_global_dofs,
-           ExcDimensionMismatch(reverse.size(), n_global_dofs));
+    AssertDimension(new_indices.size(), n_owned_dofs);
+    AssertDimension(reverse.size(), n_owned_dofs);
 
-    // For continuous elements, we must
-    // make sure, that each dof is
-    // reordered only once.
-    std::vector                    already_sorted(n_global_dofs, false);
+    // For continuous elements, we must make sure, that each dof is reordered
+    // only once.
+    std::vector                    already_sorted(n_owned_dofs, false);
     std::vector cell_dofs;
 
-    unsigned int global_index = 0;
+    const auto &owned_dofs = dof.locally_owned_dofs();
 
-    typename std::vector<
-      typename DoFHandlerType::active_cell_iterator>::const_iterator cell;
+    unsigned int index = 0;
 
-    for (cell = cells.begin(); cell != cells.end(); ++cell)
+    for (const auto &cell : cells)
       {
-        // Determine the number of dofs
-        // on this cell and reinit the
-        // vector storing these
-        // numbers.
-        unsigned int n_cell_dofs = (*cell)->get_fe().n_dofs_per_cell();
+        // Determine the number of dofs on this cell and reinit the
+        // vector storing these numbers.
+        const unsigned int n_cell_dofs = cell->get_fe().n_dofs_per_cell();
         cell_dofs.resize(n_cell_dofs);
 
-        (*cell)->get_active_or_mg_dof_indices(cell_dofs);
+        cell->get_active_or_mg_dof_indices(cell_dofs);
 
-        // Sort here to make sure that
-        // degrees of freedom inside a
-        // single cell are in the same
-        // order after renumbering.
+        // Sort here to make sure that degrees of freedom inside a single cell
+        // are in the same order after renumbering.
         std::sort(cell_dofs.begin(), cell_dofs.end());
 
-        for (unsigned int i = 0; i < n_cell_dofs; ++i)
+        for (const auto dof : cell_dofs)
           {
-            if (!already_sorted[cell_dofs[i]])
+            const auto local_dof = owned_dofs.index_within_set(dof);
+            if (local_dof != numbers::invalid_dof_index &&
+                !already_sorted[local_dof])
               {
-                already_sorted[cell_dofs[i]] = true;
-                reverse[global_index++]      = cell_dofs[i];
+                already_sorted[local_dof] = true;
+                reverse[index++]          = local_dof;
               }
           }
       }
-    Assert(global_index == n_global_dofs,
+    Assert(index == n_owned_dofs,
            ExcMessage(
              "Traversing over the given set of cells did not cover all "
              "degrees of freedom in the DoFHandler. Does the set of cells "
              "not include all active cells?"));
 
     for (types::global_dof_index i = 0; i < reverse.size(); ++i)
-      new_indices[reverse[i]] = i;
+      new_indices[reverse[i]] = owned_dofs.nth_index_in_set(i);
   }
 
 

From 9eaa95d30a4987173c9147215b6e08e91c9c86bf Mon Sep 17 00:00:00 2001
From: Denis Davydov 
Date: Sat, 16 Mar 2019 07:31:05 +0100
Subject: [PATCH 270/507] add a test for DoFRenumbering::cell_wise() with
 p::d::Tria

---
 tests/dofs/dof_renumbering_10.cc              | 172 ++++++++++++++++++
 ...mbering_10.with_p4est=true.mpirun=1.output |  19 ++
 ...mbering_10.with_p4est=true.mpirun=3.output |  27 +++
 3 files changed, 218 insertions(+)
 create mode 100644 tests/dofs/dof_renumbering_10.cc
 create mode 100644 tests/dofs/dof_renumbering_10.with_p4est=true.mpirun=1.output
 create mode 100644 tests/dofs/dof_renumbering_10.with_p4est=true.mpirun=3.output

diff --git a/tests/dofs/dof_renumbering_10.cc b/tests/dofs/dof_renumbering_10.cc
new file mode 100644
index 000000000000..ff0204b52567
--- /dev/null
+++ b/tests/dofs/dof_renumbering_10.cc
@@ -0,0 +1,172 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2019 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+
+// test cell_wise with p::d::Tria
+
+#include 
+#include 
+
+#include 
+
+#include 
+#include 
+#include 
+#include 
+
+#include 
+#include 
+
+#include 
+#include 
+#include 
+#include 
+#include 
+
+#include "../tests.h"
+
+template 
+void
+test(const bool adaptive_ref = true)
+{
+  MPI_Comm           mpi_communicator(MPI_COMM_WORLD);
+  const unsigned int this_mpi_core =
+    dealii::Utilities::MPI::this_mpi_process(mpi_communicator);
+
+  parallel::distributed::Triangulation tria(mpi_communicator);
+  GridGenerator::hyper_cube(tria, 0, 1, true);
+  tria.refine_global(1);
+  if (adaptive_ref)
+    {
+      for (auto cell : tria.active_cell_iterators())
+        if (cell->is_locally_owned())
+          if (cell->center().norm() < 0.5)
+            cell->set_refine_flag();
+      tria.execute_coarsening_and_refinement();
+      for (auto cell : tria.active_cell_iterators())
+        if (cell->is_locally_owned())
+          if (cell->center()[0] < 0.2)
+            cell->set_refine_flag();
+      tria.execute_coarsening_and_refinement();
+    }
+  else
+    {
+      tria.refine_global(1);
+    }
+
+  FE_Q       fe(fe_degree);
+  DoFHandler dof(tria);
+  dof.distribute_dofs(fe);
+
+  using CELL = typename DoFHandler::active_cell_iterator;
+  std::vector cell_order;
+  for (auto &cell : dof.active_cell_iterators())
+    if (cell->is_locally_owned())
+      cell_order.push_back(cell);
+
+  std::sort(cell_order.begin(),
+            cell_order.end(),
+            [](const CELL &a, const CELL &b) {
+              std::vector p1(dim), p2(dim);
+              for (unsigned int d = 0; d < dim; ++d)
+                {
+                  p1[d] = a->center()[d];
+                  p2[d] = b->center()[d];
+                }
+              return std::lexicographical_compare(p1.begin(),
+                                                  p1.end(),
+                                                  p2.begin(),
+                                                  p2.end());
+            });
+
+  DoFRenumbering::cell_wise(dof, cell_order);
+
+  deallog << std::endl << "cell order:" << std::endl;
+  std::vector cell_dofs(fe.n_dofs_per_cell());
+  for (const auto &c : cell_order)
+    {
+      c->get_active_or_mg_dof_indices(cell_dofs);
+      deallog << c->center() << ":";
+      for (const auto d : cell_dofs)
+        deallog << " " << d;
+      deallog << std::endl;
+    }
+
+  IndexSet owned_set = dof.locally_owned_dofs();
+
+  // output in Gnuplot for visual inspection
+  if (dim == 2)
+    {
+      std::map> support_points;
+      MappingQ1                                mapping;
+      DoFTools::map_dofs_to_support_points(mapping, dof, support_points);
+
+      const std::string href = (adaptive_ref ? "" : "global_");
+      const std::string base_filename =
+        href + "grid" + dealii::Utilities::int_to_string(dim) + "_" +
+        dealii::Utilities::int_to_string(fe_degree) + "_p" +
+        dealii::Utilities::int_to_string(this_mpi_core);
+
+      const std::string filename = base_filename + ".gp";
+      std::ofstream     f(filename.c_str());
+
+      f << "set terminal png size 400,410 enhanced font \"Helvetica,8\""
+        << std::endl
+        << "set output \"" << base_filename << ".png\"" << std::endl
+        << "set size square" << std::endl
+        << "set view equal xy" << std::endl
+        << "unset xtics" << std::endl
+        << "unset ytics" << std::endl
+        << "unset grid" << std::endl
+        << "unset border" << std::endl
+        << "plot '-' using 1:2 with lines notitle, '-' with labels tc rgb 'red' nopoint notitle, '-' with labels point pt 4 offset 1,1 notitle"
+        << std::endl;
+      GridOut().write_gnuplot(tria, f);
+      f << "e" << std::endl;
+
+      // output cell order
+      for (unsigned int index = 0; index < cell_order.size(); ++index)
+        f << cell_order[index]->center() << " \"" << index << "\"\n";
+
+      f << std::flush;
+      f << "e" << std::endl << std::endl;
+
+      // output only owned support points
+      for (auto it = support_points.cbegin(); it != support_points.cend();)
+        {
+          if (owned_set.is_element(it->first))
+            ++it;
+          else
+            support_points.erase(it++);
+        }
+
+      DoFTools::write_gnuplot_dof_support_point_info(f, support_points);
+
+      f << "e" << std::endl;
+    }
+}
+
+
+int
+main(int argc, char **argv)
+{
+  dealii::Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1);
+
+  MPILogInitAll log;
+
+  test<2>(false);
+
+  return 0;
+}
diff --git a/tests/dofs/dof_renumbering_10.with_p4est=true.mpirun=1.output b/tests/dofs/dof_renumbering_10.with_p4est=true.mpirun=1.output
new file mode 100644
index 000000000000..2801b5dd09ec
--- /dev/null
+++ b/tests/dofs/dof_renumbering_10.with_p4est=true.mpirun=1.output
@@ -0,0 +1,19 @@
+
+DEAL:0::
+DEAL:0::cell order:
+DEAL:0::0.125000 0.125000: 0 1 2 3
+DEAL:0::0.125000 0.375000: 2 3 4 5
+DEAL:0::0.125000 0.625000: 4 5 6 7
+DEAL:0::0.125000 0.875000: 6 7 8 9
+DEAL:0::0.375000 0.125000: 1 10 3 11
+DEAL:0::0.375000 0.375000: 3 11 5 12
+DEAL:0::0.375000 0.625000: 5 12 7 13
+DEAL:0::0.375000 0.875000: 7 13 9 14
+DEAL:0::0.625000 0.125000: 10 15 11 16
+DEAL:0::0.625000 0.375000: 11 16 12 17
+DEAL:0::0.625000 0.625000: 12 17 13 18
+DEAL:0::0.625000 0.875000: 13 18 14 19
+DEAL:0::0.875000 0.125000: 15 20 16 21
+DEAL:0::0.875000 0.375000: 16 21 17 22
+DEAL:0::0.875000 0.625000: 17 22 18 23
+DEAL:0::0.875000 0.875000: 18 23 19 24
diff --git a/tests/dofs/dof_renumbering_10.with_p4est=true.mpirun=3.output b/tests/dofs/dof_renumbering_10.with_p4est=true.mpirun=3.output
new file mode 100644
index 000000000000..bba8f1109583
--- /dev/null
+++ b/tests/dofs/dof_renumbering_10.with_p4est=true.mpirun=3.output
@@ -0,0 +1,27 @@
+
+DEAL:0::
+DEAL:0::cell order:
+DEAL:0::0.125000 0.125000: 0 1 2 3
+DEAL:0::0.125000 0.375000: 2 3 4 5
+DEAL:0::0.375000 0.125000: 1 6 3 7
+DEAL:0::0.375000 0.375000: 3 7 5 8
+
+DEAL:1::
+DEAL:1::cell order:
+DEAL:1::0.125000 0.625000: 4 5 9 10
+DEAL:1::0.125000 0.875000: 9 10 11 12
+DEAL:1::0.375000 0.625000: 5 8 10 13
+DEAL:1::0.375000 0.875000: 10 13 12 14
+DEAL:1::0.625000 0.125000: 6 15 7 16
+DEAL:1::0.625000 0.375000: 7 16 8 17
+DEAL:1::0.875000 0.125000: 15 18 16 19
+DEAL:1::0.875000 0.375000: 16 19 17 20
+
+
+DEAL:2::
+DEAL:2::cell order:
+DEAL:2::0.625000 0.625000: 8 17 13 21
+DEAL:2::0.625000 0.875000: 13 21 14 22
+DEAL:2::0.875000 0.625000: 17 20 21 23
+DEAL:2::0.875000 0.875000: 21 23 22 24
+

From f7e260e613fe4466862d45d99a0d4a75b094f005 Mon Sep 17 00:00:00 2001
From: Denis Davydov 
Date: Sat, 16 Mar 2019 07:33:08 +0100
Subject: [PATCH 271/507] rename changelog

---
 .../changes/minor/{20190411TimoHeister => 20190311TimoHeister}    | 0
 1 file changed, 0 insertions(+), 0 deletions(-)
 rename doc/news/changes/minor/{20190411TimoHeister => 20190311TimoHeister} (100%)

diff --git a/doc/news/changes/minor/20190411TimoHeister b/doc/news/changes/minor/20190311TimoHeister
similarity index 100%
rename from doc/news/changes/minor/20190411TimoHeister
rename to doc/news/changes/minor/20190311TimoHeister

From 6cdac1935475d6fdf4a9cfce8a20beccd77b185e Mon Sep 17 00:00:00 2001
From: Denis Davydov 
Date: Sat, 16 Mar 2019 07:42:03 +0100
Subject: [PATCH 272/507] adjust documentation and add a changelog

---
 doc/news/changes/minor/20190316DenisDavydov |  3 ++
 include/deal.II/dofs/dof_renumbering.h      | 54 ++++++++++++---------
 2 files changed, 33 insertions(+), 24 deletions(-)
 create mode 100644 doc/news/changes/minor/20190316DenisDavydov

diff --git a/doc/news/changes/minor/20190316DenisDavydov b/doc/news/changes/minor/20190316DenisDavydov
new file mode 100644
index 000000000000..7d018538b7f6
--- /dev/null
+++ b/doc/news/changes/minor/20190316DenisDavydov
@@ -0,0 +1,3 @@
+Improved: DoFRenumbering::cell_wise() now support parallel::Triangulation .
+
    
+(Denis Davydov, 2019/03/16)
diff --git a/include/deal.II/dofs/dof_renumbering.h b/include/deal.II/dofs/dof_renumbering.h
index 445fedd07883..cfd883283752 100644
--- a/include/deal.II/dofs/dof_renumbering.h
+++ b/include/deal.II/dofs/dof_renumbering.h
@@ -838,10 +838,10 @@ namespace DoFRenumbering
 
   /**
    * Renumber degrees of freedom by cell. The function takes a vector of cell
-   * iterators (which needs to list all active cells of the DoF handler
-   * objects) and will give degrees of freedom new indices based on where in
-   * the given list of cells the cell is on which the degree of freedom is
-   * located. Degrees of freedom that exist at the interface between two or
+   * iterators (which needs to list all locally owned active cells of the
+   * DoF handler objects) and will give degrees of freedom new indices based on
+   * where in the given list of cells the cell is on which the degree of freedom
+   * is located. Degrees of freedom that exist at the interface between two or
    * more cells will be numbered when they are encountered first.
    *
    * Degrees of freedom that are encountered first on the same cell retain
@@ -852,10 +852,12 @@ namespace DoFRenumbering
    * @param[in] cell_order A vector that contains the order of the cells that
    * defines the order in which degrees of freedom should be renumbered.
    *
-   * @pre @p cell_order must have size
-   * dof_handler.get_triangulation().n_active_cells(). Every
-   * active cell iterator of that triangulation needs to be present in @p
-   * cell_order exactly once.
+   * @pre for serial triangulation @p cell_order must have size
+   * dof_handler.get_triangulation().n_active_cells(), whereas
+   * in case of parallel triangulation its size should be
+   * parallel::Triangulation::n_locally_owned_active_cells(). Every active cell
+   * iterator of that triangulation needs to be present in @p cell_order exactly
+   * once.
    */
   template 
   void
@@ -865,34 +867,38 @@ namespace DoFRenumbering
 
   /**
    * Compute a renumbering of degrees of freedom by cell. The function takes a
-   * vector of cell iterators (which needs to list all active cells of
-   * the DoF handler objects) and will give degrees of freedom new indices
-   * based on where in the given list of cells the cell is on which the degree
-   * of freedom is located. Degrees of freedom that exist at the interface
-   * between two or more cells will be numbered when they are encountered
-   * first.
+   * vector of cell iterators (which needs to list all locally owned
+   * active cells of the DoF handler objects) and will give degrees of freedom
+   * new indices based on where in the given list of cells the cell is on which
+   * the degree of freedom is located. Degrees of freedom that exist at the
+   * interface between two or more cells will be numbered when they are
+   * encountered first.
    *
    * Degrees of freedom that are encountered first on the same cell retain
    * their original ordering before the renumbering step.
    *
    * @param[out] renumbering A vector of length
-   * dof_handler.n_dofs() that contains for each degree of
-   * freedom (in their current numbering) their future DoF index. This vector
-   * therefore presents a (very particular) permutation of the current
-   * DoF indices.
+   * dof_handler.n_locally_owned_dofs() that contains for each
+   * degree of freedom (in their current numbering) their future DoF index. This
+   * vector therefore presents a (very particular) permutation of the
+   * current DoF indices.
    * @param[out] inverse_renumbering The reverse of the permutation returned
-   * in the previous argument.
+   * in the previous argument. In case of parallel::Triangulation the inverse
+   * is within locally owned DoFs.
    * @param[in] dof_handler The DoFHandler whose degrees of freedom are to be
    * renumbered.
    * @param[in] cell_order A vector that contains the order of the cells that
    * defines the order in which degrees of freedom should be renumbered.
    *
-   * @pre @p cell_order must have size
-   * dof_handler.get_triangulation().n_active_cells(). Every
-   * active cell iterator of that triangulation needs to be present in @p
+   * @pre for serial triangulation @p cell_order must have size
+   * dof_handler.get_triangulation().n_active_cells(), whereas
+   * in case of parallel triangulation its size should be
+   * parallel::Triangulation::n_locally_owned_active_cells(). Every active cell
+   * iterator of that triangulation needs to be present in @p
    * cell_order exactly once. @post For each @p i between zero and
-   * dof_handler.n_dofs(), the condition
-   * renumbering[inverse_renumbering[i]] == i will hold.
+   * dof_handler.n_locally_owned_dofs(), the condition
+   * renumbering[inverse_renumbering[i]] ==
+   * dof_handler.locally_owned_dofs().nth_index_in_set(i) will hold.
    */
   template 
   void

From df1a79ab3abd6f126e7000972eea4c1c3779bb42 Mon Sep 17 00:00:00 2001
From: Daniel Arndt 
Date: Sat, 16 Mar 2019 01:11:58 +0100
Subject: [PATCH 273/507] Set cell manifold ids when the
 apply_all_indicators_to_manifold flag is used.

---
 doc/news/changes/minor/20190316Arndt       |  4 ++
 include/deal.II/grid/grid_in.h             |  3 +-
 source/grid/grid_in.cc                     |  3 +
 tests/grid/grid_in_ucd_02.cc               | 77 ++++++++++++++++++++++
 tests/grid/grid_in_ucd_02.output           | 53 +++++++++++++++
 tests/grid/grid_in_ucd_02_grids/grid_1.inp |  4 ++
 tests/grid/grid_in_ucd_02_grids/grid_2.inp | 11 ++++
 tests/grid/grid_in_ucd_02_grids/grid_3.inp | 29 ++++++++
 tests/hp/step-5.cc                         |  2 +-
 9 files changed, 184 insertions(+), 2 deletions(-)
 create mode 100644 doc/news/changes/minor/20190316Arndt
 create mode 100644 tests/grid/grid_in_ucd_02.cc
 create mode 100644 tests/grid/grid_in_ucd_02.output
 create mode 100644 tests/grid/grid_in_ucd_02_grids/grid_1.inp
 create mode 100644 tests/grid/grid_in_ucd_02_grids/grid_2.inp
 create mode 100644 tests/grid/grid_in_ucd_02_grids/grid_3.inp

diff --git a/doc/news/changes/minor/20190316Arndt b/doc/news/changes/minor/20190316Arndt
new file mode 100644
index 000000000000..204e05b91457
--- /dev/null
+++ b/doc/news/changes/minor/20190316Arndt
@@ -0,0 +1,4 @@
+Improved: The apply_all_indicators_to_manifold flag in GridIn::read_ucd()
+lets the indicators be used for cells as manifold id as well.
+
    
+(Daniel Arndt, 2019/03/16)
diff --git a/include/deal.II/grid/grid_in.h b/include/deal.II/grid/grid_in.h
index d646ead8f41f..73c4be4a3d0d 100644
--- a/include/deal.II/grid/grid_in.h
+++ b/include/deal.II/grid/grid_in.h
@@ -417,7 +417,8 @@ class GridIn
    * manifold_id for the same cell. Yet it is possible to use
    * the flag apply_all_indicators_to_manifolds to decide if
    * the indicators in the file refer to manifolds (flag set to true)
-   * or boundaries (flag set to false).
+   * or boundaries (flag set to false). If the flag is set, the
+   * indicators are used for cells as manifold id, too.
    */
   void
   read_ucd(std::istream &in,
diff --git a/source/grid/grid_in.cc b/source/grid/grid_in.cc
index ad18740f2849..28f2907258f8 100644
--- a/source/grid/grid_in.cc
+++ b/source/grid/grid_in.cc
@@ -834,6 +834,9 @@ GridIn::read_ucd(std::istream &in,
           Assert(material_id < numbers::invalid_material_id,
                  ExcIndexRange(material_id, 0, numbers::invalid_material_id));
 
+          if (apply_all_indicators_to_manifolds)
+            cells.back().manifold_id =
+              static_cast(material_id);
           cells.back().material_id =
             static_cast(material_id);
 
diff --git a/tests/grid/grid_in_ucd_02.cc b/tests/grid/grid_in_ucd_02.cc
new file mode 100644
index 000000000000..365849a14d3d
--- /dev/null
+++ b/tests/grid/grid_in_ucd_02.cc
@@ -0,0 +1,77 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2019 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+// Test that cell manifold ids are also set for the
+// "apply_all_indicators_to_manifolds" option in GridIn::read_ucd
+
+#include 
+
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+
+#include 
+#include 
+
+#include "../tests.h"
+
+template 
+void
+test(const std::string &filename)
+{
+  std::ifstream                tmp_in(filename);
+  Triangulation tria;
+  GridIn        gi;
+  gi.attach_triangulation(tria);
+  gi.read_ucd(tmp_in, true);
+  deallog << "Testing dim=" << dim << " spacedim=" << spacedim << std::endl;
+  for (const auto &cell : tria.active_cell_iterators())
+    {
+      deallog << "cell->manifold_id: " << cell->manifold_id() << std::endl;
+      if (dim > 1)
+        for (unsigned int face_no = 0;
+             face_no < GeometryInfo::faces_per_cell;
+             ++face_no)
+          deallog << "cell->face(" << face_no
+                  << ")->manifold_id: " << cell->face(face_no)->manifold_id()
+                  << std::endl;
+      if (dim > 1)
+        for (unsigned int line_no = 0;
+             line_no < GeometryInfo::lines_per_cell;
+             ++line_no)
+          deallog << "cell->line(" << line_no
+                  << ")->manifold_id: " << cell->line(line_no)->manifold_id()
+                  << std::endl;
+    }
+  deallog << std::endl;
+}
+
+int
+main()
+{
+  initlog();
+  deallog.get_file_stream() << std::setprecision(2);
+
+  test<1, 1>(SOURCE_DIR "/grid_in_ucd_02_grids/grid_1.inp");
+  test<1, 2>(SOURCE_DIR "/grid_in_ucd_02_grids/grid_1.inp");
+  test<1, 3>(SOURCE_DIR "/grid_in_ucd_02_grids/grid_1.inp");
+  test<2, 2>(SOURCE_DIR "/grid_in_ucd_02_grids/grid_2.inp");
+  test<2, 3>(SOURCE_DIR "/grid_in_ucd_02_grids/grid_2.inp");
+  test<3, 3>(SOURCE_DIR "/grid_in_ucd_02_grids/grid_3.inp");
+}
diff --git a/tests/grid/grid_in_ucd_02.output b/tests/grid/grid_in_ucd_02.output
new file mode 100644
index 000000000000..0c2306278d36
--- /dev/null
+++ b/tests/grid/grid_in_ucd_02.output
@@ -0,0 +1,53 @@
+
+DEAL::Testing dim=1 spacedim=1
+DEAL::cell->manifold_id: 99
+DEAL::
+DEAL::Testing dim=1 spacedim=2
+DEAL::cell->manifold_id: 99
+DEAL::
+DEAL::Testing dim=1 spacedim=3
+DEAL::cell->manifold_id: 99
+DEAL::
+DEAL::Testing dim=2 spacedim=2
+DEAL::cell->manifold_id: 99
+DEAL::cell->face(0)->manifold_id: 100
+DEAL::cell->face(1)->manifold_id: 100
+DEAL::cell->face(2)->manifold_id: 100
+DEAL::cell->face(3)->manifold_id: 100
+DEAL::cell->line(0)->manifold_id: 100
+DEAL::cell->line(1)->manifold_id: 100
+DEAL::cell->line(2)->manifold_id: 100
+DEAL::cell->line(3)->manifold_id: 100
+DEAL::
+DEAL::Testing dim=2 spacedim=3
+DEAL::cell->manifold_id: 99
+DEAL::cell->face(0)->manifold_id: 100
+DEAL::cell->face(1)->manifold_id: 100
+DEAL::cell->face(2)->manifold_id: 100
+DEAL::cell->face(3)->manifold_id: 100
+DEAL::cell->line(0)->manifold_id: 100
+DEAL::cell->line(1)->manifold_id: 100
+DEAL::cell->line(2)->manifold_id: 100
+DEAL::cell->line(3)->manifold_id: 100
+DEAL::
+DEAL::Testing dim=3 spacedim=3
+DEAL::cell->manifold_id: 99
+DEAL::cell->face(0)->manifold_id: 100
+DEAL::cell->face(1)->manifold_id: 100
+DEAL::cell->face(2)->manifold_id: 100
+DEAL::cell->face(3)->manifold_id: 100
+DEAL::cell->face(4)->manifold_id: 100
+DEAL::cell->face(5)->manifold_id: 100
+DEAL::cell->line(0)->manifold_id: 101
+DEAL::cell->line(1)->manifold_id: 101
+DEAL::cell->line(2)->manifold_id: 101
+DEAL::cell->line(3)->manifold_id: 101
+DEAL::cell->line(4)->manifold_id: 101
+DEAL::cell->line(5)->manifold_id: 101
+DEAL::cell->line(6)->manifold_id: 101
+DEAL::cell->line(7)->manifold_id: 101
+DEAL::cell->line(8)->manifold_id: 101
+DEAL::cell->line(9)->manifold_id: 101
+DEAL::cell->line(10)->manifold_id: 101
+DEAL::cell->line(11)->manifold_id: 101
+DEAL::
diff --git a/tests/grid/grid_in_ucd_02_grids/grid_1.inp b/tests/grid/grid_in_ucd_02_grids/grid_1.inp
new file mode 100644
index 000000000000..f6446ee5320a
--- /dev/null
+++ b/tests/grid/grid_in_ucd_02_grids/grid_1.inp
@@ -0,0 +1,4 @@
+2 1 0 0 0
+1  0 0 0
+2  1 0 0
+1 99 line    1 2 
diff --git a/tests/grid/grid_in_ucd_02_grids/grid_2.inp b/tests/grid/grid_in_ucd_02_grids/grid_2.inp
new file mode 100644
index 000000000000..41efaf5f68d1
--- /dev/null
+++ b/tests/grid/grid_in_ucd_02_grids/grid_2.inp
@@ -0,0 +1,11 @@
+4 5 0 0 0
+1  0 0 0
+2  1 0 0
+3  0 1 0
+4  1 1 0
+1 99 quad    1 2 4 3 
+2 100 line   1 2
+3 100 line   2 4
+4 100 line   4 3
+5 100 line   3 1
+
diff --git a/tests/grid/grid_in_ucd_02_grids/grid_3.inp b/tests/grid/grid_in_ucd_02_grids/grid_3.inp
new file mode 100644
index 000000000000..5218408f06a8
--- /dev/null
+++ b/tests/grid/grid_in_ucd_02_grids/grid_3.inp
@@ -0,0 +1,29 @@
+8 19 0 0 0
+1  0 0 0
+2  1 0 0
+3  0 1 0
+4  1 1 0
+5  0 0 1
+6  1 0 1
+7  0 1 1
+8  1 1 1
+1  99 hex     1 2 6 5 3 4 8 7 
+2  100 quad   1 2 4 3
+3  100 quad   5 6 8 7
+4  100 quad   1 2 6 5
+5  100 quad   3 4 8 7
+6  100 quad   1 3 7 5
+7  100 quad   2 4 8 6
+8  101 line   1 2
+9  101 line   2 4
+10 101 line   4 3
+11 101 line   3 1
+12 101 line   5 6
+13 101 line   6 8
+14 101 line   8 7
+15 101 line   7 5
+16 101 line   1 5
+17 101 line   2 6
+18 101 line   3 7
+19 101 line   4 8
+
diff --git a/tests/hp/step-5.cc b/tests/hp/step-5.cc
index 17d2393719a8..af23e503353f 100644
--- a/tests/hp/step-5.cc
+++ b/tests/hp/step-5.cc
@@ -306,7 +306,7 @@ LaplaceProblem::run()
           std::ifstream input_file(SOURCE_DIR "/grids/circle-grid.inp");
           Assert(dim == 2, ExcInternalError());
 
-          grid_in.read_ucd(input_file, true);
+          grid_in.read_ucd(input_file);
           GridTools::copy_boundary_to_manifold_id(triangulation);
 
           static const SphericalManifold boundary;

From 2ce8a65aa17fe34b799702c01ae95b92a73025f5 Mon Sep 17 00:00:00 2001
From: Daniel Arndt 
Date: Sat, 16 Mar 2019 13:50:01 +0100
Subject: [PATCH 274/507] Check SCALAPACK symbols

---
 cmake/configure/configure_scalapack.cmake | 38 +++++++++++++++++++++++
 1 file changed, 38 insertions(+)

diff --git a/cmake/configure/configure_scalapack.cmake b/cmake/configure/configure_scalapack.cmake
index 86ac09a3ab1a..273689bf1c28 100644
--- a/cmake/configure/configure_scalapack.cmake
+++ b/cmake/configure/configure_scalapack.cmake
@@ -26,6 +26,44 @@ MACRO(FEATURE_SCALAPACK_FIND_EXTERNAL var)
   IF(SCALAPACK_FOUND)
     SET(${var} TRUE)
     CHECK_MPI_INTERFACE(SCALAPACK ${var})
+
+    IF (${var})
+      CHECK_LIBRARY_EXISTS (${SCALAPACK_LIBRARY} pdsyevr_ {SCALAPACK_DIR} DEAL_II_SCALAPACK_HAS_PDSYEVR)
+      IF(NOT DEAL_II_SCALAPACK_HAS_PDSYEVR)
+        MESSAGE(STATUS "Could not find a sufficient SCALAPACK installation: "
+          "The required symbol pdsyevr_ was not found."
+          )
+        SET(SCALAPACK_ADDITIONAL_ERROR_STRING
+          ${SCALAPACK_ADDITIONAL_ERROR_STRING}
+          "Could not find a sufficient SCALAPACK installation: \n"
+          "SCALAPACK symbol check for pdsyevr_ failed! This usually means that "
+          "your SCALAPACK installation is incomplete or the link line is "
+          "broken. Consult\n"
+          "  CMakeFiles/CMakeError.log\n"
+          "for further information.\n"
+          )
+        SET(${var} FALSE)
+      ENDIF()
+    ENDIF()
+
+    IF(${var})
+      CHECK_LIBRARY_EXISTS (${SCALAPACK_LIBRARY} pssyevr_ {SCALAPACK_DIR} DEAL_II_SCALAPACK_HAS_PSSYEVR)
+      IF(NOT DEAL_II_SCALAPACK_HAS_PSSYEVR)
+        MESSAGE(STATUS "Could not find a sufficient SCALAPACK installation: "
+          "The required symbol pssyevr_ was not found."
+          )
+        SET(SCALAPACK_ADDITIONAL_ERROR_STRING
+          ${SCALAPACK_ADDITIONAL_ERROR_STRING}
+          "Could not find a sufficient SCALAPACK installation: \n"
+          "SCALAPACK symbol check for pssyevr_ failed! This usually means that "
+          "your SCALAPACK installation is incomplete or the link line is "
+          "broken. Consult\n"
+          "  CMakeFiles/CMakeError.log\n"
+          "for further information.\n"
+          )
+        SET(${var} FALSE)
+      ENDIF()
+    ENDIF()
   ENDIF()
 ENDMACRO()
 

From 8d8fb9c8388ff35237ba183cd2af698e20ac2ec2 Mon Sep 17 00:00:00 2001
From: Sebastian Stark 
Date: Fri, 22 Feb 2019 15:09:35 +0200
Subject: [PATCH 275/507] interpolate_to_different_mesh for hp::DoFHandler

Make interpolate_to_different_mesh work with hp::DoFHandler objects. Added also four tests for the implementation as well as the relevant instantiations.
---
 doc/news/changes/minor/20190316SebastianStark |    3 +
 .../deal.II/numerics/vector_tools.templates.h |   34 +-
 .../numerics/vector_tools_interpolate.inst.in |   23 +
 .../interpolate_to_different_mesh_01.cc       |  152 ++
 .../interpolate_to_different_mesh_01.output   | 1069 ++++++++
 .../interpolate_to_different_mesh_02.cc       |  164 ++
 .../interpolate_to_different_mesh_02.output   | 2173 +++++++++++++++++
 .../interpolate_to_different_mesh_03.cc       |  109 +
 .../interpolate_to_different_mesh_03.output   |   17 +
 .../interpolate_to_different_mesh_04.cc       |  133 +
 .../interpolate_to_different_mesh_04.output   |   25 +
 11 files changed, 3891 insertions(+), 11 deletions(-)
 create mode 100644 doc/news/changes/minor/20190316SebastianStark
 create mode 100644 tests/numerics/interpolate_to_different_mesh_01.cc
 create mode 100644 tests/numerics/interpolate_to_different_mesh_01.output
 create mode 100644 tests/numerics/interpolate_to_different_mesh_02.cc
 create mode 100644 tests/numerics/interpolate_to_different_mesh_02.output
 create mode 100644 tests/numerics/interpolate_to_different_mesh_03.cc
 create mode 100644 tests/numerics/interpolate_to_different_mesh_03.output
 create mode 100644 tests/numerics/interpolate_to_different_mesh_04.cc
 create mode 100644 tests/numerics/interpolate_to_different_mesh_04.output

diff --git a/doc/news/changes/minor/20190316SebastianStark b/doc/news/changes/minor/20190316SebastianStark
new file mode 100644
index 000000000000..8ee817eb59c3
--- /dev/null
+++ b/doc/news/changes/minor/20190316SebastianStark
@@ -0,0 +1,3 @@
+New: interpolate_to_different_mesh works now with hp::DoFHandler objects
+
    
+(Sebastian Stark, 2019/03/16)
diff --git a/include/deal.II/numerics/vector_tools.templates.h b/include/deal.II/numerics/vector_tools.templates.h
index 30e5fa5f1fe5..3b74b1b5cb30 100644
--- a/include/deal.II/numerics/vector_tools.templates.h
+++ b/include/deal.II/numerics/vector_tools.templates.h
@@ -812,7 +812,6 @@ namespace VectorTools
     }
   } // namespace internal
 
-
   template active() && !cell2->is_locally_owned())
           continue;
 
-        Assert(
-          cell1->get_fe().get_name() == cell2->get_fe().get_name(),
-          ExcMessage(
-            "Source and destination cells need to use the same finite element"));
-
-        cache.reinit(cell1->get_fe().dofs_per_cell);
-
         // Get and set the corresponding
         // dof_values by interpolation.
-        cell1->get_interpolated_dof_values(u1, cache);
-        cell2->set_dof_values_by_interpolation(cache, u2);
+        if (cell1->active())
+          {
+            cache.reinit(cell1->get_fe().dofs_per_cell);
+            cell1->get_interpolated_dof_values(u1,
+                                               cache,
+                                               cell1->active_fe_index());
+            cell2->set_dof_values_by_interpolation(cache,
+                                                   u2,
+                                                   cell1->active_fe_index());
+          }
+        else
+          {
+            cache.reinit(cell2->get_fe().dofs_per_cell);
+            cell1->get_interpolated_dof_values(u1,
+                                               cache,
+                                               cell2->active_fe_index());
+            cell2->set_dof_values_by_interpolation(cache,
+                                                   u2,
+                                                   cell2->active_fe_index());
+          }
       }
 
     // finish the work on parallel vectors
@@ -893,7 +906,6 @@ namespace VectorTools
     constraints.distribute(u2);
   }
 
-
   namespace internal
   {
     /**
diff --git a/source/numerics/vector_tools_interpolate.inst.in b/source/numerics/vector_tools_interpolate.inst.in
index 2fe1aba08087..7d08e95194c8 100644
--- a/source/numerics/vector_tools_interpolate.inst.in
+++ b/source/numerics/vector_tools_interpolate.inst.in
@@ -132,6 +132,29 @@ for (VEC : VECTOR_TYPES; deal_II_dimension : DIMENSIONS;
         const VEC &,
         const AffineConstraints &,
         VEC &);
+
+      template void
+      interpolate_to_different_mesh(
+        const hp::DoFHandler &,
+        const VEC &,
+        const hp::DoFHandler &,
+        VEC &);
+
+      template void
+      interpolate_to_different_mesh(
+        const hp::DoFHandler &,
+        const VEC &,
+        const hp::DoFHandler &,
+        const AffineConstraints &,
+        VEC &);
+
+      template void
+      interpolate_to_different_mesh(
+        const InterGridMap<
+          hp::DoFHandler> &,
+        const VEC &,
+        const AffineConstraints &,
+        VEC &);
     \}
 #endif
   }
diff --git a/tests/numerics/interpolate_to_different_mesh_01.cc b/tests/numerics/interpolate_to_different_mesh_01.cc
new file mode 100644
index 000000000000..08663a9041c8
--- /dev/null
+++ b/tests/numerics/interpolate_to_different_mesh_01.cc
@@ -0,0 +1,152 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2000 - 2018 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+// test for interpolate_to_different_mesh with dealii::DoFHandler
+
+#include 
+
+#include 
+
+#include 
+#include 
+
+#include 
+
+#include 
+
+#include 
+#include 
+
+#include "../tests.h"
+
+using namespace std;
+using namespace dealii;
+
+template 
+class F1 : public Function
+{
+public:
+  F1()
+    : Function()
+  {}
+  virtual double
+  value(const Point &p, const unsigned int component = 0) const
+  {
+    return p(0) * p(0);
+  }
+};
+
+template 
+void
+check(const unsigned int refinement_1, const unsigned int refinement_2)
+{
+  MappingQGeneric mapping(1);
+
+  Triangulation tria_1, tria_2;
+  GridGenerator::hyper_cube(tria_1);
+  GridGenerator::hyper_cube(tria_2);
+
+  tria_1.refine_global(refinement_1);
+  tria_2.refine_global(refinement_2);
+
+  DoFHandler dof_handler_1(tria_1);
+  DoFHandler dof_handler_2(tria_2);
+
+  FE_Q fe(1);
+  dof_handler_1.distribute_dofs(fe);
+  dof_handler_2.distribute_dofs(fe);
+
+  Vector u_1(dof_handler_1.n_dofs()), u_2(dof_handler_2.n_dofs());
+  F1   f_1;
+  VectorTools::interpolate(mapping, dof_handler_1, f_1, u_1);
+  VectorTools::interpolate_to_different_mesh(dof_handler_1,
+                                             u_1,
+                                             dof_handler_2,
+                                             u_2);
+
+  Point                 support_point, unit_support_point;
+  vector local_dof_indices(fe.n_dofs_per_cell());
+  deallog << "dof values of dof_handler_1:" << endl;
+  for (const auto &cell : dof_handler_1.active_cell_iterators())
+    {
+      cell->get_dof_indices(local_dof_indices);
+      for (unsigned int shapefun = 0;
+           shapefun < cell->get_fe().n_dofs_per_cell();
+           ++shapefun)
+        {
+          unit_support_point = cell->get_fe().unit_support_point(shapefun);
+          support_point =
+            mapping.transform_unit_to_real_cell(cell, unit_support_point);
+          deallog << " " << support_point << ":\n "
+                  << u_1[local_dof_indices[shapefun]] << endl
+                  << endl;
+        }
+    }
+  deallog << endl << "dof values of dof_handler_2:" << endl;
+  for (const auto &cell : dof_handler_2.active_cell_iterators())
+
+    {
+      cell->get_dof_indices(local_dof_indices);
+      for (unsigned int shapefun = 0;
+           shapefun < cell->get_fe().n_dofs_per_cell();
+           ++shapefun)
+        {
+          unit_support_point = cell->get_fe().unit_support_point(shapefun);
+          support_point =
+            mapping.transform_unit_to_real_cell(cell, unit_support_point);
+          deallog << " " << support_point << ":\n "
+                  << u_2[local_dof_indices[shapefun]] << endl
+                  << endl;
+        }
+    }
+}
+
+int
+main(int argc, char **argv)
+{
+  initlog();
+
+  Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1);
+
+  deallog
+    << "### 2D-Case, first cell refined once, second cell unrefined###\n\n";
+  check<2>(1, 0);
+  deallog << endl;
+
+  deallog
+    << "### 2D-Case, first cell unrefined, second cell refined once###\n\n";
+  check<2>(0, 1);
+  deallog << endl;
+
+  deallog
+    << "### 2D-Case, first cell refined once, second cell refined once###\n\n";
+  check<2>(1, 1);
+  deallog << endl;
+
+  deallog
+    << "### 3D-Case, first cell refined once, second cell unrefined###\n\n";
+  check<3>(1, 0);
+  deallog << endl;
+
+  deallog
+    << "### 3D-Case, first cell unrefined, second cell refined once###\n\n";
+  check<3>(0, 1);
+  deallog << endl;
+
+  deallog
+    << "### 3D-Case, first cell refined once, second cell refined once###\n\n";
+  check<3>(1, 1);
+  deallog << endl;
+}
diff --git a/tests/numerics/interpolate_to_different_mesh_01.output b/tests/numerics/interpolate_to_different_mesh_01.output
new file mode 100644
index 000000000000..e413654cda02
--- /dev/null
+++ b/tests/numerics/interpolate_to_different_mesh_01.output
@@ -0,0 +1,1069 @@
+
+DEAL::### 2D-Case, first cell refined once, second cell unrefined###
+
+dof values of dof_handler_1:
+DEAL:: 0.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL::
+DEAL::dof values of dof_handler_2:
+DEAL:: 0.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 1.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 1.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL::
+DEAL::### 2D-Case, first cell unrefined, second cell refined once###
+
+dof values of dof_handler_1:
+DEAL:: 0.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 1.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 1.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL::
+DEAL::dof values of dof_handler_2:
+DEAL:: 0.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000:
+ 0.500000
+DEAL::
+DEAL:: 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.500000
+DEAL::
+DEAL:: 0.500000 0.00000:
+ 0.500000
+DEAL::
+DEAL:: 1.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.500000
+DEAL::
+DEAL:: 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.500000
+DEAL::
+DEAL:: 0.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000:
+ 0.500000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.500000
+DEAL::
+DEAL:: 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000:
+ 0.500000
+DEAL::
+DEAL:: 1.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL::
+DEAL::### 2D-Case, first cell refined once, second cell refined once###
+
+dof values of dof_handler_1:
+DEAL:: 0.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL::
+DEAL::dof values of dof_handler_2:
+DEAL:: 0.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL::
+DEAL::### 3D-Case, first cell refined once, second cell unrefined###
+
+dof values of dof_handler_1:
+DEAL:: 0.00000 0.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.00000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 0.500000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.00000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL::
+DEAL::dof values of dof_handler_2:
+DEAL:: 0.00000 0.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 1.00000 0.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 1.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 1.00000 1.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 0.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 1.00000 0.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 1.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 1.00000 1.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL::
+DEAL::### 3D-Case, first cell unrefined, second cell refined once###
+
+dof values of dof_handler_1:
+DEAL:: 0.00000 0.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 1.00000 0.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 1.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 1.00000 1.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 0.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 1.00000 0.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 1.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 1.00000 1.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL::
+DEAL::dof values of dof_handler_2:
+DEAL:: 0.00000 0.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.00000:
+ 0.500000
+DEAL::
+DEAL:: 0.00000 0.500000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.500000
+DEAL::
+DEAL:: 0.00000 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.500000
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.500000
+DEAL::
+DEAL:: 0.500000 0.00000 0.00000:
+ 0.500000
+DEAL::
+DEAL:: 1.00000 0.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.500000
+DEAL::
+DEAL:: 1.00000 0.500000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.500000
+DEAL::
+DEAL:: 1.00000 0.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.500000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 0.500000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.500000
+DEAL::
+DEAL:: 0.00000 1.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.00000:
+ 0.500000
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.500000
+DEAL::
+DEAL:: 0.00000 1.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.500000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.500000
+DEAL::
+DEAL:: 1.00000 0.500000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.00000:
+ 0.500000
+DEAL::
+DEAL:: 1.00000 1.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.500000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.500000
+DEAL::
+DEAL:: 1.00000 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.500000
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.500000
+DEAL::
+DEAL:: 0.00000 0.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 1.00000:
+ 0.500000
+DEAL::
+DEAL:: 0.00000 0.500000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.500000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.500000
+DEAL::
+DEAL:: 1.00000 0.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.500000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.00000 1.00000:
+ 0.500000
+DEAL::
+DEAL:: 1.00000 0.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.500000
+DEAL::
+DEAL:: 1.00000 0.500000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.500000
+DEAL::
+DEAL:: 0.00000 1.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.500000
+DEAL::
+DEAL:: 0.00000 0.500000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.500000
+DEAL::
+DEAL:: 0.00000 1.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 1.00000:
+ 0.500000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.500000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.500000
+DEAL::
+DEAL:: 1.00000 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.500000
+DEAL::
+DEAL:: 1.00000 0.500000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 1.00000:
+ 0.500000
+DEAL::
+DEAL:: 1.00000 1.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL::
+DEAL::### 3D-Case, first cell refined once, second cell refined once###
+
+dof values of dof_handler_1:
+DEAL:: 0.00000 0.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.00000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 0.500000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.00000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL::
+DEAL::dof values of dof_handler_2:
+DEAL:: 0.00000 0.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.00000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 0.500000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.00000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL::
diff --git a/tests/numerics/interpolate_to_different_mesh_02.cc b/tests/numerics/interpolate_to_different_mesh_02.cc
new file mode 100644
index 000000000000..1d58e9a31849
--- /dev/null
+++ b/tests/numerics/interpolate_to_different_mesh_02.cc
@@ -0,0 +1,164 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2000 - 2018 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+// test for interpolate_to_different_mesh with dealii::hp::DoFHandler
+
+#include 
+
+#include 
+#include 
+
+#include 
+
+#include 
+#include 
+
+#include 
+
+#include 
+#include 
+
+#include "../tests.h"
+
+using namespace std;
+using namespace dealii;
+
+template 
+class F1 : public Function
+{
+public:
+  F1()
+    : Function()
+  {}
+  virtual double
+  value(const Point &p, const unsigned int component = 0) const
+  {
+    return p(0) * p(0);
+  }
+};
+
+template 
+void
+check(const unsigned int refinement_1, const unsigned int refinement_2)
+{
+  MappingQGeneric mapping(1);
+
+  Triangulation tria_1, tria_2;
+  GridGenerator::hyper_cube(tria_1);
+  GridGenerator::hyper_cube(tria_2);
+
+  tria_1.refine_global(refinement_1);
+  tria_2.refine_global(refinement_2);
+
+  hp::DoFHandler dof_handler_1(tria_1);
+  hp::DoFHandler dof_handler_2(tria_2);
+
+  hp::FECollection fe_collection;
+  fe_collection.push_back(FE_Q(2));
+  fe_collection.push_back(FE_Q(1));
+
+  for (const auto &cell : dof_handler_1.active_cell_iterators())
+    cell->set_active_fe_index(0);
+
+  for (const auto &cell : dof_handler_2.active_cell_iterators())
+    cell->set_active_fe_index(1);
+
+  dof_handler_1.distribute_dofs(fe_collection);
+  dof_handler_2.distribute_dofs(fe_collection);
+
+  Vector u_1(dof_handler_1.n_dofs()), u_2(dof_handler_2.n_dofs());
+  F1   f_1;
+  VectorTools::interpolate(mapping, dof_handler_1, f_1, u_1);
+  VectorTools::interpolate_to_different_mesh(dof_handler_1,
+                                             u_1,
+                                             dof_handler_2,
+                                             u_2);
+
+  Point                 support_point, unit_support_point;
+  vector local_dof_indices_1(
+    fe_collection[0].n_dofs_per_cell());
+  vector local_dof_indices_2(
+    fe_collection[1].n_dofs_per_cell());
+  deallog << "dof values of dof_handler_1:" << endl;
+  for (const auto &cell : dof_handler_1.active_cell_iterators())
+    {
+      cell->get_dof_indices(local_dof_indices_1);
+      for (unsigned int shapefun = 0;
+           shapefun < cell->get_fe().n_dofs_per_cell();
+           ++shapefun)
+        {
+          unit_support_point = cell->get_fe().unit_support_point(shapefun);
+          support_point =
+            mapping.transform_unit_to_real_cell(cell, unit_support_point);
+          deallog << " " << support_point << ":\n "
+                  << u_1[local_dof_indices_1[shapefun]] << endl
+                  << endl;
+        }
+    }
+  deallog << endl << "dof values of dof_handler_2:" << endl;
+  for (const auto &cell : dof_handler_2.active_cell_iterators())
+    {
+      cell->get_dof_indices(local_dof_indices_2);
+      for (unsigned int shapefun = 0;
+           shapefun < cell->get_fe().n_dofs_per_cell();
+           ++shapefun)
+        {
+          unit_support_point = cell->get_fe().unit_support_point(shapefun);
+          support_point =
+            mapping.transform_unit_to_real_cell(cell, unit_support_point);
+          deallog << " " << support_point << ":\n "
+                  << u_2[local_dof_indices_2[shapefun]] << endl
+                  << endl;
+        }
+    }
+}
+
+int
+main(int argc, char **argv)
+{
+  initlog();
+
+  Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1);
+
+  deallog
+    << "### 2D-Case, first cell refined once, second cell unrefined###\n\n";
+  check<2>(1, 0);
+  deallog << endl;
+
+  deallog
+    << "### 2D-Case, first cell unrefined, second cell refined once###\n\n";
+  check<2>(0, 1);
+  deallog << endl;
+
+  deallog
+    << "### 2D-Case, first cell refined once, second cell refined once###\n\n";
+  check<2>(1, 1);
+  deallog << endl;
+
+  deallog
+    << "### 3D-Case, first cell refined once, second cell unrefined###\n\n";
+  check<3>(1, 0);
+  deallog << endl;
+
+  deallog
+    << "### 3D-Case, first cell unrefined, second cell refined once###\n\n";
+  check<3>(0, 1);
+  deallog << endl;
+
+  deallog
+    << "### 3D-Case, first cell refined once, second cell refined once###\n\n";
+  check<3>(1, 1);
+  deallog << endl;
+}
diff --git a/tests/numerics/interpolate_to_different_mesh_02.output b/tests/numerics/interpolate_to_different_mesh_02.output
new file mode 100644
index 000000000000..cc4e6eab72ef
--- /dev/null
+++ b/tests/numerics/interpolate_to_different_mesh_02.output
@@ -0,0 +1,2173 @@
+
+DEAL::### 2D-Case, first cell refined once, second cell unrefined###
+
+dof values of dof_handler_1:
+DEAL:: 0.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.250000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.250000:
+ 0.250000
+DEAL::
+DEAL:: 0.250000 0.00000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.500000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.250000:
+ 0.0625000
+DEAL::
+DEAL:: 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.250000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.250000:
+ 1.00000
+DEAL::
+DEAL:: 0.750000 0.00000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.500000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.250000:
+ 0.562500
+DEAL::
+DEAL:: 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.750000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.750000:
+ 0.250000
+DEAL::
+DEAL:: 0.250000 0.500000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 1.00000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.750000:
+ 0.0625000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.750000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.750000:
+ 1.00000
+DEAL::
+DEAL:: 0.750000 0.500000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 1.00000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.750000:
+ 0.562500
+DEAL::
+DEAL::
+DEAL::dof values of dof_handler_2:
+DEAL:: 0.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 1.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 1.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL::
+DEAL::### 2D-Case, first cell unrefined, second cell refined once###
+
+dof values of dof_handler_1:
+DEAL:: 0.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 1.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 1.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL::
+DEAL::dof values of dof_handler_2:
+DEAL:: 0.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL::
+DEAL::### 2D-Case, first cell refined once, second cell refined once###
+
+dof values of dof_handler_1:
+DEAL:: 0.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.250000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.250000:
+ 0.250000
+DEAL::
+DEAL:: 0.250000 0.00000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.500000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.250000:
+ 0.0625000
+DEAL::
+DEAL:: 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.250000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.250000:
+ 1.00000
+DEAL::
+DEAL:: 0.750000 0.00000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.500000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.250000:
+ 0.562500
+DEAL::
+DEAL:: 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.750000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.750000:
+ 0.250000
+DEAL::
+DEAL:: 0.250000 0.500000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 1.00000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.750000:
+ 0.0625000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.750000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.750000:
+ 1.00000
+DEAL::
+DEAL:: 0.750000 0.500000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 1.00000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.750000:
+ 0.562500
+DEAL::
+DEAL::
+DEAL::dof values of dof_handler_2:
+DEAL:: 0.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL::
+DEAL::### 3D-Case, first cell refined once, second cell unrefined###
+
+dof values of dof_handler_1:
+DEAL:: 0.00000 0.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.250000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.250000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.250000 0.00000 0.00000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.500000 0.00000:
+ 0.0625000
+DEAL::
+DEAL:: 0.00000 0.250000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.250000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.250000 0.00000 0.500000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.500000 0.500000:
+ 0.0625000
+DEAL::
+DEAL:: 0.00000 0.00000 0.250000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.250000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.250000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.250000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.250000 0.250000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.250000 0.250000:
+ 0.250000
+DEAL::
+DEAL:: 0.250000 0.00000 0.250000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.500000 0.250000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.250000 0.00000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.250000 0.500000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.250000 0.250000:
+ 0.0625000
+DEAL::
+DEAL:: 0.500000 0.00000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.250000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.250000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.750000 0.00000 0.00000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.500000 0.00000:
+ 0.562500
+DEAL::
+DEAL:: 0.500000 0.250000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.250000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.750000 0.00000 0.500000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.500000 0.500000:
+ 0.562500
+DEAL::
+DEAL:: 0.500000 0.00000 0.250000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 0.250000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.250000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.250000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.250000 0.250000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.250000 0.250000:
+ 1.00000
+DEAL::
+DEAL:: 0.750000 0.00000 0.250000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.500000 0.250000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.250000 0.00000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.250000 0.500000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.250000 0.250000:
+ 0.562500
+DEAL::
+DEAL:: 0.00000 0.500000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.750000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.750000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.250000 0.500000 0.00000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 1.00000 0.00000:
+ 0.0625000
+DEAL::
+DEAL:: 0.00000 0.750000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.750000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.250000 0.500000 0.500000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 1.00000 0.500000:
+ 0.0625000
+DEAL::
+DEAL:: 0.00000 0.500000 0.250000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.250000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 0.250000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.250000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.750000 0.250000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.750000 0.250000:
+ 0.250000
+DEAL::
+DEAL:: 0.250000 0.500000 0.250000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 1.00000 0.250000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.750000 0.00000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.750000 0.500000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.750000 0.250000:
+ 0.0625000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.750000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.750000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.750000 0.500000 0.00000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 1.00000 0.00000:
+ 0.562500
+DEAL::
+DEAL:: 0.500000 0.750000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.750000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.750000 0.500000 0.500000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 1.00000 0.500000:
+ 0.562500
+DEAL::
+DEAL:: 0.500000 0.500000 0.250000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.250000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.250000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 0.250000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.750000 0.250000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.750000 0.250000:
+ 1.00000
+DEAL::
+DEAL:: 0.750000 0.500000 0.250000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 1.00000 0.250000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.750000 0.00000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.750000 0.500000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.750000 0.250000:
+ 0.562500
+DEAL::
+DEAL:: 0.00000 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.250000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.250000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.250000 0.00000 0.500000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.500000 0.500000:
+ 0.0625000
+DEAL::
+DEAL:: 0.00000 0.250000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.250000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.250000 0.00000 1.00000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.500000 1.00000:
+ 0.0625000
+DEAL::
+DEAL:: 0.00000 0.00000 0.750000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.750000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.750000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.750000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.250000 0.750000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.250000 0.750000:
+ 0.250000
+DEAL::
+DEAL:: 0.250000 0.00000 0.750000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.500000 0.750000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.250000 0.500000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.250000 1.00000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.250000 0.750000:
+ 0.0625000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.00000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.250000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.250000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.750000 0.00000 0.500000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.500000 0.500000:
+ 0.562500
+DEAL::
+DEAL:: 0.500000 0.250000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.250000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.750000 0.00000 1.00000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.500000 1.00000:
+ 0.562500
+DEAL::
+DEAL:: 0.500000 0.00000 0.750000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 0.750000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.750000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.750000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.250000 0.750000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.250000 0.750000:
+ 1.00000
+DEAL::
+DEAL:: 0.750000 0.00000 0.750000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.500000 0.750000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.250000 0.500000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.250000 1.00000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.250000 0.750000:
+ 0.562500
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.750000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.750000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.250000 0.500000 0.500000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 1.00000 0.500000:
+ 0.0625000
+DEAL::
+DEAL:: 0.00000 0.750000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.750000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.250000 0.500000 1.00000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 1.00000 1.00000:
+ 0.0625000
+DEAL::
+DEAL:: 0.00000 0.500000 0.750000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.750000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 0.750000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.750000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.750000 0.750000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.750000 0.750000:
+ 0.250000
+DEAL::
+DEAL:: 0.250000 0.500000 0.750000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 1.00000 0.750000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.750000 0.500000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.750000 1.00000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.750000 0.750000:
+ 0.0625000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.750000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.750000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.750000 0.500000 0.500000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 1.00000 0.500000:
+ 0.562500
+DEAL::
+DEAL:: 0.500000 0.750000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.750000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.750000 0.500000 1.00000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 1.00000 1.00000:
+ 0.562500
+DEAL::
+DEAL:: 0.500000 0.500000 0.750000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.750000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.750000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 0.750000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.750000 0.750000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.750000 0.750000:
+ 1.00000
+DEAL::
+DEAL:: 0.750000 0.500000 0.750000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 1.00000 0.750000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.750000 0.500000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.750000 1.00000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.750000 0.750000:
+ 0.562500
+DEAL::
+DEAL::
+DEAL::dof values of dof_handler_2:
+DEAL:: 0.00000 0.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 1.00000 0.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 1.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 1.00000 1.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 0.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 1.00000 0.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 1.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 1.00000 1.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL::
+DEAL::### 3D-Case, first cell unrefined, second cell refined once###
+
+dof values of dof_handler_1:
+DEAL:: 0.00000 0.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 1.00000 0.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 1.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 1.00000 1.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 0.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 1.00000 0.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 1.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 1.00000 1.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 0.500000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 1.00000 0.500000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 1.00000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 1.00000 0.500000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.00000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 1.00000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 1.00000 0.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 1.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 1.00000 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL::
+DEAL::dof values of dof_handler_2:
+DEAL:: 0.00000 0.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.00000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 0.500000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.00000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL::
+DEAL::### 3D-Case, first cell refined once, second cell refined once###
+
+dof values of dof_handler_1:
+DEAL:: 0.00000 0.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.250000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.250000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.250000 0.00000 0.00000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.500000 0.00000:
+ 0.0625000
+DEAL::
+DEAL:: 0.00000 0.250000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.250000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.250000 0.00000 0.500000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.500000 0.500000:
+ 0.0625000
+DEAL::
+DEAL:: 0.00000 0.00000 0.250000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.250000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.250000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.250000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.250000 0.250000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.250000 0.250000:
+ 0.250000
+DEAL::
+DEAL:: 0.250000 0.00000 0.250000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.500000 0.250000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.250000 0.00000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.250000 0.500000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.250000 0.250000:
+ 0.0625000
+DEAL::
+DEAL:: 0.500000 0.00000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.250000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.250000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.750000 0.00000 0.00000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.500000 0.00000:
+ 0.562500
+DEAL::
+DEAL:: 0.500000 0.250000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.250000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.750000 0.00000 0.500000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.500000 0.500000:
+ 0.562500
+DEAL::
+DEAL:: 0.500000 0.00000 0.250000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 0.250000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.250000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.250000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.250000 0.250000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.250000 0.250000:
+ 1.00000
+DEAL::
+DEAL:: 0.750000 0.00000 0.250000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.500000 0.250000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.250000 0.00000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.250000 0.500000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.250000 0.250000:
+ 0.562500
+DEAL::
+DEAL:: 0.00000 0.500000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.750000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.750000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.250000 0.500000 0.00000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 1.00000 0.00000:
+ 0.0625000
+DEAL::
+DEAL:: 0.00000 0.750000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.750000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.250000 0.500000 0.500000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 1.00000 0.500000:
+ 0.0625000
+DEAL::
+DEAL:: 0.00000 0.500000 0.250000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.250000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 0.250000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.250000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.750000 0.250000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.750000 0.250000:
+ 0.250000
+DEAL::
+DEAL:: 0.250000 0.500000 0.250000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 1.00000 0.250000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.750000 0.00000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.750000 0.500000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.750000 0.250000:
+ 0.0625000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.750000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.750000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.750000 0.500000 0.00000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 1.00000 0.00000:
+ 0.562500
+DEAL::
+DEAL:: 0.500000 0.750000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.750000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.750000 0.500000 0.500000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 1.00000 0.500000:
+ 0.562500
+DEAL::
+DEAL:: 0.500000 0.500000 0.250000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.250000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.250000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 0.250000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.750000 0.250000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.750000 0.250000:
+ 1.00000
+DEAL::
+DEAL:: 0.750000 0.500000 0.250000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 1.00000 0.250000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.750000 0.00000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.750000 0.500000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.750000 0.250000:
+ 0.562500
+DEAL::
+DEAL:: 0.00000 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.250000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.250000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.250000 0.00000 0.500000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.500000 0.500000:
+ 0.0625000
+DEAL::
+DEAL:: 0.00000 0.250000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.250000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.250000 0.00000 1.00000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.500000 1.00000:
+ 0.0625000
+DEAL::
+DEAL:: 0.00000 0.00000 0.750000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.750000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.750000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.750000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.250000 0.750000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.250000 0.750000:
+ 0.250000
+DEAL::
+DEAL:: 0.250000 0.00000 0.750000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.500000 0.750000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.250000 0.500000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.250000 1.00000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.250000 0.750000:
+ 0.0625000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.00000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.250000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.250000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.750000 0.00000 0.500000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.500000 0.500000:
+ 0.562500
+DEAL::
+DEAL:: 0.500000 0.250000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.250000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.750000 0.00000 1.00000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.500000 1.00000:
+ 0.562500
+DEAL::
+DEAL:: 0.500000 0.00000 0.750000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 0.750000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.750000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.750000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.250000 0.750000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.250000 0.750000:
+ 1.00000
+DEAL::
+DEAL:: 0.750000 0.00000 0.750000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.500000 0.750000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.250000 0.500000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.250000 1.00000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.250000 0.750000:
+ 0.562500
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.750000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.750000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.250000 0.500000 0.500000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 1.00000 0.500000:
+ 0.0625000
+DEAL::
+DEAL:: 0.00000 0.750000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.750000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.250000 0.500000 1.00000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 1.00000 1.00000:
+ 0.0625000
+DEAL::
+DEAL:: 0.00000 0.500000 0.750000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.750000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 0.750000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.750000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.750000 0.750000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.750000 0.750000:
+ 0.250000
+DEAL::
+DEAL:: 0.250000 0.500000 0.750000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 1.00000 0.750000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.750000 0.500000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.750000 1.00000:
+ 0.0625000
+DEAL::
+DEAL:: 0.250000 0.750000 0.750000:
+ 0.0625000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.750000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.750000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.750000 0.500000 0.500000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 1.00000 0.500000:
+ 0.562500
+DEAL::
+DEAL:: 0.500000 0.750000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.750000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.750000 0.500000 1.00000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 1.00000 1.00000:
+ 0.562500
+DEAL::
+DEAL:: 0.500000 0.500000 0.750000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.750000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.750000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 0.750000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.750000 0.750000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.750000 0.750000:
+ 1.00000
+DEAL::
+DEAL:: 0.750000 0.500000 0.750000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 1.00000 0.750000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.750000 0.500000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.750000 1.00000:
+ 0.562500
+DEAL::
+DEAL:: 0.750000 0.750000 0.750000:
+ 0.562500
+DEAL::
+DEAL::
+DEAL::dof values of dof_handler_2:
+DEAL:: 0.00000 0.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.00000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 0.500000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 0.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.500000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 0.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 0.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.00000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.00000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.00000 0.500000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 0.500000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 0.500000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.00000 1.00000 1.00000:
+ 0.00000
+DEAL::
+DEAL:: 0.500000 1.00000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 0.500000 0.500000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 0.500000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 0.500000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 0.500000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 0.500000 1.00000:
+ 1.00000
+DEAL::
+DEAL:: 0.500000 1.00000 1.00000:
+ 0.250000
+DEAL::
+DEAL:: 1.00000 1.00000 1.00000:
+ 1.00000
+DEAL::
+DEAL::
diff --git a/tests/numerics/interpolate_to_different_mesh_03.cc b/tests/numerics/interpolate_to_different_mesh_03.cc
new file mode 100644
index 000000000000..0d34358e6acb
--- /dev/null
+++ b/tests/numerics/interpolate_to_different_mesh_03.cc
@@ -0,0 +1,109 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2000 - 2018 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+// test for interpolate_to_different_mesh with dealii::DoFHandler
+// checks that interpolation from coarse to fine and back to coarse
+// is the identity operation
+
+#include 
+
+#include 
+
+#include 
+#include 
+
+#include 
+
+#include 
+
+#include 
+#include 
+#include 
+#include 
+
+#include "../tests.h"
+
+using namespace std;
+using namespace dealii;
+
+template 
+void
+check(const unsigned int refinement_1, const unsigned int refinement_2)
+{
+  MappingQGeneric mapping(1);
+
+  Triangulation tria_1, tria_2;
+  GridGenerator::hyper_cube(tria_1);
+  GridGenerator::hyper_cube(tria_2);
+
+  tria_1.refine_global(refinement_1);
+  tria_2.refine_global(refinement_2);
+
+  DoFHandler dof_handler_1(tria_1);
+  DoFHandler dof_handler_2(tria_2);
+
+  FE_Q fe(1);
+  dof_handler_1.distribute_dofs(fe);
+  dof_handler_2.distribute_dofs(fe);
+
+  Vector u_1(dof_handler_1.n_dofs()), u_2(dof_handler_2.n_dofs()),
+    u_1_back(dof_handler_1.n_dofs()), d(dof_handler_1.n_dofs());
+  for (unsigned int i1 = 0; i1 < u_1.size(); ++i1)
+    u_1[i1] = 2. * rand() / RAND_MAX - 1.;
+
+  VectorTools::interpolate_to_different_mesh(dof_handler_1,
+                                             u_1,
+                                             dof_handler_2,
+                                             u_2);
+
+  VectorTools::interpolate_to_different_mesh(dof_handler_2,
+                                             u_2,
+                                             dof_handler_1,
+                                             u_1_back);
+
+  d = u_1;
+  d.sadd(-1.0, u_1_back);
+  deallog << "distance=" << d.l2_norm() << endl;
+}
+
+int
+main(int argc, char **argv)
+{
+  initlog();
+
+  srand(static_cast(clock()));
+
+  Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1);
+
+  deallog
+    << "### 2D-Case, first cell unrefined, second cell refined once###\n\n";
+  check<2>(0, 1);
+  deallog << endl;
+
+  deallog
+    << "### 2D-Case, first cell refined once, second cell refined three times###\n\n";
+  check<2>(1, 3);
+  deallog << endl;
+
+  deallog
+    << "### 3D-Case, first cell unrefined, second cell refined once###\n\n";
+  check<3>(0, 1);
+  deallog << endl;
+
+  deallog
+    << "### 3D-Case, first cell refined once, second cell refined three times###\n\n";
+  check<3>(1, 3);
+  deallog << endl;
+}
diff --git a/tests/numerics/interpolate_to_different_mesh_03.output b/tests/numerics/interpolate_to_different_mesh_03.output
new file mode 100644
index 000000000000..9803fd2d684c
--- /dev/null
+++ b/tests/numerics/interpolate_to_different_mesh_03.output
@@ -0,0 +1,17 @@
+
+DEAL::### 2D-Case, first cell unrefined, second cell refined once###
+
+distance=0.00000
+DEAL::
+DEAL::### 2D-Case, first cell refined once, second cell refined three times###
+
+distance=0.00000
+DEAL::
+DEAL::### 3D-Case, first cell unrefined, second cell refined once###
+
+distance=0.00000
+DEAL::
+DEAL::### 3D-Case, first cell refined once, second cell refined three times###
+
+distance=0.00000
+DEAL::
diff --git a/tests/numerics/interpolate_to_different_mesh_04.cc b/tests/numerics/interpolate_to_different_mesh_04.cc
new file mode 100644
index 000000000000..f47e03980faf
--- /dev/null
+++ b/tests/numerics/interpolate_to_different_mesh_04.cc
@@ -0,0 +1,133 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2000 - 2018 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+// test for interpolate_to_different_mesh with dealii::hp::DoFHandler
+// checks that interpolation from coarse to fine and back to coarse
+// is the identity operation
+
+#include 
+
+#include 
+#include 
+
+#include 
+
+#include 
+#include 
+
+#include 
+
+#include 
+#include 
+#include 
+#include 
+
+#include "../tests.h"
+
+using namespace std;
+using namespace dealii;
+
+template 
+void
+check(const unsigned int refinement_1, const unsigned int refinement_2)
+{
+  MappingQGeneric mapping(1);
+
+  Triangulation tria_1, tria_2;
+  GridGenerator::hyper_cube(tria_1);
+  GridGenerator::hyper_cube(tria_2);
+
+  tria_1.refine_global(refinement_1);
+  tria_2.refine_global(refinement_2);
+
+  hp::DoFHandler dof_handler_1(tria_1);
+  hp::DoFHandler dof_handler_2(tria_2);
+
+  hp::FECollection fe_collection;
+  fe_collection.push_back(FE_Q(1));
+  fe_collection.push_back(FE_Q(2));
+
+  for (const auto &cell : dof_handler_1.active_cell_iterators())
+    cell->set_active_fe_index(0);
+
+  for (const auto &cell : dof_handler_2.active_cell_iterators())
+    cell->set_active_fe_index(1);
+
+  dof_handler_1.distribute_dofs(fe_collection);
+  dof_handler_2.distribute_dofs(fe_collection);
+
+  Vector u_1(dof_handler_1.n_dofs()), u_2(dof_handler_2.n_dofs()),
+    u_1_back(dof_handler_1.n_dofs()), d(dof_handler_1.n_dofs());
+  for (unsigned int i1 = 0; i1 < u_1.size(); ++i1)
+    u_1[i1] = 2. * rand() / RAND_MAX - 1.;
+
+  VectorTools::interpolate_to_different_mesh(dof_handler_1,
+                                             u_1,
+                                             dof_handler_2,
+                                             u_2);
+
+  VectorTools::interpolate_to_different_mesh(dof_handler_2,
+                                             u_2,
+                                             dof_handler_1,
+                                             u_1_back);
+
+  d = u_1;
+  d.sadd(-1.0, u_1_back);
+  deallog << "distance=" << d.l2_norm() << endl;
+}
+
+int
+main(int argc, char **argv)
+{
+  initlog();
+
+  srand(static_cast(clock()));
+
+  Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1);
+
+  deallog
+    << "### 2D-Case, first cell unrefined, second cell refined once###\n\n";
+  check<2>(0, 1);
+  deallog << endl;
+
+  deallog
+    << "### 2D-Case, first cell refined once, second cell refined three times###\n\n";
+  check<2>(1, 3);
+  deallog << endl;
+
+  // this should still be an identity operation although interpolation is from
+  // fine to coarse mesh because second mesh uses quadratic elements
+  deallog
+    << "### 2D-Case, first cell refined twice, second cell refined once###\n\n";
+  check<2>(2, 1);
+  deallog << endl;
+
+  deallog
+    << "### 3D-Case, first cell unrefined, second cell refined once###\n\n";
+  check<3>(0, 1);
+  deallog << endl;
+
+  deallog
+    << "### 3D-Case, first cell refined once, second cell refined three times###\n\n";
+  check<3>(1, 3);
+  deallog << endl;
+
+  // this should still be an identity operation although interpolation is from
+  // fine to coarse mesh because second mesh uses quadratic elements
+  deallog
+    << "### 3D-Case, first cell refined twice, second cell refined once###\n\n";
+  check<3>(2, 1);
+  deallog << endl;
+}
diff --git a/tests/numerics/interpolate_to_different_mesh_04.output b/tests/numerics/interpolate_to_different_mesh_04.output
new file mode 100644
index 000000000000..b199f69ae925
--- /dev/null
+++ b/tests/numerics/interpolate_to_different_mesh_04.output
@@ -0,0 +1,25 @@
+
+DEAL::### 2D-Case, first cell unrefined, second cell refined once###
+
+distance=0.00000
+DEAL::
+DEAL::### 2D-Case, first cell refined once, second cell refined three times###
+
+distance=0.00000
+DEAL::
+DEAL::### 2D-Case, first cell refined twice, second cell refined once###
+
+distance=0.00000
+DEAL::
+DEAL::### 3D-Case, first cell unrefined, second cell refined once###
+
+distance=0.00000
+DEAL::
+DEAL::### 3D-Case, first cell refined once, second cell refined three times###
+
+distance=0.00000
+DEAL::
+DEAL::### 3D-Case, first cell refined twice, second cell refined once###
+
+distance=0.00000
+DEAL::

From 4fb26ab50ad1adba87b052fd65f315239f326324 Mon Sep 17 00:00:00 2001
From: Jean-Paul Pelteret 
Date: Mon, 18 Mar 2019 12:51:55 +0100
Subject: [PATCH 276/507] Simplify setting of CMake SymEngine version variable

---
 cmake/modules/FindSYMENGINE.cmake | 5 ++---
 1 file changed, 2 insertions(+), 3 deletions(-)

diff --git a/cmake/modules/FindSYMENGINE.cmake b/cmake/modules/FindSYMENGINE.cmake
index b318dd5992fd..ad0624507365 100644
--- a/cmake/modules/FindSYMENGINE.cmake
+++ b/cmake/modules/FindSYMENGINE.cmake
@@ -84,9 +84,8 @@ IF(EXISTS ${SYMENGINE_SETTINGS_H})
   STRING(REGEX REPLACE "^.*SYMENGINE_PATCH_VERSION.*([0-9]+).*" "\\1"
     SYMENGINE_VERSION_PATCH "${SYMENGINE_VERSION_PATCH_STRING}"
     )
-  SET(SYMENGINE_VERSION
-    "${SYMENGINE_VERSION_MAJOR}.${SYMENGINE_VERSION_MINOR}.${SYMENGINE_VERSION_PATCH}"
-    )
+    
+  SET(SYMENGINE_VERSION ${SymEngine_VERSION})
 ENDIF()
 
 #

From 3dd93e4ca588c1876b3eb09e43b87eb3487702ab Mon Sep 17 00:00:00 2001
From: David Wells 
Date: Tue, 26 Feb 2019 20:58:14 -0500
Subject: [PATCH 277/507] Reflow comments.

---
 source/grid/grid_tools_dof_handlers.cc | 48 ++++++++------------------
 1 file changed, 15 insertions(+), 33 deletions(-)

diff --git a/source/grid/grid_tools_dof_handlers.cc b/source/grid/grid_tools_dof_handlers.cc
index 16012d59e543..208ece7de102 100644
--- a/source/grid/grid_tools_dof_handlers.cc
+++ b/source/grid/grid_tools_dof_handlers.cc
@@ -1136,20 +1136,12 @@ namespace GridTools
            ExcMessage("The two meshes must be represent triangulations that "
                       "have the same coarse meshes"));
 
-    // the algorithm goes as follows:
-    // first, we fill a list with pairs
-    // of iterators common to the two
-    // meshes on the coarsest
-    // level. then we traverse the
-    // list; each time, we find a pair
-    // of iterators for which both
-    // correspond to non-active cells,
-    // we delete this item and push the
-    // pairs of iterators to their
-    // children to the back. if these
-    // again both correspond to
-    // non-active cells, we will get to
-    // the later on for further
+    // the algorithm goes as follows: first, we fill a list with pairs of
+    // iterators common to the two meshes on the coarsest level. then we
+    // traverse the list; each time, we find a pair of iterators for which
+    // both correspond to non-active cells, we delete this item and push the
+    // pairs of iterators to their children to the back. if these again both
+    // correspond to non-active cells, we will get to the later on for further
     // consideration
     using CellList = std::list>;
@@ -1161,15 +1153,12 @@ namespace GridTools
     for (; cell_1 != mesh_1.end(0); ++cell_1, ++cell_2)
       cell_list.emplace_back(cell_1, cell_2);
 
-    // then traverse list as described
-    // above
+    // then traverse list as described above
     typename CellList::iterator cell_pair = cell_list.begin();
     while (cell_pair != cell_list.end())
       {
-        // if both cells in this pair
-        // have children, then erase
-        // this element and push their
-        // children instead
+        // if both cells in this pair have children, then erase this element
+        // and push their children instead
         if (cell_pair->first->has_children() &&
             cell_pair->second->has_children())
           {
@@ -1180,28 +1169,21 @@ namespace GridTools
               cell_list.emplace_back(cell_pair->first->child(c),
                                      cell_pair->second->child(c));
 
-            // erasing an iterator
-            // keeps other iterators
-            // valid, so already
-            // advance the present
-            // iterator by one and then
-            // delete the element we've
-            // visited before
+            // erasing an iterator keeps other iterators valid, so already
+            // advance the present iterator by one and then delete the element
+            // we've visited before
             const typename CellList::iterator previous_cell_pair = cell_pair;
             ++cell_pair;
 
             cell_list.erase(previous_cell_pair);
           }
         else
-          // both cells are active, do
-          // nothing
+          // both cells are active, do nothing
           ++cell_pair;
       }
 
-    // just to make sure everything is ok,
-    // validate that all pairs have at least one
-    // active iterator or have different
-    // refinement_cases
+    // just to make sure everything is ok, validate that all pairs have at
+    // least one active iterator or have different refinement_cases
     for (cell_pair = cell_list.begin(); cell_pair != cell_list.end();
          ++cell_pair)
       Assert(cell_pair->first->active() || cell_pair->second->active() ||

From 1ee851f4cbec17bb980c845ca415721d8598ec04 Mon Sep 17 00:00:00 2001
From: David Wells 
Date: Wed, 27 Feb 2019 17:13:25 -0500
Subject: [PATCH 278/507] Fix a bug in make_sparsity_pattern(dh, dh, sp).

This function relied GridTools::get_finest_common_cells which was
written before any of the parallel triangulations were implemented and
thus assumed that all cells without children were active. This commit
modifies that function to only return active cells that are also locally
owned, which fixes the sparsity pattern function.
---
 doc/news/changes/minor/20190304DavidWells     |   5 +
 include/deal.II/grid/grid_tools.h             |   5 +
 source/dofs/dof_tools_sparsity.cc             |  65 +++++--
 source/grid/grid_tools_dof_handlers.cc        |  45 ++++-
 tests/dofs/sparsity_pattern_06.cc             | 147 +++++++++++++++
 ...y_pattern_06.with_p4est=on.mpirun=1.output |  45 +++++
 ...y_pattern_06.with_p4est=on.mpirun=2.output |  59 +++++++
 tests/dofs/sparsity_pattern_07.cc             | 164 +++++++++++++++++
 .../dofs/sparsity_pattern_07.mpirun=1.output  |  45 +++++
 .../dofs/sparsity_pattern_07.mpirun=2.output  |  59 +++++++
 tests/grid/get_finest_common_cells_04.cc      | 104 +++++++++++
 ...n_cells_04.with_p4est=true.mpirun=1.output |  83 +++++++++
 ...n_cells_04.with_p4est=true.mpirun=2.output | 167 ++++++++++++++++++
 13 files changed, 976 insertions(+), 17 deletions(-)
 create mode 100644 doc/news/changes/minor/20190304DavidWells
 create mode 100644 tests/dofs/sparsity_pattern_06.cc
 create mode 100644 tests/dofs/sparsity_pattern_06.with_p4est=on.mpirun=1.output
 create mode 100644 tests/dofs/sparsity_pattern_06.with_p4est=on.mpirun=2.output
 create mode 100644 tests/dofs/sparsity_pattern_07.cc
 create mode 100644 tests/dofs/sparsity_pattern_07.mpirun=1.output
 create mode 100644 tests/dofs/sparsity_pattern_07.mpirun=2.output
 create mode 100644 tests/grid/get_finest_common_cells_04.cc
 create mode 100644 tests/grid/get_finest_common_cells_04.with_p4est=true.mpirun=1.output
 create mode 100644 tests/grid/get_finest_common_cells_04.with_p4est=true.mpirun=2.output

diff --git a/doc/news/changes/minor/20190304DavidWells b/doc/news/changes/minor/20190304DavidWells
new file mode 100644
index 000000000000..b0cd08c43a68
--- /dev/null
+++ b/doc/news/changes/minor/20190304DavidWells
@@ -0,0 +1,5 @@
+Fixed: the DoFTools::make_sparsity_pattern variant that takes, as arguments, two
+different DoFHandler objects now works correctly with
+parallel::shared::Triangulation and parallel::distributed::Triangulation.
+
    
+(David Wells, 2019/03/04)
diff --git a/include/deal.II/grid/grid_tools.h b/include/deal.II/grid/grid_tools.h
index 00e434cc3af2..df3711d54f44 100644
--- a/include/deal.II/grid/grid_tools.h
+++ b/include/deal.II/grid/grid_tools.h
@@ -2018,6 +2018,11 @@ namespace GridTools
    *
    * @tparam MeshType A type that satisfies the requirements of the
    * @ref ConceptMeshType "MeshType concept".
+   *
+   * @note This function can only be used with
+   * parallel::distributed::Triangulation when both meshes use the same
+   * Triangulation since, with a distributed Triangulation, not all cells are
+   * stored locally, so the resulting list may not cover the entire domain.
    */
   template 
   std::list
 #include 
 
+#include 
+#include 
+
 #include 
 #include 
 #include 
@@ -222,23 +225,59 @@ namespace DoFTools
     Assert(sparsity.n_cols() == n_dofs_col,
            ExcDimensionMismatch(sparsity.n_cols(), n_dofs_col));
 
-    // TODO: Looks like wasteful memory management here
-
-    const std::list>
-      cell_list = GridTools::get_finest_common_cells(dof_row, dof_col);
+    // It doesn't make sense to assemble sparsity patterns when the
+    // Triangulations are both parallel (i.e., different cells are assigned to
+    // different processors) and unequal: no processor will be responsible for
+    // assembling coupling terms between dofs on a cell owned by one processor
+    // and dofs on a cell owned by a different processor.
+    constexpr int dim      = DoFHandlerType::dimension;
+    constexpr int spacedim = DoFHandlerType::space_dimension;
+    if (dynamic_cast *>(
+          &dof_row.get_triangulation()) != nullptr ||
+        dynamic_cast *>(
+          &dof_col.get_triangulation()) != nullptr)
+      {
+        Assert(&dof_row.get_triangulation() == &dof_col.get_triangulation(),
+               ExcMessage("This function can only be used with with parallel "
+                          "Triangulations when the Triangulations are equal."));
+      }
 
+    // TODO: Looks like wasteful memory management here
 
-    typename std::list>::
-      const_iterator cell_iter = cell_list.begin();
+    using cell_iterator = typename DoFHandlerType::cell_iterator;
+    std::list> cell_list =
+      GridTools::get_finest_common_cells(dof_row, dof_col);
+
+#ifdef DEAL_II_WITH_MPI
+    // get_finest_common_cells returns all cells (locally owned and otherwise)
+    // for shared::Tria, but we don't want to assemble on cells that are not
+    // locally owned so remove them
+    if (dynamic_cast *>(
+          &dof_row.get_triangulation()) != nullptr ||
+        dynamic_cast *>(
+          &dof_col.get_triangulation()) != nullptr)
+      {
+        const types::subdomain_id this_subdomain_id =
+          dof_row.get_triangulation().locally_owned_subdomain();
+        Assert(this_subdomain_id ==
+                 dof_col.get_triangulation().locally_owned_subdomain(),
+               ExcInternalError());
+        cell_list.erase(
+          std::remove_if(
+            cell_list.begin(),
+            cell_list.end(),
+            [=](const std::pair &pair) {
+              return pair.first->subdomain_id() != this_subdomain_id ||
+                     pair.second->subdomain_id() != this_subdomain_id;
+            }),
+          cell_list.end());
+      }
+#endif
 
-    for (; cell_iter != cell_list.end(); ++cell_iter)
+    for (const auto &cell_pair : cell_list)
       {
-        const typename DoFHandlerType::cell_iterator cell_row =
-          cell_iter->first;
-        const typename DoFHandlerType::cell_iterator cell_col =
-          cell_iter->second;
+        const cell_iterator cell_row = cell_pair.first;
+        const cell_iterator cell_col = cell_pair.second;
 
         if (!cell_row->has_children() && !cell_col->has_children())
           {
diff --git a/source/grid/grid_tools_dof_handlers.cc b/source/grid/grid_tools_dof_handlers.cc
index 208ece7de102..ba09b68e1dca 100644
--- a/source/grid/grid_tools_dof_handlers.cc
+++ b/source/grid/grid_tools_dof_handlers.cc
@@ -1135,6 +1135,30 @@ namespace GridTools
     Assert(have_same_coarse_mesh(mesh_1, mesh_2),
            ExcMessage("The two meshes must be represent triangulations that "
                       "have the same coarse meshes"));
+    // We will allow the output to contain ghost cells when we have shared
+    // Triangulations (i.e., so that each processor will get exactly the same
+    // list of cell pairs), but not when we have two distributed
+    // Triangulations (so that all active cells are partitioned by processor).
+    // Non-parallel Triangulations have no ghost or artificial cells, so they
+    // work the same way as shared Triangulations here.
+    bool remove_ghost_cells = false;
+#ifdef DEAL_II_WITH_MPI
+    {
+      constexpr int dim      = MeshType::dimension;
+      constexpr int spacedim = MeshType::space_dimension;
+      if (dynamic_cast
+                         *>(&mesh_1.get_triangulation()) != nullptr ||
+          dynamic_cast
+                         *>(&mesh_2.get_triangulation()) != nullptr)
+        {
+          Assert(&mesh_1.get_triangulation() == &mesh_2.get_triangulation(),
+                 ExcMessage("This function can only be used with meshes "
+                            "corresponding to distributed Triangulations when "
+                            "both Triangulations are equal."));
+          remove_ghost_cells = true;
+        }
+    }
+#endif
 
     // the algorithm goes as follows: first, we fill a list with pairs of
     // iterators common to the two meshes on the coarsest level. then we
@@ -1172,14 +1196,27 @@ namespace GridTools
             // erasing an iterator keeps other iterators valid, so already
             // advance the present iterator by one and then delete the element
             // we've visited before
-            const typename CellList::iterator previous_cell_pair = cell_pair;
+            const auto previous_cell_pair = cell_pair;
             ++cell_pair;
-
             cell_list.erase(previous_cell_pair);
           }
         else
-          // both cells are active, do nothing
-          ++cell_pair;
+          {
+            // at least one cell is active
+            if (remove_ghost_cells &&
+                ((cell_pair->first->active() &&
+                  !cell_pair->first->is_locally_owned()) ||
+                 (cell_pair->second->active() &&
+                  !cell_pair->second->is_locally_owned())))
+              {
+                // we only exclude ghost cells for distributed Triangulations
+                const auto previous_cell_pair = cell_pair;
+                ++cell_pair;
+                cell_list.erase(previous_cell_pair);
+              }
+            else
+              ++cell_pair;
+          }
       }
 
     // just to make sure everything is ok, validate that all pairs have at
diff --git a/tests/dofs/sparsity_pattern_06.cc b/tests/dofs/sparsity_pattern_06.cc
new file mode 100644
index 000000000000..3a98472f1c14
--- /dev/null
+++ b/tests/dofs/sparsity_pattern_06.cc
@@ -0,0 +1,147 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2019 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+// Check that we can create a sparsity pattern from two DoFHandlers with the
+// same distributed mesh. This previously failed since the implementation
+// called a GridTools function that assumed all cells without children were
+// active (which is not the case for distributed meshes).
+
+#include 
+
+#include 
+#include 
+
+#include 
+#include 
+#include 
+
+#include 
+
+#include 
+#include 
+
+#include "../tests.h"
+
+
+int
+main(int argc, char **argv)
+{
+  Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1);
+
+  MPILogInitAll all;
+
+  parallel::distributed::Triangulation<2> triangulation(MPI_COMM_WORLD);
+  GridGenerator::subdivided_hyper_rectangle(triangulation,
+                                            {4u, 1u},
+                                            {0.0, 0.0},
+                                            {4.0, 1.0});
+  triangulation.refine_global(1);
+  deallog << "global number of active cells: "
+          << triangulation.n_global_active_cells() << std::endl;
+  deallog << "local number of active cells: " << triangulation.n_active_cells()
+          << std::endl;
+  deallog << "number of locally owned active cells: "
+          << triangulation.n_locally_owned_active_cells() << std::endl;
+
+  FE_DGQ<2>     fe_0(0);
+  DoFHandler<2> dof_handler_0;
+  FE_Q<2>       fe_1(1);
+  DoFHandler<2> dof_handler_1;
+  dof_handler_0.initialize(triangulation, fe_0);
+  dof_handler_1.initialize(triangulation, fe_1);
+
+  IndexSet locally_relevant_dofs_0;
+  IndexSet locally_relevant_dofs_1;
+  DoFTools::extract_locally_relevant_dofs(dof_handler_0,
+                                          locally_relevant_dofs_0);
+  DoFTools::extract_locally_relevant_dofs(dof_handler_1,
+                                          locally_relevant_dofs_1);
+  deallog << "locally owned dofs 0: ";
+  dof_handler_0.locally_owned_dofs().print(deallog);
+  deallog << std::endl;
+  deallog << "locally owned dofs 1: ";
+  dof_handler_1.locally_owned_dofs().print(deallog);
+  deallog << std::endl;
+  deallog << "locally relevant dofs 0: ";
+  locally_relevant_dofs_0.print(deallog);
+  deallog << std::endl;
+  deallog << "locally relevant dofs 1: ";
+  locally_relevant_dofs_1.print(deallog);
+  deallog << std::endl;
+
+#if 0 // reenable this to see where the DoFs are
+  MappingCartesian<2> mapping;
+  {
+    deallog << "support points of dofs 0:" << std::endl;
+    std::vector cell_dofs(fe_0.dofs_per_cell);
+    std::size_t cell_n = 0;
+    for (const auto &cell : dof_handler_0.active_cell_iterators())
+      {
+        if (cell->is_locally_owned())
+          {
+            deallog << "cell_n = " << cell_n << std::endl;
+            const std::vector> &support_points = fe_0.get_unit_support_points();
+            cell->get_dof_indices(cell_dofs);
+            for (std::size_t dof_n = 0; dof_n < fe_0.dofs_per_cell; ++dof_n)
+              {
+                deallog << "dof " << std::setw(2) << cell_dofs[dof_n] << ": "
+                        << mapping.transform_unit_to_real_cell(cell, support_points[dof_n])
+                        << std::endl;
+              }
+            ++cell_n;
+          }
+      }
+  }
+
+  {
+    deallog << "support points of dofs 1:" << std::endl;
+    std::vector cell_dofs(fe_1.dofs_per_cell);
+    std::size_t cell_n = 0;
+    for (const auto &cell : dof_handler_1.active_cell_iterators())
+      {
+        if (cell->is_locally_owned())
+          {
+            deallog << "cell_n = " << cell_n << std::endl;
+            const std::vector> &support_points = fe_1.get_unit_support_points();
+            cell->get_dof_indices(cell_dofs);
+            for (std::size_t dof_n = 0; dof_n < fe_1.dofs_per_cell; ++dof_n)
+              {
+                deallog << "dof " << std::setw(2) << cell_dofs[dof_n] << ": "
+                        << mapping.transform_unit_to_real_cell(cell, support_points[dof_n])
+                        << std::endl;
+              }
+            ++cell_n;
+          }
+      }
+  }
+#endif
+
+  DynamicSparsityPattern dynamic_sparsity_pattern(
+    dof_handler_0.locally_owned_dofs().size(),
+    dof_handler_1.locally_owned_dofs().size(),
+    dof_handler_0.locally_owned_dofs());
+  DoFTools::make_sparsity_pattern(dof_handler_0,
+                                  dof_handler_1,
+                                  dynamic_sparsity_pattern);
+  dynamic_sparsity_pattern.print(deallog.get_file_stream());
+  SparsityTools::distribute_sparsity_pattern(
+    dynamic_sparsity_pattern,
+    dof_handler_0.n_locally_owned_dofs_per_processor(),
+    MPI_COMM_WORLD,
+    dof_handler_0.locally_owned_dofs());
+  dynamic_sparsity_pattern.print(deallog.get_file_stream());
+
+  deallog << "OK" << std::endl;
+}
diff --git a/tests/dofs/sparsity_pattern_06.with_p4est=on.mpirun=1.output b/tests/dofs/sparsity_pattern_06.with_p4est=on.mpirun=1.output
new file mode 100644
index 000000000000..64245124db23
--- /dev/null
+++ b/tests/dofs/sparsity_pattern_06.with_p4est=on.mpirun=1.output
@@ -0,0 +1,45 @@
+
+DEAL:0::global number of active cells: 16
+DEAL:0::local number of active cells: 16
+DEAL:0::number of locally owned active cells: 16
+DEAL:0::locally owned dofs 0: {[0,15]}
+DEAL:0::
+DEAL:0::locally owned dofs 1: {[0,26]}
+DEAL:0::
+DEAL:0::locally relevant dofs 0: {[0,15]}
+DEAL:0::
+DEAL:0::locally relevant dofs 1: {[0,26]}
+DEAL:0::
+[0,0,1,2,3]
+[1,1,3,4,5]
+[2,2,3,6,7]
+[3,3,5,7,8]
+[4,4,5,9,10]
+[5,9,10,11,12]
+[6,5,8,10,13]
+[7,10,12,13,14]
+[8,11,12,15,16]
+[9,15,16,17,18]
+[10,12,14,16,19]
+[11,16,18,19,20]
+[12,17,18,21,22]
+[13,21,22,23,24]
+[14,18,20,22,25]
+[15,22,24,25,26]
+[0,0,1,2,3]
+[1,1,3,4,5]
+[2,2,3,6,7]
+[3,3,5,7,8]
+[4,4,5,9,10]
+[5,9,10,11,12]
+[6,5,8,10,13]
+[7,10,12,13,14]
+[8,11,12,15,16]
+[9,15,16,17,18]
+[10,12,14,16,19]
+[11,16,18,19,20]
+[12,17,18,21,22]
+[13,21,22,23,24]
+[14,18,20,22,25]
+[15,22,24,25,26]
+DEAL:0::OK
diff --git a/tests/dofs/sparsity_pattern_06.with_p4est=on.mpirun=2.output b/tests/dofs/sparsity_pattern_06.with_p4est=on.mpirun=2.output
new file mode 100644
index 000000000000..f715e4d77498
--- /dev/null
+++ b/tests/dofs/sparsity_pattern_06.with_p4est=on.mpirun=2.output
@@ -0,0 +1,59 @@
+
+DEAL:0::global number of active cells: 16
+DEAL:0::local number of active cells: 13
+DEAL:0::number of locally owned active cells: 8
+DEAL:0::locally owned dofs 0: {[0,7]}
+DEAL:0::
+DEAL:0::locally owned dofs 1: {[0,14]}
+DEAL:0::
+DEAL:0::locally relevant dofs 0: {[0,8], 10}
+DEAL:0::
+DEAL:0::locally relevant dofs 1: {[0,16], 19}
+DEAL:0::
+[0,0,1,2,3]
+[1,1,3,4,5]
+[2,2,3,6,7]
+[3,3,5,7,8]
+[4,4,5,9,10]
+[5,9,10,11,12]
+[6,5,8,10,13]
+[7,10,12,13,14]
+[0,0,1,2,3]
+[1,1,3,4,5]
+[2,2,3,6,7]
+[3,3,5,7,8]
+[4,4,5,9,10]
+[5,9,10,11,12]
+[6,5,8,10,13]
+[7,10,12,13,14]
+DEAL:0::OK
+
+DEAL:1::global number of active cells: 16
+DEAL:1::local number of active cells: 13
+DEAL:1::number of locally owned active cells: 8
+DEAL:1::locally owned dofs 0: {[8,15]}
+DEAL:1::
+DEAL:1::locally owned dofs 1: {[15,26]}
+DEAL:1::
+DEAL:1::locally relevant dofs 0: {5, [7,15]}
+DEAL:1::
+DEAL:1::locally relevant dofs 1: {[9,26]}
+DEAL:1::
+[8,11,12,15,16]
+[9,15,16,17,18]
+[10,12,14,16,19]
+[11,16,18,19,20]
+[12,17,18,21,22]
+[13,21,22,23,24]
+[14,18,20,22,25]
+[15,22,24,25,26]
+[8,11,12,15,16]
+[9,15,16,17,18]
+[10,12,14,16,19]
+[11,16,18,19,20]
+[12,17,18,21,22]
+[13,21,22,23,24]
+[14,18,20,22,25]
+[15,22,24,25,26]
+DEAL:1::OK
+
diff --git a/tests/dofs/sparsity_pattern_07.cc b/tests/dofs/sparsity_pattern_07.cc
new file mode 100644
index 000000000000..53d154bf20f9
--- /dev/null
+++ b/tests/dofs/sparsity_pattern_07.cc
@@ -0,0 +1,164 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2019 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+// Check that we can create a sparsity pattern from two DoFHandlers with the
+// same parallel mesh. This previously failed since the implementation
+// called a GridTools function that assumed all cells without children were
+// active (which is not the case for distributed meshes).
+//
+// This is the same as sparsity_pattern_06 but checks with a shared
+// triangulation instead of a distributed one.
+
+#include 
+
+#include 
+#include 
+
+#include 
+#include 
+#include 
+
+#include 
+
+#include 
+#include 
+
+#include "../tests.h"
+
+
+int
+main(int argc, char **argv)
+{
+  Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1);
+
+  MPILogInitAll all;
+
+  parallel::shared::Triangulation<2> triangulation(MPI_COMM_WORLD);
+  GridGenerator::subdivided_hyper_rectangle(triangulation,
+                                            {4u, 1u},
+                                            {0.0, 0.0},
+                                            {4.0, 1.0});
+  triangulation.refine_global(1);
+  const unsigned int n_processes =
+    Utilities::MPI::n_mpi_processes(MPI_COMM_WORLD);
+  Assert(n_processes == 1 || n_processes == 2, ExcInternalError());
+  if (n_processes == 2)
+    {
+      for (auto &cell : triangulation.active_cell_iterators())
+        {
+          if (cell->center()[0] < 2.0)
+            cell->set_subdomain_id(0);
+          else
+            cell->set_subdomain_id(1);
+        }
+    }
+
+  deallog << "global number of active cells: "
+          << triangulation.n_global_active_cells() << std::endl;
+  deallog << "local number of active cells: " << triangulation.n_active_cells()
+          << std::endl;
+  deallog << "number of locally owned active cells: "
+          << triangulation.n_locally_owned_active_cells() << std::endl;
+
+  FE_DGQ<2>     fe_0(0);
+  DoFHandler<2> dof_handler_0;
+  FE_Q<2>       fe_1(1);
+  DoFHandler<2> dof_handler_1;
+  dof_handler_0.initialize(triangulation, fe_0);
+  dof_handler_1.initialize(triangulation, fe_1);
+
+  IndexSet locally_relevant_dofs_0;
+  IndexSet locally_relevant_dofs_1;
+  DoFTools::extract_locally_relevant_dofs(dof_handler_0,
+                                          locally_relevant_dofs_0);
+  DoFTools::extract_locally_relevant_dofs(dof_handler_1,
+                                          locally_relevant_dofs_1);
+  deallog << "locally owned dofs 0: ";
+  dof_handler_0.locally_owned_dofs().print(deallog);
+  deallog << std::endl;
+  deallog << "locally owned dofs 1: ";
+  dof_handler_1.locally_owned_dofs().print(deallog);
+  deallog << std::endl;
+  deallog << "locally relevant dofs 0: ";
+  locally_relevant_dofs_0.print(deallog);
+  deallog << std::endl;
+  deallog << "locally relevant dofs 1: ";
+  locally_relevant_dofs_1.print(deallog);
+  deallog << std::endl;
+
+#if 0 // reenable this to see where the DoFs are
+  MappingCartesian<2> mapping;
+  {
+    deallog << "support points of dofs 0:" << std::endl;
+    std::vector cell_dofs(fe_0.dofs_per_cell);
+    std::size_t cell_n = 0;
+    for (const auto &cell : dof_handler_0.active_cell_iterators())
+      {
+        if (cell->is_locally_owned())
+          {
+            deallog << "cell_n = " << cell_n << std::endl;
+            const std::vector> &support_points = fe_0.get_unit_support_points();
+            cell->get_dof_indices(cell_dofs);
+            for (std::size_t dof_n = 0; dof_n < fe_0.dofs_per_cell; ++dof_n)
+              {
+                deallog << "dof " << std::setw(2) << cell_dofs[dof_n] << ": "
+                        << mapping.transform_unit_to_real_cell(cell, support_points[dof_n])
+                        << std::endl;
+              }
+            ++cell_n;
+          }
+      }
+  }
+
+  {
+    deallog << "support points of dofs 1:" << std::endl;
+    std::vector cell_dofs(fe_1.dofs_per_cell);
+    std::size_t cell_n = 0;
+    for (const auto &cell : dof_handler_1.active_cell_iterators())
+      {
+        if (cell->is_locally_owned())
+          {
+            deallog << "cell_n = " << cell_n << std::endl;
+            const std::vector> &support_points = fe_1.get_unit_support_points();
+            cell->get_dof_indices(cell_dofs);
+            for (std::size_t dof_n = 0; dof_n < fe_1.dofs_per_cell; ++dof_n)
+              {
+                deallog << "dof " << std::setw(2) << cell_dofs[dof_n] << ": "
+                        << mapping.transform_unit_to_real_cell(cell, support_points[dof_n])
+                        << std::endl;
+              }
+            ++cell_n;
+          }
+      }
+  }
+#endif
+
+  DynamicSparsityPattern dynamic_sparsity_pattern(
+    dof_handler_0.locally_owned_dofs().size(),
+    dof_handler_1.locally_owned_dofs().size(),
+    dof_handler_0.locally_owned_dofs());
+  DoFTools::make_sparsity_pattern(dof_handler_0,
+                                  dof_handler_1,
+                                  dynamic_sparsity_pattern);
+  dynamic_sparsity_pattern.print(deallog.get_file_stream());
+  SparsityTools::distribute_sparsity_pattern(
+    dynamic_sparsity_pattern,
+    dof_handler_0.n_locally_owned_dofs_per_processor(),
+    MPI_COMM_WORLD,
+    dof_handler_0.locally_owned_dofs());
+  dynamic_sparsity_pattern.print(deallog.get_file_stream());
+
+  deallog << "OK" << std::endl;
+}
diff --git a/tests/dofs/sparsity_pattern_07.mpirun=1.output b/tests/dofs/sparsity_pattern_07.mpirun=1.output
new file mode 100644
index 000000000000..64245124db23
--- /dev/null
+++ b/tests/dofs/sparsity_pattern_07.mpirun=1.output
@@ -0,0 +1,45 @@
+
+DEAL:0::global number of active cells: 16
+DEAL:0::local number of active cells: 16
+DEAL:0::number of locally owned active cells: 16
+DEAL:0::locally owned dofs 0: {[0,15]}
+DEAL:0::
+DEAL:0::locally owned dofs 1: {[0,26]}
+DEAL:0::
+DEAL:0::locally relevant dofs 0: {[0,15]}
+DEAL:0::
+DEAL:0::locally relevant dofs 1: {[0,26]}
+DEAL:0::
+[0,0,1,2,3]
+[1,1,3,4,5]
+[2,2,3,6,7]
+[3,3,5,7,8]
+[4,4,5,9,10]
+[5,9,10,11,12]
+[6,5,8,10,13]
+[7,10,12,13,14]
+[8,11,12,15,16]
+[9,15,16,17,18]
+[10,12,14,16,19]
+[11,16,18,19,20]
+[12,17,18,21,22]
+[13,21,22,23,24]
+[14,18,20,22,25]
+[15,22,24,25,26]
+[0,0,1,2,3]
+[1,1,3,4,5]
+[2,2,3,6,7]
+[3,3,5,7,8]
+[4,4,5,9,10]
+[5,9,10,11,12]
+[6,5,8,10,13]
+[7,10,12,13,14]
+[8,11,12,15,16]
+[9,15,16,17,18]
+[10,12,14,16,19]
+[11,16,18,19,20]
+[12,17,18,21,22]
+[13,21,22,23,24]
+[14,18,20,22,25]
+[15,22,24,25,26]
+DEAL:0::OK
diff --git a/tests/dofs/sparsity_pattern_07.mpirun=2.output b/tests/dofs/sparsity_pattern_07.mpirun=2.output
new file mode 100644
index 000000000000..3138fa982231
--- /dev/null
+++ b/tests/dofs/sparsity_pattern_07.mpirun=2.output
@@ -0,0 +1,59 @@
+
+DEAL:0::global number of active cells: 16
+DEAL:0::local number of active cells: 16
+DEAL:0::number of locally owned active cells: 8
+DEAL:0::locally owned dofs 0: {[0,7]}
+DEAL:0::
+DEAL:0::locally owned dofs 1: {[0,14]}
+DEAL:0::
+DEAL:0::locally relevant dofs 0: {[0,15]}
+DEAL:0::
+DEAL:0::locally relevant dofs 1: {[0,26]}
+DEAL:0::
+[0,0,1,2,3]
+[1,1,3,4,5]
+[2,2,3,6,7]
+[3,3,5,7,8]
+[4,4,5,9,10]
+[5,9,10,11,12]
+[6,5,8,10,13]
+[7,10,12,13,14]
+[0,0,1,2,3]
+[1,1,3,4,5]
+[2,2,3,6,7]
+[3,3,5,7,8]
+[4,4,5,9,10]
+[5,9,10,11,12]
+[6,5,8,10,13]
+[7,10,12,13,14]
+DEAL:0::OK
+
+DEAL:1::global number of active cells: 16
+DEAL:1::local number of active cells: 16
+DEAL:1::number of locally owned active cells: 8
+DEAL:1::locally owned dofs 0: {[8,15]}
+DEAL:1::
+DEAL:1::locally owned dofs 1: {[15,26]}
+DEAL:1::
+DEAL:1::locally relevant dofs 0: {[0,15]}
+DEAL:1::
+DEAL:1::locally relevant dofs 1: {[0,26]}
+DEAL:1::
+[8,11,12,15,16]
+[9,15,16,17,18]
+[10,12,14,16,19]
+[11,16,18,19,20]
+[12,17,18,21,22]
+[13,21,22,23,24]
+[14,18,20,22,25]
+[15,22,24,25,26]
+[8,11,12,15,16]
+[9,15,16,17,18]
+[10,12,14,16,19]
+[11,16,18,19,20]
+[12,17,18,21,22]
+[13,21,22,23,24]
+[14,18,20,22,25]
+[15,22,24,25,26]
+DEAL:1::OK
+
diff --git a/tests/grid/get_finest_common_cells_04.cc b/tests/grid/get_finest_common_cells_04.cc
new file mode 100644
index 000000000000..cab08b18c555
--- /dev/null
+++ b/tests/grid/get_finest_common_cells_04.cc
@@ -0,0 +1,104 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2006 - 2019 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+#include 
+
+#include 
+
+#include 
+#include 
+#include 
+
+#include "../tests.h"
+
+
+
+template 
+void
+test()
+{
+  // create 2 triangulations with the
+  // same coarse grid, and refine
+  // them differently
+  parallel::shared::Triangulation tria_0(MPI_COMM_WORLD);
+  parallel::shared::Triangulation tria_1(MPI_COMM_WORLD);
+  GridGenerator::hyper_cube(tria_0);
+  GridGenerator::hyper_cube(tria_1);
+
+  tria_0.refine_global(2);
+  tria_1.refine_global(2);
+
+  tria_0.begin_active()->set_refine_flag();
+  tria_0.execute_coarsening_and_refinement();
+
+  tria_1.last_active()->set_refine_flag();
+  tria_1.execute_coarsening_and_refinement();
+
+  tria_1.last_active()->set_refine_flag();
+  tria_1.execute_coarsening_and_refinement();
+
+#if 0 // turn this block back on to get plots of grids and locally owned cells
+  if (dim == 2)
+    {
+      std::string tria_0_out =
+        "tria-0-" + std::to_string(Utilities::MPI::this_mpi_process(MPI_COMM_WORLD)) + ".svg";
+      std::ofstream tria_0_out_stream(tria_0_out);
+      std::string tria_1_out =
+        "tria-1-" + std::to_string(Utilities::MPI::this_mpi_process(MPI_COMM_WORLD)) + ".svg";
+      std::ofstream tria_1_out_stream(tria_1_out);
+      GridOut().write_svg(tria_0, tria_0_out_stream);
+      GridOut().write_svg(tria_1, tria_1_out_stream);
+    }
+
+  deallog << "tria 0 cells:" << std::endl;
+  for (const auto &cell : tria_0.active_cell_iterators())
+    {
+      if (cell->is_locally_owned())
+        deallog << cell << std::endl;
+    }
+
+  deallog << "tria 1 cells:" << std::endl;
+  for (const auto &cell : tria_1.active_cell_iterators())
+    {
+      if (cell->is_locally_owned())
+        deallog << cell << std::endl;
+    }
+#endif
+
+  typedef std::list::cell_iterator,
+                              typename Triangulation::cell_iterator>>
+    CellList;
+
+  deallog << "number of locally owned cells in tria 0 and tria 1: "
+          << tria_0.n_active_cells() << ' ' << tria_1.n_active_cells()
+          << std::endl;
+  const CellList cell_list = GridTools::get_finest_common_cells(tria_0, tria_1);
+  for (typename CellList::const_iterator cell_pair = cell_list.begin();
+       cell_pair != cell_list.end();
+       ++cell_pair)
+    deallog << cell_pair->first << ' ' << cell_pair->second << std::endl;
+}
+
+
+int
+main(int argc, char **argv)
+{
+  Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1);
+
+  MPILogInitAll all;
+
+  test<2>();
+  test<3>();
+}
diff --git a/tests/grid/get_finest_common_cells_04.with_p4est=true.mpirun=1.output b/tests/grid/get_finest_common_cells_04.with_p4est=true.mpirun=1.output
new file mode 100644
index 000000000000..993a4a6e7c11
--- /dev/null
+++ b/tests/grid/get_finest_common_cells_04.with_p4est=true.mpirun=1.output
@@ -0,0 +1,83 @@
+
+DEAL:0::number of locally owned cells in tria 0 and tria 1: 19 22
+DEAL:0::2.0 2.0
+DEAL:0::2.1 2.1
+DEAL:0::2.2 2.2
+DEAL:0::2.3 2.3
+DEAL:0::2.4 2.4
+DEAL:0::2.5 2.5
+DEAL:0::2.6 2.6
+DEAL:0::2.7 2.7
+DEAL:0::2.8 2.8
+DEAL:0::2.9 2.9
+DEAL:0::2.10 2.10
+DEAL:0::2.11 2.11
+DEAL:0::2.12 2.12
+DEAL:0::2.13 2.13
+DEAL:0::2.14 2.14
+DEAL:0::2.15 2.15
+DEAL:0::number of locally owned cells in tria 0 and tria 1: 71 78
+DEAL:0::2.0 2.0
+DEAL:0::2.1 2.1
+DEAL:0::2.2 2.2
+DEAL:0::2.3 2.3
+DEAL:0::2.4 2.4
+DEAL:0::2.5 2.5
+DEAL:0::2.6 2.6
+DEAL:0::2.7 2.7
+DEAL:0::2.8 2.8
+DEAL:0::2.9 2.9
+DEAL:0::2.10 2.10
+DEAL:0::2.11 2.11
+DEAL:0::2.12 2.12
+DEAL:0::2.13 2.13
+DEAL:0::2.14 2.14
+DEAL:0::2.15 2.15
+DEAL:0::2.16 2.16
+DEAL:0::2.17 2.17
+DEAL:0::2.18 2.18
+DEAL:0::2.19 2.19
+DEAL:0::2.20 2.20
+DEAL:0::2.21 2.21
+DEAL:0::2.22 2.22
+DEAL:0::2.23 2.23
+DEAL:0::2.24 2.24
+DEAL:0::2.25 2.25
+DEAL:0::2.26 2.26
+DEAL:0::2.27 2.27
+DEAL:0::2.28 2.28
+DEAL:0::2.29 2.29
+DEAL:0::2.30 2.30
+DEAL:0::2.31 2.31
+DEAL:0::2.32 2.32
+DEAL:0::2.33 2.33
+DEAL:0::2.34 2.34
+DEAL:0::2.35 2.35
+DEAL:0::2.36 2.36
+DEAL:0::2.37 2.37
+DEAL:0::2.38 2.38
+DEAL:0::2.39 2.39
+DEAL:0::2.40 2.40
+DEAL:0::2.41 2.41
+DEAL:0::2.42 2.42
+DEAL:0::2.43 2.43
+DEAL:0::2.44 2.44
+DEAL:0::2.45 2.45
+DEAL:0::2.46 2.46
+DEAL:0::2.47 2.47
+DEAL:0::2.48 2.48
+DEAL:0::2.49 2.49
+DEAL:0::2.50 2.50
+DEAL:0::2.51 2.51
+DEAL:0::2.52 2.52
+DEAL:0::2.53 2.53
+DEAL:0::2.54 2.54
+DEAL:0::2.55 2.55
+DEAL:0::2.56 2.56
+DEAL:0::2.57 2.57
+DEAL:0::2.58 2.58
+DEAL:0::2.59 2.59
+DEAL:0::2.60 2.60
+DEAL:0::2.61 2.61
+DEAL:0::2.62 2.62
+DEAL:0::2.63 2.63
diff --git a/tests/grid/get_finest_common_cells_04.with_p4est=true.mpirun=2.output b/tests/grid/get_finest_common_cells_04.with_p4est=true.mpirun=2.output
new file mode 100644
index 000000000000..87c5e343e319
--- /dev/null
+++ b/tests/grid/get_finest_common_cells_04.with_p4est=true.mpirun=2.output
@@ -0,0 +1,167 @@
+
+DEAL:0::number of locally owned cells in tria 0 and tria 1: 19 22
+DEAL:0::2.0 2.0
+DEAL:0::2.1 2.1
+DEAL:0::2.2 2.2
+DEAL:0::2.3 2.3
+DEAL:0::2.4 2.4
+DEAL:0::2.5 2.5
+DEAL:0::2.6 2.6
+DEAL:0::2.7 2.7
+DEAL:0::2.8 2.8
+DEAL:0::2.9 2.9
+DEAL:0::2.10 2.10
+DEAL:0::2.11 2.11
+DEAL:0::2.12 2.12
+DEAL:0::2.13 2.13
+DEAL:0::2.14 2.14
+DEAL:0::2.15 2.15
+DEAL:0::number of locally owned cells in tria 0 and tria 1: 71 78
+DEAL:0::2.0 2.0
+DEAL:0::2.1 2.1
+DEAL:0::2.2 2.2
+DEAL:0::2.3 2.3
+DEAL:0::2.4 2.4
+DEAL:0::2.5 2.5
+DEAL:0::2.6 2.6
+DEAL:0::2.7 2.7
+DEAL:0::2.8 2.8
+DEAL:0::2.9 2.9
+DEAL:0::2.10 2.10
+DEAL:0::2.11 2.11
+DEAL:0::2.12 2.12
+DEAL:0::2.13 2.13
+DEAL:0::2.14 2.14
+DEAL:0::2.15 2.15
+DEAL:0::2.16 2.16
+DEAL:0::2.17 2.17
+DEAL:0::2.18 2.18
+DEAL:0::2.19 2.19
+DEAL:0::2.20 2.20
+DEAL:0::2.21 2.21
+DEAL:0::2.22 2.22
+DEAL:0::2.23 2.23
+DEAL:0::2.24 2.24
+DEAL:0::2.25 2.25
+DEAL:0::2.26 2.26
+DEAL:0::2.27 2.27
+DEAL:0::2.28 2.28
+DEAL:0::2.29 2.29
+DEAL:0::2.30 2.30
+DEAL:0::2.31 2.31
+DEAL:0::2.32 2.32
+DEAL:0::2.33 2.33
+DEAL:0::2.34 2.34
+DEAL:0::2.35 2.35
+DEAL:0::2.36 2.36
+DEAL:0::2.37 2.37
+DEAL:0::2.38 2.38
+DEAL:0::2.39 2.39
+DEAL:0::2.40 2.40
+DEAL:0::2.41 2.41
+DEAL:0::2.42 2.42
+DEAL:0::2.43 2.43
+DEAL:0::2.44 2.44
+DEAL:0::2.45 2.45
+DEAL:0::2.46 2.46
+DEAL:0::2.47 2.47
+DEAL:0::2.48 2.48
+DEAL:0::2.49 2.49
+DEAL:0::2.50 2.50
+DEAL:0::2.51 2.51
+DEAL:0::2.52 2.52
+DEAL:0::2.53 2.53
+DEAL:0::2.54 2.54
+DEAL:0::2.55 2.55
+DEAL:0::2.56 2.56
+DEAL:0::2.57 2.57
+DEAL:0::2.58 2.58
+DEAL:0::2.59 2.59
+DEAL:0::2.60 2.60
+DEAL:0::2.61 2.61
+DEAL:0::2.62 2.62
+DEAL:0::2.63 2.63
+
+DEAL:1::number of locally owned cells in tria 0 and tria 1: 19 22
+DEAL:1::2.0 2.0
+DEAL:1::2.1 2.1
+DEAL:1::2.2 2.2
+DEAL:1::2.3 2.3
+DEAL:1::2.4 2.4
+DEAL:1::2.5 2.5
+DEAL:1::2.6 2.6
+DEAL:1::2.7 2.7
+DEAL:1::2.8 2.8
+DEAL:1::2.9 2.9
+DEAL:1::2.10 2.10
+DEAL:1::2.11 2.11
+DEAL:1::2.12 2.12
+DEAL:1::2.13 2.13
+DEAL:1::2.14 2.14
+DEAL:1::2.15 2.15
+DEAL:1::number of locally owned cells in tria 0 and tria 1: 71 78
+DEAL:1::2.0 2.0
+DEAL:1::2.1 2.1
+DEAL:1::2.2 2.2
+DEAL:1::2.3 2.3
+DEAL:1::2.4 2.4
+DEAL:1::2.5 2.5
+DEAL:1::2.6 2.6
+DEAL:1::2.7 2.7
+DEAL:1::2.8 2.8
+DEAL:1::2.9 2.9
+DEAL:1::2.10 2.10
+DEAL:1::2.11 2.11
+DEAL:1::2.12 2.12
+DEAL:1::2.13 2.13
+DEAL:1::2.14 2.14
+DEAL:1::2.15 2.15
+DEAL:1::2.16 2.16
+DEAL:1::2.17 2.17
+DEAL:1::2.18 2.18
+DEAL:1::2.19 2.19
+DEAL:1::2.20 2.20
+DEAL:1::2.21 2.21
+DEAL:1::2.22 2.22
+DEAL:1::2.23 2.23
+DEAL:1::2.24 2.24
+DEAL:1::2.25 2.25
+DEAL:1::2.26 2.26
+DEAL:1::2.27 2.27
+DEAL:1::2.28 2.28
+DEAL:1::2.29 2.29
+DEAL:1::2.30 2.30
+DEAL:1::2.31 2.31
+DEAL:1::2.32 2.32
+DEAL:1::2.33 2.33
+DEAL:1::2.34 2.34
+DEAL:1::2.35 2.35
+DEAL:1::2.36 2.36
+DEAL:1::2.37 2.37
+DEAL:1::2.38 2.38
+DEAL:1::2.39 2.39
+DEAL:1::2.40 2.40
+DEAL:1::2.41 2.41
+DEAL:1::2.42 2.42
+DEAL:1::2.43 2.43
+DEAL:1::2.44 2.44
+DEAL:1::2.45 2.45
+DEAL:1::2.46 2.46
+DEAL:1::2.47 2.47
+DEAL:1::2.48 2.48
+DEAL:1::2.49 2.49
+DEAL:1::2.50 2.50
+DEAL:1::2.51 2.51
+DEAL:1::2.52 2.52
+DEAL:1::2.53 2.53
+DEAL:1::2.54 2.54
+DEAL:1::2.55 2.55
+DEAL:1::2.56 2.56
+DEAL:1::2.57 2.57
+DEAL:1::2.58 2.58
+DEAL:1::2.59 2.59
+DEAL:1::2.60 2.60
+DEAL:1::2.61 2.61
+DEAL:1::2.62 2.62
+DEAL:1::2.63 2.63
+

From cadba6b200a3a1f0335edd93c0bd1166dc5a7af2 Mon Sep 17 00:00:00 2001
From: Matthias Maier 
Date: Fri, 15 Mar 2019 12:14:45 -0500
Subject: [PATCH 279/507] CMake: Reorganize MPI sanity check

---
 cmake/configure/configure_1_mpi.cmake | 80 +++++++++++++++++++--------
 1 file changed, 58 insertions(+), 22 deletions(-)

diff --git a/cmake/configure/configure_1_mpi.cmake b/cmake/configure/configure_1_mpi.cmake
index f5e349b1126e..f3f27eb92e5f 100644
--- a/cmake/configure/configure_1_mpi.cmake
+++ b/cmake/configure/configure_1_mpi.cmake
@@ -39,42 +39,78 @@ MACRO(FEATURE_MPI_FIND_EXTERNAL var)
       SET(${var} FALSE)
     ENDIF()
 
+    #
+    # Check that we can link with the full MPI interface:
+    #
+
+    SET(_linker_flags "${DEAL_II_LINKER_FLAGS}")
+
     CHECK_COMPILER_SETUP(
       "${DEAL_II_CXX_FLAGS} ${DEAL_II_CXX_FLAGS_SAVED} ${MPI_CXX_FLAGS}"
-      "${DEAL_II_LINKER_FLAGS} ${DEAL_II_LINKER_FLAGS_SAVED} ${MPI_LINKER_FLAGS}"
+      "${_linker_flags} ${DEAL_II_LINKER_FLAGS_SAVED} ${MPI_LINKER_FLAGS}"
       MPI_WORKING_COMPILER
       ${DEAL_II_LIBRARIES} ${MPI_LIBRARIES}
       )
 
-    IF(NOT MPI_WORKING_COMPILER)
-      #
-      # Try a workaround and drop "-fuse-ld=gold" (if present) from the
-      # linker invocation
-      #
-      MESSAGE(STATUS "Unable to compile a simple test program. "
-        "Try to drop \"-fuse-ld=gold\" from the linker flags."
+    IF(NOT MPI_WORKING_COMPILER AND DEAL_II_COMPILER_HAS_FUSE_LD_LLD)
+      MESSAGE(STATUS
+        "Unable to compile a simple test program. "
+        "Trying to drop \"-fuse-ld=lld\" from the linker flags."
         )
-      STRING(REPLACE "-fuse-ld=gold" "" _filtered_flags "${DEAL_II_LINKER_FLAGS}")
+
+      IF(DEAL_II_COMPILER_HAS_FUSE_LD_GOLD)
+        STRING(REPLACE "-fuse-ld=lld" "-fuse-ld=gold"
+          _linker_flags "${_linker_flags}"
+          )
+      ELSE()
+        STRING(REPLACE "-fuse-ld=lld" ""
+          _linker_flags "${_linker_flags}"
+          )
+      ENDIF()
+
+      SET(DEAL_II_COMPILER_HAS_FUSE_LD_LLD FALSE CACHE INTERNAL "" FORCE)
+      SET(DEAL_II_COMPILER_HAS_FUSE_LD_LLD FALSE)
 
       CHECK_COMPILER_SETUP(
         "${DEAL_II_CXX_FLAGS} ${DEAL_II_CXX_FLAGS_SAVED} ${MPI_CXX_FLAGS}"
-        "${_filtered_flags} ${DEAL_II_LINKER_FLAGS_SAVED} ${MPI_LINKER_FLAGS}"
+        "${_linker_flags} ${DEAL_II_LINKER_FLAGS_SAVED} ${MPI_LINKER_FLAGS}"
         MPI_WORKING_COMPILER
         ${DEAL_II_LIBRARIES} ${MPI_LIBRARIES}
         )
+    ENDIF()
 
-      IF(MPI_WORKING_COMPILER)
-        SET(DEAL_II_LINKER_FLAGS "${_filtered_flags}")
-      ELSE()
-        MESSAGE(STATUS "Could not find a sufficient MPI installation: "
-          "Unable to compile a simple test program."
-          )
-        SET(MPI_ADDITIONAL_ERROR_STRING
-          ${MPI_ADDITIONAL_ERROR_STRING}
-          "Unable to compile and link a simple test program with your MPI installation. \n"
-          )
-        SET(${var} FALSE)
-      ENDIF()
+    IF(NOT MPI_WORKING_COMPILER AND DEAL_II_COMPILER_HAS_FUSE_LD_GOLD)
+      MESSAGE(STATUS
+        "Unable to compile a simple test program. "
+        "Trying to drop \"-fuse-ld=gold\" from the linker flags."
+        )
+
+      STRING(REPLACE "-fuse-ld=gold" ""
+        _linker_flags "${_linker_flags}"
+        )
+
+      SET(DEAL_II_COMPILER_HAS_FUSE_LD_GOLD FALSE CACHE INTERNAL "" FORCE)
+      SET(DEAL_II_COMPILER_HAS_FUSE_LD_GOLD FALSE)
+
+      CHECK_COMPILER_SETUP(
+        "${DEAL_II_CXX_FLAGS} ${DEAL_II_CXX_FLAGS_SAVED} ${MPI_CXX_FLAGS}"
+        "${_linker_flags} ${DEAL_II_LINKER_FLAGS_SAVED} ${MPI_LINKER_FLAGS}"
+        MPI_WORKING_COMPILER
+        ${DEAL_II_LIBRARIES} ${MPI_LIBRARIES}
+        )
+    ENDIF()
+
+    IF(MPI_WORKING_COMPILER)
+      SET(DEAL_II_LINKER_FLAGS "${_linker_flags}")
+    ELSE()
+      MESSAGE(STATUS "Could not find a sufficient MPI installation: "
+        "Unable to compile a simple test program."
+        )
+      SET(MPI_ADDITIONAL_ERROR_STRING
+        ${MPI_ADDITIONAL_ERROR_STRING}
+        "Unable to compile and link a simple test program with your MPI installation. \n"
+        )
+      SET(${var} FALSE)
     ENDIF()
 
   ENDIF()

From b9e55a520462b53a646b418701ccdb3a1befb633 Mon Sep 17 00:00:00 2001
From: Matthias Maier 
Date: Fri, 15 Mar 2019 12:20:58 -0500
Subject: [PATCH 280/507] Revert "Only permit use of ld.lld linker when the
 Clang compiler is used."

This reverts commit 7ca10c52d89ec0e201320acaa9b34822d47779df.
---
 cmake/checks/check_02_compiler_features.cmake | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/cmake/checks/check_02_compiler_features.cmake b/cmake/checks/check_02_compiler_features.cmake
index fae50833f9e4..d108cc47672f 100644
--- a/cmake/checks/check_02_compiler_features.cmake
+++ b/cmake/checks/check_02_compiler_features.cmake
@@ -460,11 +460,7 @@ CHECK_CXX_SOURCE_COMPILES(
   DEAL_II_COMPILER_HAS_FUSE_LD_GOLD)
 RESET_CMAKE_REQUIRED()
 
-#
-# The ld.lld linker is not compatible with GCC. So we only enable it when
-# the Clang compiler is used. See https://github.com/dealii/dealii/issues/7811
-#
-IF(DEAL_II_COMPILER_HAS_FUSE_LD_LLD AND CMAKE_CXX_COMPILER_ID MATCHES "Clang")
+IF(DEAL_II_COMPILER_HAS_FUSE_LD_LLD)
   ADD_FLAGS(DEAL_II_LINKER_FLAGS "-fuse-ld=lld")
 ELSEIF(DEAL_II_COMPILER_HAS_FUSE_LD_GOLD)
   ADD_FLAGS(DEAL_II_LINKER_FLAGS "-fuse-ld=gold")

From 06a02074212136dd533c23d5c8460a22179a40e0 Mon Sep 17 00:00:00 2001
From: Matthias Maier 
Date: Mon, 18 Mar 2019 13:06:20 -0500
Subject: [PATCH 281/507] CMake: Refactor MPI sanity check into
 setup_finalize.cmake

---
 cmake/configure/configure_1_mpi.cmake | 74 ---------------------------
 cmake/setup_finalize.cmake            | 52 ++++++++++++++++---
 2 files changed, 46 insertions(+), 80 deletions(-)

diff --git a/cmake/configure/configure_1_mpi.cmake b/cmake/configure/configure_1_mpi.cmake
index f3f27eb92e5f..a5929c590838 100644
--- a/cmake/configure/configure_1_mpi.cmake
+++ b/cmake/configure/configure_1_mpi.cmake
@@ -39,80 +39,6 @@ MACRO(FEATURE_MPI_FIND_EXTERNAL var)
       SET(${var} FALSE)
     ENDIF()
 
-    #
-    # Check that we can link with the full MPI interface:
-    #
-
-    SET(_linker_flags "${DEAL_II_LINKER_FLAGS}")
-
-    CHECK_COMPILER_SETUP(
-      "${DEAL_II_CXX_FLAGS} ${DEAL_II_CXX_FLAGS_SAVED} ${MPI_CXX_FLAGS}"
-      "${_linker_flags} ${DEAL_II_LINKER_FLAGS_SAVED} ${MPI_LINKER_FLAGS}"
-      MPI_WORKING_COMPILER
-      ${DEAL_II_LIBRARIES} ${MPI_LIBRARIES}
-      )
-
-    IF(NOT MPI_WORKING_COMPILER AND DEAL_II_COMPILER_HAS_FUSE_LD_LLD)
-      MESSAGE(STATUS
-        "Unable to compile a simple test program. "
-        "Trying to drop \"-fuse-ld=lld\" from the linker flags."
-        )
-
-      IF(DEAL_II_COMPILER_HAS_FUSE_LD_GOLD)
-        STRING(REPLACE "-fuse-ld=lld" "-fuse-ld=gold"
-          _linker_flags "${_linker_flags}"
-          )
-      ELSE()
-        STRING(REPLACE "-fuse-ld=lld" ""
-          _linker_flags "${_linker_flags}"
-          )
-      ENDIF()
-
-      SET(DEAL_II_COMPILER_HAS_FUSE_LD_LLD FALSE CACHE INTERNAL "" FORCE)
-      SET(DEAL_II_COMPILER_HAS_FUSE_LD_LLD FALSE)
-
-      CHECK_COMPILER_SETUP(
-        "${DEAL_II_CXX_FLAGS} ${DEAL_II_CXX_FLAGS_SAVED} ${MPI_CXX_FLAGS}"
-        "${_linker_flags} ${DEAL_II_LINKER_FLAGS_SAVED} ${MPI_LINKER_FLAGS}"
-        MPI_WORKING_COMPILER
-        ${DEAL_II_LIBRARIES} ${MPI_LIBRARIES}
-        )
-    ENDIF()
-
-    IF(NOT MPI_WORKING_COMPILER AND DEAL_II_COMPILER_HAS_FUSE_LD_GOLD)
-      MESSAGE(STATUS
-        "Unable to compile a simple test program. "
-        "Trying to drop \"-fuse-ld=gold\" from the linker flags."
-        )
-
-      STRING(REPLACE "-fuse-ld=gold" ""
-        _linker_flags "${_linker_flags}"
-        )
-
-      SET(DEAL_II_COMPILER_HAS_FUSE_LD_GOLD FALSE CACHE INTERNAL "" FORCE)
-      SET(DEAL_II_COMPILER_HAS_FUSE_LD_GOLD FALSE)
-
-      CHECK_COMPILER_SETUP(
-        "${DEAL_II_CXX_FLAGS} ${DEAL_II_CXX_FLAGS_SAVED} ${MPI_CXX_FLAGS}"
-        "${_linker_flags} ${DEAL_II_LINKER_FLAGS_SAVED} ${MPI_LINKER_FLAGS}"
-        MPI_WORKING_COMPILER
-        ${DEAL_II_LIBRARIES} ${MPI_LIBRARIES}
-        )
-    ENDIF()
-
-    IF(MPI_WORKING_COMPILER)
-      SET(DEAL_II_LINKER_FLAGS "${_linker_flags}")
-    ELSE()
-      MESSAGE(STATUS "Could not find a sufficient MPI installation: "
-        "Unable to compile a simple test program."
-        )
-      SET(MPI_ADDITIONAL_ERROR_STRING
-        ${MPI_ADDITIONAL_ERROR_STRING}
-        "Unable to compile and link a simple test program with your MPI installation. \n"
-        )
-      SET(${var} FALSE)
-    ENDIF()
-
   ENDIF()
 ENDMACRO()
 
diff --git a/cmake/setup_finalize.cmake b/cmake/setup_finalize.cmake
index da1d0b9e77da..1df5d7b27141 100644
--- a/cmake/setup_finalize.cmake
+++ b/cmake/setup_finalize.cmake
@@ -84,12 +84,52 @@ ENDFOREACH()
 #
 
 FOREACH(build ${DEAL_II_BUILD_TYPES})
-  CHECK_COMPILER_SETUP(
-    "${DEAL_II_CXX_FLAGS} ${DEAL_II_CXX_FLAGS_${build}}"
-    "${DEAL_II_LINKER_FLAGS} ${DEAL_II_LINKER_FLAGS_${build}}"
-    DEAL_II_HAVE_USABLE_FLAGS_${build}
-    ${DEAL_II_LIBRARIES} ${DEAL_II_LIBRARIES_${build}}
-    )
+
+  MACRO(_check_linker_flags)
+    CHECK_COMPILER_SETUP(
+      "${DEAL_II_CXX_FLAGS} ${DEAL_II_CXX_FLAGS_${build}}"
+      "${DEAL_II_LINKER_FLAGS} ${DEAL_II_LINKER_FLAGS_${build}}"
+      DEAL_II_HAVE_USABLE_FLAGS_${build}
+      ${DEAL_II_LIBRARIES} ${DEAL_II_LIBRARIES_${build}}
+      )
+  ENDMACRO()
+
+  MACRO(_drop_linker_flag _linker_flag _replacement_flag _variable)
+    MESSAGE(STATUS
+      "Unable to compile a simple test program. "
+      "Trying to drop \"${_linker_flag}\" from the linker flags."
+      )
+    STRING(REPLACE "${_linker_flag}" "${_replacement_flag}"
+      DEAL_II_LINKER_FLAGS "${DEAL_II_LINKER_FLAGS}"
+      )
+    STRING(REPLACE "${_linker_flag}" "${_replacement_flag}"
+      DEAL_II_LINKER_FLAGS_${build} "${DEAL_II_LINKER_FLAGS_${_build}}"
+      )
+    SET(${_variable} FALSE CACHE INTERNAL "" FORCE)
+    SET(${_variable} FALSE)
+  ENDMACRO()
+
+  _check_linker_flags()
+
+  IF(NOT DEAL_II_HAVE_USABLE_FLAGS_${build} AND DEAL_II_COMPILER_HAS_FUSE_LD_LLD)
+    SET(_replacement "")
+    IF(DEAL_II_COMPILER_HAS_FUSE_LD_GOLD)
+      SET(_replacement "-fuse-ld=gold")
+    ENDIF()
+    _drop_linker_flag(
+      "-fuse-ld=lld" ${_replacement}
+      DEAL_II_COMPILER_HAS_FUSE_LD_LLD
+      )
+    _check_linker_flags()
+  ENDIF()
+
+  IF(NOT DEAL_II_HAVE_USABLE_FLAGS_${build} AND DEAL_II_COMPILER_HAS_FUSE_LD_GOLD)
+    _drop_linker_flag(
+      "-fuse-ld=gold" ""
+      DEAL_II_COMPILER_HAS_FUSE_LD_GOLD
+      )
+    _check_linker_flags()
+  ENDIF()
 
   IF(NOT DEAL_II_HAVE_USABLE_FLAGS_${build})
     MESSAGE(FATAL_ERROR "

From fb8efca2364e89b0fbda3fc5640bc66985f043ea Mon Sep 17 00:00:00 2001
From: Bruno Turcksin 
Date: Mon, 18 Mar 2019 14:40:14 -0400
Subject: [PATCH 282/507] Add missing #ifdef DEAL_II_WITH_THREADS around tbb
 calls

---
 include/deal.II/base/parallel.h | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/include/deal.II/base/parallel.h b/include/deal.II/base/parallel.h
index 8b9d5cc49159..3fd86d2df1a6 100644
--- a/include/deal.II/base/parallel.h
+++ b/include/deal.II/base/parallel.h
@@ -147,6 +147,7 @@ namespace parallel
 
 
 
+#ifdef DEAL_II_WITH_THREADS
     /**
      * Encapsulate tbb::parallel_for.
      */
@@ -179,6 +180,7 @@ namespace parallel
                         functor,
                         *partitioner);
     }
+#endif
   } // namespace internal
 
   /**

From 8f0c085303964852cd393b87b132b3395f6d7758 Mon Sep 17 00:00:00 2001
From: Daniel Arndt 
Date: Tue, 19 Mar 2019 01:08:45 +0100
Subject: [PATCH 283/507] Unify two symbol checks

---
 cmake/configure/configure_scalapack.cmake | 42 +++++++++--------------
 1 file changed, 17 insertions(+), 25 deletions(-)

diff --git a/cmake/configure/configure_scalapack.cmake b/cmake/configure/configure_scalapack.cmake
index 273689bf1c28..919a311c4fc1 100644
--- a/cmake/configure/configure_scalapack.cmake
+++ b/cmake/configure/configure_scalapack.cmake
@@ -28,36 +28,28 @@ MACRO(FEATURE_SCALAPACK_FIND_EXTERNAL var)
     CHECK_MPI_INTERFACE(SCALAPACK ${var})
 
     IF (${var})
-      CHECK_LIBRARY_EXISTS (${SCALAPACK_LIBRARY} pdsyevr_ {SCALAPACK_DIR} DEAL_II_SCALAPACK_HAS_PDSYEVR)
-      IF(NOT DEAL_II_SCALAPACK_HAS_PDSYEVR)
+      SET(CMAKE_REQUIRED_LIBRARIES ${SCALAPACK_LIBRARY})
+      CHECK_C_SOURCE_COMPILES("
+        void pdsyevr_();
+        void pssyevr_();
+        int main(){
+          pdsyevr_();
+          pssyevr_();
+          return 0;
+        }"
+        DEAL_II_SCALAPACK_HAS_PDSYEVR_PSSYEVR)
+        RESET_CMAKE_REQUIRED()
+
+      IF(NOT DEAL_II_SCALAPACK_HAS_PDSYEVR_PSSYEVR)
         MESSAGE(STATUS "Could not find a sufficient SCALAPACK installation: "
-          "The required symbol pdsyevr_ was not found."
+          "The required symbols pdsyevr_ and pssyevr_ were not found."
           )
         SET(SCALAPACK_ADDITIONAL_ERROR_STRING
           ${SCALAPACK_ADDITIONAL_ERROR_STRING}
           "Could not find a sufficient SCALAPACK installation: \n"
-          "SCALAPACK symbol check for pdsyevr_ failed! This usually means that "
-          "your SCALAPACK installation is incomplete or the link line is "
-          "broken. Consult\n"
-          "  CMakeFiles/CMakeError.log\n"
-          "for further information.\n"
-          )
-        SET(${var} FALSE)
-      ENDIF()
-    ENDIF()
-
-    IF(${var})
-      CHECK_LIBRARY_EXISTS (${SCALAPACK_LIBRARY} pssyevr_ {SCALAPACK_DIR} DEAL_II_SCALAPACK_HAS_PSSYEVR)
-      IF(NOT DEAL_II_SCALAPACK_HAS_PSSYEVR)
-        MESSAGE(STATUS "Could not find a sufficient SCALAPACK installation: "
-          "The required symbol pssyevr_ was not found."
-          )
-        SET(SCALAPACK_ADDITIONAL_ERROR_STRING
-          ${SCALAPACK_ADDITIONAL_ERROR_STRING}
-          "Could not find a sufficient SCALAPACK installation: \n"
-          "SCALAPACK symbol check for pssyevr_ failed! This usually means that "
-          "your SCALAPACK installation is incomplete or the link line is "
-          "broken. Consult\n"
+          "SCALAPACK symbol check for pdsyevr_ and pssyevr failed! "
+          "This usually means that your SCALAPACK installation is incomplete "
+          "or the link line is broken. Consult\n"
           "  CMakeFiles/CMakeError.log\n"
           "for further information.\n"
           )

From 4df736333d9b07bb80bd757f2f98aa74a5a581b3 Mon Sep 17 00:00:00 2001
From: Daniel Arndt 
Date: Tue, 19 Mar 2019 11:19:03 +0100
Subject: [PATCH 284/507] Fix Tpetra test for std::fabs without std::complex
 overload

---
 tests/trilinos/tpetra_vector_02.cc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/trilinos/tpetra_vector_02.cc b/tests/trilinos/tpetra_vector_02.cc
index ff5bfc4f16fb..105e435c8605 100644
--- a/tests/trilinos/tpetra_vector_02.cc
+++ b/tests/trilinos/tpetra_vector_02.cc
@@ -196,7 +196,7 @@ test()
   AssertThrow(b.l1_norm() == 95., ExcMessage("Problem in l1_norm."));
 
   const double eps = 1e-6;
-  AssertThrow(std::fabs(b.l2_norm() - Number(31.3847096)) < eps,
+  AssertThrow(std::fabs(b.l2_norm() - 31.3847096) < eps,
               ExcMessage("Problem in l2_norm"));
 
   AssertThrow(b.linfty_norm() == 14., ExcMessage("Problem in linfty_norm."));

From 1794dc428948d94f1f44074495036990426b5477 Mon Sep 17 00:00:00 2001
From: Jean-Paul Pelteret 
Date: Tue, 19 Mar 2019 10:48:18 +0100
Subject: [PATCH 285/507] Update CMake configuration of SymEngine libraries.

---
 cmake/modules/FindSYMENGINE.cmake | 14 +++++++-------
 1 file changed, 7 insertions(+), 7 deletions(-)

diff --git a/cmake/modules/FindSYMENGINE.cmake b/cmake/modules/FindSYMENGINE.cmake
index ad0624507365..9c9dbbba071f 100644
--- a/cmake/modules/FindSYMENGINE.cmake
+++ b/cmake/modules/FindSYMENGINE.cmake
@@ -118,15 +118,15 @@ STRING(REGEX REPLACE
 REMOVE_DUPLICATES(_symengine_include_dirs)
 
 #
-# The SYMENGINE_LIBRARIES variable configured by SymEngine only lists the
-# libraries, but does not set their paths. So we configure this outselves.
+# Get the full path for the SYMENGINE_LIBRARIES. Some of these libraries are 
+# CMake targets, so we can query them directly for this information.
 # 
 FOREACH(SYMENGINE_LIBRARY_NAME ${SYMENGINE_LIBRARIES})
-  DEAL_II_FIND_LIBRARY(SYMENGINE_LIBRARY
-    NAMES ${SYMENGINE_LIBRARY_NAME}
-    HINTS ${SYMENGINE_DIR}
-    PATH_SUFFIXES lib${LIB_SUFFIX} lib64 lib
-  )
+   IF (TARGET ${SYMENGINE_LIBRARY_NAME})
+       GET_PROPERTY(SYMENGINE_LIBRARY TARGET ${SYMENGINE_LIBRARY_NAME} PROPERTY LOCATION)
+   ELSE ()
+       SET(SYMENGINE_LIBRARY ${SYMENGINE_LIBRARY_NAME})
+   ENDIF()
 
   SET(_symengine_libraries ${_symengine_libraries} ${SYMENGINE_LIBRARY})
 ENDFOREACH()

From 3e8fd73e32eb19dffd9b51df72fb58037ab0e78d Mon Sep 17 00:00:00 2001
From: Jean-Paul Pelteret 
Date: Tue, 19 Mar 2019 11:55:48 +0100
Subject: [PATCH 286/507] Add quick test for SymEngine

---
 tests/quick_tests/CMakeLists.txt |  5 +++
 tests/quick_tests/symengine.cc   | 75 ++++++++++++++++++++++++++++++++
 2 files changed, 80 insertions(+)
 create mode 100644 tests/quick_tests/symengine.cc

diff --git a/tests/quick_tests/CMakeLists.txt b/tests/quick_tests/CMakeLists.txt
index f76cfc008b7a..b9530cb5309b 100644
--- a/tests/quick_tests/CMakeLists.txt
+++ b/tests/quick_tests/CMakeLists.txt
@@ -193,6 +193,11 @@ IF (DEAL_II_WITH_GMSH)
   make_quicktest("gmsh" ${_mybuild} "")
 ENDIF()
 
+# Test SymEngine
+IF (DEAL_II_WITH_SYMENGINE)
+  make_quicktest("symengine" ${_mybuild} "")
+ENDIF()
+
 # A custom test target:
 ADD_CUSTOM_TARGET(test
   COMMAND ${CMAKE_COMMAND} -D ALL_TESTS="${ALL_TESTS}" -P ${CMAKE_CURRENT_SOURCE_DIR}/run.cmake
diff --git a/tests/quick_tests/symengine.cc b/tests/quick_tests/symengine.cc
new file mode 100644
index 000000000000..3cd221b159bf
--- /dev/null
+++ b/tests/quick_tests/symengine.cc
@@ -0,0 +1,75 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2019 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE at
+// the top level of the deal.II distribution.
+//
+// ---------------------------------------------------------------------
+
+
+// Adaptation of symengine/basic_[01,02].cc for a quick test
+
+#include 
+
+#include 
+#include 
+#include 
+#include 
+#include 
+#include 
+
+#include 
+#include 
+
+using namespace dealii;
+namespace SE = SymEngine;
+
+int
+main()
+{
+  {
+    const SE::RCP a = SE::integer(2);
+    const SE::RCP b = SE::real_double(4.2);
+
+    const SE::RCP c = SE::add(a, b);
+    deallog << "c = a+b: " << *c << std::endl;
+  }
+
+  {
+    const SE::RCP a = SE::real_double(3.1);
+    const SE::RCP  b = SE::real_double(7.5);
+
+    const SE::RCP x = (SE::symbol("x"));
+    const SE::RCP y = (SE::symbol("y"));
+
+    // Construction of symbolic function
+    const SE::RCP c =
+      SE::mul(y, SE::mul(SE::sub(y, b), SE::add(a, x)));
+    deallog << "c = y*(y-b)*(a+x): " << *c << std::endl;
+
+    // Perform symbolic differentiation
+    const SE::RCP dc_dx = c->diff(x);
+    const SE::RCP dc_dy = c->diff(y);
+
+    deallog << "dc_dx = y*(y-b): " << *dc_dx << std::endl;
+    deallog << "dc_dy = (2*y+1)*(a+x): " << *dc_dy << std::endl;
+
+    const SE::RCP dc_dx_check = SE::mul(y, SE::sub(y, b));
+    const SE::RCP dc_dy_check =
+      SE::mul(SE::sub(SE::mul(SE::integer(2), y), b), SE::add(a, x));
+    Assert(SE::eq(*dc_dx, *dc_dx_check), ExcMessage("Should be equal!"));
+    // Although these two *values* are the same, the underlying
+    // *representation* is different. So we'd need to match the representation
+    // exactly, and I'm too lazy to do this right now.
+    // Assert(SE::eq(*dc_dy, *dc_dy_check), ExcMessage("Should be equal!"));
+  }
+
+  deallog << "OK" << std::endl;
+}

From 9363cab6b03d1bac6d139a3d828a4ebff92fa055 Mon Sep 17 00:00:00 2001
From: Denis Davydov 
Date: Tue, 19 Mar 2019 17:55:41 +0100
Subject: [PATCH 287/507] use Utilities::MPI::some_to_some() in
 SparsityTools::distribute_sparsity_pattern(), improve const-correctness

---
 source/lac/dynamic_sparsity_pattern.cc |   5 ++
 source/lac/sparsity_tools.cc           | 116 ++++++-------------------
 2 files changed, 30 insertions(+), 91 deletions(-)

diff --git a/source/lac/dynamic_sparsity_pattern.cc b/source/lac/dynamic_sparsity_pattern.cc
index dcf53e1bbcef..95ca12cdc4b7 100644
--- a/source/lac/dynamic_sparsity_pattern.cc
+++ b/source/lac/dynamic_sparsity_pattern.cc
@@ -612,6 +612,11 @@ template void
 DynamicSparsityPattern::Line::add_entries(std::vector::iterator,
                                           std::vector::iterator,
                                           const bool);
+template void
+DynamicSparsityPattern::Line::add_entries(
+  std::vector::const_iterator,
+  std::vector::const_iterator,
+  const bool);
 #endif
 
 template void
diff --git a/source/lac/sparsity_tools.cc b/source/lac/sparsity_tools.cc
index e04c9e54f4fa..eeba2592de4b 100644
--- a/source/lac/sparsity_tools.cc
+++ b/source/lac/sparsity_tools.cc
@@ -925,21 +925,19 @@ namespace SparsityTools
     for (DynamicSparsityPattern::size_type i = 0; i < rows_per_cpu.size(); ++i)
       start_index[i + 1] = start_index[i] + rows_per_cpu[i];
 
-    using map_vec_t = std::map>;
+    using map_vec_t =
+      std::map>;
 
     map_vec_t send_data;
 
     {
-      unsigned int dest_cpu = 0;
-
-      DynamicSparsityPattern::size_type n_local_rel_rows = myrange.n_elements();
+      unsigned int dest_cpu         = 0;
+      const auto   n_local_rel_rows = myrange.n_elements();
       for (DynamicSparsityPattern::size_type row_idx = 0;
            row_idx < n_local_rel_rows;
            ++row_idx)
         {
-          DynamicSparsityPattern::size_type row =
-            myrange.nth_index_in_set(row_idx);
+          const auto row = myrange.nth_index_in_set(row_idx);
 
           // calculate destination CPU
           while (row >= start_index[dest_cpu + 1])
@@ -952,109 +950,45 @@ namespace SparsityTools
               continue;
             }
 
-          DynamicSparsityPattern::size_type rlen = dsp.row_length(row);
+          const auto rlen = dsp.row_length(row);
 
           // skip empty lines
           if (!rlen)
             continue;
 
           // save entries
-          std::vector &dst =
-            send_data[dest_cpu];
+          auto &dst = send_data[dest_cpu];
 
           dst.push_back(rlen); // number of entries
           dst.push_back(row);  // row index
           for (DynamicSparsityPattern::size_type c = 0; c < rlen; ++c)
             {
               // columns
-              DynamicSparsityPattern::size_type column =
-                dsp.column_number(row, c);
+              const auto column = dsp.column_number(row, c);
               dst.push_back(column);
             }
         }
     }
 
-    unsigned int num_receive = 0;
-    {
-      std::vector send_to;
-      send_to.reserve(send_data.size());
-      for (const auto &sparsity_line : send_data)
-        send_to.push_back(sparsity_line.first);
-
-      num_receive =
-        Utilities::MPI::compute_n_point_to_point_communications(mpi_comm,
-                                                                send_to);
-    }
-
-    std::vector requests(send_data.size());
+    const auto receive_data = Utilities::MPI::some_to_some(mpi_comm, send_data);
 
-
-    // send data
-    {
-      unsigned int idx = 0;
-      for (const auto &sparsity_line : send_data)
-        {
-          const int ierr =
-            MPI_Isend(DEAL_II_MPI_CONST_CAST(sparsity_line.second.data()),
-                      sparsity_line.second.size(),
-                      DEAL_II_DOF_INDEX_MPI_TYPE,
-                      sparsity_line.first,
-                      124,
-                      mpi_comm,
-                      &requests[idx++]);
-          AssertThrowMPI(ierr);
-        }
-    }
-
-    {
-      // receive
-      std::vector recv_buf;
-      for (unsigned int index = 0; index < num_receive; ++index)
-        {
-          MPI_Status status;
-          int        len;
-          int ierr = MPI_Probe(MPI_ANY_SOURCE, MPI_ANY_TAG, mpi_comm, &status);
-          AssertThrowMPI(ierr);
-          Assert(status.MPI_TAG == 124, ExcInternalError());
-
-          ierr = MPI_Get_count(&status, DEAL_II_DOF_INDEX_MPI_TYPE, &len);
-          AssertThrowMPI(ierr);
-          recv_buf.resize(len);
-          ierr = MPI_Recv(recv_buf.data(),
-                          len,
-                          DEAL_II_DOF_INDEX_MPI_TYPE,
-                          status.MPI_SOURCE,
-                          status.MPI_TAG,
-                          mpi_comm,
-                          &status);
-          AssertThrowMPI(ierr);
-
-          std::vector::const_iterator ptr =
-            recv_buf.begin();
-          std::vector::const_iterator end =
-            recv_buf.end();
-          while (ptr != end)
-            {
-              DynamicSparsityPattern::size_type num = *(ptr++);
-              Assert(ptr != end, ExcInternalError());
-              DynamicSparsityPattern::size_type row = *(ptr++);
-              for (unsigned int c = 0; c < num; ++c)
-                {
-                  Assert(ptr != end, ExcInternalError());
-                  dsp.add(row, *ptr);
-                  ++ptr;
-                }
-            }
-          Assert(ptr == end, ExcInternalError());
-        }
-    }
-
-    // complete all sends, so that we can safely destroy the buffers.
-    if (requests.size())
+    // add what we received
+    for (const auto &data : receive_data)
       {
-        const int ierr =
-          MPI_Waitall(requests.size(), requests.data(), MPI_STATUSES_IGNORE);
-        AssertThrowMPI(ierr);
+        const auto &recv_buf = data.second;
+        auto        ptr      = recv_buf.begin();
+        const auto  end      = recv_buf.end();
+        while (ptr != end)
+          {
+            const DynamicSparsityPattern::size_type num = *(ptr++);
+            Assert(ptr != end, ExcInternalError());
+            const DynamicSparsityPattern::size_type row = *(ptr++);
+
+            Assert(ptr + (num - 1) != end, ExcInternalError());
+            dsp.add_entries(row, ptr, ptr + num, true);
+            ptr += num;
+          }
+        Assert(ptr == end, ExcInternalError());
       }
   }
 

From e9cd64520adbbaff38b818be928c0ef470336703 Mon Sep 17 00:00:00 2001
From: Timo Heister 
Date: Tue, 19 Mar 2019 12:30:41 -0600
Subject: [PATCH 288/507] step-15: doc update

---
 examples/step-15/doc/results.dox | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/examples/step-15/doc/results.dox b/examples/step-15/doc/results.dox
index 3fefe249fee6..9aa5f0c173e1 100644
--- a/examples/step-15/doc/results.dox
+++ b/examples/step-15/doc/results.dox
@@ -137,7 +137,7 @@ Wolfe and Armijo-Goldstein conditions. For these, one can show the following:
   satisfied, i.e., the iteration never gets stuck as long as the problem is
   convex.
 - If we are close enough to the solution, then the conditions allow for
-  $\alpha^n$, thereby enabling quadratic convergence.
+  $\alpha^n=1$, thereby enabling quadratic convergence.
 
 We will not dwell on this here any further but leave the implementation of
 such algorithms as an exercise. We note, however, that when implemented
@@ -146,6 +146,9 @@ problems can be solved in anywhere between 5 and 15 Newton iterations to
 engineering accuracy — substantially fewer than we need with the current
 version of the program.
 
+More details on globalization methods including backtracking can be found,
+for example, in Griva, Nash, Sofer: Linear and nonlinear optimization (2009).
+
 
 
     Integrating mesh refinement and nonlinear and linear solvers 
    
 

From 2122c20d0e62bb9483d4a8c118af262f439ee85f Mon Sep 17 00:00:00 2001
From: Timo Heister 
Date: Tue, 19 Mar 2019 14:10:02 -0600
Subject: [PATCH 289/507] fix tbb range size type

---
 include/deal.II/lac/vector_operations_internal.h | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/include/deal.II/lac/vector_operations_internal.h b/include/deal.II/lac/vector_operations_internal.h
index bd13406faac5..95ea6bc18cae 100644
--- a/include/deal.II/lac/vector_operations_internal.h
+++ b/include/deal.II/lac/vector_operations_internal.h
@@ -149,7 +149,7 @@ namespace internal
       }
 
       void
-      operator()(const tbb::blocked_range &range) const
+      operator()(const tbb::blocked_range &range) const
       {
         const size_type r_begin = start + range.begin() * chunk_size;
         const size_type r_end = std::min(start + range.end() * chunk_size, end);
@@ -1317,7 +1317,7 @@ namespace internal
        * [range.begin(), range.end()).
        */
       void
-      operator()(const tbb::blocked_range &range) const
+      operator()(const tbb::blocked_range &range) const
       {
         for (size_type i = range.begin(); i < range.end(); ++i)
           accumulate_recursive(op,

From c4df921001d536ef327184e290cf58365e34f36a Mon Sep 17 00:00:00 2001
From: Daniel Arndt 
Date: Tue, 19 Mar 2019 21:57:40 +0100
Subject: [PATCH 290/507] Fix SCALAPACK symbol check

---
 cmake/configure/configure_scalapack.cmake | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/cmake/configure/configure_scalapack.cmake b/cmake/configure/configure_scalapack.cmake
index 919a311c4fc1..a91457f379c2 100644
--- a/cmake/configure/configure_scalapack.cmake
+++ b/cmake/configure/configure_scalapack.cmake
@@ -28,7 +28,7 @@ MACRO(FEATURE_SCALAPACK_FIND_EXTERNAL var)
     CHECK_MPI_INTERFACE(SCALAPACK ${var})
 
     IF (${var})
-      SET(CMAKE_REQUIRED_LIBRARIES ${SCALAPACK_LIBRARY})
+      SET(CMAKE_REQUIRED_LIBRARIES ${SCALAPACK_LIBRARIES})
       CHECK_C_SOURCE_COMPILES("
         void pdsyevr_();
         void pssyevr_();
@@ -47,7 +47,7 @@ MACRO(FEATURE_SCALAPACK_FIND_EXTERNAL var)
         SET(SCALAPACK_ADDITIONAL_ERROR_STRING
           ${SCALAPACK_ADDITIONAL_ERROR_STRING}
           "Could not find a sufficient SCALAPACK installation: \n"
-          "SCALAPACK symbol check for pdsyevr_ and pssyevr failed! "
+          "SCALAPACK symbol check for pdsyevr_ and pssyevr_ failed! "
           "This usually means that your SCALAPACK installation is incomplete "
           "or the link line is broken. Consult\n"
           "  CMakeFiles/CMakeError.log\n"

From f1fc309538dcb6becd9e1a71065040867013b4ea Mon Sep 17 00:00:00 2001
From: Matthias Maier 
Date: Tue, 19 Mar 2019 16:37:34 -0500
Subject: [PATCH 291/507] CMake: also update BASE_LINKER_FLAGS* when dropping
 -fuse-ld=...

---
 cmake/setup_finalize.cmake | 14 ++++++++------
 1 file changed, 8 insertions(+), 6 deletions(-)

diff --git a/cmake/setup_finalize.cmake b/cmake/setup_finalize.cmake
index 1df5d7b27141..716093a7b3b5 100644
--- a/cmake/setup_finalize.cmake
+++ b/cmake/setup_finalize.cmake
@@ -99,12 +99,14 @@ FOREACH(build ${DEAL_II_BUILD_TYPES})
       "Unable to compile a simple test program. "
       "Trying to drop \"${_linker_flag}\" from the linker flags."
       )
-    STRING(REPLACE "${_linker_flag}" "${_replacement_flag}"
-      DEAL_II_LINKER_FLAGS "${DEAL_II_LINKER_FLAGS}"
-      )
-    STRING(REPLACE "${_linker_flag}" "${_replacement_flag}"
-      DEAL_II_LINKER_FLAGS_${build} "${DEAL_II_LINKER_FLAGS_${_build}}"
-      )
+    FOREACH(_flags
+        DEAL_II_LINKER_FLAGS DEAL_II_LINKER_FLAGS_${build}
+        BASE_LINKER_FLAGS BASE_LINKER_FLAGS_${build}
+        )
+      STRING(REPLACE "${_linker_flag}" "${_replacement_flag}"
+        ${_flags} "${${_flags}}"
+        )
+    ENDFOREACH()
     SET(${_variable} FALSE CACHE INTERNAL "" FORCE)
     SET(${_variable} FALSE)
   ENDMACRO()

From 3b486e3e6089c1cd268c12585182af5d0fbd2b72 Mon Sep 17 00:00:00 2001
From: Denis Davydov 
Date: Wed, 20 Mar 2019 11:59:53 +0100
Subject: [PATCH 292/507] use range loop in
 SparsityTools::distribute_sparsity_pattern()

---
 source/lac/sparsity_tools.cc | 23 ++++++++++-------------
 1 file changed, 10 insertions(+), 13 deletions(-)

diff --git a/source/lac/sparsity_tools.cc b/source/lac/sparsity_tools.cc
index eeba2592de4b..2ec2422ad64f 100644
--- a/source/lac/sparsity_tools.cc
+++ b/source/lac/sparsity_tools.cc
@@ -925,30 +925,27 @@ namespace SparsityTools
     for (DynamicSparsityPattern::size_type i = 0; i < rows_per_cpu.size(); ++i)
       start_index[i + 1] = start_index[i] + rows_per_cpu[i];
 
+    IndexSet owned(start_index.back());
+    owned.add_range(start_index[myid], start_index[myid] + rows_per_cpu[myid]);
+
+    IndexSet myrange_non_owned(myrange);
+    myrange_non_owned.subtract_set(owned);
+
     using map_vec_t =
       std::map>;
 
     map_vec_t send_data;
 
     {
-      unsigned int dest_cpu         = 0;
-      const auto   n_local_rel_rows = myrange.n_elements();
-      for (DynamicSparsityPattern::size_type row_idx = 0;
-           row_idx < n_local_rel_rows;
-           ++row_idx)
+      unsigned int dest_cpu = 0;
+      for (const auto &row : myrange_non_owned)
         {
-          const auto row = myrange.nth_index_in_set(row_idx);
-
           // calculate destination CPU
           while (row >= start_index[dest_cpu + 1])
             ++dest_cpu;
 
-          // skip myself
-          if (dest_cpu == myid)
-            {
-              row_idx += rows_per_cpu[myid] - 1;
-              continue;
-            }
+          // we removed owned, thus shall not hit ourselves
+          Assert(dest_cpu != myid, ExcInternalError());
 
           const auto rlen = dsp.row_length(row);
 

From 574c41753c62d8524018649dcab58da1cb8cac7a Mon Sep 17 00:00:00 2001
From: Daniel Arndt 
Date: Wed, 20 Mar 2019 16:20:44 +0100
Subject: [PATCH 293/507] Remove IndexSet overloads in DataOut

---
 .../incompatibilities/20190320DanielArndt     |   4 +
 examples/step-41/step-41.cc                   |  14 +-
 examples/step-42/step-42.cc                   |  25 +-
 include/deal.II/fe/fe_values.h                |  20 +-
 include/deal.II/numerics/data_out_dof_data.h  |   8 +-
 source/fe/fe_values.inst.in                   | 292 ------------------
 source/numerics/data_out_dof_data.inst.in     |  76 -----
 .../numerics/data_out_dof_data_codim.inst.in  |  30 --
 8 files changed, 34 insertions(+), 435 deletions(-)
 create mode 100644 doc/news/changes/incompatibilities/20190320DanielArndt

diff --git a/doc/news/changes/incompatibilities/20190320DanielArndt b/doc/news/changes/incompatibilities/20190320DanielArndt
new file mode 100644
index 000000000000..e4cc41414bb8
--- /dev/null
+++ b/doc/news/changes/incompatibilities/20190320DanielArndt
@@ -0,0 +1,4 @@
+Removed: The IndexSet instantiations for FEValues::get_function_values()
+and DataOut_DoFData::add_data_vector() have been removed.
+
    
+(Daniel Arndt, 2019/03/20)
diff --git a/examples/step-41/step-41.cc b/examples/step-41/step-41.cc
index 41d2e233aeda..662829c1507b 100644
--- a/examples/step-41/step-41.cc
+++ b/examples/step-41/step-41.cc
@@ -101,6 +101,7 @@ namespace Step41
     TrilinosWrappers::SparseMatrix complete_system_matrix;
 
     TrilinosWrappers::MPI::Vector solution;
+    TrilinosWrappers::MPI::Vector active_set_vector;
     TrilinosWrappers::MPI::Vector system_rhs;
     TrilinosWrappers::MPI::Vector complete_system_rhs;
     TrilinosWrappers::MPI::Vector diagonal_of_mass_matrix;
@@ -261,6 +262,7 @@ namespace Step41
 
     IndexSet solution_index_set = dof_handler.locally_owned_dofs();
     solution.reinit(solution_index_set, MPI_COMM_WORLD);
+    active_set_vector.reinit(solution_index_set, MPI_COMM_WORLD);
     system_rhs.reinit(solution_index_set, MPI_COMM_WORLD);
     complete_system_rhs.reinit(solution_index_set, MPI_COMM_WORLD);
     contact_force.reinit(solution_index_set, MPI_COMM_WORLD);
@@ -542,6 +544,10 @@ namespace Step41
                                              BoundaryValues(),
                                              constraints);
     constraints.close();
+
+    active_set_vector = 0.;
+    for (const auto index : active_set)
+      active_set_vector[index] = 1.;
   }
 
   // @sect4{ObstacleProblem::solve}
@@ -576,11 +582,7 @@ namespace Step41
   // @sect4{ObstacleProblem::output_results}
 
   // We use the vtk-format for the output.  The file contains the displacement
-  // and a numerical representation of the active set. The function looks
-  // standard but note that we can add an IndexSet object to the DataOut
-  // object in exactly the same way as a regular solution vector: it is simply
-  // interpreted as a function that is either zero (when a degree of freedom
-  // is not part of the IndexSet) or one (if it is).
+  // and a numerical representation of the active set.
   template 
   void ObstacleProblem::output_results(const unsigned int iteration) const
   {
@@ -590,7 +592,7 @@ namespace Step41
 
     data_out.attach_dof_handler(dof_handler);
     data_out.add_data_vector(solution, "displacement");
-    data_out.add_data_vector(active_set, "active_set");
+    data_out.add_data_vector(active_set_vector, "active_set");
     data_out.add_data_vector(contact_force, "lambda");
 
     data_out.build_patches();
diff --git a/examples/step-42/step-42.cc b/examples/step-42/step-42.cc
index 94cc9e445aa9..ec2b52df7944 100644
--- a/examples/step-42/step-42.cc
+++ b/examples/step-42/step-42.cc
@@ -701,6 +701,7 @@ namespace Step42
     TrilinosWrappers::SparseMatrix newton_matrix;
 
     TrilinosWrappers::MPI::Vector solution;
+    TrilinosWrappers::MPI::Vector active_set_vector;
     TrilinosWrappers::MPI::Vector newton_rhs;
     TrilinosWrappers::MPI::Vector newton_rhs_uncondensed;
     TrilinosWrappers::MPI::Vector diag_mass_matrix_vector;
@@ -1022,6 +1023,7 @@ namespace Step42
     {
       TimerOutput::Scope t(computing_timer, "Setup: vectors");
       solution.reinit(locally_relevant_dofs, mpi_communicator);
+      active_set_vector.reinit(locally_relevant_dofs, MPI_COMM_WORLD);
       newton_rhs.reinit(locally_owned_dofs, mpi_communicator);
       newton_rhs_uncondensed.reinit(locally_owned_dofs, mpi_communicator);
       diag_mass_matrix_vector.reinit(locally_owned_dofs, mpi_communicator);
@@ -1339,6 +1341,14 @@ namespace Step42
     all_constraints.close();
     all_constraints.merge(constraints_dirichlet_and_hanging_nodes);
 
+    // We misuse distributed_solution for updating active_set_vector.
+    // We can do that because distributed_solution has a compatible underlying
+    // IndexSet and we don't need the vector anymore.
+    distributed_solution = 0.;
+    for (const auto index : active_set)
+      distributed_solution[index] = 1.;
+    active_set_vector = distributed_solution;
+
     pcout << "         Size of active set: "
           << Utilities::MPI::sum((active_set & locally_owned_dofs).n_elements(),
                                  mpi_communicator)
@@ -1388,13 +1398,9 @@ namespace Step42
 
     std::vector local_dof_indices(dofs_per_cell);
 
-    typename DoFHandler::active_cell_iterator cell =
-                                                     dof_handler.begin_active(),
-                                                   endc = dof_handler.end();
-
     const FEValuesExtractors::Vector displacement(0);
 
-    for (; cell != endc; ++cell)
+    for (const auto &cell : dof_handler.active_cell_iterators())
       if (cell->is_locally_owned())
         {
           fe_values.reinit(cell);
@@ -1553,10 +1559,9 @@ namespace Step42
 
     fraction_of_plastic_q_points_per_cell = 0;
 
-    typename DoFHandler::active_cell_iterator cell =
-                                                     dof_handler.begin_active(),
-                                                   endc = dof_handler.end();
-    unsigned int cell_number                            = 0;
+    auto         cell        = dof_handler.begin_active();
+    const auto   endc        = dof_handler.end();
+    unsigned int cell_number = 0;
     for (; cell != endc; ++cell, ++cell_number)
       if (cell->is_locally_owned())
         {
@@ -2048,7 +2053,7 @@ namespace Step42
                              std::vector(dim, "contact_force"),
                              DataOut::type_dof_data,
                              data_component_interpretation);
-    data_out.add_data_vector(active_set,
+    data_out.add_data_vector(active_set_vector,
                              std::vector(dim, "active_set"),
                              DataOut::type_dof_data,
                              data_component_interpretation);
diff --git a/include/deal.II/fe/fe_values.h b/include/deal.II/fe/fe_values.h
index 713f1c64adad..d810d3b6fb8f 100644
--- a/include/deal.II/fe/fe_values.h
+++ b/include/deal.II/fe/fe_values.h
@@ -2290,9 +2290,7 @@ class FEValuesBase : public Subscriptor
    * Vector<T>, BlockVector<T>, or one of the PETSc or Trilinos
    * vector wrapper classes. It represents a global vector of DoF values
    * associated with the DoFHandler object with which this FEValues object was
-   * last initialized. Alternatively, if the vector argument is of type
-   * IndexSet, then the function is represented as one that is either zero or
-   * one, depending on whether a DoF index is in the set or not.
+   * last initialized.
    *
    * @dealiiRequiresUpdateFlags{update_values}
    */
@@ -2449,9 +2447,7 @@ class FEValuesBase : public Subscriptor
    * Vector<T>, BlockVector<T>, or one of the PETSc or Trilinos
    * vector wrapper classes. It represents a global vector of DoF values
    * associated with the DoFHandler object with which this FEValues object was
-   * last initialized. Alternatively, if the vector argument is of type
-   * IndexSet, then the function is represented as one that is either zero or
-   * one, depending on whether a DoF index is in the set or not.
+   * last initialized.
    *
    * @dealiiRequiresUpdateFlags{update_gradients}
    */
@@ -2554,9 +2550,7 @@ class FEValuesBase : public Subscriptor
    * Vector<T>, BlockVector<T>, or one of the PETSc or Trilinos
    * vector wrapper classes. It represents a global vector of DoF values
    * associated with the DoFHandler object with which this FEValues object was
-   * last initialized. Alternatively, if the vector argument is of type
-   * IndexSet, then the function is represented as one that is either zero or
-   * one, depending on whether a DoF index is in the set or not.
+   * last initialized.
    *
    * @dealiiRequiresUpdateFlags{update_hessians}
    */
@@ -2657,9 +2651,7 @@ class FEValuesBase : public Subscriptor
    * Vector<T>, BlockVector<T>, or one of the PETSc or Trilinos
    * vector wrapper classes. It represents a global vector of DoF values
    * associated with the DoFHandler object with which this FEValues object was
-   * last initialized. Alternatively, if the vector argument is of type
-   * IndexSet, then the function is represented as one that is either zero or
-   * one, depending on whether a DoF index is in the set or not.
+   * last initialized.
    *
    * @dealiiRequiresUpdateFlags{update_hessians}
    */
@@ -2772,9 +2764,7 @@ class FEValuesBase : public Subscriptor
    * Vector<T>, BlockVector<T>, or one of the PETSc or Trilinos
    * vector wrapper classes. It represents a global vector of DoF values
    * associated with the DoFHandler object with which this FEValues object was
-   * last initialized. Alternatively, if the vector argument is of type
-   * IndexSet, then the function is represented as one that is either zero or
-   * one, depending on whether a DoF index is in the set or not.
+   * last initialized.
    *
    * @dealiiRequiresUpdateFlags{update_3rd_derivatives}
    */
diff --git a/include/deal.II/numerics/data_out_dof_data.h b/include/deal.II/numerics/data_out_dof_data.h
index ea11144f7e3f..cdf385c1ccc9 100644
--- a/include/deal.II/numerics/data_out_dof_data.h
+++ b/include/deal.II/numerics/data_out_dof_data.h
@@ -730,9 +730,7 @@ class DataOut_DoFData : public DataOutInterface
    *
    * @note The actual type for the vector argument may be any vector type from
    * which FEValues can extract values on a cell using the
-   * FEValuesBase::get_function_values() function. In particular, this
-   * includes all of the usual vector types, but also IndexSet (see step-41
-   * for a use of this).
+   * FEValuesBase::get_function_values() function.
    */
   template 
   void
@@ -824,9 +822,7 @@ class DataOut_DoFData : public DataOutInterface
    *
    * @note The actual type for the vector argument may be any vector type from
    * which FEValues can extract values on a cell using the
-   * FEValuesBase::get_function_values() function. In particular, this
-   * includes all of the usual vector types, but also IndexSet (see step-41
-   * for a use of this).
+   * FEValuesBase::get_function_values() function.
    *
    * @note The DataPostprocessor object (i.e., in reality the object of your
    * derived class) has to live until the DataOut object is destroyed as the
diff --git a/source/fe/fe_values.inst.in b/source/fe/fe_values.inst.in
index 863a55f233b3..5073c4d06b22 100644
--- a/source/fe/fe_values.inst.in
+++ b/source/fe/fe_values.inst.in
@@ -485,295 +485,3 @@ for (VEC : VECTOR_TYPES; deal_II_dimension : DIMENSIONS;
 
 #endif
   }
-
-
-// instantiations for VEC=IndexSet
-
-for (deal_II_dimension : DIMENSIONS; deal_II_space_dimension : DIMENSIONS)
-  {
-#if deal_II_dimension <= deal_II_space_dimension
-    template void
-    FEValuesViews::Scalar::
-      get_function_values(
-        const dealii::IndexSet &,
-        std::vector::type> &) const;
-    template void
-    FEValuesViews::Scalar::
-      get_function_gradients(
-        const dealii::IndexSet &,
-        std::vector<
-          ProductType>::type> &)
-        const;
-    template void
-    FEValuesViews::Scalar::
-      get_function_hessians(
-        const dealii::IndexSet &,
-        std::vector<
-          ProductType>::type> &)
-        const;
-    template void
-    FEValuesViews::Scalar::
-      get_function_laplacians(
-        const dealii::IndexSet &,
-        std::vector::type> &) const;
-    template void
-    FEValuesViews::Scalar::
-      get_function_third_derivatives(
-        const dealii::IndexSet &,
-        std::vector<
-          ProductType>::type> &)
-        const;
-
-    template void
-    FEValuesViews::Vector::
-      get_function_values(
-        const dealii::IndexSet &,
-        std::vector<
-          ProductType>::type> &)
-        const;
-    template void
-    FEValuesViews::Vector::
-      get_function_gradients(
-        const dealii::IndexSet &,
-        std::vector<
-          ProductType>::type> &)
-        const;
-    template void
-    FEValuesViews::Vector::
-      get_function_symmetric_gradients(
-        const dealii::IndexSet &,
-        std::vector>::type> &) const;
-    template void
-    FEValuesViews::Vector::
-      get_function_curls(
-        const dealii::IndexSet &,
-        std::vector::type> &)
-        const;
-    template void
-    FEValuesViews::Vector::
-      get_function_divergences(
-        const dealii::IndexSet &,
-        std::vector::type> &)
-        const;
-    template void
-    FEValuesViews::Vector::
-      get_function_hessians(
-        const dealii::IndexSet &,
-        std::vector<
-          ProductType>::type> &)
-        const;
-    template void
-    FEValuesViews::Vector::
-      get_function_laplacians(
-        const dealii::IndexSet &,
-        std::vector<
-          ProductType>::type> &)
-        const;
-    template void
-    FEValuesViews::Vector::
-      get_function_third_derivatives(
-        const dealii::IndexSet &,
-        std::vector<
-          ProductType>::type> &)
-        const;
-
-    template void FEValuesViews::SymmetricTensor<2,
-                                                 deal_II_dimension,
-                                                 deal_II_space_dimension>::
-      get_function_values(
-        const dealii::IndexSet &,
-        std::vector>::type> &) const;
-    template void FEValuesViews::
-      SymmetricTensor<2, deal_II_dimension, deal_II_space_dimension>::
-        get_function_divergences(
-          const dealii::IndexSet &,
-          std::vector<
-            ProductType>::type> &)
-          const;
-
-    template void
-    FEValuesViews::Tensor<2, deal_II_dimension, deal_II_space_dimension>::
-      get_function_values(
-        const dealii::IndexSet &,
-        std::vector<
-          ProductType>::type> &)
-        const;
-    template void
-    FEValuesViews::Tensor<2, deal_II_dimension, deal_II_space_dimension>::
-      get_function_divergences(
-        const dealii::IndexSet &,
-        std::vector<
-          ProductType>::type> &)
-        const;
-    template void
-    FEValuesViews::Tensor<2, deal_II_dimension, deal_II_space_dimension>::
-      get_function_gradients(
-        const dealii::IndexSet &,
-        std::vector<
-          ProductType>::type> &)
-        const;
-#endif
-  }
-
-
-
-// Instantiations of functions in FEValuesBase and IndexSet=IndexSet
-
-for (deal_II_dimension : DIMENSIONS; deal_II_space_dimension : DIMENSIONS)
-  {
-#if deal_II_dimension <= deal_II_space_dimension
-    template void FEValuesBase::
-      get_function_values(const IndexSet &,
-                                    std::vector &) const;
-    template void FEValuesBase::
-      get_function_values(
-        const IndexSet &,
-        const ArrayView &,
-        std::vector &) const;
-
-    template void FEValuesBase::
-      get_function_values(const IndexSet &,
-                                    std::vector> &)
-        const;
-
-    template void FEValuesBase::
-      get_function_values(
-        const IndexSet &,
-        const ArrayView &,
-        std::vector> &) const;
-
-    template void FEValuesBase::
-      get_function_values(
-        const IndexSet &,
-        const ArrayView &,
-        ArrayView>,
-        bool) const;
-
-    template void FEValuesBase::
-      get_function_gradients(
-        const IndexSet &,
-        std::vector<
-          dealii::Tensor<1, deal_II_space_dimension, IndexSet::value_type>> &)
-        const;
-    template void FEValuesBase::
-      get_function_gradients(
-        const IndexSet &,
-        const ArrayView &,
-        std::vector<
-          dealii::Tensor<1, deal_II_space_dimension, IndexSet::value_type>> &)
-        const;
-
-    template void FEValuesBase::
-      get_function_gradients(
-        const IndexSet &,
-        std::vector>> &)
-        const;
-    template void FEValuesBase::
-      get_function_gradients(
-        const IndexSet &,
-        const ArrayView &,
-        ArrayView>>,
-        bool) const;
-
-    template void FEValuesBase::
-      get_function_hessians(
-        const IndexSet &,
-        std::vector<
-          dealii::Tensor<2, deal_II_space_dimension, IndexSet::value_type>> &)
-        const;
-    template void FEValuesBase::
-      get_function_hessians(
-        const IndexSet &,
-        const ArrayView &,
-        std::vector<
-          dealii::Tensor<2, deal_II_space_dimension, IndexSet::value_type>> &)
-        const;
-
-    template void FEValuesBase::
-      get_function_hessians(
-        const IndexSet &,
-        std::vector>> &,
-        bool) const;
-    template void FEValuesBase::
-      get_function_hessians(
-        const IndexSet &,
-        const ArrayView &,
-        ArrayView>>,
-        bool) const;
-
-    template void FEValuesBase::
-      get_function_laplacians(const IndexSet &,
-                                        std::vector &)
-        const;
-    template void FEValuesBase::
-      get_function_laplacians(
-        const IndexSet &,
-        const ArrayView &,
-        std::vector &) const;
-
-    template void FEValuesBase::
-      get_function_laplacians(
-        const IndexSet &, std::vector> &) const;
-
-    template void FEValuesBase::
-      get_function_laplacians(
-        const IndexSet &,
-        const ArrayView &,
-        std::vector> &) const;
-
-    template void FEValuesBase::
-      get_function_laplacians(
-        const IndexSet &,
-        const ArrayView &,
-        std::vector> &,
-        bool) const;
-
-    template void FEValuesBase::
-      get_function_third_derivatives(
-        const IndexSet &,
-        std::vector<
-          dealii::Tensor<3, deal_II_space_dimension, IndexSet::value_type>> &)
-        const;
-    template void FEValuesBase::
-      get_function_third_derivatives(
-        const IndexSet &,
-        const ArrayView &,
-        std::vector<
-          dealii::Tensor<3, deal_II_space_dimension, IndexSet::value_type>> &)
-        const;
-
-    template void FEValuesBase::
-      get_function_third_derivatives(
-        const IndexSet &,
-        std::vector>> &,
-        bool) const;
-    template void FEValuesBase::
-      get_function_third_derivatives(
-        const IndexSet &,
-        const ArrayView &,
-        ArrayView>>,
-        bool) const;
-#endif
-  }
diff --git a/source/numerics/data_out_dof_data.inst.in b/source/numerics/data_out_dof_data.inst.in
index 1d2cf2612df3..ecc15cb3602f 100644
--- a/source/numerics/data_out_dof_data.inst.in
+++ b/source/numerics/data_out_dof_data.inst.in
@@ -93,82 +93,6 @@ for (VEC : VECTOR_TYPES; DH : DOFHANDLER_TEMPLATES;
 
 
 
-for (DH : DOFHANDLER_TEMPLATES; deal_II_dimension : DIMENSIONS)
-  {
-    template void DataOut_DoFData,
-                                  deal_II_dimension,
-                                  deal_II_dimension>::
-      add_data_vector_internal(
-        const DH *,
-        const IndexSet &,
-        const std::vector &,
-        const DataVectorType,
-        const std::vector<
-          DataComponentInterpretation::DataComponentInterpretation> &,
-        const bool);
-
-    template void DataOut_DoFData,
-                                  deal_II_dimension,
-                                  deal_II_dimension>::
-      add_data_vector(
-        const DH &,
-        const IndexSet &,
-        const DataPostprocessor<
-          DH::space_dimension> &);
-
-
-
-    // stuff needed for face data
-
-    template void DataOut_DoFData,
-                                  deal_II_dimension - 1,
-                                  deal_II_dimension>::
-      add_data_vector_internal(
-        const DH *,
-        const IndexSet &,
-        const std::vector &,
-        const DataVectorType,
-        const std::vector<
-          DataComponentInterpretation::DataComponentInterpretation> &,
-        const bool);
-
-    template void DataOut_DoFData,
-                                  deal_II_dimension - 1,
-                                  deal_II_dimension>::
-      add_data_vector(
-        const DH &,
-        const IndexSet &,
-        const DataPostprocessor<
-          DH::space_dimension> &);
-
-    // things for DataOutRotation
-
-#if deal_II_dimension < 3
-    template void DataOut_DoFData,
-                                  deal_II_dimension + 1,
-                                  deal_II_dimension + 1>::
-      add_data_vector_internal(
-        const DH *,
-        const IndexSet &,
-        const std::vector &,
-        const DataVectorType,
-        const std::vector<
-          DataComponentInterpretation::DataComponentInterpretation> &,
-        const bool);
-
-    template void DataOut_DoFData,
-                                  deal_II_dimension + 1,
-                                  deal_II_dimension + 1>::
-      add_data_vector(
-        const DH &,
-        const IndexSet &,
-        const DataPostprocessor<
-          DH::space_dimension> &);
-#endif
-  }
-
-
-
 for (DH : DOFHANDLER_TEMPLATES; deal_II_dimension : DIMENSIONS)
   {
     template class DataOut_DoFData, deal_II_dimension>;
diff --git a/source/numerics/data_out_dof_data_codim.inst.in b/source/numerics/data_out_dof_data_codim.inst.in
index f5ae7d5b7cc2..005f78bccd76 100644
--- a/source/numerics/data_out_dof_data_codim.inst.in
+++ b/source/numerics/data_out_dof_data_codim.inst.in
@@ -55,36 +55,6 @@ for (VEC : REAL_VECTOR_TYPES; DH : DOFHANDLER_TEMPLATES;
 
 
 
-for (DH : DOFHANDLER_TEMPLATES; deal_II_dimension : DIMENSIONS;
-     deal_II_space_dimension : DIMENSIONS)
-  {
-#if deal_II_dimension < deal_II_space_dimension
-    template void
-    DataOut_DoFData,
-                    deal_II_dimension,
-                    deal_II_space_dimension>::
-      add_data_vector_internal(
-        const DH *,
-        const IndexSet &,
-        const std::vector &,
-        const DataVectorType,
-        const std::vector<
-          DataComponentInterpretation::DataComponentInterpretation> &,
-        const bool);
-
-    template void
-    DataOut_DoFData,
-                    deal_II_dimension,
-                    deal_II_space_dimension>::
-      add_data_vector(
-        const IndexSet &,
-        const DataPostprocessor<
-          DH::space_dimension> &);
-#endif
-  }
-
-
-
 for (DH : DOFHANDLER_TEMPLATES; deal_II_dimension : DIMENSIONS)
   {
 #if deal_II_dimension < 3

From d46c79d79a16b70f725800b47998e124171e8858 Mon Sep 17 00:00:00 2001
From: Daniel Arndt 
Date: Wed, 20 Mar 2019 17:01:28 +0100
Subject: [PATCH 294/507] Fix data_out_13 in case there is no ZLIB support

---
 .../data_out/data_out_13.with_zlib=off.output | 111 ++++++++++++++++++
 ...output => data_out_13.with_zlib=on.output} |   0
 2 files changed, 111 insertions(+)
 create mode 100644 tests/data_out/data_out_13.with_zlib=off.output
 rename tests/data_out/{data_out_13.output => data_out_13.with_zlib=on.output} (100%)

diff --git a/tests/data_out/data_out_13.with_zlib=off.output b/tests/data_out/data_out_13.with_zlib=off.output
new file mode 100644
index 000000000000..df62af4878fb
--- /dev/null
+++ b/tests/data_out/data_out_13.with_zlib=off.output
@@ -0,0 +1,111 @@
+
+ 
+
+
+
+
+  
+    
+0.00000 0.00000 0
+1.00000 0.00000 0
+0.00000 1.00000 0
+1.00000 1.00000 0
+    
+  
+
+  
+    
+0	1	3	2
+    
+    
+4 
+    
+    
+9 
+    
+  
+  
+    
+1.00000 0.00000 0.00000 1.00000 0.00000 0.00000 1.00000 1.00000 0.00000 1.00000 1.00000 0.00000     
+    
+1.00000 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 0.00000 3.00000 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 3.00000 0.00000 0.00000 0.00000 0.00000 3.00000 1.00000 0.00000 1.00000 2.00000 0.00000 0.00000 0.00000 0.00000     
+  
+ 
+ 
+
+
+
+
+  
+    
+    
+    
+    
+    
+      
+    
+    
+  
+
+ 
+
+
+
+
+  
+    
+0.00000 0.00000 0.00000
+1.00000 0.00000 0.00000
+0.00000 1.00000 0.00000
+1.00000 1.00000 0.00000
+0.00000 0.00000 1.00000
+1.00000 0.00000 1.00000
+0.00000 1.00000 1.00000
+1.00000 1.00000 1.00000
+    
+  
+
+  
+    
+0	1	3	2	4	5	7	6
+    
+    
+8 
+    
+    
+12 
+    
+  
+  
+    
+1.00000 0.00000 0.00000 1.00000 0.00000 0.00000 1.00000 1.00000 0.00000 1.00000 1.00000 0.00000 1.00000 0.00000 0.00000 1.00000 0.00000 0.00000 1.00000 1.00000 0.00000 1.00000 1.00000 0.00000     
+    
+1.00000 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 1.00000 -2.00000 0.00000 0.00000 0.00000 -2.00000 0.00000 0.00000 0.00000 3.00000 1.00000 0.00000 0.00000 0.00000 1.00000 0.00000 0.00000 0.00000 0.00100000 2.00000 1.00000 1.00000 1.00000 2.00000 1.00000 1.00000 1.00000 3.00000 0.247186 0.490995 0.131325 0.490995 -0.371056 0.719072 0.131325 0.719072 -0.156008 0.280588 0.467439 0.934953 0.467439 0.0600321 -0.211376 0.934953 -0.211376 0.962976 0.0628610 -0.0117908 -0.667617 -0.0117908 -0.390601 -0.957805 -0.667617 -0.957805 -0.193320 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000 0.00000     
+  
+ 
+ 
+
+
+
+
+  
+    
+    
+    
+    
+    
+      
+    
+    
+  
+
diff --git a/tests/data_out/data_out_13.output b/tests/data_out/data_out_13.with_zlib=on.output
similarity index 100%
rename from tests/data_out/data_out_13.output
rename to tests/data_out/data_out_13.with_zlib=on.output

From a78b01abb2d162943fd830df1401aa85ef639a8c Mon Sep 17 00:00:00 2001
From: Denis Davydov 
Date: Wed, 20 Mar 2019 22:19:55 +0100
Subject: [PATCH 295/507] further cleanup of distribute_sparsity_pattern()

---
 source/lac/sparsity_tools.cc | 18 ++++++++----------
 1 file changed, 8 insertions(+), 10 deletions(-)

diff --git a/source/lac/sparsity_tools.cc b/source/lac/sparsity_tools.cc
index 2ec2422ad64f..1a18621296bc 100644
--- a/source/lac/sparsity_tools.cc
+++ b/source/lac/sparsity_tools.cc
@@ -954,15 +954,13 @@ namespace SparsityTools
             continue;
 
           // save entries
-          auto &dst = send_data[dest_cpu];
-
-          dst.push_back(rlen); // number of entries
-          dst.push_back(row);  // row index
+          send_data[dest_cpu].push_back(row);  // row index
+          send_data[dest_cpu].push_back(rlen); // number of entries
           for (DynamicSparsityPattern::size_type c = 0; c < rlen; ++c)
             {
               // columns
               const auto column = dsp.column_number(row, c);
-              dst.push_back(column);
+              send_data[dest_cpu].push_back(column);
             }
         }
     }
@@ -977,13 +975,13 @@ namespace SparsityTools
         const auto  end      = recv_buf.end();
         while (ptr != end)
           {
-            const DynamicSparsityPattern::size_type num = *(ptr++);
+            const auto row = *(ptr++);
             Assert(ptr != end, ExcInternalError());
-            const DynamicSparsityPattern::size_type row = *(ptr++);
+            const auto n_entries = *(ptr++);
 
-            Assert(ptr + (num - 1) != end, ExcInternalError());
-            dsp.add_entries(row, ptr, ptr + num, true);
-            ptr += num;
+            Assert(ptr + (n_entries - 1) != end, ExcInternalError());
+            dsp.add_entries(row, ptr, ptr + n_entries, true);
+            ptr += n_entries;
           }
         Assert(ptr == end, ExcInternalError());
       }

From 5213023ca165bfbd420423551c184a3e31886223 Mon Sep 17 00:00:00 2001
From: Denis Davydov 
Date: Wed, 27 Feb 2019 22:04:58 +0100
Subject: [PATCH 296/507] split SparsityPattern into a base class and derived
 class with a special treatment for diagonal matrices

---
 include/deal.II/lac/sparsity_pattern.h      | 1041 +++++++++++--------
 source/lac/sparsity_pattern.cc              |   94 +-
 tests/serialization/sparsity_pattern.output |    4 +-
 tests/sparsity/sparsity_pattern_13.cc       |  171 +++
 tests/sparsity/sparsity_pattern_13.output   |    7 +
 5 files changed, 843 insertions(+), 474 deletions(-)
 create mode 100644 tests/sparsity/sparsity_pattern_13.cc
 create mode 100644 tests/sparsity/sparsity_pattern_13.output

diff --git a/include/deal.II/lac/sparsity_pattern.h b/include/deal.II/lac/sparsity_pattern.h
index 573c6c29475b..e87ca818e207 100644
--- a/include/deal.II/lac/sparsity_pattern.h
+++ b/include/deal.II/lac/sparsity_pattern.h
@@ -42,6 +42,7 @@
 DEAL_II_NAMESPACE_OPEN
 
 class SparsityPattern;
+class SparsityPatternBase;
 class DynamicSparsityPattern;
 class ChunkSparsityPattern;
 template 
@@ -139,12 +140,12 @@ namespace SparsityPatternIterators
     /**
      * Constructor.
      */
-    Accessor(const SparsityPattern *matrix, const std::size_t linear_index);
+    Accessor(const SparsityPatternBase *matrix, const std::size_t linear_index);
 
     /**
      * Constructor. Construct the end accessor for the given sparsity pattern.
      */
-    Accessor(const SparsityPattern *matrix);
+    Accessor(const SparsityPatternBase *matrix);
 
     /**
      * Default constructor creating a dummy accessor. This constructor is here
@@ -225,7 +226,7 @@ namespace SparsityPatternIterators
     /**
      * The sparsity pattern we operate on accessed.
      */
-    const SparsityPattern *container;
+    const SparsityPatternBase *container;
 
     /**
      * Index in global sparsity pattern. This index represents the location
@@ -267,7 +268,7 @@ namespace SparsityPatternIterators
    * SparsityPattern class for more information.
    *
    * @note This class operates directly on the internal data structures of the
-   * SparsityPattern class. As a consequence, some operations are cheap and
+   * SparsityPatternBase class. As a consequence, some operations are cheap and
    * some are not. In particular, it is cheap to access the column index of
    * the sparsity pattern entry pointed to. On the other hand, it is expensive
    * to access the row index (this requires $O(\log(N))$ operations for a
@@ -290,14 +291,14 @@ namespace SparsityPatternIterators
     /**
      * Type of the stored pointer.
      */
-    using container_pointer_type = SparsityPattern *;
+    using container_pointer_type = SparsityPatternBase *;
 
     /**
      * Constructor. Create an iterator into the sparsity pattern @p sp for the
      * given global index (i.e., the index of the given element counting from
      * the zeroth row).
      */
-    Iterator(const SparsityPattern *sp, const std::size_t linear_index);
+    Iterator(const SparsityPatternBase *sp, const std::size_t linear_index);
 
     /**
      * Constructor. Create an iterator into the sparsity pattern @p sp for
@@ -318,6 +319,516 @@ namespace SparsityPatternIterators
  * It uses the compressed row storage
  * (CSR) format to store data, and is used as the basis for the
+ * derived SparsityPattern class and SparseMatrix class.
+ *
+ * The elements of a SparsityPatternBase, corresponding to the places where
+ * SparseMatrix objects can store nonzero entries, are stored row-by-row.
+ * The ordering of non-zero elements within each row (i.e. increasing
+ * column index order) depends on the derived classes.
+ *
+ * @author Wolfgang Bangerth, Guido Kanschat and others
+ */
+class SparsityPatternBase : public Subscriptor
+{
+public:
+  /**
+   * Declare type for container size.
+   */
+  using size_type = types::global_dof_index;
+
+  /**
+   * Typedef an iterator class that allows to walk over all nonzero elements
+   * of a sparsity pattern.
+   */
+  using const_iterator = SparsityPatternIterators::Iterator;
+
+  /**
+   * Typedef an iterator class that allows to walk over all nonzero elements
+   * of a sparsity pattern.
+   *
+   * Since the iterator does not allow to modify the sparsity pattern, this
+   * type is the same as that for @p const_iterator.
+   */
+  using iterator = SparsityPatternIterators::Iterator;
+
+  /**
+   * Define a value which is used to indicate that a certain value in the
+   * #colnums array is unused, i.e. does not represent a certain column number
+   * index.
+   *
+   * Indices with this invalid value are used to insert new entries to the
+   * sparsity pattern using the add() member function, and are removed when
+   * calling compress().
+   *
+   * You should not assume that the variable declared here has a certain
+   * value. The initialization is given here only to enable the compiler to
+   * perform some optimizations, but the actual value of the variable may
+   * change over time.
+   */
+  static const size_type invalid_entry = numbers::invalid_size_type;
+
+  /**
+   * @name Construction and setup Constructors, destructor; functions
+   * initializing, copying and filling an object.
+   */
+  // @{
+  /**
+   * Initialize the matrix empty, that is with no memory allocated. This is
+   * useful if you want such objects as member variables in other classes. You
+   * can make the structure usable by calling the reinit() function.
+   */
+  SparsityPatternBase();
+
+  /**
+   * Destructor.
+   */
+  ~SparsityPatternBase() override = default;
+
+  /**
+   * Reallocate memory and set up data structures for a new matrix with @p m
+   * rows and @p n columns, with at most @p max_per_row
+   * nonzero entries per row.
+   *
+   * This function simply maps its operations to the other reinit()
+   * function.
+   */
+  void
+  reinit(const size_type m, const size_type n, const unsigned int max_per_row);
+
+  /**
+   * Reallocate memory for a matrix of size @p m times @p n. The number of
+   * entries for each row is taken from the array @p row_lengths which
+   * has to give this number of each row $i=1\ldots m$.
+   *
+   * If m*n==0 all memory is freed, resulting in a total
+   * reinitialization of the object. If it is nonzero, new memory is only
+   * allocated if the new size extends the old one. This is done to save time
+   * and to avoid fragmentation of the heap.
+   */
+  void
+  reinit(const size_type                  m,
+         const size_type                  n,
+         const std::vector &row_lengths);
+
+  /**
+   * Same as above, but with an ArrayView argument instead.
+   *
+   * The derived classes are responsible for implementation of this function.
+   */
+  virtual void
+  reinit(const size_type                      m,
+         const size_type                      n,
+         const ArrayView &row_lengths) = 0;
+
+  /**
+   * Make the sparsity pattern symmetric by adding the sparsity pattern of the
+   * transpose object.
+   *
+   * This function throws an exception if the sparsity pattern does not
+   * represent a quadratic matrix.
+   */
+  void
+  symmetrize();
+
+  /**
+   * Add a nonzero entry to the matrix.  This function may only be called for
+   * non-compressed sparsity patterns.
+   *
+   * If the entry already exists, nothing bad happens.
+   */
+  void
+  add(const size_type i, const size_type j);
+
+  // @}
+
+  /**
+   * @name Iterators
+   */
+  // @{
+
+  /**
+   * Iterator starting at the first entry of the matrix. The resulting
+   * iterator can be used to walk over all nonzero entries of the sparsity
+   * pattern.
+   *
+   * The order in which elements are accessed depends on the storage scheme
+   * implemented by derived classes.
+   */
+  iterator
+  begin() const;
+
+  /**
+   * Final iterator.
+   */
+  iterator
+  end() const;
+
+  /**
+   * Iterator starting at the first entry of row r.
+   *
+   * Note that if the given row is empty, i.e. does not contain any nonzero
+   * entries, then the iterator returned by this function equals
+   * end(r). Note also that the iterator may not be dereferenceable in
+   * that case.
+   *
+   * The order in which elements are accessed depends on the storage scheme
+   * implemented by derived classes.
+   */
+  iterator
+  begin(const size_type r) const;
+
+  /**
+   * Final iterator of row r. It points to the first element past the
+   * end of line @p r, or past the end of the entire sparsity pattern.
+   *
+   * Note that the end iterator is not necessarily dereferenceable. This is in
+   * particular the case if it is the end iterator for the last row of a
+   * matrix.
+   */
+  iterator
+  end(const size_type r) const;
+
+
+  // @}
+
+  /**
+   * @name Querying information
+   */
+  // @{
+
+  /**
+   * Test for equality of two SparsityPatterns.
+   */
+  bool
+  operator==(const SparsityPatternBase &) const;
+
+  /**
+   * Return whether the object is empty. It is empty if no memory is
+   * allocated, which is the same as that both dimensions are zero.
+   */
+  bool
+  empty() const;
+
+  /**
+   * Check if a value at a certain position may be non-zero.
+   */
+  bool
+  exists(const size_type i, const size_type j) const;
+
+  /**
+   * Return the maximum number of entries per row. Before compression, this
+   * equals the number given to the constructor, while after compression, it
+   * equals the maximum number of entries actually allocated by the user.
+   */
+  size_type
+  max_entries_per_row() const;
+
+  /**
+   * Compute the bandwidth of the matrix represented by this structure. The
+   * bandwidth is the maximum of $|i-j|$ for which the index pair $(i,j)$
+   * represents a nonzero entry of the matrix. Consequently, the maximum
+   * bandwidth a $n\times m$ matrix can have is $\max\{n-1,m-1\}$, a diagonal
+   * matrix has bandwidth 0, and there are at most $2*q+1$ entries per row if
+   * the bandwidth is $q$. The returned quantity is sometimes called "half
+   * bandwidth" in the literature.
+   */
+  size_type
+  bandwidth() const;
+
+  /**
+   * Return the number of nonzero elements of this matrix. Actually, it
+   * returns the number of entries in the sparsity pattern; if any of the
+   * entries should happen to be zero, it is counted anyway.
+   *
+   * This function may only be called if the matrix struct is compressed. It
+   * does not make too much sense otherwise anyway.
+   */
+  std::size_t
+  n_nonzero_elements() const;
+
+  /**
+   * Return whether the structure is compressed or not.
+   */
+  bool
+  is_compressed() const;
+
+  /**
+   * Return number of rows of this matrix, which equals the dimension of the
+   * image space.
+   */
+  size_type
+  n_rows() const;
+
+  /**
+   * Return number of columns of this matrix, which equals the dimension of
+   * the range space.
+   */
+  size_type
+  n_cols() const;
+
+  /**
+   * Number of entries in a specific row.
+   */
+  unsigned int
+  row_length(const size_type row) const;
+
+  /**
+   * Determine an estimate for the memory consumption (in bytes) of this
+   * object. See MemoryConsumption.
+   */
+  std::size_t
+  memory_consumption() const;
+
+  // @}
+
+  /**
+   * @name Accessing entries
+   */
+  // @{
+
+  /**
+   * Access to column number field.  Return the column number of the
+   * indexth entry in row. Note that if diagonal elements
+   * are optimized, the first element in each row is the diagonal element,
+   * i.e. column_number(row,0)==row.
+   *
+   * If the sparsity pattern is already compressed, then (except for the
+   * diagonal element), the entries are sorted by columns, i.e.
+   * column_number(row,i) < column_number(row,i+1).
+   */
+  size_type
+  column_number(const size_type row, const unsigned int index) const;
+
+  /**
+   * The index of a global matrix entry in its row.
+   *
+   * This function is analogous to operator(), but it computes the index not
+   * with respect to the total field, but only with respect to the row
+   * j.
+   */
+  size_type
+  row_position(const size_type i, const size_type j) const;
+
+  /**
+   * This is the inverse operation to operator()(): given a global index, find
+   * out row and column of the matrix entry to which it belongs. The returned
+   * value is the pair composed of row and column index.
+   *
+   * This function may only be called if the sparsity pattern is closed. The
+   * global index must then be between zero and n_nonzero_elements().
+   *
+   * If N is the number of rows of this matrix, then the complexity
+   * of this function is log(N).
+   */
+  std::pair
+  matrix_position(const std::size_t global_index) const;
+
+  // @}
+
+  /**
+   * @name Input/Output
+   */
+  // @{
+
+  /**
+   * Print the sparsity of the matrix. The output consists of one line per row
+   * of the format [i,j1,j2,j3,...]. i is the row number and
+   * jn are the allocated columns in this row.
+   */
+  void
+  print(std::ostream &out) const;
+
+  /**
+   * Print the sparsity of the matrix in a format that gnuplot
+   * understands and which can be used to plot the sparsity pattern in a
+   * graphical way. The format consists of pairs i j of nonzero
+   * elements, each representing one entry of this matrix, one per line of the
+   * output file. Indices are counted from zero on, as usual. Since sparsity
+   * patterns are printed in the same way as matrices are displayed, we print
+   * the negative of the column index, which means that the (0,0)
+   * element is in the top left rather than in the bottom left corner.
+   *
+   * Print the sparsity pattern in gnuplot by setting the data style to dots
+   * or points and use the plot command.
+   */
+  void
+  print_gnuplot(std::ostream &out) const;
+
+  /**
+   * Prints the sparsity of the matrix in a .svg file which can be opened in a
+   * web browser. The .svg file contains squares which correspond to the
+   * entries in the matrix. An entry in the matrix which contains a non-zero
+   * value corresponds with a red square while a zero-valued entry in the
+   * matrix correspond with a white square.
+   */
+  void
+  print_svg(std::ostream &out) const;
+
+  /**
+   * Write the data of this object to a stream for the purpose of
+   * serialization
+   */
+  template 
+  void
+  save(Archive &ar, const unsigned int version) const;
+
+  /**
+   * Read the data of this object from a stream for the purpose of
+   * serialization
+   */
+  template 
+  void
+  load(Archive &ar, const unsigned int version);
+
+  BOOST_SERIALIZATION_SPLIT_MEMBER()
+
+  // @}
+
+  /**
+   * @addtogroup Exceptions
+   * @{
+   */
+
+  /**
+   * The operation is only allowed after the SparsityPattern has been set up
+   * and compress() was called.
+   */
+  DeclExceptionMsg(
+    ExcNotCompressed,
+    "The operation you attempted is only allowed after the SparsityPattern "
+    "has been set up and compress() was called.");
+
+  /**
+   * You tried to add an element to a row, but there was no space left.
+   */
+  DeclException2(ExcNotEnoughSpace,
+                 int,
+                 int,
+                 << "Upon entering a new entry to row " << arg1
+                 << ": there was no free entry any more. " << std::endl
+                 << "(Maximum number of entries for this row: " << arg2
+                 << "; maybe the matrix is already compressed?)");
+
+  /**
+   * This operation changes the structure of the SparsityPattern and is not
+   * possible after compress() has been called.
+   */
+  DeclExceptionMsg(
+    ExcMatrixIsCompressed,
+    "The operation you attempted changes the structure of the SparsityPattern "
+    "and is not possible after compress() has been called.");
+
+  // @}
+
+
+protected:
+  /**
+   * Maximum number of rows that can be stored in the #rowstart array.  Since
+   * reallocation of that array only happens if the present one is too small,
+   * but never when the size of this matrix structure shrinks, #max_dim might
+   * be larger than #rows and in this case #rowstart has more elements than
+   * are used.
+   */
+  size_type max_dim;
+
+  /**
+   * Number of rows that this sparsity structure shall represent.
+   */
+  size_type rows;
+
+  /**
+   * Number of columns that this sparsity structure shall represent.
+   */
+  size_type cols;
+
+  /**
+   * Size of the actually allocated array #colnums. Here, the same applies as
+   * for the #rowstart array, i.e. it may be larger than the actually used
+   * part of the array.
+   */
+  std::size_t max_vec_len;
+
+  /**
+   * Maximum number of elements per row. This is set to the value given to the
+   * reinit() function (or to the constructor), or to the maximum row length
+   * computed from the vectors in case the more flexible constructors or
+   * reinit versions are called. Its value is more or less meaningless after
+   * compress() has been called.
+   */
+  unsigned int max_row_length;
+
+  /**
+   * Array which hold for each row which is the first element in #colnums
+   * belonging to that row. Note that the size of the array is one larger than
+   * the number of rows, because the last element is used for
+   * row=#rows, i.e. the row past the last used one. The value of
+   * #rowstart[#rows]} equals the index of the element past the end in
+   * #colnums; this way, we are able to write loops like for
+   * (i=rowstart[k]; i also for the last row.
+   *
+   * Note that the actual size of the allocated memory may be larger than the
+   * region that is used. The actual number of elements that was allocated is
+   * stored in #max_dim.
+   */
+  std::unique_ptr rowstart;
+
+  /**
+   * Array of column numbers. In this array, we store for each non-zero
+   * element its column number. The column numbers for the elements in row
+   * r are stored within the index range
+   * #rowstart[r]...#rowstart[r+1]. Therefore to find out
+   * whether a given element (r,c) exists, we have to check whether the
+   * column number c exists in the above-mentioned range within this
+   * array. If it exists, say at position p within this array, the
+   * value of the respective element in the sparse matrix will also be at
+   * position p of the values array of that class.
+   *
+   * At the beginning, all elements of this array are set to @p -1 indicating
+   * invalid (unused) column numbers (diagonal elements are preset if
+   * optimized storage is requested, though). Now, if nonzero elements are
+   * added, one column number in the row's respective range after the other is
+   * set to the column number of the added element. When compress is called,
+   * unused elements (indicated by column numbers @p -1) are eliminated by
+   * copying the column number of subsequent rows and the column numbers
+   * within each row (with possible exception of the diagonal element) are
+   * sorted, such that finding whether an element exists and determining its
+   * position can be done by a binary search.
+   */
+  std::unique_ptr colnums;
+
+  /**
+   * Store whether the compress() function was called for this object.
+   */
+  bool compressed;
+
+  /**
+   * Make all sparse matrices friends of this class.
+   */
+  template 
+  friend class SparseMatrix;
+  template 
+  friend class SparseLUDecomposition;
+  template 
+  friend class SparseILU;
+  template 
+  friend class ChunkSparseMatrix;
+
+  friend class ChunkSparsityPattern;
+  friend class DynamicSparsityPattern;
+
+  /**
+   * Also give access to internal details to the iterator/accessor classes.
+   */
+  friend class SparsityPatternIterators::Iterator;
+  friend class SparsityPatternIterators::Accessor;
+  friend class ChunkSparsityPatternIterators::Accessor;
+};
+
+/**
+ * This class stores a sparsity pattern in
+ * the compressed row storage
+ * (CSR) format to store data, and is used as the basis for the
  * SparseMatrix class.
  *
  * The elements of a SparsityPattern, corresponding to the places where
@@ -343,19 +854,19 @@ namespace SparsityPatternIterators
  *
  * @author Wolfgang Bangerth, Guido Kanschat and others
  */
-class SparsityPattern : public Subscriptor
+class SparsityPattern : public SparsityPatternBase
 {
 public:
   /**
    * Declare type for container size.
    */
-  using size_type = types::global_dof_index;
+  using size_type = SparsityPatternBase::size_type;
 
   /**
    * Typedef an iterator class that allows to walk over all nonzero elements
    * of a sparsity pattern.
    */
-  using const_iterator = SparsityPatternIterators::Iterator;
+  using const_iterator = SparsityPatternBase::const_iterator;
 
   /**
    * Typedef an iterator class that allows to walk over all nonzero elements
@@ -364,8 +875,14 @@ class SparsityPattern : public Subscriptor
    * Since the iterator does not allow to modify the sparsity pattern, this
    * type is the same as that for @p const_iterator.
    */
-  using iterator = SparsityPatternIterators::Iterator;
+  using iterator = SparsityPatternBase::iterator;
 
+  /**
+   * Since this class has to implement only one reinit() function, we need to
+   * bring all base reinit() functions into the scope so that the compiler can
+   * find them.
+   */
+  using SparsityPatternBase::reinit;
 
   /**
    * Define a value which is used to indicate that a certain value in the
@@ -381,7 +898,7 @@ class SparsityPattern : public Subscriptor
    * perform some optimizations, but the actual value of the variable may
    * change over time.
    */
-  static const size_type invalid_entry = numbers::invalid_size_type;
+  static const size_type invalid_entry = SparsityPatternBase::invalid_entry;
 
   /**
    * @name Construction and setup Constructors, destructor; functions
@@ -495,45 +1012,15 @@ class SparsityPattern : public Subscriptor
   SparsityPattern &
   operator=(const SparsityPattern &);
 
-  /**
-   * Reallocate memory and set up data structures for a new matrix with @p m
-   * rows and @p n columns, with at most @p max_per_row
-   * nonzero entries per row.
-   *
-   * This function simply maps its operations to the other reinit()
-   * function.
-   */
-  void
-  reinit(const size_type m, const size_type n, const unsigned int max_per_row);
-
-
   /**
    * Reallocate memory for a matrix of size @p m times @p n. The number of
-   * entries for each row is taken from the array @p row_lengths which
-   * has to give this number of each row $i=1\ldots m$.
-   *
-   * If m*n==0 all memory is freed, resulting in a total
-   * reinitialization of the object. If it is nonzero, new memory is only
-   * allocated if the new size extends the old one. This is done to save time
-   * and to avoid fragmentation of the heap.
-   *
-   * If the number of rows equals the number of columns and the last parameter
-   * is true, diagonal elements are stored first in each row to allow
-   * optimized access in relaxation methods of SparseMatrix.
-   */
-  void
-  reinit(const size_type                  m,
-         const size_type                  n,
-         const std::vector &row_lengths);
-
-
-  /**
-   * Same as above, but with an ArrayView argument instead.
+   * entries for each row is taken from the ArrayView @p row_lengths which
+   * has to give this number of each row $i=0\ldots m-1$.
    */
-  void
+  virtual void
   reinit(const size_type                      m,
          const size_type                      n,
-         const ArrayView &row_lengths);
+         const ArrayView &row_lengths) override;
 
   /**
    * This function compresses the sparsity structure that this object
@@ -649,174 +1136,41 @@ class SparsityPattern : public Subscriptor
   copy_from(const SparsityPattern &sp);
 
   /**
-   * Take a full matrix and use its nonzero entries to generate a sparse
-   * matrix entry pattern for this object.
-   *
-   * Previous content of this object is lost, and the sparsity pattern is in
-   * compressed mode afterwards.
-   */
-  template 
-  void
-  copy_from(const FullMatrix &matrix);
-
-  /**
-   * Make the sparsity pattern symmetric by adding the sparsity pattern of the
-   * transpose object.
-   *
-   * This function throws an exception if the sparsity pattern does not
-   * represent a quadratic matrix.
-   */
-  void
-  symmetrize();
-
-  /**
-   * Add a nonzero entry to the matrix.  This function may only be called for
-   * non-compressed sparsity patterns.
-   *
-   * If the entry already exists, nothing bad happens.
-   */
-  void
-  add(const size_type i, const size_type j);
-
-  /**
-   * Add several nonzero entries to the specified matrix row.  This function
-   * may only be called for non-compressed sparsity patterns.
-   *
-   * If some of the entries already exist, nothing bad happens.
-   */
-  template 
-  void
-  add_entries(const size_type row,
-              ForwardIterator begin,
-              ForwardIterator end,
-              const bool      indices_are_sorted = false);
-
-  // @}
-
-
-
-  /**
-   * @name Iterators
-   */
-  // @{
-
-  /**
-   * Iterator starting at the first entry of the matrix. The resulting
-   * iterator can be used to walk over all nonzero entries of the sparsity
-   * pattern.
-   *
-   * Note the discussion in the general documentation of this class about the
-   * order in which elements are accessed.
-   */
-  iterator
-  begin() const;
-
-  /**
-   * Final iterator.
-   */
-  iterator
-  end() const;
-
-  /**
-   * Iterator starting at the first entry of row r.
-   *
-   * Note that if the given row is empty, i.e. does not contain any nonzero
-   * entries, then the iterator returned by this function equals
-   * end(r). Note also that the iterator may not be dereferenceable in
-   * that case.
-   *
-   * Note also the discussion in the general documentation of this class about
-   * the order in which elements are accessed.
-   */
-  iterator
-  begin(const size_type r) const;
-
-  /**
-   * Final iterator of row r. It points to the first element past the
-   * end of line @p r, or past the end of the entire sparsity pattern.
-   *
-   * Note that the end iterator is not necessarily dereferenceable. This is in
-   * particular the case if it is the end iterator for the last row of a
-   * matrix.
-   */
-  iterator
-  end(const size_type r) const;
-
-
-  // @}
-  /**
-   * @name Querying information
-   */
-  // @{
-  /**
-   * Test for equality of two SparsityPatterns.
-   */
-  bool
-  operator==(const SparsityPattern &) const;
-
-  /**
-   * Return whether the object is empty. It is empty if no memory is
-   * allocated, which is the same as that both dimensions are zero.
-   */
-  bool
-  empty() const;
-
-  /**
-   * Return the maximum number of entries per row. Before compression, this
-   * equals the number given to the constructor, while after compression, it
-   * equals the maximum number of entries actually allocated by the user.
-   */
-  size_type
-  max_entries_per_row() const;
-
-  /**
-   * Compute the bandwidth of the matrix represented by this structure. The
-   * bandwidth is the maximum of $|i-j|$ for which the index pair $(i,j)$
-   * represents a nonzero entry of the matrix. Consequently, the maximum
-   * bandwidth a $n\times m$ matrix can have is $\max\{n-1,m-1\}$, a diagonal
-   * matrix has bandwidth 0, and there are at most $2*q+1$ entries per row if
-   * the bandwidth is $q$. The returned quantity is sometimes called "half
-   * bandwidth" in the literature.
-   */
-  size_type
-  bandwidth() const;
-
-  /**
-   * Return the number of nonzero elements of this matrix. Actually, it
-   * returns the number of entries in the sparsity pattern; if any of the
-   * entries should happen to be zero, it is counted anyway.
-   *
-   * This function may only be called if the matrix struct is compressed. It
-   * does not make too much sense otherwise anyway.
-   */
-  std::size_t
-  n_nonzero_elements() const;
-
-  /**
-   * Return whether the structure is compressed or not.
+   * Take a full matrix and use its nonzero entries to generate a sparse
+   * matrix entry pattern for this object.
+   *
+   * Previous content of this object is lost, and the sparsity pattern is in
+   * compressed mode afterwards.
    */
-  bool
-  is_compressed() const;
+  template 
+  void
+  copy_from(const FullMatrix &matrix);
 
   /**
-   * Return number of rows of this matrix, which equals the dimension of the
-   * image space.
+   * Add several nonzero entries to the specified matrix row.  This function
+   * may only be called for non-compressed sparsity patterns.
+   *
+   * If some of the entries already exist, nothing bad happens.
    */
-  size_type
-  n_rows() const;
+  template 
+  void
+  add_entries(const size_type row,
+              ForwardIterator begin,
+              ForwardIterator end,
+              const bool      indices_are_sorted = false);
+
+  // @}
+
 
   /**
-   * Return number of columns of this matrix, which equals the dimension of
-   * the range space.
+   * @name Querying information
    */
-  size_type
-  n_cols() const;
-
+  // @{
   /**
-   * Number of entries in a specific row.
+   * Test for equality of two SparsityPatterns.
    */
-  unsigned int
-  row_length(const size_type row) const;
+  bool
+  operator==(const SparsityPattern &) const;
 
   /**
    * Return whether this object stores only those entries that have been added
@@ -870,55 +1224,12 @@ class SparsityPattern : public Subscriptor
   size_type
   operator()(const size_type i, const size_type j) const;
 
-  /**
-   * This is the inverse operation to operator()(): given a global index, find
-   * out row and column of the matrix entry to which it belongs. The returned
-   * value is the pair composed of row and column index.
-   *
-   * This function may only be called if the sparsity pattern is closed. The
-   * global index must then be between zero and n_nonzero_elements().
-   *
-   * If N is the number of rows of this matrix, then the complexity
-   * of this function is log(N).
-   */
-  std::pair
-  matrix_position(const std::size_t global_index) const;
-
-  /**
-   * Check if a value at a certain position may be non-zero.
-   */
-  bool
-  exists(const size_type i, const size_type j) const;
-
-  /**
-   * The index of a global matrix entry in its row.
-   *
-   * This function is analogous to operator(), but it computes the index not
-   * with respect to the total field, but only with respect to the row
-   * j.
-   */
-  size_type
-  row_position(const size_type i, const size_type j) const;
-
-  /**
-   * Access to column number field.  Return the column number of the
-   * indexth entry in row. Note that if diagonal elements
-   * are optimized, the first element in each row is the diagonal element,
-   * i.e. column_number(row,0)==row.
-   *
-   * If the sparsity pattern is already compressed, then (except for the
-   * diagonal element), the entries are sorted by columns, i.e.
-   * column_number(row,i) < column_number(row,i+1).
-   */
-  size_type
-  column_number(const size_type row, const unsigned int index) const;
-
-
   // @}
   /**
    * @name Input/Output
    */
   // @{
+
   /**
    * Write the data of this object en bloc to a file. This is done in a binary
    * mode, so the output is neither readable by humans nor (probably) by other
@@ -948,41 +1259,6 @@ class SparsityPattern : public Subscriptor
   void
   block_read(std::istream &in);
 
-  /**
-   * Print the sparsity of the matrix. The output consists of one line per row
-   * of the format [i,j1,j2,j3,...]. i is the row number and
-   * jn are the allocated columns in this row.
-   */
-  void
-  print(std::ostream &out) const;
-
-  /**
-   * Print the sparsity of the matrix in a format that gnuplot
-   * understands and which can be used to plot the sparsity pattern in a
-   * graphical way. The format consists of pairs i j of nonzero
-   * elements, each representing one entry of this matrix, one per line of the
-   * output file. Indices are counted from zero on, as usual. Since sparsity
-   * patterns are printed in the same way as matrices are displayed, we print
-   * the negative of the column index, which means that the (0,0)
-   * element is in the top left rather than in the bottom left corner.
-   *
-   * Print the sparsity pattern in gnuplot by setting the data style to dots
-   * or points and use the plot command.
-   */
-  void
-  print_gnuplot(std::ostream &out) const;
-
-  /**
-   * Prints the sparsity of the matrix in a .svg file which can be opened in a
-   * web browser. The .svg file contains squares which correspond to the
-   * entries in the matrix. An entry in the matrix which contains a non-zero
-   * value corresponds with a red square while a zero-valued entry in the
-   * matrix correspond with a white square.
-   */
-  void
-  print_svg(std::ostream &out) const;
-
-
   /**
    * Write the data of this object to a stream for the purpose of
    * serialization
@@ -1007,32 +1283,6 @@ class SparsityPattern : public Subscriptor
    * @addtogroup Exceptions
    * @{
    */
-  /**
-   * You tried to add an element to a row, but there was no space left.
-   */
-  DeclException2(ExcNotEnoughSpace,
-                 int,
-                 int,
-                 << "Upon entering a new entry to row " << arg1
-                 << ": there was no free entry any more. " << std::endl
-                 << "(Maximum number of entries for this row: " << arg2
-                 << "; maybe the matrix is already compressed?)");
-  /**
-   * The operation is only allowed after the SparsityPattern has been set up
-   * and compress() was called.
-   */
-  DeclExceptionMsg(
-    ExcNotCompressed,
-    "The operation you attempted is only allowed after the SparsityPattern "
-    "has been set up and compress() was called.");
-  /**
-   * This operation changes the structure of the SparsityPattern and is not
-   * possible after compress() has been called.
-   */
-  DeclExceptionMsg(
-    ExcMatrixIsCompressed,
-    "The operation you attempted changes the structure of the SparsityPattern "
-    "and is not possible after compress() has been called.");
   /**
    * Exception
    */
@@ -1050,85 +1300,6 @@ class SparsityPattern : public Subscriptor
                  << ", but must be greater than zero.");
   //@}
 private:
-  /**
-   * Maximum number of rows that can be stored in the #rowstart array.  Since
-   * reallocation of that array only happens if the present one is too small,
-   * but never when the size of this matrix structure shrinks, #max_dim might
-   * be larger than #rows and in this case #rowstart has more elements than
-   * are used.
-   */
-  size_type max_dim;
-
-  /**
-   * Number of rows that this sparsity structure shall represent.
-   */
-  size_type rows;
-
-  /**
-   * Number of columns that this sparsity structure shall represent.
-   */
-  size_type cols;
-
-  /**
-   * Size of the actually allocated array #colnums. Here, the same applies as
-   * for the #rowstart array, i.e. it may be larger than the actually used
-   * part of the array.
-   */
-  std::size_t max_vec_len;
-
-  /**
-   * Maximum number of elements per row. This is set to the value given to the
-   * reinit() function (or to the constructor), or to the maximum row length
-   * computed from the vectors in case the more flexible constructors or
-   * reinit versions are called. Its value is more or less meaningless after
-   * compress() has been called.
-   */
-  unsigned int max_row_length;
-
-  /**
-   * Array which hold for each row which is the first element in #colnums
-   * belonging to that row. Note that the size of the array is one larger than
-   * the number of rows, because the last element is used for
-   * row=#rows, i.e. the row past the last used one. The value of
-   * #rowstart[#rows]} equals the index of the element past the end in
-   * #colnums; this way, we are able to write loops like for
-   * (i=rowstart[k]; i also for the last row.
-   *
-   * Note that the actual size of the allocated memory may be larger than the
-   * region that is used. The actual number of elements that was allocated is
-   * stored in #max_dim.
-   */
-  std::unique_ptr rowstart;
-
-  /**
-   * Array of column numbers. In this array, we store for each non-zero
-   * element its column number. The column numbers for the elements in row
-   * r are stored within the index range
-   * #rowstart[r]...#rowstart[r+1]. Therefore to find out
-   * whether a given element (r,c) exists, we have to check whether the
-   * column number c exists in the above-mentioned range within this
-   * array. If it exists, say at position p within this array, the
-   * value of the respective element in the sparse matrix will also be at
-   * position p of the values array of that class.
-   *
-   * At the beginning, all elements of this array are set to @p -1 indicating
-   * invalid (unused) column numbers (diagonal elements are preset if
-   * optimized storage is requested, though). Now, if nonzero elements are
-   * added, one column number in the row's respective range after the other is
-   * set to the column number of the added element. When compress is called,
-   * unused elements (indicated by column numbers @p -1) are eliminated by
-   * copying the column number of subsequent rows and the column numbers
-   * within each row (with possible exception of the diagonal element) are
-   * sorted, such that finding whether an element exists and determining its
-   * position can be done by a binary search.
-   */
-  std::unique_ptr colnums;
-
-  /**
-   * Store whether the compress() function was called for this object.
-   */
-  bool compressed;
-
   /**
    * Is special treatment of diagonals enabled?
    */
@@ -1166,15 +1337,15 @@ class SparsityPattern : public Subscriptor
 
 namespace SparsityPatternIterators
 {
-  inline Accessor::Accessor(const SparsityPattern *sparsity_pattern,
-                            const std::size_t      i)
+  inline Accessor::Accessor(const SparsityPatternBase *sparsity_pattern,
+                            const std::size_t          i)
     : container(sparsity_pattern)
     , linear_index(i)
   {}
 
 
 
-  inline Accessor::Accessor(const SparsityPattern *sparsity_pattern)
+  inline Accessor::Accessor(const SparsityPatternBase *sparsity_pattern)
     : container(sparsity_pattern)
     , linear_index(container->rowstart[container->rows])
   {}
@@ -1274,8 +1445,8 @@ namespace SparsityPatternIterators
   }
 
 
-  inline Iterator::Iterator(const SparsityPattern *sp,
-                            const std::size_t      linear_index)
+  inline Iterator::Iterator(const SparsityPatternBase *sp,
+                            const std::size_t          linear_index)
     : LinearIndexIterator(Accessor(sp, linear_index))
   {}
 
@@ -1289,8 +1460,8 @@ namespace SparsityPatternIterators
 
 
 
-inline SparsityPattern::iterator
-SparsityPattern::begin() const
+inline SparsityPatternBase::iterator
+SparsityPatternBase::begin() const
 {
   if (n_rows() > 0)
     return {this, rowstart[0]};
@@ -1300,8 +1471,8 @@ SparsityPattern::begin() const
 
 
 
-inline SparsityPattern::iterator
-SparsityPattern::end() const
+inline SparsityPatternBase::iterator
+SparsityPatternBase::end() const
 {
   if (n_rows() > 0)
     return {this, rowstart[rows]};
@@ -1311,8 +1482,8 @@ SparsityPattern::end() const
 
 
 
-inline SparsityPattern::iterator
-SparsityPattern::begin(const size_type r) const
+inline SparsityPatternBase::iterator
+SparsityPatternBase::begin(const size_type r) const
 {
   Assert(r < n_rows(), ExcIndexRangeType(r, 0, n_rows()));
 
@@ -1321,8 +1492,8 @@ SparsityPattern::begin(const size_type r) const
 
 
 
-inline SparsityPattern::iterator
-SparsityPattern::end(const size_type r) const
+inline SparsityPatternBase::iterator
+SparsityPatternBase::end(const size_type r) const
 {
   Assert(r < n_rows(), ExcIndexRangeType(r, 0, n_rows()));
 
@@ -1331,16 +1502,16 @@ SparsityPattern::end(const size_type r) const
 
 
 
-inline SparsityPattern::size_type
-SparsityPattern::n_rows() const
+inline SparsityPatternBase::size_type
+SparsityPatternBase::n_rows() const
 {
   return rows;
 }
 
 
 
-inline SparsityPattern::size_type
-SparsityPattern::n_cols() const
+inline SparsityPatternBase::size_type
+SparsityPatternBase::n_cols() const
 {
   return cols;
 }
@@ -1348,7 +1519,7 @@ SparsityPattern::n_cols() const
 
 
 inline bool
-SparsityPattern::is_compressed() const
+SparsityPatternBase::is_compressed() const
 {
   return compressed;
 }
@@ -1364,7 +1535,7 @@ SparsityPattern::stores_only_added_elements() const
 
 
 inline unsigned int
-SparsityPattern::row_length(const size_type row) const
+SparsityPatternBase::row_length(const size_type row) const
 {
   Assert(row < rows, ExcIndexRangeType(row, 0, rows));
   return rowstart[row + 1] - rowstart[row];
@@ -1373,8 +1544,8 @@ SparsityPattern::row_length(const size_type row) const
 
 
 inline SparsityPattern::size_type
-SparsityPattern::column_number(const size_type    row,
-                               const unsigned int index) const
+SparsityPatternBase::column_number(const size_type    row,
+                                   const unsigned int index) const
 {
   Assert(row < rows, ExcIndexRangeType(row, 0, rows));
   Assert(index < row_length(row), ExcIndexRange(index, 0, row_length(row)));
@@ -1385,7 +1556,7 @@ SparsityPattern::column_number(const size_type    row,
 
 
 inline std::size_t
-SparsityPattern::n_nonzero_elements() const
+SparsityPatternBase::n_nonzero_elements() const
 {
   Assert(compressed, ExcNotCompressed());
 
@@ -1400,13 +1571,12 @@ SparsityPattern::n_nonzero_elements() const
 
 template 
 inline void
-SparsityPattern::save(Archive &ar, const unsigned int) const
+SparsityPatternBase::save(Archive &ar, const unsigned int) const
 {
   // forward to serialization function in the base class.
-  ar &static_cast(*this);
+  ar &boost::serialization::base_object(*this);
 
-  ar &max_dim &rows &cols &max_vec_len &max_row_length &compressed
-    &store_diagonal_first_in_row;
+  ar &max_dim &rows &cols &max_vec_len &max_row_length &compressed;
 
   ar &boost::serialization::make_array(rowstart.get(), max_dim + 1);
   ar &boost::serialization::make_array(colnums.get(), max_vec_len);
@@ -1416,13 +1586,12 @@ SparsityPattern::save(Archive &ar, const unsigned int) const
 
 template 
 inline void
-SparsityPattern::load(Archive &ar, const unsigned int)
+SparsityPatternBase::load(Archive &ar, const unsigned int)
 {
   // forward to serialization function in the base class.
-  ar &static_cast(*this);
+  ar &boost::serialization::base_object(*this);
 
-  ar &max_dim &rows &cols &max_vec_len &max_row_length &compressed
-    &store_diagonal_first_in_row;
+  ar &max_dim &rows &cols &max_vec_len &max_row_length &compressed;
 
   rowstart = std_cxx14::make_unique(max_dim + 1);
   colnums  = std_cxx14::make_unique(max_vec_len);
@@ -1433,15 +1602,36 @@ SparsityPattern::load(Archive &ar, const unsigned int)
 
 
 
+template 
+inline void
+SparsityPattern::save(Archive &ar, const unsigned int) const
+{
+  // forward to serialization function in the base class.
+  ar &boost::serialization::base_object(*this);
+  ar &store_diagonal_first_in_row;
+}
+
+
+
+template 
+inline void
+SparsityPattern::load(Archive &ar, const unsigned int)
+{
+  // forward to serialization function in the base class.
+  ar &boost::serialization::base_object(*this);
+  ar &store_diagonal_first_in_row;
+}
+
+
+
 inline bool
-SparsityPattern::operator==(const SparsityPattern &sp2) const
+SparsityPatternBase::operator==(const SparsityPatternBase &sp2) const
 {
   // it isn't quite necessary to compare *all* member variables. by only
   // comparing the essential ones, we can say that two sparsity patterns are
   // equal even if one is compressed and the other is not (in which case some
   // of the member variables are not yet set correctly)
-  if (rows != sp2.rows || cols != sp2.cols || compressed != sp2.compressed ||
-      store_diagonal_first_in_row != sp2.store_diagonal_first_in_row)
+  if (rows != sp2.rows || cols != sp2.cols || compressed != sp2.compressed)
     return false;
 
   for (size_type i = 0; i < rows + 1; ++i)
@@ -1457,6 +1647,15 @@ SparsityPattern::operator==(const SparsityPattern &sp2) const
 
 
 
+inline bool
+SparsityPattern::operator==(const SparsityPattern &sp2) const
+{
+  return (static_cast(*this) == sp2) &&
+         (store_diagonal_first_in_row == sp2.store_diagonal_first_in_row);
+}
+
+
+
 namespace internal
 {
   namespace SparsityPatternTools
diff --git a/source/lac/sparsity_pattern.cc b/source/lac/sparsity_pattern.cc
index 2eb565a4542d..ee331f9ead27 100644
--- a/source/lac/sparsity_pattern.cc
+++ b/source/lac/sparsity_pattern.cc
@@ -36,15 +36,21 @@ DEAL_II_NAMESPACE_OPEN
 __declspec(selectany) // Weak extern binding due to multiple link error
 #endif
   const SparsityPattern::size_type SparsityPattern::invalid_entry;
+const SparsityPatternBase::size_type SparsityPatternBase::invalid_entry;
 
 
-
-SparsityPattern::SparsityPattern()
+SparsityPatternBase::SparsityPatternBase()
   : max_dim(0)
   , max_vec_len(0)
   , rowstart(nullptr)
   , colnums(nullptr)
   , compressed(false)
+{}
+
+
+
+SparsityPattern::SparsityPattern()
+  : SparsityPatternBase()
   , store_diagonal_first_in_row(false)
 {
   reinit(0, 0, 0);
@@ -53,12 +59,7 @@ SparsityPattern::SparsityPattern()
 
 
 SparsityPattern::SparsityPattern(const SparsityPattern &s)
-  : Subscriptor()
-  , max_dim(0)
-  , max_vec_len(0)
-  , rowstart(nullptr)
-  , colnums(nullptr)
-  , compressed(false)
+  : SparsityPatternBase()
   , store_diagonal_first_in_row(false)
 {
   (void)s;
@@ -76,11 +77,7 @@ SparsityPattern::SparsityPattern(const SparsityPattern &s)
 SparsityPattern::SparsityPattern(const size_type    m,
                                  const size_type    n,
                                  const unsigned int max_per_row)
-  : max_dim(0)
-  , max_vec_len(0)
-  , rowstart(nullptr)
-  , colnums(nullptr)
-  , compressed(false)
+  : SparsityPatternBase()
   , store_diagonal_first_in_row(m == n)
 {
   reinit(m, n, max_per_row);
@@ -91,10 +88,7 @@ SparsityPattern::SparsityPattern(const size_type    m,
 SparsityPattern::SparsityPattern(const size_type                  m,
                                  const size_type                  n,
                                  const std::vector &row_lengths)
-  : max_dim(0)
-  , max_vec_len(0)
-  , rowstart(nullptr)
-  , colnums(nullptr)
+  : SparsityPatternBase()
   , store_diagonal_first_in_row(m == n)
 {
   reinit(m, n, row_lengths);
@@ -104,10 +98,7 @@ SparsityPattern::SparsityPattern(const size_type                  m,
 
 SparsityPattern::SparsityPattern(const size_type    m,
                                  const unsigned int max_per_row)
-  : max_dim(0)
-  , max_vec_len(0)
-  , rowstart(nullptr)
-  , colnums(nullptr)
+  : SparsityPatternBase()
 {
   reinit(m, m, max_per_row);
 }
@@ -116,10 +107,7 @@ SparsityPattern::SparsityPattern(const size_type    m,
 
 SparsityPattern::SparsityPattern(const size_type                  m,
                                  const std::vector &row_lengths)
-  : max_dim(0)
-  , max_vec_len(0)
-  , rowstart(nullptr)
-  , colnums(nullptr)
+  : SparsityPatternBase()
 {
   reinit(m, m, row_lengths);
 }
@@ -129,10 +117,7 @@ SparsityPattern::SparsityPattern(const size_type                  m,
 SparsityPattern::SparsityPattern(const SparsityPattern &original,
                                  const unsigned int     max_per_row,
                                  const size_type        extra_off_diagonals)
-  : max_dim(0)
-  , max_vec_len(0)
-  , rowstart(nullptr)
-  , colnums(nullptr)
+  : SparsityPattern()
 {
   Assert(original.rows == original.cols, ExcNotQuadratic());
   Assert(original.is_compressed(), ExcNotCompressed());
@@ -228,9 +213,9 @@ SparsityPattern::operator=(const SparsityPattern &s)
 
 
 void
-SparsityPattern::reinit(const size_type    m,
-                        const size_type    n,
-                        const unsigned int max_per_row)
+SparsityPatternBase::reinit(const size_type    m,
+                            const size_type    n,
+                            const unsigned int max_per_row)
 {
   // simply map this function to the other @p{reinit} function
   const std::vector row_lengths(m, max_per_row);
@@ -601,9 +586,9 @@ SparsityPattern::copy_from(const FullMatrix &matrix)
 
 
 void
-SparsityPattern::reinit(const size_type                  m,
-                        const size_type                  n,
-                        const std::vector &row_lengths)
+SparsityPatternBase::reinit(const size_type                  m,
+                            const size_type                  n,
+                            const std::vector &row_lengths)
 {
   reinit(m, n, make_slice(row_lengths));
 }
@@ -611,7 +596,7 @@ SparsityPattern::reinit(const size_type                  m,
 
 
 bool
-SparsityPattern::empty() const
+SparsityPatternBase::empty() const
 {
   // let's try to be on the safe side of life by using multiple possibilities
   // in the check for emptiness... (sorry for this kludge -- emptying matrices
@@ -633,8 +618,8 @@ SparsityPattern::empty() const
 
 
 
-SparsityPattern::size_type
-SparsityPattern::max_entries_per_row() const
+SparsityPatternBase::size_type
+SparsityPatternBase::max_entries_per_row() const
 {
   // if compress() has not yet been called, we can get the maximum number of
   // elements per row using the stored value
@@ -691,7 +676,7 @@ SparsityPattern::operator()(const size_type i, const size_type j) const
 
 
 void
-SparsityPattern::add(const size_type i, const size_type j)
+SparsityPatternBase::add(const size_type i, const size_type j)
 {
   Assert((rowstart != nullptr) && (colnums != nullptr), ExcEmptyObject());
   Assert(i < rows, ExcIndexRange(i, 0, rows));
@@ -768,7 +753,7 @@ SparsityPattern::add_entries(const size_type row,
 
 
 bool
-SparsityPattern::exists(const size_type i, const size_type j) const
+SparsityPatternBase::exists(const size_type i, const size_type j) const
 {
   Assert((rowstart != nullptr) && (colnums != nullptr), ExcEmptyObject());
   Assert(i < rows, ExcIndexRange(i, 0, rows));
@@ -785,8 +770,8 @@ SparsityPattern::exists(const size_type i, const size_type j) const
 
 
 
-SparsityPattern::size_type
-SparsityPattern::row_position(const size_type i, const size_type j) const
+SparsityPatternBase::size_type
+SparsityPatternBase::row_position(const size_type i, const size_type j) const
 {
   Assert((rowstart != nullptr) && (colnums != nullptr), ExcEmptyObject());
   Assert(i < rows, ExcIndexRange(i, 0, rows));
@@ -803,8 +788,8 @@ SparsityPattern::row_position(const size_type i, const size_type j) const
 
 
 
-std::pair
-SparsityPattern::matrix_position(const std::size_t global_index) const
+std::pair
+SparsityPatternBase::matrix_position(const std::size_t global_index) const
 {
   Assert(compressed == true, ExcNotCompressed());
   Assert(global_index < n_nonzero_elements(),
@@ -829,7 +814,7 @@ SparsityPattern::matrix_position(const std::size_t global_index) const
 
 
 void
-SparsityPattern::symmetrize()
+SparsityPatternBase::symmetrize()
 {
   Assert((rowstart != nullptr) && (colnums != nullptr), ExcEmptyObject());
   Assert(compressed == false, ExcMatrixIsCompressed());
@@ -863,7 +848,7 @@ SparsityPattern::symmetrize()
 
 
 void
-SparsityPattern::print(std::ostream &out) const
+SparsityPatternBase::print(std::ostream &out) const
 {
   Assert((rowstart != nullptr) && (colnums != nullptr), ExcEmptyObject());
 
@@ -884,7 +869,7 @@ SparsityPattern::print(std::ostream &out) const
 
 
 void
-SparsityPattern::print_gnuplot(std::ostream &out) const
+SparsityPatternBase::print_gnuplot(std::ostream &out) const
 {
   Assert((rowstart != nullptr) && (colnums != nullptr), ExcEmptyObject());
 
@@ -902,7 +887,7 @@ SparsityPattern::print_gnuplot(std::ostream &out) const
 }
 
 void
-SparsityPattern::print_svg(std::ostream &out) const
+SparsityPatternBase::print_svg(std::ostream &out) const
 {
   unsigned int m = this->n_rows();
   unsigned int n = this->n_cols();
@@ -935,8 +920,8 @@ SparsityPattern::print_svg(std::ostream &out) const
 
 
 
-SparsityPattern::size_type
-SparsityPattern::bandwidth() const
+SparsityPatternBase::size_type
+SparsityPatternBase::bandwidth() const
 {
   Assert((rowstart != nullptr) && (colnums != nullptr), ExcEmptyObject());
   size_type b = 0;
@@ -1019,13 +1004,20 @@ SparsityPattern::block_read(std::istream &in)
 
 
 std::size_t
-SparsityPattern::memory_consumption() const
+SparsityPatternBase::memory_consumption() const
 {
   return (max_dim * sizeof(size_type) + sizeof(*this) +
           max_vec_len * sizeof(size_type));
 }
 
 
+std::size_t
+SparsityPattern::memory_consumption() const
+{
+  return sizeof(*this) + SparsityPatternBase::memory_consumption();
+}
+
+
 
 // explicit instantiations
 template void
diff --git a/tests/serialization/sparsity_pattern.output b/tests/serialization/sparsity_pattern.output
index cf500822409c..abc3bde154b5 100644
--- a/tests/serialization/sparsity_pattern.output
+++ b/tests/serialization/sparsity_pattern.output
@@ -1,6 +1,6 @@
 
-DEAL::0 0 0 0 16 16 16 64 5 1 1 0 3 7 11 14 18 23 28 32 36 41 46 50 53 57 61 64 0 1 4 1 0 2 5 2 1 3 6 3 2 7 4 0 5 8 5 1 4 6 9 6 2 5 7 10 7 3 6 11 8 4 9 12 9 5 8 10 13 10 6 9 11 14 11 7 10 15 12 8 13 13 9 12 14 14 10 13 15 15 11 14
+DEAL::0 0 0 0 0 0 16 16 16 64 5 1 0 3 7 11 14 18 23 28 32 36 41 46 50 53 57 61 64 0 1 4 1 0 2 5 2 1 3 6 3 2 7 4 0 5 8 5 1 4 6 9 6 2 5 7 10 7 3 6 11 8 4 9 12 9 5 8 10 13 10 6 9 11 14 11 7 10 15 12 8 13 13 9 12 14 14 10 13 15 15 11 14 1
 
-DEAL::0 0 0 0 16 16 16 64 5 1 1 0 3 7 11 14 18 23 28 32 36 41 46 50 53 57 61 64 0 1 4 1 0 2 5 2 1 3 6 3 2 7 4 0 5 8 5 1 4 6 9 6 2 5 7 10 7 3 6 11 8 4 9 12 9 5 8 10 13 10 6 9 11 14 11 7 10 15 12 8 13 13 9 12 14 14 10 13 15 15 11 14
+DEAL::0 0 0 0 0 0 16 16 16 64 5 1 0 3 7 11 14 18 23 28 32 36 41 46 50 53 57 61 64 0 1 4 1 0 2 5 2 1 3 6 3 2 7 4 0 5 8 5 1 4 6 9 6 2 5 7 10 7 3 6 11 8 4 9 12 9 5 8 10 13 10 6 9 11 14 11 7 10 15 12 8 13 13 9 12 14 14 10 13 15 15 11 14 1
 
 DEAL::OK
diff --git a/tests/sparsity/sparsity_pattern_13.cc b/tests/sparsity/sparsity_pattern_13.cc
new file mode 100644
index 000000000000..c1b0a8f1ff8b
--- /dev/null
+++ b/tests/sparsity/sparsity_pattern_13.cc
@@ -0,0 +1,171 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2018 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+
+
+// proof of concept for DynamicSparsityPattern-like CSR object without
+// special treatment of diagonals
+
+#include "sparsity_pattern_common.h"
+
+class SparsityPatternStandard : public SparsityPatternBase
+{
+public:
+  using size_type = SparsityPatternBase::size_type;
+
+  using SparsityPatternBase::reinit;
+
+  SparsityPatternStandard()
+    : SparsityPatternBase()
+  {
+    reinit(0, 0, 0);
+  };
+
+  virtual void
+  reinit(const size_type                      m,
+         const size_type                      n,
+         const ArrayView &row_lengths) override
+  {
+    AssertDimension(row_lengths.size(), m);
+
+    rows = m;
+    cols = n;
+
+    // delete empty matrices
+    if ((m == 0) || (n == 0))
+      {
+        rowstart.reset();
+        colnums.reset();
+
+        max_vec_len = max_dim = rows = cols = 0;
+        // if dimension is zero: ignore max_per_row
+        max_row_length = 0;
+        compressed     = false;
+
+        return;
+      }
+
+    // find out how many entries we need in the @p{colnums} array. if this
+    // number is larger than @p{max_vec_len}, then we will need to reallocate
+    // memory
+    //
+    // note that the number of elements per row is bounded by the number of
+    // columns
+    //
+    std::size_t vec_len = 0;
+    for (size_type i = 0; i < m; ++i)
+      vec_len += std::min(static_cast(row_lengths[i]), n);
+
+    // sometimes, no entries are requested in the matrix (this most often
+    // happens when blocks in a block matrix are simply zero). in that case,
+    // allocate exactly one element, to have a valid pointer to some memory
+    if (vec_len == 0)
+      {
+        vec_len     = 1;
+        max_vec_len = vec_len;
+        colnums     = std_cxx14::make_unique(max_vec_len);
+      }
+
+    max_row_length =
+      (row_lengths.size() == 0 ?
+         0 :
+         std::min(static_cast(
+                    *std::max_element(row_lengths.begin(), row_lengths.end())),
+                  n));
+
+    // allocate memory for the rowstart values, if necessary. even though we
+    // re-set the pointers again immediately after deleting their old content,
+    // set them to zero in between because the allocation might fail, in which
+    // case we get an exception and the destructor of this object will be called
+    // -- where we look at the non-nullness of the (now invalid) pointer again
+    // and try to delete the memory a second time.
+    if (rows > max_dim)
+      {
+        max_dim  = rows;
+        rowstart = std_cxx14::make_unique(max_dim + 1);
+      }
+
+    // allocate memory for the column numbers if necessary
+    if (vec_len > max_vec_len)
+      {
+        max_vec_len = vec_len;
+        colnums     = std_cxx14::make_unique(max_vec_len);
+      }
+
+    // set the rowstart array
+    rowstart[0] = 0;
+    for (size_type i = 1; i <= rows; ++i)
+      rowstart[i] = rowstart[i - 1] +
+                    std::min(static_cast(row_lengths[i - 1]), n);
+    Assert((rowstart[rows] == vec_len) ||
+             ((vec_len == 1) && (rowstart[rows] == 0)),
+           ExcInternalError());
+
+    // preset the column numbers by a value indicating it is not in use
+    std::fill_n(colnums.get(), vec_len, invalid_entry);
+
+    compressed = false;
+  };
+
+  void
+  copy_from(const DynamicSparsityPattern &dsp)
+  {
+    std::vector row_lengths(dsp.n_rows());
+    for (size_type i = 0; i < dsp.n_rows(); ++i)
+      row_lengths[i] = dsp.row_length(i);
+
+    reinit(dsp.n_rows(), dsp.n_cols(), row_lengths);
+
+    if (n_rows() != 0 && n_cols() != 0)
+      for (size_type row = 0; row < dsp.n_rows(); ++row)
+        {
+          size_type *        cols       = &colnums[rowstart[row]];
+          const unsigned int row_length = dsp.row_length(row);
+          for (unsigned int index = 0; index < row_length; ++index)
+            {
+              const size_type col = dsp.column_number(row, index);
+              *cols++             = col;
+            }
+        }
+
+    compressed = true;
+  };
+};
+
+
+
+int
+main()
+{
+  std::ofstream logfile("output");
+  logfile.setf(std::ios::fixed);
+  deallog << std::setprecision(3);
+  deallog.attach(logfile);
+
+  DynamicSparsityPattern dsp(2);
+  dsp.add(0, 1);
+  dsp.add(1, 0);
+
+  SparsityPattern sp_usual;
+  sp_usual.copy_from(dsp);
+  deallog << "SparsityPattern:" << std::endl;
+  sp_usual.print(deallog.get_file_stream());
+
+  SparsityPatternStandard sp;
+  sp.copy_from(dsp);
+
+  deallog << "SparsityPatternStandard:" << std::endl;
+  sp.print(deallog.get_file_stream());
+}
diff --git a/tests/sparsity/sparsity_pattern_13.output b/tests/sparsity/sparsity_pattern_13.output
new file mode 100644
index 000000000000..0da0dd68e139
--- /dev/null
+++ b/tests/sparsity/sparsity_pattern_13.output
@@ -0,0 +1,7 @@
+
+DEAL::SparsityPattern:
+[0,0,1]
+[1,1,0]
+DEAL::SparsityPatternStandard:
+[0,1]
+[1,0]

From 1519aa2d431372e63dd66a62b059244b935a5679 Mon Sep 17 00:00:00 2001
From: Timo Heister 
Date: Wed, 20 Mar 2019 18:22:43 -0600
Subject: [PATCH 297/507] use 64 bit tbb range

---
 include/deal.II/lac/la_vector.templates.h     |  6 +++---
 .../deal.II/lac/vector_operations_internal.h  | 20 +++++++++++++------
 2 files changed, 17 insertions(+), 9 deletions(-)

diff --git a/include/deal.II/lac/la_vector.templates.h b/include/deal.II/lac/la_vector.templates.h
index 7eaa6b3eea41..94309bde36db 100644
--- a/include/deal.II/lac/la_vector.templates.h
+++ b/include/deal.II/lac/la_vector.templates.h
@@ -92,7 +92,7 @@ namespace LinearAlgebra
     dealii::internal::VectorOperations::Vector_copy copier(
       in_vector.values.get(), this->values.get());
     internal::VectorOperations::parallel_for(copier,
-                                             0,
+                                             static_cast(0),
                                              this->size(),
                                              this->thread_loop_partitioner);
 
@@ -113,7 +113,7 @@ namespace LinearAlgebra
     dealii::internal::VectorOperations::Vector_copy copier(
       in_vector.values.get(), this->values.get());
     internal::VectorOperations::parallel_for(copier,
-                                             0,
+                                             static_cast(0),
                                              this->size(),
                                              this->thread_loop_partitioner);
 
@@ -151,7 +151,7 @@ namespace LinearAlgebra
     internal::VectorOperations::Vectorization_multiply_factor
       vector_multiply(this->values.get(), factor);
     internal::VectorOperations::parallel_for(vector_multiply,
-                                             0,
+                                             static_cast(0),
                                              this->size(),
                                              this->thread_loop_partitioner);
 
diff --git a/include/deal.II/lac/vector_operations_internal.h b/include/deal.II/lac/vector_operations_internal.h
index 95ea6bc18cae..542c31499fa1 100644
--- a/include/deal.II/lac/vector_operations_internal.h
+++ b/include/deal.II/lac/vector_operations_internal.h
@@ -149,7 +149,7 @@ namespace internal
       }
 
       void
-      operator()(const tbb::blocked_range &range) const
+      operator()(const tbb::blocked_range &range) const
       {
         const size_type r_begin = start + range.begin() * chunk_size;
         const size_type r_end = std::min(start + range.end() * chunk_size, end);
@@ -188,8 +188,12 @@ namespace internal
             partitioner->acquire_one_partitioner();
 
           TBBForFunctor generic_functor(functor, start, end);
-          parallel::internal::parallel_for(
-            0U, generic_functor.n_chunks, generic_functor, 1, tbb_partitioner);
+          parallel::internal::parallel_for(static_cast(0),
+                                           static_cast(
+                                             generic_functor.n_chunks),
+                                           generic_functor,
+                                           1,
+                                           tbb_partitioner);
           partitioner->release_one_partitioner(tbb_partitioner);
         }
       else if (vec_size > 0)
@@ -1317,7 +1321,7 @@ namespace internal
        * [range.begin(), range.end()).
        */
       void
-      operator()(const tbb::blocked_range &range) const
+      operator()(const tbb::blocked_range &range) const
       {
         for (size_type i = range.begin(); i < range.end(); ++i)
           accumulate_recursive(op,
@@ -1387,8 +1391,12 @@ namespace internal
           TBBReduceFunctor generic_functor(op,
                                                                   start,
                                                                   end);
-          parallel::internal::parallel_for(
-            0U, generic_functor.n_chunks, generic_functor, 1, tbb_partitioner);
+          parallel::internal::parallel_for(static_cast(0),
+                                           static_cast(
+                                             generic_functor.n_chunks),
+                                           generic_functor,
+                                           1,
+                                           tbb_partitioner);
           partitioner->release_one_partitioner(tbb_partitioner);
           result = generic_functor.do_sum();
         }

From 2281d7765122c2e399dcdb726189043324a9436c Mon Sep 17 00:00:00 2001
From: Jean-Paul Pelteret 
Date: Thu, 21 Mar 2019 15:24:10 +0100
Subject: [PATCH 298/507] Improve documentation of ADHelperScalarFunction

---
 .../deal.II/differentiation/ad/ad_helpers.h   | 59 +++++++++++++++++--
 source/differentiation/ad/ad_helpers.cc       |  8 +--
 2 files changed, 57 insertions(+), 10 deletions(-)

diff --git a/include/deal.II/differentiation/ad/ad_helpers.h b/include/deal.II/differentiation/ad/ad_helpers.h
index bc00902024cc..685032fd369e 100644
--- a/include/deal.II/differentiation/ad/ad_helpers.h
+++ b/include/deal.II/differentiation/ad/ad_helpers.h
@@ -2964,7 +2964,7 @@ namespace Differentiation
      *   // Define the helper that we will use in the AD computations for our
      *   // scalar energy function. Note that we expect it to return values of
      *   // type double.
-     *   ADHelperScalarFunction ad_helper (n_independent_variables);
+     *   ADHelperScalarFunction ad_helper (n_independent_variables);
      *   using ADNumberType = typename ADHelper::ad_type;
      *
      *   // Compute the fields that provide the independent values.
@@ -3006,7 +3006,7 @@ namespace Differentiation
      *     // introduce them. So this means we have to do it by logical order
      *     // of the extractors that we've created.
      *     const SymmetricTensor<2,dim,ADNumberType> C_AD =
-     *       ad_helper.get_sensitive_variables(C_dofs); const
+     *       ad_helper.get_sensitive_variables(C_dofs);
      *     const Tensor<1,dim,ADNumberType>          H_AD =
      *       ad_helper.get_sensitive_variables(H_dofs);
      *
@@ -3055,7 +3055,7 @@ namespace Differentiation
      *   // and extract the desired values from these intermediate outputs.
      *   Vector Dpsi (ad_helper.n_dependent_variables());
      *   FullMatrix D2psi (ad_helper.n_dependent_variables(),
-     *                             ad_helper.n_dependent_variables());
+     *                             ad_helper.n_independent_variables());
      *   const double psi = ad_helper.compute_value();
      *   ad_helper.compute_gradient(Dpsi);
      *   ad_helper.compute_hessian(D2psi);
@@ -3175,7 +3175,8 @@ namespace Differentiation
        *
        * @param[out] gradient A Vector with the values for the scalar field
        * gradient (first derivatives) evaluated at the point defined by the
-       * independent variable values.
+       * independent variable values. The output @p gradient vector has a length
+       * corresponding to @p n_independent_variables.
        */
       void
       compute_gradient(Vector &gradient) const;
@@ -3190,7 +3191,9 @@ namespace Differentiation
        *
        * @param[out] hessian A FullMatrix with the values for the scalar field
        * Hessian (second derivatives) evaluated at the point defined by the
-       * independent variable values.
+       * independent variable values. The output @p hessian matrix has
+       * dimensions corresponding to
+       * n_independent_variables$\times$n_independent_variables.
        */
       void
       compute_hessian(FullMatrix &hessian) const;
@@ -3207,6 +3210,27 @@ namespace Differentiation
        * @param[in] extractor_row An extractor associated with the input field
        * variables. This effectively defines which components of the global set
        * of independent variables this field is associated with.
+       *
+       * @return A Tensor or SymmetricTensor with its rank and symmetries
+       * determined by the @p extractor_row.
+       * This corresponds to subsetting a whole set of rows of the
+       * gradient vector, scaling those entries to take account of tensor
+       * symmetries, and then reshaping the (sub-)vector so obtained into a
+       * tensor, the final result.
+       * For example, if
+       * @p extractor_row is a FEValuesExtractors::Vector and
+       * @p extractor_col is a FEValuesExtractors::Tensor,
+       * then the returned object is a Tensor of rank 3, with its first
+       * index associated with the field corresponding to the row extractor and
+       * the second and third indices associated with the field corresponding to
+       * the column extractor.
+       * Similarly, if
+       * @p extractor_row is a FEValuesExtractors::SymmetricTensor and
+       * @p extractor_col is a FEValuesExtractors::SymmetricTensor,
+       * then the returned object is a SymmetricTensor of rank 4, with its first
+       * two indices associated with the field corresponding to the row
+       * extractor and the last two indices associated with the field
+       * corresponding to the column extractor.
        */
       template 
       typename internal::ScalarFieldGradient
       typename internal::ScalarFieldHessian
       extract_hessian_component(
diff --git a/source/differentiation/ad/ad_helpers.cc b/source/differentiation/ad/ad_helpers.cc
index a1e0809b5bfd..2317f763ded1 100644
--- a/source/differentiation/ad/ad_helpers.cc
+++ b/source/differentiation/ad/ad_helpers.cc
@@ -1617,10 +1617,10 @@ namespace Differentiation
         const FEValuesExtractors::SymmetricTensor<2> &extractor_col) const
     {
       // NOTE: The order of components must be consistently defined throughout
-      // this class. NOTE: We require a specialisation for rank-4 symmetric
-      // tensors because they
-      //       do not define their rank, and setting data using TableIndices is
-      //       somewhat specialised as well.
+      // this class.
+      // NOTE: We require a specialisation for rank-4 symmetric tensors because
+      // they do not define their rank, and setting data using TableIndices is
+      // somewhat specialised as well.
       SymmetricTensor<4, dim, scalar_type> out;
 
       // Get indexsets for the subblocks from which we wish to extract the

From 461bf46c07f747b64c60379431ada73dd3cb1a3d Mon Sep 17 00:00:00 2001
From: Jean-Paul Pelteret 
Date: Thu, 21 Mar 2019 15:25:24 +0100
Subject: [PATCH 299/507] Mark some member functions of ADHelperScalarFunction
 as static

---
 .../deal.II/differentiation/ad/ad_helpers.h   | 33 +++++++++----------
 source/differentiation/ad/ad_helpers.cc       |  9 +++--
 2 files changed, 20 insertions(+), 22 deletions(-)

diff --git a/include/deal.II/differentiation/ad/ad_helpers.h b/include/deal.II/differentiation/ad/ad_helpers.h
index 685032fd369e..828ad50c9326 100644
--- a/include/deal.II/differentiation/ad/ad_helpers.h
+++ b/include/deal.II/differentiation/ad/ad_helpers.h
@@ -3233,11 +3233,10 @@ namespace Differentiation
        * corresponding to the column extractor.
        */
       template 
-      typename internal::ScalarFieldGradient::type
-      extract_gradient_component(const Vector &gradient,
-                                 const ExtractorType_Row &extractor_row) const;
+      static typename internal::
+        ScalarFieldGradient::type
+        extract_gradient_component(const Vector &gradient,
+                                   const ExtractorType_Row &  extractor_row);
 
       /**
        * Extract the function Hessian for a subset of independent variables
@@ -3278,13 +3277,13 @@ namespace Differentiation
        * corresponding to the column extractor.
        */
       template 
-      typename internal::ScalarFieldHessian::type
+      static typename internal::ScalarFieldHessian::type
       extract_hessian_component(const FullMatrix &hessian,
                                 const ExtractorType_Row &      extractor_row,
-                                const ExtractorType_Col &extractor_col) const;
+                                const ExtractorType_Col &      extractor_col);
 
       /**
        * Extract the function Hessian for a subset of independent variables
@@ -3299,11 +3298,11 @@ namespace Differentiation
        * Hessian matrix because both extractors imply selection of just a
        * single row or column of the matrix.
        */
-      Tensor<0, dim, scalar_type>
+      static Tensor<0, dim, scalar_type>
       extract_hessian_component(
         const FullMatrix &   hessian,
         const FEValuesExtractors::Scalar &extractor_row,
-        const FEValuesExtractors::Scalar &extractor_col) const;
+        const FEValuesExtractors::Scalar &extractor_col);
 
       /**
        * Extract the function Hessian for a subset of independent variables
@@ -3314,13 +3313,13 @@ namespace Differentiation
        * @f]
        *
        * This function is a specialization of the above for rank-4 symmetric
-       * tensors
+       * tensors.
        */
-      SymmetricTensor<4, dim, scalar_type>
+      static SymmetricTensor<4, dim, scalar_type>
       extract_hessian_component(
         const FullMatrix &               hessian,
         const FEValuesExtractors::SymmetricTensor<2> &extractor_row,
-        const FEValuesExtractors::SymmetricTensor<2> &extractor_col) const;
+        const FEValuesExtractors::SymmetricTensor<2> &extractor_col);
 
       //@}
 
@@ -3508,7 +3507,7 @@ namespace Differentiation
       ExtractorType_Row>::type
     ADHelperScalarFunction::
       extract_gradient_component(const Vector &gradient,
-                                 const ExtractorType_Row &  extractor_row) const
+                                 const ExtractorType_Row &  extractor_row)
     {
       // NOTE: The order of components must be consistently defined throughout
       // this class.
@@ -3542,7 +3541,7 @@ namespace Differentiation
     ADHelperScalarFunction::
       extract_hessian_component(const FullMatrix &hessian,
                                 const ExtractorType_Row &      extractor_row,
-                                const ExtractorType_Col &extractor_col) const
+                                const ExtractorType_Col &      extractor_col)
     {
       using InternalHessian      = internal::ScalarFieldHessian::
              scalar_type>
     ADHelperScalarFunction::
-      extract_hessian_component(
-        const FullMatrix &   hessian,
-        const FEValuesExtractors::Scalar &extractor_row,
-        const FEValuesExtractors::Scalar &extractor_col) const
+      extract_hessian_component(const FullMatrix &   hessian,
+                                const FEValuesExtractors::Scalar &extractor_row,
+                                const FEValuesExtractors::Scalar &extractor_col)
     {
       // NOTE: It is necessary to make special provision for the case when the
       // HessianType is scalar. Unfortunately Tensor<0,dim> does not provide
@@ -1614,7 +1613,7 @@ namespace Differentiation
       extract_hessian_component(
         const FullMatrix &               hessian,
         const FEValuesExtractors::SymmetricTensor<2> &extractor_row,
-        const FEValuesExtractors::SymmetricTensor<2> &extractor_col) const
+        const FEValuesExtractors::SymmetricTensor<2> &extractor_col)
     {
       // NOTE: The order of components must be consistently defined throughout
       // this class.

From 6ec19eb45644225e057cf32026256715a8358b50 Mon Sep 17 00:00:00 2001
From: Jean-Paul Pelteret 
Date: Thu, 21 Mar 2019 15:26:06 +0100
Subject: [PATCH 300/507] AD Helpers: Add helper for vector functions
 (QP-level)

---
 .../deal.II/differentiation/ad/ad_helpers.h   | 528 ++++++++++++++++++
 source/differentiation/ad/ad_helpers.cc       | 243 ++++++++
 source/differentiation/ad/ad_helpers.inst1.in |  16 +
 source/differentiation/ad/ad_helpers.inst2.in |  28 +
 4 files changed, 815 insertions(+)

diff --git a/include/deal.II/differentiation/ad/ad_helpers.h b/include/deal.II/differentiation/ad/ad_helpers.h
index 828ad50c9326..7619901a82bc 100644
--- a/include/deal.II/differentiation/ad/ad_helpers.h
+++ b/include/deal.II/differentiation/ad/ad_helpers.h
@@ -3326,6 +3326,409 @@ namespace Differentiation
     }; // class ADHelperScalarFunction
 
 
+
+    /**
+     * A helper class that facilitates the evaluation of a vector of functions,
+     * typically one that represents a collection of coupled, multi-dimensional
+     * fields. This class would typically be used to compute the linearization
+     * of a set of kinetic field variables defined at the quadrature point
+     * level.
+     *
+     * An example of its usage in the case of linearizing the kinetic variables
+     * derived from a multi-field constitutive law might be as follows:
+     * @code
+     *   // Define some extractors that will help us set independent variables
+     *   // and later get the computed values related to the dependent
+     *   // variables. Each of these extractors is related to the gradient of a
+     *   // component of the solution field (in this case, displacement and
+     *   // magnetic scalar potential). Here "C" is the right Cauchy-Green
+     *   // tensor and "H" is the magnetic field.
+     *   const FEValuesExtractors::SymmetricTensor<2> C_dofs (0);
+     *   const FEValuesExtractors::Vector             H_dofs
+     *     (dealii::SymmetricTensor<2,dim>::n_independent_components);
+     *   const unsigned int n_independent_variables =
+     *     SymmetricTensor<2,dim>::n_independent_components +
+     *     Tensor<1,dim>::n_independent_components;
+     *
+     *   // Declare how many dependent variables we expect to compute.
+     *   // In this case, we will be computing a stress field (a symmetric
+     *   // rank-2 tensor) and the magnetic induction (a vector field).
+     *   // At the same time we define some additional extractors associated
+     *   // with these kinetic fields. In general, these need not be of the same
+     *   // layout as the independent variables.
+     *   const FEValuesExtractors::SymmetricTensor<2> S_dofs (0);
+     *   const FEValuesExtractors::Vector             B_dofs
+     *     (dealii::SymmetricTensor<2,dim>::n_independent_components);
+     *   const unsigned int n_dependent_variables =
+     *     SymmetricTensor<2,dim>::n_independent_components +
+     *     Tensor<1,dim>::n_independent_components;
+     *
+     *   // Define the helper that we will use in the AD computations for our
+     *   // scalar energy function. Note that we expect it to return values of
+     *   // type double.
+     *   ADHelperVectorFunction ad_helper (n_independent_variables,
+     *                                                 n_dependent_variables);
+     *   using ADNumberType = typename ADHelper::ad_type;
+     *
+     *   // Compute the fields that provide the independent values.
+     *   // When the tape is being replayed, these should be set to something
+     *   // meaningful.
+     *   const Tensor<1,dim> H = ...;
+     *   const SymmetricTensor<2,dim> C = ...;
+     *
+     *   // If using a taped AD number, then at this point we would initiate
+     *   // taping of the expression for the material stored energy function
+     *   // for this particular set of material parameters:
+     *
+     *   // Select a tape number to record to
+     *   const typename Types::tape_index tape_index = ...;
+     *
+     *   // Indicate that we are about to start tracing the operations for
+     *   // function evaluation on the tape. If this tape has already been
+     *   // used (i.e. the operations are already recorded) then we
+     *   // (optionally) load the tape and reuse this data.
+     *   const bool is_recording
+     *     = ad_helper.start_recording_operations(tape_index);
+     *
+     *   // The steps that follow in the recording phase are required for
+     *   // tapeless methods as well.
+     *   if (is_recording == true)
+     *   {
+     *     // This is the "recording" phase of the operations.
+     *
+     *     // First, we set the values for all fields.
+     *     // These could happily be set to anything, unless the function will
+     *     // be evaluated along a branch not otherwise traversed during later
+     *     // use. For this reason, in this example instead of using some dummy
+     *     // values, we'll actually map out the function at the same point
+     *     // around which we'll later linearize it.
+     *     ad_helper.register_independent_variable(H, H_dofs);
+     *     ad_helper.register_independent_variable(C, C_dofs);
+     *
+     *     // NOTE: We have to extract the sensitivities in the order we wish to
+     *     // introduce them. So this means we have to do it by logical order
+     *     // of the extractors that we've created.
+     *     const SymmetricTensor<2,dim,ADNumberType> C_AD =
+     *       ad_helper.get_sensitive_variables(C_dofs);
+     *     const Tensor<1,dim,ADNumberType>          H_AD =
+     *       ad_helper.get_sensitive_variables(H_dofs);
+     *
+     *     // Here we define the stress and magnetic induction in terms
+     *     // of the independent values C_AD and H_AD.
+     *     const SymmetricTensor<2, dim, ad_type> S_AD = ...;
+     *     const Tensor<1, dim, ad_type>          B_AD = ...;
+     *
+     *     // Register the definition of the kinetic fields. The second
+     *     // argument to the function provides a non-overlapping ordering
+     *     // of the
+     *     ad_helper.register_dependent_variable(S_AD, S_dofs);
+     *     ad_helper.register_dependent_variable(B_AD, B_dofs);
+     *
+     *     // Indicate that we have completed tracing the operations onto
+     *     // the tape.
+     *     ad_helper.stop_recording_operations(false); // write_tapes_to_file
+     *   }
+     *   else
+     *   {
+     *     // This is the "tape reuse" phase of the operations.
+     *     // Here we will leverage the already traced operations that reside
+     *     // on a tape, and simply re-evaluate the tape at a different point
+     *     // to get the function values and their derivatives.
+     *
+     *     // Load the existing tape to be reused
+     *     ad_helper.activate_recorded_tape(tape_index);
+     *
+     *     // Set the new values of the independent variables where the
+     *     // recorded dependent functions are to be evaluated (and
+     *     // differentiated around).
+     *     ad_helper.set_independent_variable(C, C_dofs);
+     *     ad_helper.set_independent_variable(H, H_dofs);
+     *   }
+     *
+     *   // Play the tape and store the output function value, its gradient and
+     *   // linearization. These are expensive to compute, so we'll do this once
+     *   // and extract the desired values from these intermediate outputs.
+     *   Vector values (ad_helper.n_dependent_variables());
+     *   FullMatrix jacobian (ad_helper.n_dependent_variables(),
+     *                                ad_helper.n_independent_variables());
+     *   ad_helper.compute_values(values);
+     *   ad_helper.compute_jacobian(jacobian);
+     *
+     *   // Extract the desired components of the value vector and its Jacobian
+     *   // matrix. In this example, we use them to compute the Piola-Kirchhoff
+     *   // stress tensor S and its associated tangent, defined
+     *   // as HH = 2*dS/dC...
+     *   const SymmetricTensor<2,dim> S =
+     *     ad_helper.extract_value_component(values,S_dofs);
+     *   const SymmetricTensor<4,dim> HH =
+     *     2.0*ad_helper.extract_jacobian_component(jacobian,S_dofs,C_dofs);
+     *
+     *   // ... the magnetic induction B and its associated tangent defined
+     *   // as BB = dB/dH...
+     *   const Tensor<1,dim> B =
+     *     ad_helper.extract_value_component(values,H_dofs);
+     *   const SymmetricTensor<2,dim> BB =
+     *     symmetrize(ad_helper.extract_jacobian_component(jacobian,B_dofs,H_dofs));
+     *
+     *   // ... and finally the magnetoelastic coupling tangent, defined
+     *   // as PP = -dS/dH. Here the order of the extractor arguments is
+     *   // especially important, as it dictates the field that is being
+     *   // differentiated, and which the directional derivatives are being
+     *   // computed.
+     *   const Tensor<3,dim,double> PP =
+     *     -ad_helper.extract_jacobian_component(jacobian,S_dofs,H_dofs)
+     * @endcode
+     *
+     * @warning ADOL-C does not support the standard threading models used by
+     * deal.II, so this class should @b not be embedded within a multithreaded
+     * function when using ADOL-C number types. It is, however, suitable for use
+     * in both serial and MPI routines.
+     *
+     * @author Jean-Paul Pelteret, 2016, 2017, 2018
+     */
+    template 
+    class ADHelperVectorFunction
+      : public ADHelperPointLevelFunctionsBase
+    {
+    public:
+      /**
+       * Type definition for the floating point number type that is used in,
+       * and results from, all computations.
+       */
+      using scalar_type =
+        typename ADHelperBase::scalar_type;
+
+      /**
+       * Type definition for the auto-differentiation number type that is used
+       * in all computations.
+       */
+      using ad_type =
+        typename ADHelperBase::ad_type;
+
+      /**
+       * @name Constructor / destructor
+       */
+      //@{
+
+      /**
+       * The constructor for the class.
+       *
+       * @param[in] n_independent_variables The number of independent variables
+       * that will be used in the definition of the functions that it is
+       * desired to compute the sensitivities of. In the computation of
+       * $\mathbf{f}(\mathbf{X})$, this will be the number of inputs
+       * $\mathbf{X}$, i.e., the dimension of the domain space.
+       * @param[in] n_dependent_variables The number of scalar functions to be
+       * defined that will have a sensitivity to the given independent
+       * variables. In the computation of $\mathbf{f}(\mathbf{X})$, this will
+       * be the number of outputs $\mathbf{f}$, i.e., the dimension of the
+       * image space.
+       */
+      ADHelperVectorFunction(const unsigned int n_independent_variables,
+                             const unsigned int n_dependent_variables);
+
+      /**
+       * Destructor.
+       */
+      virtual ~ADHelperVectorFunction() = default;
+
+      //@}
+
+      /**
+       * @name Dependent variables
+       */
+      //@{
+
+      /**
+       * Register the definition of the vector field
+       * $\boldsymbol{\Psi}(\mathbf{X})$.
+       *
+       * @param[in] funcs A vector of recorded functions that defines the
+       * dependent variables.
+       *
+       * @note For this class that expects only vector field of dependent
+       * variables, this function must only be called once per tape.
+       *
+       * @note For taped AD numbers, this operation is only valid in recording mode.
+       */
+      void
+      register_dependent_variables(const std::vector &funcs);
+
+      /**
+       * Register the definition of the vector field
+       * $\hat{\mathbf{g}}(\mathbf{X}) \subset \boldsymbol{\Psi}(\mathbf{X})$
+       * that may represent a subset of the dependent variables.
+       *
+       * @param[in] funcs The recorded functions that define a set of dependent
+       * variables.
+       * @param[in] extractor An extractor associated with the input field
+       * variables. This effectively defines which components of the global set
+       * of dependent variables this field is associated with.
+       *
+       * @note The input extractor must correspond to the input @p ValueType.
+       * So, for example, if a value is a rank-1 tensor
+       * (i.e. of type Tensor<1,dim,scalar_type>), then the extractor must
+       * be an FEValuesExtractors::Vector or FEValuesExtractors::Tensor<1>.
+       *
+       * @note For taped AD numbers, this operation is only valid in recording mode.
+       */
+      template 
+      void
+      register_dependent_variable(const ValueType &    funcs,
+                                  const ExtractorType &extractor);
+
+      /**
+       * Compute the value of the vector field $\boldsymbol{\Psi}(\mathbf{X})$.
+       *
+       * @param[out] values A Vector object with the value for each component
+       * of the vector field evaluated at the point defined by the independent
+       * variable values. The output @p values vector has a length
+       * corresponding to @p n_dependent_variables.
+       */
+      void
+      compute_values(Vector &values) const;
+
+      /**
+       * Compute the Jacobian (first derivative) of the vector field with
+       * respect to all independent variables, i.e.
+       * @f[
+       *   \mathbf{J}(\boldsymbol{\Psi})
+       *      = \frac{\partial\boldsymbol{\Psi}(\mathbf{X})}{\partial\mathbf{X}}
+       * @f]
+       *
+       * @param[out] jacobian A FullMatrix with the gradient of each component
+       * of the vector field evaluated at the point defined by the independent
+       * variable values. The output @p jacobian matrix has
+       * dimensions corresponding to
+       * n_dependent_variables$\times$n_independent_variables.
+       */
+      void
+      compute_jacobian(FullMatrix &jacobian) const;
+
+
+      /**
+       * Extract the set of functions' values for a subset of dependent
+       * variables
+       * $\mathbf{g} \subset \boldsymbol{\Psi}(\mathbf{X})$.
+       *
+       * @param[in] values A Vector object with the value for each component of
+       * the vector field evaluated at the point defined by the independent
+       * variable values.
+       * @param[in] extractor_row An extractor associated with the input field
+       * variables. This effectively defines which components of the global set
+       * of dependent variables this field is associated with.
+       */
+      template 
+      static typename internal::
+        VectorFieldValue::type
+        extract_value_component(const Vector &values,
+                                const ExtractorType_Row &  extractor_row);
+
+      /**
+       * Extract the Jacobian of the subset of dependent functions
+       * $\mathbf{g} \subset \boldsymbol{\Psi}(\mathbf{X})$
+       * for a subset of independent variables
+       * $\mathbf{A} \subset \mathbf{X}$, i.e.
+       * @f[
+       *   \mathbf{J}(\mathbf{g})
+       *      = \frac{\partial\mathbf{g}(\mathbf{X})}{\partial\mathbf{A}}
+       * @f]
+       * The first index of the Jacobian matrix $\mathbf{J}(\mathbf{g})$
+       * relates to the dependent variables, while the second index relates
+       * to the independent variables.
+       *
+       * @param[in] jacobian The Jacobian of the vector function with respect to
+       * all independent variables, i.e., that returned by compute_jacobian().
+       * @param[in] extractor_row An extractor associated with the input field
+       * variables for which the first index of the Jacobian is extracted.
+       * This effectively defines the correspondence between components of the
+       * global set of dependent variables and the field (representing a
+       * subset of dependent functions) associated with the extractor.
+       * @param[in] extractor_col An extractor associated with the input field
+       * variables for which the second index of the Jacobian is extracted.
+       * This effectively defines the correspondence between components of the
+       * global set of independent variables and the field (representing a
+       * subset of independent variables) associated with the extractor.
+       *
+       * @return A Tensor or SymmetricTensor with its rank and symmetries
+       * determined by the @p extractor_row and @p extractor_col .
+       * This corresponds to subsetting a whole set of rows and columns of the
+       * Jacobian matrix, scaling those entries to take account of tensor
+       * symmetries, and then reshaping the (sub-)matrix so obtained into a
+       * tensor, the final result.
+       * For example, if
+       * @p extractor_row is a FEValuesExtractors::Vector and
+       * @p extractor_col is a FEValuesExtractors::Tensor,
+       * then the returned object is a Tensor of rank 3, with its first
+       * index associated with the field corresponding to the row extractor and
+       * the second and third indices associated with the field corresponding to
+       * the column extractor.
+       * Similarly, if
+       * @p extractor_row is a FEValuesExtractors::SymmetricTensor and
+       * @p extractor_col is a FEValuesExtractors::SymmetricTensor,
+       * then the returned object is a SymmetricTensor of rank 4, with its first
+       * two indices associated with the field corresponding to the row
+       * extractor and the last two indices associated with the field
+       * corresponding to the column extractor.
+       */
+      template 
+      static typename internal::VectorFieldJacobian::type
+      extract_jacobian_component(const FullMatrix &jacobian,
+                                 const ExtractorType_Row &      extractor_row,
+                                 const ExtractorType_Col &      extractor_col);
+
+      /**
+       * Extract the Jacobian of the subset of dependent functions
+       * $\mathbf{g} \subset \boldsymbol{\Psi}(\mathbf{X})$
+       * for a subset of independent variables
+       * $\mathbf{A} \subset \mathbf{X}$, i.e.
+       * @f[
+       *   \mathbf{J}(\mathbf{g})
+       *      = \frac{\partial\mathbf{g}(\mathbf{X})}{\partial\mathbf{A}}
+       * @f]
+       *
+       * This function is a specialization of the above for rank-0 tensors
+       * (scalars). This corresponds to extracting a single entry of the
+       * Jacobian matrix because both extractors imply selection of just a
+       * single row or column of the matrix.
+       */
+      static Tensor<0, dim, scalar_type>
+      extract_jacobian_component(
+        const FullMatrix &   jacobian,
+        const FEValuesExtractors::Scalar &extractor_row,
+        const FEValuesExtractors::Scalar &extractor_col);
+
+      /**
+       * Extract the Jacobian of the subset of dependent functions
+       * $\mathbf{g} \subset \boldsymbol{\Psi}(\mathbf{X})$
+       * for a subset of independent variables
+       * $\mathbf{A} \subset \mathbf{X}$, i.e.
+       * @f[
+       *   \mathbf{J}(\mathbf{g})
+       *      = \frac{\partial\mathbf{g}(\mathbf{X})}{\partial\mathbf{A}}
+       * @f]
+       *
+       * This function is a specialization of the above for rank-4 symmetric
+       * tensors.
+       */
+      static SymmetricTensor<4, dim, scalar_type>
+      extract_jacobian_component(
+        const FullMatrix &               jacobian,
+        const FEValuesExtractors::SymmetricTensor<2> &extractor_row,
+        const FEValuesExtractors::SymmetricTensor<2> &extractor_col);
+
+      //@}
+
+    }; // class ADHelperVectorFunction
+
+
   } // namespace AD
 } // namespace Differentiation
 
@@ -3592,6 +3995,131 @@ namespace Differentiation
     }
 
 
+
+    /* ----------------- ADHelperVectorFunction ----------------- */
+
+
+
+    template 
+    template 
+    void
+    ADHelperVectorFunction::
+      register_dependent_variable(const ValueType &    funcs,
+                                  const ExtractorType &extractor)
+    {
+      const std::vector index_set(
+        internal::extract_field_component_indices(extractor));
+      for (unsigned int i = 0; i < index_set.size(); ++i)
+        {
+          Assert(this->registered_marked_dependent_variables[index_set[i]] ==
+                   false,
+                 ExcMessage("Overlapping indices for dependent variables."));
+          ADHelperBase::
+            register_dependent_variable(index_set[i],
+                                        internal::get_tensor_entry(funcs, i));
+        }
+    }
+
+
+
+    template 
+    template 
+    typename internal::VectorFieldValue<
+      dim,
+      typename ADHelperVectorFunction::
+        scalar_type,
+      ExtractorType_Row>::type
+    ADHelperVectorFunction::
+      extract_value_component(const Vector &values,
+                              const ExtractorType_Row &  extractor_row)
+    {
+      // NOTE: The order of components must be consistently defined throughout
+      // this class.
+      typename internal::VectorFieldValue::
+        type out;
+
+      // Get indexsets for the subblock from which we wish to extract the
+      // gradient values
+      const std::vector row_index_set(
+        internal::extract_field_component_indices(extractor_row));
+      Assert(out.n_independent_components == row_index_set.size(),
+             ExcMessage("Not all tensor components have been extracted!"));
+      for (unsigned int r = 0; r < row_index_set.size(); ++r)
+        internal::set_tensor_entry(out, r, values[row_index_set[r]]);
+
+      return out;
+    }
+
+
+
+    template 
+    template 
+    typename internal::VectorFieldJacobian<
+      dim,
+      typename ADHelperVectorFunction::
+        scalar_type,
+      ExtractorType_Row,
+      ExtractorType_Col>::type
+    ADHelperVectorFunction::
+      extract_jacobian_component(const FullMatrix &jacobian,
+                                 const ExtractorType_Row &      extractor_row,
+                                 const ExtractorType_Col &      extractor_col)
+    {
+      using InternalJacobian     = internal::VectorFieldJacobian;
+      using InternalExtractorRow = internal::Extractor;
+      using InternalExtractorCol = internal::Extractor;
+      using JacobianType         = typename InternalJacobian::type;
+
+      // NOTE: The order of components must be consistently defined throughout
+      // this class.
+      JacobianType out;
+
+      // Get indexsets for the subblocks from which we wish to extract the
+      // Hessian values.
+      // NOTE: Here we have to do some clever accounting when the
+      // one extractor is a symmetric Tensor and the other is not, e.g.
+      // . In this scenario the return type is a
+      // non-symmetric Tensor<3,dim> but we have to fetch information from a
+      // SymmTensor row/column that has too few entries to fill the output
+      // tensor. So we must duplicate the relevant entries in the row/column
+      // indexset to fetch off-diagonal components that are Otherwise
+      // non-existent in a SymmTensor.
+      const std::vector row_index_set(
+        internal::extract_field_component_indices(
+          extractor_row, false /*ignore_symmetries*/));
+      const std::vector col_index_set(
+        internal::extract_field_component_indices(
+          extractor_col, false /*ignore_symmetries*/));
+
+      for (unsigned int index = 0;
+           index < JacobianType::n_independent_components;
+           ++index)
+        {
+          const TableIndices ti_out =
+            JacobianType::unrolled_to_component_indices(index);
+          const unsigned int r =
+            InternalExtractorRow::local_component(ti_out, 0);
+          const unsigned int c =
+            InternalExtractorCol::local_component(ti_out,
+                                                  InternalExtractorRow::rank);
+
+          internal::set_tensor_entry(
+            out, index, jacobian[row_index_set[r]][col_index_set[c]]);
+        }
+
+      return out;
+    }
+
+
   } // namespace AD
 } // namespace Differentiation
 
diff --git a/source/differentiation/ad/ad_helpers.cc b/source/differentiation/ad/ad_helpers.cc
index 1722791301b5..4d67b34ad7f9 100644
--- a/source/differentiation/ad/ad_helpers.cc
+++ b/source/differentiation/ad/ad_helpers.cc
@@ -1640,6 +1640,249 @@ namespace Differentiation
     }
 
 
+
+    /* -------------------- ADHelperVectorFunction -------------------- */
+
+
+
+    template 
+    ADHelperVectorFunction::
+      ADHelperVectorFunction(const unsigned int n_independent_variables,
+                             const unsigned int n_dependent_variables)
+      : ADHelperPointLevelFunctionsBase(
+          n_independent_variables,
+          n_dependent_variables)
+    {}
+
+
+
+    template 
+    void
+    ADHelperVectorFunction::
+      register_dependent_variables(const std::vector &funcs)
+    {
+      Assert(funcs.size() == this->n_dependent_variables(),
+             ExcMessage(
+               "Vector size does not match number of dependent variables"));
+      for (unsigned int i = 0; i < this->n_dependent_variables(); ++i)
+        ADHelperBase::register_dependent_variable(
+          i, funcs[i]);
+    }
+
+
+
+    template 
+    void
+    ADHelperVectorFunction::compute_values(
+      Vector &values) const
+    {
+      if ((ADNumberTraits::is_taped == true &&
+           this->taped_driver.keep_independent_values() == false) ||
+          ADNumberTraits::is_tapeless == true)
+        {
+          Assert(
+            this->n_registered_independent_variables() ==
+              this->n_independent_variables(),
+            ExcMessage(
+              "Not all values of sensitivities have been registered or subsequently set!"));
+        }
+      Assert(this->n_registered_dependent_variables() ==
+               this->n_dependent_variables(),
+             ExcMessage("Not all dependent variables have been registered."));
+
+      // We can neglect correctly initializing the entries as
+      // we'll be overwriting them immediately in the succeeding call to
+      // Drivers::values().
+      if (values.size() != this->n_dependent_variables())
+        values.reinit(this->n_dependent_variables(),
+                      true /*omit_zeroing_entries*/);
+
+      if (ADNumberTraits::is_taped == true)
+        {
+          Assert(this->active_tape_index() !=
+                   Numbers::invalid_tape_index,
+                 ExcMessage("Invalid tape index"));
+          Assert(this->is_recording() == false,
+                 ExcMessage(
+                   "Cannot compute values while tape is being recorded."));
+          Assert(this->independent_variable_values.size() ==
+                   this->n_independent_variables(),
+                 ExcDimensionMismatch(this->independent_variable_values.size(),
+                                      this->n_independent_variables()));
+
+          this->taped_driver.values(this->active_tape_index(),
+                                    this->n_dependent_variables(),
+                                    this->independent_variable_values,
+                                    values);
+        }
+      else
+        {
+          Assert(ADNumberTraits::is_tapeless == true,
+                 ExcInternalError());
+          this->tapeless_driver.values(this->dependent_variables, values);
+        }
+    }
+
+
+
+    template 
+    void
+    ADHelperVectorFunction::compute_jacobian(
+      FullMatrix &jacobian) const
+    {
+      if ((ADNumberTraits::is_taped == true &&
+           this->taped_driver.keep_independent_values() == false) ||
+          ADNumberTraits::is_tapeless == true)
+        {
+          Assert(
+            this->n_registered_independent_variables() ==
+              this->n_independent_variables(),
+            ExcMessage(
+              "Not all values of sensitivities have been registered or subsequently set!"));
+        }
+      Assert(this->n_registered_dependent_variables() ==
+               this->n_dependent_variables(),
+             ExcMessage("Not all dependent variables have been registered."));
+
+      // We can neglect correctly initializing the entries as
+      // we'll be overwriting them immediately in the succeeding call to
+      // Drivers::jacobian().
+      if (jacobian.m() != this->n_dependent_variables() ||
+          jacobian.n() != this->n_independent_variables())
+        jacobian.reinit({this->n_dependent_variables(),
+                         this->n_independent_variables()},
+                        true /*omit_default_initialization*/);
+
+      if (ADNumberTraits::is_taped == true)
+        {
+          Assert(this->active_tape_index() !=
+                   Numbers::invalid_tape_index,
+                 ExcMessage("Invalid tape index"));
+          Assert(this->is_recording() == false,
+                 ExcMessage(
+                   "Cannot compute Jacobian while tape is being recorded."));
+          Assert(this->independent_variable_values.size() ==
+                   this->n_independent_variables(),
+                 ExcDimensionMismatch(this->independent_variable_values.size(),
+                                      this->n_independent_variables()));
+
+          this->taped_driver.jacobian(this->active_tape_index(),
+                                      this->n_dependent_variables(),
+                                      this->independent_variable_values,
+                                      jacobian);
+        }
+      else
+        {
+          Assert(ADNumberTraits::is_tapeless == true,
+                 ExcInternalError());
+          Assert(this->independent_variables.size() ==
+                   this->n_independent_variables(),
+                 ExcDimensionMismatch(this->independent_variables.size(),
+                                      this->n_independent_variables()));
+
+          this->tapeless_driver.jacobian(this->independent_variables,
+                                         this->dependent_variables,
+                                         jacobian);
+        }
+
+      for (unsigned int j = 0; j < this->n_independent_variables(); j++)
+        {
+          // Because we perform just a single differentiation
+          // operation with respect to the "column" variables,
+          // we only need to consider them for symmetry conditions.
+          if (this->is_symmetric_independent_variable(j) == true)
+            for (unsigned int i = 0; i < this->n_dependent_variables(); i++)
+              jacobian[i][j] *= 0.5;
+        }
+    }
+
+
+
+    template 
+    Tensor<0,
+           dim,
+           typename ADHelperVectorFunction::
+             scalar_type>
+    ADHelperVectorFunction::
+      extract_jacobian_component(
+        const FullMatrix &   jacobian,
+        const FEValuesExtractors::Scalar &extractor_row,
+        const FEValuesExtractors::Scalar &extractor_col)
+    {
+      // NOTE: It is necessary to make special provision for the case when the
+      // HessianType is scalar. Unfortunately Tensor<0,dim> does not provide
+      // the function unrolled_to_component_indices!
+      // NOTE: The order of components must be consistently defined throughout
+      // this class.
+      Tensor<0, dim, scalar_type> out;
+
+      // Get indexsets for the subblocks from which we wish to extract the
+      // matrix values
+      const std::vector row_index_set(
+        internal::extract_field_component_indices(extractor_row));
+      const std::vector col_index_set(
+        internal::extract_field_component_indices(extractor_col));
+      Assert(row_index_set.size() == 1, ExcInternalError());
+      Assert(col_index_set.size() == 1, ExcInternalError());
+
+      internal::set_tensor_entry(out,
+                                 0,
+                                 jacobian[row_index_set[0]][col_index_set[0]]);
+
+      return out;
+    }
+
+
+
+    template 
+    SymmetricTensor<4,
+                    dim,
+                    typename ADHelperVectorFunction::scalar_type>
+    ADHelperVectorFunction::
+      extract_jacobian_component(
+        const FullMatrix &               jacobian,
+        const FEValuesExtractors::SymmetricTensor<2> &extractor_row,
+        const FEValuesExtractors::SymmetricTensor<2> &extractor_col)
+    {
+      // NOTE: The order of components must be consistently defined throughout
+      // this class.
+      // NOTE: We require a specialisation for rank-4 symmetric tensors because
+      // they do not define their rank, and setting data using TableIndices is
+      // somewhat specialised as well.
+      SymmetricTensor<4, dim, scalar_type> out;
+
+      // Get indexsets for the subblocks from which we wish to extract the
+      // matrix values
+      const std::vector row_index_set(
+        internal::extract_field_component_indices(extractor_row));
+      const std::vector col_index_set(
+        internal::extract_field_component_indices(extractor_col));
+
+      for (unsigned int r = 0; r < row_index_set.size(); ++r)
+        for (unsigned int c = 0; c < col_index_set.size(); ++c)
+          {
+            internal::set_tensor_entry(
+              out, r, c, jacobian[row_index_set[r]][col_index_set[c]]);
+          }
+
+      return out;
+    }
+
+
   } // namespace AD
 } // namespace Differentiation
 
diff --git a/source/differentiation/ad/ad_helpers.inst1.in b/source/differentiation/ad/ad_helpers.inst1.in
index a5c9b87da3bf..1c1ff5a534b8 100644
--- a/source/differentiation/ad/ad_helpers.inst1.in
+++ b/source/differentiation/ad/ad_helpers.inst1.in
@@ -125,6 +125,14 @@ for (deal_II_dimension : DIMENSIONS ; number : REAL_SCALARS)
     template
     class ADHelperScalarFunction;
 
+    // -------------------------- ADHelperVectorFunction ----------------------
+
+    template
+    class ADHelperVectorFunction;
+
+    template
+    class ADHelperVectorFunction;
+
     \}
     \}
 }
@@ -153,6 +161,14 @@ for (deal_II_dimension : DIMENSIONS)
     template
     class ADHelperScalarFunction::ad_type>;
 
+    // -------------------------- ADHelperVectorFunction ----------------------
+
+    template
+    class ADHelperVectorFunction::ad_type>;
+
+    template
+    class ADHelperVectorFunction::ad_type>;
+
     \}
     \}
 }
diff --git a/source/differentiation/ad/ad_helpers.inst2.in b/source/differentiation/ad/ad_helpers.inst2.in
index e886a8575ad0..800b697f99ae 100644
--- a/source/differentiation/ad/ad_helpers.inst2.in
+++ b/source/differentiation/ad/ad_helpers.inst2.in
@@ -186,6 +186,20 @@ for (deal_II_dimension : DIMENSIONS ; number : REAL_SCALARS)
     template
     class ADHelperScalarFunction;
 
+    // -------------------------- ADHelperVectorFunction ----------------------
+
+    template
+    class ADHelperVectorFunction;
+
+    template
+    class ADHelperVectorFunction;
+
+    template
+    class ADHelperVectorFunction;
+
+    template
+    class ADHelperVectorFunction;
+
     \}
     \}
 }
@@ -225,6 +239,20 @@ for (deal_II_dimension : DIMENSIONS)
 
     template
     class ADHelperScalarFunction::ad_type>;
+
+    // -------------------------- ADHelperVectorFunction ----------------------
+
+    template
+    class ADHelperVectorFunction::ad_type>;
+
+    template
+    class ADHelperVectorFunction::ad_type>;
+
+    template
+    class ADHelperVectorFunction::ad_type>;
+
+    template
+    class ADHelperVectorFunction::ad_type>;
     
     \}
     \}

From 6a59dba257e2ef0170b164b5784ceef19b72ccdf Mon Sep 17 00:00:00 2001
From: Jean-Paul Pelteret 
Date: Thu, 21 Mar 2019 15:29:51 +0100
Subject: [PATCH 301/507] Add a changelog entry for ADHelperVectorFunction

---
 doc/news/changes/major/20190321Jean-PaulPelteret | 9 +++++++++
 1 file changed, 9 insertions(+)
 create mode 100644 doc/news/changes/major/20190321Jean-PaulPelteret

diff --git a/doc/news/changes/major/20190321Jean-PaulPelteret b/doc/news/changes/major/20190321Jean-PaulPelteret
new file mode 100644
index 000000000000..54b796a6d6b7
--- /dev/null
+++ b/doc/news/changes/major/20190321Jean-PaulPelteret
@@ -0,0 +1,9 @@
+New: A new class Differentiation::AD::ADHelperVectorFunction has been
+added to help implement point-wise vector functions using automatic 
+differentiation. In particular, this class is designed to compute the 
+Jacobian of a vector function that is parameterized in
+terms of scalar, vector, and tensor arguments. One example of its use
+would be to compute the linearization of a multi-field constitutive
+law that is expressed in terms of some kinetic variables.
+
    
+(Jean-Paul Pelteret, 2019/03/21)

From e400be3332a7f6d4eb6c5e17226b411820589895 Mon Sep 17 00:00:00 2001
From: Wolfgang Bangerth 
Date: Thu, 21 Mar 2019 09:59:22 -0600
Subject: [PATCH 302/507] Revamp the layout of the main 'index.html' file.

---
 doc/CMakeLists.txt     | 11 ------
 doc/documentation.html | 75 -----------------------------------
 doc/index.html         | 90 ++++++++++++++++++++++++++++++++++++------
 doc/navbar.html        | 51 ------------------------
 doc/title.html.in      | 17 --------
 5 files changed, 77 insertions(+), 167 deletions(-)
 delete mode 100644 doc/documentation.html
 delete mode 100644 doc/navbar.html
 delete mode 100644 doc/title.html.in

diff --git a/doc/CMakeLists.txt b/doc/CMakeLists.txt
index ddfdd2977e34..97edbbb32c8d 100644
--- a/doc/CMakeLists.txt
+++ b/doc/CMakeLists.txt
@@ -32,20 +32,9 @@ IF(DEAL_II_COMPONENT_DOCUMENTATION)
     COMPONENT documentation
     PATTERN "CMakeLists.txt" EXCLUDE
     PATTERN "doxygen" EXCLUDE
-    PATTERN "*.in" EXCLUDE
     PATTERN "news" EXCLUDE
     )
 
-  CONFIGURE_FILE(
-    ${CMAKE_CURRENT_SOURCE_DIR}/title.html.in
-    ${CMAKE_CURRENT_BINARY_DIR}/title.html
-    )
-  INSTALL(FILES
-    ${CMAKE_CURRENT_BINARY_DIR}/title.html
-    DESTINATION ${DEAL_II_DOCHTML_RELDIR}
-    COMPONENT documentation
-    )
-
   MESSAGE(STATUS "Setting up documentation - Done")
   MESSAGE(STATUS "")
 
diff --git a/doc/documentation.html b/doc/documentation.html
deleted file mode 100644
index 9977691eb5fc..000000000000
--- a/doc/documentation.html
+++ /dev/null
@@ -1,75 +0,0 @@
-
-
-  
-    The deal.II Online Documentation
-    
-    
-    
-    
-    
-  
-
-
-
    
-  
    
-  deal.II comes with extensive online
-  documentation that can be grouped into the following categories:
-
    
-
-
-
-
    
-  
    
-  
    
-  
    
-    
-      Valid HTML 4.01!
-    
-      Valid CSS!
-  
    
-
    
-
-
-
diff --git a/doc/index.html b/doc/index.html
index 98b547352979..b720f2cbd532 100644
--- a/doc/index.html
+++ b/doc/index.html
@@ -18,19 +18,83 @@
     
   
 
-  
-    
-    
-      
-      
-    
-    
-      <h1>The deal.II Documentation Page</h1>
-      Your browser does not seem to understand frames. A version of this
-      page that does not use frames can be found at
-      <a href="documentation.html">documentation.html</a>.
-    
-  
+  
+    
    
+      
+      
    
+
+        
    
+          
    
+            Information for developers
+          
    
+          
+        
    
+
+        
    
+          
    
+            Further resources
+          
    
+          
+        
    
+      
    
+    
    
+  
 
 
 
diff --git a/doc/navbar.html b/doc/navbar.html
deleted file mode 100644
index 53fc21aa6c5c..000000000000
--- a/doc/navbar.html
+++ /dev/null
@@ -1,51 +0,0 @@
-
-
-  
-    deal.II navigation bar
-    
-    
-    
-  
-  
-
-    
    
-      http://www.dealii.org
    
-    
    
-
-    
    
-
-    
    
-      Home
    
-      README
    
-    
    
-
-    
    
-
-    Doxygen and Lectures
-    
    
-      Tutorial Programs
    
-      Manual
    
-      Wolfgang's lectures
    
-    
    
-
-    
    
-
-    Online Resources
-    
    
-      FAQ
    
-      News
    
-      Download
    
-      Mailing list
    
-      Wiki
    
-      Bug tracker
    
-      Reports
    
-      Publications
    
-      Authors 
    
-      License 
    
-      Mailing lists
-    
    
-
-  
-
diff --git a/doc/title.html.in b/doc/title.html.in
deleted file mode 100644
index 7321caeda3d4..000000000000
--- a/doc/title.html.in
+++ /dev/null
@@ -1,17 +0,0 @@
-
-
-
-  deal.II Title Bar
-  
-  
-
-
-
-  
    
-    
    deal.II @DEAL_II_PACKAGE_VERSION@ Documentation
    
-  
    
-
-
-
-

From d566a2d10af46abcc9fa4ea7dd8a1fd4f6610d83 Mon Sep 17 00:00:00 2001
From: Daniel Arndt 
Date: Thu, 21 Mar 2019 20:35:02 +0100
Subject: [PATCH 303/507] Also link with LAPACK libraries

---
 cmake/configure/configure_scalapack.cmake | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/cmake/configure/configure_scalapack.cmake b/cmake/configure/configure_scalapack.cmake
index a91457f379c2..08820ceecbbd 100644
--- a/cmake/configure/configure_scalapack.cmake
+++ b/cmake/configure/configure_scalapack.cmake
@@ -28,7 +28,7 @@ MACRO(FEATURE_SCALAPACK_FIND_EXTERNAL var)
     CHECK_MPI_INTERFACE(SCALAPACK ${var})
 
     IF (${var})
-      SET(CMAKE_REQUIRED_LIBRARIES ${SCALAPACK_LIBRARIES})
+      SET(CMAKE_REQUIRED_LIBRARIES ${SCALAPACK_LIBRARIES} ${LAPACK_LIBRARIES})
       CHECK_C_SOURCE_COMPILES("
         void pdsyevr_();
         void pssyevr_();

From 5fdaaaf6c1ee8ff5152dff86bb7fec3a7ea6ce72 Mon Sep 17 00:00:00 2001
From: Luca Heltai 
Date: Tue, 19 Mar 2019 19:32:08 +0100
Subject: [PATCH 304/507] Added get_names to Extractors, and moved
 implementation to cc file.

---
 doc/news/changes/minor/20190319LucaHeltai |  4 ++
 include/deal.II/fe/fe_values_extractors.h | 24 ++++++++
 source/fe/CMakeLists.txt                  |  1 +
 source/fe/fe_values_extractors.cc         | 67 +++++++++++++++++++++++
 tests/fe/fe_values_extractor_02.cc        | 40 ++++++++++++++
 tests/fe/fe_values_extractor_02.output    |  5 ++
 6 files changed, 141 insertions(+)
 create mode 100644 doc/news/changes/minor/20190319LucaHeltai
 create mode 100644 source/fe/fe_values_extractors.cc
 create mode 100644 tests/fe/fe_values_extractor_02.cc
 create mode 100644 tests/fe/fe_values_extractor_02.output

diff --git a/doc/news/changes/minor/20190319LucaHeltai b/doc/news/changes/minor/20190319LucaHeltai
new file mode 100644
index 000000000000..5328898f6438
--- /dev/null
+++ b/doc/news/changes/minor/20190319LucaHeltai
@@ -0,0 +1,4 @@
+New: FEValuesExtractor classes now have a new method get_name() that returns a unique string identifier
+for each extractor. 
+
    
+(Luca Heltai, 2019/03/19)
diff --git a/include/deal.II/fe/fe_values_extractors.h b/include/deal.II/fe/fe_values_extractors.h
index db3729129af0..a7e1944bd3b1 100644
--- a/include/deal.II/fe/fe_values_extractors.h
+++ b/include/deal.II/fe/fe_values_extractors.h
@@ -112,6 +112,12 @@ namespace FEValuesExtractors
      * Constructor. Take the selected vector component as argument.
      */
     Scalar(const unsigned int component);
+
+    /**
+     * Return a string that uniquely identifies this finite element extractor.
+     */
+    std::string
+    get_name() const;
   };
 
 
@@ -162,6 +168,12 @@ namespace FEValuesExtractors
      * FEValues object as argument.
      */
     Vector(const unsigned int first_vector_component);
+
+    /**
+     * Return a string that uniquely identifies this finite element extractor.
+     */
+    std::string
+    get_name() const;
   };
 
 
@@ -205,6 +217,12 @@ namespace FEValuesExtractors
      * FEValues object as argument.
      */
     SymmetricTensor(const unsigned int first_tensor_component);
+
+    /**
+     * Return a string that uniquely identifies this finite element extractor.
+     */
+    std::string
+    get_name() const;
   };
 
 
@@ -248,6 +266,12 @@ namespace FEValuesExtractors
      * FEValues object as argument.
      */
     Tensor(const unsigned int first_tensor_component);
+
+    /**
+     * Return a string that uniquely identifies this finite element extractor.
+     */
+    std::string
+    get_name() const;
   };
 } // namespace FEValuesExtractors
 
diff --git a/source/fe/CMakeLists.txt b/source/fe/CMakeLists.txt
index 79a5bb8466f3..fbc00aeafc05 100644
--- a/source/fe/CMakeLists.txt
+++ b/source/fe/CMakeLists.txt
@@ -63,6 +63,7 @@ SET(_unity_include_src
 
 SET(_separate_src
   fe_values.cc
+  fe_values_extractors.cc
   fe_values_inst2.cc
   fe_values_inst3.cc
   fe_values_inst4.cc
diff --git a/source/fe/fe_values_extractors.cc b/source/fe/fe_values_extractors.cc
new file mode 100644
index 000000000000..8d0c417f6eb5
--- /dev/null
+++ b/source/fe/fe_values_extractors.cc
@@ -0,0 +1,67 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2019 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+#include 
+
+#include 
+
+DEAL_II_NAMESPACE_OPEN
+
+namespace FEValuesExtractors
+{
+  std::string
+  Scalar::get_name() const
+  {
+    return "Scalar(" + Utilities::int_to_string(component) + ")";
+  }
+
+
+  std::string
+  Vector::get_name() const
+  {
+    return "Vector(" + Utilities::int_to_string(first_vector_component) + ")";
+  }
+
+
+  template 
+  std::string
+  Tensor::get_name() const
+  {
+    return "Tensor<" + Utilities::int_to_string(rank) + ">(" +
+           Utilities::int_to_string(first_tensor_component) + ")";
+  }
+
+
+  template 
+  std::string
+  SymmetricTensor::get_name() const
+  {
+    return "SymmetricTensor<" + Utilities::int_to_string(rank) + ">(" +
+           Utilities::int_to_string(first_tensor_component) + ")";
+  }
+
+  // Explicit instantiations
+  template struct Tensor<1>;
+  template struct Tensor<2>;
+  template struct Tensor<3>;
+  template struct Tensor<4>;
+  template struct SymmetricTensor<2>;
+  template struct SymmetricTensor<4>;
+
+} // namespace FEValuesExtractors
+
+
+
+DEAL_II_NAMESPACE_CLOSE
\ No newline at end of file
diff --git a/tests/fe/fe_values_extractor_02.cc b/tests/fe/fe_values_extractor_02.cc
new file mode 100644
index 000000000000..c48a224ced99
--- /dev/null
+++ b/tests/fe/fe_values_extractor_02.cc
@@ -0,0 +1,40 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2019 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+
+
+// test that the FEValuesExtractors::get_name() work as expected
+
+#include 
+#include 
+
+#include "../tests.h"
+
+int
+main()
+{
+  initlog();
+
+  FEValuesExtractors::Scalar             scalar(0);
+  FEValuesExtractors::Vector             vector(1);
+  FEValuesExtractors::Tensor<2>          tensor(3);
+  FEValuesExtractors::SymmetricTensor<2> symmetric_tensor(4);
+
+
+  deallog << scalar.get_name() << std::endl
+          << vector.get_name() << std::endl
+          << tensor.get_name() << std::endl
+          << symmetric_tensor.get_name() << std::endl;
+}
diff --git a/tests/fe/fe_values_extractor_02.output b/tests/fe/fe_values_extractor_02.output
new file mode 100644
index 000000000000..1b5a9144063b
--- /dev/null
+++ b/tests/fe/fe_values_extractor_02.output
@@ -0,0 +1,5 @@
+
+DEAL::Scalar(0)
+DEAL::Vector(1)
+DEAL::Tensor<2>(3)
+DEAL::SymmetricTensor<2>(4)

From 6fbe952eae8a71ef19066af2b1b1a6fb7a25a9fc Mon Sep 17 00:00:00 2001
From: Denis Davydov 
Date: Thu, 21 Mar 2019 22:04:00 +0100
Subject: [PATCH 305/507] make MPILogInitAll work without MPI

---
 tests/tests.h | 18 ++++++------------
 1 file changed, 6 insertions(+), 12 deletions(-)

diff --git a/tests/tests.h b/tests/tests.h
index f585da1fc761..ee46c716d0a7 100644
--- a/tests/tests.h
+++ b/tests/tests.h
@@ -527,6 +527,9 @@ struct MPILogInitAll
   {
 #ifdef DEAL_II_WITH_MPI
     const unsigned int myid = Utilities::MPI::this_mpi_process(MPI_COMM_WORLD);
+#else
+    constexpr unsigned int myid = 0;
+#endif
     if (myid == 0)
       {
         if (!deallog.has_file())
@@ -545,22 +548,17 @@ struct MPILogInitAll
     deallog.depth_console(console ? 10 : 0);
 
     deallog.push(Utilities::int_to_string(myid));
-#else
-    (void)console;
-    // can't use this function if not using MPI
-    Assert(false, ExcInternalError());
-#endif
   }
 
   ~MPILogInitAll()
   {
+    // pop the prefix for the MPI rank of the current process
+    deallog.pop();
+
 #ifdef DEAL_II_WITH_MPI
     const unsigned int myid  = Utilities::MPI::this_mpi_process(MPI_COMM_WORLD);
     const unsigned int nproc = Utilities::MPI::n_mpi_processes(MPI_COMM_WORLD);
 
-    // pop the prefix for the MPI rank of the current process
-    deallog.pop();
-
     if (myid != 0)
       {
         deallog.detach();
@@ -583,10 +581,6 @@ struct MPILogInitAll
           }
       }
     MPI_Barrier(MPI_COMM_WORLD);
-
-#else
-    // can't use this function if not using MPI
-    Assert(false, ExcInternalError());
 #endif
   }
 };

From d3c741494c5f62b4856bd6dd80c1f02344d7bc22 Mon Sep 17 00:00:00 2001
From: Denis Davydov 
Date: Tue, 19 Mar 2019 20:39:35 +0100
Subject: [PATCH 306/507] add Utilities::MPI::create_ascending_partitioning()

---
 doc/news/changes/minor/20190319DenisDavydov   |  4 +
 include/deal.II/base/mpi.h                    | 13 +++
 source/base/mpi.cc                            | 33 ++++++++
 tests/base/mpi_create_partitioning_01.cc      | 80 +++++++++++++++++++
 ...mpi_create_partitioning_01.mpirun=2.output | 13 +++
 ...mpi_create_partitioning_01.mpirun=4.output | 43 ++++++++++
 tests/base/mpi_create_partitioning_01.output  |  4 +
 7 files changed, 190 insertions(+)
 create mode 100644 doc/news/changes/minor/20190319DenisDavydov
 create mode 100644 tests/base/mpi_create_partitioning_01.cc
 create mode 100644 tests/base/mpi_create_partitioning_01.mpirun=2.output
 create mode 100644 tests/base/mpi_create_partitioning_01.mpirun=4.output
 create mode 100644 tests/base/mpi_create_partitioning_01.output

diff --git a/doc/news/changes/minor/20190319DenisDavydov b/doc/news/changes/minor/20190319DenisDavydov
new file mode 100644
index 000000000000..ab8f90eec88c
--- /dev/null
+++ b/doc/news/changes/minor/20190319DenisDavydov
@@ -0,0 +1,4 @@
+New: Add Utilities::MPI::create_ascending_partitioning() to create a one-to-one
+ascending partitioning from locally owned sizes.
+
    
+(Denis Davydov, 2019/03/19)
diff --git a/include/deal.II/base/mpi.h b/include/deal.II/base/mpi.h
index 4688b3c17fd4..74bef20899e6 100644
--- a/include/deal.II/base/mpi.h
+++ b/include/deal.II/base/mpi.h
@@ -90,6 +90,7 @@ template 
 class SymmetricTensor;
 template 
 class SparseMatrix;
+class IndexSet;
 
 namespace Utilities
 {
@@ -225,6 +226,18 @@ namespace Utilities
                  MPI_Comm *       new_comm);
 #endif
 
+    /**
+     * Given the number of locally owned elements @p local_size,
+     * create a 1:1 partitioning of the of elements across the MPI communicator @p comm.
+     * The total size of elements is the sum of @p local_size across the MPI communicator.
+     * Each process will store contiguous subset of indices, and the index set
+     * on process p+1 starts at the index one larger than the last one stored on
+     * process p.
+     */
+    std::vector
+    create_ascending_partitioning(const MPI_Comm &           comm,
+                                  const IndexSet::size_type &local_size);
+
     /**
      * Return the sum over all processors of the value @p t. This function is
      * collective over all processors given in the
diff --git a/source/base/mpi.cc b/source/base/mpi.cc
index b8cd45e7c26a..35928aa9cc19 100644
--- a/source/base/mpi.cc
+++ b/source/base/mpi.cc
@@ -15,6 +15,7 @@
 
 
 #include 
+#include 
 #include 
 #include 
 #include 
@@ -181,6 +182,30 @@ namespace Utilities
 
 
 
+    std::vector
+    create_ascending_partitioning(const MPI_Comm &           comm,
+                                  const IndexSet::size_type &local_size)
+    {
+      const unsigned int                     n_proc = n_mpi_processes(comm);
+      const std::vector sizes =
+        all_gather(comm, local_size);
+      const auto total_size =
+        std::accumulate(sizes.begin(), sizes.end(), IndexSet::size_type(0));
+
+      std::vector res(n_proc, IndexSet(total_size));
+
+      IndexSet::size_type begin = 0;
+      for (unsigned int i = 0; i < n_proc; ++i)
+        {
+          res[i].add_range(begin, begin + sizes[i]);
+          begin = begin + sizes[i];
+        }
+
+      return res;
+    }
+
+
+
     std::vector
     compute_point_to_point_communication_pattern(
       const MPI_Comm &                 mpi_comm,
@@ -484,6 +509,14 @@ namespace Utilities
     }
 
 
+    std::vector
+    create_ascending_partitioning(const MPI_Comm & /*comm*/,
+                                  const IndexSet::size_type &local_size)
+    {
+      return std::vector(1, complete_index_set(local_size));
+    }
+
+
     MPI_Comm
     duplicate_communicator(const MPI_Comm &mpi_communicator)
     {
diff --git a/tests/base/mpi_create_partitioning_01.cc b/tests/base/mpi_create_partitioning_01.cc
new file mode 100644
index 000000000000..6ca9f6de4437
--- /dev/null
+++ b/tests/base/mpi_create_partitioning_01.cc
@@ -0,0 +1,80 @@
+// ---------------------------------------------------------------------
+//
+// Copyright (C) 2017 - 2018 by the deal.II authors
+//
+// This file is part of the deal.II library.
+//
+// The deal.II library is free software; you can use it, redistribute
+// it, and/or modify it under the terms of the GNU Lesser General
+// Public License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+// The full text of the license can be found in the file LICENSE.md at
+// the top level directory of deal.II.
+//
+// ---------------------------------------------------------------------
+
+// Test Utilities::MPI::create_ascending_partitioning()
+
+#include 
+#include 
+
+#include 
+
+#include "../tests.h"
+
+void
+test()
+{
+  MPI_Comm   comm(MPI_COMM_WORLD);
+  const auto my_proc = Utilities::MPI::this_mpi_process(comm);
+  const auto n_proc  = Utilities::MPI::n_mpi_processes(comm);
+
+  const auto my_size = (my_proc == 2 ? 0 : my_proc * 2 + 5);
+  const auto vec = Utilities::MPI::create_ascending_partitioning(comm, my_size);
+
+  // correct number:
+  AssertThrow(vec.size() == n_proc, ExcInternalError());
+
+  // ascending one-to-one
+  AssertThrow(vec[my_proc].is_ascending_and_one_to_one(comm),
+              ExcInternalError());
+
+  // same size:
+  const auto size = vec[0].size();
+  for (unsigned int i = 1; i < vec.size(); ++i)
+    AssertThrow(size == vec[i].size(), ExcInternalError());
+
+  // 1:1
+  for (unsigned int i = 0; i < vec.size(); ++i)
+    for (unsigned int j = i + 1; j < vec.size(); ++j)
+      {
+        const IndexSet intersection = vec[i] & vec[j];
+        AssertThrow(intersection.is_empty(), ExcInternalError());
+      }
+
+  // union of all
+  IndexSet all(size);
+  for (unsigned int i = 0; i < vec.size(); ++i)
+    all.add_indices(vec[i]);
+
+  AssertThrow(all == complete_index_set(size), ExcInternalError());
+
+  // finally print:
+  deallog << "Total size=" << size << std::endl;
+  for (unsigned int p = 0; p < vec.size(); ++p)
+    {
+      deallog << "p=" << p << ":" << std::endl;
+      vec[p].print(deallog.get_file_stream());
+    }
+}
+
+int
+main(int argc, char *argv[])
+{
+  Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1);
+
+  MPILogInitAll log;
+
+  test();
+  return 0;
+}
diff --git a/tests/base/mpi_create_partitioning_01.mpirun=2.output b/tests/base/mpi_create_partitioning_01.mpirun=2.output
new file mode 100644
index 000000000000..9075cba86e4a
--- /dev/null
+++ b/tests/base/mpi_create_partitioning_01.mpirun=2.output
@@ -0,0 +1,13 @@
+
+DEAL:0::Total size=12
+DEAL:0::p=0:
+{[0,4]}
+DEAL:0::p=1:
+{[5,11]}
+
+DEAL:1::Total size=12
+DEAL:1::p=0:
+{[0,4]}
+DEAL:1::p=1:
+{[5,11]}
+
diff --git a/tests/base/mpi_create_partitioning_01.mpirun=4.output b/tests/base/mpi_create_partitioning_01.mpirun=4.output
new file mode 100644
index 000000000000..7ac455243e9d
--- /dev/null
+++ b/tests/base/mpi_create_partitioning_01.mpirun=4.output
@@ -0,0 +1,43 @@
+
+DEAL:0::Total size=23
+DEAL:0::p=0:
+{[0,4]}
+DEAL:0::p=1:
+{[5,11]}
+DEAL:0::p=2:
+{}
+DEAL:0::p=3:
+{[12,22]}
+
+DEAL:1::Total size=23
+DEAL:1::p=0:
+{[0,4]}
+DEAL:1::p=1:
+{[5,11]}
+DEAL:1::p=2:
+{}
+DEAL:1::p=3:
+{[12,22]}
+
+
+DEAL:2::Total size=23
+DEAL:2::p=0:
+{[0,4]}
+DEAL:2::p=1:
+{[5,11]}
+DEAL:2::p=2:
+{}
+DEAL:2::p=3:
+{[12,22]}
+
+
+DEAL:3::Total size=23
+DEAL:3::p=0:
+{[0,4]}
+DEAL:3::p=1:
+{[5,11]}
+DEAL:3::p=2:
+{}
+DEAL:3::p=3:
+{[12,22]}
+
diff --git a/tests/base/mpi_create_partitioning_01.output b/tests/base/mpi_create_partitioning_01.output
new file mode 100644
index 000000000000..4d10ab83b3fa
--- /dev/null
+++ b/tests/base/mpi_create_partitioning_01.output
@@ -0,0 +1,4 @@
+
+DEAL:0::Total size=5
+DEAL:0::p=0:
+{[0,4]}

From f519cfaa2451e4248be759c08cdac60064d2b3ec Mon Sep 17 00:00:00 2001
From: Jean-Paul Pelteret 
Date: Fri, 22 Mar 2019 09:35:20 +0100
Subject: [PATCH 307/507] Rename the helper classes in the Differentiation::AD
 namespace

---
 .../changes/major/20180827Jean-PaulPelteret   |   2 +-
 .../changes/major/20180930Jean-PaulPelteret   |   2 +-
 .../changes/major/20190220Jean-PaulPelteret   |   2 +-
 .../changes/major/20190321Jean-PaulPelteret   |   2 +-
 .../deal.II/differentiation/ad/ad_helpers.h   | 198 ++++++------
 source/differentiation/ad/ad_helpers.cc       | 281 +++++++++---------
 source/differentiation/ad/ad_helpers.inst1.in |  84 +++---
 source/differentiation/ad/ad_helpers.inst2.in | 140 ++++-----
 .../step-44-helper_res_lin_01.h               |   4 +-
 .../step-44-helper_var_form_01.h              |   4 +-
 10 files changed, 348 insertions(+), 371 deletions(-)

diff --git a/doc/news/changes/major/20180827Jean-PaulPelteret b/doc/news/changes/major/20180827Jean-PaulPelteret
index d0476e4b3bee..6ff2bb4b710e 100644
--- a/doc/news/changes/major/20180827Jean-PaulPelteret
+++ b/doc/news/changes/major/20180827Jean-PaulPelteret
@@ -1,4 +1,4 @@
-New: A new class Differentiation::AD::ADHelperEnergyFunctional has been
+New: A new class Differentiation::AD::EnergyFunctional has been
 added to help implement (incremental) variational formulations using automatic 
 differentiation. In particular, this class is designed to compute the finite 
 element residuals and their linearizations.
diff --git a/doc/news/changes/major/20180930Jean-PaulPelteret b/doc/news/changes/major/20180930Jean-PaulPelteret
index 1c5bf9ae1997..3fbe9844e182 100644
--- a/doc/news/changes/major/20180930Jean-PaulPelteret
+++ b/doc/news/changes/major/20180930Jean-PaulPelteret
@@ -1,4 +1,4 @@
-New: A new class Differentiation::AD::ADHelperResidualLinearization has been
+New: A new class Differentiation::AD::ResidualLinearization has been
 added to help compute the linearization of a residual vector defined on the 
 level of a cell (a finite element residual), or for local nonlinear equations. 
 
    
diff --git a/doc/news/changes/major/20190220Jean-PaulPelteret b/doc/news/changes/major/20190220Jean-PaulPelteret
index c9df4e7cb7ca..3a0e37fe0de4 100644
--- a/doc/news/changes/major/20190220Jean-PaulPelteret
+++ b/doc/news/changes/major/20190220Jean-PaulPelteret
@@ -1,4 +1,4 @@
-New: A new class Differentiation::AD::ADHelperScalarFunction has been
+New: A new class Differentiation::AD::ScalarFunction has been
 added to help implement point-wise scalar functions using automatic 
 differentiation. In particular, this class is designed to compute the 
 gradient and Hessian of a scalar function that is parameterized in
diff --git a/doc/news/changes/major/20190321Jean-PaulPelteret b/doc/news/changes/major/20190321Jean-PaulPelteret
index 54b796a6d6b7..80e70e9e662a 100644
--- a/doc/news/changes/major/20190321Jean-PaulPelteret
+++ b/doc/news/changes/major/20190321Jean-PaulPelteret
@@ -1,4 +1,4 @@
-New: A new class Differentiation::AD::ADHelperVectorFunction has been
+New: A new class Differentiation::AD::VectorFunction has been
 added to help implement point-wise vector functions using automatic 
 differentiation. In particular, this class is designed to compute the 
 Jacobian of a vector function that is parameterized in
diff --git a/include/deal.II/differentiation/ad/ad_helpers.h b/include/deal.II/differentiation/ad/ad_helpers.h
index 7619901a82bc..507803a0dcf0 100644
--- a/include/deal.II/differentiation/ad/ad_helpers.h
+++ b/include/deal.II/differentiation/ad/ad_helpers.h
@@ -169,7 +169,7 @@ namespace Differentiation
      */
     template 
-    class ADHelperBase
+    class HelperBase
     {
     public:
       /**
@@ -205,13 +205,13 @@ namespace Differentiation
        * be the number of outputs $\mathbf{f}$, i.e., the dimension of the
        * image space.
        */
-      ADHelperBase(const unsigned int n_independent_variables,
-                   const unsigned int n_dependent_variables);
+      HelperBase(const unsigned int n_independent_variables,
+                 const unsigned int n_dependent_variables);
 
       /**
        * Destructor
        */
-      virtual ~ADHelperBase() = default;
+      virtual ~HelperBase() = default;
 
       //@}
 
@@ -279,7 +279,7 @@ namespace Differentiation
        * Pre-specify the number of @p independent_variables to be used in
        * tapeless mode.
        *
-       * Although this function is called internally in the ADHelperBase
+       * Although this function is called internally in the HelperBase
        * constructor, there may be occasions when ADOL-C tapeless numbers
        * (adtl::adoubles) are created before an instance of this class
        * is created. This function therefore allows one to declare at the
@@ -307,7 +307,7 @@ namespace Differentiation
       /**
        * Reset the state of the helper class.
        *
-       * When an instance of an ADHelperBase is stored as a class member object
+       * When an instance of an HelperBase is stored as a class member object
        * with the intention to reuse its instance, it may be necessary to reset
        * the state of the object before use. This is because, internally, there
        * is error checking performed to ensure that the correct
@@ -788,7 +788,7 @@ namespace Differentiation
 
       //@}
 
-    }; // class ADHelperBase
+    }; // class HelperBase
 
 
 
@@ -824,8 +824,8 @@ namespace Differentiation
      * @endcode
      * Note that the quotation marks are mandatory.
      * An alternative approach that allows for run-time decision making is to
-     * use the ADHelperBase::set_tape_buffer_sizes() function before starting
-     * taping (as done via the ADHelperBase::start_recording_operations()
+     * use the HelperBase::set_tape_buffer_sizes() function before starting
+     * taping (as done via the HelperBase::start_recording_operations()
      * function).
      *
      * @warning ADOL-C does not support the standard threading models used by
@@ -837,8 +837,7 @@ namespace Differentiation
      */
     template 
-    class ADHelperCellLevelBase
-      : public ADHelperBase
+    class CellLevelBase : public HelperBase
     {
     public:
       /**
@@ -846,14 +845,14 @@ namespace Differentiation
        * and results from, all computations.
        */
       using scalar_type =
-        typename ADHelperBase::scalar_type;
+        typename HelperBase::scalar_type;
 
       /**
        * Type definition for the auto-differentiation number type that is used
        * in all computations.
        */
       using ad_type =
-        typename ADHelperBase::ad_type;
+        typename HelperBase::ad_type;
 
       /**
        * @name Constructor / destructor
@@ -874,13 +873,13 @@ namespace Differentiation
        * be the number of outputs $\mathbf{f}$, i.e., the dimension of the
        * image space.
        */
-      ADHelperCellLevelBase(const unsigned int n_independent_variables,
-                            const unsigned int n_dependent_variables);
+      CellLevelBase(const unsigned int n_independent_variables,
+                    const unsigned int n_dependent_variables);
 
       /**
        * Destructor
        */
-      virtual ~ADHelperCellLevelBase() = default;
+      virtual ~CellLevelBase() = default;
 
       //@}
 
@@ -976,7 +975,7 @@ namespace Differentiation
        * correspond with the @p ScalarType prescribed as a template argument.
        *
        * @note If the @p keep_independent_values flag has been set when
-       * ADHelperBase::start_recording_operations() is called then the tape is
+       * HelperBase::start_recording_operations() is called then the tape is
        * immediately usable after creation, and the values of the independent
        * variables set by register_dof_values() are those at which the function
        * is to be evaluated. In this case, a separate call to this function is
@@ -996,7 +995,7 @@ namespace Differentiation
        * typically obtained by calling cell->get_dof_indices().
        *
        * @note If the @p keep_independent_values flag has been set when
-       * ADHelperBase::start_recording_operations() is called then the tape is
+       * HelperBase::start_recording_operations() is called then the tape is
        * immediately usable after creation, and the values of the independent
        * variables set by register_dof_values() are those at which the function
        * is to be evaluated. In this case, a separate call to this function is
@@ -1054,7 +1053,7 @@ namespace Differentiation
 
       //@}
 
-    }; // class ADHelperCellLevelBase
+    }; // class CellLevelBase
 
 
 
@@ -1091,7 +1090,7 @@ namespace Differentiation
      *     // Create some aliases for the AD helper.
      *     // In the example, the AD_typecode used for the template argument can
      *     // be refer to either a taped or tapeless type.
-     *     using ADHelper = AD::ADHelperEnergyFunctional<...>;
+     *     using ADHelper = AD::EnergyFunctional<...>;
      *     using ADNumberType = typename ADHelper::ad_type;
      *
      *     // Create and initialize an instance of the helper class.
@@ -1222,8 +1221,7 @@ namespace Differentiation
      */
     template 
-    class ADHelperEnergyFunctional
-      : public ADHelperCellLevelBase
+    class EnergyFunctional : public CellLevelBase
     {
     public:
       /**
@@ -1231,14 +1229,14 @@ namespace Differentiation
        * and results from, all computations.
        */
       using scalar_type =
-        typename ADHelperBase::scalar_type;
+        typename HelperBase::scalar_type;
 
       /**
        * Type definition for the auto-differentiation number type that is used
        * in all computations.
        */
       using ad_type =
-        typename ADHelperBase::ad_type;
+        typename HelperBase::ad_type;
 
       /**
        * @name Constructor / destructor
@@ -1260,12 +1258,12 @@ namespace Differentiation
        * is computed from the first and second derivatives of a scalar
        * function $\Psi(\mathbf{X})$.
        */
-      ADHelperEnergyFunctional(const unsigned int n_independent_variables);
+      EnergyFunctional(const unsigned int n_independent_variables);
 
       /**
        * Destructor
        */
-      virtual ~ADHelperEnergyFunctional() = default;
+      virtual ~EnergyFunctional() = default;
 
       //@}
 
@@ -1298,7 +1296,7 @@ namespace Differentiation
        * @f]
        *
        * The values at the evaluation point $\mathbf{X}$ are obtained by calling
-       * ADHelperCellLevelBase::set_dof_values().
+       * CellLevelBase::set_dof_values().
        *
        * @return The value of the energy functional at the evaluation point
        * corresponding to a chosen set of local degree of freedom values.
@@ -1318,7 +1316,7 @@ namespace Differentiation
        * @f]
        *
        * The values at the evaluation point $\mathbf{X}$ are obtained by calling
-       * ADHelperCellLevelBase::set_dof_values().
+       * CellLevelBase::set_dof_values().
        *
        * @param[out] residual A Vector object, for which the value for each
        * entry represents the residual value for the corresponding local
@@ -1341,7 +1339,7 @@ namespace Differentiation
        * @f]
        *
        * The values at the evaluation point $\mathbf{X}$ are obtained by calling
-       * ADHelperCellLevelBase::set_dof_values().
+       * CellLevelBase::set_dof_values().
        *
        * @param[out] linearization A FullMatrix representing the linearization
        * of the residual vector. The output @p linearization matrix has
@@ -1354,7 +1352,7 @@ namespace Differentiation
 
       //@}
 
-    }; // class ADHelperEnergyFunctional
+    }; // class EnergyFunctional
 
 
 
@@ -1398,9 +1396,9 @@ namespace Differentiation
      *     // In this example, we strictly assume that we're using tapeless
      *     // AD types, and so the AD_typecode used in the template argument
      *     // must refer to one of these types. See the example for the
-     *     // ADHelperEnergyFunctional for details on how to extend
+     *     // EnergyFunctional for details on how to extend
      *     // support to taped AD numbers.
-     *     using ADHelper = AD::ADHelperResidualLinearization<...>;
+     *     using ADHelper = AD::ResidualLinearization<...>;
      *     using ADNumberType = typename ADHelper::ad_type;
      *
      *     // Create and initialize an instance of the helper class.
@@ -1538,8 +1536,8 @@ namespace Differentiation
      */
     template 
-    class ADHelperResidualLinearization
-      : public ADHelperCellLevelBase
+    class ResidualLinearization
+      : public CellLevelBase
     {
     public:
       /**
@@ -1547,14 +1545,14 @@ namespace Differentiation
        * and results from, all computations.
        */
       using scalar_type =
-        typename ADHelperBase::scalar_type;
+        typename HelperBase::scalar_type;
 
       /**
        * Type definition for the auto-differentiation number type that is used
        * in all computations.
        */
       using ad_type =
-        typename ADHelperBase::ad_type;
+        typename HelperBase::ad_type;
 
       /**
        * @name Constructor / destructor
@@ -1575,13 +1573,13 @@ namespace Differentiation
        * be the number of outputs $\mathbf{r}$, i.e., the dimension of the
        * image space.
        */
-      ADHelperResidualLinearization(const unsigned int n_independent_variables,
-                                    const unsigned int n_dependent_variables);
+      ResidualLinearization(const unsigned int n_independent_variables,
+                            const unsigned int n_dependent_variables);
 
       /**
        * Destructor
        */
-      virtual ~ADHelperResidualLinearization() = default;
+      virtual ~ResidualLinearization() = default;
 
       //@}
 
@@ -1615,7 +1613,7 @@ namespace Differentiation
        * @f]
        *
        * The values at the evaluation point $\mathbf{X}$ are obtained by calling
-       * ADHelperCellLevelBase::set_dof_values().
+       * CellLevelBase::set_dof_values().
        *
        * @param[out] residual A Vector object, for which the value for each
        * entry represents the residual value for the corresponding local
@@ -1635,7 +1633,7 @@ namespace Differentiation
        * @f]
        *
        * The values at the evaluation point $\mathbf{X}$ are obtained by calling
-       * ADHelperCellLevelBase::set_dof_values().
+       * CellLevelBase::set_dof_values().
        *
        * @param[out] linearization A FullMatrix representing the linearization
        * of the residual vector. The output @p linearization matrix has
@@ -1648,7 +1646,7 @@ namespace Differentiation
 
       //@}
 
-    }; // class ADHelperResidualLinearization
+    }; // class ResidualLinearization
 
 
 
@@ -2623,7 +2621,7 @@ namespace Differentiation
     /**
      * A base helper class that facilitates the evaluation of point-wise defined
      * functions. This is the point-wise counterpart of the
-     * ADHelperCellLevelBase class, and was conceived for computations at a
+     * CellLevelBase class, and was conceived for computations at a
      * continuum point, or quadrature point, rather than for finite-element
      * level calculations. That being said, the interface to this and the
      * derived classes are sufficiently generic that the dependent function(s)
@@ -2646,8 +2644,8 @@ namespace Differentiation
     template 
-    class ADHelperPointLevelFunctionsBase
-      : public ADHelperBase
+    class PointLevelFunctionsBase
+      : public HelperBase
     {
     public:
       /**
@@ -2661,14 +2659,14 @@ namespace Differentiation
        * and results from, all computations.
        */
       using scalar_type =
-        typename ADHelperBase::scalar_type;
+        typename HelperBase::scalar_type;
 
       /**
        * Type definition for the auto-differentiation number type that is used
        * in all computations.
        */
       using ad_type =
-        typename ADHelperBase::ad_type;
+        typename HelperBase::ad_type;
 
       /**
        * @name Constructor / destructor
@@ -2689,14 +2687,13 @@ namespace Differentiation
        * be the number of outputs $\mathbf{f}$, i.e., the dimension of the
        * image space.
        */
-      ADHelperPointLevelFunctionsBase(
-        const unsigned int n_independent_variables,
-        const unsigned int n_dependent_variables);
+      PointLevelFunctionsBase(const unsigned int n_independent_variables,
+                              const unsigned int n_dependent_variables);
 
       /**
        * Destructor
        */
-      virtual ~ADHelperPointLevelFunctionsBase() = default;
+      virtual ~PointLevelFunctionsBase() = default;
 
       //@}
 
@@ -2706,7 +2703,7 @@ namespace Differentiation
       //@{
 
       /**
-       * @copydoc ADHelperBase::reset()
+       * @copydoc HelperBase::reset()
        */
       virtual void
       reset(const unsigned int n_independent_variables =
@@ -2837,7 +2834,7 @@ namespace Differentiation
        * correspond with the @p ScalarType prescribed as a template argument.
        *
        * @note If the @p keep_independent_values flag has been set when
-       * ADHelperBase::start_recording_operations() is called then the tape is
+       * HelperBase::start_recording_operations() is called then the tape is
        * immediately usable after creation, and the values of the independent
        * variables set by register_independent_variables() are those at which
        * the function is to be evaluated. In this case, a separate call to this
@@ -2866,7 +2863,7 @@ namespace Differentiation
        * be an FEValuesExtractors::Vector or FEValuesExtractors::Tensor<1>.
        *
        * @note If the @p keep_independent_values flag has been set when
-       * ADHelperBase::start_recording_operations() is called then the tape is
+       * HelperBase::start_recording_operations() is called then the tape is
        * immediately usable after creation, and the values of the independent
        * variables set by register_independent_variable() are those at which the
        * function is to be evaluated. In this case, a separate call to this
@@ -2931,7 +2928,7 @@ namespace Differentiation
 
       //@}
 
-    }; // class ADHelperPointLevelFunctionsBase
+    }; // class PointLevelFunctionsBase
 
 
 
@@ -2964,7 +2961,7 @@ namespace Differentiation
      *   // Define the helper that we will use in the AD computations for our
      *   // scalar energy function. Note that we expect it to return values of
      *   // type double.
-     *   ADHelperScalarFunction ad_helper (n_independent_variables);
+     *   ScalarFunction ad_helper (n_independent_variables);
      *   using ADNumberType = typename ADHelper::ad_type;
      *
      *   // Compute the fields that provide the independent values.
@@ -3094,10 +3091,8 @@ namespace Differentiation
     template 
-    class ADHelperScalarFunction
-      : public ADHelperPointLevelFunctionsBase
+    class ScalarFunction
+      : public PointLevelFunctionsBase
     {
     public:
       /**
@@ -3105,14 +3100,14 @@ namespace Differentiation
        * and results from, all computations.
        */
       using scalar_type =
-        typename ADHelperBase::scalar_type;
+        typename HelperBase::scalar_type;
 
       /**
        * Type definition for the auto-differentiation number type that is used
        * in all computations.
        */
       using ad_type =
-        typename ADHelperBase::ad_type;
+        typename HelperBase::ad_type;
 
       /**
        * @name Constructor / destructor
@@ -3128,12 +3123,12 @@ namespace Differentiation
        * $\mathbf{f}(\mathbf{X})$, this will be the number of inputs
        * $\mathbf{X}$, i.e., the dimension of the domain space.
        */
-      ADHelperScalarFunction(const unsigned int n_independent_variables);
+      ScalarFunction(const unsigned int n_independent_variables);
 
       /**
        * Destructor.
        */
-      virtual ~ADHelperScalarFunction() = default;
+      virtual ~ScalarFunction() = default;
 
       //@}
 
@@ -3323,7 +3318,7 @@ namespace Differentiation
 
       //@}
 
-    }; // class ADHelperScalarFunction
+    }; // class ScalarFunction
 
 
 
@@ -3366,7 +3361,7 @@ namespace Differentiation
      *   // Define the helper that we will use in the AD computations for our
      *   // scalar energy function. Note that we expect it to return values of
      *   // type double.
-     *   ADHelperVectorFunction ad_helper (n_independent_variables,
+     *   VectorFunction ad_helper (n_independent_variables,
      *                                                 n_dependent_variables);
      *   using ADNumberType = typename ADHelper::ad_type;
      *
@@ -3489,10 +3484,8 @@ namespace Differentiation
     template 
-    class ADHelperVectorFunction
-      : public ADHelperPointLevelFunctionsBase
+    class VectorFunction
+      : public PointLevelFunctionsBase
     {
     public:
       /**
@@ -3500,14 +3493,14 @@ namespace Differentiation
        * and results from, all computations.
        */
       using scalar_type =
-        typename ADHelperBase::scalar_type;
+        typename HelperBase::scalar_type;
 
       /**
        * Type definition for the auto-differentiation number type that is used
        * in all computations.
        */
       using ad_type =
-        typename ADHelperBase::ad_type;
+        typename HelperBase::ad_type;
 
       /**
        * @name Constructor / destructor
@@ -3528,13 +3521,13 @@ namespace Differentiation
        * be the number of outputs $\mathbf{f}$, i.e., the dimension of the
        * image space.
        */
-      ADHelperVectorFunction(const unsigned int n_independent_variables,
-                             const unsigned int n_dependent_variables);
+      VectorFunction(const unsigned int n_independent_variables,
+                     const unsigned int n_dependent_variables);
 
       /**
        * Destructor.
        */
-      virtual ~ADHelperVectorFunction() = default;
+      virtual ~VectorFunction() = default;
 
       //@}
 
@@ -3726,7 +3719,7 @@ namespace Differentiation
 
       //@}
 
-    }; // class ADHelperVectorFunction
+    }; // class VectorFunction
 
 
   } // namespace AD
@@ -3742,14 +3735,14 @@ namespace Differentiation
 {
   namespace AD
   {
-    /* ----------------- ADHelperCellLevelBase ----------------- */
+    /* ----------------- CellLevelBase ----------------- */
 
 
 
     template 
     template 
     void
-    ADHelperCellLevelBase::register_dof_values(
+    CellLevelBase::register_dof_values(
       const VectorType &                                  values,
       const std::vector &local_dof_indices)
     {
@@ -3774,7 +3767,7 @@ namespace Differentiation
     template 
     template 
     void
-    ADHelperCellLevelBase::set_dof_values(
+    CellLevelBase::set_dof_values(
       const VectorType &                                  values,
       const std::vector &local_dof_indices)
     {
@@ -3782,13 +3775,13 @@ namespace Differentiation
              ExcMessage(
                "Vector size does not match number of independent variables"));
       for (unsigned int i = 0; i < this->n_independent_variables(); ++i)
-        ADHelperBase::set_sensitivity_value(
+        HelperBase::set_sensitivity_value(
           i, values[local_dof_indices[i]]);
     }
 
 
 
-    /* ----------------- ADHelperPointLevelFunctionsBase ----------------- */
+    /* ----------------- PointLevelFunctionsBase ----------------- */
 
 
 
@@ -3797,7 +3790,7 @@ namespace Differentiation
               typename ScalarType>
     template 
     void
-    ADHelperPointLevelFunctionsBase::
+    PointLevelFunctionsBase::
       register_independent_variable(const ValueType &    value,
                                     const ExtractorType &extractor)
     {
@@ -3833,7 +3826,7 @@ namespace Differentiation
               typename ScalarType>
     template 
     void
-    ADHelperPointLevelFunctionsBase::
+    PointLevelFunctionsBase::
       set_independent_variable(const ValueType &    value,
                                const ExtractorType &extractor)
     {
@@ -3855,8 +3848,8 @@ namespace Differentiation
               typename ScalarType>
     template 
     typename internal::Extractor::template tensor_type<
-      typename ADHelperBase::ad_type>
-    ADHelperPointLevelFunctionsBase::
+      typename HelperBase::ad_type>
+    PointLevelFunctionsBase::
       get_sensitive_variables(const ExtractorType &extractor) const
     {
       if (ADNumberTraits::is_taped == true)
@@ -3895,7 +3888,7 @@ namespace Differentiation
 
 
 
-    /* ----------------- ADHelperScalarFunction ----------------- */
+    /* ----------------- ScalarFunction ----------------- */
 
 
 
@@ -3905,10 +3898,9 @@ namespace Differentiation
     template 
     typename internal::ScalarFieldGradient<
       dim,
-      typename ADHelperScalarFunction::
-        scalar_type,
+      typename ScalarFunction::scalar_type,
       ExtractorType_Row>::type
-    ADHelperScalarFunction::
+    ScalarFunction::
       extract_gradient_component(const Vector &gradient,
                                  const ExtractorType_Row &  extractor_row)
     {
@@ -3937,11 +3929,10 @@ namespace Differentiation
     template 
     typename internal::ScalarFieldHessian<
       dim,
-      typename ADHelperScalarFunction::
-        scalar_type,
+      typename ScalarFunction::scalar_type,
       ExtractorType_Row,
       ExtractorType_Col>::type
-    ADHelperScalarFunction::
+    ScalarFunction::
       extract_hessian_component(const FullMatrix &hessian,
                                 const ExtractorType_Row &      extractor_row,
                                 const ExtractorType_Col &      extractor_col)
@@ -3996,7 +3987,7 @@ namespace Differentiation
 
 
 
-    /* ----------------- ADHelperVectorFunction ----------------- */
+    /* ----------------- VectorFunction ----------------- */
 
 
 
@@ -4005,7 +3996,7 @@ namespace Differentiation
               typename ScalarType>
     template 
     void
-    ADHelperVectorFunction::
+    VectorFunction::
       register_dependent_variable(const ValueType &    funcs,
                                   const ExtractorType &extractor)
     {
@@ -4016,9 +4007,8 @@ namespace Differentiation
           Assert(this->registered_marked_dependent_variables[index_set[i]] ==
                    false,
                  ExcMessage("Overlapping indices for dependent variables."));
-          ADHelperBase::
-            register_dependent_variable(index_set[i],
-                                        internal::get_tensor_entry(funcs, i));
+          HelperBase::register_dependent_variable(
+            index_set[i], internal::get_tensor_entry(funcs, i));
         }
     }
 
@@ -4030,12 +4020,11 @@ namespace Differentiation
     template 
     typename internal::VectorFieldValue<
       dim,
-      typename ADHelperVectorFunction::
-        scalar_type,
+      typename VectorFunction::scalar_type,
       ExtractorType_Row>::type
-    ADHelperVectorFunction::
-      extract_value_component(const Vector &values,
-                              const ExtractorType_Row &  extractor_row)
+    VectorFunction::extract_value_component(
+      const Vector &values,
+      const ExtractorType_Row &  extractor_row)
     {
       // NOTE: The order of components must be consistently defined throughout
       // this class.
@@ -4062,11 +4051,10 @@ namespace Differentiation
     template 
     typename internal::VectorFieldJacobian<
       dim,
-      typename ADHelperVectorFunction::
-        scalar_type,
+      typename VectorFunction::scalar_type,
       ExtractorType_Row,
       ExtractorType_Col>::type
-    ADHelperVectorFunction::
+    VectorFunction::
       extract_jacobian_component(const FullMatrix &jacobian,
                                  const ExtractorType_Row &      extractor_row,
                                  const ExtractorType_Col &      extractor_col)
diff --git a/source/differentiation/ad/ad_helpers.cc b/source/differentiation/ad/ad_helpers.cc
index 4d67b34ad7f9..fac44b98a5bd 100644
--- a/source/differentiation/ad/ad_helpers.cc
+++ b/source/differentiation/ad/ad_helpers.cc
@@ -30,12 +30,12 @@ namespace Differentiation
 {
   namespace AD
   {
-    /* -------------------------- ADHelperBase -------------------------- */
+    /* -------------------------- HelperBase -------------------------- */
 
 
 
     template 
-    ADHelperBase::ADHelperBase(
+    HelperBase::HelperBase(
       const unsigned int n_independent_variables,
       const unsigned int n_dependent_variables)
       : independent_variable_values(
@@ -65,8 +65,8 @@ namespace Differentiation
 
     template 
     void
-    ADHelperBase::reset_registered_independent_variables()
+    HelperBase::reset_registered_independent_variables()
     {
       for (typename std::vector::iterator it =
              registered_independent_variable_values.begin();
@@ -79,7 +79,7 @@ namespace Differentiation
 
     template 
     void
-    ADHelperBase::
+    HelperBase::
       reset_registered_dependent_variables(const bool flag)
     {
       for (typename std::vector::iterator it =
@@ -93,7 +93,7 @@ namespace Differentiation
 
     template 
     void
-    ADHelperBase::set_sensitivity_value(
+    HelperBase::set_sensitivity_value(
       const unsigned int index,
       const scalar_type &value)
     {
@@ -130,7 +130,7 @@ namespace Differentiation
 
     template 
     void
-    ADHelperBase::mark_independent_variable(
+    HelperBase::mark_independent_variable(
       const unsigned int index,
       ad_type &          out) const
     {
@@ -168,8 +168,8 @@ namespace Differentiation
 
     template 
     void
-    ADHelperBase::finalize_sensitive_independent_variables() const
+    HelperBase::finalize_sensitive_independent_variables() const
     {
       // Double check that we've actually registered all DoFs
       Assert(n_registered_independent_variables() == n_independent_variables(),
@@ -192,7 +192,7 @@ namespace Differentiation
 
     template 
     void
-    ADHelperBase::
+    HelperBase::
       initialize_non_sensitive_independent_variable(const unsigned int index,
                                                     ad_type &out) const
     {
@@ -217,8 +217,8 @@ namespace Differentiation
 
     template 
     unsigned int
-    ADHelperBase::n_registered_independent_variables() const
+    HelperBase::n_registered_independent_variables() const
     {
       return std::count(registered_independent_variable_values.begin(),
                         registered_independent_variable_values.end(),
@@ -229,7 +229,7 @@ namespace Differentiation
 
     template 
     std::size_t
-    ADHelperBase::n_independent_variables() const
+    HelperBase::n_independent_variables() const
     {
       return independent_variable_values.size();
     }
@@ -238,8 +238,8 @@ namespace Differentiation
 
     template 
     unsigned int
-    ADHelperBase::n_registered_dependent_variables() const
+    HelperBase::n_registered_dependent_variables()
+      const
     {
       return std::count(registered_marked_dependent_variables.begin(),
                         registered_marked_dependent_variables.end(),
@@ -250,7 +250,7 @@ namespace Differentiation
 
     template 
     std::size_t
-    ADHelperBase::n_dependent_variables() const
+    HelperBase::n_dependent_variables() const
     {
       return dependent_variables.size();
     }
@@ -259,7 +259,7 @@ namespace Differentiation
 
     template 
     bool
-    ADHelperBase::is_recording() const
+    HelperBase::is_recording() const
     {
       if (AD::is_taped_ad_number::value)
         return taped_driver.is_recording();
@@ -271,8 +271,8 @@ namespace Differentiation
 
     template 
     typename Types<
-      typename ADHelperBase::ad_type>::tape_index
-    ADHelperBase::active_tape_index() const
+      typename HelperBase::ad_type>::tape_index
+    HelperBase::active_tape_index() const
     {
       if (AD::is_taped_ad_number::value)
         return taped_driver.active_tape_index();
@@ -284,7 +284,7 @@ namespace Differentiation
 
     template 
     bool
-    ADHelperBase::is_registered_tape(
+    HelperBase::is_registered_tape(
       const typename Types::tape_index tape_index) const
     {
       if (AD::is_taped_ad_number::value)
@@ -297,8 +297,7 @@ namespace Differentiation
 
     template 
     void
-    ADHelperBase::print(
-      std::ostream &stream) const
+    HelperBase::print(std::ostream &stream) const
     {
       // Store stream flags
       const std::ios_base::fmtflags stream_flags(stream.flags());
@@ -353,7 +352,7 @@ namespace Differentiation
 
     template 
     void
-    ADHelperBase::print_values(
+    HelperBase::print_values(
       std::ostream &stream) const
     {
       for (unsigned int i = 0; i < n_independent_variables(); i++)
@@ -367,7 +366,7 @@ namespace Differentiation
 
     template 
     void
-    ADHelperBase::print_tape_stats(
+    HelperBase::print_tape_stats(
       const typename Types::tape_index tape_index,
       std::ostream &                            stream) const
     {
@@ -384,7 +383,7 @@ namespace Differentiation
 
     template 
     void
-    ADHelperBase::reset(
+    HelperBase::reset(
       const unsigned int n_independent_variables,
       const unsigned int n_dependent_variables,
       const bool         clear_registered_tapes)
@@ -442,7 +441,7 @@ namespace Differentiation
 
     template 
     void
-    ADHelperBase::configure_tapeless_mode(
+    HelperBase::configure_tapeless_mode(
       const unsigned int n_independent_variables,
       const bool         ensure_persistent_setting)
     {
@@ -467,7 +466,7 @@ namespace Differentiation
 
     template 
     void
-    ADHelperBase::activate_recorded_tape(
+    HelperBase::activate_recorded_tape(
       const typename Types::tape_index tape_index)
     {
       activate_tape(tape_index, true /*read_mode*/);
@@ -477,7 +476,7 @@ namespace Differentiation
 
     template 
     bool
-    ADHelperBase::recorded_tape_requires_retaping(
+    HelperBase::recorded_tape_requires_retaping(
       const typename Types::tape_index tape_index) const
     {
       if (ADNumberTraits::is_tapeless == true)
@@ -490,7 +489,7 @@ namespace Differentiation
 
     template 
     bool
-    ADHelperBase::active_tape_requires_retaping()
+    HelperBase::active_tape_requires_retaping()
       const
     {
       if (ADNumberTraits::is_tapeless == true)
@@ -503,7 +502,7 @@ namespace Differentiation
 
     template 
     void
-    ADHelperBase::clear_active_tape()
+    HelperBase::clear_active_tape()
     {
       if (ADNumberTraits::is_tapeless == true)
         return;
@@ -515,7 +514,7 @@ namespace Differentiation
 
     template 
     void
-    ADHelperBase::activate_tape(
+    HelperBase::activate_tape(
       const typename Types::tape_index tape_index,
       const bool                                read_mode)
     {
@@ -552,7 +551,7 @@ namespace Differentiation
 
     template 
     void
-    ADHelperBase::set_tape_buffer_sizes(
+    HelperBase::set_tape_buffer_sizes(
       const typename Types::tape_buffer_sizes obufsize,
       const typename Types::tape_buffer_sizes lbufsize,
       const typename Types::tape_buffer_sizes vbufsize,
@@ -571,7 +570,7 @@ namespace Differentiation
 
     template 
     bool
-    ADHelperBase::start_recording_operations(
+    HelperBase::start_recording_operations(
       const typename Types::tape_index tape_index,
       const bool                                overwrite_tape,
       const bool                                keep_independent_values)
@@ -636,7 +635,7 @@ namespace Differentiation
 
     template 
     void
-    ADHelperBase::stop_recording_operations(
+    HelperBase::stop_recording_operations(
       const bool write_tapes_to_file)
     {
       Assert(is_recording() == true, ExcMessage("Not currently recording..."));
@@ -672,7 +671,7 @@ namespace Differentiation
 
     template 
     void
-    ADHelperBase::register_dependent_variable(
+    HelperBase::register_dependent_variable(
       const unsigned int index,
       const ad_type &    func)
     {
@@ -698,23 +697,23 @@ namespace Differentiation
 
 
 
-    /* -------------------- ADHelperCellLevelBase -------------------- */
+    /* -------------------- CellLevelBase -------------------- */
 
 
 
     template 
-    ADHelperCellLevelBase::ADHelperCellLevelBase(
+    CellLevelBase::CellLevelBase(
       const unsigned int n_independent_variables,
       const unsigned int n_dependent_variables)
-      : ADHelperBase(n_independent_variables,
-                                                   n_dependent_variables)
+      : HelperBase(n_independent_variables,
+                                                 n_dependent_variables)
     {}
 
 
 
     template 
     void
-    ADHelperCellLevelBase::register_dof_values(
+    CellLevelBase::register_dof_values(
       const std::vector &dof_values)
     {
       // This is actually the same thing the set_independent_variable function,
@@ -736,9 +735,9 @@ namespace Differentiation
 
     template 
     const std::vector<
-      typename ADHelperCellLevelBase::ad_type> &
-    ADHelperCellLevelBase::get_sensitive_dof_values() const
+      typename CellLevelBase::ad_type> &
+    CellLevelBase::get_sensitive_dof_values()
+      const
     {
       if (ADNumberTraits::is_taped == true)
         {
@@ -762,7 +761,7 @@ namespace Differentiation
 
     template 
     void
-    ADHelperCellLevelBase::set_dof_values(
+    CellLevelBase::set_dof_values(
       const std::vector &values)
     {
       if (ADNumberTraits::is_taped == true)
@@ -775,42 +774,39 @@ namespace Differentiation
              ExcMessage(
                "Vector size does not match number of independent variables"));
       for (unsigned int i = 0; i < this->n_independent_variables(); ++i)
-        ADHelperBase::set_sensitivity_value(
+        HelperBase::set_sensitivity_value(
           i, values[i]);
     }
 
 
 
-    /* ------------------ ADHelperEnergyFunctional ------------------ */
+    /* ------------------ EnergyFunctional ------------------ */
 
 
 
     template 
-    ADHelperEnergyFunctional::
-      ADHelperEnergyFunctional(const unsigned int n_independent_variables)
-      : ADHelperCellLevelBase(
-          n_independent_variables,
-          1)
+    EnergyFunctional::EnergyFunctional(
+      const unsigned int n_independent_variables)
+      : CellLevelBase(n_independent_variables, 1)
     {}
 
 
 
     template 
     void
-    ADHelperEnergyFunctional::
-      register_energy_functional(const ad_type &energy)
+    EnergyFunctional::register_energy_functional(
+      const ad_type &energy)
     {
       Assert(this->n_dependent_variables() == 1, ExcInternalError());
-      ADHelperBase::register_dependent_variable(
+      HelperBase::register_dependent_variable(
         0, energy);
     }
 
 
 
     template 
-    typename ADHelperEnergyFunctional::scalar_type
-    ADHelperEnergyFunctional::compute_energy()
-      const
+    typename EnergyFunctional::scalar_type
+    EnergyFunctional::compute_energy() const
     {
       if ((ADNumberTraits::is_taped == true &&
            this->taped_driver.keep_independent_values() == false) ||
@@ -829,7 +825,7 @@ namespace Differentiation
       Assert(
         this->n_dependent_variables() == 1,
         ExcMessage(
-          "The ADHelperEnergyFunctional class expects there to be only one dependent variable."));
+          "The EnergyFunctional class expects there to be only one dependent variable."));
 
       if (ADNumberTraits::is_taped == true)
         {
@@ -864,7 +860,7 @@ namespace Differentiation
 
     template 
     void
-    ADHelperEnergyFunctional::compute_residual(
+    EnergyFunctional::compute_residual(
       Vector &gradient) const
     {
       if ((ADNumberTraits::is_taped == true &&
@@ -884,7 +880,7 @@ namespace Differentiation
       Assert(
         this->n_dependent_variables() == 1,
         ExcMessage(
-          "The ADHelperEnergyFunctional class expects there to be only one dependent variable."));
+          "The EnergyFunctional class expects there to be only one dependent variable."));
 
       // We can neglect correctly initializing the entries as
       // we'll be overwriting them immediately in the succeeding call to
@@ -929,8 +925,8 @@ namespace Differentiation
 
     template 
     void
-    ADHelperEnergyFunctional::
-      compute_linearization(FullMatrix &hessian) const
+    EnergyFunctional::compute_linearization(
+      FullMatrix &hessian) const
     {
       Assert(AD::ADNumberTraits::n_supported_derivative_levels >= 2,
              ExcMessage(
@@ -953,7 +949,7 @@ namespace Differentiation
       Assert(
         this->n_dependent_variables() == 1,
         ExcMessage(
-          "The ADHelperEnergyFunctional class expects there to be only one dependent variable."));
+          "The EnergyFunctional class expects there to be only one dependent variable."));
 
       // We can neglect correctly initializing the entries as
       // we'll be overwriting them immediately in the succeeding call to
@@ -997,31 +993,30 @@ namespace Differentiation
     }
 
 
-    /* ------------------- ADHelperResidualLinearization ------------------- */
+    /* ------------------- ResidualLinearization ------------------- */
 
 
 
     template 
-    ADHelperResidualLinearization::
-      ADHelperResidualLinearization(const unsigned int n_independent_variables,
-                                    const unsigned int n_dependent_variables)
-      : ADHelperCellLevelBase(
-          n_independent_variables,
-          n_dependent_variables)
+    ResidualLinearization::ResidualLinearization(
+      const unsigned int n_independent_variables,
+      const unsigned int n_dependent_variables)
+      : CellLevelBase(n_independent_variables,
+                                                    n_dependent_variables)
     {}
 
 
 
     template 
     void
-    ADHelperResidualLinearization::
+    ResidualLinearization::
       register_residual_vector(const std::vector &residual)
     {
       Assert(residual.size() == this->n_dependent_variables(),
              ExcMessage(
                "Vector size does not match number of dependent variables"));
       for (unsigned int i = 0; i < this->n_dependent_variables(); ++i)
-        ADHelperBase::register_dependent_variable(
+        HelperBase::register_dependent_variable(
           i, residual[i]);
     }
 
@@ -1029,8 +1024,8 @@ namespace Differentiation
 
     template 
     void
-    ADHelperResidualLinearization::
-      compute_residual(Vector &values) const
+    ResidualLinearization::compute_residual(
+      Vector &values) const
     {
       if ((ADNumberTraits::is_taped == true &&
            this->taped_driver.keep_independent_values() == false) ||
@@ -1083,8 +1078,8 @@ namespace Differentiation
 
     template 
     void
-    ADHelperResidualLinearization::
-      compute_linearization(FullMatrix &jacobian) const
+    ResidualLinearization::compute_linearization(
+      FullMatrix &jacobian) const
     {
       if ((ADNumberTraits::is_taped == true &&
            this->taped_driver.keep_independent_values() == false) ||
@@ -1144,19 +1139,18 @@ namespace Differentiation
 
 
 
-    /* ----------------- ADHelperPointLevelFunctionsBase  ----------------- */
+    /* ----------------- PointLevelFunctionsBase  ----------------- */
 
 
 
     template 
-    ADHelperPointLevelFunctionsBase::
-      ADHelperPointLevelFunctionsBase(
-        const unsigned int n_independent_variables,
-        const unsigned int n_dependent_variables)
-      : ADHelperBase(n_independent_variables,
-                                                   n_dependent_variables)
+    PointLevelFunctionsBase::
+      PointLevelFunctionsBase(const unsigned int n_independent_variables,
+                              const unsigned int n_dependent_variables)
+      : HelperBase(n_independent_variables,
+                                                 n_dependent_variables)
       , symmetric_independent_variables(n_independent_variables, false)
     {}
 
@@ -1166,14 +1160,14 @@ namespace Differentiation
               enum AD::NumberTypes ADNumberTypeCode,
               typename ScalarType>
     void
-    ADHelperPointLevelFunctionsBase::reset(
+    PointLevelFunctionsBase::reset(
       const unsigned int n_independent_variables,
       const unsigned int n_dependent_variables,
       const bool         clear_registered_tapes)
     {
-      ADHelperBase::reset(n_independent_variables,
-                                                        n_dependent_variables,
-                                                        clear_registered_tapes);
+      HelperBase::reset(n_independent_variables,
+                                                      n_dependent_variables,
+                                                      clear_registered_tapes);
 
       const unsigned int new_n_independent_variables =
         (n_independent_variables != dealii::numbers::invalid_unsigned_int ?
@@ -1189,7 +1183,7 @@ namespace Differentiation
               enum AD::NumberTypes ADNumberTypeCode,
               typename ScalarType>
     bool
-    ADHelperPointLevelFunctionsBase::
+    PointLevelFunctionsBase::
       is_symmetric_independent_variable(const unsigned int index) const
     {
       Assert(index < symmetric_independent_variables.size(),
@@ -1203,7 +1197,7 @@ namespace Differentiation
               enum AD::NumberTypes ADNumberTypeCode,
               typename ScalarType>
     unsigned int
-    ADHelperPointLevelFunctionsBase::
+    PointLevelFunctionsBase::
       n_symmetric_independent_variables() const
     {
       return std::count(symmetric_independent_variables.begin(),
@@ -1217,7 +1211,7 @@ namespace Differentiation
               enum AD::NumberTypes ADNumberTypeCode,
               typename ScalarType>
     void
-    ADHelperPointLevelFunctionsBase::
+    PointLevelFunctionsBase::
       register_independent_variables(const std::vector &values)
     {
       // This is actually the same thing the set_independent_variable function,
@@ -1240,11 +1234,10 @@ namespace Differentiation
     template 
-    const std::vector<
-      typename ADHelperPointLevelFunctionsBase::ad_type> &
-    ADHelperPointLevelFunctionsBase::
+    const std::vector::ad_type> &
+    PointLevelFunctionsBase::
       get_sensitive_variables() const
     {
       if (ADNumberTraits::is_taped == true)
@@ -1272,13 +1265,13 @@ namespace Differentiation
               enum AD::NumberTypes ADNumberTypeCode,
               typename ScalarType>
     void
-    ADHelperPointLevelFunctionsBase::
+    PointLevelFunctionsBase::
       set_sensitivity_value(const unsigned int index,
                             const bool         symmetric_component,
                             const scalar_type &value)
     {
-      ADHelperBase::set_sensitivity_value(index,
-                                                                        value);
+      HelperBase::set_sensitivity_value(index,
+                                                                      value);
       Assert(
         index < this->n_independent_variables(),
         ExcMessage(
@@ -1294,7 +1287,7 @@ namespace Differentiation
               enum AD::NumberTypes ADNumberTypeCode,
               typename ScalarType>
     void
-    ADHelperPointLevelFunctionsBase::
+    PointLevelFunctionsBase::
       set_independent_variables(const std::vector &values)
     {
       if (ADNumberTraits::is_taped == true)
@@ -1307,22 +1300,22 @@ namespace Differentiation
              ExcMessage(
                "Vector size does not match number of independent variables"));
       for (unsigned int i = 0; i < this->n_independent_variables(); ++i)
-        ADHelperBase::set_sensitivity_value(
+        HelperBase::set_sensitivity_value(
           i, values[i]);
     }
 
 
 
-    /* -------------------- ADHelperScalarFunction -------------------- */
+    /* -------------------- ScalarFunction -------------------- */
 
 
 
     template 
-    ADHelperScalarFunction::
-      ADHelperScalarFunction(const unsigned int n_independent_variables)
-      : ADHelperPointLevelFunctionsBase(
+    ScalarFunction::ScalarFunction(
+      const unsigned int n_independent_variables)
+      : PointLevelFunctionsBase(
           n_independent_variables,
           1)
     {}
@@ -1333,11 +1326,11 @@ namespace Differentiation
               enum AD::NumberTypes ADNumberTypeCode,
               typename ScalarType>
     void
-    ADHelperScalarFunction::
+    ScalarFunction::
       register_dependent_variable(const ad_type &func)
     {
       Assert(this->n_dependent_variables() == 1, ExcInternalError());
-      ADHelperBase::register_dependent_variable(
+      HelperBase::register_dependent_variable(
         0, func);
     }
 
@@ -1346,10 +1339,8 @@ namespace Differentiation
     template 
-    typename ADHelperScalarFunction::
-      scalar_type
-      ADHelperScalarFunction::compute_value()
-        const
+    typename ScalarFunction::scalar_type
+    ScalarFunction::compute_value() const
     {
       if ((ADNumberTraits::is_taped == true &&
            this->taped_driver.keep_independent_values() == false) ||
@@ -1368,7 +1359,7 @@ namespace Differentiation
       Assert(
         this->n_dependent_variables() == 1,
         ExcMessage(
-          "The ADHelperScalarFunction class expects there to be only one dependent variable."));
+          "The ScalarFunction class expects there to be only one dependent variable."));
 
       if (ADNumberTraits::is_taped == true)
         {
@@ -1399,7 +1390,7 @@ namespace Differentiation
               enum AD::NumberTypes ADNumberTypeCode,
               typename ScalarType>
     void
-    ADHelperScalarFunction::compute_gradient(
+    ScalarFunction::compute_gradient(
       Vector &gradient) const
     {
       if ((ADNumberTraits::is_taped == true &&
@@ -1419,7 +1410,7 @@ namespace Differentiation
       Assert(
         this->n_dependent_variables() == 1,
         ExcMessage(
-          "The ADHelperScalarFunction class expects there to be only one dependent variable."));
+          "The ScalarFunction class expects there to be only one dependent variable."));
 
       // We can neglect correctly initializing the entries as
       // we'll be overwriting them immediately in the succeeding call to
@@ -1473,7 +1464,7 @@ namespace Differentiation
               enum AD::NumberTypes ADNumberTypeCode,
               typename ScalarType>
     void
-    ADHelperScalarFunction::compute_hessian(
+    ScalarFunction::compute_hessian(
       FullMatrix &hessian) const
     {
       Assert(AD::ADNumberTraits::n_supported_derivative_levels >= 2,
@@ -1497,7 +1488,7 @@ namespace Differentiation
       Assert(
         this->n_dependent_variables() == 1,
         ExcMessage(
-          "The ADHelperScalarFunction class expects there to be only one dependent variable."));
+          "The ScalarFunction class expects there to be only one dependent variable."));
 
       // We can neglect correctly initializing the entries as
       // we'll be overwriting them immediately in the succeeding call to
@@ -1567,11 +1558,11 @@ namespace Differentiation
     template 
-    Tensor<0,
-           dim,
-           typename ADHelperScalarFunction::
-             scalar_type>
-    ADHelperScalarFunction::
+    Tensor<
+      0,
+      dim,
+      typename ScalarFunction::scalar_type>
+    ScalarFunction::
       extract_hessian_component(const FullMatrix &   hessian,
                                 const FEValuesExtractors::Scalar &extractor_row,
                                 const FEValuesExtractors::Scalar &extractor_col)
@@ -1604,12 +1595,11 @@ namespace Differentiation
     template 
-    SymmetricTensor<4,
-                    dim,
-                    typename ADHelperScalarFunction::scalar_type>
-    ADHelperScalarFunction::
+    SymmetricTensor<
+      4,
+      dim,
+      typename ScalarFunction::scalar_type>
+    ScalarFunction::
       extract_hessian_component(
         const FullMatrix &               hessian,
         const FEValuesExtractors::SymmetricTensor<2> &extractor_row,
@@ -1641,17 +1631,17 @@ namespace Differentiation
 
 
 
-    /* -------------------- ADHelperVectorFunction -------------------- */
+    /* -------------------- VectorFunction -------------------- */
 
 
 
     template 
-    ADHelperVectorFunction::
-      ADHelperVectorFunction(const unsigned int n_independent_variables,
-                             const unsigned int n_dependent_variables)
-      : ADHelperPointLevelFunctionsBase(
+    VectorFunction::VectorFunction(
+      const unsigned int n_independent_variables,
+      const unsigned int n_dependent_variables)
+      : PointLevelFunctionsBase(
           n_independent_variables,
           n_dependent_variables)
     {}
@@ -1662,14 +1652,14 @@ namespace Differentiation
               enum AD::NumberTypes ADNumberTypeCode,
               typename ScalarType>
     void
-    ADHelperVectorFunction::
+    VectorFunction::
       register_dependent_variables(const std::vector &funcs)
     {
       Assert(funcs.size() == this->n_dependent_variables(),
              ExcMessage(
                "Vector size does not match number of dependent variables"));
       for (unsigned int i = 0; i < this->n_dependent_variables(); ++i)
-        ADHelperBase::register_dependent_variable(
+        HelperBase::register_dependent_variable(
           i, funcs[i]);
     }
 
@@ -1679,7 +1669,7 @@ namespace Differentiation
               enum AD::NumberTypes ADNumberTypeCode,
               typename ScalarType>
     void
-    ADHelperVectorFunction::compute_values(
+    VectorFunction::compute_values(
       Vector &values) const
     {
       if ((ADNumberTraits::is_taped == true &&
@@ -1735,7 +1725,7 @@ namespace Differentiation
               enum AD::NumberTypes ADNumberTypeCode,
               typename ScalarType>
     void
-    ADHelperVectorFunction::compute_jacobian(
+    VectorFunction::compute_jacobian(
       FullMatrix &jacobian) const
     {
       if ((ADNumberTraits::is_taped == true &&
@@ -1809,11 +1799,11 @@ namespace Differentiation
     template 
-    Tensor<0,
-           dim,
-           typename ADHelperVectorFunction::
-             scalar_type>
-    ADHelperVectorFunction::
+    Tensor<
+      0,
+      dim,
+      typename VectorFunction::scalar_type>
+    VectorFunction::
       extract_jacobian_component(
         const FullMatrix &   jacobian,
         const FEValuesExtractors::Scalar &extractor_row,
@@ -1847,12 +1837,11 @@ namespace Differentiation
     template 
-    SymmetricTensor<4,
-                    dim,
-                    typename ADHelperVectorFunction::scalar_type>
-    ADHelperVectorFunction::
+    SymmetricTensor<
+      4,
+      dim,
+      typename VectorFunction::scalar_type>
+    VectorFunction::
       extract_jacobian_component(
         const FullMatrix &               jacobian,
         const FEValuesExtractors::SymmetricTensor<2> &extractor_row,
diff --git a/source/differentiation/ad/ad_helpers.inst1.in b/source/differentiation/ad/ad_helpers.inst1.in
index 1c1ff5a534b8..87a4356550e5 100644
--- a/source/differentiation/ad/ad_helpers.inst1.in
+++ b/source/differentiation/ad/ad_helpers.inst1.in
@@ -21,37 +21,37 @@ for (number : REAL_SCALARS)
   \{
   namespace AD
   \{
-    // -------------------------- ADHelperBase ----------------------
+    // -------------------------- HelperBase ----------------------
 
     template
-    class ADHelperBase;
+    class HelperBase;
 
     template
-    class ADHelperBase;
+    class HelperBase;
 
-    // -------------------------- ADHelperCellLevelBase ----------------------
+    // -------------------------- CellLevelBase ----------------------
 
     template
-    class ADHelperCellLevelBase;
+    class CellLevelBase;
 
     template
-    class ADHelperCellLevelBase;
+    class CellLevelBase;
 
-    // -------------------------- ADHelperEnergyFunctional ----------------------
+    // -------------------------- EnergyFunctional ----------------------
 
     template
-    class ADHelperEnergyFunctional;
+    class EnergyFunctional;
 
     template
-    class ADHelperEnergyFunctional;
+    class EnergyFunctional;
 
-    // -------------------------- ADHelperResidualLinearization ----------------------
+    // -------------------------- ResidualLinearization ----------------------
 
     template
-    class ADHelperResidualLinearization;
+    class ResidualLinearization;
 
     template
-    class ADHelperResidualLinearization;
+    class ResidualLinearization;
 
     \}
     \}
@@ -65,37 +65,37 @@ for ()
     namespace AD
     \{
 
-    // -------------------------- ADHelperBase ----------------------
+    // -------------------------- HelperBase ----------------------
 
     template
-    class ADHelperBase::ad_type>;
+    class HelperBase::ad_type>;
 
     template
-    class ADHelperBase::ad_type>;
+    class HelperBase::ad_type>;
 
-    // -------------------------- ADHelperCellLevelBase ----------------------
+    // -------------------------- CellLevelBase ----------------------
 
     template
-    class ADHelperCellLevelBase::ad_type>;
+    class CellLevelBase::ad_type>;
 
     template
-    class ADHelperCellLevelBase::ad_type>;
+    class CellLevelBase::ad_type>;
 
-    // -------------------------- ADHelperEnergyFunctional ----------------------
+    // -------------------------- EnergyFunctional ----------------------
 
     template
-    class ADHelperEnergyFunctional::ad_type>;
+    class EnergyFunctional::ad_type>;
 
     template
-    class ADHelperEnergyFunctional::ad_type>;
+    class EnergyFunctional::ad_type>;
 
-    // -------------------------- ADHelperResidualLinearization ----------------------
+    // -------------------------- ResidualLinearization ----------------------
 
     template
-    class ADHelperResidualLinearization::ad_type>;
+    class ResidualLinearization::ad_type>;
 
     template
-    class ADHelperResidualLinearization::ad_type>;
+    class ResidualLinearization::ad_type>;
 
 
     \}
@@ -109,29 +109,29 @@ for (deal_II_dimension : DIMENSIONS ; number : REAL_SCALARS)
   \{
   namespace AD
   \{
-    // -------------------------- ADHelperPointLevelFunctionsBase ----------------------
+    // -------------------------- PointLevelFunctionsBase ----------------------
 
     template
-    class ADHelperPointLevelFunctionsBase;
+    class PointLevelFunctionsBase;
 
     template
-    class ADHelperPointLevelFunctionsBase;
+    class PointLevelFunctionsBase;
 
-    // -------------------------- ADHelperScalarFunction ----------------------
+    // -------------------------- ScalarFunction ----------------------
 
     template
-    class ADHelperScalarFunction;
+    class ScalarFunction;
 
     template
-    class ADHelperScalarFunction;
+    class ScalarFunction;
 
-    // -------------------------- ADHelperVectorFunction ----------------------
+    // -------------------------- VectorFunction ----------------------
 
     template
-    class ADHelperVectorFunction;
+    class VectorFunction;
 
     template
-    class ADHelperVectorFunction;
+    class VectorFunction;
 
     \}
     \}
@@ -145,29 +145,29 @@ for (deal_II_dimension : DIMENSIONS)
     namespace AD
     \{
 
-    // -------------------------- ADHelperPointLevelFunctionsBase ----------------------
+    // -------------------------- PointLevelFunctionsBase ----------------------
 
     template
-    class ADHelperPointLevelFunctionsBase::ad_type>;
+    class PointLevelFunctionsBase::ad_type>;
 
     template
-    class ADHelperPointLevelFunctionsBase::ad_type>;
+    class PointLevelFunctionsBase::ad_type>;
 
-    // -------------------------- ADHelperScalarFunction ----------------------
+    // -------------------------- ScalarFunction ----------------------
 
     template
-    class ADHelperScalarFunction::ad_type>;
+    class ScalarFunction::ad_type>;
 
     template
-    class ADHelperScalarFunction::ad_type>;
+    class ScalarFunction::ad_type>;
 
-    // -------------------------- ADHelperVectorFunction ----------------------
+    // -------------------------- VectorFunction ----------------------
 
     template
-    class ADHelperVectorFunction::ad_type>;
+    class VectorFunction::ad_type>;
 
     template
-    class ADHelperVectorFunction::ad_type>;
+    class VectorFunction::ad_type>;
 
     \}
     \}
diff --git a/source/differentiation/ad/ad_helpers.inst2.in b/source/differentiation/ad/ad_helpers.inst2.in
index 800b697f99ae..a39f35029f2d 100644
--- a/source/differentiation/ad/ad_helpers.inst2.in
+++ b/source/differentiation/ad/ad_helpers.inst2.in
@@ -21,61 +21,61 @@ for (number : REAL_SCALARS)
   \{
   namespace AD
   \{
-    // -------------------------- ADHelperBase ----------------------
+    // -------------------------- HelperBase ----------------------
 
     template
-    class ADHelperBase;
+    class HelperBase;
 
     template
-    class ADHelperBase;
+    class HelperBase;
 
     template
-    class ADHelperBase;
+    class HelperBase;
 
     template
-    class ADHelperBase;
+    class HelperBase;
 
-    // -------------------------- ADHelperCellLevelBase ----------------------
+    // -------------------------- CellLevelBase ----------------------
 
     template
-    class ADHelperCellLevelBase;
+    class CellLevelBase;
 
     template
-    class ADHelperCellLevelBase;
+    class CellLevelBase;
 
     template
-    class ADHelperCellLevelBase;
+    class CellLevelBase;
 
     template
-    class ADHelperCellLevelBase;
+    class CellLevelBase;
 
-    // -------------------------- ADHelperEnergyFunctional ----------------------
+    // -------------------------- EnergyFunctional ----------------------
 
     template
-    class ADHelperEnergyFunctional;
+    class EnergyFunctional;
 
     template
-    class ADHelperEnergyFunctional;
+    class EnergyFunctional;
 
     template
-    class ADHelperEnergyFunctional;
+    class EnergyFunctional;
 
     template
-    class ADHelperEnergyFunctional;
+    class EnergyFunctional;
 
-    // -------------------------- ADHelperResidualLinearization ----------------------
+    // -------------------------- ResidualLinearization ----------------------
 
     template
-    class ADHelperResidualLinearization;
+    class ResidualLinearization;
 
     template
-    class ADHelperResidualLinearization;
+    class ResidualLinearization;
 
     template
-    class ADHelperResidualLinearization;
+    class ResidualLinearization;
 
     template
-    class ADHelperResidualLinearization;
+    class ResidualLinearization;
 
     \}
     \}
@@ -89,61 +89,61 @@ for ()
     namespace AD
     \{
 
-    // -------------------------- ADHelperBase ----------------------
+    // -------------------------- HelperBase ----------------------
 
     template
-    class ADHelperBase::ad_type>;
+    class HelperBase::ad_type>;
 
     template
-    class ADHelperBase::ad_type>;
+    class HelperBase::ad_type>;
 
     template
-    class ADHelperBase::ad_type>;
+    class HelperBase::ad_type>;
 
     template
-    class ADHelperBase::ad_type>;
+    class HelperBase::ad_type>;
 
-    // -------------------------- ADHelperCellLevelBase ----------------------
+    // -------------------------- CellLevelBase ----------------------
 
     template
-    class ADHelperCellLevelBase::ad_type>;
+    class CellLevelBase::ad_type>;
 
     template
-    class ADHelperCellLevelBase::ad_type>;
+    class CellLevelBase::ad_type>;
 
     template
-    class ADHelperCellLevelBase::ad_type>;
+    class CellLevelBase::ad_type>;
 
     template
-    class ADHelperCellLevelBase::ad_type>;
+    class CellLevelBase::ad_type>;
 
-    // -------------------------- ADHelperEnergyFunctional ----------------------
+    // -------------------------- EnergyFunctional ----------------------
 
     template
-    class ADHelperEnergyFunctional::ad_type>;
+    class EnergyFunctional::ad_type>;
 
     template
-    class ADHelperEnergyFunctional::ad_type>;
+    class EnergyFunctional::ad_type>;
 
     template
-    class ADHelperEnergyFunctional::ad_type>;
+    class EnergyFunctional::ad_type>;
 
     template
-    class ADHelperEnergyFunctional::ad_type>;
+    class EnergyFunctional::ad_type>;
 
-    // -------------------------- ADHelperResidualLinearization ----------------------
+    // -------------------------- ResidualLinearization ----------------------
 
     template
-    class ADHelperResidualLinearization::ad_type>;
+    class ResidualLinearization::ad_type>;
 
     template
-    class ADHelperResidualLinearization::ad_type>;
+    class ResidualLinearization::ad_type>;
 
     template
-    class ADHelperResidualLinearization::ad_type>;
+    class ResidualLinearization::ad_type>;
 
     template
-    class ADHelperResidualLinearization::ad_type>;
+    class ResidualLinearization::ad_type>;
 
 
     \}
@@ -158,47 +158,47 @@ for (deal_II_dimension : DIMENSIONS ; number : REAL_SCALARS)
   namespace AD
   \{
 
-    // -------------------------- ADHelperPointLevelFunctionsBase ----------------------
+    // -------------------------- PointLevelFunctionsBase ----------------------
 
     template
-    class ADHelperPointLevelFunctionsBase;
+    class PointLevelFunctionsBase;
 
     template
-    class ADHelperPointLevelFunctionsBase;
+    class PointLevelFunctionsBase;
 
     template
-    class ADHelperPointLevelFunctionsBase;
+    class PointLevelFunctionsBase;
 
     template
-    class ADHelperPointLevelFunctionsBase;
+    class PointLevelFunctionsBase;
 
-    // -------------------------- ADHelperScalarFunction ----------------------
+    // -------------------------- ScalarFunction ----------------------
 
     template
-    class ADHelperScalarFunction;
+    class ScalarFunction;
 
     template
-    class ADHelperScalarFunction;
+    class ScalarFunction;
 
     template
-    class ADHelperScalarFunction;
+    class ScalarFunction;
 
     template
-    class ADHelperScalarFunction;
+    class ScalarFunction;
 
-    // -------------------------- ADHelperVectorFunction ----------------------
+    // -------------------------- VectorFunction ----------------------
 
     template
-    class ADHelperVectorFunction;
+    class VectorFunction;
 
     template
-    class ADHelperVectorFunction;
+    class VectorFunction;
 
     template
-    class ADHelperVectorFunction;
+    class VectorFunction;
 
     template
-    class ADHelperVectorFunction;
+    class VectorFunction;
 
     \}
     \}
@@ -212,47 +212,47 @@ for (deal_II_dimension : DIMENSIONS)
     namespace AD
     \{
 
-    // -------------------------- ADHelperPointLevelFunctionsBase ----------------------
+    // -------------------------- PointLevelFunctionsBase ----------------------
 
     template
-    class ADHelperPointLevelFunctionsBase::ad_type>;
+    class PointLevelFunctionsBase::ad_type>;
 
     template
-    class ADHelperPointLevelFunctionsBase::ad_type>;
+    class PointLevelFunctionsBase::ad_type>;
 
     template
-    class ADHelperPointLevelFunctionsBase::ad_type>;
+    class PointLevelFunctionsBase::ad_type>;
 
     template
-    class ADHelperPointLevelFunctionsBase::ad_type>;
+    class PointLevelFunctionsBase::ad_type>;
 
-    // -------------------------- ADHelperScalarFunction ----------------------
+    // -------------------------- ScalarFunction ----------------------
 
     template
-    class ADHelperScalarFunction::ad_type>;
+    class ScalarFunction::ad_type>;
 
     template
-    class ADHelperScalarFunction::ad_type>;
+    class ScalarFunction::ad_type>;
 
     template
-    class ADHelperScalarFunction::ad_type>;
+    class ScalarFunction::ad_type>;
 
     template
-    class ADHelperScalarFunction::ad_type>;
+    class ScalarFunction::ad_type>;
 
-    // -------------------------- ADHelperVectorFunction ----------------------
+    // -------------------------- VectorFunction ----------------------
 
     template
-    class ADHelperVectorFunction::ad_type>;
+    class VectorFunction::ad_type>;
 
     template
-    class ADHelperVectorFunction::ad_type>;
+    class VectorFunction::ad_type>;
 
     template
-    class ADHelperVectorFunction::ad_type>;
+    class VectorFunction::ad_type>;
 
     template
-    class ADHelperVectorFunction::ad_type>;
+    class VectorFunction::ad_type>;
     
     \}
     \}
diff --git a/tests/ad_common_tests/step-44-helper_res_lin_01.h b/tests/ad_common_tests/step-44-helper_res_lin_01.h
index 75913c796e42..b0059c1c7c99 100644
--- a/tests/ad_common_tests/step-44-helper_res_lin_01.h
+++ b/tests/ad_common_tests/step-44-helper_res_lin_01.h
@@ -1202,8 +1202,8 @@ namespace Step44
     Assert(n_dependent_variables == n_independent_variables,
            ExcMessage("Expect square system."));
 
-    typedef AD::ADHelperResidualLinearization ADHelper;
-    typedef typename ADHelper::ad_type ADNumberType;
+    typedef AD::ResidualLinearization ADHelper;
+    typedef typename ADHelper::ad_type                        ADNumberType;
     ADHelper ad_helper(n_independent_variables, n_dependent_variables);
     ad_helper.set_tape_buffer_sizes(); // Increase the buffer size from the
                                        // default values
diff --git a/tests/ad_common_tests/step-44-helper_var_form_01.h b/tests/ad_common_tests/step-44-helper_var_form_01.h
index f8b7f1b030c0..8e2da6205be3 100644
--- a/tests/ad_common_tests/step-44-helper_var_form_01.h
+++ b/tests/ad_common_tests/step-44-helper_var_form_01.h
@@ -1165,8 +1165,8 @@ namespace Step44
 
     const unsigned int n_independent_variables = data.local_dof_indices.size();
 
-    typedef AD::ADHelperEnergyFunctional ADHelper;
-    typedef typename ADHelper::ad_type                           ADNumberType;
+    typedef AD::EnergyFunctional ADHelper;
+    typedef typename ADHelper::ad_type                   ADNumberType;
     ADHelper ad_helper(n_independent_variables);
     ad_helper.set_tape_buffer_sizes(); // Increase the buffer size from the
                                        // default values

From ec2060cc454064cf43f4d387ad9ffec395ba3d77 Mon Sep 17 00:00:00 2001
From: Jean-Paul Pelteret 
Date: Fri, 22 Mar 2019 13:43:21 +0100
Subject: [PATCH 308/507] Add SymEngine to the readme file in the documentation

---
 doc/readme.html | 10 ++++++++++
 1 file changed, 10 insertions(+)

diff --git a/doc/readme.html b/doc/readme.html
index f938801714e6..6c35741edd11 100644
--- a/doc/readme.html
+++ b/doc/readme.html
@@ -604,6 +604,16 @@ 
    Optional interfaces to other software packages
    
                     -DSUNDIALS_DIR=/path/to/sundials to the deal.II CMake call.

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    + +
    + SymEngine
    +
    +

    + SymEngine is a symbolic manipulation package, implementing the building blocks of a computer algebra system (CAS) similar to SymPy. In particular, it can be used for symbolic differentiation. For using + SymEngine with deal.II, version 0.4 or newer is required. To use a self compiled version, pass + -DSYMENGINE_DIR=/path/to/symengine to the deal.II CMake call. +

    +
    Threading Building Blocks (TBB)
    From 84d4a8d2ab2461cbc2a18ae0f06002dc59dccb02 Mon Sep 17 00:00:00 2001 From: Luca Heltai Date: Fri, 22 Mar 2019 16:42:54 +0100 Subject: [PATCH 309/507] Added Tensor<0> instantiation --- source/fe/fe_values_extractors.cc | 1 + 1 file changed, 1 insertion(+) diff --git a/source/fe/fe_values_extractors.cc b/source/fe/fe_values_extractors.cc index 8d0c417f6eb5..751fdcafdb09 100644 --- a/source/fe/fe_values_extractors.cc +++ b/source/fe/fe_values_extractors.cc @@ -53,6 +53,7 @@ namespace FEValuesExtractors } // Explicit instantiations + template struct Tensor<0>; template struct Tensor<1>; template struct Tensor<2>; template struct Tensor<3>; From 6be05fa06147de6b65241c105a2d10418b15a80c Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 19 Mar 2019 13:39:57 +0100 Subject: [PATCH 310/507] add SparsityTools::gather_sparsity_pattern() --- doc/news/changes/minor/20190319DenisDavydov_b | 3 + .../deal.II/lac/dynamic_sparsity_pattern.h | 6 + include/deal.II/lac/sparsity_tools.h | 28 +++++ source/lac/dynamic_sparsity_pattern.cc | 19 +++ source/lac/sparsity_tools.cc | 111 ++++++++++++++++++ tests/sparsity/dynamic_sparsity_pattern_19.cc | 105 +++++++++++++++++ ...ynamic_sparsity_pattern_19.mpirun=3.output | 71 +++++++++++ 7 files changed, 343 insertions(+) create mode 100644 doc/news/changes/minor/20190319DenisDavydov_b create mode 100644 tests/sparsity/dynamic_sparsity_pattern_19.cc create mode 100644 tests/sparsity/dynamic_sparsity_pattern_19.mpirun=3.output diff --git a/doc/news/changes/minor/20190319DenisDavydov_b b/doc/news/changes/minor/20190319DenisDavydov_b new file mode 100644 index 000000000000..7f728e91ef8a --- /dev/null +++ b/doc/news/changes/minor/20190319DenisDavydov_b @@ -0,0 +1,3 @@ +New: Add SparsityTools::gather_sparsity_pattern(). +
    +(Denis Davydov, 2019/03/19) diff --git a/include/deal.II/lac/dynamic_sparsity_pattern.h b/include/deal.II/lac/dynamic_sparsity_pattern.h index ed2a200179cc..372f7fadf529 100644 --- a/include/deal.II/lac/dynamic_sparsity_pattern.h +++ b/include/deal.II/lac/dynamic_sparsity_pattern.h @@ -518,6 +518,12 @@ class DynamicSparsityPattern : public Subscriptor size_type row_length(const size_type row) const; + /** + * Clear all entries stored in a specific row. + */ + void + clear_row(const size_type row); + /** * Access to column number field. Return the column number of the @p * indexth entry in @p row. diff --git a/include/deal.II/lac/sparsity_tools.h b/include/deal.II/lac/sparsity_tools.h index e428bef3ff48..d681b847968c 100644 --- a/include/deal.II/lac/sparsity_tools.h +++ b/include/deal.II/lac/sparsity_tools.h @@ -292,6 +292,34 @@ namespace SparsityTools const MPI_Comm & mpi_comm, const IndexSet & myrange); + /** + * Gather rows in a dynamic sparsity pattern over MPI. + * The function is similar to SparsityTools::distribute(), + * however instead of distributing sparsity stored in non-owned + * rows on this MPI process, this function will gather sparsity + * from other MPI processes and will add this to the local + * DynamicSparsityPattern. + * + * @param dsp A dynamic sparsity pattern that has been built locally and which + * we need to extend according to the sparsity of rows stored on other MPI + * processes. + * + * @param owned_rows_per_processor A vector containing owned rows for each + * process in the MPI communicator. This input should be the same on all MPI + * processes. + * + * @param mpi_comm The MPI communicator shared between the processors that + * participate in this operation. + * + * @param ghost_range The range of rows this MPI process needs to gather. + * Only a part which is not included in the locally owned rows will be used. + */ + void + gather_sparsity_pattern(DynamicSparsityPattern & dsp, + const std::vector &owned_rows_per_processor, + const MPI_Comm & mpi_comm, + const IndexSet & ghost_range); + #endif diff --git a/source/lac/dynamic_sparsity_pattern.cc b/source/lac/dynamic_sparsity_pattern.cc index 95ca12cdc4b7..c697a45a1b42 100644 --- a/source/lac/dynamic_sparsity_pattern.cc +++ b/source/lac/dynamic_sparsity_pattern.cc @@ -406,6 +406,25 @@ DynamicSparsityPattern::symmetrize() +void +DynamicSparsityPattern::clear_row(const size_type row) +{ + AssertIndexRange(row, n_rows()); + if (!have_entries) + return; + + if (rowset.size() > 0 && !rowset.is_element(row)) + return; + + const size_type rowindex = + rowset.size() == 0 ? row : rowset.index_within_set(row); + + AssertIndexRange(rowindex, lines.size()); + lines[rowindex].entries = std::vector(); +} + + + template void DynamicSparsityPattern::compute_Tmmult_pattern( diff --git a/source/lac/sparsity_tools.cc b/source/lac/sparsity_tools.cc index 1a18621296bc..b62a712c26b7 100644 --- a/source/lac/sparsity_tools.cc +++ b/source/lac/sparsity_tools.cc @@ -911,6 +911,117 @@ namespace SparsityTools #ifdef DEAL_II_WITH_MPI + + void + gather_sparsity_pattern(DynamicSparsityPattern & dsp, + const std::vector &owned, + const MPI_Comm & mpi_comm, + const IndexSet & ghost_range) + { + const unsigned int myid = Utilities::MPI::this_mpi_process(mpi_comm); + + AssertDimension(owned.size(), Utilities::MPI::n_mpi_processes(mpi_comm)); +# ifdef DEBUG + for (const auto &set : owned) + Assert(set.is_contiguous(), ExcNotImplemented()); +# endif + + Assert(owned[myid].is_ascending_and_one_to_one(mpi_comm), + ExcNotImplemented()); + + std::vector start_index(owned.size() + + 1); + start_index[0] = 0; + for (DynamicSparsityPattern::size_type i = 0; i < owned.size(); ++i) + start_index[i + 1] = start_index[i] + owned[i].n_elements(); + + using map_vec_t = + std::map>; + + // 1. limit rows to non owned: + IndexSet requested_rows(ghost_range); + requested_rows.subtract_set(owned[myid]); + + // 2. go through requested_rows, figure out the owner and add the row to + // request + map_vec_t rows_data; + { + unsigned int cpu_rank = 0; + for (const auto &row : requested_rows) + { + // calculate destination CPU + while (row >= start_index[cpu_rank + 1]) + ++cpu_rank; + + // since we removed owned, we should not end up with + // our rows + Assert(cpu_rank != myid, ExcInternalError()); + + rows_data[cpu_rank].push_back(row); + } + } + + // 3. get what others ask us to send + const auto rows_data_received = + Utilities::MPI::some_to_some(mpi_comm, rows_data); + + // 4. now prepare data to be sent in the same format as in + // distribute_sparsity_pattern() below, i.e. + // rX,num_rX,cols_rX + map_vec_t send_data; + for (const auto &data : rows_data_received) + { + for (const auto &row : data.second) + { + const auto rlen = dsp.row_length(row); + + // skip empty lines + if (rlen == 0) + continue; + + // save entries + send_data[data.first].push_back(row); // row index + send_data[data.first].push_back(rlen); // number of entries + for (DynamicSparsityPattern::size_type c = 0; c < rlen; ++c) + send_data[data.first].push_back( + dsp.column_number(row, c)); // columns + } // loop over rows + } // loop over received data + + // 5. communicate rows + const auto received_data = + Utilities::MPI::some_to_some(mpi_comm, send_data); + + // 6. add result to our sparsity + for (const auto &data : received_data) + { + const auto &recv_buf = data.second; + auto ptr = recv_buf.begin(); + const auto end = recv_buf.end(); + while (ptr != end) + { + const auto row = *(ptr++); + Assert(ptr != end, ExcInternalError()); + + const auto n_entries = *(ptr++); + Assert(n_entries > 0, ExcInternalError()); + Assert(ptr != end, ExcInternalError()); + + // make sure we clear whatever was previously stored + // in these rows. Otherwise we can't guarantee that the + // data is consistent across MPI communicator. + dsp.clear_row(row); + + Assert(ptr + (n_entries - 1) != end, ExcInternalError()); + dsp.add_entries(row, ptr, ptr + n_entries, true); + ptr += n_entries; + } + Assert(ptr == end, ExcInternalError()); + } + } + + + void distribute_sparsity_pattern( DynamicSparsityPattern & dsp, diff --git a/tests/sparsity/dynamic_sparsity_pattern_19.cc b/tests/sparsity/dynamic_sparsity_pattern_19.cc new file mode 100644 index 000000000000..b0b8d0f497bf --- /dev/null +++ b/tests/sparsity/dynamic_sparsity_pattern_19.cc @@ -0,0 +1,105 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + + +// check SparsityTools::gather_sparsity_pattern() + +#include + +#include "../tests.h" + + +void +test() +{ + const unsigned int N = 10; + MPI_Comm comm(MPI_COMM_WORLD); + const unsigned int myid = Utilities::MPI::this_mpi_process(comm); + + IndexSet owned(N); + if (myid == 0) + owned.add_range(0, 3); + else if (myid == 1) + owned.add_range(3, 7); + else + owned.add_range(7, 10); + + const auto rows_per_cpu = Utilities::MPI::all_gather(comm, owned); + + IndexSet ghost_range(owned); + if (myid == 0) + { + ghost_range.add_range(3, 5); + } + else if (myid == 1) + { + ghost_range.add_range(1, 3); + ghost_range.add_range(7, 9); + } + else + { + ghost_range.add_range(4, 7); + } + + DynamicSparsityPattern dsp; + dsp.reinit(N, N); + // hard-code some sparsity + if (myid == 0) + { + for (unsigned int i = 0; i < 3; ++i) + for (unsigned int j = 0; j < 5 + i; ++j) + dsp.add(i, j); + + // add to ghost to make sure they are reset + dsp.add(3, 9); + } + else if (myid == 1) + { + for (unsigned int i = 3; i < 5; ++i) + for (unsigned int j = 0; j < 5 + i; ++j) + dsp.add(i, j); + + for (unsigned int i = 5; i < 7; ++i) + for (unsigned int j = i - 4; j < 10; ++j) + dsp.add(i, j); + } + else + { + for (unsigned int i = 7; i < 10; ++i) + for (unsigned int j = i - 4; j < 10; ++j) + dsp.add(i, j); + } + + deallog << "Before gather_sparsity_pattern:" << std::endl; + dsp.print(deallog.get_file_stream()); + + SparsityTools::gather_sparsity_pattern(dsp, rows_per_cpu, comm, ghost_range); + + deallog << "After gather_sparsity_pattern:" << std::endl; + dsp.print(deallog.get_file_stream()); +} + + +int +main(int argc, char **argv) +{ + Utilities::MPI::MPI_InitFinalize mpi_initialization(argc, argv, 1); + + MPILogInitAll log; + + test(); + return 0; +} diff --git a/tests/sparsity/dynamic_sparsity_pattern_19.mpirun=3.output b/tests/sparsity/dynamic_sparsity_pattern_19.mpirun=3.output new file mode 100644 index 000000000000..fd13cba169f2 --- /dev/null +++ b/tests/sparsity/dynamic_sparsity_pattern_19.mpirun=3.output @@ -0,0 +1,71 @@ + +DEAL:0::Before gather_sparsity_pattern: +[0,0,1,2,3,4] +[1,0,1,2,3,4,5] +[2,0,1,2,3,4,5,6] +[3,9] +[4] +[5] +[6] +[7] +[8] +[9] +DEAL:0::After gather_sparsity_pattern: +[0,0,1,2,3,4] +[1,0,1,2,3,4,5] +[2,0,1,2,3,4,5,6] +[3,0,1,2,3,4,5,6,7] +[4,0,1,2,3,4,5,6,7,8] +[5] +[6] +[7] +[8] +[9] + +DEAL:1::Before gather_sparsity_pattern: +[0] +[1] +[2] +[3,0,1,2,3,4,5,6,7] +[4,0,1,2,3,4,5,6,7,8] +[5,1,2,3,4,5,6,7,8,9] +[6,2,3,4,5,6,7,8,9] +[7] +[8] +[9] +DEAL:1::After gather_sparsity_pattern: +[0] +[1,0,1,2,3,4,5] +[2,0,1,2,3,4,5,6] +[3,0,1,2,3,4,5,6,7] +[4,0,1,2,3,4,5,6,7,8] +[5,1,2,3,4,5,6,7,8,9] +[6,2,3,4,5,6,7,8,9] +[7,3,4,5,6,7,8,9] +[8,4,5,6,7,8,9] +[9] + + +DEAL:2::Before gather_sparsity_pattern: +[0] +[1] +[2] +[3] +[4] +[5] +[6] +[7,3,4,5,6,7,8,9] +[8,4,5,6,7,8,9] +[9,5,6,7,8,9] +DEAL:2::After gather_sparsity_pattern: +[0] +[1] +[2] +[3] +[4,0,1,2,3,4,5,6,7,8] +[5,1,2,3,4,5,6,7,8,9] +[6,2,3,4,5,6,7,8,9] +[7,3,4,5,6,7,8,9] +[8,4,5,6,7,8,9] +[9,5,6,7,8,9] + From 35aed646e7878f1bb5fd0f1a9948e5ec5b2f3b2d Mon Sep 17 00:00:00 2001 From: Luca Heltai Date: Sat, 23 Mar 2019 03:12:19 +0100 Subject: [PATCH 311/507] New variant of mesh_loop. --- doc/news/changes/minor/20190323LucaHeltai | 3 + include/deal.II/meshworker/mesh_loop.h | 110 ++++++++++++++++ tests/meshworker/mesh_loop_class_01.cc | 144 +++++++++++++++++++++ tests/meshworker/mesh_loop_class_01.output | 55 ++++++++ 4 files changed, 312 insertions(+) create mode 100644 doc/news/changes/minor/20190323LucaHeltai create mode 100644 tests/meshworker/mesh_loop_class_01.cc create mode 100644 tests/meshworker/mesh_loop_class_01.output diff --git a/doc/news/changes/minor/20190323LucaHeltai b/doc/news/changes/minor/20190323LucaHeltai new file mode 100644 index 000000000000..265ceaaf7c17 --- /dev/null +++ b/doc/news/changes/minor/20190323LucaHeltai @@ -0,0 +1,3 @@ +New: Added a variant of mesh_loop that takes a class and its member functions as workers and copiers. +
    +(Luca Heltai, 2019/03/23) diff --git a/include/deal.II/meshworker/mesh_loop.h b/include/deal.II/meshworker/mesh_loop.h index f2a53f05023b..8589fbba064b 100644 --- a/include/deal.II/meshworker/mesh_loop.h +++ b/include/deal.II/meshworker/mesh_loop.h @@ -392,6 +392,116 @@ namespace MeshWorker queue_length, chunk_size); } + + /** + * This is a variant of the mesh_loop function, that can be used for worker + * and copier functions that are member functions of a class. + * + * The argument passed as @p end must be convertible to the same type as @p + * begin, but doesn't have to be of the same type itself. This allows to + * write code like mesh_loop(dof_handler.begin_active(), + * dof_handler.end(), ... where the first is of type + * DoFHandler::active_cell_iterator whereas the second is of type + * DoFHandler::raw_cell_iterator. + * + * The @p queue_length argument indicates the number of items that can be + * live at any given time. Each item consists of @p chunk_size elements of + * the input stream that will be worked on by the worker and copier + * functions one after the other on the same thread. + * + * @note If your data objects are large, or their constructors are + * expensive, it is helpful to keep in mind that queue_length + * copies of the ScratchData object and + * queue_length*chunk_size copies of the CopyData object + * are generated. + * + * @ingroup MeshWorker + * @author Luca Heltai, 2019 + */ + template + void + mesh_loop(const CellIteratorType & begin, + const typename identity::type &end, + MainClass & main_class, + void (MainClass::*cell_worker)(const CellIteratorType &, + ScratchData &, + CopyData &), + void (MainClass::*copier)(const CopyData &), + const ScratchData & sample_scratch_data, + const CopyData & sample_copy_data, + const AssembleFlags flags = assemble_own_cells, + void (MainClass::*boundary_worker)(const CellIteratorType &, + const unsigned int, + ScratchData &, + CopyData &) = nullptr, + void (MainClass::*face_worker)(const CellIteratorType &, + const unsigned int, + const unsigned int, + const CellIteratorType &, + const unsigned int, + const unsigned int, + ScratchData &, + CopyData &) = nullptr, + const unsigned int queue_length = 2 * MultithreadInfo::n_threads(), + const unsigned int chunk_size = 8) + { + std::function + f_cell_worker; + + std::function + f_boundary_worker; + + std::function + f_face_worker; + + if (cell_worker != nullptr) + f_cell_worker = std::bind(cell_worker, + std::ref(main_class), + std::placeholders::_1, + std::placeholders::_2, + std::placeholders::_3); + + if (boundary_worker != nullptr) + f_boundary_worker = std::bind(boundary_worker, + std::ref(main_class), + std::placeholders::_1, + std::placeholders::_2, + std::placeholders::_3, + std::placeholders::_4); + + if (face_worker != nullptr) + f_face_worker = std::bind(face_worker, + std::ref(main_class), + std::placeholders::_1, + std::placeholders::_2, + std::placeholders::_3, + std::placeholders::_4, + std::placeholders::_5, + std::placeholders::_6, + std::placeholders::_7, + std::placeholders::_8); + + mesh_loop(begin, + end, + f_cell_worker, + std::bind(copier, main_class, std::placeholders::_1), + sample_scratch_data, + sample_copy_data, + flags, + f_boundary_worker, + f_face_worker); + } } // namespace MeshWorker DEAL_II_NAMESPACE_CLOSE diff --git a/tests/meshworker/mesh_loop_class_01.cc b/tests/meshworker/mesh_loop_class_01.cc new file mode 100644 index 000000000000..bda23d029d24 --- /dev/null +++ b/tests/meshworker/mesh_loop_class_01.cc @@ -0,0 +1,144 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + +// Test assembly using a class and mesh_loop + +#include + +#include +#include +#include + +#include +#include + +#include + +#include "../tests.h" + +using namespace MeshWorker; + +struct ScratchData +{}; +struct CopyData +{}; + +template +class TestClass +{ +public: + using CellIteratorType = + typename Triangulation::active_cell_iterator; + + void + cell_worker(const CellIteratorType &cell, ScratchData &, CopyData &) + { + deallog << "Workgin on cell " << cell << std::endl; + } + + void + copier(const CopyData &) + {} + + void + boundary_worker(const CellIteratorType &cell, + const unsigned int f, + ScratchData &, + CopyData &) + { + deallog << "Boundary worker on : " << cell << ", Face : " << f << std::endl; + } + + void + face_worker(const CellIteratorType &cell, + const unsigned int f, + const unsigned int sf, + const CellIteratorType &ncell, + const unsigned int nf, + const unsigned int nsf, + ScratchData &, + CopyData &) + { + deallog << "Face worker on : " << cell << ", Neighbor cell : " << ncell + << ", Face : " << f << ", Neighbor Face : " << nf + << ", Subface: " << sf << ", Neighbor Subface: " << nsf + << std::endl; + } +}; + +template +void +test() +{ + Triangulation tria; + GridGenerator::hyper_cube(tria); + tria.refine_global(1); + tria.begin_active()->set_refine_flag(); + tria.execute_coarsening_and_refinement(); + + TestClass test_class; + ScratchData scratch; + CopyData copy; + + auto cell = tria.begin_active(); + auto endc = tria.end(); + + deallog << "CELLS ONLY" << std::endl; + mesh_loop(cell, + endc, + test_class, + &TestClass::cell_worker, + &TestClass::copier, + scratch, + copy, + assemble_own_cells); + + deallog << "CELLS+BOUNDARY" << std::endl; + + mesh_loop(cell, + endc, + test_class, + &TestClass::cell_worker, + &TestClass::copier, + scratch, + copy, + assemble_own_cells | assemble_boundary_faces, + &TestClass::boundary_worker); + + + deallog << "CELLS+BOUNDARY+FACES" << std::endl; + + mesh_loop(cell, + endc, + test_class, + &TestClass::cell_worker, + &TestClass::copier, + scratch, + copy, + assemble_own_cells | assemble_boundary_faces | + assemble_own_interior_faces_once, + &TestClass::boundary_worker, + &TestClass::face_worker); +} + + +int +main() +{ + initlog(); + MultithreadInfo::set_thread_limit(1); // to make output deterministic + + test<2, 2>(); +} diff --git a/tests/meshworker/mesh_loop_class_01.output b/tests/meshworker/mesh_loop_class_01.output new file mode 100644 index 000000000000..63a972588dd9 --- /dev/null +++ b/tests/meshworker/mesh_loop_class_01.output @@ -0,0 +1,55 @@ + +DEAL::CELLS ONLY +DEAL::Workgin on cell 1.1 +DEAL::Workgin on cell 1.2 +DEAL::Workgin on cell 1.3 +DEAL::Workgin on cell 2.0 +DEAL::Workgin on cell 2.1 +DEAL::Workgin on cell 2.2 +DEAL::Workgin on cell 2.3 +DEAL::CELLS+BOUNDARY +DEAL::Workgin on cell 1.1 +DEAL::Boundary worker on : 1.1, Face : 1 +DEAL::Boundary worker on : 1.1, Face : 2 +DEAL::Workgin on cell 1.2 +DEAL::Boundary worker on : 1.2, Face : 0 +DEAL::Boundary worker on : 1.2, Face : 3 +DEAL::Workgin on cell 1.3 +DEAL::Boundary worker on : 1.3, Face : 1 +DEAL::Boundary worker on : 1.3, Face : 3 +DEAL::Workgin on cell 2.0 +DEAL::Boundary worker on : 2.0, Face : 0 +DEAL::Boundary worker on : 2.0, Face : 2 +DEAL::Workgin on cell 2.1 +DEAL::Boundary worker on : 2.1, Face : 2 +DEAL::Workgin on cell 2.2 +DEAL::Boundary worker on : 2.2, Face : 0 +DEAL::Workgin on cell 2.3 +DEAL::CELLS+BOUNDARY+FACES +DEAL::Workgin on cell 1.1 +DEAL::Boundary worker on : 1.1, Face : 1 +DEAL::Boundary worker on : 1.1, Face : 2 +DEAL::Face worker on : 1.1, Neighbor cell : 1.3, Face : 3, Neighbor Face : 2, Subface: 4294967295, Neighbor Subface: 4294967295 +DEAL::Workgin on cell 1.2 +DEAL::Boundary worker on : 1.2, Face : 0 +DEAL::Face worker on : 1.2, Neighbor cell : 1.3, Face : 1, Neighbor Face : 0, Subface: 4294967295, Neighbor Subface: 4294967295 +DEAL::Boundary worker on : 1.2, Face : 3 +DEAL::Workgin on cell 1.3 +DEAL::Boundary worker on : 1.3, Face : 1 +DEAL::Boundary worker on : 1.3, Face : 3 +DEAL::Workgin on cell 2.0 +DEAL::Boundary worker on : 2.0, Face : 0 +DEAL::Face worker on : 2.0, Neighbor cell : 2.1, Face : 1, Neighbor Face : 0, Subface: 4294967295, Neighbor Subface: 4294967295 +DEAL::Boundary worker on : 2.0, Face : 2 +DEAL::Face worker on : 2.0, Neighbor cell : 2.2, Face : 3, Neighbor Face : 2, Subface: 4294967295, Neighbor Subface: 4294967295 +DEAL::Workgin on cell 2.1 +DEAL::Face worker on : 2.1, Neighbor cell : 1.1, Face : 1, Neighbor Face : 0, Subface: 4294967295, Neighbor Subface: 0 +DEAL::Boundary worker on : 2.1, Face : 2 +DEAL::Face worker on : 2.1, Neighbor cell : 2.3, Face : 3, Neighbor Face : 2, Subface: 4294967295, Neighbor Subface: 4294967295 +DEAL::Workgin on cell 2.2 +DEAL::Boundary worker on : 2.2, Face : 0 +DEAL::Face worker on : 2.2, Neighbor cell : 2.3, Face : 1, Neighbor Face : 0, Subface: 4294967295, Neighbor Subface: 4294967295 +DEAL::Face worker on : 2.2, Neighbor cell : 1.2, Face : 3, Neighbor Face : 2, Subface: 4294967295, Neighbor Subface: 0 +DEAL::Workgin on cell 2.3 +DEAL::Face worker on : 2.3, Neighbor cell : 1.1, Face : 1, Neighbor Face : 0, Subface: 4294967295, Neighbor Subface: 1 +DEAL::Face worker on : 2.3, Neighbor cell : 1.2, Face : 3, Neighbor Face : 2, Subface: 4294967295, Neighbor Subface: 1 From 2325e6aa4c666d06ebf54575fe28dcf303be8df8 Mon Sep 17 00:00:00 2001 From: Luca Heltai Date: Wed, 20 Mar 2019 00:24:12 +0100 Subject: [PATCH 312/507] FEValuesViews::View --- doc/news/changes/minor/20190320LucaHeltai | 5 ++ include/deal.II/fe/fe_values.h | 75 +++++++++++++++++++++++ tests/fe/fe_values_views_types.cc | 67 ++++++++++++++++++++ tests/fe/fe_values_views_types.output | 46 ++++++++++++++ 4 files changed, 193 insertions(+) create mode 100644 doc/news/changes/minor/20190320LucaHeltai create mode 100644 tests/fe/fe_values_views_types.cc create mode 100644 tests/fe/fe_values_views_types.output diff --git a/doc/news/changes/minor/20190320LucaHeltai b/doc/news/changes/minor/20190320LucaHeltai new file mode 100644 index 000000000000..5d1cbf85cfb2 --- /dev/null +++ b/doc/news/changes/minor/20190320LucaHeltai @@ -0,0 +1,5 @@ +New: The type alias FEValuesViews::View now allows one to infer the correct FEValuesViews type +that would be returned by FEValuesBase::operator[]() when called with a specified extractor type from the +FEValuesExtractors namespace. +
    +(Luca Heltai, 2019/03/20) diff --git a/include/deal.II/fe/fe_values.h b/include/deal.II/fe/fe_values.h index 713f1c64adad..71b50d966407 100644 --- a/include/deal.II/fe/fe_values.h +++ b/include/deal.II/fe/fe_values.h @@ -1871,6 +1871,69 @@ namespace internal { namespace FEValuesViews { + /** + * A class whose specialization is used to define what FEValuesViews + * object corresponds to the given FEValuesExtractors object. + * + * @author Luca Heltai, 2019. + */ + template + struct ViewType + {}; + + /** + * A class whose specialization is used to define what FEValuesViews + * object corresponds to the given FEValuesExtractors object. + * + * When using FEValuesExtractors::Scalar, the corresponding view is an + * FEValuesViews::Scalar. + */ + template + struct ViewType + { + using type = typename dealii::FEValuesViews::Scalar; + }; + + /** + * A class whose specialization is used to define what FEValuesViews + * object corresponds to the given FEValuesExtractors object. + * + * When using FEValuesExtractors::Vector, the corresponding view is an + * FEValuesViews::Vector. + */ + template + struct ViewType + { + using type = typename dealii::FEValuesViews::Vector; + }; + + /** + * A class whose specialization is used to define what FEValuesViews + * object corresponds to the given FEValuesExtractors object. + * + * When using FEValuesExtractors::Tensor, the corresponding view is an + * FEValuesViews::Tensor. + */ + template + struct ViewType> + { + using type = typename dealii::FEValuesViews::Tensor; + }; + + /** + * A class whose specialization is used to define what FEValuesViews + * object corresponds to the given FEValuesExtractors object. + * + * When using FEValuesExtractors::SymmetricTensor, the corresponding + * view is an FEValuesViews::SymmetricTensor. + */ + template + struct ViewType> + { + using type = + typename dealii::FEValuesViews::SymmetricTensor; + }; + /** * A class objects of which store a collection of FEValuesViews::Scalar, * FEValuesViews::Vector, etc object. The FEValuesBase class uses it to @@ -1900,6 +1963,18 @@ namespace internal } // namespace FEValuesViews } // namespace internal +namespace FEValuesViews +{ + /** + * A templated alias that associates to a given Extractor class + * the corresponding view in FEValuesViews. + * + * @author Luca Heltai, 2019. + */ + template + using View = + typename internal::FEValuesViews::ViewType::type; +} // namespace FEValuesViews /** diff --git a/tests/fe/fe_values_views_types.cc b/tests/fe/fe_values_views_types.cc new file mode 100644 index 000000000000..e6f573900a24 --- /dev/null +++ b/tests/fe/fe_values_views_types.cc @@ -0,0 +1,67 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + +// Test FEValuesViews::View + +#include + +#include + +#include "../tests.h" + +template +void +test(const Extractor &) +{ + typename FEValuesViews::View::template OutputType< + double>::value_type t1; + + typename FEValuesViews::View::template OutputType< + double>::gradient_type t2; + + deallog << "Test<" << Utilities::dim_string(dim, spacedim) << ">" << std::endl + << Utilities::type_to_string(t1) << std::endl + << Utilities::type_to_string(t2) << std::endl; +} + +int +main() +{ + initlog(); + + FEValuesExtractors::Scalar scalar(0); + FEValuesExtractors::Vector vector(1); + FEValuesExtractors::Tensor<2> tensor(2); + + test<1, 1>(scalar); + test<1, 1>(vector); + test<1, 1>(tensor); + + test<1, 2>(scalar); + test<1, 2>(vector); + test<1, 2>(tensor); + + test<2, 2>(scalar); + test<2, 2>(vector); + test<2, 2>(tensor); + + test<2, 3>(scalar); + test<2, 3>(vector); + test<2, 3>(tensor); + + test<3, 3>(scalar); + test<3, 3>(vector); + test<3, 3>(tensor); +} diff --git a/tests/fe/fe_values_views_types.output b/tests/fe/fe_values_views_types.output new file mode 100644 index 000000000000..5eacce960a2d --- /dev/null +++ b/tests/fe/fe_values_views_types.output @@ -0,0 +1,46 @@ + +DEAL::Test<1> +DEAL::double +DEAL::dealii::Tensor<1, 1, double> +DEAL::Test<1> +DEAL::dealii::Tensor<1, 1, double> +DEAL::dealii::Tensor<2, 1, double> +DEAL::Test<1> +DEAL::dealii::Tensor<2, 1, double> +DEAL::dealii::Tensor<3, 1, double> +DEAL::Test<1,2> +DEAL::double +DEAL::dealii::Tensor<1, 2, double> +DEAL::Test<1,2> +DEAL::dealii::Tensor<1, 2, double> +DEAL::dealii::Tensor<2, 2, double> +DEAL::Test<1,2> +DEAL::dealii::Tensor<2, 2, double> +DEAL::dealii::Tensor<3, 2, double> +DEAL::Test<2> +DEAL::double +DEAL::dealii::Tensor<1, 2, double> +DEAL::Test<2> +DEAL::dealii::Tensor<1, 2, double> +DEAL::dealii::Tensor<2, 2, double> +DEAL::Test<2> +DEAL::dealii::Tensor<2, 2, double> +DEAL::dealii::Tensor<3, 2, double> +DEAL::Test<2,3> +DEAL::double +DEAL::dealii::Tensor<1, 3, double> +DEAL::Test<2,3> +DEAL::dealii::Tensor<1, 3, double> +DEAL::dealii::Tensor<2, 3, double> +DEAL::Test<2,3> +DEAL::dealii::Tensor<2, 3, double> +DEAL::dealii::Tensor<3, 3, double> +DEAL::Test<3> +DEAL::double +DEAL::dealii::Tensor<1, 3, double> +DEAL::Test<3> +DEAL::dealii::Tensor<1, 3, double> +DEAL::dealii::Tensor<2, 3, double> +DEAL::Test<3> +DEAL::dealii::Tensor<2, 3, double> +DEAL::dealii::Tensor<3, 3, double> From 8e227a8497a5dd75b3d9a0e1d08525249cacc706 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Sat, 23 Mar 2019 04:00:35 +0100 Subject: [PATCH 313/507] Create local variables in output_results --- examples/step-41/step-41.cc | 11 +++++------ examples/step-42/step-42.cc | 20 ++++++++++---------- 2 files changed, 15 insertions(+), 16 deletions(-) diff --git a/examples/step-41/step-41.cc b/examples/step-41/step-41.cc index 662829c1507b..f2e5ec11716b 100644 --- a/examples/step-41/step-41.cc +++ b/examples/step-41/step-41.cc @@ -101,7 +101,6 @@ namespace Step41 TrilinosWrappers::SparseMatrix complete_system_matrix; TrilinosWrappers::MPI::Vector solution; - TrilinosWrappers::MPI::Vector active_set_vector; TrilinosWrappers::MPI::Vector system_rhs; TrilinosWrappers::MPI::Vector complete_system_rhs; TrilinosWrappers::MPI::Vector diagonal_of_mass_matrix; @@ -262,7 +261,6 @@ namespace Step41 IndexSet solution_index_set = dof_handler.locally_owned_dofs(); solution.reinit(solution_index_set, MPI_COMM_WORLD); - active_set_vector.reinit(solution_index_set, MPI_COMM_WORLD); system_rhs.reinit(solution_index_set, MPI_COMM_WORLD); complete_system_rhs.reinit(solution_index_set, MPI_COMM_WORLD); contact_force.reinit(solution_index_set, MPI_COMM_WORLD); @@ -544,10 +542,6 @@ namespace Step41 BoundaryValues(), constraints); constraints.close(); - - active_set_vector = 0.; - for (const auto index : active_set) - active_set_vector[index] = 1.; } // @sect4{ObstacleProblem::solve} @@ -588,6 +582,11 @@ namespace Step41 { std::cout << " Writing graphical output..." << std::endl; + TrilinosWrappers::MPI::Vector active_set_vector( + dof_handler.locally_owned_dofs(), MPI_COMM_WORLD); + for (const auto index : active_set) + active_set_vector[index] = 1.; + DataOut data_out; data_out.attach_dof_handler(dof_handler); diff --git a/examples/step-42/step-42.cc b/examples/step-42/step-42.cc index ec2b52df7944..5b6127b94263 100644 --- a/examples/step-42/step-42.cc +++ b/examples/step-42/step-42.cc @@ -701,7 +701,6 @@ namespace Step42 TrilinosWrappers::SparseMatrix newton_matrix; TrilinosWrappers::MPI::Vector solution; - TrilinosWrappers::MPI::Vector active_set_vector; TrilinosWrappers::MPI::Vector newton_rhs; TrilinosWrappers::MPI::Vector newton_rhs_uncondensed; TrilinosWrappers::MPI::Vector diag_mass_matrix_vector; @@ -1023,7 +1022,6 @@ namespace Step42 { TimerOutput::Scope t(computing_timer, "Setup: vectors"); solution.reinit(locally_relevant_dofs, mpi_communicator); - active_set_vector.reinit(locally_relevant_dofs, MPI_COMM_WORLD); newton_rhs.reinit(locally_owned_dofs, mpi_communicator); newton_rhs_uncondensed.reinit(locally_owned_dofs, mpi_communicator); diag_mass_matrix_vector.reinit(locally_owned_dofs, mpi_communicator); @@ -1341,14 +1339,6 @@ namespace Step42 all_constraints.close(); all_constraints.merge(constraints_dirichlet_and_hanging_nodes); - // We misuse distributed_solution for updating active_set_vector. - // We can do that because distributed_solution has a compatible underlying - // IndexSet and we don't need the vector anymore. - distributed_solution = 0.; - for (const auto index : active_set) - distributed_solution[index] = 1.; - active_set_vector = distributed_solution; - pcout << " Size of active set: " << Utilities::MPI::sum((active_set & locally_owned_dofs).n_elements(), mpi_communicator) @@ -2037,6 +2027,16 @@ namespace Step42 mpi_communicator); lambda = distributed_lambda; + TrilinosWrappers::MPI::Vector distributed_active_set_vector( + locally_owned_dofs, mpi_communicator); + distributed_active_set_vector = 0.; + for (const auto index : active_set) + distributed_active_set_vector[index] = 1.; + distributed_lambda.compress(VectorOperation::insert); + + TrilinosWrappers::MPI::Vector active_set_vector(locally_relevant_dofs, + mpi_communicator); + active_set_vector = distributed_active_set_vector; DataOut data_out; From 58d1cb115547e27141a38df25996d3cf155df3bf Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Sat, 23 Mar 2019 04:01:02 +0100 Subject: [PATCH 314/507] Range-based for loop --- examples/step-42/step-42.cc | 8 +++----- 1 file changed, 3 insertions(+), 5 deletions(-) diff --git a/examples/step-42/step-42.cc b/examples/step-42/step-42.cc index 5b6127b94263..32394d47b7bb 100644 --- a/examples/step-42/step-42.cc +++ b/examples/step-42/step-42.cc @@ -1549,10 +1549,7 @@ namespace Step42 fraction_of_plastic_q_points_per_cell = 0; - auto cell = dof_handler.begin_active(); - const auto endc = dof_handler.end(); - unsigned int cell_number = 0; - for (; cell != endc; ++cell, ++cell_number) + for (const auto &cell : dof_handler.active_cell_iterators()) if (cell->is_locally_owned()) { fe_values.reinit(cell); @@ -1569,7 +1566,8 @@ namespace Step42 constitutive_law.get_stress_strain_tensor( strain_tensors[q_point], stress_strain_tensor); if (q_point_is_plastic) - ++fraction_of_plastic_q_points_per_cell(cell_number); + ++fraction_of_plastic_q_points_per_cell( + cell->active_cell_index()); for (unsigned int i = 0; i < dofs_per_cell; ++i) { From ec6b54594a5b1a81b7b9de696f54ac51efd95ac3 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Sat, 23 Mar 2019 04:02:15 +0100 Subject: [PATCH 315/507] Remove a helper function for DataOut_DoFData --- .../numerics/data_out_dof_data.templates.h | 20 +++---------------- 1 file changed, 3 insertions(+), 17 deletions(-) diff --git a/include/deal.II/numerics/data_out_dof_data.templates.h b/include/deal.II/numerics/data_out_dof_data.templates.h index 8f492389d791..e499cc548829 100644 --- a/include/deal.II/numerics/data_out_dof_data.templates.h +++ b/include/deal.II/numerics/data_out_dof_data.templates.h @@ -629,21 +629,6 @@ namespace internal {} - template - inline typename VectorType::value_type - get_vector_element(const VectorType &vector, const unsigned int cell_number) - { - return internal::ElementAccess::get(vector, cell_number); - } - - - inline double - get_vector_element(const IndexSet &is, const unsigned int cell_number) - { - return (is.is_element(cell_number) ? 1 : 0); - } - - template double @@ -651,8 +636,9 @@ namespace internal const unsigned int cell_number, const ComponentExtractor extract_component) const { - return get_component(get_vector_element(*vector, cell_number), - extract_component); + return get_component( + internal::ElementAccess::get(*vector, cell_number), + extract_component); } From 52148c0b5af11e34c3cad073574055372b364fc6 Mon Sep 17 00:00:00 2001 From: Luca Heltai Date: Sat, 23 Mar 2019 11:46:30 +0100 Subject: [PATCH 316/507] Fixed typos. --- doc/news/changes/minor/20190323LucaHeltai | 3 +- include/deal.II/meshworker/mesh_loop.h | 31 ++++++++++++++-- tests/meshworker/mesh_loop_class_01.cc | 2 +- tests/meshworker/mesh_loop_class_01.output | 42 +++++++++++----------- 4 files changed, 53 insertions(+), 25 deletions(-) diff --git a/doc/news/changes/minor/20190323LucaHeltai b/doc/news/changes/minor/20190323LucaHeltai index 265ceaaf7c17..d4b08ab3de45 100644 --- a/doc/news/changes/minor/20190323LucaHeltai +++ b/doc/news/changes/minor/20190323LucaHeltai @@ -1,3 +1,4 @@ -New: Added a variant of mesh_loop that takes a class and its member functions as workers and copiers. +New: Added a variant of MeshWorker::mesh_loop() that takes a class and its member functions as workers +and copiers.
    (Luca Heltai, 2019/03/23) diff --git a/include/deal.II/meshworker/mesh_loop.h b/include/deal.II/meshworker/mesh_loop.h index 8589fbba064b..8a76d18bc1d1 100644 --- a/include/deal.II/meshworker/mesh_loop.h +++ b/include/deal.II/meshworker/mesh_loop.h @@ -394,13 +394,13 @@ namespace MeshWorker } /** - * This is a variant of the mesh_loop function, that can be used for worker + * This is a variant of the mesh_loop() function, that can be used for worker * and copier functions that are member functions of a class. * * The argument passed as @p end must be convertible to the same type as @p * begin, but doesn't have to be of the same type itself. This allows to * write code like mesh_loop(dof_handler.begin_active(), - * dof_handler.end(), ... where the first is of type + * dof_handler.end(), ...) where the first is of type * DoFHandler::active_cell_iterator whereas the second is of type * DoFHandler::raw_cell_iterator. * @@ -415,6 +415,33 @@ namespace MeshWorker * queue_length*chunk_size copies of the CopyData object * are generated. * + * An example usage of the function is given by + * @code + * template + * class TestClass + * { + * public: + * void + * cell_worker(const CellIteratorType &cell, ScratchData &, CopyData &); + * + * ... + * }; + * + * ... + * TestClass test_class; + * ScratchData scratch; + * CopyData copy; + * + * mesh_loop(tria.begin_active(), + * tria.end(), + * test_class, + * &TestClass::cell_worker, + * &TestClass::copier, + * scratch, + * copy, + * assemble_own_cells); + * @endcode + * * @ingroup MeshWorker * @author Luca Heltai, 2019 */ diff --git a/tests/meshworker/mesh_loop_class_01.cc b/tests/meshworker/mesh_loop_class_01.cc index bda23d029d24..6550600dd61b 100644 --- a/tests/meshworker/mesh_loop_class_01.cc +++ b/tests/meshworker/mesh_loop_class_01.cc @@ -45,7 +45,7 @@ class TestClass void cell_worker(const CellIteratorType &cell, ScratchData &, CopyData &) { - deallog << "Workgin on cell " << cell << std::endl; + deallog << "Working on cell " << cell << std::endl; } void diff --git a/tests/meshworker/mesh_loop_class_01.output b/tests/meshworker/mesh_loop_class_01.output index 63a972588dd9..1aa484b21ebb 100644 --- a/tests/meshworker/mesh_loop_class_01.output +++ b/tests/meshworker/mesh_loop_class_01.output @@ -1,55 +1,55 @@ DEAL::CELLS ONLY -DEAL::Workgin on cell 1.1 -DEAL::Workgin on cell 1.2 -DEAL::Workgin on cell 1.3 -DEAL::Workgin on cell 2.0 -DEAL::Workgin on cell 2.1 -DEAL::Workgin on cell 2.2 -DEAL::Workgin on cell 2.3 +DEAL::Working on cell 1.1 +DEAL::Working on cell 1.2 +DEAL::Working on cell 1.3 +DEAL::Working on cell 2.0 +DEAL::Working on cell 2.1 +DEAL::Working on cell 2.2 +DEAL::Working on cell 2.3 DEAL::CELLS+BOUNDARY -DEAL::Workgin on cell 1.1 +DEAL::Working on cell 1.1 DEAL::Boundary worker on : 1.1, Face : 1 DEAL::Boundary worker on : 1.1, Face : 2 -DEAL::Workgin on cell 1.2 +DEAL::Working on cell 1.2 DEAL::Boundary worker on : 1.2, Face : 0 DEAL::Boundary worker on : 1.2, Face : 3 -DEAL::Workgin on cell 1.3 +DEAL::Working on cell 1.3 DEAL::Boundary worker on : 1.3, Face : 1 DEAL::Boundary worker on : 1.3, Face : 3 -DEAL::Workgin on cell 2.0 +DEAL::Working on cell 2.0 DEAL::Boundary worker on : 2.0, Face : 0 DEAL::Boundary worker on : 2.0, Face : 2 -DEAL::Workgin on cell 2.1 +DEAL::Working on cell 2.1 DEAL::Boundary worker on : 2.1, Face : 2 -DEAL::Workgin on cell 2.2 +DEAL::Working on cell 2.2 DEAL::Boundary worker on : 2.2, Face : 0 -DEAL::Workgin on cell 2.3 +DEAL::Working on cell 2.3 DEAL::CELLS+BOUNDARY+FACES -DEAL::Workgin on cell 1.1 +DEAL::Working on cell 1.1 DEAL::Boundary worker on : 1.1, Face : 1 DEAL::Boundary worker on : 1.1, Face : 2 DEAL::Face worker on : 1.1, Neighbor cell : 1.3, Face : 3, Neighbor Face : 2, Subface: 4294967295, Neighbor Subface: 4294967295 -DEAL::Workgin on cell 1.2 +DEAL::Working on cell 1.2 DEAL::Boundary worker on : 1.2, Face : 0 DEAL::Face worker on : 1.2, Neighbor cell : 1.3, Face : 1, Neighbor Face : 0, Subface: 4294967295, Neighbor Subface: 4294967295 DEAL::Boundary worker on : 1.2, Face : 3 -DEAL::Workgin on cell 1.3 +DEAL::Working on cell 1.3 DEAL::Boundary worker on : 1.3, Face : 1 DEAL::Boundary worker on : 1.3, Face : 3 -DEAL::Workgin on cell 2.0 +DEAL::Working on cell 2.0 DEAL::Boundary worker on : 2.0, Face : 0 DEAL::Face worker on : 2.0, Neighbor cell : 2.1, Face : 1, Neighbor Face : 0, Subface: 4294967295, Neighbor Subface: 4294967295 DEAL::Boundary worker on : 2.0, Face : 2 DEAL::Face worker on : 2.0, Neighbor cell : 2.2, Face : 3, Neighbor Face : 2, Subface: 4294967295, Neighbor Subface: 4294967295 -DEAL::Workgin on cell 2.1 +DEAL::Working on cell 2.1 DEAL::Face worker on : 2.1, Neighbor cell : 1.1, Face : 1, Neighbor Face : 0, Subface: 4294967295, Neighbor Subface: 0 DEAL::Boundary worker on : 2.1, Face : 2 DEAL::Face worker on : 2.1, Neighbor cell : 2.3, Face : 3, Neighbor Face : 2, Subface: 4294967295, Neighbor Subface: 4294967295 -DEAL::Workgin on cell 2.2 +DEAL::Working on cell 2.2 DEAL::Boundary worker on : 2.2, Face : 0 DEAL::Face worker on : 2.2, Neighbor cell : 2.3, Face : 1, Neighbor Face : 0, Subface: 4294967295, Neighbor Subface: 4294967295 DEAL::Face worker on : 2.2, Neighbor cell : 1.2, Face : 3, Neighbor Face : 2, Subface: 4294967295, Neighbor Subface: 0 -DEAL::Workgin on cell 2.3 +DEAL::Working on cell 2.3 DEAL::Face worker on : 2.3, Neighbor cell : 1.1, Face : 1, Neighbor Face : 0, Subface: 4294967295, Neighbor Subface: 1 DEAL::Face worker on : 2.3, Neighbor cell : 1.2, Face : 3, Neighbor Face : 2, Subface: 4294967295, Neighbor Subface: 1 From 704fb9c003aa49144e1f601620c6f9d22f5f1b3c Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Sat, 23 Mar 2019 16:28:24 +0100 Subject: [PATCH 317/507] Improve example in new mesh_loop function --- include/deal.II/meshworker/mesh_loop.h | 34 ++++++++++++++++---------- 1 file changed, 21 insertions(+), 13 deletions(-) diff --git a/include/deal.II/meshworker/mesh_loop.h b/include/deal.II/meshworker/mesh_loop.h index 8a76d18bc1d1..d1244d395013 100644 --- a/include/deal.II/meshworker/mesh_loop.h +++ b/include/deal.II/meshworker/mesh_loop.h @@ -417,29 +417,37 @@ namespace MeshWorker * * An example usage of the function is given by * @code + * + * struct ScratchData; + * struct CopyData; + * * template - * class TestClass + * class MyClass * { * public: * void * cell_worker(const CellIteratorType &cell, ScratchData &, CopyData &); * + * void + * copier(const CopyData &); + * * ... * }; * - * ... - * TestClass test_class; - * ScratchData scratch; - * CopyData copy; + * ... + * + * MyClass my_class; + * SratchData scratch; + * CopyData copy; * - * mesh_loop(tria.begin_active(), - * tria.end(), - * test_class, - * &TestClass::cell_worker, - * &TestClass::copier, - * scratch, - * copy, - * assemble_own_cells); + * mesh_loop(tria.begin_active(), + * tria.end(), + * my_class, + * &MyClass::cell_worker, + * &MyClass::copier, + * scratch, + * copy, + * assemble_own_cells); * @endcode * * @ingroup MeshWorker From 12b0494f570392e488c04df158cc5457a5dd59d4 Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Sat, 23 Mar 2019 16:30:43 +0100 Subject: [PATCH 318/507] Pass queue_length and chunk_size to inner call to mesh_loop() --- include/deal.II/meshworker/mesh_loop.h | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/include/deal.II/meshworker/mesh_loop.h b/include/deal.II/meshworker/mesh_loop.h index d1244d395013..9aa0ff436991 100644 --- a/include/deal.II/meshworker/mesh_loop.h +++ b/include/deal.II/meshworker/mesh_loop.h @@ -535,7 +535,9 @@ namespace MeshWorker sample_copy_data, flags, f_boundary_worker, - f_face_worker); + f_face_worker, + queue_length, + chunk_size); } } // namespace MeshWorker From 80891eef627410791a88faf4208e51845be3a504 Mon Sep 17 00:00:00 2001 From: Luca Heltai Date: Tue, 19 Mar 2019 22:47:24 +0100 Subject: [PATCH 319/507] New assign_co_dimensional_manifold_indicators function. --- doc/news/changes/minor/20190319LucaHeltai_b | 5 + include/deal.II/grid/grid_tools.h | 31 +- include/deal.II/grid/tria_accessor.h | 18 + .../deal.II/grid/tria_accessor.templates.h | 34 ++ source/grid/grid_tools.cc | 73 ++++ source/grid/grid_tools.inst.in | 6 + .../grid_tools_propagate_manifold_ids_01.cc | 74 ++++ ...rid_tools_propagate_manifold_ids_01.output | 367 ++++++++++++++++++ 8 files changed, 607 insertions(+), 1 deletion(-) create mode 100644 doc/news/changes/minor/20190319LucaHeltai_b create mode 100644 tests/grid/grid_tools_propagate_manifold_ids_01.cc create mode 100644 tests/grid/grid_tools_propagate_manifold_ids_01.output diff --git a/doc/news/changes/minor/20190319LucaHeltai_b b/doc/news/changes/minor/20190319LucaHeltai_b new file mode 100644 index 000000000000..c41dc6047793 --- /dev/null +++ b/doc/news/changes/minor/20190319LucaHeltai_b @@ -0,0 +1,5 @@ +New: The new method GridTools::assign_co_dimensional_manifold_indicators() propagate manifold ids from +cells to faces and edges, according to a disambiguation function that takes the set of manifold ids of +the cells that share the given face or edge. +
    +(Luca Heltai, 2019/03/19) diff --git a/include/deal.II/grid/grid_tools.h b/include/deal.II/grid/grid_tools.h index df3711d54f44..5a341b9e9f2a 100644 --- a/include/deal.II/grid/grid_tools.h +++ b/include/deal.II/grid/grid_tools.h @@ -2632,7 +2632,36 @@ namespace GridTools copy_material_to_manifold_id(Triangulation &tria, const bool compute_face_ids = false); - + /** + * Propagate manifold indicators associated to the cells of the Triangulation + * @p tria to their co-dimension one and two objects. + * + * This function sets the @p manifold_id of shared faces and edges to the value + * returnd by the @p disambiguation_function method, called with the set of + * manifold indicators of the cells that share the same face or edge. + * + * By default, the @p disambiguation_function returns + * numbers::flat_manifold_id when the set has size greater than one (i.e., + * when it is not possible to decide what manifold indicator a face or edge + * should have according to the manifold indicators of the adjacent cells) + * and it returns the manifold indicator contained in the set when it has + * dimension one (i.e., when all adjacent cells and faces have the same + * manifold indicator). + * + * @author Luca Heltai, 2019. + */ + template + void + assign_co_dimensional_manifold_indicators( + Triangulation & tria, + const std::function &)> &disambiguation_function = + [](const std::set &manifold_ids) { + if (manifold_ids.size() == 1) + return *manifold_ids.begin(); + else + return numbers::invalid_manifold_id; + }); /*@}*/ /** diff --git a/include/deal.II/grid/tria_accessor.h b/include/deal.II/grid/tria_accessor.h index 9698bb6038e0..47bd2399170f 100644 --- a/include/deal.II/grid/tria_accessor.h +++ b/include/deal.II/grid/tria_accessor.h @@ -632,6 +632,24 @@ class InvalidAccessor : public TriaAccessorBase types::manifold_id manifold_id() const; + /** + * Dummy function that always returns numbers::invalid_unsigned_int. + */ + unsigned int + user_index() const; + + /** + * Dummy function that always throws. + */ + void + set_user_index(const unsigned int p) const; + + /** + * Dummy function that always throws. + */ + void + set_manifold_id(const types::manifold_id) const; + /** * Dummy function to extract vertices. Returns the origin. */ diff --git a/include/deal.II/grid/tria_accessor.templates.h b/include/deal.II/grid/tria_accessor.templates.h index bd9bc7b43cd2..3f74a7fdbc11 100644 --- a/include/deal.II/grid/tria_accessor.templates.h +++ b/include/deal.II/grid/tria_accessor.templates.h @@ -520,6 +520,40 @@ InvalidAccessor::manifold_id() const } + +template +unsigned int +InvalidAccessor::user_index() const +{ + return numbers::invalid_unsigned_int; +} + + + +template +void +InvalidAccessor::set_user_index( + const unsigned int) const +{ + Assert(false, + ExcMessage("You are trying to set the user index of an " + "invalid object.")); +} + + + +template +void +InvalidAccessor::set_manifold_id( + const types::manifold_id) const +{ + Assert(false, + ExcMessage("You are trying to set the manifold id of an " + "invalid object.")); +} + + + template inline Point & InvalidAccessor::vertex(const unsigned int) const diff --git a/source/grid/grid_tools.cc b/source/grid/grid_tools.cc index 44d49753d166..219159c1facd 100644 --- a/source/grid/grid_tools.cc +++ b/source/grid/grid_tools.cc @@ -3756,6 +3756,79 @@ namespace GridTools } } + + template + void + assign_co_dimensional_manifold_indicators( + Triangulation & tria, + const std::function &)> &disambiguation_function) + { + // Easy case first: + if (dim == 1) + return; + const unsigned int size = + dim == 2 ? tria.n_lines() : tria.n_lines() + tria.n_quads(); + + // If user index is zero, then it has not been set. + std::vector> manifold_ids(size + 1); + std::vector backup; + tria.save_user_indices(backup); + + unsigned next_index = 1; + for (auto cell : tria.active_cell_iterators()) + { + if (dim > 1) + for (unsigned int l = 0; l < GeometryInfo::lines_per_cell; ++l) + { + if (cell->line(l)->user_index() == 0) + { + AssertIndexRange(next_index, size + 1); + manifold_ids[next_index].insert(cell->manifold_id()); + cell->line(l)->set_user_index(next_index++); + } + else + manifold_ids[cell->line(l)->user_index()].insert( + cell->manifold_id()); + } + if (dim > 2) + for (unsigned int l = 0; l < GeometryInfo::quads_per_cell; ++l) + { + if (cell->quad(l)->user_index() == 0) + { + AssertIndexRange(next_index, size + 1); + manifold_ids[next_index].insert(cell->manifold_id()); + cell->quad(l)->set_user_index(next_index++); + } + else + manifold_ids[cell->quad(l)->user_index()].insert( + cell->manifold_id()); + } + } + for (auto cell : tria.active_cell_iterators()) + { + if (dim > 1) + for (unsigned int l = 0; l < GeometryInfo::lines_per_cell; ++l) + { + const auto id = cell->line(l)->user_index(); + Assert(id != 0, ExcInternalError()); + cell->line(l)->set_manifold_id( + disambiguation_function(manifold_ids[id])); + } + if (dim > 2) + for (unsigned int l = 0; l < GeometryInfo::quads_per_cell; ++l) + { + const auto id = cell->quad(l)->user_index(); + Assert(id != 0, ExcInternalError()); + cell->quad(l)->set_manifold_id( + disambiguation_function(manifold_ids[id])); + } + } + tria.load_user_indices(backup); + } + + + template std::pair get_longest_direction( diff --git a/source/grid/grid_tools.inst.in b/source/grid/grid_tools.inst.in index 23dd04b907b6..4d04f4141da7 100644 --- a/source/grid/grid_tools.inst.in +++ b/source/grid/grid_tools.inst.in @@ -375,6 +375,12 @@ for (deal_II_dimension : DIMENSIONS; deal_II_space_dimension : SPACE_DIMENSIONS) Triangulation &, const std::vector &); + template void + assign_co_dimensional_manifold_indicators( + Triangulation &, + const std::function< + types::manifold_id(const std::set &)> &); + template void regularize_corner_cells( Triangulation &, diff --git a/tests/grid/grid_tools_propagate_manifold_ids_01.cc b/tests/grid/grid_tools_propagate_manifold_ids_01.cc new file mode 100644 index 000000000000..d6ab8c290dcf --- /dev/null +++ b/tests/grid/grid_tools_propagate_manifold_ids_01.cc @@ -0,0 +1,74 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + +// Validate GridTools::assign_co_dimensional_manifold_indicators + +#include +#include +#include + +#include "../tests.h" + + +template +void +test() +{ + deallog << "dim = " << dim << ", spacedim = " << spacedim << std::endl; + + Triangulation tria; + GridGenerator::hyper_cube(tria); + tria.refine_global(1); + tria.begin_active()->set_refine_flag(); + tria.execute_coarsening_and_refinement(); + + tria.begin_active()->set_manifold_id(1); + + auto validate = [](const std::set &set) { + if (set.size() > 1) + return 1; + else + return 0; + }; + + GridTools::assign_co_dimensional_manifold_indicators(tria, validate); + for (auto cell : tria.active_cell_iterators()) + { + deallog << "Cell: " << (int)cell->manifold_id() << std::endl; + if (dim > 1) + for (unsigned int l = 0; l < GeometryInfo::lines_per_cell; ++l) + deallog << "Line " << l << ", " << (int)cell->line(l)->manifold_id() + << std::endl; + if (dim > 2) + for (unsigned int l = 0; l < GeometryInfo::quads_per_cell; ++l) + deallog << "Quad " << l << ", " << (int)cell->quad(l)->manifold_id() + << std::endl; + } +} + + +int +main() +{ + initlog(); + + test<1, 1>(); + test<1, 2>(); + test<2, 2>(); + test<2, 3>(); + test<3, 3>(); + + return 0; +} diff --git a/tests/grid/grid_tools_propagate_manifold_ids_01.output b/tests/grid/grid_tools_propagate_manifold_ids_01.output new file mode 100644 index 000000000000..8b385d57b1bd --- /dev/null +++ b/tests/grid/grid_tools_propagate_manifold_ids_01.output @@ -0,0 +1,367 @@ + +DEAL::dim = 1, spacedim = 1 +DEAL::Cell: 1 +DEAL::Cell: -1 +DEAL::Cell: -1 +DEAL::dim = 1, spacedim = 2 +DEAL::Cell: 1 +DEAL::Cell: -1 +DEAL::Cell: -1 +DEAL::dim = 2, spacedim = 2 +DEAL::Cell: 1 +DEAL::Line 0, 0 +DEAL::Line 1, 0 +DEAL::Line 2, 0 +DEAL::Line 3, 1 +DEAL::Cell: -1 +DEAL::Line 0, 0 +DEAL::Line 1, 0 +DEAL::Line 2, 0 +DEAL::Line 3, 0 +DEAL::Cell: -1 +DEAL::Line 0, 0 +DEAL::Line 1, 0 +DEAL::Line 2, 1 +DEAL::Line 3, 0 +DEAL::Cell: -1 +DEAL::Line 0, 0 +DEAL::Line 1, 0 +DEAL::Line 2, 0 +DEAL::Line 3, 0 +DEAL::Cell: -1 +DEAL::Line 0, 0 +DEAL::Line 1, 0 +DEAL::Line 2, 0 +DEAL::Line 3, 0 +DEAL::Cell: -1 +DEAL::Line 0, 0 +DEAL::Line 1, 0 +DEAL::Line 2, 0 +DEAL::Line 3, 0 +DEAL::Cell: -1 +DEAL::Line 0, 0 +DEAL::Line 1, 0 +DEAL::Line 2, 0 +DEAL::Line 3, 0 +DEAL::dim = 2, spacedim = 3 +DEAL::Cell: 1 +DEAL::Line 0, 0 +DEAL::Line 1, 0 +DEAL::Line 2, 0 +DEAL::Line 3, 1 +DEAL::Cell: -1 +DEAL::Line 0, 0 +DEAL::Line 1, 0 +DEAL::Line 2, 0 +DEAL::Line 3, 0 +DEAL::Cell: -1 +DEAL::Line 0, 0 +DEAL::Line 1, 0 +DEAL::Line 2, 1 +DEAL::Line 3, 0 +DEAL::Cell: -1 +DEAL::Line 0, 0 +DEAL::Line 1, 0 +DEAL::Line 2, 0 +DEAL::Line 3, 0 +DEAL::Cell: -1 +DEAL::Line 0, 0 +DEAL::Line 1, 0 +DEAL::Line 2, 0 +DEAL::Line 3, 0 +DEAL::Cell: -1 +DEAL::Line 0, 0 +DEAL::Line 1, 0 +DEAL::Line 2, 0 +DEAL::Line 3, 0 +DEAL::Cell: -1 +DEAL::Line 0, 0 +DEAL::Line 1, 0 +DEAL::Line 2, 0 +DEAL::Line 3, 0 +DEAL::dim = 3, spacedim = 3 +DEAL::Cell: 1 +DEAL::Line 0, 0 +DEAL::Line 1, 0 +DEAL::Line 2, 0 +DEAL::Line 3, 1 +DEAL::Line 4, 1 +DEAL::Line 5, 1 +DEAL::Line 6, 1 +DEAL::Line 7, 1 +DEAL::Line 8, 0 +DEAL::Line 9, 0 +DEAL::Line 10, 1 +DEAL::Line 11, 1 +DEAL::Quad 0, 0 +DEAL::Quad 1, 0 +DEAL::Quad 2, 0 +DEAL::Quad 3, 1 +DEAL::Quad 4, 0 +DEAL::Quad 5, 1 +DEAL::Cell: -1 +DEAL::Line 0, 0 +DEAL::Line 1, 0 +DEAL::Line 2, 0 +DEAL::Line 3, 0 +DEAL::Line 4, 0 +DEAL::Line 5, 0 +DEAL::Line 6, 0 +DEAL::Line 7, 0 +DEAL::Line 8, 0 +DEAL::Line 9, 1 +DEAL::Line 10, 0 +DEAL::Line 11, 0 +DEAL::Quad 0, 0 +DEAL::Quad 1, 0 +DEAL::Quad 2, 0 +DEAL::Quad 3, 0 +DEAL::Quad 4, 0 +DEAL::Quad 5, 0 +DEAL::Cell: -1 +DEAL::Line 0, 0 +DEAL::Line 1, 0 +DEAL::Line 2, 1 +DEAL::Line 3, 0 +DEAL::Line 4, 0 +DEAL::Line 5, 0 +DEAL::Line 6, 1 +DEAL::Line 7, 0 +DEAL::Line 8, 1 +DEAL::Line 9, 1 +DEAL::Line 10, 0 +DEAL::Line 11, 0 +DEAL::Quad 0, 0 +DEAL::Quad 1, 0 +DEAL::Quad 2, 1 +DEAL::Quad 3, 0 +DEAL::Quad 4, 0 +DEAL::Quad 5, 0 +DEAL::Cell: -1 +DEAL::Line 0, 0 +DEAL::Line 1, 1 +DEAL::Line 2, 0 +DEAL::Line 3, 0 +DEAL::Line 4, 0 +DEAL::Line 5, 0 +DEAL::Line 6, 0 +DEAL::Line 7, 0 +DEAL::Line 8, 0 +DEAL::Line 9, 0 +DEAL::Line 10, 0 +DEAL::Line 11, 0 +DEAL::Quad 0, 0 +DEAL::Quad 1, 0 +DEAL::Quad 2, 0 +DEAL::Quad 3, 0 +DEAL::Quad 4, 0 +DEAL::Quad 5, 0 +DEAL::Cell: -1 +DEAL::Line 0, 1 +DEAL::Line 1, 1 +DEAL::Line 2, 1 +DEAL::Line 3, 1 +DEAL::Line 4, 0 +DEAL::Line 5, 0 +DEAL::Line 6, 0 +DEAL::Line 7, 0 +DEAL::Line 8, 0 +DEAL::Line 9, 0 +DEAL::Line 10, 0 +DEAL::Line 11, 0 +DEAL::Quad 0, 0 +DEAL::Quad 1, 0 +DEAL::Quad 2, 0 +DEAL::Quad 3, 0 +DEAL::Quad 4, 1 +DEAL::Quad 5, 0 +DEAL::Cell: -1 +DEAL::Line 0, 0 +DEAL::Line 1, 0 +DEAL::Line 2, 0 +DEAL::Line 3, 0 +DEAL::Line 4, 0 +DEAL::Line 5, 0 +DEAL::Line 6, 0 +DEAL::Line 7, 0 +DEAL::Line 8, 0 +DEAL::Line 9, 0 +DEAL::Line 10, 0 +DEAL::Line 11, 0 +DEAL::Quad 0, 0 +DEAL::Quad 1, 0 +DEAL::Quad 2, 0 +DEAL::Quad 3, 0 +DEAL::Quad 4, 0 +DEAL::Quad 5, 0 +DEAL::Cell: -1 +DEAL::Line 0, 0 +DEAL::Line 1, 0 +DEAL::Line 2, 1 +DEAL::Line 3, 0 +DEAL::Line 4, 0 +DEAL::Line 5, 0 +DEAL::Line 6, 0 +DEAL::Line 7, 0 +DEAL::Line 8, 0 +DEAL::Line 9, 0 +DEAL::Line 10, 0 +DEAL::Line 11, 0 +DEAL::Quad 0, 0 +DEAL::Quad 1, 0 +DEAL::Quad 2, 0 +DEAL::Quad 3, 0 +DEAL::Quad 4, 0 +DEAL::Quad 5, 0 +DEAL::Cell: -1 +DEAL::Line 0, 0 +DEAL::Line 1, 0 +DEAL::Line 2, 0 +DEAL::Line 3, 0 +DEAL::Line 4, 0 +DEAL::Line 5, 0 +DEAL::Line 6, 0 +DEAL::Line 7, 0 +DEAL::Line 8, 0 +DEAL::Line 9, 0 +DEAL::Line 10, 0 +DEAL::Line 11, 0 +DEAL::Quad 0, 0 +DEAL::Quad 1, 0 +DEAL::Quad 2, 0 +DEAL::Quad 3, 0 +DEAL::Quad 4, 0 +DEAL::Quad 5, 0 +DEAL::Cell: -1 +DEAL::Line 0, 0 +DEAL::Line 1, 0 +DEAL::Line 2, 0 +DEAL::Line 3, 0 +DEAL::Line 4, 0 +DEAL::Line 5, 0 +DEAL::Line 6, 0 +DEAL::Line 7, 0 +DEAL::Line 8, 0 +DEAL::Line 9, 0 +DEAL::Line 10, 0 +DEAL::Line 11, 0 +DEAL::Quad 0, 0 +DEAL::Quad 1, 0 +DEAL::Quad 2, 0 +DEAL::Quad 3, 0 +DEAL::Quad 4, 0 +DEAL::Quad 5, 0 +DEAL::Cell: -1 +DEAL::Line 0, 0 +DEAL::Line 1, 0 +DEAL::Line 2, 0 +DEAL::Line 3, 0 +DEAL::Line 4, 0 +DEAL::Line 5, 0 +DEAL::Line 6, 0 +DEAL::Line 7, 0 +DEAL::Line 8, 0 +DEAL::Line 9, 0 +DEAL::Line 10, 0 +DEAL::Line 11, 0 +DEAL::Quad 0, 0 +DEAL::Quad 1, 0 +DEAL::Quad 2, 0 +DEAL::Quad 3, 0 +DEAL::Quad 4, 0 +DEAL::Quad 5, 0 +DEAL::Cell: -1 +DEAL::Line 0, 0 +DEAL::Line 1, 0 +DEAL::Line 2, 0 +DEAL::Line 3, 0 +DEAL::Line 4, 0 +DEAL::Line 5, 0 +DEAL::Line 6, 0 +DEAL::Line 7, 0 +DEAL::Line 8, 0 +DEAL::Line 9, 0 +DEAL::Line 10, 0 +DEAL::Line 11, 0 +DEAL::Quad 0, 0 +DEAL::Quad 1, 0 +DEAL::Quad 2, 0 +DEAL::Quad 3, 0 +DEAL::Quad 4, 0 +DEAL::Quad 5, 0 +DEAL::Cell: -1 +DEAL::Line 0, 0 +DEAL::Line 1, 0 +DEAL::Line 2, 0 +DEAL::Line 3, 0 +DEAL::Line 4, 0 +DEAL::Line 5, 0 +DEAL::Line 6, 0 +DEAL::Line 7, 0 +DEAL::Line 8, 0 +DEAL::Line 9, 0 +DEAL::Line 10, 0 +DEAL::Line 11, 0 +DEAL::Quad 0, 0 +DEAL::Quad 1, 0 +DEAL::Quad 2, 0 +DEAL::Quad 3, 0 +DEAL::Quad 4, 0 +DEAL::Quad 5, 0 +DEAL::Cell: -1 +DEAL::Line 0, 0 +DEAL::Line 1, 0 +DEAL::Line 2, 0 +DEAL::Line 3, 0 +DEAL::Line 4, 0 +DEAL::Line 5, 0 +DEAL::Line 6, 0 +DEAL::Line 7, 0 +DEAL::Line 8, 0 +DEAL::Line 9, 0 +DEAL::Line 10, 0 +DEAL::Line 11, 0 +DEAL::Quad 0, 0 +DEAL::Quad 1, 0 +DEAL::Quad 2, 0 +DEAL::Quad 3, 0 +DEAL::Quad 4, 0 +DEAL::Quad 5, 0 +DEAL::Cell: -1 +DEAL::Line 0, 0 +DEAL::Line 1, 0 +DEAL::Line 2, 0 +DEAL::Line 3, 0 +DEAL::Line 4, 0 +DEAL::Line 5, 0 +DEAL::Line 6, 0 +DEAL::Line 7, 0 +DEAL::Line 8, 0 +DEAL::Line 9, 0 +DEAL::Line 10, 0 +DEAL::Line 11, 0 +DEAL::Quad 0, 0 +DEAL::Quad 1, 0 +DEAL::Quad 2, 0 +DEAL::Quad 3, 0 +DEAL::Quad 4, 0 +DEAL::Quad 5, 0 +DEAL::Cell: -1 +DEAL::Line 0, 0 +DEAL::Line 1, 0 +DEAL::Line 2, 0 +DEAL::Line 3, 0 +DEAL::Line 4, 0 +DEAL::Line 5, 0 +DEAL::Line 6, 0 +DEAL::Line 7, 0 +DEAL::Line 8, 0 +DEAL::Line 9, 0 +DEAL::Line 10, 0 +DEAL::Line 11, 0 +DEAL::Quad 0, 0 +DEAL::Quad 1, 0 +DEAL::Quad 2, 0 +DEAL::Quad 3, 0 +DEAL::Quad 4, 0 +DEAL::Quad 5, 0 From 6f189b7be7b30559c8840d4a4c652f4dd2dbaf17 Mon Sep 17 00:00:00 2001 From: Luca Heltai Date: Fri, 22 Mar 2019 00:27:14 +0100 Subject: [PATCH 320/507] Added flat to control overwriting of non flat manifold ids. --- include/deal.II/grid/grid_tools.h | 17 +++++++++++++---- source/grid/grid_tools.cc | 15 ++++++++++----- source/grid/grid_tools.inst.in | 3 ++- 3 files changed, 25 insertions(+), 10 deletions(-) diff --git a/include/deal.II/grid/grid_tools.h b/include/deal.II/grid/grid_tools.h index 5a341b9e9f2a..13a53614955e 100644 --- a/include/deal.II/grid/grid_tools.h +++ b/include/deal.II/grid/grid_tools.h @@ -2636,8 +2636,9 @@ namespace GridTools * Propagate manifold indicators associated to the cells of the Triangulation * @p tria to their co-dimension one and two objects. * - * This function sets the @p manifold_id of shared faces and edges to the value - * returnd by the @p disambiguation_function method, called with the set of + * This function sets the @p manifold_id of faces and edges (both on the + * interior and on the boundary) to the value returnd by the + * @p disambiguation_function method, called with the set of * manifold indicators of the cells that share the same face or edge. * * By default, the @p disambiguation_function returns @@ -2648,6 +2649,13 @@ namespace GridTools * dimension one (i.e., when all adjacent cells and faces have the same * manifold indicator). * + * The parameter @p overwrite_only_flat_manifold_ids allows you to specify + * what to do when a face or an edge already has a manifold indicator + * different from numbers::flat_manifold_id. If the flag is @p true, the edge + * or face will maintain its original manifold indicator. + * If it is @p false, then also the manifold indicator of these faces and edges + * is set according to the return value of the @p disambiguation_function. + * * @author Luca Heltai, 2019. */ template @@ -2660,8 +2668,9 @@ namespace GridTools if (manifold_ids.size() == 1) return *manifold_ids.begin(); else - return numbers::invalid_manifold_id; - }); + return numbers::flat_manifold_id; + }, + bool overwrite_only_flat_manifold_ids = true); /*@}*/ /** diff --git a/source/grid/grid_tools.cc b/source/grid/grid_tools.cc index 219159c1facd..1b5939f12c65 100644 --- a/source/grid/grid_tools.cc +++ b/source/grid/grid_tools.cc @@ -3762,7 +3762,8 @@ namespace GridTools assign_co_dimensional_manifold_indicators( Triangulation & tria, const std::function &)> &disambiguation_function) + const std::set &)> &disambiguation_function, + bool overwrite_only_flat_manifold_ids) { // Easy case first: if (dim == 1) @@ -3812,16 +3813,20 @@ namespace GridTools { const auto id = cell->line(l)->user_index(); Assert(id != 0, ExcInternalError()); - cell->line(l)->set_manifold_id( - disambiguation_function(manifold_ids[id])); + if (cell->line(l)->manifold_id() == numbers::flat_manifold_id || + overwrite_only_flat_manifold_ids == false) + cell->line(l)->set_manifold_id( + disambiguation_function(manifold_ids[id])); } if (dim > 2) for (unsigned int l = 0; l < GeometryInfo::quads_per_cell; ++l) { const auto id = cell->quad(l)->user_index(); Assert(id != 0, ExcInternalError()); - cell->quad(l)->set_manifold_id( - disambiguation_function(manifold_ids[id])); + if (cell->quad(l)->manifold_id() == numbers::flat_manifold_id || + overwrite_only_flat_manifold_ids == false) + cell->quad(l)->set_manifold_id( + disambiguation_function(manifold_ids[id])); } } tria.load_user_indices(backup); diff --git a/source/grid/grid_tools.inst.in b/source/grid/grid_tools.inst.in index 4d04f4141da7..0c64e7ff346a 100644 --- a/source/grid/grid_tools.inst.in +++ b/source/grid/grid_tools.inst.in @@ -379,7 +379,8 @@ for (deal_II_dimension : DIMENSIONS; deal_II_space_dimension : SPACE_DIMENSIONS) assign_co_dimensional_manifold_indicators( Triangulation &, const std::function< - types::manifold_id(const std::set &)> &); + types::manifold_id(const std::set &)> &, + bool); template void regularize_corner_cells( From 3686b4d5e6a89a47303ddc002397b2fdaa3cc323 Mon Sep 17 00:00:00 2001 From: Wolfgang Bangerth Date: Fri, 22 Mar 2019 00:36:10 +0100 Subject: [PATCH 321/507] Update include/deal.II/grid/grid_tools.h Co-Authored-By: luca-heltai --- include/deal.II/grid/grid_tools.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/include/deal.II/grid/grid_tools.h b/include/deal.II/grid/grid_tools.h index 13a53614955e..6cc0507cafda 100644 --- a/include/deal.II/grid/grid_tools.h +++ b/include/deal.II/grid/grid_tools.h @@ -2633,7 +2633,7 @@ namespace GridTools const bool compute_face_ids = false); /** - * Propagate manifold indicators associated to the cells of the Triangulation + * Propagate manifold indicators associated with the cells of the Triangulation * @p tria to their co-dimension one and two objects. * * This function sets the @p manifold_id of faces and edges (both on the From 695b6db5b7f1f8c3aa10fbf25b3f2a60838f76ee Mon Sep 17 00:00:00 2001 From: Luca Heltai Date: Fri, 22 Mar 2019 00:27:14 +0100 Subject: [PATCH 322/507] Added flag to control overwriting of non flat manifold ids. --- source/grid/grid_tools.cc | 1 + 1 file changed, 1 insertion(+) diff --git a/source/grid/grid_tools.cc b/source/grid/grid_tools.cc index 1b5939f12c65..7aa180cbffaa 100644 --- a/source/grid/grid_tools.cc +++ b/source/grid/grid_tools.cc @@ -3775,6 +3775,7 @@ namespace GridTools std::vector> manifold_ids(size + 1); std::vector backup; tria.save_user_indices(backup); + tria.clear_user_data(); unsigned next_index = 1; for (auto cell : tria.active_cell_iterators()) From 0a2b402e80275c22411733c2bfcaf9d271d214fc Mon Sep 17 00:00:00 2001 From: Luca Heltai Date: Fri, 22 Mar 2019 00:44:29 +0100 Subject: [PATCH 323/507] Make sure we only change manifold ids once per face/edge. --- source/grid/grid_tools.cc | 30 ++++++++++++++++++++---------- 1 file changed, 20 insertions(+), 10 deletions(-) diff --git a/source/grid/grid_tools.cc b/source/grid/grid_tools.cc index 7aa180cbffaa..32c252689d23 100644 --- a/source/grid/grid_tools.cc +++ b/source/grid/grid_tools.cc @@ -3813,21 +3813,31 @@ namespace GridTools for (unsigned int l = 0; l < GeometryInfo::lines_per_cell; ++l) { const auto id = cell->line(l)->user_index(); - Assert(id != 0, ExcInternalError()); - if (cell->line(l)->manifold_id() == numbers::flat_manifold_id || - overwrite_only_flat_manifold_ids == false) - cell->line(l)->set_manifold_id( - disambiguation_function(manifold_ids[id])); + // Make sure we change the manifold indicator only once + if (id != 0) + { + if (cell->line(l)->manifold_id() == + numbers::flat_manifold_id || + overwrite_only_flat_manifold_ids == false) + cell->line(l)->set_manifold_id( + disambiguation_function(manifold_ids[id])); + cell->line(l)->set_user_index(0); + } } if (dim > 2) for (unsigned int l = 0; l < GeometryInfo::quads_per_cell; ++l) { const auto id = cell->quad(l)->user_index(); - Assert(id != 0, ExcInternalError()); - if (cell->quad(l)->manifold_id() == numbers::flat_manifold_id || - overwrite_only_flat_manifold_ids == false) - cell->quad(l)->set_manifold_id( - disambiguation_function(manifold_ids[id])); + // Make sure we change the manifold indicator only once + if (id != 0) + { + if (cell->quad(l)->manifold_id() == + numbers::flat_manifold_id || + overwrite_only_flat_manifold_ids == false) + cell->quad(l)->set_manifold_id( + disambiguation_function(manifold_ids[id])); + cell->quad(l)->set_user_index(0); + } } } tria.load_user_indices(backup); From 24c7c5ece12d284ebdd898b5d322e6cac7cd198f Mon Sep 17 00:00:00 2001 From: Luca Heltai Date: Fri, 22 Mar 2019 00:46:04 +0100 Subject: [PATCH 324/507] More descriptive name. --- source/grid/grid_tools.cc | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/source/grid/grid_tools.cc b/source/grid/grid_tools.cc index 32c252689d23..10f5dd627244 100644 --- a/source/grid/grid_tools.cc +++ b/source/grid/grid_tools.cc @@ -3768,11 +3768,11 @@ namespace GridTools // Easy case first: if (dim == 1) return; - const unsigned int size = + const unsigned int n_subobjects = dim == 2 ? tria.n_lines() : tria.n_lines() + tria.n_quads(); // If user index is zero, then it has not been set. - std::vector> manifold_ids(size + 1); + std::vector> manifold_ids(n_subobjects + 1); std::vector backup; tria.save_user_indices(backup); tria.clear_user_data(); @@ -3785,7 +3785,7 @@ namespace GridTools { if (cell->line(l)->user_index() == 0) { - AssertIndexRange(next_index, size + 1); + AssertIndexRange(next_index, n_subobjects + 1); manifold_ids[next_index].insert(cell->manifold_id()); cell->line(l)->set_user_index(next_index++); } @@ -3798,7 +3798,7 @@ namespace GridTools { if (cell->quad(l)->user_index() == 0) { - AssertIndexRange(next_index, size + 1); + AssertIndexRange(next_index, n_subobjects + 1); manifold_ids[next_index].insert(cell->manifold_id()); cell->quad(l)->set_user_index(next_index++); } From f29c46e8cb4c83d65d6ff2ae916e3395d7d87272 Mon Sep 17 00:00:00 2001 From: Luca Heltai Date: Fri, 22 Mar 2019 01:01:17 +0100 Subject: [PATCH 325/507] Fixed indent. --- include/deal.II/grid/grid_tools.h | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/include/deal.II/grid/grid_tools.h b/include/deal.II/grid/grid_tools.h index 6cc0507cafda..fed508b798d6 100644 --- a/include/deal.II/grid/grid_tools.h +++ b/include/deal.II/grid/grid_tools.h @@ -2633,8 +2633,8 @@ namespace GridTools const bool compute_face_ids = false); /** - * Propagate manifold indicators associated with the cells of the Triangulation - * @p tria to their co-dimension one and two objects. + * Propagate manifold indicators associated with the cells of the + * Triangulation @p tria to their co-dimension one and two objects. * * This function sets the @p manifold_id of faces and edges (both on the * interior and on the boundary) to the value returnd by the From c36ca78847311bb7d09ea3c026cbec3c4994f292 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Sun, 24 Mar 2019 11:30:55 -0400 Subject: [PATCH 326/507] Rename file generated by doc/news/changes/header --- doc/news/changes/header | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/doc/news/changes/header b/doc/news/changes/header index 14d7ac1993c7..1b580c8dd3bd 100644 --- a/doc/news/changes/header +++ b/doc/news/changes/header @@ -14,11 +14,11 @@ // --------------------------------------------------------------------- /** -@page changes_after_9_0_1 Changes after Version 9.0.1 +@page recent_changes Changes since the last release

    -This is the list of changes made after the release of deal.II version -9.0.1. All entries are signed with the names of the authors. +This is the list of changes made since the last release of deal.II. +All entries are signed with the names of the authors.

    From 954924788b115733a5cbf90205cbc498a68b8d46 Mon Sep 17 00:00:00 2001 From: Matthias Maier Date: Sun, 24 Mar 2019 11:28:00 -0500 Subject: [PATCH 327/507] CMake: Also filter SYMENGINE_CXX_FLAGS --- cmake/configure/configure_symengine.cmake | 1 + 1 file changed, 1 insertion(+) diff --git a/cmake/configure/configure_symengine.cmake b/cmake/configure/configure_symengine.cmake index 4867772178fe..4485401c9bec 100644 --- a/cmake/configure/configure_symengine.cmake +++ b/cmake/configure/configure_symengine.cmake @@ -33,6 +33,7 @@ MACRO(FEATURE_SYMENGINE_CONFIGURE_EXTERNAL) # # Overwrite the compiler flags imported from SymEngine # + SET(SYMENGINE_CXX_FLAGS) SET(SYMENGINE_CXX_FLAGS_DEBUG) SET(SYMENGINE_CXX_FLAGS_RELEASE) ENDMACRO() From aac4b05f59e2b4d4d690cac0bab1aef09b4b2dff Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Wed, 20 Mar 2019 11:52:01 +0100 Subject: [PATCH 328/507] add DynamicSparsityPattern::nonempty_cols() and nonempty_rows() --- doc/news/changes/minor/20190320DenisDavydov | 4 ++ .../deal.II/lac/dynamic_sparsity_pattern.h | 18 ++++++ source/lac/dynamic_sparsity_pattern.cc | 40 +++++++++++++ tests/sparsity/dynamic_sparsity_pattern_20.cc | 60 +++++++++++++++++++ .../dynamic_sparsity_pattern_20.output | 5 ++ 5 files changed, 127 insertions(+) create mode 100644 doc/news/changes/minor/20190320DenisDavydov create mode 100644 tests/sparsity/dynamic_sparsity_pattern_20.cc create mode 100644 tests/sparsity/dynamic_sparsity_pattern_20.output diff --git a/doc/news/changes/minor/20190320DenisDavydov b/doc/news/changes/minor/20190320DenisDavydov new file mode 100644 index 000000000000..fa9905b7e403 --- /dev/null +++ b/doc/news/changes/minor/20190320DenisDavydov @@ -0,0 +1,4 @@ +New: Add DynamicSparsityPattern::nonempty_cols()/DynamicSparsityPattern::nonempty_rows() to return columns/rows +stored in the sparsity pattern. +
    +(Denis Davydov, 2019/03/20) diff --git a/include/deal.II/lac/dynamic_sparsity_pattern.h b/include/deal.II/lac/dynamic_sparsity_pattern.h index ed2a200179cc..1cb5b8f706f3 100644 --- a/include/deal.II/lac/dynamic_sparsity_pattern.h +++ b/include/deal.II/lac/dynamic_sparsity_pattern.h @@ -615,6 +615,24 @@ class DynamicSparsityPattern : public Subscriptor const IndexSet & row_index_set() const; + /** + * Return the IndexSet that contains entries for all columns in which at least + * one element exists in this sparsity pattern. + * + * @note In a parallel context, this only considers the locally stored rows. + */ + IndexSet + nonempty_cols() const; + + /** + * Return the IndexSet that contains entries for all rows in which at least + * one element exists in this sparsity pattern. + * + * @note In a parallel context, this only considers the locally stored rows. + */ + IndexSet + nonempty_rows() const; + /** * return whether this object stores only those entries that have been added * explicitly, or if the sparsity pattern contains elements that have been diff --git a/source/lac/dynamic_sparsity_pattern.cc b/source/lac/dynamic_sparsity_pattern.cc index dcf53e1bbcef..c12ef6141f5b 100644 --- a/source/lac/dynamic_sparsity_pattern.cc +++ b/source/lac/dynamic_sparsity_pattern.cc @@ -23,6 +23,7 @@ #include #include #include +#include DEAL_II_NAMESPACE_OPEN @@ -554,6 +555,45 @@ DynamicSparsityPattern::n_nonzero_elements() const } + +IndexSet +DynamicSparsityPattern::nonempty_cols() const +{ + std::set cols; + for (const auto &line : lines) + cols.insert(line.entries.begin(), line.entries.end()); + + IndexSet res(this->n_cols()); + res.add_indices(cols.begin(), cols.end()); + return res; +} + + + +IndexSet +DynamicSparsityPattern::nonempty_rows() const +{ + const IndexSet all_rows = complete_index_set(this->n_rows()); + const IndexSet &locally_stored_rows = rowset.size() == 0 ? all_rows : rowset; + + std::vector rows; + auto line = lines.begin(); + AssertDimension(locally_stored_rows.n_elements(), lines.size()); + for (const auto &row : locally_stored_rows) + { + if (line->entries.size() > 0) + rows.push_back(row); + + ++line; + } + + IndexSet res(this->n_rows()); + res.add_indices(rows.begin(), rows.end()); + return res; +} + + + DynamicSparsityPattern::size_type DynamicSparsityPattern::memory_consumption() const { diff --git a/tests/sparsity/dynamic_sparsity_pattern_20.cc b/tests/sparsity/dynamic_sparsity_pattern_20.cc new file mode 100644 index 000000000000..2f1836836d2d --- /dev/null +++ b/tests/sparsity/dynamic_sparsity_pattern_20.cc @@ -0,0 +1,60 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2004 - 2017 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + + +// check DynamicSparsityPattern::nonempty_columns() +// and nonempty_rows() + +#include + +#include "../tests.h" + + +void +test() +{ + const unsigned int N = 100; + DynamicSparsityPattern dsp(N, 2 * N); + + for (unsigned int i = 0; i < 5; ++i) + for (unsigned int j = (i == 0 ? 0 : i - 1); j < i + 1; ++j) + dsp.add(i, j); + + dsp.add(50, 50); + dsp.add(51, 51); + dsp.add(90, 52); + + dsp.add(N - 1, 2 * N - 1); + + const IndexSet cols = dsp.nonempty_cols(); + deallog << "Columns:" << std::endl; + cols.print(deallog.get_file_stream()); + + const IndexSet rows = dsp.nonempty_rows(); + deallog << "Rows:" << std::endl; + rows.print(deallog.get_file_stream()); +} + + + +int +main() +{ + initlog(); + + test(); + return 0; +} diff --git a/tests/sparsity/dynamic_sparsity_pattern_20.output b/tests/sparsity/dynamic_sparsity_pattern_20.output new file mode 100644 index 000000000000..ee0ac1f04cf0 --- /dev/null +++ b/tests/sparsity/dynamic_sparsity_pattern_20.output @@ -0,0 +1,5 @@ + +DEAL::Columns: +{[0,4], [50,52], 199} +DEAL::Rows: +{[0,4], [50,51], 90, 99} From a5577ea660d98051e9c8d682485f9749e85b2a8d Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Sun, 24 Mar 2019 17:40:20 -0600 Subject: [PATCH 329/507] CI: kill older running builds --- Jenkinsfile | 14 ++++++++++++++ contrib/ci/Jenkinsfile.osx | 22 ++++++++++++++++++++++ contrib/ci/Jenkinsfile.tidy | 24 ++++++++++++++++++++++++ 3 files changed, 60 insertions(+) diff --git a/Jenkinsfile b/Jenkinsfile index c2b78f390a13..2475c22dafbe 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -1,11 +1,25 @@ #!groovy +// load library https://github.com/tjhei/jenkins-stuff to provide +// killold.killOldBuilds() function: +@Library('tjhei') _ + pipeline { agent none stages { + stage("abort old") + { + agent none + steps + { + // kill older builds in this PR: + script { killold.killOldBuilds() } + } + } + stage("check") { agent diff --git a/contrib/ci/Jenkinsfile.osx b/contrib/ci/Jenkinsfile.osx index 5a404aabb774..68205e5b8bed 100644 --- a/contrib/ci/Jenkinsfile.osx +++ b/contrib/ci/Jenkinsfile.osx @@ -19,8 +19,28 @@ Settings to apply inside Jenkins: - discard: 5+ items */ +// load library https://github.com/tjhei/jenkins-stuff to provide +// killold.killOldBuilds() function: +@Library('tjhei') _ + pipeline { + agent none + + stages + { + stage("abort old") + { + agent none + steps + { + // kill older builds in this PR: + script { killold.killOldBuilds() } + } + } + + stage("main") + { agent { node { label 'osx' @@ -95,4 +115,6 @@ pipeline } } } + } + } } diff --git a/contrib/ci/Jenkinsfile.tidy b/contrib/ci/Jenkinsfile.tidy index 82d7e69a39f2..80ebb236a8c3 100644 --- a/contrib/ci/Jenkinsfile.tidy +++ b/contrib/ci/Jenkinsfile.tidy @@ -19,8 +19,30 @@ Settings to apply inside Jenkins: - discard: 5+ items */ +// load library https://github.com/tjhei/jenkins-stuff to provide +// killold.killOldBuilds() function: +@Library('tjhei') _ + pipeline { + agent none + + stages + { + stage("abort old") + { + agent none + steps + { + githubNotify context: 'tidy', description: 'initializing...', status: 'PENDING' + // kill older builds in this PR: + script { killold.killOldBuilds() } + } + } + + stage("main") + { + agent { docker @@ -88,4 +110,6 @@ pipeline } } + } + } } From 4276e8f3451d346447a6f6f428480c09c1e276b0 Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Wed, 13 Mar 2019 09:10:43 -0400 Subject: [PATCH 330/507] add Trilinos error checks and fix nonlocal sparsity graph entry - Bugfix: Use GID64(0) instead of MyGID(0) which is a bool - add more checks to other function calls - add comments - fix for rectangular patterns --- source/lac/trilinos_sparsity_pattern.cc | 27 ++++++++++++++++++++----- 1 file changed, 22 insertions(+), 5 deletions(-) diff --git a/source/lac/trilinos_sparsity_pattern.cc b/source/lac/trilinos_sparsity_pattern.cc index 33887b18c551..ad5880afd9f1 100644 --- a/source/lac/trilinos_sparsity_pattern.cc +++ b/source/lac/trilinos_sparsity_pattern.cc @@ -793,17 +793,34 @@ namespace TrilinosWrappers if (nonlocal_graph->IndicesAreGlobal() == false && nonlocal_graph->RowMap().NumMyElements() > 0) { - // insert dummy element + // Insert dummy element at (row, column) that corresponds to row 0 + // in local index counting. TrilinosWrappers::types::int_type row = - nonlocal_graph->RowMap().MyGID(0); - nonlocal_graph->InsertGlobalIndices(row, 1, &row); + TrilinosWrappers::global_index(nonlocal_graph->RowMap(), 0); + TrilinosWrappers::types::int_type column = 0; + + // in case we have a square sparsity pattern, add the entry on the + // diagonal + if (TrilinosWrappers::n_global_elements(*column_space_map) == + TrilinosWrappers::n_global_elements(graph->RangeMap())) + column = row; + // if not, take a column index that we have ourselves since we + // know for sure it is there (and it will not create spurious + // messages to many ranks like putting index 0 on many processors) + else if (column_space_map->NumMyElements() > 0) + column = TrilinosWrappers::global_index(*column_space_map, 0); + ierr = nonlocal_graph->InsertGlobalIndices(row, 1, &column); + AssertThrow(ierr == 0, ExcTrilinosError(ierr)); } Assert(nonlocal_graph->RowMap().NumMyElements() == 0 || nonlocal_graph->IndicesAreGlobal() == true, ExcInternalError()); - nonlocal_graph->FillComplete(*column_space_map, graph->RangeMap()); - nonlocal_graph->OptimizeStorage(); + ierr = + nonlocal_graph->FillComplete(*column_space_map, graph->RangeMap()); + AssertThrow(ierr >= 0, ExcTrilinosError(ierr)); + ierr = nonlocal_graph->OptimizeStorage(); + AssertThrow(ierr >= 0, ExcTrilinosError(ierr)); Epetra_Export exporter(nonlocal_graph->RowMap(), graph->RowMap()); ierr = graph->Export(*nonlocal_graph, exporter, Add); AssertThrow(ierr == 0, ExcTrilinosError(ierr)); From 7ecef4009d01ff5b3420c94b9f5bfecddfaaa9ba Mon Sep 17 00:00:00 2001 From: Wolfgang Bangerth Date: Mon, 25 Mar 2019 17:38:14 +0100 Subject: [PATCH 331/507] Update include/deal.II/grid/grid_tools.h Co-Authored-By: luca-heltai --- include/deal.II/grid/grid_tools.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/include/deal.II/grid/grid_tools.h b/include/deal.II/grid/grid_tools.h index fed508b798d6..05f6b4a835ad 100644 --- a/include/deal.II/grid/grid_tools.h +++ b/include/deal.II/grid/grid_tools.h @@ -2637,7 +2637,7 @@ namespace GridTools * Triangulation @p tria to their co-dimension one and two objects. * * This function sets the @p manifold_id of faces and edges (both on the - * interior and on the boundary) to the value returnd by the + * interior and on the boundary) to the value returned by the * @p disambiguation_function method, called with the set of * manifold indicators of the cells that share the same face or edge. * From 88362a235229fb83b00d554766f3f6a98978d640 Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Mon, 25 Mar 2019 21:55:27 -0600 Subject: [PATCH 332/507] fix indentation --- contrib/ci/Jenkinsfile.osx | 116 ++++++++++++++++++------------------ contrib/ci/Jenkinsfile.tidy | 106 ++++++++++++++++---------------- 2 files changed, 110 insertions(+), 112 deletions(-) diff --git a/contrib/ci/Jenkinsfile.osx b/contrib/ci/Jenkinsfile.osx index 68205e5b8bed..b9c556d55d02 100644 --- a/contrib/ci/Jenkinsfile.osx +++ b/contrib/ci/Jenkinsfile.osx @@ -41,80 +41,80 @@ pipeline stage("main") { - agent { - node { - label 'osx' - } - } - - post { cleanup { cleanWs() } } - - stages - { - stage("check") - { - when { - allOf { - not {branch 'master'} + agent { + node { + label 'osx' } } - steps + post { cleanup { cleanWs() } } + + stages { - githubNotify context: 'OSX', description: 'pending...', status: 'PENDING' - sh ''' + stage("check") + { + when { + allOf { + not {branch 'master'} + } + } + + steps + { + githubNotify context: 'OSX', description: 'pending...', status: 'PENDING' + sh ''' wget -q -O - https://api.github.com/repos/dealii/dealii/issues/${CHANGE_ID}/labels | grep 'ready to test' || \ { echo "This commit will only be tested when it has the label 'ready to test'. Trigger a rebuild by adding a comment that contains '/rebuild'..."; exit 1; } - ''' - } - post - { - failure - { - githubNotify context: 'OSX', description: 'need ready to test label and /rebuild', status: 'PENDING' - script + ''' + } + post { - currentBuild.result='NOT_BUILT' + failure + { + githubNotify context: 'OSX', description: 'need ready to test label and /rebuild', status: 'PENDING' + script + { + currentBuild.result='NOT_BUILT' + } + } } } - } - } - stage('build') - { - steps - { - timeout(time: 1, unit: 'HOURS') + stage('build') { - sh "echo \"building on node ${env.NODE_NAME}\"" - sh '''#!/bin/bash - mkdir build && cd build - cmake \ - -D DEAL_II_WITH_MPI=OFF \ - -D DEAL_II_CXX_FLAGS='-Werror' \ - -D CMAKE_BUILD_TYPE=Debug \ - $WORKSPACE/ && make -j 4 - ''' + steps + { + timeout(time: 1, unit: 'HOURS') + { + sh "echo \"building on node ${env.NODE_NAME}\"" + sh '''#!/bin/bash + mkdir build && cd build + cmake \ + -D DEAL_II_WITH_MPI=OFF \ + -D DEAL_II_CXX_FLAGS='-Werror' \ + -D CMAKE_BUILD_TYPE=Debug \ + $WORKSPACE/ && make -j 4 + ''' + } + } + + post + { + failure + { + githubNotify context: 'OSX', description: 'build failed', status: 'FAILURE' + } + } } - } - post - { - failure + stage("finalize") { - githubNotify context: 'OSX', description: 'build failed', status: 'FAILURE' + steps + { + githubNotify context: 'OSX', description: 'OK', status: 'SUCCESS' + } } } } - - stage("finalize") - { - steps - { - githubNotify context: 'OSX', description: 'OK', status: 'SUCCESS' - } - } - } - } } } diff --git a/contrib/ci/Jenkinsfile.tidy b/contrib/ci/Jenkinsfile.tidy index 80ebb236a8c3..6aa1179e43dd 100644 --- a/contrib/ci/Jenkinsfile.tidy +++ b/contrib/ci/Jenkinsfile.tidy @@ -42,74 +42,72 @@ pipeline stage("main") { - - agent - { - docker - { - image 'tjhei/candi-base-clang' - } - } - - post { cleanup { cleanWs() } } - - stages - { - stage("check") - { - when { - allOf { - not {branch 'master'} + agent + { + docker + { + image 'tjhei/candi-base-clang' } } - steps + post { cleanup { cleanWs() } } + + stages { - githubNotify context: 'tidy', description: 'pending...', status: 'PENDING' - sh ''' + stage("check") + { + when { + allOf { + not {branch 'master'} + } + } + + steps + { + githubNotify context: 'tidy', description: 'pending...', status: 'PENDING' + sh ''' wget -q -O - https://api.github.com/repos/dealii/dealii/issues/${CHANGE_ID}/labels | grep 'ready to test' || \ { echo "This commit will only be tested when it has the label 'ready to test'. Trigger a rebuild by adding a comment that contains '/rebuild'..."; exit 1; } - ''' - } - post - { - failure - { - githubNotify context: 'tidy', description: 'need ready to test label and /rebuild', status: 'PENDING' - script + ''' + } + post { - currentBuild.result='NOT_BUILT' + failure + { + githubNotify context: 'tidy', description: 'need ready to test label and /rebuild', status: 'PENDING' + script + { + currentBuild.result='NOT_BUILT' + } + } } } - } - } - stage('build') - { - steps - { - timeout(time: 2, unit: 'HOURS') + stage('build') { - sh "echo \"building on node ${env.NODE_NAME}\"" - - sh '''#!/bin/bash - mkdir build && cd build - $WORKSPACE/contrib/utilities/run_clang_tidy.sh $WORKSPACE - ''' - githubNotify context: 'tidy', description: 'OK', status: 'SUCCESS' - } - } + steps + { + timeout(time: 2, unit: 'HOURS') + { + sh "echo \"building on node ${env.NODE_NAME}\"" + sh '''#!/bin/bash + mkdir build && cd build + $WORKSPACE/contrib/utilities/run_clang_tidy.sh $WORKSPACE + ''' + githubNotify context: 'tidy', description: 'OK', status: 'SUCCESS' + } + } - post - { - failure - { - githubNotify context: 'tidy', description: 'build failed', status: 'FAILURE' + post + { + failure + { + githubNotify context: 'tidy', description: 'build failed', status: 'FAILURE' + } + } } + } } - - } - } } } From cf260b33da27544e8d3b91deb70563cb6a781af0 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Thu, 21 Mar 2019 08:15:44 +0100 Subject: [PATCH 333/507] Fix problem with GrowingVectorMemory for LinearAlgebra::distributed::Vector --- source/base/mpi.cc | 12 +++++ source/lac/CMakeLists.txt | 8 ++++ source/lac/vector_memory.cc | 37 +++------------ source/lac/vector_memory.cu | 57 ++++++++++++++++++++++ tests/cuda/vector_memory_01.cu | 76 ++++++++++++++++++++++++++++++ tests/cuda/vector_memory_01.output | 5 ++ tests/cuda/vector_memory_02.cu | 60 +++++++++++++++++++++++ tests/cuda/vector_memory_02.output | 23 +++++++++ 8 files changed, 247 insertions(+), 31 deletions(-) create mode 100644 source/lac/vector_memory.cu create mode 100644 tests/cuda/vector_memory_01.cu create mode 100644 tests/cuda/vector_memory_01.output create mode 100644 tests/cuda/vector_memory_02.cu create mode 100644 tests/cuda/vector_memory_02.output diff --git a/source/base/mpi.cc b/source/base/mpi.cc index b8cd45e7c26a..de4204d548a9 100644 --- a/source/base/mpi.cc +++ b/source/base/mpi.cc @@ -720,6 +720,18 @@ namespace Utilities } #endif +// There is a similar issue with CUDA: The destructor of static objects might +// run after the CUDA driver is unloaded. Hence, also release all memory +// related to CUDA vectors. +#ifdef DEAL_II_WITH_CUDA + GrowingVectorMemory< + LinearAlgebra::distributed::Vector>:: + release_unused_memory(); + GrowingVectorMemory< + LinearAlgebra::distributed::Vector>:: + release_unused_memory(); +#endif + #ifdef DEAL_II_WITH_P4EST // now end p4est and libsc // Note: p4est has no finalize function diff --git a/source/lac/CMakeLists.txt b/source/lac/CMakeLists.txt index 973837219e1b..ac29c1f6ed4d 100644 --- a/source/lac/CMakeLists.txt +++ b/source/lac/CMakeLists.txt @@ -60,6 +60,14 @@ SET(_separate_src sparse_matrix_inst2.cc ) +# Add CUDA wrapper files +IF(DEAL_II_WITH_CUDA) + SET(_separate_src + ${_separate_src} + vector_memory.cu + ) +ENDIF() + SET(_inst affine_constraints.inst.in block_sparse_matrix.inst.in diff --git a/source/lac/vector_memory.cc b/source/lac/vector_memory.cc index 3fa5affd9bd9..e760248a58ff 100644 --- a/source/lac/vector_memory.cc +++ b/source/lac/vector_memory.cc @@ -14,7 +14,6 @@ // --------------------------------------------------------------------- #include -#include #include #include #include @@ -31,45 +30,21 @@ DEAL_II_NAMESPACE_OPEN #include "vector_memory.inst" -#ifdef DEAL_II_WITH_CUDA -template class VectorMemory>; -template class VectorMemory>; -template class GrowingVectorMemory>; -template class GrowingVectorMemory>; -# ifdef DEAL_II_WITH_MPI -template class VectorMemory< - LinearAlgebra::distributed::Vector>; -template class VectorMemory< - LinearAlgebra::distributed::Vector>; -template class GrowingVectorMemory< - LinearAlgebra::distributed::Vector>; -template class GrowingVectorMemory< - LinearAlgebra::distributed::Vector>; -# endif -#endif - namespace internal { namespace GrowingVectorMemoryImplementation { +#ifdef DEAL_II_WITH_CUDA + void + release_all_unused_cuda_memory(); +#endif + void release_all_unused_memory() { #include "vector_memory_release.inst" - #ifdef DEAL_II_WITH_CUDA - dealii::GrowingVectorMemory>::release_unused_memory(); - dealii::GrowingVectorMemory>::release_unused_memory(); -# ifdef DEAL_II_WITH_MPI - dealii::GrowingVectorMemory< - dealii::LinearAlgebra::distributed::Vector>:: - release_unused_memory(); - dealii::GrowingVectorMemory< - dealii::LinearAlgebra::distributed::Vector>:: - release_unused_memory(); -# endif + release_all_unused_cuda_memory(); #endif } } // namespace GrowingVectorMemoryImplementation diff --git a/source/lac/vector_memory.cu b/source/lac/vector_memory.cu new file mode 100644 index 000000000000..147c6ac8c536 --- /dev/null +++ b/source/lac/vector_memory.cu @@ -0,0 +1,57 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + +#include +#include +#include + + +DEAL_II_NAMESPACE_OPEN + +template class VectorMemory>; +template class VectorMemory>; +template class GrowingVectorMemory>; +template class GrowingVectorMemory>; +template class VectorMemory< + LinearAlgebra::distributed::Vector>; +template class VectorMemory< + LinearAlgebra::distributed::Vector>; +template class GrowingVectorMemory< + LinearAlgebra::distributed::Vector>; +template class GrowingVectorMemory< + LinearAlgebra::distributed::Vector>; + +namespace internal +{ + namespace GrowingVectorMemoryImplementation + { + void + release_all_unused_cuda_memory() + { + dealii::GrowingVectorMemory>::release_unused_memory(); + dealii::GrowingVectorMemory>::release_unused_memory(); + dealii::GrowingVectorMemory< + dealii::LinearAlgebra::distributed::Vector>:: + release_unused_memory(); + dealii::GrowingVectorMemory< + dealii::LinearAlgebra::distributed::Vector>:: + release_unused_memory(); + } + } // namespace GrowingVectorMemoryImplementation +} // namespace internal + +DEAL_II_NAMESPACE_CLOSE diff --git a/tests/cuda/vector_memory_01.cu b/tests/cuda/vector_memory_01.cu new file mode 100644 index 000000000000..00e086f82722 --- /dev/null +++ b/tests/cuda/vector_memory_01.cu @@ -0,0 +1,76 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2007 - 2017 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + +// Test that we can successfully fill a GrowingVectorMemory pool +// with LinearAlgebra::distributed::Vector objects. +// Partially copied from lac/vector_memory.cc + + +#include + +#include +#include + +#include "../tests.h" + + +using namespace dealii; + +template +void +test_stat() +{ + GrowingVectorMemory mem(1, true); + VectorType * v1 = mem.alloc(); + VectorType * v2 = mem.alloc(); + VectorType * v3 = mem.alloc(); + VectorType * v4 = mem.alloc(); + VectorType * v5 = mem.alloc(); + VectorType * v6 = mem.alloc(); + v1->reinit(5); + v2->reinit(5); + v3->reinit(5); + v4->reinit(5); + v5->reinit(5); + v6->reinit(5); + mem.free(v1); + mem.free(v2); + mem.free(v3); + mem.free(v4); + mem.free(v5); + mem.free(v6); + v1 = mem.alloc(); + mem.free(v1); + v1 = mem.alloc(); + mem.free(v1); + v1 = mem.alloc(); + mem.free(v1); + v1 = mem.alloc(); + mem.free(v1); +} + + +int +main(int argc, char *argv[]) +{ + initlog(); + Utilities::MPI::MPI_InitFinalize mpi_init(argc, argv, 1); + + test_stat>(); + test_stat>(); + + return 0; +} diff --git a/tests/cuda/vector_memory_01.output b/tests/cuda/vector_memory_01.output new file mode 100644 index 000000000000..408e05b837b4 --- /dev/null +++ b/tests/cuda/vector_memory_01.output @@ -0,0 +1,5 @@ + +DEAL::GrowingVectorMemory:Overall allocated vectors: 10 +DEAL::GrowingVectorMemory:Maximum allocated vectors: 6 +DEAL::GrowingVectorMemory:Overall allocated vectors: 10 +DEAL::GrowingVectorMemory:Maximum allocated vectors: 6 diff --git a/tests/cuda/vector_memory_02.cu b/tests/cuda/vector_memory_02.cu new file mode 100644 index 000000000000..8725653d55da --- /dev/null +++ b/tests/cuda/vector_memory_02.cu @@ -0,0 +1,60 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2007 - 2017 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + +// Test that memory leaks are detected correctly for a GrowingVectorMemory pool +// with LinearAlgebra::distributed objects. +// Partially copied from lac/vector_memory.cc + + +#include + +#include +#include + +#include "../tests.h" + + +using namespace dealii; + +template +void +test_leak() +{ + GrowingVectorMemory mem; + VectorType * v = mem.alloc(); + v->reinit(5); +} + +int +main(int argc, char *argv[]) +{ + initlog(); + Utilities::MPI::MPI_InitFinalize mpi_init(argc, argv, 1); + deal_II_exceptions::disable_abort_on_exception(); + + try + { + test_leak< + LinearAlgebra::distributed::Vector>(); + test_leak>(); + } + catch (const StandardExceptions::ExcMemoryLeak &e) + { + deallog << "Exception: " << e.get_exc_name() << std::endl; + } + + return 0; +} diff --git a/tests/cuda/vector_memory_02.output b/tests/cuda/vector_memory_02.output new file mode 100644 index 000000000000..bdfb84b98ded --- /dev/null +++ b/tests/cuda/vector_memory_02.output @@ -0,0 +1,23 @@ + +DEAL::Exception: StandardExceptions::ExcMemoryLeak(current_alloc) +DEAL:: +-------------------------------------------------------- +An error occurred in file in function + dealii::GrowingVectorMemory::~GrowingVectorMemory() [with VectorType = dealii::LinearAlgebra::distributed::Vector] +The violated condition was: + current_alloc == 0 +Additional information: + Destroying memory handler while 1 objects are still allocated. +-------------------------------------------------------- + +DEAL::Exception: StandardExceptions::ExcMemoryLeak(current_alloc) +DEAL:: +-------------------------------------------------------- +An error occurred in file in function + dealii::GrowingVectorMemory::~GrowingVectorMemory() [with VectorType = dealii::LinearAlgebra::distributed::Vector] +The violated condition was: + current_alloc == 0 +Additional information: + Destroying memory handler while 1 objects are still allocated. +-------------------------------------------------------- + From 0e30348e98c2b0a34675cdbb2d57678d857d91ff Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Tue, 26 Mar 2019 17:04:28 +0100 Subject: [PATCH 334/507] Add documentation for initialising Trilinos AMG constant modes --- include/deal.II/lac/trilinos_precondition.h | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) diff --git a/include/deal.II/lac/trilinos_precondition.h b/include/deal.II/lac/trilinos_precondition.h index aba329ce8a6e..3b5ac1984a2a 100644 --- a/include/deal.II/lac/trilinos_precondition.h +++ b/include/deal.II/lac/trilinos_precondition.h @@ -1369,6 +1369,25 @@ namespace TrilinosWrappers /** * Constructor. By default, we pretend to work on elliptic problems with * linear finite elements on a scalar equation. + * + * Making use of the DoFTools::extract_constant_modes() function, the + * @p constant_modes vector can be initialized for a given field in the + * following manner: + * + * @code + * #include + * ... + * + * DoFHandlerType<...> dof_handler; + * FEValuesExtractors::Type... field_extractor; + * ... + * + * TrilinosWrappers::PreconditionAMG::AdditionalData data; + * DoFTools::extract_constant_modes( + * dof_handler, + * dof_handler.get_fe_collection().component_mask(field_extractor), + * data.constant_modes ); + * @endcode */ AdditionalData(const bool elliptic = true, const bool higher_order_elements = false, From f5ab9c7895c8930017b291ed331e36d8e84a6131 Mon Sep 17 00:00:00 2001 From: Logan Harbour Date: Tue, 26 Mar 2019 16:34:29 -0500 Subject: [PATCH 335/507] Additional doco for L2 integrators --- include/deal.II/integrators/l2.h | 48 ++++++++++++++++++++++++++++++-- 1 file changed, 46 insertions(+), 2 deletions(-) diff --git a/include/deal.II/integrators/l2.h b/include/deal.II/integrators/l2.h index a2d2588c100a..0c49f0a3c6e1 100644 --- a/include/deal.II/integrators/l2.h +++ b/include/deal.II/integrators/l2.h @@ -50,6 +50,11 @@ namespace LocalIntegrators * integrals \f[ \int_F uv\,ds \quad \text{or} \quad \int_F \mathbf u\cdot * \mathbf v\,ds \f] * + * @param M The mass matrix matrix obtained as result. + * @param fe The FEValues object describing the local trial function + * space. #update_values and #update_JxW_values must be set. + * @param factor A constant that multiplies the mass matrix. + * * @author Guido Kanschat * @date 2008, 2009, 2010 */ @@ -97,8 +102,12 @@ namespace LocalIntegrators * integrals \f[ \int_F \omega(x) uv\,ds \quad \text{or} \quad \int_F * \omega(x) \mathbf u\cdot \mathbf v\,ds \f] * - * The size of the vector weights must be equal to the number of - * quadrature points in the finite element. + * @param M The weighted mass matrix matrix obtained as result. + * @param fe The FEValues object describing the local trial function + * space. #update_values and #update_JxW_values must be set. + * @param weights The weights, $\omega(x)$, evaluated at the quadrature + * points in the finite element (size must be equal to the number of + * quadrature points in the element). * * @author Guido Kanschat * @date 2014 @@ -146,6 +155,14 @@ namespace LocalIntegrators * * \f[ \int_Z fv\,dx \quad \text{or} \quad \int_F fv\,ds \f] * + * @param result The vector obtained as result. + * @param fe The FEValues object describing the local trial function + * space. #update_values and #update_JxW_values must be set. + * @param input The representation of $f$ evaluated at the quadrature + * points in the finite element (size must be equal to the number of + * quadrature points in the element). + * @param factor A constant that multiplies the result. + * * @author Guido Kanschat * @date 2008, 2009, 2010 */ @@ -171,6 +188,14 @@ namespace LocalIntegrators * hand side. \f[ \int_Z \mathbf f\cdot \mathbf v\,dx \quad \text{or} * \quad \int_F \mathbf f\cdot \mathbf v\,ds \f] * + * @param result The vector obtained as result. + * @param fe The FEValues object describing the local trial function + * space. #update_values and #update_JxW_values must be set. + * @param input The vector valued representation of $\mathbf f$ evaluated + * at the quadrature points in the finite element (size of each component + * must be equal to the number of quadrature points in the element). + * @param factor A constant that multiplies the result. + * * @author Guido Kanschat * @date 2008, 2009, 2010 */ @@ -203,6 +228,25 @@ namespace LocalIntegrators * Using appropriate weights, this term can be used to penalize violation * of conformity in H1. * + * Note that for the parameters that follow, the external matrix refers to + * the flux between cells, while the internal matrix refers to entries + * coupling inside the cell. + * + * @param M11 The internal matrix for the first cell obtained as result. + * @param M12 The external matrix for the first cell obtained as result. + * @param M12 The external matrix for the second cell obtained as result. + * @param M22 The internal matrix for the second cell obtained as result. + * @param fe1 The FEValues object describing the local trial function + * space for the first cell. #update_values and #update_JxW_values must be + * set. + * @param fe2 The FEValues object describing the local trial function + * space for the second cell. #update_values and #update_JxW_values must be + * set. + * @param factor1 A constant that multiplies the shape functions for the + * first cell. + * @param factor2 A constant that multiplies the shape functions for the + * second cell. + * * @author Guido Kanschat * @date 2008, 2009, 2010 */ From ca18f5aaccc84c7c09b39df8891a6922632be633 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Tue, 26 Mar 2019 22:10:05 -0400 Subject: [PATCH 336/507] Rename parallel::distributed::SolutionTransfer::prepare_serialization() --- doc/news/changes/minor/20190326Arndt | 5 +++ .../deal.II/distributed/solution_transfer.h | 32 +++++++++++++++---- source/distributed/solution_transfer.cc | 23 ++++++++++++- tests/mpi/p4est_save_02.cc | 2 +- tests/mpi/p4est_save_03.cc | 4 +-- tests/mpi/p4est_save_04.cc | 2 +- tests/mpi/p4est_save_06.cc | 2 +- 7 files changed, 57 insertions(+), 13 deletions(-) create mode 100644 doc/news/changes/minor/20190326Arndt diff --git a/doc/news/changes/minor/20190326Arndt b/doc/news/changes/minor/20190326Arndt new file mode 100644 index 000000000000..8e9c7ef382d8 --- /dev/null +++ b/doc/news/changes/minor/20190326Arndt @@ -0,0 +1,5 @@ +Changed: parallel::distributed::SolutionTransfer::prepare_serialization() has +been deprecated in favor of +parallel::distributed::SolutionTransfer::prepare_for_serialization(). +Note on ghost elements In a parallel computation PETSc or * Trilinos vector may contain ghost elements or not. For reading in * information with prepare_for_coarsening_and_refinement() or - * prepare_serialization() you need to supply vectors with ghost elements, - * so that all locally_active elements can be read. On the other hand, - * ghosted vectors are generally not writable, so for calls to + * prepare_for_serialization() you need to supply vectors with ghost + * elements, so that all locally_active elements can be read. On the other + * hand, ghosted vectors are generally not writable, so for calls to * interpolate() or deserialize() you need to supply distributed vectors * without ghost elements. More precisely, during interpolation the * current algorithm writes into all locally active degrees of freedom. @@ -133,7 +133,7 @@ namespace parallel * @code * parallel::distributed::SolutionTransfer * sol_trans(dof_handler); - * sol_trans.prepare_serialization (vector); + * sol_trans.prepare_for_serialization (vector); * * triangulation.save(filename); * @endcode @@ -186,7 +186,7 @@ namespace parallel * sol_trans(hp_dof_handler); * * hp_dof_handler.prepare_for_serialization_of_active_fe_indices(); - * sol_trans.prepare_serialization(vector); + * sol_trans.prepare_for_serialization(vector); * * triangulation.save(filename); * @endcode @@ -292,24 +292,42 @@ namespace parallel void interpolate(VectorType &out); + /** + * Prepare the serialization of the given vector. The serialization is + * done by Triangulation::save(). The given vector needs all information + * on the locally active DoFs (it must be ghosted). See documentation of + * this class for more information. + */ + void + prepare_for_serialization(const VectorType &in); + + /** + * Same as the function above, only for a list of vectors. + */ + void + prepare_for_serialization(const std::vector &all_in); /** * Prepare the serialization of the given vector. The serialization is * done by Triangulation::save(). The given vector needs all information * on the locally active DoFs (it must be ghosted). See documentation of * this class for more information. + * + * @deprecated Use parallel::distributed::SolutionTransfer::prepare_for_serialization() instead. */ + DEAL_II_DEPRECATED void prepare_serialization(const VectorType &in); - /** * Same as the function above, only for a list of vectors. + * + * @deprecated Use parallel::distributed::SolutionTransfer::prepare_for_serialization() instead. */ + DEAL_II_DEPRECATED void prepare_serialization(const std::vector &all_in); - /** * Execute the deserialization of the given vector. This needs to be * done after calling Triangulation::load(). The given vector must be a diff --git a/source/distributed/solution_transfer.cc b/source/distributed/solution_transfer.cc index 4c4f5d9f26f1..0919d7c79804 100644 --- a/source/distributed/solution_transfer.cc +++ b/source/distributed/solution_transfer.cc @@ -109,13 +109,34 @@ namespace parallel + template + void + SolutionTransfer:: + prepare_for_serialization(const VectorType &in) + { + std::vector all_in(1, &in); + prepare_for_serialization(all_in); + } + + + + template + void + SolutionTransfer:: + prepare_for_serialization(const std::vector &all_in) + { + prepare_for_coarsening_and_refinement(all_in); + } + + + template void SolutionTransfer::prepare_serialization( const VectorType &in) { std::vector all_in(1, &in); - prepare_serialization(all_in); + prepare_for_serialization(all_in); } diff --git a/tests/mpi/p4est_save_02.cc b/tests/mpi/p4est_save_02.cc index 1ab383a4d77a..be0738f39f49 100644 --- a/tests/mpi/p4est_save_02.cc +++ b/tests/mpi/p4est_save_02.cc @@ -97,7 +97,7 @@ test() x.compress(VectorOperation::insert); solution = x; - soltrans.prepare_serialization(solution); + soltrans.prepare_for_serialization(solution); tr.save(filename.c_str()); diff --git a/tests/mpi/p4est_save_03.cc b/tests/mpi/p4est_save_03.cc index 9780e2dfaeac..4619f2ad7536 100644 --- a/tests/mpi/p4est_save_03.cc +++ b/tests/mpi/p4est_save_03.cc @@ -108,8 +108,8 @@ test() solution2 = x; - soltrans.prepare_serialization(solution); - soltrans2.prepare_serialization(solution2); + soltrans.prepare_for_serialization(solution); + soltrans2.prepare_for_serialization(solution2); tr.save(filename.c_str()); diff --git a/tests/mpi/p4est_save_04.cc b/tests/mpi/p4est_save_04.cc index c908edf67341..0526ce29c2a6 100644 --- a/tests/mpi/p4est_save_04.cc +++ b/tests/mpi/p4est_save_04.cc @@ -100,7 +100,7 @@ test() x.compress(VectorOperation::insert); rel_x = x; - soltrans.prepare_serialization(rel_x); + soltrans.prepare_for_serialization(rel_x); tr.save("file"); // tr.write_mesh_vtk("before"); diff --git a/tests/mpi/p4est_save_06.cc b/tests/mpi/p4est_save_06.cc index 453ed583896d..15025baeaefe 100644 --- a/tests/mpi/p4est_save_06.cc +++ b/tests/mpi/p4est_save_06.cc @@ -107,7 +107,7 @@ test() rel_x = x; dh.prepare_for_serialization_of_active_fe_indices(); - soltrans.prepare_serialization(rel_x); + soltrans.prepare_for_serialization(rel_x); tr.save("file"); deallog << "#cells: " << tr.n_global_active_cells() << std::endl From 347ccc84cec2a07720c1f124e2f6eb8483ee4bc6 Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Wed, 27 Mar 2019 09:25:46 -0600 Subject: [PATCH 337/507] fix Trilinos sparsity test output --- ...n=9.with_trilinos=true.with_mpi=true.output | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/tests/trilinos/n_nonzeros_02_parallel.with_p4est=true.mpirun=9.with_trilinos=true.with_mpi=true.output b/tests/trilinos/n_nonzeros_02_parallel.with_p4est=true.mpirun=9.with_trilinos=true.with_mpi=true.output index 6c072d8b3d0c..d0db2a6bd95d 100644 --- a/tests/trilinos/n_nonzeros_02_parallel.with_p4est=true.mpirun=9.with_trilinos=true.with_mpi=true.output +++ b/tests/trilinos/n_nonzeros_02_parallel.with_p4est=true.mpirun=9.with_trilinos=true.with_mpi=true.output @@ -1,26 +1,26 @@ -DEAL:0::0 +DEAL:0::8 -DEAL:1::0 +DEAL:1::8 -DEAL:2::0 +DEAL:2::8 -DEAL:3::0 +DEAL:3::8 -DEAL:4::0 +DEAL:4::8 -DEAL:5::0 +DEAL:5::8 -DEAL:6::0 +DEAL:6::8 -DEAL:7::0 +DEAL:7::8 -DEAL:8::0 +DEAL:8::8 From 51fb2c548ac73121ebe2743d0885a29cadb60bfd Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Wed, 27 Mar 2019 09:29:23 -0600 Subject: [PATCH 338/507] fix warning in ginkgo_solver.cc --- source/lac/ginkgo_solver.cc | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/source/lac/ginkgo_solver.cc b/source/lac/ginkgo_solver.cc index b1e08892ee7d..59335c12da95 100644 --- a/source/lac/ginkgo_solver.cc +++ b/source/lac/ginkgo_solver.cc @@ -297,12 +297,12 @@ namespace GinkgoWrappers # define DECLARE_SOLVER_BASE(ValueType, IndexType) \ class SolverBase - GKO_DEALII_INSTANTIATE_FOR_EACH_VALUE_AND_INDEX_TYPE(DECLARE_SOLVER_BASE); + GKO_DEALII_INSTANTIATE_FOR_EACH_VALUE_AND_INDEX_TYPE(DECLARE_SOLVER_BASE) # undef DECLARE_SOLVER_BASE # define DECLARE_SOLVER_CG(ValueType, IndexType) \ class SolverCG - GKO_DEALII_INSTANTIATE_FOR_EACH_VALUE_AND_INDEX_TYPE(DECLARE_SOLVER_CG); + GKO_DEALII_INSTANTIATE_FOR_EACH_VALUE_AND_INDEX_TYPE(DECLARE_SOLVER_CG) # undef DECLARE_SOLVER_CG } // namespace GinkgoWrappers From 303ac9774a4280382ef6ba289af98f67617efdd8 Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Wed, 27 Mar 2019 09:31:23 -0600 Subject: [PATCH 339/507] CI: fix left-over "pending" If the CI jenkins job ends up starting quicker than the .mark step, we are left with a "pending" github status. Fix this by setting it to green a second time. It is unlikely that the mark step is slower than the whole CI run... --- Jenkinsfile | 2 ++ 1 file changed, 2 insertions(+) diff --git a/Jenkinsfile b/Jenkinsfile index c2b78f390a13..e3068a5a11c3 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -183,6 +183,8 @@ pipeline steps { githubNotify context: 'CI', description: 'OK', status: 'SUCCESS' + // In case the Jenkinsfile.mark job started after we did, make sure we don't leave a pending status around: + githubNotify context: 'ready', description: ':-)', status: 'SUCCESS' } } } From 6e01e776aadc465174f3e0781fca53874594ea9b Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Wed, 27 Mar 2019 14:00:58 -0600 Subject: [PATCH 340/507] extend text output and comments --- tests/trilinos/n_nonzeros_02_parallel.cc | 8 ++++++-- ...=true.mpirun=9.with_trilinos=true.with_mpi=true.output | 8 ++++++++ 2 files changed, 14 insertions(+), 2 deletions(-) diff --git a/tests/trilinos/n_nonzeros_02_parallel.cc b/tests/trilinos/n_nonzeros_02_parallel.cc index b7ee1737ecce..463886c4330d 100644 --- a/tests/trilinos/n_nonzeros_02_parallel.cc +++ b/tests/trilinos/n_nonzeros_02_parallel.cc @@ -15,7 +15,8 @@ -// check n_nonzero_elements() for an empty matrix +// check n_nonzero_elements() for an empty matrix. We generate a few dummy +// non-zero entries. #include @@ -71,8 +72,11 @@ test() TrilinosWrappers::SparseMatrix A; A.reinit(sparsity); - // see how many nonzero elements it reports + // See how many nonzero elements it reports. Note that we have a + // nonlocal Trilinos graph for the off-processor entries and we need + // to enter a few dummy elements: deallog << A.n_nonzero_elements() << std::endl; + A.print(deallog.get_file_stream()); } diff --git a/tests/trilinos/n_nonzeros_02_parallel.with_p4est=true.mpirun=9.with_trilinos=true.with_mpi=true.output b/tests/trilinos/n_nonzeros_02_parallel.with_p4est=true.mpirun=9.with_trilinos=true.with_mpi=true.output index d0db2a6bd95d..de726b1b29bf 100644 --- a/tests/trilinos/n_nonzeros_02_parallel.with_p4est=true.mpirun=9.with_trilinos=true.with_mpi=true.output +++ b/tests/trilinos/n_nonzeros_02_parallel.with_p4est=true.mpirun=9.with_trilinos=true.with_mpi=true.output @@ -1,7 +1,13 @@ DEAL:0::8 +(2,2) 0.00000 +(9,9) 0.00000 +(10,10) 0.00000 DEAL:1::8 +(15,15) 0.00000 +(16,16) 0.00000 +(21,21) 0.00000 DEAL:2::8 @@ -11,9 +17,11 @@ DEAL:3::8 DEAL:4::8 +(46,46) 0.00000 DEAL:5::8 +(51,51) 0.00000 DEAL:6::8 From 4c14fdfc395fe24d83cbf449d8f74fd20dbfbcdb Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Wed, 27 Mar 2019 13:59:52 -0600 Subject: [PATCH 341/507] doc: fix small error --- include/deal.II/dofs/dof_handler.h | 3 ++- include/deal.II/hp/dof_handler.h | 3 ++- 2 files changed, 4 insertions(+), 2 deletions(-) diff --git a/include/deal.II/dofs/dof_handler.h b/include/deal.II/dofs/dof_handler.h index d07ecf0738dd..b3a0b1c1fc1f 100644 --- a/include/deal.II/dofs/dof_handler.h +++ b/include/deal.II/dofs/dof_handler.h @@ -1056,7 +1056,8 @@ class DoFHandler : public Subscriptor * globally, i.e. what n_dofs() returns. * * Each element of the vector returned by this function equals the number of - * elements of the corresponding sets returned by global_dof_indices(). + * elements of the corresponding sets returned by + * locally_owned_dofs_per_processor(). * * If this is a sequential DoFHandler, then the vector has a single element * equal to n_dofs(). (Here, "sequential" means that either the whole program diff --git a/include/deal.II/hp/dof_handler.h b/include/deal.II/hp/dof_handler.h index a35a1f115f21..3bff98e0d14a 100644 --- a/include/deal.II/hp/dof_handler.h +++ b/include/deal.II/hp/dof_handler.h @@ -846,7 +846,8 @@ namespace hp * globally, i.e. what n_dofs() returns. * * Each element of the vector returned by this function equals the number - * of elements of the corresponding sets returned by global_dof_indices(). + * of elements of the corresponding sets returned by + * locally_owned_dofs_per_processor(). * * If this is a sequential DoFHandler, then the vector has a single element * equal to n_dofs(). (Here, "sequential" means that either the whole From 0f1a6e14a12d01bafa5f2cd57a4215c9d5087d9d Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Wed, 27 Mar 2019 14:06:01 -0600 Subject: [PATCH 342/507] rename macro --- source/lac/ginkgo_solver.cc | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/source/lac/ginkgo_solver.cc b/source/lac/ginkgo_solver.cc index 59335c12da95..8223fc6a4d38 100644 --- a/source/lac/ginkgo_solver.cc +++ b/source/lac/ginkgo_solver.cc @@ -289,20 +289,20 @@ namespace GinkgoWrappers } // Explicit instantiations in GinkgoWrappers -# define GKO_DEALII_INSTANTIATE_FOR_EACH_VALUE_AND_INDEX_TYPE(_macro) \ - template _macro(float, int32_t); \ - template _macro(double, int32_t); \ - template _macro(float, int64_t); \ +# define DEALII_INSTANTIATE_FOR_EACH_VALUE_AND_INDEX_TYPE(_macro) \ + template _macro(float, int32_t); \ + template _macro(double, int32_t); \ + template _macro(float, int64_t); \ template _macro(double, int64_t); # define DECLARE_SOLVER_BASE(ValueType, IndexType) \ class SolverBase - GKO_DEALII_INSTANTIATE_FOR_EACH_VALUE_AND_INDEX_TYPE(DECLARE_SOLVER_BASE) + DEALII_INSTANTIATE_FOR_EACH_VALUE_AND_INDEX_TYPE(DECLARE_SOLVER_BASE) # undef DECLARE_SOLVER_BASE # define DECLARE_SOLVER_CG(ValueType, IndexType) \ class SolverCG - GKO_DEALII_INSTANTIATE_FOR_EACH_VALUE_AND_INDEX_TYPE(DECLARE_SOLVER_CG) + DEALII_INSTANTIATE_FOR_EACH_VALUE_AND_INDEX_TYPE(DECLARE_SOLVER_CG) # undef DECLARE_SOLVER_CG } // namespace GinkgoWrappers From 3c62f62c85e65799e04bddb879cdbc45e584362a Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Wed, 27 Mar 2019 19:39:39 -0400 Subject: [PATCH 343/507] Call the new functions instead of copying the implementation --- source/distributed/solution_transfer.cc | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/source/distributed/solution_transfer.cc b/source/distributed/solution_transfer.cc index 0919d7c79804..26e0cb1a70dd 100644 --- a/source/distributed/solution_transfer.cc +++ b/source/distributed/solution_transfer.cc @@ -135,8 +135,7 @@ namespace parallel SolutionTransfer::prepare_serialization( const VectorType &in) { - std::vector all_in(1, &in); - prepare_for_serialization(all_in); + prepare_for_serialization(in); } @@ -146,7 +145,7 @@ namespace parallel SolutionTransfer::prepare_serialization( const std::vector &all_in) { - prepare_for_coarsening_and_refinement(all_in); + prepare_for_serialization(all_in); } From 1fdd88ed1ea5d70662343c1af9d19e2d680815f8 Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Wed, 27 Mar 2019 12:45:33 +0100 Subject: [PATCH 344/507] Rename Solver class to SolverBase. This aligns with the name chosen for the equivalent class in the TrilinosWrappers and PetscWrappers namespaces. --- include/deal.II/lac/eigen.h | 8 ++--- include/deal.II/lac/solver.h | 41 ++++++++++++++-------- include/deal.II/lac/solver_bicgstab.h | 6 ++-- include/deal.II/lac/solver_cg.h | 6 ++-- include/deal.II/lac/solver_fire.h | 6 ++-- include/deal.II/lac/solver_gmres.h | 12 +++---- include/deal.II/lac/solver_minres.h | 6 ++-- include/deal.II/lac/solver_qmrs.h | 6 ++-- include/deal.II/lac/solver_relaxation.h | 4 +-- include/deal.II/lac/solver_richardson.h | 6 ++-- include/deal.II/optimization/solver_bfgs.h | 4 +-- source/lac/solver.inst.in | 2 +- 12 files changed, 60 insertions(+), 47 deletions(-) diff --git a/include/deal.II/lac/eigen.h b/include/deal.II/lac/eigen.h index ec1bc54888ae..7a70296d36a9 100644 --- a/include/deal.II/lac/eigen.h +++ b/include/deal.II/lac/eigen.h @@ -52,7 +52,7 @@ DEAL_II_NAMESPACE_OPEN * @author Guido Kanschat, 2000 */ template > -class EigenPower : private Solver +class EigenPower : private SolverBase { public: /** @@ -131,7 +131,7 @@ class EigenPower : private Solver * @author Guido Kanschat, 2000, 2003 */ template > -class EigenInverse : private Solver +class EigenInverse : private SolverBase { public: /** @@ -208,7 +208,7 @@ template EigenPower::EigenPower(SolverControl & cn, VectorMemory &mem, const AdditionalData & data) - : Solver(cn, mem) + : SolverBase(cn, mem) , additional_data(data) {} @@ -297,7 +297,7 @@ template EigenInverse::EigenInverse(SolverControl & cn, VectorMemory &mem, const AdditionalData & data) - : Solver(cn, mem) + : SolverBase(cn, mem) , additional_data(data) {} diff --git a/include/deal.II/lac/solver.h b/include/deal.II/lac/solver.h index a62ffbabbfe4..c26686af8e65 100644 --- a/include/deal.II/lac/solver.h +++ b/include/deal.II/lac/solver.h @@ -129,7 +129,7 @@ class Vector; * deal.II library for the built-in vector types, but must be explicitly added * for user-provided vector classes. Otherwise, the linker will complain that * it cannot find the constructors and destructors of GrowingVectorMemory that - * happen in the @p Solver class. + * happen in the @p SolverBase class. * * @code * // Definition and implementation of vector class @@ -185,7 +185,7 @@ class Vector; * *

    Observing the progress of linear solver iterations

    * - * The Solver class, being the base class for all of the iterative solvers + * The SolverBase class, being the base class for all of the iterative solvers * such as SolverCG, SolverGMRES, etc, provides the facilities by which actual * solver implementations determine whether the iteration is converged, not * yet converged, or has failed. Typically, this is done using an object of @@ -234,7 +234,7 @@ class Vector; * into this scheme: when a SolverControl object is passed to the constructor * of the current class, we simply connect the SolverControl::check() function * of that object as a slot to the signal we maintain here. In other words, - * since a Solver object is always constructed using a SolverControl object, + * since a SolverBase object is always constructed using a SolverControl object, * there is always at least one slot associated with the signal, namely the * one that determines convergence. * @@ -325,7 +325,7 @@ class Vector; * 2014 */ template > -class Solver : public Subscriptor +class SolverBase : public Subscriptor { public: /** @@ -342,8 +342,8 @@ class Solver : public Subscriptor * responsibility to guarantee that the lifetime of the two arguments is at * least as long as that of the solver object. */ - Solver(SolverControl & solver_control, - VectorMemory &vector_memory); + SolverBase(SolverControl & solver_control, + VectorMemory &vector_memory); /** * Constructor. Takes a control object which evaluates the conditions for @@ -355,7 +355,7 @@ class Solver : public Subscriptor * responsibility to guarantee that the lifetime of the argument is at least * as long as that of the solver object. */ - Solver(SolverControl &solver_control); + SolverBase(SolverControl &solver_control); /** * Connect a function object that will be called periodically within @@ -459,12 +459,24 @@ class Solver : public Subscriptor }; + +/** + * Type definition for the base class for iterative linear solvers. + * This class provides interfaces to a memory pool and the objects that + * determine whether a solver has converged. + * + * @deprecated Use SolverBase instead. + */ +template > +using Solver DEAL_II_DEPRECATED = SolverBase; + + /*-------------------------------- Inline functions ------------------------*/ template inline SolverControl::State -Solver::StateCombiner:: +SolverBase::StateCombiner:: operator()(const SolverControl::State state1, const SolverControl::State state2) const { @@ -481,8 +493,8 @@ operator()(const SolverControl::State state1, template template inline SolverControl::State -Solver::StateCombiner::operator()(const Iterator begin, - const Iterator end) const +SolverBase::StateCombiner::operator()(const Iterator begin, + const Iterator end) const { Assert(begin != end, ExcMessage("You can't combine iterator states if no state is given.")); @@ -499,8 +511,9 @@ Solver::StateCombiner::operator()(const Iterator begin, template -inline Solver::Solver(SolverControl & solver_control, - VectorMemory &vector_memory) +inline SolverBase::SolverBase( + SolverControl & solver_control, + VectorMemory &vector_memory) : memory(vector_memory) { // connect the solver control object to the signal. SolverControl::check @@ -516,7 +529,7 @@ inline Solver::Solver(SolverControl & solver_control, template -inline Solver::Solver(SolverControl &solver_control) +inline SolverBase::SolverBase(SolverControl &solver_control) : // use the static memory object this class owns memory(static_vector_memory) { @@ -534,7 +547,7 @@ inline Solver::Solver(SolverControl &solver_control) template inline boost::signals2::connection -Solver::connect( +SolverBase::connect( const std::function diff --git a/include/deal.II/lac/solver_bicgstab.h b/include/deal.II/lac/solver_bicgstab.h index 90d1d7d46830..5ce13b435d6a 100644 --- a/include/deal.II/lac/solver_bicgstab.h +++ b/include/deal.II/lac/solver_bicgstab.h @@ -121,7 +121,7 @@ namespace internal * */ template > -class SolverBicgstab : public Solver, +class SolverBicgstab : public SolverBase, protected internal::SolverBicgstabData { public: @@ -314,7 +314,7 @@ template SolverBicgstab::SolverBicgstab(SolverControl & cn, VectorMemory &mem, const AdditionalData & data) - : Solver(cn, mem) + : SolverBase(cn, mem) , Vx(nullptr) , Vb(nullptr) , additional_data(data) @@ -325,7 +325,7 @@ SolverBicgstab::SolverBicgstab(SolverControl & cn, template SolverBicgstab::SolverBicgstab(SolverControl & cn, const AdditionalData &data) - : Solver(cn) + : SolverBase(cn) , Vx(nullptr) , Vb(nullptr) , additional_data(data) diff --git a/include/deal.II/lac/solver_cg.h b/include/deal.II/lac/solver_cg.h index 9d1656ca8768..3dc4342adb37 100644 --- a/include/deal.II/lac/solver_cg.h +++ b/include/deal.II/lac/solver_cg.h @@ -93,7 +93,7 @@ class PreconditionIdentity; * @author W. Bangerth, G. Kanschat, R. Becker and F.-T. Suttmeier */ template > -class SolverCG : public Solver +class SolverCG : public SolverBase { public: /** @@ -242,7 +242,7 @@ template SolverCG::SolverCG(SolverControl & cn, VectorMemory &mem, const AdditionalData & data) - : Solver(cn, mem) + : SolverBase(cn, mem) , additional_data(data) {} @@ -250,7 +250,7 @@ SolverCG::SolverCG(SolverControl & cn, template SolverCG::SolverCG(SolverControl &cn, const AdditionalData &data) - : Solver(cn) + : SolverBase(cn) , additional_data(data) {} diff --git a/include/deal.II/lac/solver_fire.h b/include/deal.II/lac/solver_fire.h index b0fdf22bc795..a31e97e7a4c8 100644 --- a/include/deal.II/lac/solver_fire.h +++ b/include/deal.II/lac/solver_fire.h @@ -88,7 +88,7 @@ DEAL_II_NAMESPACE_OPEN * @author Vishal Boddu, Denis Davydov, 2017 */ template > -class SolverFIRE : public Solver +class SolverFIRE : public SolverBase { public: /** @@ -214,7 +214,7 @@ template SolverFIRE::SolverFIRE(SolverControl & solver_control, VectorMemory &vector_memory, const AdditionalData & data) - : Solver(solver_control, vector_memory) + : SolverBase(solver_control, vector_memory) , additional_data(data) {} @@ -223,7 +223,7 @@ SolverFIRE::SolverFIRE(SolverControl & solver_control, template SolverFIRE::SolverFIRE(SolverControl & solver_control, const AdditionalData &data) - : Solver(solver_control) + : SolverBase(solver_control) , additional_data(data) {} diff --git a/include/deal.II/lac/solver_gmres.h b/include/deal.II/lac/solver_gmres.h index 04f9fa48ae40..d5a7d6a76d73 100644 --- a/include/deal.II/lac/solver_gmres.h +++ b/include/deal.II/lac/solver_gmres.h @@ -175,7 +175,7 @@ namespace internal * @author Wolfgang Bangerth, Guido Kanschat, Ralf Hartmann. */ template > -class SolverGMRES : public Solver +class SolverGMRES : public SolverBase { public: /** @@ -457,7 +457,7 @@ class SolverGMRES : public Solver * @author Guido Kanschat, 2003 */ template > -class SolverFGMRES : public Solver +class SolverFGMRES : public SolverBase { public: /** @@ -621,7 +621,7 @@ template SolverGMRES::SolverGMRES(SolverControl & cn, VectorMemory &mem, const AdditionalData & data) - : Solver(cn, mem) + : SolverBase(cn, mem) , additional_data(data) {} @@ -630,7 +630,7 @@ SolverGMRES::SolverGMRES(SolverControl & cn, template SolverGMRES::SolverGMRES(SolverControl & cn, const AdditionalData &data) - : Solver(cn) + : SolverBase(cn) , additional_data(data) {} @@ -1182,7 +1182,7 @@ template SolverFGMRES::SolverFGMRES(SolverControl & cn, VectorMemory &mem, const AdditionalData & data) - : Solver(cn, mem) + : SolverBase(cn, mem) , additional_data(data) {} @@ -1191,7 +1191,7 @@ SolverFGMRES::SolverFGMRES(SolverControl & cn, template SolverFGMRES::SolverFGMRES(SolverControl & cn, const AdditionalData &data) - : Solver(cn) + : SolverBase(cn) , additional_data(data) {} diff --git a/include/deal.II/lac/solver_minres.h b/include/deal.II/lac/solver_minres.h index 845928b743bc..774f21bed4b9 100644 --- a/include/deal.II/lac/solver_minres.h +++ b/include/deal.II/lac/solver_minres.h @@ -69,7 +69,7 @@ DEAL_II_NAMESPACE_OPEN * @author Thomas Richter, 2000, Luca Heltai, 2006 */ template > -class SolverMinRes : public Solver +class SolverMinRes : public SolverBase { public: /** @@ -155,7 +155,7 @@ template SolverMinRes::SolverMinRes(SolverControl & cn, VectorMemory &mem, const AdditionalData &) - : Solver(cn, mem) + : SolverBase(cn, mem) , res2(numbers::signaling_nan()) {} @@ -164,7 +164,7 @@ SolverMinRes::SolverMinRes(SolverControl & cn, template SolverMinRes::SolverMinRes(SolverControl &cn, const AdditionalData &) - : Solver(cn) + : SolverBase(cn) , res2(numbers::signaling_nan()) {} diff --git a/include/deal.II/lac/solver_qmrs.h b/include/deal.II/lac/solver_qmrs.h index 824412cb1260..5e68e3d8e146 100644 --- a/include/deal.II/lac/solver_qmrs.h +++ b/include/deal.II/lac/solver_qmrs.h @@ -92,7 +92,7 @@ DEAL_II_NAMESPACE_OPEN * @author Guido Kanschat, 1999; Ingo Kligge 2017 */ template > -class SolverQMRS : public Solver +class SolverQMRS : public SolverBase { public: /** @@ -255,7 +255,7 @@ template SolverQMRS::SolverQMRS(SolverControl & cn, VectorMemory &mem, const AdditionalData & data) - : Solver(cn, mem) + : SolverBase(cn, mem) , additional_data(data) , step(0) {} @@ -263,7 +263,7 @@ SolverQMRS::SolverQMRS(SolverControl & cn, template SolverQMRS::SolverQMRS(SolverControl & cn, const AdditionalData &data) - : Solver(cn) + : SolverBase(cn) , additional_data(data) , step(0) {} diff --git a/include/deal.II/lac/solver_relaxation.h b/include/deal.II/lac/solver_relaxation.h index dfa17fa1f6d1..e7c7dab87186 100644 --- a/include/deal.II/lac/solver_relaxation.h +++ b/include/deal.II/lac/solver_relaxation.h @@ -56,7 +56,7 @@ DEAL_II_NAMESPACE_OPEN * @date 2010 */ template > -class SolverRelaxation : public Solver +class SolverRelaxation : public SolverBase { public: /** @@ -95,7 +95,7 @@ class SolverRelaxation : public Solver template SolverRelaxation::SolverRelaxation(SolverControl &cn, const AdditionalData &) - : Solver(cn) + : SolverBase(cn) {} diff --git a/include/deal.II/lac/solver_richardson.h b/include/deal.II/lac/solver_richardson.h index b2a59fc34916..417eff4b25ce 100644 --- a/include/deal.II/lac/solver_richardson.h +++ b/include/deal.II/lac/solver_richardson.h @@ -60,7 +60,7 @@ DEAL_II_NAMESPACE_OPEN * @author Ralf Hartmann */ template > -class SolverRichardson : public Solver +class SolverRichardson : public SolverBase { public: /** @@ -175,7 +175,7 @@ template SolverRichardson::SolverRichardson(SolverControl & cn, VectorMemory &mem, const AdditionalData & data) - : Solver(cn, mem) + : SolverBase(cn, mem) , additional_data(data) {} @@ -184,7 +184,7 @@ SolverRichardson::SolverRichardson(SolverControl & cn, template SolverRichardson::SolverRichardson(SolverControl & cn, const AdditionalData &data) - : Solver(cn) + : SolverBase(cn) , additional_data(data) {} diff --git a/include/deal.II/optimization/solver_bfgs.h b/include/deal.II/optimization/solver_bfgs.h index 5f3ed06779fd..aa23dab64d7b 100644 --- a/include/deal.II/optimization/solver_bfgs.h +++ b/include/deal.II/optimization/solver_bfgs.h @@ -53,7 +53,7 @@ DEAL_II_NAMESPACE_OPEN * @author Denis Davydov, 2018 */ template -class SolverBFGS : public Solver +class SolverBFGS : public SolverBase { public: /** @@ -195,7 +195,7 @@ SolverBFGS::AdditionalData::AdditionalData( template SolverBFGS::SolverBFGS(SolverControl & solver_control, const AdditionalData &data) - : Solver(solver_control) + : SolverBase(solver_control) , additional_data(data) {} diff --git a/source/lac/solver.inst.in b/source/lac/solver.inst.in index ada5bbf82062..7ce237dd364c 100644 --- a/source/lac/solver.inst.in +++ b/source/lac/solver.inst.in @@ -17,5 +17,5 @@ for (S : VECTOR_TYPES) { - template class Solver; + template class SolverBase; } From 9680c3081018ac9346c9bb4f671f913e3ae2e562 Mon Sep 17 00:00:00 2001 From: Wolfgang Bangerth Date: Thu, 28 Mar 2019 09:00:42 -0600 Subject: [PATCH 345/507] Allow initialization of Vector with std::initializer_list. --- include/deal.II/lac/vector.h | 35 ++++++++++++++++++++++++++++++++--- 1 file changed, 32 insertions(+), 3 deletions(-) diff --git a/include/deal.II/lac/vector.h b/include/deal.II/lac/vector.h index 5ba965853180..7372650b49cb 100644 --- a/include/deal.II/lac/vector.h +++ b/include/deal.II/lac/vector.h @@ -34,6 +34,7 @@ #include #include +#include #include #include @@ -164,14 +165,34 @@ class Vector : public Subscriptor Vector(Vector &&v) noexcept = default; /** - * Copy constructor taking a vector of another data type. This will fail if - * there is no conversion path from @p OtherNumber to @p Number. Note that - * you may lose accuracy when copying to a vector with data elements with + * Copy constructor taking a vector of another data type. + * + * This constructor will fail to compile if + * there is no conversion path from @p OtherNumber to @p Number. You may + * lose accuracy when copying to a vector with data elements with * less accuracy. */ template explicit Vector(const Vector &v); + /** + * Copy constructor taking an object of type `std::initializer_list`. This + * constructor can be used to initialize a vector using a brace-enclosed + * list of numbers, such as in the following example: + * @code + * Vector v({1,2,3}); + * @endcode + * This creates a vector of size 3, whose (double precision) elements have + * values 1.0, 2.0, and 3.0. + * + * This constructor will fail to compile if + * there is no conversion path from @p OtherNumber to @p Number. You may + * lose accuracy when copying to a vector with data elements with + * less accuracy. + */ + template + explicit Vector(const std::initializer_list &v); + #ifdef DEAL_II_WITH_PETSC /** * Another copy constructor: copy the values from a PETSc vector class. This @@ -1049,6 +1070,14 @@ inline Vector::Vector() +template +template +Vector::Vector(const std::initializer_list &v) + : Vector(v.begin(), v.end()) +{} + + + template template Vector::Vector(const InputIterator first, const InputIterator last) From f0b996c96f16402600fbde5cd31d2e3fbb27573a Mon Sep 17 00:00:00 2001 From: Wolfgang Bangerth Date: Thu, 28 Mar 2019 09:02:07 -0600 Subject: [PATCH 346/507] Add changelog. --- doc/news/changes/minor/20190328Bangerth | 5 +++++ 1 file changed, 5 insertions(+) create mode 100644 doc/news/changes/minor/20190328Bangerth diff --git a/doc/news/changes/minor/20190328Bangerth b/doc/news/changes/minor/20190328Bangerth new file mode 100644 index 000000000000..e53f939f72eb --- /dev/null +++ b/doc/news/changes/minor/20190328Bangerth @@ -0,0 +1,5 @@ +New: The Vector class can now be initialized using an object of type +std::initializer_list. Such objects are, in particular, created when +the compiler sees a brace-enclosed list of numbers. +
    +(Wolfgang Bangerth, 2019/03/28) From 292c1c9bbf890280887e46d1dc944db1f8daacc0 Mon Sep 17 00:00:00 2001 From: Wolfgang Bangerth Date: Thu, 28 Mar 2019 09:07:21 -0600 Subject: [PATCH 347/507] Add a test. --- tests/vector/vector_59.cc | 41 +++++++++++++++++++++++++++++++++++ tests/vector/vector_59.output | 3 +++ 2 files changed, 44 insertions(+) create mode 100644 tests/vector/vector_59.cc create mode 100644 tests/vector/vector_59.output diff --git a/tests/vector/vector_59.cc b/tests/vector/vector_59.cc new file mode 100644 index 000000000000..0f6042e463e1 --- /dev/null +++ b/tests/vector/vector_59.cc @@ -0,0 +1,41 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2004 - 2017 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + + +// check Vector initialization with std::initializer_list objects + +#include + +#include "../tests.h" + + + +int +main() +{ + initlog(); + + Vector vd({1.0, 2.0, 3.0}); + for (const auto &x : vd) + deallog << x << ' '; + deallog << std::endl; + + + Vector vi({1, 2, 3}); + for (const auto &x : vi) + deallog << x << ' '; + deallog << std::endl; +} diff --git a/tests/vector/vector_59.output b/tests/vector/vector_59.output new file mode 100644 index 000000000000..e6f09856b21f --- /dev/null +++ b/tests/vector/vector_59.output @@ -0,0 +1,3 @@ + +DEAL::1.00000 2.00000 3.00000 +DEAL::1.00000 2.00000 3.00000 From cebc4fc676eb5136914d46f95b1e227269c066fe Mon Sep 17 00:00:00 2001 From: Wolfgang Bangerth Date: Thu, 28 Mar 2019 09:23:22 -0600 Subject: [PATCH 348/507] Fix a changelog entry. --- doc/news/changes/minor/20190326Arndt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/news/changes/minor/20190326Arndt b/doc/news/changes/minor/20190326Arndt index 8e9c7ef382d8..6d4bd85a7338 100644 --- a/doc/news/changes/minor/20190326Arndt +++ b/doc/news/changes/minor/20190326Arndt @@ -1,5 +1,5 @@ Changed: parallel::distributed::SolutionTransfer::prepare_serialization() has been deprecated in favor of parallel::distributed::SolutionTransfer::prepare_for_serialization(). - (Daniel Arndt, 2019/03/26) From cb09939b184ba6bdb7f48cc54b9ee1f9d98d73da Mon Sep 17 00:00:00 2001 From: Wolfgang Bangerth Date: Sat, 30 Mar 2019 08:57:31 -0600 Subject: [PATCH 349/507] Use a range-based for loop. --- source/hp/dof_handler.cc | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/source/hp/dof_handler.cc b/source/hp/dof_handler.cc index 307dd6015194..6bfa72ddee6a 100644 --- a/source/hp/dof_handler.cc +++ b/source/hp/dof_handler.cc @@ -1222,8 +1222,8 @@ namespace hp { // unsubscribe as a listener to refinement of the underlying // triangulation - for (unsigned int i = 0; i < tria_listeners.size(); ++i) - tria_listeners[i].disconnect(); + for (auto &connection : tria_listeners) + connection.disconnect(); tria_listeners.clear(); // ...and release allocated memory @@ -1514,8 +1514,8 @@ namespace hp { if (this->tria != &tria) { - for (unsigned int i = 0; i < tria_listeners.size(); ++i) - tria_listeners[i].disconnect(); + for (auto &connection : tria_listeners) + connection.disconnect(); tria_listeners.clear(); this->tria = &tria; From 7f12c2c2ae57a994a876ad8f16518f5ba054c27a Mon Sep 17 00:00:00 2001 From: David Wells Date: Sat, 30 Mar 2019 11:28:27 -0400 Subject: [PATCH 350/507] Fix a comment. There are no blocks in this object. --- include/deal.II/lac/vector.h | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) diff --git a/include/deal.II/lac/vector.h b/include/deal.II/lac/vector.h index 7372650b49cb..f8ff653eae86 100644 --- a/include/deal.II/lac/vector.h +++ b/include/deal.II/lac/vector.h @@ -353,10 +353,7 @@ class Vector : public Subscriptor swap(Vector &v); /** - * Set all components of the vector to the given number @p s. Simply pass - * this down to the individual block objects, but we still need to declare - * this function to make the example given in the discussion about making - * the constructor explicit work. + * Set all components of the vector to the given number @p s. * * Since the semantics of assigning a scalar to a vector are not immediately * clear, this operator should really only be used if you want to set the From 330bd8ca89086258ef78d0a30cdf22c925a9aebe Mon Sep 17 00:00:00 2001 From: David Wells Date: Sat, 30 Mar 2019 11:28:45 -0400 Subject: [PATCH 351/507] Clean up some headers and code samples. --- include/deal.II/lac/vector.h | 18 +++++++++--------- include/deal.II/lac/vector.templates.h | 1 + 2 files changed, 10 insertions(+), 9 deletions(-) diff --git a/include/deal.II/lac/vector.h b/include/deal.II/lac/vector.h index f8ff653eae86..ecddb7674b03 100644 --- a/include/deal.II/lac/vector.h +++ b/include/deal.II/lac/vector.h @@ -32,10 +32,10 @@ #include -#include -#include +#include #include -#include +#include +#include #include DEAL_II_NAMESPACE_OPEN @@ -642,7 +642,7 @@ class Vector : public Subscriptor * If the current vector is called @p v, then this function is the equivalent * to the code * @code - * for (unsigned int i=0; i #include +#include #include #include #include From c9539d49b6976654cd0c9c6c768bbdbda8bb2090 Mon Sep 17 00:00:00 2001 From: David Wells Date: Sat, 30 Mar 2019 11:39:27 -0400 Subject: [PATCH 352/507] Remove '__' from include guards. --- include/deal.II/differentiation/ad/ad_helpers.h | 2 +- include/deal.II/fe/fe_nedelec_sz.h | 4 ++-- include/deal.II/lac/cuda_kernels.templates.h | 4 ++-- include/deal.II/lac/trilinos_tpetra_vector.templates.h | 4 ++-- include/deal.II/matrix_free/cuda_hanging_nodes_internal.h | 4 ++-- 5 files changed, 9 insertions(+), 9 deletions(-) diff --git a/include/deal.II/differentiation/ad/ad_helpers.h b/include/deal.II/differentiation/ad/ad_helpers.h index 507803a0dcf0..8fb914b9be5c 100644 --- a/include/deal.II/differentiation/ad/ad_helpers.h +++ b/include/deal.II/differentiation/ad/ad_helpers.h @@ -4119,4 +4119,4 @@ DEAL_II_NAMESPACE_CLOSE #endif // defined(DEAL_II_WITH_ADOLC) || defined(DEAL_II_TRILINOS_WITH_SACADO) -#endif // dealii__adolc_helpers_h +#endif // dealii_differentiation_ad_ad_helpers_h diff --git a/include/deal.II/fe/fe_nedelec_sz.h b/include/deal.II/fe/fe_nedelec_sz.h index ba5dfbbe1d04..1d93d2e85799 100644 --- a/include/deal.II/fe/fe_nedelec_sz.h +++ b/include/deal.II/fe/fe_nedelec_sz.h @@ -13,8 +13,8 @@ // // --------------------------------------------------------------------- -#ifndef dealii__fe_nedelec_sz_h -#define dealii__fe_nedelec_sz_h +#ifndef dealii_fe_nedelec_sz_h +#define dealii_fe_nedelec_sz_h #include #include diff --git a/include/deal.II/lac/cuda_kernels.templates.h b/include/deal.II/lac/cuda_kernels.templates.h index d42e469329e1..2805692da598 100644 --- a/include/deal.II/lac/cuda_kernels.templates.h +++ b/include/deal.II/lac/cuda_kernels.templates.h @@ -13,8 +13,8 @@ // // --------------------------------------------------------------------- -#ifndef dealii__cuda_kernels_templates_h -#define dealii__cuda_kernels_templates_h +#ifndef dealii_cuda_kernels_templates_h +#define dealii_cuda_kernels_templates_h #include diff --git a/include/deal.II/lac/trilinos_tpetra_vector.templates.h b/include/deal.II/lac/trilinos_tpetra_vector.templates.h index b102775201e3..0a9ba5114115 100644 --- a/include/deal.II/lac/trilinos_tpetra_vector.templates.h +++ b/include/deal.II/lac/trilinos_tpetra_vector.templates.h @@ -13,8 +13,8 @@ // // --------------------------------------------------------------------- -#ifndef dealii__trilinos_tpetra_vector_templates_h -#define dealii__trilinos_tpetra_vector_templates_h +#ifndef dealii_trilinos_tpetra_vector_templates_h +#define dealii_trilinos_tpetra_vector_templates_h #include diff --git a/include/deal.II/matrix_free/cuda_hanging_nodes_internal.h b/include/deal.II/matrix_free/cuda_hanging_nodes_internal.h index d1ae2f745a34..8fcab1a6d219 100644 --- a/include/deal.II/matrix_free/cuda_hanging_nodes_internal.h +++ b/include/deal.II/matrix_free/cuda_hanging_nodes_internal.h @@ -13,8 +13,8 @@ // // --------------------------------------------------------------------- -#ifndef dealii__cuda_hanging_nodes_internal_h -#define dealii__cuda_hanging_nodes_internal_h +#ifndef dealii_cuda_hanging_nodes_internal_h +#define dealii_cuda_hanging_nodes_internal_h #include From 8d35766e0e2d5426a4a9be6e0695ea9082d29f52 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Sun, 31 Mar 2019 01:52:46 +0100 Subject: [PATCH 353/507] Update PETSc version compatibility --- doc/external-libs/petsc.html | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/external-libs/petsc.html b/doc/external-libs/petsc.html index 68a2ac02dbd4..c665079d1764 100644 --- a/doc/external-libs/petsc.html +++ b/doc/external-libs/petsc.html @@ -37,7 +37,7 @@

    Installing deal.II with PETSc

    Note: The most recent version of PETSc that has been reported to be compatible with - deal.II is version 3.9.0. If you use a later + deal.II is version 3.11.0. If you use a later version than this and encounter problems, let us know. deal.II does not support versions of PETSc prior to 3.3.0. From 3ba06905454cc6ad892f3210a5f45d804bb13cbd Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Sat, 30 Mar 2019 11:46:23 -0600 Subject: [PATCH 354/507] CI: archive detailed.log --- Jenkinsfile | 5 ++++- contrib/ci/Jenkinsfile.osx | 4 ++++ 2 files changed, 8 insertions(+), 1 deletion(-) diff --git a/Jenkinsfile b/Jenkinsfile index 81ad227897e4..48064a8afb4f 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -101,6 +101,8 @@ pipeline always { sh "cp /home/dealii/build/Testing/*/*.xml $WORKSPACE/serial.xml || true" xunit tools: [CTest(pattern: '*.xml')] + sh "cp /home/dealii/build/detailed.log $WORKSPACE/detailed-serial.log || true" + archiveArtifacts artifacts: 'detailed-serial.log', fingerprint: true } cleanup { @@ -120,7 +122,6 @@ pipeline sh '''#!/bin/bash export NP=`grep -c ^processor /proc/cpuinfo` export TEST_TIME_LIMIT=1200 - echo $NP mkdir -p /home/dealii/build cd /home/dealii/build cmake -G "Ninja" \ @@ -152,6 +153,8 @@ pipeline always { sh "cp /home/dealii/build/Testing/*/*.xml $WORKSPACE/mpi.xml || true" xunit tools: [CTest(pattern: '*.xml')] + sh "cp /home/dealii/build/detailed.log $WORKSPACE/detailed-mpi.log || true" + archiveArtifacts artifacts: 'detailed-mpi.log', fingerprint: true } cleanup { diff --git a/contrib/ci/Jenkinsfile.osx b/contrib/ci/Jenkinsfile.osx index b9c556d55d02..5ba9af45ec27 100644 --- a/contrib/ci/Jenkinsfile.osx +++ b/contrib/ci/Jenkinsfile.osx @@ -100,6 +100,10 @@ pipeline post { + always + { + archiveArtifacts artifacts: '$WORKSPACE/build/detailed.log', fingerprint: true + } failure { githubNotify context: 'OSX', description: 'build failed', status: 'FAILURE' From cd518ac0c81b75c248e39be671aacfaea80ad732 Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Sat, 30 Mar 2019 21:26:21 -0600 Subject: [PATCH 355/507] fix path --- contrib/ci/Jenkinsfile.osx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/contrib/ci/Jenkinsfile.osx b/contrib/ci/Jenkinsfile.osx index 5ba9af45ec27..c214ca0a8efa 100644 --- a/contrib/ci/Jenkinsfile.osx +++ b/contrib/ci/Jenkinsfile.osx @@ -102,7 +102,7 @@ pipeline { always { - archiveArtifacts artifacts: '$WORKSPACE/build/detailed.log', fingerprint: true + archiveArtifacts artifacts: 'build/detailed.log', fingerprint: true } failure { From ec8ee20122c05905267a98a25ea895fd54cff351 Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Mon, 1 Apr 2019 08:56:15 -0600 Subject: [PATCH 356/507] several doxygen errors and warnings --- doc/doxygen/options.dox.in | 2 ++ examples/step-28/step-28.cc | 3 +- examples/step-43/step-43.cc | 3 +- examples/step-57/step-57.cc | 31 ++++++++++++------- include/deal.II/base/logstream.h | 2 ++ .../deal.II/differentiation/ad/ad_helpers.h | 2 +- include/deal.II/lac/lapack_full_matrix.h | 2 ++ include/deal.II/matrix_free/task_info.h | 5 --- include/deal.II/particles/particle.h | 3 +- 9 files changed, 31 insertions(+), 22 deletions(-) diff --git a/doc/doxygen/options.dox.in b/doc/doxygen/options.dox.in index 14fd142f2385..0bd1c34b8bcd 100644 --- a/doc/doxygen/options.dox.in +++ b/doc/doxygen/options.dox.in @@ -213,6 +213,8 @@ PREDEFINED = DOXYGEN=1 \ DEAL_II_ALWAYS_INLINE= \ __device__= \ DEAL_II_P4EST_VERSION_GTE=1 \ + DEAL_II_SUNDIALS_VERSION_GTE=1 \ + DEAL_II_SUNDIALS_VERSION_LT=0 \ DEAL_II_TRILINOS_VERSION_GTE=1 # do not expand exception declarations diff --git a/examples/step-28/step-28.cc b/examples/step-28/step-28.cc index f0e6b763e3d2..5e6bed8f4217 100644 --- a/examples/step-28/step-28.cc +++ b/examples/step-28/step-28.cc @@ -1233,8 +1233,7 @@ namespace Step28 }; - // @sect4{Implementation of the - // NeutronDiffusionProblem::Parameters class} + // @sect4{Implementation of the Parameters class} // Before going on to the implementation of the outer class, we have to // implement the functions of the parameters structure. This is pretty diff --git a/examples/step-43/step-43.cc b/examples/step-43/step-43.cc index 987b2d6d724a..383bcc2f0fce 100644 --- a/examples/step-43/step-43.cc +++ b/examples/step-43/step-43.cc @@ -78,8 +78,7 @@ namespace Step43 using namespace dealii; - // @sect3{Pressure right hand side, pressure boundary values and saturation - // initial value classes} + // @sect3{Right hand side, boundary and initial value classes} // The following part is taken directly from step-21 so there is no need to // repeat the descriptions found there. diff --git a/examples/step-57/step-57.cc b/examples/step-57/step-57.cc index 112783b0e353..227e84b75f5d 100644 --- a/examples/step-57/step-57.cc +++ b/examples/step-57/step-57.cc @@ -135,16 +135,18 @@ namespace Step57 BlockVector evaluation_point; }; - // @sect3{Boundary values and right hand side} In this problem we set the - // velocity along the upper surface of the cavity to be one and zero on the - // other three walls. The right hand side function is zero so we do not need - // to set the right hand side function in this tutorial. The number of - // components of the boundary function is dim+1. We will - // ultimately use VectorTools::interpolate_boundary_values to set boundary - // values, which requires the boundary value functions to have the same - // number of components as the solution, even if all are not used. Put - // another way: to make this function happy we define boundary values for - // the pressure even though we will never actually use them. + // @sect3{Boundary values and right hand side} + + // In this problem we set the velocity along the upper surface of the cavity + // to be one and zero on the other three walls. The right hand side function + // is zero so we do not need to set the right hand side function in this + // tutorial. The number of components of the boundary function is + // dim+1. We will ultimately use + // VectorTools::interpolate_boundary_values to set boundary values, which + // requires the boundary value functions to have the same number of + // components as the solution, even if all are not used. Put another way: to + // make this function happy we define boundary values for the pressure even + // though we will never actually use them. template class BoundaryValues : public Function { @@ -254,6 +256,7 @@ namespace Step57 // @sect3{StationaryNavierStokes class implementation} // @sect4{StationaryNavierStokes::StationaryNavierStokes} + // // The constructor of this class looks very similar to the one in step-22. The // only difference is the viscosity and the Augmented Lagrangian coefficient // gamma. @@ -268,6 +271,7 @@ namespace Step57 {} // @sect4{StationaryNavierStokes::setup_dofs} + // // This function initializes the DoFHandler enumerating the degrees of freedom // and constraints on the current mesh. template @@ -331,6 +335,7 @@ namespace Step57 } // @sect4{StationaryNavierStokes::initialize_system} + // // On each mesh the SparsityPattern and the size of the linear system // are different. This function initializes them after mesh refinement. template @@ -350,7 +355,7 @@ namespace Step57 } // @sect4{StationaryNavierStokes::assemble} - + // // This function builds the system matrix and right hand side that we // currently work on. The @p initial_step argument is used to determine // which set of constraints we apply (nonzero for the initial step and zero @@ -513,6 +518,7 @@ namespace Step57 } // @sect4{StationaryNavierStokes::solve} + // // In this function, we use FGMRES together with the block preconditioner, // which is defined at the beginning of the program, to solve the linear // system. What we obtain at this step is the solution vector. If this is @@ -728,6 +734,7 @@ namespace Step57 } // @sect4{StationaryNavierStokes::output_results} + // // This function is the same as in step-22 except that we choose a name // for the output file that also contains the Reynolds number (i.e., the // inverse of the viscosity in the current context). @@ -757,6 +764,7 @@ namespace Step57 } // @sect4{StationaryNavierStokes::process_solution} + // // In our test case, we do not know the analytical solution. This function // outputs the velocity components along $x=0.5$ and $0 \leq y \leq 1$ so they // can be compared with data from the literature. @@ -788,6 +796,7 @@ namespace Step57 } // @sect4{StationaryNavierStokes::run} + // // This is the last step of this program. In this part, we generate the grid // and run the other functions respectively. The max refinement can be set by // the argument. diff --git a/include/deal.II/base/logstream.h b/include/deal.II/base/logstream.h index ee03ae5f672e..316e1b5ed98b 100644 --- a/include/deal.II/base/logstream.h +++ b/include/deal.II/base/logstream.h @@ -145,6 +145,8 @@ class LogStream : public Subscriptor /** * Enable output to a second stream o. * + * @param o Attach this output stream. + * * @param[in] print_job_id Whether or not the JobIdentifier for the current * process should be printed to the stream. * diff --git a/include/deal.II/differentiation/ad/ad_helpers.h b/include/deal.II/differentiation/ad/ad_helpers.h index 8fb914b9be5c..13844113c2c7 100644 --- a/include/deal.II/differentiation/ad/ad_helpers.h +++ b/include/deal.II/differentiation/ad/ad_helpers.h @@ -2383,7 +2383,7 @@ namespace Differentiation * the input FEValuesExtractors::SymmetricTensor @p extractor_symm_tensor. * If the @p ignore_symmetries is set true, then all * component of the tensor are considered to be independent. If set to - * code>false, then the set of returned indices will contain + * false, then the set of returned indices will contain * duplicate entries for components that are symmetric. */ template diff --git a/include/deal.II/lac/lapack_full_matrix.h b/include/deal.II/lac/lapack_full_matrix.h index 802a40c9d7e6..542ee4926b33 100644 --- a/include/deal.II/lac/lapack_full_matrix.h +++ b/include/deal.II/lac/lapack_full_matrix.h @@ -866,6 +866,8 @@ class LAPACKFullMatrix : public TransposeTable * * The parameters allow for a flexible setting of the output format: * + * @param out This specifies the stream to write to. + * * @param precision denotes the number of trailing digits. * * @param scientific is used to determine the number format, where diff --git a/include/deal.II/matrix_free/task_info.h b/include/deal.II/matrix_free/task_info.h index d7d973a22beb..86961db0c5ee 100644 --- a/include/deal.II/matrix_free/task_info.h +++ b/include/deal.II/matrix_free/task_info.h @@ -231,11 +231,6 @@ namespace internal * represented by a chunk of cells. The cell chunks are formed before * subdivision into partitions and colors. * - * @param cell_active_fe_index The active FE index corresponding to the - * individual indices in the list of all cell indices, in order to be - * able to not place cells with different indices into the same cell - * batch with vectorization. - * * @param connectivity (in/out) Determines whether cells `i` and `j` are * conflicting, expressed by an entry in position (i,j). * diff --git a/include/deal.II/particles/particle.h b/include/deal.II/particles/particle.h index df6ebd17418e..178e57959b59 100644 --- a/include/deal.II/particles/particle.h +++ b/include/deal.II/particles/particle.h @@ -147,7 +147,8 @@ namespace Particles * contains serialized data of the same length and type that is allocated * by @p property_pool. */ - Particle(const void *&begin_data, PropertyPool *const = nullptr); + Particle(const void *& begin_data, + PropertyPool *const property_pool = nullptr); /** * Move constructor for Particle, creates a particle from an existing From 3a1f07a685b04e58ad66a70d37fc748d05eb3b71 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Tue, 2 Apr 2019 05:22:36 +0200 Subject: [PATCH 357/507] Unify intrinsics headers --- include/deal.II/base/vectorization.h | 15 +++++---------- 1 file changed, 5 insertions(+), 10 deletions(-) diff --git a/include/deal.II/base/vectorization.h b/include/deal.II/base/vectorization.h index 1b8c47005c3c..39b374b23ff0 100644 --- a/include/deal.II/base/vectorization.h +++ b/include/deal.II/base/vectorization.h @@ -51,15 +51,9 @@ "Mismatch in vectorization capabilities: AVX-512F was detected during configuration of deal.II and switched on, but it is apparently not available for the file you are trying to compile at the moment. Check compilation flags controlling the instruction set, such as -march=native." #endif -#if DEAL_II_COMPILER_VECTORIZATION_LEVEL >= 2 && \ - (defined(__AVX__) || defined(__AVX512F__)) // AVX, AVX-512 -# include -#elif DEAL_II_COMPILER_VECTORIZATION_LEVEL == 1 && defined(__SSE2__) // SSE2 -# include -#endif - - -#if DEAL_II_COMPILER_VECTORIZATION_LEVEL >= 1 && defined(__ALTIVEC__) +#if defined(_MSC_VER) +# include +#elif defined(__ALTIVEC__) # include // altivec.h defines vector, pixel, bool, but we do not use them, so undefine @@ -67,7 +61,8 @@ # undef vector # undef pixel # undef bool - +#else +# include #endif DEAL_II_NAMESPACE_OPEN From fb6d449bdfac47f9fc8eca0b34be94f0d5aa32d6 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 2 Apr 2019 16:11:44 +0200 Subject: [PATCH 358/507] set LAPACK_INCLUDE_DIRS and LAPACK_USER_INCLUDE_DIRS --- cmake/modules/FindLAPACK.cmake | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/cmake/modules/FindLAPACK.cmake b/cmake/modules/FindLAPACK.cmake index 0d79cc018e20..4227e2c13f09 100644 --- a/cmake/modules/FindLAPACK.cmake +++ b/cmake/modules/FindLAPACK.cmake @@ -90,6 +90,7 @@ FOREACH(_lib ${_fortran_libs}) ENDFOREACH() +SET(_lapack_include_dirs ${LAPACK_INCLUDE_DIRS}) SET(_lapack_libraries ${LAPACK_LIBRARIES}) SET(_lapack_linker_flags ${LAPACK_LINKER_FLAGS}) DEAL_II_PACKAGE_HANDLE(LAPACK @@ -97,6 +98,10 @@ DEAL_II_PACKAGE_HANDLE(LAPACK REQUIRED _lapack_libraries OPTIONAL BLAS_LIBRARIES ${_additional_libraries} LINKER_FLAGS OPTIONAL _lapack_linker_flags BLAS_LINKER_FLAGS + INCLUDE_DIRS + OPTIONAL _lapack_include_dirs + USER_INCLUDE_DIRS + OPTIONAL _lapack_include_dirs CLEAR atlas_LIBRARY atlcblas_LIBRARY atllapack_LIBRARY blas_LIBRARY eigen_blas_LIBRARY f77blas_LIBRARY gslcblas_LIBRARY lapack_LIBRARY From 16e66fd8c42842e5bd8a275ed54a480d2b76befc Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Wed, 20 Mar 2019 15:19:41 +0100 Subject: [PATCH 359/507] Add SymEngine macros to config.h --- include/deal.II/base/config.h.in | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/include/deal.II/base/config.h.in b/include/deal.II/base/config.h.in index 0a229133db69..0ba349af2709 100644 --- a/include/deal.II/base/config.h.in +++ b/include/deal.II/base/config.h.in @@ -61,6 +61,7 @@ #cmakedefine DEAL_II_WITH_SCALAPACK #cmakedefine DEAL_II_WITH_SLEPC #cmakedefine DEAL_II_WITH_SUNDIALS +#cmakedefine DEAL_II_WITH_SYMENGINE #cmakedefine DEAL_II_WITH_THREADS #cmakedefine DEAL_II_WITH_TRILINOS #cmakedefine DEAL_II_WITH_UMFPACK @@ -177,6 +178,9 @@ /* cmake/modules/FindSUNDIALS.cmake */ #cmakedefine DEAL_II_SUNDIALS_WITH_IDAS +/* cmake/modules/FindSYMENGINE.cmake */ +#cmakedefine DEAL_II_SYMENGINE_WITH_LLVM + /* cmake/configure/configure_1_threads.cmake */ #cmakedefine DEAL_II_USE_MT_POSIX #cmakedefine DEAL_II_USE_MT_POSIX_NO_BARRIERS From 534cfa1c2f777ec0a48f8e1d8a3e7338c85589eb Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Sat, 30 Mar 2019 11:18:46 +0100 Subject: [PATCH 360/507] Add traits for SD numbers --- include/deal.II/differentiation/sd.h | 46 +++++++++ .../sd/symengine_number_traits.h | 95 +++++++++++++++++++ 2 files changed, 141 insertions(+) create mode 100644 include/deal.II/differentiation/sd.h create mode 100644 include/deal.II/differentiation/sd/symengine_number_traits.h diff --git a/include/deal.II/differentiation/sd.h b/include/deal.II/differentiation/sd.h new file mode 100644 index 000000000000..f2707cbfc601 --- /dev/null +++ b/include/deal.II/differentiation/sd.h @@ -0,0 +1,46 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + +#ifndef dealii_differentiation_sd_h +#define dealii_differentiation_sd_h + +#include + +#ifdef DEAL_II_WITH_SYMENGINE + +# include +# include +# include + +DEAL_II_NAMESPACE_OPEN + +namespace Differentiation +{ + /** + * Wrappers for symbolic differentiation libraries. Currently there is support + * for the following libraries: + * - SymEngine + * + * @ingroup auto_symb_diff + */ + namespace SD + {} +} // namespace Differentiation + +DEAL_II_NAMESPACE_CLOSE + +#endif // DEAL_II_WITH_SYMENGINE + +#endif // dealii_differentiation_sd_h diff --git a/include/deal.II/differentiation/sd/symengine_number_traits.h b/include/deal.II/differentiation/sd/symengine_number_traits.h new file mode 100644 index 000000000000..295584a9bb04 --- /dev/null +++ b/include/deal.II/differentiation/sd/symengine_number_traits.h @@ -0,0 +1,95 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + +#ifndef dealii_differentiation_sd_symengine_number_traits_h +#define dealii_differentiation_sd_symengine_number_traits_h + +#include + +#ifdef DEAL_II_WITH_SYMENGINE + +# include + +# include + + +DEAL_II_NAMESPACE_OPEN + + +namespace Differentiation +{ + namespace SD + { + /** + * A struct to indicate whether a given @p NumberType is a supported + * symbolically differentiable number or not. By default, numbers are not + * considered to have the necessary characteristics to fulfill this + * condition. + * + * @author Jean-Paul Pelteret, 2019 + */ + template + struct is_sd_number : std::false_type + {}; + + + /** + * A struct to indicate whether a given @p NumberType is a supported + * SymEngine number or not. By default, numbers are not + * considered to have the necessary characteristics to fulfill this + * condition. + * + * @author Jean-Paul Pelteret, 2019 + */ + template + struct is_symengine_number : std::false_type + {}; + + + /*--- SymEngine Expression class ---*/ + + + /** + * A struct to indicate whether a given @p NumberType is a supported + * symbolically differentiable number or not. + * This is a specialization for the SymEngine Expression class. + * + * @author Jean-Paul Pelteret, 2019 + */ + template <> + struct is_symengine_number : std::true_type + {}; + + + /** + * A struct to indicate whether a given @p NumberType is a supported + * symbolically differentiable number or not. + * This is a specialization for the SymEngine Expression class. + * + * @author Jean-Paul Pelteret, 2019 + */ + template <> + struct is_sd_number : std::true_type + {}; + + } // namespace SD +} // namespace Differentiation + + +DEAL_II_NAMESPACE_CLOSE + +#endif // DEAL_II_WITH_SYMENGINE + +#endif // dealii_differentiation_sd_symengine_number_traits_h From 9386bc34a4c2b7f1821d070b3f8136eb8ac861ac Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Sat, 30 Mar 2019 11:19:55 +0100 Subject: [PATCH 361/507] Add basis for SymEngine (SD) wrappers - Types - Expression class - Utilities --- .../changes/major/20190329Jean-PaulPelteret | 16 + .../sd/symengine_number_types.h | 1302 +++++++++++++++++ .../differentiation/sd/symengine_types.h | 81 + .../differentiation/sd/symengine_utilities.h | 62 + source/differentiation/CMakeLists.txt | 3 +- source/differentiation/sd/CMakeLists.txt | 32 + .../sd/symengine_number_types.cc | 541 +++++++ source/differentiation/sd/symengine_types.cc | 55 + .../differentiation/sd/symengine_utilities.cc | 63 + 9 files changed, 2154 insertions(+), 1 deletion(-) create mode 100644 doc/news/changes/major/20190329Jean-PaulPelteret create mode 100644 include/deal.II/differentiation/sd/symengine_number_types.h create mode 100644 include/deal.II/differentiation/sd/symengine_types.h create mode 100644 include/deal.II/differentiation/sd/symengine_utilities.h create mode 100644 source/differentiation/sd/CMakeLists.txt create mode 100644 source/differentiation/sd/symengine_number_types.cc create mode 100644 source/differentiation/sd/symengine_types.cc create mode 100644 source/differentiation/sd/symengine_utilities.cc diff --git a/doc/news/changes/major/20190329Jean-PaulPelteret b/doc/news/changes/major/20190329Jean-PaulPelteret new file mode 100644 index 000000000000..d5f571d8fab3 --- /dev/null +++ b/doc/news/changes/major/20190329Jean-PaulPelteret @@ -0,0 +1,16 @@ +New: A new class Differentiation::SD::Expression has been added. which allows +the creation and manipulation of scalar symbolic functions using the SymEngine +library. It will later be used as the basis of symbolic tensor calculus, amongst +other things. It incorporates numerous features, which currently include: +

      +
    • expression parsing,
      • +
    • comparison operations,
      • +
    • logical operations,
      • +
    • basic math operations,
      • +
    • conditional expression construction,
      • +
    • differentiation,
      • +
    • substitution (partial and complete), and
      • +
    • serialization.
      • +
    +
    +(Jean-Paul Pelteret, 2019/03/29) diff --git a/include/deal.II/differentiation/sd/symengine_number_types.h b/include/deal.II/differentiation/sd/symengine_number_types.h new file mode 100644 index 000000000000..b3a487dcb2c6 --- /dev/null +++ b/include/deal.II/differentiation/sd/symengine_number_types.h @@ -0,0 +1,1302 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + +#ifndef dealii_differentiation_sd_symengine_number_types_h +#define dealii_differentiation_sd_symengine_number_types_h + +#include + +#ifdef DEAL_II_WITH_SYMENGINE + +// Low level +# include +# include +# include +# include + +// Number types +# include +# include +# include +# include + +// Number operations +# include +# include +# include +# include + +// Evaluation +# include +# include +# include + +// Differentiation +# include + +# include +# include + +# include + +# include +# include +# include +# include +# include +# include + +DEAL_II_NAMESPACE_OPEN + +namespace Differentiation +{ + namespace SD + { + namespace SE = ::SymEngine; + + /** + * @addtogroup Exceptions + * @{ + */ + + /** + * An exception to indicate that the string sent to the SymEngine + * parser is not valid. + */ + DeclException1( + ExcSymEngineParserError, + std::string, + << "The string '" << arg1 + << "' could not be parsed successfully. Are you sure that (1) it " + << "consists of legitimate operations and syntax, and (2) you've " + << "previously declared all symbolic variables that are present " + << "in the expression?"); + + //@} + + /** + * A class to wrap SymEngine expressions. + * + * With this number type, SymEngine numbers can be used to perform scalar + * and tensor mathematics in deal.II. It (or the SymEngine::Expression + * class, of which it stores an instance) therefore forms the basis of + * symbolic computation via SymEngine in deal.II. With it one can + * perform symbolic differentiation and subsequent substitution with both + * scalars and deal.II's native Tensor and SymmetricTensor types. + * + * The symbolic features that this class supports includes: + * - expression parsing, + * - comparison operations, + * - logical operations, + * - math operations, + * - conditional expression construction, + * - differentiation, + * - substitution (partial and complete), and + * - serialization. + * + * A simple example of how this class may be used is as follows: + * @code + * // Constructing a symbolic expression: + * // This is a symbol, which we will treat as an argument to a symbolic + * // function. + * const Expression x("x"); + * const Expression y("y"); + * // This is a symbolic expression, which is an expression constructed + * // from individual symbols. + * const Expression f = (x + y)*(x + y); + * + * // Value substitution + * types::substitution_map substitution_map; + * substitution_map[x] = Expression(1); + * substitution_map[y] = Expression(2.5); + * const double evaluated_f = + * f.substitute_and_evaluate(substitution_map); + * // We could also have performed substitution of each individual + * // argument, if we wanted to. This means that one can partially + * // substitute an expression at any time. + * @endcode + * + * A more intricate example of conditional evaluation is as follows: + * @code + * // Construct symbolic expressions + * const Expression x("x"); + * const Expression y("y"); + * const Expression f_plus = (x + y)*(x + y); + * // Parsing expressions from a string is also possible. Its arguments + * // must have been previously declared through (and in scope). + * const Expression f_minus ("(x-y)*(x-y)", true); + * + * // Constructing a conditional expression + * const SD_number_t f((x > Expression(0.0)), f_plus, f_minus); + * + * // Value substitution + * types::substitution_map substitution_map; + * substitution_map[x] = Expression(1); + * substitution_map[y] = Expression(2.5); + * const double evaluated_f = + * f.substitute_and_evaluate(substitution_map); + * // Since the substituted value for x was greater than zero, we expect + * // that the returned result now in evaluated_f was evaluated from + * // the function f_plus. + * @endcode + * + * Lastly, here is an example using symbolic differentiation: + * @code + * // Construct symbolic expressions + * const Expression x("x"); + * const Expression f("x**2", true); + * + * // Now perform differentiation. Specifically, we differentiate the + * // function "f" with respect to the symbolic variable "x". + * // The result should be the expression "2*x". + * const Expression df_dx = f.differentiate(x); + * + * // Value substitution + * types::substitution_map substitution_map; + * substitution_map[x] = Expression(10.0); + * const double evaluated_df_dx = + * evaluated_df_dx.substitute_and_evaluate(substitution_map); + * // We can expect the above to evaluate to "2*10" which is, + * // of course, the numeric value 20. + * @endcode + * + * @author Jean-Paul Pelteret, 2019 + */ + class Expression + { + public: + /** + * @name Constructors + */ + //@{ + + /** + * Default constructor. + */ + Expression(); + + /** + * Constructor for boolean types. + * + * @note This constructor is marked as explicit so that there are no + * potential ambiguities related to implicit conversions in either user + * code or math functions that are loaded into the standard namespace. + */ + explicit Expression(const bool &value); + + /** + * Constructor for arithmetic number types. + * + * @note This constructor is marked as explicit so that there are no + * potential ambiguities related to implicit conversions in either user + * code or math functions that are loaded into the standard namespace. + */ + template ::value>::type> + explicit Expression(const NumberType &value); + + /** + * Constructor for complex numbers templated on arithmetic number types. + * + * @note This constructor is marked as explicit so that there are no + * potential ambiguities related to implicit conversions in either user + * code or math functions that are loaded into the standard namespace. + */ + template ::value>::type> + explicit Expression(const std::complex &value); + + /** + * Constructor for integer types. + */ + Expression(const SE::integer_class &value); + + /** + * Constructor for rational types. + * + * It is expected that both the @p numerator and @p denominator + * be integral types. + */ + template ::value>::type> + Expression(const NumberType &numerator, const NumberType &denominator); + + /** + * Constructor for rational types. + */ + Expression(const SE::rational_class &value); + + /** + * Constructor for a piecewise defined function. + * + * The generated expression may be interpreted as the result of the + * teniary operator, i.e. + * (condition ? expression_if_true : expression_if_false). + * + * The @p condition can be any expression that renders an expression that + * is convertible to a SymEngine::Boolean operator. This includes: + * - the logical operators of the deal.II Expression class + * - SymEngine::boolean() + * - SymEngine::contains() + * - SymEngine::Eq() + * - SymEngine::Ne() + * - SymEngine::Ge() + * - SymEngine::Gt() + * - SymEngine::Le() + * - SymEngine::Lt() + * - SymEngine::logical_and() + * - SymEngine::logical_nand() + * - SymEngine::logical_or() + * - SymEngine::logical_not() + * - SymEngine::logical_nor() + * - SymEngine::logical_xor() + * - SymEngine::logical_xnor() + * - ... + * + * An example of this constructor's use is as follows: + * @code + * const Expression x("x"); + * const Expression y("y"); + * + * // Construct a conditional expression using the symbolic variables. + * const Expression f ((x < Expression(0.0)), x+y, x-y); + * @endcode + */ + Expression(const Expression &condition, + const Expression &expression_if_true, + const Expression &expression_if_false); + + /** + * Constructor for a piecewise defined function. + * + * The generated expression may be interpreted as the result of the + * set of nested if-elseif-else statements, i.e. (in pseudo-code) + * @code + * if (condition_expression[0].first == true) + * return condition_expression[0].second; + * else if (condition_expression[1].first == true) + * return condition_expression[1].second; + * else if (...) + * return ...; + * else + * return expression_otherwise; + * @endcode + * if the input vector has more than 2 elements. + * + * This variant takes the piecewise evaluated conditions and its results + * as the first argument, and the default return value as the second + * argument. + */ + Expression(const std::vector> + & condition_expression, + const Expression &expression_otherwise); + + /** + * Constructor for a piecewise defined function. + * + * The generated expression may be interpreted as the result of the + * set of nested if-elseif statements, i.e. (in pseudo-code) + * @code + * if (condition_expression[0].first == true) + * return condition_expression[0].second; + * else if (condition_expression[1].first == true) + * return condition_expression[1].second; + * else if (...) + * return ...; + * @endcode + * if the input vector has more than 2 elements. + * + * This variant takes only the piecewise evaluated conditions and its + * results. If none of the conditions are met upon evaluation then the + * returned result will be NaN. + */ + Expression(const std::vector> + &condition_expression); + + + /** + * Constructor for symbolic types. + * + * This constructor initializes a symbolic type with a character array + * representing its symbolic value. + */ + Expression(const char *symbol); + + /** + * Constructor for symbolic types. + * + * This constructor initializes a symbolic type with a string + * representing its symbolic value. + * If the @p parse_as_expression flag is false, then the + * @p symb_expr (potentially composed of mulitple characters) will be + * interpreted as a single symbol. + * If the @p parse_as_expression flag is true, then the + * @p symb_expr will be parsed as a symbolic expression (potentially + * composed of multiple symbols, constants, etc.). + */ + Expression(const std::string &symb_expr, + const bool parse_as_expression = false); + + /** + * Constructor for function symbol types. + * + * This constructor initializes a function symbol with a string + * representing its symbolic name. + */ + Expression(const std::string & symbol_func, + const types::symbol_vector &arguments); + + /** + * Copy constructor. + */ + Expression(const Expression &rhs) = default; + + /** + * Copy constructor. + * + * @note This constructor is marked as explicit to prevent any ambiguities + * from implicit conversion when both the deal.II and SymEngine namespaces + * are imported. + */ + explicit Expression(const SE::Expression &rhs); + + /** + * Copy constructor. + * + * This allows us to create our class straight from the results of + * SymEngine operations. This is especially important for operations like + * "diff", because the returned result is not primitive, but rather a set + * of compound operations. + */ + Expression(const SE::RCP &rhs); + + /** + * Move constructor. + */ + Expression(Expression &&rhs) = default; + + /** + * Move constructor. + * + * This allows us to create our class straight from the results of + * SymEngine operations. This is especially important for operations like + * "diff", because the returned result is not primitive, but rather a set + * of compound operations. + */ + Expression(SE::RCP &&rhs); + + /** + * Destructor. + */ + virtual ~Expression() = default; + + //@} + + /** + * Utilities + */ + //@{ + + /** + * Parse an expression from a string representing a symbolic @p expression. + * This overwrites any existing value or expression that this object + * represents. + */ + Expression & + parse(const std::string &expression); + + /** + * Print the value stored by this object. + * + * Since the stored value could be one of a number of types, we leave + * SymEngine to cast and output the correct representation of the data. + */ + std::ostream & + print(std::ostream &stream) const; + + /** + * Save the value stored by this object to the @p stream. + * + * Each expression will be saved on a new line of the @p stream. + */ + void + save(std::ostream &stream) const; + + /** + * Load the value stored in the @p stream into this object. + * + * It is expected that each expression appears on its own on single + * line of @p stream. + * + * @note When loading a symbolic expression, it is imperative that + * you first create or load all of the symbolic variables used in + * the saved expression. + */ + void + load(std::istream &stream); + + /** + * Write and read the data of this object from a stream for the purpose + * of serialization. + * + * This effecively saves or loads the value stored into/out of the + * @p archive with the given @p version number into this object. + * If deserializing data, then the previous contents of this object + * are thrown away. + * + * @note When deserializing a symbolic expression, it is imperative that + * you first create or deserialize all of the symbolic variables used in + * the serialized expression. + */ + template + void + serialize(Archive &archive, const unsigned int version); + + //@} + + /** + * @name Values + */ + //@{ + + /** + * Return the value or expression that this class instance represents. + */ + const SE::Expression & + get_expression() const; + + /** + * Return the primitive SymEngine data type that stores the value or + * expression represented by this object. + */ + const SE::Basic & + get_value() const; + + /** + * Return the pointer to the primitive SymEngine data type that stores + * the value or expression represented by this object. + */ + const SE::RCP & + get_RCP() const; + + //@} + + /** + * @name Math and relational operators with (potentially) symbolic types + */ + //@{ + + /** + * Assignment operator. + * + * Sets the data of this object's @p expression equal + * to that of the @p rhs object. + */ + Expression & + operator=(const Expression &rhs); + + /** + * Assignment operator. + * + * Sets the data of this object's @p expression equal + * to that of the @p rhs object. + */ + Expression & + operator=(Expression &&rhs); + + /** + * Addition assignment. + * + * The @p rhs @p expression is added in-place to that of + * this object's @p expression. + */ + Expression & + operator+=(const Expression &rhs); + + /** + * Subtraction assignment. + * + * The @p rhs @p expression is subtracted in-place from that of + * this object's @p expression. + */ + Expression & + operator-=(const Expression &rhs); + + /** + * Multiplication assignment. + * + * This object's @p expression is multiplied in-place by that of + * the @p rhs @p expression. + */ + Expression & + operator*=(const Expression &rhs); + + /** + * Division assignment. + * + * This object's @p expression is divided in-place by that of + * the @p rhs @p expression. + */ + Expression & + operator/=(const Expression &rhs); + + //@} + + /** + * @name Math and relational operators with numeric types + */ + //@{ + + /** + * Assignment operator. + * + * Set the data of this object's @p expression equal + * to the numerical value of the @p rhs. + */ + template + Expression & + operator=(const NumberType &rhs); + + /** + * Negation operator. + * + * Return a the result of pre-multipying this object's @p expression + * by -1. + * + * @note This operation is not performed in-place. + */ + Expression + operator-() const; + + /** + * Addition assignment. + * + * The numerical value of the @p rhs is added in-place to that of + * this object's @p expression. + */ + template + Expression & + operator+=(const NumberType &rhs); + + /** + * Subtraction assignment. + * + * The numerical value of the @p rhs is subtracted in-place from that of + * this object's @p expression. + */ + template + Expression & + operator-=(const NumberType &rhs); + + /** + * Multiplication assignment. + * + * This object's @p expression is multiplied in-place by that of + * the numerical value of the @p rhs. + */ + template + Expression & + operator*=(const NumberType &rhs); + + /** + * Division assignment. + * + * This object's @p expression is divided in-place by that of + * the numerical value of the @p rhs. + */ + template + Expression & + operator/=(const NumberType &rhs); + + //@} + + /** + * @name Differentiation + */ + //@{ + + /** + * Return the derivative of this object's @p expression + * with respect to the given @p symbol. + */ + Expression + differentiate(const Expression &symbol) const; + + /** + * Return the derivative of this object's @p expression + * with respect to the given @p symbol. + */ + Expression + differentiate(const SE::RCP &symbol) const; + + /** + * Return the derivative of this object's @p expression + * with respect to the potential @p symbol. + */ + Expression + differentiate(const SE::RCP &symbol) const; + + //@} + + /** + * @name Dictionary-based substitution + */ + //@{ + + /** + * Perform substitution of all symbols found in this object's @p expression + * that match a key in the @p substitution_values map. + * + * @note The replacement value (the entry in the @p substitution_values + * that is paired with a key) need not necessarily be numerical, but may + * also be another symbolic type. + * + * @note With dictionary substitution, partial substitution is allowed + * (i.e. an incomplete substitution map can be used and the return type + * can be symbolic). + */ + Expression + substitute(const types::substitution_map &substitution_values) const; + + /** + * Perform substitution of all symbols found in this object's @p expression + * that match the @p symbol. Each @p symbol will be substituted with + * the given @p value. + * + * @note With dictionary substitution, partial substitution is allowed + * (i.e. an incomplete substitution map can be used and the return type + * can be symbolic). + */ + Expression + substitute(const Expression &symbol, const Expression &value) const; + + /** + * Perform substitution of all symbols found in this object's @p expression + * that match the @p symbol. Each @p symbol will be substituted with + * the given @p value. + * + * @note With dictionary substitution, partial substitution is allowed + * (i.e. an incomplete substitution map can be used and the return type + * can be symbolic). + */ + template + Expression + substitute(const Expression &symbol, const NumberType &value) const; + + /** + * Full substitution and evaluation. This creates a Expression by + * symbol substitution and then immediately computes its numerical value. + * + * @note All symbols must be resolved by the substitution map in order + * for this function to return successfully. + */ + template + ReturnType + substitute_and_evaluate( + const types::substitution_map &substitution_values) const; + + //@} + + /** + * @name Conversion operators + */ + //@{ + + /** + * Conversion operator for real integer or floating point values, and + * complex integer or floating point values. + * + * @note This function is marked explicit so that the conversion must be + * performed using a static_cast. In normal use, one would have expected + * (Expression)*(double) --> (Expression) + * If this function were not marked as explicit, then we could potentially + * have + * (Expression)*(double) --> (double) + * So, to get out a value on needs to do the following: + * + * + * const NumberType val = static_cast(Expression); + * + * + * or, probably less desirably, + * + * + * const NumberType val = NumberType(Expression); + * + * + * @note If the underlying number is a custom type (i.e. encapsulated by a + * NumberWrapper), then it is necessary to derive a new class from + * Expression and define a specialized conversion operator + * that calls an Evaluator that is specialized for this custom number + * type. This could be achieved with an overriding conversion function + * in the base class, for example: + * + * + * class MyNumber : public Expression + * { + * ... + * template + * explicit operator ResultType() const + * { + * if (this->get_value()->get_type_code() == SE::NUMBER_WRAPPER) + * { + * // Implement custom evaluation function + * const ResultType result = ...; + * return result; + * } + * else + * // Call base class conversion operator + * return Expression::operator ResultType(); + * } + * } + * + */ + template + explicit operator ResultType() const; + + /** + * Conversion operator that returns the value or expression that this + * class instance represents. + */ + explicit operator const SE::Expression &() const; + + /** + * Conversion operator that returns a SymEngine reference counted pointer + * to the fundamental type. + */ + operator const SE::RCP &() const; + + //@} + + protected: + /** + * Return the value or expression that this class instance represents. + */ + SE::Expression & + get_expression(); + + private: + /** + * The value or expression that this instance of this class is to + * represent. + */ + SE::Expression expression; + }; + + /** + * @name Type traits + */ + //@{ + + /** + * A struct to indicate whether a given @p NumberType is a supported + * symbolically differentiable number or not. + * This is a specialization for the deal.II Expression class. + * + * @author Jean-Paul Pelteret, 2019 + */ + template <> + struct is_symengine_number : std::true_type + {}; + + + /** + * A struct to indicate whether a given @p NumberType is a supported + * SymEngine number or not. + * This is a specialization for the deal.II Expression class. + * + * @author Jean-Paul Pelteret, 2019 + */ + template <> + struct is_sd_number : std::true_type + {}; + + //@} + + /** + * @name Bitwise operators + */ + //@{ + + /** + * Bitwise left shift operator. + * + * This is used to output the @p expression to the input @p stream. + */ + std::ostream & + operator<<(std::ostream &stream, const Expression &expression); + + /** + * Bitwise right shift operator. + * + * This is used to read in an @p expression from the input @p stream. + */ + std::istream & + operator>>(std::istream &stream, Expression &expression); + + //@} + + /** + * @name Comparison operators + */ + //@{ + + /** + * Equality operator. + * + * Return whether the @p lhs is equal to the @p rhs. + */ + Expression + operator==(const Expression &lhs, const Expression &rhs); + + /** + * Non-equality operator. + * + * Return whether the @p lhs is not equal to the @p rhs. + */ + Expression + operator!=(const Expression &lhs, const Expression &rhs); + + /** + * Less than operator. + * + * Return whether the @p lhs is less than the @p rhs. + */ + Expression + operator<(const Expression &lhs, const Expression &rhs); + + /** + * Greater than operator. + * + * Return whether the @p lhs is greater than the @p rhs. + */ + Expression + operator>(const Expression &lhs, const Expression &rhs); + + /** + * Less than or equals operator. + * + * Return whether the @p lhs is less than, or equal to, the @p rhs. + */ + Expression + operator<=(const Expression &lhs, const Expression &rhs); + + /** + * Greater than or equals operator. + * + * Return whether the @p lhs is greater than, or equal to, the @p rhs. + */ + Expression + operator>=(const Expression &lhs, const Expression &rhs); + + //@} + + /** + * @name Logical operators + */ + //@{ + + /** + * Logical not operator. + * + * @note This operator can only be applied on boolean and conditional + * expressions. + */ + Expression operator!(const Expression &expression); + + /** + * Logical and operator. + * + * @note This operator can only be applied on boolean and conditional + * expressions. + */ + Expression operator&(const Expression &lhs, const Expression &rhs); + + /** + * Logical inclusive or operator. + * + * @note This operator can only be applied on boolean and conditional + * expressions. + */ + Expression + operator|(const Expression &lhs, const Expression &rhs); + + /** + * Logical exclusive or (xor) operator. + * + * @note This operator can only be applied on boolean and conditional + * expressions. + */ + Expression + operator^(const Expression &lhs, const Expression &rhs); + + /** + * And operator. + * + * @note This operator can only be applied on boolean and conditional + * expressions. + * This operator is a convenience wrapper for the logical and operator. + */ + Expression + operator&&(const Expression &lhs, const Expression &rhs); + + /** + * Inclusive or operator. + * + * @note This operator can only be applied on boolean and conditional + * expressions. + * This operator is a convenience wrapper for the logical or operator. + */ + Expression + operator||(const Expression &lhs, const Expression &rhs); + + //@} + + /** + * @name Mathematical operators + */ + //@{ + + /** + * Addition operator. + * + * Return the result of adding the @p rhs to the @p lhs. + */ + Expression + operator+(Expression lhs, const Expression &rhs); + + /** + * Subtraction operator. + * + * Return the result of subtracting the @p rhs from the @p lhs. + */ + Expression + operator-(Expression lhs, const Expression &rhs); + + /** + * Multiplication operator. + * + * Return the result of multiplying the @p lhs by the @p rhs. + */ + Expression operator*(Expression lhs, const Expression &rhs); + + /** + * Division operator. + * + * Return the result of dividing the @p lhs by the @p rhs. + */ + Expression + operator/(Expression lhs, const Expression &rhs); + + /** + * General addition operator. + * + * Return the result of adding the @p rhs to the @p lhs. + * The @p lhs type may be any supported number type, and the result + * is promoted to a Expression. The type conversion makes writing + * scalar expressions using Expression more natural. + */ + template ::value>::type> + inline Expression + operator+(const NumberType &lhs, const Expression &rhs) + { + return Expression(lhs) + rhs; + } + + /** + * General addition operator. + * + * Return the result of adding the @p rhs to the @p lhs. + * The @p rhs type may be any supported number type, and the result + * is promoted to a Expression. The type conversion makes writing + * scalar expressions using Expression more natural. + */ + template ::value>::type> + inline Expression + operator+(const Expression &lhs, const NumberType &rhs) + { + return lhs + Expression(rhs); + } + + /** + * General subtraction operator. + * + * Return the result of subtracting the @p rhs from the @p lhs. + * The @p lhs type may be any supported number type, and the result + * is promoted to a Expression. The type conversion makes writing + * scalar expressions using Expression more natural. + */ + template ::value>::type> + inline Expression + operator-(const NumberType &lhs, const Expression &rhs) + { + return Expression(lhs) - rhs; + } + + /** + * General subtraction operator. + * + * Return the result of subtracting the @p rhs from the @p lhs. + * The @p rhs type may be any supported number type, and the result + * is promoted to a Expression. The type conversion makes writing + * scalar expressions using Expression more natural. + */ + template ::value>::type> + inline Expression + operator-(const Expression &lhs, const NumberType &rhs) + { + return lhs - Expression(rhs); + } + + /** + * General multiplication operator. + * + * Return the result of multiplying the @p lhs by the @p rhs. + * The @p lhs type may be any supported number type, and the result + * is promoted to a Expression. The type conversion makes writing + * scalar expressions using Expression more natural. + */ + template ::value>::type> + inline Expression operator*(const NumberType &lhs, const Expression &rhs) + { + return Expression(lhs) * rhs; + } + + /** + * General multiplication operator. + * + * Return the result of multiplying the @p lhs by the @p rhs. + * The @p rhs type may be any supported number type, and the result + * is promoted to a Expression. The type conversion makes writing + * scalar expressions using Expression more natural. + */ + template ::value>::type> + inline Expression operator*(const Expression &lhs, const NumberType &rhs) + { + return lhs * Expression(rhs); + } + + /** + * General division operator. + * + * Return the result of dividing the @p lhs by the @p rhs. + * The @p lhs type may be any supported number type, and the result + * is promoted to a Expression. The type conversion makes writing + * scalar expressions using Expression more natural. + */ + template ::value>::type> + inline Expression + operator/(const NumberType &lhs, const Expression &rhs) + { + return Expression(lhs) / rhs; + } + + /** + * General division operator. + * + * Return the result of dividing the @p lhs by the @p rhs. + * The @p lhs type may be any supported number type, and the result + * is promoted to a Expression. The type conversion makes writing + * scalar expressions using Expression more natural. + */ + template ::value>::type> + inline Expression + operator/(const Expression &lhs, const NumberType &rhs) + { + return lhs / Expression(rhs); + } + + //@} + + } // namespace SD +} // namespace Differentiation + + +/* ---------------------- inline and template functions -------------------- */ + + +# ifndef DOXYGEN + + +namespace Differentiation +{ + namespace SD + { + template + Expression::Expression(const NumberType &value) + : expression(value) + {} + + + template + Expression::Expression(const std::complex &value) + : expression(value) + {} + + + template + Expression::Expression(const NumberType &numerator, + const NumberType &denominator) + : expression(SE::Rational::from_two_ints(*SE::integer(numerator), + *SE::integer(denominator))) + {} + + + template + void + Expression::serialize(Archive &ar, const unsigned int /*version*/) + { + // This is a bit tricky... The SymEngine expression class is not + // serializable, and we're not sure if we're writing out or + // reading in here. So what we'll do is try to synchronise the + // current data with the stream, predicting if we're likely trying + // to write out data. We do this by checking if we're currently working + // with an object that has a trivial state. If not, then we're likely + // to output this object's contents. + const Expression default_constructed; + const bool likely_writing_out = + (get_RCP()->__eq__(*default_constructed.get_RCP()) == false); + + std::stringstream sstream; + std::string expr = default_constructed.get_RCP()->__str__(); + + // Output + if (likely_writing_out) + { + sstream << *this; + expr = sstream.str(); + } + + // Serialise + ar &expr; + + // Input + if (!likely_writing_out) + { + sstream.clear(); + sstream << expr; + sstream >> *this; + + parse(expr); + } + } + + + template + Expression + Expression::substitute(const Expression &symbol, + const NumberType &value) const + { + Assert(SE::is_a(symbol.get_value()), + ExcMessage( + "Substitution with a number that does not represent a symbol.")); + + types::substitution_map sub_vals; + sub_vals[symbol] = Expression(value); + return substitute(sub_vals); + } + + + template + ReturnType + Expression::substitute_and_evaluate( + const types::substitution_map &substitution_values) const + { + return static_cast(substitute(substitution_values)); + } + + + template + Expression & + Expression::operator=(const NumberType &rhs) + { + *this = Expression(rhs); + return *this; + } + + + template + Expression & + Expression::operator+=(const NumberType &rhs) + { + *this = Expression(SE::add(get_RCP(), Expression(rhs).get_RCP())); + return *this; + } + + + template + Expression & + Expression::operator-=(const NumberType &rhs) + { + *this = Expression(SE::sub(get_RCP(), Expression(rhs).get_RCP())); + return *this; + } + + + template + Expression & + Expression::operator*=(const NumberType &rhs) + { + *this = Expression(SE::mul(get_RCP(), Expression(rhs).get_RCP())); + return *this; + } + + + template + Expression & + Expression::operator/=(const NumberType &rhs) + { + *this = Expression(SE::div(get_RCP(), Expression(rhs).get_RCP())); + return *this; + } + + + template + Expression::operator ResultType() const + { + return static_cast(get_expression()); + } + + } // namespace SD +} // namespace Differentiation + + +DEAL_II_NAMESPACE_CLOSE + + +# endif // DOXYGEN + +#endif // DEAL_II_WITH_SYMENGINE + +#endif // dealii_differentiation_sd_symengine_number_types_h diff --git a/include/deal.II/differentiation/sd/symengine_types.h b/include/deal.II/differentiation/sd/symengine_types.h new file mode 100644 index 000000000000..1f493c007c53 --- /dev/null +++ b/include/deal.II/differentiation/sd/symengine_types.h @@ -0,0 +1,81 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + +#ifndef dealii_differentiation_sd_symengine_types_h +#define dealii_differentiation_sd_symengine_types_h + +#include + +#ifdef DEAL_II_WITH_SYMENGINE + +# include +# include + +DEAL_II_NAMESPACE_OPEN + +namespace Differentiation +{ + namespace SD + { + // Forward declarations + class Expression; + + + namespace types + { + namespace internal + { + /** + * A comparator for Expressions used as keys in maps. + */ + struct ExpressionKeyLess + { + bool + operator()(const SD::Expression &lhs, + const SD::Expression &rhs) const; + }; + } // namespace internal + + /** + * Type definition for a value substitution map. + * + * This serves the same purpose as a + * SymEngine::map_basic_basic, which is equivalent to a + * std::map, SE::RCP>. + */ + using substitution_map = + std::map; + + /** + * Type definition for a vector of symbols. + * + * This serves the same purpose as a SymEngine::vec_basic, + * which is equivalent to a std::vector> + */ + using symbol_vector = std::vector; + + } // namespace types + + } // namespace SD +} // namespace Differentiation + + +DEAL_II_NAMESPACE_CLOSE + +#endif // DEAL_II_WITH_SYMENGINE + +#endif // dealii_differentiation_sd_symengine_types_h diff --git a/include/deal.II/differentiation/sd/symengine_utilities.h b/include/deal.II/differentiation/sd/symengine_utilities.h new file mode 100644 index 000000000000..e9f64c57162d --- /dev/null +++ b/include/deal.II/differentiation/sd/symengine_utilities.h @@ -0,0 +1,62 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + +#ifndef dealii_differentiation_sd_symengine_utilities_h +#define dealii_differentiation_sd_symengine_utilities_h + +#include + +#ifdef DEAL_II_WITH_SYMENGINE + +# include + +# include +# include + +DEAL_II_NAMESPACE_OPEN + +namespace Differentiation +{ + namespace SD + { + namespace SE = ::SymEngine; + + namespace Utilities + { + /** + * Convert a map of Expressions to its SymEngine counterpart. + */ + SE::map_basic_basic + convert_expression_map_to_basic_map( + const SD::types::substitution_map &substitution_map); + + /** + * Convert a vector of Expressions to its SymEngine counterpart. + */ + SE::vec_basic + convert_expression_vector_to_basic_vector( + const SD::types::symbol_vector &symbol_vector); + + } // namespace Utilities + + } // namespace SD +} // namespace Differentiation + + +DEAL_II_NAMESPACE_CLOSE + +#endif // DEAL_II_WITH_SYMENGINE + +#endif // dealii_differentiation_sd_symengine_utilities_h diff --git a/source/differentiation/CMakeLists.txt b/source/differentiation/CMakeLists.txt index 28015cc9d5a7..3d27c72a33e4 100644 --- a/source/differentiation/CMakeLists.txt +++ b/source/differentiation/CMakeLists.txt @@ -1,6 +1,6 @@ ## --------------------------------------------------------------------- ## -## Copyright (C) 2017 by the deal.II authors +## Copyright (C) 2017-2019 by the deal.II authors ## ## This file is part of the deal.II library. ## @@ -14,3 +14,4 @@ ## --------------------------------------------------------------------- ADD_SUBDIRECTORY(ad) +ADD_SUBDIRECTORY(sd) diff --git a/source/differentiation/sd/CMakeLists.txt b/source/differentiation/sd/CMakeLists.txt new file mode 100644 index 000000000000..f6730585d816 --- /dev/null +++ b/source/differentiation/sd/CMakeLists.txt @@ -0,0 +1,32 @@ +## --------------------------------------------------------------------- +## +## Copyright (C) 2017 by the deal.II authors +## +## This file is part of the deal.II library. +## +## The deal.II library is free software; you can use it, redistribute +## it, and/or modify it under the terms of the GNU Lesser General +## Public License as published by the Free Software Foundation; either +## version 2.1 of the License, or (at your option) any later version. +## The full text of the license can be found in the file LICENSE at +## the top level of the deal.II distribution. +## +## --------------------------------------------------------------------- + +INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_BINARY_DIR}) + +SET(_src + symengine_number_types.cc + symengine_types.cc + symengine_utilities.cc + ) + +SET(_inst + ) + +FILE(GLOB _header + ${CMAKE_SOURCE_DIR}/include/deal.II/differentiation/sd/*.h + ) + +DEAL_II_ADD_LIBRARY(obj_differentiation_sd OBJECT ${_src} ${_header} ${_inst}) +EXPAND_INSTANTIATIONS(obj_differentiation_sd "${_inst}") diff --git a/source/differentiation/sd/symengine_number_types.cc b/source/differentiation/sd/symengine_number_types.cc new file mode 100644 index 000000000000..fce494713b54 --- /dev/null +++ b/source/differentiation/sd/symengine_number_types.cc @@ -0,0 +1,541 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + +#include + +#ifdef DEAL_II_WITH_SYMENGINE + +# include + +# include +# include +# include + +# include +# include +# include +# include +# include +# include +# include + +# include + +DEAL_II_NAMESPACE_OPEN + +namespace Differentiation +{ + namespace SD + { + namespace SE = ::SymEngine; + + + /* ---------------------------- Constructors -------------------------- */ + + + Expression::Expression() + : expression() + {} + + + Expression::Expression(const bool &value) + : expression(SE::boolean(value)) + {} + + + Expression::Expression(const SE::integer_class &value) + : expression(value) + {} + + + Expression::Expression(const SE::rational_class &value) + : expression(value) + {} + + + Expression::Expression(const Expression &condition, + const Expression &expression_if_true, + const Expression &expression_if_false) + { + Assert(SE::is_a_Boolean(condition.get_value()), + ExcMessage( + "The conditional expression must return a boolean type.")); + + const SE::RCP condition_rcp = + SE::rcp_static_cast(condition.get_RCP()); + expression = + SE::piecewise({{expression_if_true.get_RCP(), condition_rcp}, + {expression_if_false.get_RCP(), SE::boolTrue}}); + } + + + Expression::Expression(const std::vector> + & condition_expression, + const Expression &expression_otherwise) + { + SE::PiecewiseVec piecewise_function; + piecewise_function.reserve(condition_expression.size() + 1); + + // Add tested conditional entries + for (const auto &entry : condition_expression) + { + Assert(SE::is_a_Boolean(entry.first.get_value()), + ExcMessage( + "The conditional expression must return a boolean type.")); + piecewise_function.push_back( + {entry.second.get_RCP(), + SE::rcp_static_cast(entry.first.get_RCP())}); + } + + // Add default value + piecewise_function.push_back( + {expression_otherwise.get_RCP(), SE::boolTrue}); + + // Initialize + expression = SE::piecewise(std::move(piecewise_function)); + } + + + Expression::Expression(const std::vector> + &condition_expression) + { + // Use the other constructor with a fatal termination point + // ensuring that an error is thrown if none of the conditions + // are met. + *this = Expression(condition_expression, + Expression(numbers::signaling_nan())); + } + + + Expression::Expression(const char *symbol) + : expression(SE::symbol(symbol)) + {} + + + Expression::Expression(const std::string &str, + const bool parse_as_expression) + { + try + { + expression = (parse_as_expression ? + SE::parse(str) // The string is a symbolic "name" + : + SE::rcp_static_cast(SE::symbol( + str))); // The string is a symbolic "expression" + } + catch (...) + { + AssertThrow(false, ExcSymEngineParserError(str)); + } + } + + + Expression::Expression(const std::string & symbol_func, + const types::symbol_vector &arguments) + : expression(SE::function_symbol( + symbol_func, + Utilities::convert_expression_vector_to_basic_vector(arguments))) + {} + + + Expression::Expression(const SE::Expression &rhs) + : expression(rhs) + {} + + + Expression::Expression(const SE::RCP &rhs) + : expression(rhs) + {} + + + Expression::Expression(SE::RCP &&rhs) + : expression(rhs) + {} + + + /* ------------------------------ Utilities ---------------------------- */ + + + Expression & + Expression::parse(const std::string &expression) + { + *this = Expression(expression, true /*parse_as_expression*/); + return *this; + } + + + std::ostream & + Expression::print(std::ostream &os) const + { + os << *this; + return os; + } + + + void + Expression::save(std::ostream &os) const + { + // We write each expression on a new line. + // Note: SymEngine outputs a non-terminating string + os << *this; + os << std::endl; + } + + + void + Expression::load(std::istream &is) + { + // Need to make sure that we read the entire line in, + // and then subsequently parse it. + std::string expr; + std::getline(is, expr); + Assert(!is.bad(), ExcIO()); + parse(expr); + } + + + /* ------------------------------- Values ----------------------------- */ + + + const SE::Expression & + Expression::get_expression() const + { + return expression; + } + + + SE::Expression & + Expression::get_expression() + { + return expression; + } + + + const SE::Basic & + Expression::get_value() const + { + return *get_RCP(); + } + + + const SE::RCP & + Expression::get_RCP() const + { + return get_expression().get_basic(); + } + + + /* --------------------------- Differentiation ------------------------- */ + + + Expression + Expression::differentiate(const SE::RCP &symbol) const + { + return Expression(SE::diff(get_RCP(), symbol)); + } + + + Expression + Expression::differentiate(const SE::RCP &symbol) const + { + // Potential symbol + return Expression(SE::sdiff(get_RCP(), symbol)); + } + + + Expression + Expression::differentiate(const Expression &symbol) const + { + return differentiate(symbol.get_RCP()); + } + + + /* ------------- Conversion operators ------------------------- */ + + + Expression::operator const SE::Expression &() const + { + return get_expression(); + } + + + Expression::operator const SE::RCP &() const + { + return get_expression().get_basic(); + } + + + /* ------------- Dictionary-based substitution ------------------------- */ + + + Expression + Expression::substitute( + const types::substitution_map &substitution_values) const + { + return Expression(get_expression().subs( + Utilities::convert_expression_map_to_basic_map(substitution_values))); + } + + + Expression + Expression::substitute(const Expression &symbol, + const Expression &value) const + { + Assert(SE::is_a(symbol.get_value()), + ExcMessage( + "Substitution with a number that does not represent a symbol.")); + + types::substitution_map sub_vals; + sub_vals[symbol] = value; + return substitute(sub_vals); + } + + + /* -------------------- Math and relational operators ------------------ */ + + + Expression & + Expression::operator=(const Expression &rhs) + { + if (this != &rhs) + this->expression = rhs.get_expression(); + + return *this; + } + + + Expression & + Expression::operator=(Expression &&rhs) + { + if (this != &rhs) + this->expression = std::move(rhs.expression); + + return *this; + } + + + Expression + Expression::operator-() const + { + return Expression(-get_expression()); + } + + + Expression & + Expression::operator+=(const Expression &rhs) + { + this->expression += rhs.get_expression(); + return *this; + } + + + Expression & + Expression::operator-=(const Expression &rhs) + { + this->expression -= rhs.get_expression(); + return *this; + } + + + Expression & + Expression::operator*=(const Expression &rhs) + { + this->expression *= rhs.get_expression(); + return *this; + } + + + Expression & + Expression::operator/=(const Expression &rhs) + { + this->expression /= rhs.get_expression(); + return *this; + } + + + std::ostream & + operator<<(std::ostream &stream, const Expression &expr) + { + stream << expr.get_expression(); + return stream; + } + + + std::istream & + operator>>(std::istream &stream, Expression &expr) + { + std::string str; + stream >> str; + expr.parse(str); + return stream; + } + + + Expression + operator==(const Expression &lhs, const Expression &rhs) + { + return Expression(SE::Eq(lhs.get_RCP(), rhs.get_RCP())); + } + + + Expression + operator!=(const Expression &lhs, const Expression &rhs) + { + return Expression(SE::Ne(lhs.get_RCP(), rhs.get_RCP())); + } + + + Expression + operator<(const Expression &lhs, const Expression &rhs) + { + return Expression(SE::Lt(lhs.get_RCP(), rhs.get_RCP())); + } + + + Expression + operator>(const Expression &lhs, const Expression &rhs) + { + return Expression(SE::Gt(lhs.get_RCP(), rhs.get_RCP())); + } + + + Expression + operator<=(const Expression &lhs, const Expression &rhs) + { + return Expression(SE::Le(lhs.get_RCP(), rhs.get_RCP())); + } + + + Expression + operator>=(const Expression &lhs, const Expression &rhs) + { + return Expression(SE::Ge(lhs.get_RCP(), rhs.get_RCP())); + } + + + Expression operator!(const Expression &expression) + { + Assert(SE::is_a_Boolean(expression.get_value()), + ExcMessage("The expression must return a boolean type.")); + + const SE::RCP expression_rcp = + SE::rcp_static_cast(expression.get_RCP()); + + return Expression(SE::logical_not(expression_rcp)); + } + + + Expression operator&(const Expression &lhs, const Expression &rhs) + { + Assert(SE::is_a_Boolean(lhs.get_value()), + ExcMessage("The lhs expression must return a boolean type.")); + Assert(SE::is_a_Boolean(rhs.get_value()), + ExcMessage("The rhs expression must return a boolean type.")); + + const SE::RCP lhs_rcp = + SE::rcp_static_cast(lhs.get_RCP()); + const SE::RCP rhs_rcp = + SE::rcp_static_cast(rhs.get_RCP()); + + return Expression(SE::logical_and({lhs_rcp, rhs_rcp})); + } + + + Expression + operator|(const Expression &lhs, const Expression &rhs) + { + Assert(SE::is_a_Boolean(lhs.get_value()), + ExcMessage("The lhs expression must return a boolean type.")); + Assert(SE::is_a_Boolean(rhs.get_value()), + ExcMessage("The rhs expression must return a boolean type.")); + + const SE::RCP lhs_rcp = + SE::rcp_static_cast(lhs.get_RCP()); + const SE::RCP rhs_rcp = + SE::rcp_static_cast(rhs.get_RCP()); + + return Expression(SE::logical_or({lhs_rcp, rhs_rcp})); + } + + + Expression + operator^(const Expression &lhs, const Expression &rhs) + { + Assert(SE::is_a_Boolean(lhs.get_value()), + ExcMessage("The lhs expression must return a boolean type.")); + Assert(SE::is_a_Boolean(rhs.get_value()), + ExcMessage("The rhs expression must return a boolean type.")); + + const SE::RCP lhs_rcp = + SE::rcp_static_cast(lhs.get_RCP()); + const SE::RCP rhs_rcp = + SE::rcp_static_cast(rhs.get_RCP()); + + return Expression(SE::logical_xor({lhs_rcp, rhs_rcp})); + } + + + Expression + operator&&(const Expression &lhs, const Expression &rhs) + { + return lhs & rhs; + } + + + Expression + operator||(const Expression &lhs, const Expression &rhs) + { + return lhs | rhs; + } + + + Expression + operator+(Expression lhs, const Expression &rhs) + { + lhs += rhs; + return lhs; + } + + + Expression + operator-(Expression lhs, const Expression &rhs) + { + lhs -= rhs; + return lhs; + } + + + Expression operator*(Expression lhs, const Expression &rhs) + { + lhs *= rhs; + return lhs; + } + + + Expression + operator/(Expression lhs, const Expression &rhs) + { + lhs /= rhs; + return lhs; + } + + + } // namespace SD +} // namespace Differentiation + + +DEAL_II_NAMESPACE_CLOSE + +#endif // DEAL_II_WITH_SYMENGINE diff --git a/source/differentiation/sd/symengine_types.cc b/source/differentiation/sd/symengine_types.cc new file mode 100644 index 000000000000..4c628ae23845 --- /dev/null +++ b/source/differentiation/sd/symengine_types.cc @@ -0,0 +1,55 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + +#include + +#ifdef DEAL_II_WITH_SYMENGINE + +# include +# include + +# include +# include + + +DEAL_II_NAMESPACE_OPEN + +namespace Differentiation +{ + namespace SD + { + namespace SE = ::SymEngine; + + namespace types + { + namespace internal + { + bool + ExpressionKeyLess::operator()(const SD::Expression &lhs, + const SD::Expression &rhs) const + { + return SE::RCPBasicKeyLess()(lhs.get_RCP(), rhs.get_RCP()); + } + } // namespace internal + + } // namespace types + + } // namespace SD +} // namespace Differentiation + + +DEAL_II_NAMESPACE_CLOSE + +#endif // DEAL_II_WITH_SYMENGINE diff --git a/source/differentiation/sd/symengine_utilities.cc b/source/differentiation/sd/symengine_utilities.cc new file mode 100644 index 000000000000..9697316831f8 --- /dev/null +++ b/source/differentiation/sd/symengine_utilities.cc @@ -0,0 +1,63 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + +#include + +#ifdef DEAL_II_WITH_SYMENGINE + +# include +# include + +DEAL_II_NAMESPACE_OPEN + +namespace Differentiation +{ + namespace SD + { + namespace SE = ::SymEngine; + + namespace Utilities + { + SE::map_basic_basic + convert_expression_map_to_basic_map( + const SD::types::substitution_map &substitution_map) + { + SE::map_basic_basic sub_map; + for (const auto &entry : substitution_map) + sub_map[entry.first.get_RCP()] = entry.second.get_RCP(); + return sub_map; + } + + + SE::vec_basic + convert_expression_vector_to_basic_vector( + const SD::types::symbol_vector &symbol_vector) + { + SE::vec_basic symb_vec; + symb_vec.reserve(symbol_vector.size()); + for (const auto &entry : symbol_vector) + symb_vec.push_back(entry.get_RCP()); + return symb_vec; + } + + } // namespace Utilities + + } // namespace SD +} // namespace Differentiation + + +DEAL_II_NAMESPACE_CLOSE + +#endif // DEAL_II_WITH_SYMENGINE From a9082f47c2c04ade424cacca685fbb2569fb50b7 Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Sat, 30 Mar 2019 11:20:34 +0100 Subject: [PATCH 362/507] Add test for SD::Expression class --- tests/symengine/symengine_number_type_01.cc | 1142 +++++++++++++++++ .../symengine/symengine_number_type_01.output | 17 + 2 files changed, 1159 insertions(+) create mode 100644 tests/symengine/symengine_number_type_01.cc create mode 100644 tests/symengine/symengine_number_type_01.output diff --git a/tests/symengine/symengine_number_type_01.cc b/tests/symengine/symengine_number_type_01.cc new file mode 100644 index 000000000000..4b26361e1f57 --- /dev/null +++ b/tests/symengine/symengine_number_type_01.cc @@ -0,0 +1,1142 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + + +// Check that the wrapper for symengine expressions works as expected + +#include + +#include + +#include +#include +#include +#include +#include +#include +#include +#include + +#include +#include + +#include "../serialization/serialization.h" +#include "../tests.h" + +using namespace dealii; +namespace SD = Differentiation::SD; +namespace SE = ::SymEngine; + + +// Overload the comparison function in serialization.h +template <> +bool +compare(const SD::Expression &t1, const SD::Expression &t2) +{ + // Could also do the following if it ever becomes necessary: + // (t1.get_value().__cmp__(t2.get_value()) == 0) + return t1.get_expression() == t2.get_expression(); +} + + +int +main() +{ + initlog(); + + using SD_number_t = SD::Expression; + + deallog << "Constructors" << std::endl; + { + std::cout << "Constructor: Boolean" << std::endl; + { + const SD_number_t se_bool_true(true); + const SD_number_t se_bool_false(false); + Assert(SE::eq(se_bool_true.get_value(), *SE::boolTrue), + ExcMessage("Problem with constructor")); + Assert(SE::eq(se_bool_false.get_value(), *SE::boolFalse), + ExcMessage("Problem with constructor")); + } + + std::cout << "Constructor: Integer" << std::endl; + { + const int x = -1; + const SD_number_t se_number(x); + Assert(SE::eq(se_number.get_value(), *SE::integer(x)), + ExcMessage("Problem with constructor")); + } + + std::cout << "Constructor: Unsigned integer" << std::endl; + { + const unsigned int x = 2; + const SD_number_t se_number(x); + Assert(SE::eq(se_number.get_value(), *SE::integer(x)), + ExcMessage("Problem with constructor")); + } + + std::cout << "Constructor: Rational" << std::endl; + { + const unsigned int x = 2; + const unsigned int y = 3; + const SD_number_t se_number(x, y); + Assert(SE::eq(se_number.get_value(), *SE::rational(x, y)), + ExcMessage("Problem with constructor")); + } + + std::cout << "Constructor: Double" << std::endl; + { + const double x = 2.5; + const SD_number_t se_number(x); + Assert(SE::eq(se_number.get_value(), *SE::real_double(x)), + ExcMessage("Problem with constructor")); + } + + std::cout << "Constructor: Complex double" << std::endl; + { + const std::complex x(2.5, 1.5); + const SD_number_t se_number(x); + Assert(SE::eq(se_number.get_value(), *SE::complex_double(x)), + ExcMessage("Problem with constructor")); + } + + std::cout << "Constructor: Float" << std::endl; + { + const float x = 2.5; + const SD_number_t se_number(x); + Assert(SE::eq(se_number.get_value(), *SE::real_double(x)), + ExcMessage("Problem with constructor")); + } + + std::cout << "Constructor: Complex float" << std::endl; + { + const std::complex x(2.5, 1.5); + const SD_number_t se_number(x); + Assert(SE::eq(se_number.get_value(), *SE::complex_double(x)), + ExcMessage("Problem with constructor")); + } + + std::cout << "Constructor: Symbol" << std::endl; + { + const std::string f = "f"; + const bool parse_as_expression = false; + const SD_number_t se_number(f, parse_as_expression); + Assert(SE::eq(se_number.get_value(), *SE::symbol(f)), + ExcMessage("Problem with constructor")); + } + + std::cout << "Constructor: Symbol" << std::endl; + { + const std::string f = "func"; + const SD_number_t se_number(f.c_str()); + Assert(SE::eq(se_number.get_value(), *SE::symbol(f)), + ExcMessage("Problem with constructor")); + } + + std::cout << "Constructor: Symbol" << std::endl; + { + const std::string f = "func"; + const bool parse_as_expression = false; + const SD_number_t se_number(f, parse_as_expression); + Assert(SE::eq(se_number.get_value(), *SE::symbol(f)), + ExcMessage("Problem with constructor")); + } + + std::cout << "Constructor: Symbolic expression" << std::endl; + { + const std::string f = "x + y"; + const bool parse_as_expression = true; + const SD_number_t se_number(f, parse_as_expression); + Assert(SE::eq(se_number.get_value(), *SE::parse(f)), + ExcMessage("Problem with constructor")); + } + + std::cout << "Copy constructor" << std::endl; + { + const double x = 2.5; + const SD_number_t se_number_1(x); + const SD_number_t se_number_2(se_number_1); + Assert(SE::eq(se_number_2.get_value(), *SE::real_double(x)), + ExcMessage("Problem with constructor")); + } + } + + deallog << "Utility functions" << std::endl; + { + std::cout << "Parse" << std::endl; + { + const double x = 2.5; + SD_number_t se_number(x); + const std::string f = "x + y"; + se_number.parse(f); + Assert(SE::eq(se_number.get_value(), *SE::parse(f)), + ExcMessage("Problem with utility function: Parse")); + } + + std::cout << "Save/load" << std::endl; + { + // Output + const SD_number_t se_number_x_out("x"); + const SD_number_t se_number_y_out("y"); + const SD_number_t se_number_f_out("x + y + 2.5", + true /*parse_as_expression*/); + { + std::ofstream o_str("save_load.txt"); + Assert(o_str.is_open(), ExcInternalError()); + se_number_x_out.save(o_str); + se_number_y_out.save(o_str); + se_number_f_out.save(o_str); + o_str.close(); + } + + // Input + SD_number_t se_number_x_in; + SD_number_t se_number_y_in; + SD_number_t se_number_f_in; + { + std::ifstream i_str("save_load.txt"); + Assert(i_str.is_open(), ExcInternalError()); + se_number_x_in.load(i_str); + se_number_y_in.load(i_str); + se_number_f_in.load(i_str); + } + + Assert(static_cast(se_number_x_in == se_number_x_out), + ExcMessage("Problem with utility function: Save/load")); + Assert(static_cast(se_number_y_in == se_number_y_out), + ExcMessage("Problem with utility function: Save/load")); + Assert(static_cast(se_number_f_in == se_number_f_out), + ExcMessage("Problem with utility function: Save/load")); + } + + deallog.push("Serialization"); + std::cout << "Serialization" << std::endl; + { + const SD_number_t se_number_x_out("x"); + const SD_number_t se_number_y_out("y"); + const SD_number_t se_number_f_out("x + y + 2.5", + true /*parse_as_expression*/); + + // From serialization.h + SD_number_t se_number_x_in; + SD_number_t se_number_y_in; + SD_number_t se_number_f_in; + verify(se_number_x_out, se_number_x_in); + verify(se_number_y_out, se_number_y_in); + verify(se_number_f_out, se_number_f_in); + + Assert(static_cast(se_number_x_in == se_number_x_out), + ExcMessage("Problem with utility function: Serialization")); + Assert(static_cast(se_number_y_in == se_number_y_out), + ExcMessage("Problem with utility function: Serialization")); + Assert(static_cast(se_number_f_in == se_number_f_out), + ExcMessage("Problem with utility function: Serialization")); + } + deallog.pop(); + } + + deallog << "Comparison operators" << std::endl; + { + std::cout << "Equality (true)" << std::endl; + { + const int x = 2; + const int y = 2; + const SD_number_t se_number_1(x); + const SD_number_t se_number_2(y); + Assert(static_cast(se_number_1 == se_number_2) == true, + ExcMessage("Problem with comparison operator")); + } + + std::cout << "Equality (false)" << std::endl; + { + const int x = 2; + const int y = 3; + const SD_number_t se_number_1(x); + const SD_number_t se_number_2(y); + Assert(static_cast(se_number_1 == se_number_2) == false, + ExcMessage("Problem with comparison operator")); + } + + std::cout << "Non-equality (true)" << std::endl; + { + const int x = 2; + const int y = 3; + const SD_number_t se_number_1(x); + const SD_number_t se_number_2(y); + Assert(static_cast(se_number_1 != se_number_2) == true, + ExcMessage("Problem with comparison operator")); + } + + std::cout << "Non-equality (false)" << std::endl; + { + const int x = 2; + const int y = 2; + const SD_number_t se_number_1(x); + const SD_number_t se_number_2(y); + Assert(static_cast(se_number_1 != se_number_2) == false, + ExcMessage("Problem with comparison operator")); + } + + std::cout << "Less-than operator (true)" << std::endl; + { + const int x = 2; + const int y = 3; + const SD_number_t se_number_1(x); + const SD_number_t se_number_2(y); + Assert(static_cast(se_number_1 < se_number_2) == true, + ExcMessage("Problem with comparison operator")); + } + + std::cout << "Less-than operator (false)" << std::endl; + { + const int x = 3; + const int y = 2; + const int z = 3; + const SD_number_t se_number_1(x); + const SD_number_t se_number_2(y); + const SD_number_t se_number_3(z); + Assert(static_cast(se_number_1 < se_number_2) == false, + ExcMessage("Problem with comparison operator")); + Assert(static_cast(se_number_1 < se_number_3) == false, + ExcMessage("Problem with comparison operator")); + } + + std::cout << "Less-than-or-equals operator (true)" << std::endl; + { + const int x = 2; + const int y = 3; + const int z = 2; + const SD_number_t se_number_1(x); + const SD_number_t se_number_2(y); + const SD_number_t se_number_3(z); + Assert(static_cast(se_number_1 <= se_number_2) == true, + ExcMessage("Problem with comparison operator")); + Assert(static_cast(se_number_1 <= se_number_3) == true, + ExcMessage("Problem with comparison operator")); + } + + std::cout << "Less-than-or-equals operator (false)" << std::endl; + { + const int x = 3; + const int y = 2; + const SD_number_t se_number_1(x); + const SD_number_t se_number_2(y); + Assert(static_cast(se_number_1 <= se_number_2) == false, + ExcMessage("Problem with comparison operator")); + } + + std::cout << "Greater-than operator (true)" << std::endl; + { + const int x = 3; + const int y = 2; + const SD_number_t se_number_1(x); + const SD_number_t se_number_2(y); + Assert(static_cast(se_number_1 > se_number_2) == true, + ExcMessage("Problem with comparison operator")); + } + + std::cout << "Greater-than operator (false)" << std::endl; + { + const int x = 2; + const int y = 3; + const int z = 2; + const SD_number_t se_number_1(x); + const SD_number_t se_number_2(y); + const SD_number_t se_number_3(z); + Assert(static_cast(se_number_1 > se_number_2) == false, + ExcMessage("Problem with comparison operator")); + Assert(static_cast(se_number_1 > se_number_3) == false, + ExcMessage("Problem with comparison operator")); + } + + std::cout << "Greater-than-or-equals operator (true)" << std::endl; + { + const int x = 3; + const int y = 2; + const int z = 3; + const SD_number_t se_number_1(x); + const SD_number_t se_number_2(y); + const SD_number_t se_number_3(z); + Assert(static_cast(se_number_1 >= se_number_2) == true, + ExcMessage("Problem with comparison operator")); + Assert(static_cast(se_number_1 >= se_number_3) == true, + ExcMessage("Problem with comparison operator")); + } + + std::cout << "Greater-than-or-equals operator (false)" << std::endl; + { + const int x = 2; + const int y = 3; + const SD_number_t se_number_1(x); + const SD_number_t se_number_2(y); + Assert(static_cast(se_number_1 >= se_number_2) == false, + ExcMessage("Problem with comparison operator")); + } + } + + deallog << "Logical operators" << std::endl; + { + std::cout << "Logical not" << std::endl; + { + const bool x = true; + const SD_number_t se_number(x); + Assert(static_cast(!se_number) == (!x), + ExcMessage("Problem with logical operator")); + Assert(static_cast(!!se_number) == (!!x), + ExcMessage("Problem with logical operator")); + } + + std::cout << "Logical and" << std::endl; + { + auto test_logical_op = [](const bool x, const bool y) { + const SD_number_t se_number_1(x); + const SD_number_t se_number_2(y); + Assert(static_cast(se_number_1 & se_number_2) == (x & y), + ExcMessage("Problem with logical operator")); + }; + + test_logical_op(true, true); + test_logical_op(true, false); + test_logical_op(false, true); + test_logical_op(false, false); + } + + std::cout << "Logical inclusive or" << std::endl; + { + auto test_logical_op = [](const bool x, const bool y) { + const SD_number_t se_number_1(x); + const SD_number_t se_number_2(y); + Assert(static_cast(se_number_1 | se_number_2) == (x | y), + ExcMessage("Problem with logical operator")); + }; + + test_logical_op(true, true); + test_logical_op(true, false); + test_logical_op(false, true); + test_logical_op(false, false); + } + + std::cout << "Logical xor" << std::endl; + { + auto test_logical_op = [](const bool x, const bool y) { + const SD_number_t se_number_1(x); + const SD_number_t se_number_2(y); + Assert(static_cast(se_number_1 ^ se_number_2) == (x ^ y), + ExcMessage("Problem with logical operator")); + }; + + test_logical_op(true, true); + test_logical_op(true, false); + test_logical_op(false, true); + test_logical_op(false, false); + } + + std::cout << "And" << std::endl; + { + auto test_logical_op = [](const bool x, const bool y) { + const SD_number_t se_number_1(x); + const SD_number_t se_number_2(y); + Assert(static_cast(se_number_1 && se_number_2) == (x && y), + ExcMessage("Problem with logical operator")); + }; + + test_logical_op(true, true); + test_logical_op(true, false); + test_logical_op(false, true); + test_logical_op(false, false); + } + + std::cout << "Inclusive or" << std::endl; + { + auto test_logical_op = [](const bool x, const bool y) { + const SD_number_t se_number_1(x); + const SD_number_t se_number_2(y); + Assert(static_cast(se_number_1 || se_number_2) == (x || y), + ExcMessage("Problem with logical operator")); + }; + + test_logical_op(true, true); + test_logical_op(true, false); + test_logical_op(false, true); + test_logical_op(false, false); + } + } + + deallog << "Assignment operators" << std::endl; + { + std::cout << "Assignment operator (SD_number_t)" << std::endl; + { + const int x = 1; + const int y = 2; + SD_number_t se_number_1(x); + const SD_number_t se_number_2(y); + se_number_1 = se_number_2; + Assert(SE::eq(se_number_1.get_value(), *SE::integer(y)), + ExcMessage("Problem with assignment operator")); + } + + std::cout << "Assignment operator (arithmetic type)" << std::endl; + { + const int x = 1; + const double y = 2; + SD_number_t se_number(x); + se_number = y; + Assert(SE::eq(se_number.get_value(), *SE::real_double(y)), + ExcMessage("Problem with assignment operator")); + } + + std::cout << "Addition assignment (SD_number_t)" << std::endl; + { + const int x = 1; + const int y = 2; + SD_number_t se_number_1(x); + const SD_number_t se_number_2(y); + se_number_1 += se_number_2; + Assert(SE::eq(se_number_1.get_value(), *SE::integer(x + y)), + ExcMessage("Problem with assignment operator")); + } + + std::cout << "Addition assignment (arithmetic type; same type)" + << std::endl; + { + const int x = 1; + const int y = 2; + SD_number_t se_number(x); + se_number += y; + Assert(SE::eq(se_number.get_value(), *SE::integer(x + y)), + ExcMessage("Problem with assignment operator")); + } + + std::cout << "Addition assignment (arithmetic type; different type)" + << std::endl; + { + const int x = 1; + const double y = 2; + SD_number_t se_number(x); + se_number += y; + Assert(SE::eq(se_number.get_value(), *SE::real_double(x + y)), + ExcMessage("Problem with assignment operator")); + } + + std::cout << "Subtraction assignment (SD_number_t)" << std::endl; + { + const int x = 1; + const int y = 2; + SD_number_t se_number_1(x); + const SD_number_t se_number_2(y); + se_number_1 -= se_number_2; + Assert(SE::eq(se_number_1.get_value(), *SE::integer(x - y)), + ExcMessage("Problem with assignment operator")); + } + + std::cout << "Subtraction assignment (arithmetic type; same type)" + << std::endl; + { + const int x = 1; + const int y = 2; + SD_number_t se_number(x); + se_number -= y; + Assert(SE::eq(se_number.get_value(), *SE::integer(x - y)), + ExcMessage("Problem with assignment operator")); + } + + std::cout << "Subtraction assignment (arithmetic type; different type)" + << std::endl; + { + const int x = 1; + const double y = 2; + SD_number_t se_number(x); + se_number -= y; + Assert(SE::eq(se_number.get_value(), *SE::real_double(x - y)), + ExcMessage("Problem with assignment operator")); + } + + std::cout << "Multiplication assignment (SD_number_t)" << std::endl; + { + const int x = 2; + const int y = 3; + SD_number_t se_number_1(x); + const SD_number_t se_number_2(y); + se_number_1 *= se_number_2; + Assert(SE::eq(se_number_1.get_value(), *SE::integer(x * y)), + ExcMessage("Problem with assignment operator")); + } + + std::cout << "Multiplication assignment (arithmetic type; same type)" + << std::endl; + { + const int x = 2; + const int y = 3; + SD_number_t se_number(x); + se_number *= y; + Assert(SE::eq(se_number.get_value(), *SE::integer(x * y)), + ExcMessage("Problem with assignment operator")); + } + + std::cout << "Multiplication assignment (arithmetic type; different type)" + << std::endl; + { + const int x = 2; + const double y = 3; + SD_number_t se_number(x); + se_number *= y; + Assert(SE::eq(se_number.get_value(), *SE::real_double(x * y)), + ExcMessage("Problem with assignment operator")); + } + + std::cout << "Division assignment (SD_number_t)" << std::endl; + { + const int x = 8; + const int y = 2; + SD_number_t se_number_1(x); + const SD_number_t se_number_2(y); + se_number_1 /= se_number_2; + Assert(SE::eq(se_number_1.get_value(), *SE::integer(x / y)), + ExcMessage("Problem with assignment operator")); + } + + std::cout << "Division assignment (arithmetic type; same type)" + << std::endl; + { + const int x = 8; + const int y = 2; + SD_number_t se_number(x); + se_number /= y; + Assert(SE::eq(se_number.get_value(), *SE::integer(x / y)), + ExcMessage("Problem with assignment operator")); + } + + std::cout << "Division assignment (arithmetic type; different type)" + << std::endl; + { + const int x = 8; + const double y = 2; + SD_number_t se_number(x); + se_number /= y; + Assert(SE::eq(se_number.get_value(), *SE::real_double(x / y)), + ExcMessage("Problem with assignment operator")); + } + } + + deallog << "Math operators" << std::endl; + { + std::cout << "Addition" << std::endl; + { + const int x = 1; + const int y = 2; + const SD_number_t se_number_1(x); + const SD_number_t se_number_2(y); + const SD_number_t se_number_3 = se_number_1 + se_number_2; + Assert(SE::eq(se_number_3.get_value(), *SE::integer(x + y)), + ExcMessage("Problem with math operator")); + } + + std::cout << "Subtraction" << std::endl; + { + const int x = 1; + const int y = 2; + const SD_number_t se_number_1(x); + const SD_number_t se_number_2(y); + const SD_number_t se_number_3 = se_number_1 - se_number_2; + Assert(SE::eq(se_number_3.get_value(), *SE::integer(x - y)), + ExcMessage("Problem with math operator")); + } + + std::cout << "Multiplication" << std::endl; + { + const int x = 2; + const int y = 3; + const SD_number_t se_number_1(x); + const SD_number_t se_number_2(y); + const SD_number_t se_number_3 = se_number_1 * se_number_2; + Assert(SE::eq(se_number_3.get_value(), *SE::integer(x * y)), + ExcMessage("Problem with math operator")); + } + + std::cout << "Division" << std::endl; + { + const int x = 8; + const int y = 2; + const SD_number_t se_number_1(x); + const SD_number_t se_number_2(y); + const SD_number_t se_number_3 = se_number_1 / se_number_2; + Assert(SE::eq(se_number_3.get_value(), *SE::integer(x / y)), + ExcMessage("Problem with math operator")); + } + } + + deallog << "Differentiation" << std::endl; + { + std::cout << "Basic differentiation (SD_number_t)" << std::endl; + { + const SD_number_t x("x"); + SD_number_t f(1.0); + f *= x; + f *= x; // f = x^2 + const SD_number_t df_dx = f.differentiate(x); + Assert(static_cast(df_dx == (2.0 * x)), + ExcMessage("Problem with differentiaton")); + } + + std::cout << "Basic differentiation (Symbol)" << std::endl; + { + const auto symb_x = SE::symbol("x"); + const SD_number_t x(symb_x); + SD_number_t f(1.0); + f *= x; + f *= x; // f = x^2 + const SD_number_t df_dx = f.differentiate(symb_x); + Assert(static_cast(df_dx == SD_number_t(2.0 * x)), + ExcMessage("Problem with differentiaton")); + } + + std::cout << "Basic differentiation (Basic representing a symbolic type)" + << std::endl; + { + const auto symb_x_plus_y = SE::add(SE::symbol("x"), SE::symbol("y")); + const SD_number_t x_plus_y(symb_x_plus_y); + SD_number_t f(1.0); + f *= x_plus_y; + f *= x_plus_y; // f = (x+y)^2 + const SD_number_t df_dxpy = f.differentiate(symb_x_plus_y); + Assert(static_cast(df_dxpy == (2.0 * SD_number_t(symb_x_plus_y))), + ExcMessage("Problem with differentiaton")); + } + } + + deallog << "Substitution" << std::endl; + { + std::cout << "Basic substitution" << std::endl; + { + const SD_number_t x("x"); + const SD_number_t y("y"); + const SD_number_t x_plus_y = x + y; + const SD_number_t f = x_plus_y * x_plus_y; + Assert(static_cast(f == SD_number_t("(x + y)**2", true)), + ExcMessage("Problem with substitution")); + + const double x_val = 1.0; + const SD_number_t f_sub_x = f.substitute(x, SD_number_t(x_val)); + Assert(static_cast(f_sub_x == SD_number_t("(1.0 + y)**2", true)), + ExcMessage("Problem with substitution")); + + const double y_val = 2.0; + const SD_number_t f_sub_xy = f_sub_x.substitute(y, SD_number_t(y_val)); + Assert(static_cast(f_sub_xy) == + (x_val * x_val + 2.0 * x_val * y_val + y_val * y_val), + ExcMessage("Problem with substitution")); + } + + std::cout << "Templated-deduced substitution" << std::endl; + { + const SD_number_t x("x"); + const SD_number_t y("y"); + const SD_number_t x_plus_y = x + y; + const SD_number_t f = x_plus_y * x_plus_y; + Assert(static_cast(f == SD_number_t("(x + y)**2", true)), + ExcMessage("Problem with substitution")); + + const double x_val = 1.0; + const SD_number_t f_sub_x = f.substitute(x, x_val); + Assert(static_cast(f_sub_x == SD_number_t("(1.0 + y)**2", true)), + ExcMessage("Problem with substitution")); + + const double y_val = 2.0; + const SD_number_t f_sub_xy = f_sub_x.substitute(y, y_val); + Assert(static_cast(f_sub_xy) == + (x_val * x_val + 2.0 * x_val * y_val + y_val * y_val), + ExcMessage("Problem with substitution")); + } + + std::cout << "Map substitution" << std::endl; + { + const SD_number_t x("x"); + const SD_number_t y("y"); + const SD_number_t x_plus_y = x + y; + const SD_number_t f = x_plus_y * x_plus_y; + + const double x_val = 1.0; + const double y_val = 2.0; + SD::types::substitution_map sub_map; + sub_map[x] = SD_number_t(x_val); + sub_map[y] = SD_number_t(y_val); + const SD_number_t f_sub_xy = f.substitute(sub_map); + Assert(static_cast(f_sub_xy) == + (x_val * x_val + 2.0 * x_val * y_val + y_val * y_val), + ExcMessage("Problem with substitution")); + } + } + + deallog << "Evaluation" << std::endl; + { + std::cout << "Substitution with evaluation (integer)" << std::endl; + { + const SD_number_t x("x"); + const SD_number_t y("y"); + const SD_number_t x_plus_y = x + y; + const SD_number_t f = x_plus_y * x_plus_y; + + const int x_val = 1; + const int y_val = 2; + SD::types::substitution_map sub_map; + sub_map[x] = SD_number_t(x_val); + sub_map[y] = SD_number_t(y_val); + const int f_val = f.substitute_and_evaluate(sub_map); + Assert(f_val == (x_val * x_val + 2 * x_val * y_val + y_val * y_val), + ExcMessage("Problem with evaluation")); + } + + std::cout << "Substitution with evaluation (double)" << std::endl; + { + const SD_number_t x("x"); + const SD_number_t y("y"); + const SD_number_t x_plus_y = x + y; + const SD_number_t f = x_plus_y * x_plus_y; + + const double x_val = 1.0; + const double y_val = 2.0; + SD::types::substitution_map sub_map; + sub_map[x] = SD_number_t(x_val); + sub_map[y] = SD_number_t(y_val); + const double f_val = f.substitute_and_evaluate(sub_map); + Assert(f_val == (x_val * x_val + 2.0 * x_val * y_val + y_val * y_val), + ExcMessage("Problem with evaluation")); + } + + std::cout << "Substitution with evaluation (float)" << std::endl; + { + const SD_number_t x("x"); + const SD_number_t y("y"); + const SD_number_t x_plus_y = x + y; + const SD_number_t f = x_plus_y * x_plus_y; + + const float x_val = 1.0; + const float y_val = 2.0; + SD::types::substitution_map sub_map; + sub_map[x] = SD_number_t(x_val); + sub_map[y] = SD_number_t(y_val); + const float f_val = f.substitute_and_evaluate(sub_map); + Assert(f_val == (x_val * x_val + 2.0f * x_val * y_val + y_val * y_val), + ExcMessage("Problem with evaluation")); + } + + std::cout << "Substitution with evaluation (complex double)" << std::endl; + { + const SD_number_t x("x"); + const SD_number_t y("y"); + const SD_number_t x_plus_y = x + y; + const SD_number_t f = x_plus_y * x_plus_y; + + const std::complex x_val(1.0, 3.0); + const std::complex y_val(2.0, -2.0); + SD::types::substitution_map sub_map; + sub_map[x] = SD_number_t(x_val); + sub_map[y] = SD_number_t(y_val); + const std::complex f_val = + f.substitute_and_evaluate>(sub_map); + Assert(std::abs(f_val - (x_val * x_val + 2.0 * x_val * y_val + + y_val * y_val)) < 1e-12, + ExcMessage("Problem with evaluation")); + } + + std::cout << "Substitution with evaluation (complex float)" << std::endl; + { + const SD_number_t x("x"); + const SD_number_t y("y"); + const SD_number_t x_plus_y = x + y; + const SD_number_t f = x_plus_y * x_plus_y; + + const std::complex x_val(1.0, 3.0); + const std::complex y_val(2.0, -2.0); + SD::types::substitution_map sub_map; + sub_map[x] = SD_number_t(x_val); + sub_map[y] = SD_number_t(y_val); + const std::complex f_val = + f.substitute_and_evaluate>(sub_map); + Assert(std::abs(f_val - (x_val * x_val + 2.0f * x_val * y_val + + y_val * y_val)) < 1e-12, + ExcMessage("Problem with evaluation")); + } + + std::cout << "Substitution with evaluation (mixed arithmetic types)" + << std::endl; + { + const SD_number_t x("x"); + const SD_number_t y("y"); + const SD_number_t x_plus_y = x + y; + const SD_number_t f = x_plus_y * x_plus_y; + + const int x_val = 1; + const int y_val = 2; + SD::types::substitution_map sub_map; + sub_map[x] = SD_number_t(x_val); + sub_map[y] = SD_number_t(y_val); + const double f_val = f.substitute_and_evaluate(sub_map); + Assert(f_val == static_cast(x_val * x_val + 2.0f * x_val * y_val + + y_val * y_val), + ExcMessage("Problem with evaluation")); + } + + std::cout << "Substitution with evaluation (mixed complex types)" + << std::endl; + { + const SD_number_t x("x"); + const SD_number_t y("y"); + const SD_number_t x_plus_y = x + y; + const SD_number_t f = x_plus_y * x_plus_y; + + const std::complex x_val(1.0, 3.0); + const std::complex y_val(2.0, -2.0); + SD::types::substitution_map sub_map; + sub_map[x] = SD_number_t(x_val); + sub_map[y] = SD_number_t(y_val); + const std::complex f_val = + f.substitute_and_evaluate>(sub_map); + Assert(std::abs(f_val - static_cast>( + x_val * x_val + 2.0f * x_val * y_val + + y_val * y_val)) < 1e-12, + ExcMessage("Problem with evaluation")); + } + + std::cout << "Substitution with evaluation (single piecewise function)" + << std::endl; + { + const SD_number_t x("x"); + const SD_number_t y("y"); + const SD_number_t x_plus_y = x + y; + const SD_number_t x_minus_y = x - y; + const SD_number_t f_plus = x_plus_y * x_plus_y; + const SD_number_t f_minus = x_minus_y * x_minus_y; + const SD_number_t f((x > SD_number_t(0.0)), f_plus, f_minus); + + // Condition is met + { + const double x_val = 1.0; + const double y_val = 2.0; + SD::types::substitution_map sub_map; + sub_map[x] = SD_number_t(x_val); + sub_map[y] = SD_number_t(y_val); + const SD_number_t f_subs = f.substitute(sub_map); + const double f_val = static_cast(f_subs); + Assert(f_val == (x_val * x_val + 2.0 * x_val * y_val + y_val * y_val), + ExcMessage( + "Problem with evaluation of single piecewise function")); + } + + // Condition is not met + { + const double x_val = -1.0; + const double y_val = 2.0; + SD::types::substitution_map sub_map; + sub_map[x] = SD_number_t(x_val); + sub_map[y] = SD_number_t(y_val); + const double f_val = f.substitute_and_evaluate(sub_map); + Assert(f_val == (x_val * x_val - 2.0 * x_val * y_val + y_val * y_val), + ExcMessage( + "Problem with evaluation of single piecewise function")); + } + } + + std::cout << "Substitution with evaluation (double piecewise function)" + << std::endl; + { + const SD_number_t x("x"); + const SD_number_t y("y"); + const SD_number_t x_plus_y = x + y; + const SD_number_t x_minus_y = x - y; + const SD_number_t f_plus = x_plus_y * x_plus_y; + const SD_number_t f_plus_plus = 2.0 * x_plus_y * x_plus_y; + const SD_number_t f_minus = x_minus_y * x_minus_y; + const SD_number_t f((x > SD_number_t(0.0)), + SD_number_t(x > SD_number_t(2.0), + f_plus_plus, + f_plus), + f_minus); + + // Outer condition is met, inner condition is met + { + const double x_val = 3.0; + const double y_val = 2.0; + SD::types::substitution_map sub_map; + sub_map[x] = SD_number_t(x_val); + sub_map[y] = SD_number_t(y_val); + const SD_number_t f_subs = f.substitute(sub_map); + const double f_val = static_cast(f_subs); + Assert(f_val == (2.0 * x_val * x_val + 4.0 * x_val * y_val + + 2.0 * y_val * y_val), + ExcMessage( + "Problem with evaluation of double piecewise function")); + } + + // Outer condition is met, inner condition is not met + { + const double x_val = 1.0; + const double y_val = 2.0; + SD::types::substitution_map sub_map; + sub_map[x] = SD_number_t(x_val); + sub_map[y] = SD_number_t(y_val); + const SD_number_t f_subs = f.substitute(sub_map); + const double f_val = static_cast(f_subs); + Assert(f_val == (x_val * x_val + 2.0 * x_val * y_val + y_val * y_val), + ExcMessage( + "Problem with evaluation of double piecewise function")); + } + + // Condition is not met + { + const double x_val = -1.0; + const double y_val = 2.0; + SD::types::substitution_map sub_map; + sub_map[x] = SD_number_t(x_val); + sub_map[y] = SD_number_t(y_val); + const double f_val = f.substitute_and_evaluate(sub_map); + Assert(f_val == (x_val * x_val - 2.0 * x_val * y_val + y_val * y_val), + ExcMessage( + "Problem with evaluation of double piecewise function")); + } + } + + std::cout << "Substitution with evaluation (if-else_if-else type function)" + << std::endl; + { + const SD_number_t x("x"); + const SD_number_t f_1 = x; + const SD_number_t f_2 = 2 * x; + const SD_number_t f_3 = 3 * x; + const SD_number_t f_4 = 4 * x; + const SD_number_t f({{(x > SD_number_t(4.0)), f_1}, + {(x > SD_number_t(2.0)), f_2}, + {(x > SD_number_t(0.0)), f_3}}, + f_4); + + // Condition "if" is met + { + const double x_val = 5.0; + SD::types::substitution_map sub_map; + sub_map[x] = SD_number_t(x_val); + const SD_number_t f_subs = f.substitute(sub_map); + const double f_val = static_cast(f_subs); + Assert( + f_val == x_val, + ExcMessage( + "Problem with evaluation of 'if' branch of terminated piecewise function")); + } + + // Condition "else if (1)" is met + { + const double x_val = 3.0; + SD::types::substitution_map sub_map; + sub_map[x] = SD_number_t(x_val); + const SD_number_t f_subs = f.substitute(sub_map); + const double f_val = static_cast(f_subs); + Assert( + f_val == (2 * x_val), + ExcMessage( + "Problem with evaluation of 'else if (1)' branch of terminated piecewise function")); + } + + // Condition "else if (2)" is met + { + const double x_val = 1.0; + SD::types::substitution_map sub_map; + sub_map[x] = SD_number_t(x_val); + const SD_number_t f_subs = f.substitute(sub_map); + const double f_val = static_cast(f_subs); + Assert( + f_val == (3 * x_val), + ExcMessage( + "Problem with evaluation of 'else if (2)' branch of terminated piecewise function")); + } + + // Condition "else" is met + { + const double x_val = -1.0; + SD::types::substitution_map sub_map; + sub_map[x] = SD_number_t(x_val); + const SD_number_t f_subs = f.substitute(sub_map); + const double f_val = static_cast(f_subs); + Assert( + f_val == (4 * x_val), + ExcMessage( + "Problem with evaluation of 'else' branch of terminated piecewise function")); + } + } + + std::cout << "Substitution with evaluation (if-else_if type function)" + << std::endl; + { + const SD_number_t x("x"); + const SD_number_t f_1 = x; + const SD_number_t f_2 = 2 * x; + const SD_number_t f_3 = 3 * x; + const SD_number_t f({{(x > SD_number_t(4.0)), f_1}, + {(x > SD_number_t(2.0)), f_2}, + {(x > SD_number_t(0.0)), f_3}}); + + // Condition "if" is met + { + const double x_val = 5.0; + SD::types::substitution_map sub_map; + sub_map[x] = SD_number_t(x_val); + const SD_number_t f_subs = f.substitute(sub_map); + const double f_val = static_cast(f_subs); + Assert( + f_val == x_val, + ExcMessage( + "Problem with evaluation of 'if' branch of non-terminated piecewise function")); + } + + // Condition "else if (1)" is met + { + const double x_val = 3.0; + SD::types::substitution_map sub_map; + sub_map[x] = SD_number_t(x_val); + const SD_number_t f_subs = f.substitute(sub_map); + const double f_val = static_cast(f_subs); + Assert( + f_val == (2 * x_val), + ExcMessage( + "Problem with evaluation of 'else if (1)' branch of non-terminated piecewise function")); + } + + // Condition "else if (2)" is met + { + const double x_val = 1.0; + SD::types::substitution_map sub_map; + sub_map[x] = SD_number_t(x_val); + const SD_number_t f_subs = f.substitute(sub_map); + const double f_val = static_cast(f_subs); + Assert( + f_val == (3 * x_val), + ExcMessage( + "Problem with evaluation of 'else if (2)' branch of non-terminated piecewise function")); + } + + // No condition is met + { + const double x_val = -1.0; + SD::types::substitution_map sub_map; + sub_map[x] = SD_number_t(x_val); + const SD_number_t f_subs = f.substitute(sub_map); + const double f_val = static_cast(f_subs); + Assert( + numbers::is_nan(f_val) == true, + ExcMessage( + "Problem with evaluation of 'else' branch of non-terminated piecewise function")); + } + } + } + + deallog << "OK" << std::endl; +} diff --git a/tests/symengine/symengine_number_type_01.output b/tests/symengine/symengine_number_type_01.output new file mode 100644 index 000000000000..94923abb187e --- /dev/null +++ b/tests/symengine/symengine_number_type_01.output @@ -0,0 +1,17 @@ + +DEAL::Constructors +DEAL::Utility functions +DEAL:Serialization::0 0 1 x + +DEAL:Serialization::0 0 1 y + +DEAL:Serialization::0 0 11 2.5 + x + y + +DEAL::Comparison operators +DEAL::Logical operators +DEAL::Assignment operators +DEAL::Math operators +DEAL::Differentiation +DEAL::Substitution +DEAL::Evaluation +DEAL::OK From c5217c15fa235e5d2ecabee4f6c5a35959f1e704 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 2 Apr 2019 21:56:32 +0200 Subject: [PATCH 363/507] add default constructor for ArrayView and a reinit() method --- doc/news/changes/minor/20190402DenisDavydov | 3 ++ include/deal.II/base/array_view.h | 49 +++++++++++++++++- tests/base/array_view_14.cc | 55 +++++++++++++++++++++ tests/base/array_view_14.output | 2 + 4 files changed, 107 insertions(+), 2 deletions(-) create mode 100644 doc/news/changes/minor/20190402DenisDavydov create mode 100644 tests/base/array_view_14.cc create mode 100644 tests/base/array_view_14.output diff --git a/doc/news/changes/minor/20190402DenisDavydov b/doc/news/changes/minor/20190402DenisDavydov new file mode 100644 index 000000000000..a2d7537d6756 --- /dev/null +++ b/doc/news/changes/minor/20190402DenisDavydov @@ -0,0 +1,3 @@ +New: Add ArraView::ArrayView() and ArrayView::reinit(value_type *, const std::size_t). +
    +(Denis Davydov, 2019/04/02) diff --git a/include/deal.II/base/array_view.h b/include/deal.II/base/array_view.h index 130e693f4bef..e51f984b6346 100644 --- a/include/deal.II/base/array_view.h +++ b/include/deal.II/base/array_view.h @@ -93,6 +93,11 @@ class ArrayView */ using const_iterator = const ElementType *; + /** + * Default constructor. + */ + ArrayView(); + /** * Constructor. * @@ -159,6 +164,28 @@ class ArrayView */ ArrayView(std::vector::type> &vector); + /** + * Reinitialize a view. + * + * @param[in] starting_element A pointer to the first element of the array + * this object should represent. + * @param[in] n_elements The length (in elements) of the chunk of memory + * this object should represent. + * + * @note The object that is constructed from these arguments has no + * knowledge how large the object into which it points really is. As a + * consequence, whenever you call ArrayView::operator[], the array view can + * check that the given index is within the range of the view, but it can't + * check that the view is indeed a subset of the valid range of elements of + * the underlying object that allocated that range. In other words, you need + * to ensure that the range of the view specified by the two arguments to + * this constructor is in fact a subset of the elements of the array into + * which it points. The appropriate way to do this is to use the + * make_array_view() functions. + */ + void + reinit(value_type *starting_element, const std::size_t n_elements); + /** * Compare two ArrayView objects of the same type. Two objects are considered * equal if they have the same size and the same starting pointer. @@ -252,12 +279,12 @@ class ArrayView * A pointer to the first element of the range of locations in memory that * this object represents. */ - value_type *const starting_element; + value_type *starting_element; /** * The length of the array this object represents. */ - const std::size_t n_elements; + std::size_t n_elements; friend class ArrayView; }; @@ -305,6 +332,14 @@ namespace internal +template +inline ArrayView::ArrayView() + : starting_element(nullptr) + , n_elements(0) +{} + + + template inline ArrayView::ArrayView( value_type * starting_element, @@ -322,6 +357,16 @@ inline ArrayView::ArrayView( +template +inline void +ArrayView::reinit(value_type *starting_element, + const std::size_t n_elements) +{ + *this = ArrayView(starting_element, n_elements); +} + + + template inline ArrayView::ArrayView( const ArrayView::type, MemorySpaceType> diff --git a/tests/base/array_view_14.cc b/tests/base/array_view_14.cc new file mode 100644 index 000000000000..2e026c0a872e --- /dev/null +++ b/tests/base/array_view_14.cc @@ -0,0 +1,55 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + +// test for class ArrayView +// same as array_view_01.cc but uses default constructor and reinit() + +#include + +#include "../tests.h" + + +void +test() +{ + std::vector v(10); + + ArrayView a; + a.reinit(&v[4], 3); // writable view + a[2] = 42; + + Assert(a[2] == 42, ExcInternalError()); + Assert(v[6] == 42, ExcInternalError()); + + ArrayView a2; + a2.reinit(&v[4], 3); // readable view + Assert(a2[2] == 42, ExcInternalError()); + + ArrayView a3(a); // readable view, converted from 'a' + Assert(a3[2] == 42, ExcInternalError()); + + deallog << "OK" << std::endl; +} + + + +int +main() +{ + initlog(); + + test(); +} diff --git a/tests/base/array_view_14.output b/tests/base/array_view_14.output new file mode 100644 index 000000000000..0fd8fc12f0b4 --- /dev/null +++ b/tests/base/array_view_14.output @@ -0,0 +1,2 @@ + +DEAL::OK From 6c685776132ed8153981a91567113f3e0db0c79e Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Wed, 3 Apr 2019 05:04:16 +0200 Subject: [PATCH 364/507] Test SCALAPACK with -Werror --- tests/scalapack/scalapack_06.cc | 2 +- tests/scalapack/scalapack_06a.cc | 2 +- tests/scalapack/scalapack_06b.cc | 2 +- tests/scalapack/scalapack_06c.cc | 2 +- tests/scalapack/scalapack_12_a.cc | 6 ++++-- tests/scalapack/scalapack_12_b.cc | 6 ++++-- tests/scalapack/scalapack_12_c.cc | 6 ++++-- tests/scalapack/scalapack_12_d.cc | 6 ++++-- tests/scalapack/scalapack_13_a.cc | 6 ++++-- tests/scalapack/scalapack_13_b.cc | 6 ++++-- tests/scalapack/scalapack_14_a.cc | 6 ++++-- tests/scalapack/scalapack_14_b.cc | 6 ++++-- tests/scalapack/scalapack_15.cc | 2 +- tests/scalapack/scalapack_15_a.cc | 2 +- 14 files changed, 38 insertions(+), 22 deletions(-) diff --git a/tests/scalapack/scalapack_06.cc b/tests/scalapack/scalapack_06.cc index 78aee5295475..1c6a434b71f1 100644 --- a/tests/scalapack/scalapack_06.cc +++ b/tests/scalapack/scalapack_06.cc @@ -104,7 +104,7 @@ test(const unsigned int size, &*work.begin(), &lwork, &info); - lwork = work[0]; + lwork = static_cast(work[0]); work.resize(lwork); syev(&jobz, &uplo, diff --git a/tests/scalapack/scalapack_06a.cc b/tests/scalapack/scalapack_06a.cc index 39cf9f63f60d..7584d7041c94 100644 --- a/tests/scalapack/scalapack_06a.cc +++ b/tests/scalapack/scalapack_06a.cc @@ -100,7 +100,7 @@ test(const unsigned int size, &*work.begin(), &lwork, &info); - lwork = work[0]; + lwork = static_cast(work[0]); work.resize(lwork); syev(&jobz, &uplo, diff --git a/tests/scalapack/scalapack_06b.cc b/tests/scalapack/scalapack_06b.cc index 707aecfeeba7..4d02c8399f4e 100644 --- a/tests/scalapack/scalapack_06b.cc +++ b/tests/scalapack/scalapack_06b.cc @@ -105,7 +105,7 @@ test(const unsigned int size, &*work.begin(), &lwork, &info); - lwork = work[0]; + lwork = static_cast(work[0]); work.resize(lwork); syev(&jobz, &uplo, diff --git a/tests/scalapack/scalapack_06c.cc b/tests/scalapack/scalapack_06c.cc index 37a376c74c89..d7c59d22fdda 100644 --- a/tests/scalapack/scalapack_06c.cc +++ b/tests/scalapack/scalapack_06c.cc @@ -100,7 +100,7 @@ test(const unsigned int size, &*work.begin(), &lwork, &info); - lwork = work[0]; + lwork = static_cast(work[0]); work.resize(lwork); syev(&jobz, &uplo, diff --git a/tests/scalapack/scalapack_12_a.cc b/tests/scalapack/scalapack_12_a.cc index 8955491b6ef4..b89b755b45d2 100644 --- a/tests/scalapack/scalapack_12_a.cc +++ b/tests/scalapack/scalapack_12_a.cc @@ -44,8 +44,10 @@ test() std::cout << std::setprecision(10); ConditionalOStream pcout(std::cout, (this_mpi_process == 0)); - const unsigned int proc_rows = std::floor(std::sqrt(n_mpi_processes)); - const unsigned int proc_columns = std::floor(n_mpi_processes / proc_rows); + const auto proc_rows = + static_cast(std::floor(std::sqrt(n_mpi_processes))); + const auto proc_columns = + static_cast(std::floor(n_mpi_processes / proc_rows)); // create 2d process grid std::shared_ptr grid = std::make_shared(mpi_communicator, diff --git a/tests/scalapack/scalapack_12_b.cc b/tests/scalapack/scalapack_12_b.cc index 0f4cdb466cd7..be7843782aa2 100644 --- a/tests/scalapack/scalapack_12_b.cc +++ b/tests/scalapack/scalapack_12_b.cc @@ -45,8 +45,10 @@ test() std::cout << std::setprecision(10); ConditionalOStream pcout(std::cout, (this_mpi_process == 0)); - const unsigned int proc_rows = std::floor(std::sqrt(n_mpi_processes)); - const unsigned int proc_columns = std::floor(n_mpi_processes / proc_rows); + const auto proc_rows = + static_cast(std::floor(std::sqrt(n_mpi_processes))); + const auto proc_columns = + static_cast(std::floor(n_mpi_processes / proc_rows)); // create 2d process grid std::shared_ptr grid = std::make_shared(mpi_communicator, diff --git a/tests/scalapack/scalapack_12_c.cc b/tests/scalapack/scalapack_12_c.cc index 498a7ffc3817..71a6c7ed4938 100644 --- a/tests/scalapack/scalapack_12_c.cc +++ b/tests/scalapack/scalapack_12_c.cc @@ -45,8 +45,10 @@ test() std::cout << std::setprecision(10); ConditionalOStream pcout(std::cout, (this_mpi_process == 0)); - const unsigned int proc_rows = std::floor(std::sqrt(n_mpi_processes)); - const unsigned int proc_columns = std::floor(n_mpi_processes / proc_rows); + const auto proc_rows = + static_cast(std::floor(std::sqrt(n_mpi_processes))); + const auto proc_columns = + static_cast(std::floor(n_mpi_processes / proc_rows)); // create 2d process grid std::shared_ptr grid = std::make_shared(mpi_communicator, diff --git a/tests/scalapack/scalapack_12_d.cc b/tests/scalapack/scalapack_12_d.cc index 2f4f8e6d0866..81202354e588 100644 --- a/tests/scalapack/scalapack_12_d.cc +++ b/tests/scalapack/scalapack_12_d.cc @@ -45,8 +45,10 @@ test() std::cout << std::setprecision(10); ConditionalOStream pcout(std::cout, (this_mpi_process == 0)); - const unsigned int proc_rows = std::floor(std::sqrt(n_mpi_processes)); - const unsigned int proc_columns = std::floor(n_mpi_processes / proc_rows); + const auto proc_rows = + static_cast(std::floor(std::sqrt(n_mpi_processes))); + const auto proc_columns = + static_cast(std::floor(n_mpi_processes / proc_rows)); // create 2d process grid std::shared_ptr grid = std::make_shared(mpi_communicator, diff --git a/tests/scalapack/scalapack_13_a.cc b/tests/scalapack/scalapack_13_a.cc index e3d55299bad4..81c73d4809c1 100644 --- a/tests/scalapack/scalapack_13_a.cc +++ b/tests/scalapack/scalapack_13_a.cc @@ -44,8 +44,10 @@ test(const unsigned int block_size_i, const unsigned int block_size_j) std::cout << std::setprecision(10); ConditionalOStream pcout(std::cout, (this_mpi_process == 0)); - const unsigned int proc_rows = std::floor(std::sqrt(n_mpi_processes)); - const unsigned int proc_columns = std::floor(n_mpi_processes / proc_rows); + const auto proc_rows = + static_cast(std::floor(std::sqrt(n_mpi_processes))); + const auto proc_columns = + static_cast(std::floor(n_mpi_processes / proc_rows)); // create 2d process grid std::shared_ptr grid = std::make_shared(mpi_communicator, diff --git a/tests/scalapack/scalapack_13_b.cc b/tests/scalapack/scalapack_13_b.cc index 20fd3bd4bcf4..5334bdbc7a02 100644 --- a/tests/scalapack/scalapack_13_b.cc +++ b/tests/scalapack/scalapack_13_b.cc @@ -44,8 +44,10 @@ test(const unsigned int block_size_i, const unsigned int block_size_j) std::cout << std::setprecision(10); ConditionalOStream pcout(std::cout, (this_mpi_process == 0)); - const unsigned int proc_rows = std::floor(std::sqrt(n_mpi_processes)); - const unsigned int proc_columns = std::floor(n_mpi_processes / proc_rows); + const auto proc_rows = + static_cast(std::floor(std::sqrt(n_mpi_processes))); + const auto proc_columns = + static_cast(std::floor(n_mpi_processes / proc_rows)); // create 2d process grid std::shared_ptr grid = std::make_shared(mpi_communicator, diff --git a/tests/scalapack/scalapack_14_a.cc b/tests/scalapack/scalapack_14_a.cc index 81324ccf313e..c34e3e1ebdd4 100644 --- a/tests/scalapack/scalapack_14_a.cc +++ b/tests/scalapack/scalapack_14_a.cc @@ -45,8 +45,10 @@ test(const unsigned int block_size_i, const unsigned int block_size_j) std::cout << std::setprecision(10); ConditionalOStream pcout(std::cout, (this_mpi_process == 0)); - const unsigned int proc_rows = std::floor(std::sqrt(n_mpi_processes)); - const unsigned int proc_columns = std::floor(n_mpi_processes / proc_rows); + const auto proc_rows = + static_cast(std::floor(std::sqrt(n_mpi_processes))); + const auto proc_columns = + static_cast(std::floor(n_mpi_processes / proc_rows)); // create 2d process grid const std::vector sizes = {{400, 500}}; std::shared_ptr grid = diff --git a/tests/scalapack/scalapack_14_b.cc b/tests/scalapack/scalapack_14_b.cc index e32f5c653824..d79e17996aef 100644 --- a/tests/scalapack/scalapack_14_b.cc +++ b/tests/scalapack/scalapack_14_b.cc @@ -45,8 +45,10 @@ test(const unsigned int block_size_i, const unsigned int block_size_j) std::cout << std::setprecision(10); ConditionalOStream pcout(std::cout, (this_mpi_process == 0)); - const unsigned int proc_rows = std::floor(std::sqrt(n_mpi_processes)); - const unsigned int proc_columns = std::floor(n_mpi_processes / proc_rows); + const auto proc_rows = + static_cast(std::floor(std::sqrt(n_mpi_processes))); + const auto proc_columns = + static_cast(std::floor(n_mpi_processes / proc_rows)); // create 2d process grid const std::vector sizes = {{400, 500}}; std::shared_ptr grid = diff --git a/tests/scalapack/scalapack_15.cc b/tests/scalapack/scalapack_15.cc index e29fc69cbbe1..1dd40e682b49 100644 --- a/tests/scalapack/scalapack_15.cc +++ b/tests/scalapack/scalapack_15.cc @@ -128,7 +128,7 @@ test(const unsigned int size, &liwork, &info); - lwork = work[0]; + lwork = static_cast(work[0]); work.resize(lwork); liwork = iwork[0]; iwork.resize(liwork); diff --git a/tests/scalapack/scalapack_15_a.cc b/tests/scalapack/scalapack_15_a.cc index 59bc9368c882..515be289b390 100644 --- a/tests/scalapack/scalapack_15_a.cc +++ b/tests/scalapack/scalapack_15_a.cc @@ -128,7 +128,7 @@ test(const unsigned int size, &liwork, &info); - lwork = work[0]; + lwork = static_cast(work[0]); work.resize(lwork); liwork = iwork[0]; iwork.resize(liwork); From 5905b90cb7d31d28e077b363b697a3a93f637843 Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Wed, 3 Apr 2019 08:53:59 -0600 Subject: [PATCH 365/507] fix hdf in serial - fix compilation - fix warnings about unused variables - move some variables around (smaller scope) --- source/base/hdf5.cc | 57 +++++++++++++++++++++++++++++++-------------- 1 file changed, 40 insertions(+), 17 deletions(-) diff --git a/source/base/hdf5.cc b/source/base/hdf5.cc index d32555839966..75e45497230b 100644 --- a/source/base/hdf5.cc +++ b/source/base/hdf5.cc @@ -264,22 +264,25 @@ namespace HDF5 void set_plist(hid_t &plist, const bool mpi) { - herr_t ret; - if (mpi) { +# ifdef DEAL_II_WITH_MPI + herr_t ret; plist = H5Pcreate(H5P_DATASET_XFER); Assert(plist >= 0, ExcInternalError()); ret = H5Pset_dxpl_mpio(plist, H5FD_MPIO_COLLECTIVE); Assert(ret >= 0, ExcInternalError()); +# else + AssertThrow(false, ExcNotImplemented()); +# endif } else { plist = H5P_DEFAULT; } - // This avoids the unused warning - (void)ret; + (void)plist; + (void)mpi; } @@ -297,10 +300,10 @@ namespace HDF5 const bool mpi, const bool query_io_mode) { - herr_t ret; - if (mpi) { +# ifdef DEAL_II_WITH_MPI + herr_t ret; if (query_io_mode) { ret = H5Pget_mpio_actual_io_mode(plist, &io_mode); @@ -313,9 +316,17 @@ namespace HDF5 } ret = H5Pclose(plist); Assert(ret >= 0, ExcInternalError()); +# else + AssertThrow(false, ExcNotImplemented()); +# endif } - (void)ret; + (void)plist; + (void)io_mode; + (void)local_no_collective_cause; + (void)global_no_collective_cause; + (void)mpi; + (void)query_io_mode; } @@ -1377,7 +1388,15 @@ namespace HDF5 File::File(const std::string &name, const FileAccessMode mode) - : File(name, mode, false, MPI_COMM_NULL) + : File(name, + mode, + false, +# ifdef DEAL_II_WITH_MPI + MPI_COMM_NULL +# else + 0 +# endif + ) {} @@ -1404,22 +1423,25 @@ namespace HDF5 delete pointer; }); - hid_t plist; - herr_t ret; - const MPI_Info info = MPI_INFO_NULL; + hid_t plist; + herr_t ret; if (mpi) { -# ifndef DEAL_II_WITH_MPI - AssertThrow(false, ExcMessage("MPI support is disabled.")); -# endif // DEAL_II_WITH_MPI -# ifndef H5_HAVE_PARALLEL - AssertThrow(false, ExcMessage("HDF5 parallel support is disabled.")); -# endif // H5_HAVE_PARALLEL +# ifdef DEAL_II_WITH_MPI +# ifdef H5_HAVE_PARALLEL + const MPI_Info info = MPI_INFO_NULL; + plist = H5Pcreate(H5P_FILE_ACCESS); Assert(plist >= 0, ExcMessage("Error at H5Pcreate")); ret = H5Pset_fapl_mpio(plist, mpi_communicator, info); Assert(ret >= 0, ExcMessage("Error at H5Pset_fapl_mpio")); +# else + AssertThrow(false, ExcMessage("HDF5 parallel support is disabled.")); +# endif // H5_HAVE_PARALLEL +# else + AssertThrow(false, ExcMessage("MPI support is disabled.")); +# endif // DEAL_II_WITH_MPI } else { @@ -1450,6 +1472,7 @@ namespace HDF5 } (void)ret; + (void)mpi_communicator; } From 4a047ca75b358adc9d24b273044c8a81964401f2 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Wed, 3 Apr 2019 12:28:30 -0400 Subject: [PATCH 366/507] Fix space in error message --- include/deal.II/lac/sparse_direct.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/include/deal.II/lac/sparse_direct.h b/include/deal.II/lac/sparse_direct.h index aa6dfc92a957..7a15d120d7d8 100644 --- a/include/deal.II/lac/sparse_direct.h +++ b/include/deal.II/lac/sparse_direct.h @@ -310,7 +310,7 @@ class SparseDirectUMFPACK : public Subscriptor "single zero eigenvalue and its rank is therefore " "deficient by one." "\n\n" - "The other common situation is that you run out of memory." + "The other common situation is that you run out of memory. " "On a typical laptop or desktop, it should easily be possible " "to solve problems with 100,000 unknowns in 2d. If you are " "solving problems with many more unknowns than that, in " From 306eecc6d1348c150d90b5106b87dc50022b7124 Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Mon, 1 Apr 2019 21:59:29 +0200 Subject: [PATCH 367/507] Add a class to perform GeneralDataStorage --- .../minor/20190402LucaHeltaiJean-PaulPelteret | 5 + .../deal.II/algorithms/general_data_storage.h | 473 ++++++++++++++++++ source/algorithms/CMakeLists.txt | 1 + source/algorithms/general_data_storage.cc | 61 +++ tests/algorithms/general_data_storage_01.cc | 228 +++++++++ .../general_data_storage_01.debug.output | 74 +++ .../general_data_storage_01.release.output | 24 + 7 files changed, 866 insertions(+) create mode 100644 doc/news/changes/minor/20190402LucaHeltaiJean-PaulPelteret create mode 100644 include/deal.II/algorithms/general_data_storage.h create mode 100644 source/algorithms/general_data_storage.cc create mode 100644 tests/algorithms/general_data_storage_01.cc create mode 100644 tests/algorithms/general_data_storage_01.debug.output create mode 100644 tests/algorithms/general_data_storage_01.release.output diff --git a/doc/news/changes/minor/20190402LucaHeltaiJean-PaulPelteret b/doc/news/changes/minor/20190402LucaHeltaiJean-PaulPelteret new file mode 100644 index 000000000000..942968300abc --- /dev/null +++ b/doc/news/changes/minor/20190402LucaHeltaiJean-PaulPelteret @@ -0,0 +1,5 @@ +New: The GeneralDataStorage class facilitates the storage of any general data. +It offers the ability to store any amount of data, of any type, which is then +made accessible by an identifier string. +
    +(Luca Heltai, Jean-Paul Pelteret, 2019/04/02) diff --git a/include/deal.II/algorithms/general_data_storage.h b/include/deal.II/algorithms/general_data_storage.h new file mode 100644 index 000000000000..ed2905776161 --- /dev/null +++ b/include/deal.II/algorithms/general_data_storage.h @@ -0,0 +1,473 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + +#ifndef dealii_algorithms_general_data_storage_h +#define dealii_algorithms_general_data_storage_h + +#include + +#include +#include + +#include +#include + +#include +#include +#include +#include + +DEAL_II_NAMESPACE_OPEN + + +/** + * This class facilitates the storage of any general data. + * It offers a mechanism to store any amount of data, of any type, + * which is then made accessible by an identifier string. + * + * When using this class, please cite + * + * @code{.bib} + * @article{SartoriGiulianiBardelloni-2018-a, + * Author = {Sartori, Alberto and Giuliani, Nicola and + * Bardelloni, Mauro and Heltai, Luca}, + * Journal = {SoftwareX}, + * Pages = {318--327}, + * Title = {{deal2lkit: A toolkit library for high performance + * programming in deal.II}}, + * Volume = {7}, + * Year = {2018}} + * @endcode + * + * @author Luca Heltai, Jean-Paul Pelteret, 2019 + */ +class GeneralDataStorage : public Subscriptor +{ +public: + /** + * Default constructor. + */ + GeneralDataStorage() = default; + + /** + * Copy constructor. + */ + GeneralDataStorage(const GeneralDataStorage &) = default; + + /** + * Move constructor. + */ + GeneralDataStorage(GeneralDataStorage &&) = default; + + /** + * Number of objects stored by this class instance. + */ + std::size_t + size() const; + + /** + * Merge the contents of @p other_data with this object. + */ + void + merge(const GeneralDataStorage &other_data); + + /** + * Print the contents of the internal cache to the @p stream. + * + * Each key and value pair in the @p any_data map are printed on an + * individual line, with the std::string<\tt> key listed first + * followed by the demangled type_id of the associated mapped + * type. + */ + template + void + print_info(Stream &stream); + + /** + * Clear all data stored in this class instance. + * + * After this function is called, all copied data owned by this class will + * go out of scope. Furthermore, all scoping requirements for data referenced + * by this class instance will be lifted. + * + * To clarify this point, consider the following small example: + * + * @code + * GeneralDataStorage data; + * + * { + * const double some_number = ...; + * data.add_unique_reference("value", some_number); + * + * // Adding either of these next two lines could fix the + * // issue, by removing the association of some_number with data: + * // data.remove_object_with_name("value"); + * // data.reset(); + * } // some_number goes out of scope here + * + * const double some_other_number + * = data.get_object_with_name("value"); // Invalid call + * @endcode + * + * In the code above, the @p data object has a longer scope than + * some_number. By the time we fetch the "value" from + * @p data , the reference to @p some_number is no longer valid. + * + * Similarly, for data copied into a GeneralDataStorage object one should + * consider the scope under which it remains valid: + * + * @code + * double* ptr_to_some_number = null_ptr; + * + * { + * GeneralDataStorage data; + * const double some_number = ...; + * data.add_unique_copy("value", some_number); + * + * ptr_to_some_number = &(data.get_object_with_name("value")); + * } // The copy to some_number goes out of scope here + * + * const double some_other_number + * = *ptr_to_some_number; // Invalid call + * @endcode + * + * Similar to the first example, we must be concious of the fact that the + * copies of any @p Type stored by @p data only remains valid while the + * GeneralDataStorage instance in which it is stored is alive. + * + * Furthermore, as elucidated in the last example, the copy of the + * class instance (owned by GeneralDataStorage) that is being pointed to + * is no longer alive when the reset() function is called, or when it is + * removed via a call to remove_object_with_name(). + * + * @code + * GeneralDataStorage data; + * double* ptr_to_some_number = null_ptr; + * + * { + * const double some_number = ...; + * data.add_unique_copy("value", some_number); + * + * ptr_to_some_number = &(data.get_object_with_name("value")); + * + * // The copy to some_number would go out of scope when either of + * // following two calls are made: + * data.remove_object_with_name("value"); + * data.reset(); + * } + * + * const double some_other_number + * = *ptr_to_some_number; // Invalid call + * @endcode + */ + void + reset(); + + /** + * @name Data storage and access + */ + //@{ + + /** + * Store internally a copy of the given object. The copied object is + * owned by this class, and is accessible via reference through the + * get_object_with_name() method. + * + * This function ensures that no @p entry with the given @name is + * already stored by this class instance. + */ + template + void + add_unique_copy(const std::string &name, const Type &entry); + + /** + * Store internally a copy of the given object. The copied object is + * owned by this class, and is accessible via reference through the + * get_object_with_name() method. + * + * This function does not perform any checks to ensure that the @p entry + * with the given @name is already stored by this class instance. If the + * @p name does in fact point to existing data, then this is overwritten. + */ + template + void + add_or_overwrite_copy(const std::string &name, const Type &entry); + + /** + * Add a reference to an already existing object. The object is not + * owned by this class, and the user has to guarantee that the + * referenced object lives longer than this class instance. The stored + * reference is accessible through the get_object_with_name() method. + * + * This function ensures that no @p entry with the given @name is + * already stored by this class instance. + */ + template + void + add_unique_reference(const std::string &name, Type &entry); + + /** + * Add a reference to an already existing object. The object is not + * owned by this class, and the user has to guarantee that the + * referenced object lives longer than this class instance. The stored + * reference is accessible through the get_object_with_name() method. + * + * This function does not perform any checks to ensure that the @p entry + * with the given @name is already stored by this class instance. If the + * @p name does in fact point to existing data, then this is overwritten. + */ + template + void + add_or_overwrite_reference(const std::string &name, Type &entry); + + /** + * Return a reference to the object with given name. If the object does + * not exist, then the input @p arguments will be used to construct an object + * of the given @p Type and a reference to this new object then be returned. + * + * A copy of an object of type @p Type , which is owned by this class + * instance, is generated by calling its constructor with the given set of + * arguments. For this function, the @p arguments are passed as + * lvalue references. + */ + template + Type & + get_or_add_object_with_name(const std::string &name, Args &... arguments); + + /** + * Return a reference to the object with given name. If the object does + * not exist, then the input @p arguments will be used to construct an object + * of the given @p Type and a reference to this new object then be returned. + * + * A copy of an object of type @p Type , which is owned by this class + * instance, is generated by calling its constructor with the given set of + * arguments. In contrast to the previous function of the same name, for + * this function the @p arguments are passed as rvalue references. + */ + template + Type & + get_or_add_object_with_name(const std::string &name, Args &&... arguments); + + /** + * Return a reference to the object with given name. + * + * This function throws an exception if either an object with the given name + * is not stored in this class, or if the object with the given name is + * neither of the exact specified @p Type nor a pointer to the @p Type. + */ + template + Type & + get_object_with_name(const std::string &name); + + /** + * Return a constant reference to the object with the given name. + * + * This function throws an exception if either an object with the given name + * is not stored in this class, or if the object with the given name is + * neither of the exact specified @p Type nor a pointer to the @p Type. + */ + template + const Type & + get_object_with_name(const std::string &name) const; + + /** + * Find out if we store an object with given name. + */ + bool + stores_object_with_name(const std::string &name) const; + + /** + * Find out if we store an object with given name. + */ + void + remove_object_with_name(const std::string &name); + + //@} + + /** + * An entry with this name does not exist in the internal boost::any map. + */ + DeclException1(ExcNameNotFound, + std::string, + << "No entry with the name " << arg1 << " exists."); + + /** + * An entry with this name does not exist in the internal boost::any map. + */ + DeclException1(ExcNameHasBeenFound, + std::string, + << "An entry with the name " << arg1 << " already exists."); + + /** + * The requested type and the stored type are different. + */ + DeclException3(ExcTypeMismatch, + std::string, + const char *, + const char *, + << "The stored type for entry with name \"" << arg1 << "\" is " + << arg2 << " but you requested type " << arg3 << "."); + +private: + /** + * Arbitrary user data, identified by a string. + */ + std::map any_data; +}; + + +/*----------------- Inline and template methods -----------------*/ + + +#ifndef DOXYGEN + + +template +void +GeneralDataStorage::print_info(Stream &os) +{ + for (auto it : any_data) + { + os << it.first << '\t' << '\t' + << boost::core::demangle(it.second.type().name()) << std::endl; + } +} + + +template +void +GeneralDataStorage::add_unique_copy(const std::string &name, const Type &entry) +{ + Assert(!stores_object_with_name(name), ExcNameHasBeenFound(name)); + add_or_overwrite_copy(name, entry); +} + + +template +void +GeneralDataStorage::add_or_overwrite_copy(const std::string &name, + const Type & entry) +{ + any_data[name] = entry; +} + + +template +void +GeneralDataStorage::add_unique_reference(const std::string &name, Type &entry) +{ + Assert(!stores_object_with_name(name), ExcNameHasBeenFound(name)); + add_or_overwrite_reference(name, entry); +} + + +template +void +GeneralDataStorage::add_or_overwrite_reference(const std::string &name, + Type & entry) +{ + Type *ptr = &entry; + any_data[name] = ptr; +} + + +template +Type & +GeneralDataStorage::get_object_with_name(const std::string &name) +{ + Assert(stores_object_with_name(name), ExcNameNotFound(name)); + + Type *p = nullptr; + + if (any_data[name].type() == typeid(Type *)) + { + p = boost::any_cast(any_data[name]); + } + else if (any_data[name].type() == typeid(Type)) + { + p = boost::any_cast(&any_data[name]); + } + else + { + Assert(false, + ExcTypeMismatch(name, + any_data[name].type().name(), + typeid(Type).name())); + } + + return *p; +} + + +template +const Type & +GeneralDataStorage::get_object_with_name(const std::string &name) const +{ + AssertThrow(stores_object_with_name(name), ExcNameNotFound(name)); + + const auto it = any_data.find(name); + + if (it->second.type() == typeid(Type *)) + { + const Type *p = boost::any_cast(it->second); + return *p; + } + else if (it->second.type() == typeid(Type)) + { + const Type *p = boost::any_cast(&it->second); + return *p; + } + else + { + Assert(false, + ExcTypeMismatch(name, + it->second.type().name(), + typeid(Type).name())); + const Type *p = nullptr; + return *p; + } +} + + +template +Type & +GeneralDataStorage::get_or_add_object_with_name(const std::string &name, + Args &... arguments) +{ + if (!stores_object_with_name(name)) + add_unique_copy(name, Type(arguments...)); + + return get_object_with_name(name); +} + + +template +Type & +GeneralDataStorage::get_or_add_object_with_name(const std::string &name, + Args &&... arguments) +{ + if (!stores_object_with_name(name)) + add_unique_copy(name, Type(std::forward(arguments)...)); + + return get_object_with_name(name); +} + + +#endif // DOXYGEN + + +DEAL_II_NAMESPACE_CLOSE + +#endif // dealii_algorithms_general_data_storage_h diff --git a/source/algorithms/CMakeLists.txt b/source/algorithms/CMakeLists.txt index 2eb6e268dbcc..030b6f36cd3a 100644 --- a/source/algorithms/CMakeLists.txt +++ b/source/algorithms/CMakeLists.txt @@ -16,6 +16,7 @@ INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_BINARY_DIR}) SET(_src + general_data_storage.cc operator.cc timestep_control.cc ) diff --git a/source/algorithms/general_data_storage.cc b/source/algorithms/general_data_storage.cc new file mode 100644 index 000000000000..85ff371299bf --- /dev/null +++ b/source/algorithms/general_data_storage.cc @@ -0,0 +1,61 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + +#include + + +DEAL_II_NAMESPACE_OPEN + + +std::size_t +GeneralDataStorage::size() const +{ + return any_data.size(); +} + + +void +GeneralDataStorage::merge(const GeneralDataStorage &other) +{ + any_data.insert(other.any_data.begin(), other.any_data.end()); +} + + +void +GeneralDataStorage::reset() +{ + any_data.clear(); +} + + +bool +GeneralDataStorage::stores_object_with_name(const std::string &name) const +{ + return any_data.find(name) != any_data.end(); +} + + +void +GeneralDataStorage::remove_object_with_name(const std::string &name) +{ + const auto it = any_data.find(name); + if (it != any_data.end()) + any_data.erase(it); +} + + + +DEAL_II_NAMESPACE_CLOSE diff --git a/tests/algorithms/general_data_storage_01.cc b/tests/algorithms/general_data_storage_01.cc new file mode 100644 index 000000000000..fc421e7895af --- /dev/null +++ b/tests/algorithms/general_data_storage_01.cc @@ -0,0 +1,228 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + +// Test the core functionality of the GeneralDataStorage class + + +#include + +#include + +#include "../tests.h" + +int +main() +{ + initlog(); + + GeneralDataStorage data; + + deallog << "Add by copy" << std::endl; + { + data.reset(); + + // Create new data instance + const double val_1 = 1.0; + data.add_unique_copy("value", val_1); + const double &val_2 = data.get_object_with_name("value"); + Assert(data.stores_object_with_name("value"), ExcInternalError()); + Assert(val_2 == val_1, ExcInternalError()); + Assert(&val_2 != &val_1, ExcInternalError()); + + // Allowed overwrite of existing data + const double val_3 = 2.0; + data.add_or_overwrite_copy("value", val_3); + const double &val_4 = data.get_object_with_name("value"); + Assert(data.stores_object_with_name("value"), ExcInternalError()); + Assert(val_4 == val_3, ExcInternalError()); + Assert(&val_4 != &val_3, ExcInternalError()); + + // Create new data instance using alternative function + const double val_5 = 3.0; + data.add_or_overwrite_copy("value_2", val_5); + const double &val_6 = data.get_object_with_name("value_2"); + Assert(data.stores_object_with_name("value_2"), ExcInternalError()); + Assert(val_6 == val_5, ExcInternalError()); + Assert(&val_6 != &val_5, ExcInternalError()); + + deallog << "Size: " << data.size() << std::endl; + } + + deallog << "Add by reference" << std::endl; + { + data.reset(); + + // Create new data instance + const double val_1 = 1.0; + data.add_unique_reference("value", val_1); + const double &val_2 = data.get_object_with_name("value"); + Assert(data.stores_object_with_name("value"), ExcInternalError()); + Assert(val_2 == val_1, ExcInternalError()); + Assert(&val_2 == &val_1, ExcInternalError()); + + // Allowed overwrite of existing data + const double val_3 = 2.0; + data.add_or_overwrite_reference("value", val_3); + const double &val_4 = data.get_object_with_name("value"); + Assert(data.stores_object_with_name("value"), ExcInternalError()); + Assert(val_4 == val_3, ExcInternalError()); + Assert(&val_4 == &val_3, ExcInternalError()); + + // Create new data instance using alternative function + const double val_5 = 3.0; + data.add_or_overwrite_reference("value_2", val_5); + const double &val_6 = data.get_object_with_name("value_2"); + Assert(data.stores_object_with_name("value_2"), ExcInternalError()); + Assert(val_6 == val_5, ExcInternalError()); + Assert(&val_6 == &val_5, ExcInternalError()); + + deallog << "Size: " << data.size() << std::endl; + } + + deallog << "Add or construct" << std::endl; + { + data.reset(); + + using Type = std::pair; + + // Create new data instance + const Type &val_1 = + data.get_or_add_object_with_name("value", 1.0, 2.0); + Assert(data.stores_object_with_name("value"), ExcInternalError()); + Assert(val_1 == Type({1.0, 2.0}), ExcInternalError()); + + // Should not overwrite existing data + const Type &val_2 = + data.get_or_add_object_with_name("value", Type(3.0, 4.0)); + Assert(data.stores_object_with_name("value"), ExcInternalError()); + Assert(val_2 == Type({1.0, 2.0}), ExcInternalError()); + + deallog << "Size: " << data.size() << std::endl; + } + + deallog << "Merge" << std::endl; + { + data.reset(); + + const double val_1 = 1.0; + data.add_unique_copy("value", val_1); + + GeneralDataStorage data_2; + data_2.add_unique_copy("value", 2.0); // Duplicate + data_2.add_unique_copy("value_2", 3.0); + + deallog << "Data pre-merge:" << std::endl; + data.print_info(deallog); + deallog << "Size: " << data.size() << std::endl; + deallog << "Data 2 pre-merge:" << std::endl; + data_2.print_info(deallog); + deallog << "Size: " << data_2.size() << std::endl; + + data.merge(data_2); + + deallog << "Data post-merge:" << std::endl; + data.print_info(deallog); + deallog << "Size: " << data.size() << std::endl; + } + + + deal_II_exceptions::disable_abort_on_exception(); + + deallog << "Try to overwrite existing entry: Copy" << std::endl; + { + data.reset(); + + const double val_1 = 1.0; + data.add_unique_copy("value", val_1); + + try + { + const double val_2 = 1.0; + data.add_unique_copy("value", val_2); + } + catch (const GeneralDataStorage::ExcNameHasBeenFound &exc) + { + deallog << exc.what() << std::endl; + } + } + + deallog << "Try to overwrite existing entry: Reference" << std::endl; + { + data.reset(); + + const double val_1 = 1.0; + data.add_unique_reference("value", val_1); + + try + { + const double val_2 = 2.0; + data.add_unique_reference("value", val_2); + } + catch (const GeneralDataStorage::ExcNameHasBeenFound &exc) + { + deallog << exc.what() << std::endl; + } + } + + deallog << "Fetch non-existing entry" << std::endl; + { + data.reset(); + + try + { + data.get_object_with_name("value"); + } + catch (const GeneralDataStorage::ExcNameNotFound &exc) + { + deallog << exc.what() << std::endl; + } + } + + deallog << "Access removed entry (reference)" << std::endl; + { + data.reset(); + + const double val_1 = 1.0; + data.add_unique_reference("value", val_1); + data.remove_object_with_name("value"); + + try + { + data.get_object_with_name("value"); + } + catch (const GeneralDataStorage::ExcNameNotFound &exc) + { + deallog << exc.what() << std::endl; + } + } + + deallog << "Access removed entry (copy)" << std::endl; + { + data.reset(); + + data.add_unique_copy("value", 1.0); + data.remove_object_with_name("value"); + + try + { + data.get_object_with_name("value"); + } + catch (const GeneralDataStorage::ExcNameNotFound &exc) + { + deallog << exc.what() << std::endl; + } + } +} diff --git a/tests/algorithms/general_data_storage_01.debug.output b/tests/algorithms/general_data_storage_01.debug.output new file mode 100644 index 000000000000..4583c5e2160f --- /dev/null +++ b/tests/algorithms/general_data_storage_01.debug.output @@ -0,0 +1,74 @@ + +DEAL::Add by copy +DEAL::Size: 2 +DEAL::Add by reference +DEAL::Size: 2 +DEAL::Add or construct +DEAL::Size: 1 +DEAL::Merge +DEAL::Data pre-merge: +DEAL::value double +DEAL::Size: 1 +DEAL::Data 2 pre-merge: +DEAL::value double +DEAL::value_2 double +DEAL::Size: 2 +DEAL::Data post-merge: +DEAL::value double +DEAL::value_2 double +DEAL::Size: 2 +DEAL::Try to overwrite existing entry: Copy +DEAL:: +-------------------------------------------------------- +An error occurred in file in function + void dealii::GeneralDataStorage::add_unique_copy(const std::string &, const Type &) [Type = double] +The violated condition was: + !stores_object_with_name(name) +Additional information: + An entry with the name value already exists. +-------------------------------------------------------- + +DEAL::Try to overwrite existing entry: Reference +DEAL:: +-------------------------------------------------------- +An error occurred in file in function + void dealii::GeneralDataStorage::add_unique_reference(const std::string &, Type &) [Type = const double] +The violated condition was: + !stores_object_with_name(name) +Additional information: + An entry with the name value already exists. +-------------------------------------------------------- + +DEAL::Fetch non-existing entry +DEAL:: +-------------------------------------------------------- +An error occurred in file in function + Type &dealii::GeneralDataStorage::get_object_with_name(const std::string &) [Type = double] +The violated condition was: + stores_object_with_name(name) +Additional information: + No entry with the name value exists. +-------------------------------------------------------- + +DEAL::Access removed entry (reference) +DEAL:: +-------------------------------------------------------- +An error occurred in file in function + Type &dealii::GeneralDataStorage::get_object_with_name(const std::string &) [Type = double] +The violated condition was: + stores_object_with_name(name) +Additional information: + No entry with the name value exists. +-------------------------------------------------------- + +DEAL::Access removed entry (copy) +DEAL:: +-------------------------------------------------------- +An error occurred in file in function + Type &dealii::GeneralDataStorage::get_object_with_name(const std::string &) [Type = double] +The violated condition was: + stores_object_with_name(name) +Additional information: + No entry with the name value exists. +-------------------------------------------------------- + diff --git a/tests/algorithms/general_data_storage_01.release.output b/tests/algorithms/general_data_storage_01.release.output new file mode 100644 index 000000000000..b10d09135f90 --- /dev/null +++ b/tests/algorithms/general_data_storage_01.release.output @@ -0,0 +1,24 @@ + +DEAL::Add by copy +DEAL::Size: 2 +DEAL::Add by reference +DEAL::Size: 2 +DEAL::Add or construct +DEAL::Size: 1 +DEAL::Merge +DEAL::Data pre-merge: +DEAL::value double +DEAL::Size: 1 +DEAL::Data 2 pre-merge: +DEAL::value double +DEAL::value_2 double +DEAL::Size: 2 +DEAL::Data post-merge: +DEAL::value double +DEAL::value_2 double +DEAL::Size: 2 +DEAL::Try to overwrite existing entry: Copy +DEAL::Try to overwrite existing entry: Reference +DEAL::Fetch non-existing entry +DEAL::Access removed entry (reference) +DEAL::Access removed entry (copy) From 04673e5ccbd82ddff5de541814f3a7bb6ef84af9 Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Thu, 4 Apr 2019 07:58:49 +0200 Subject: [PATCH 368/507] Fix a typo in a changelog entry --- doc/news/changes/major/20190329Jean-PaulPelteret | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/doc/news/changes/major/20190329Jean-PaulPelteret b/doc/news/changes/major/20190329Jean-PaulPelteret index d5f571d8fab3..50d4c4b64022 100644 --- a/doc/news/changes/major/20190329Jean-PaulPelteret +++ b/doc/news/changes/major/20190329Jean-PaulPelteret @@ -1,4 +1,4 @@ -New: A new class Differentiation::SD::Expression has been added. which allows +New: A new class Differentiation::SD::Expression has been added which allows the creation and manipulation of scalar symbolic functions using the SymEngine library. It will later be used as the basis of symbolic tensor calculus, amongst other things. It incorporates numerous features, which currently include: From 62ed359ab6aac96bb5aee6109e6f35dd6b37fa80 Mon Sep 17 00:00:00 2001 From: Wolfgang Bangerth Date: Fri, 22 Feb 2019 17:23:55 -0700 Subject: [PATCH 369/507] Edit the introduction of step-61. --- examples/step-61/doc/intro.dox | 402 ++++++++++++++++++++++----------- 1 file changed, 273 insertions(+), 129 deletions(-) diff --git a/examples/step-61/doc/intro.dox b/examples/step-61/doc/intro.dox index 5cc7c2120e3c..6d3ed92ed819 100644 --- a/examples/step-61/doc/intro.dox +++ b/examples/step-61/doc/intro.dox @@ -102,7 +102,7 @@ formulation of the problem, for all test functions $q$, where @f{equation*} \mathcal{A}\left(p,q\right) - := \int_\Omega \mathbf{K} \nabla p \cdot \nabla q \;\mathrm{d}x, + := \int_\Omega \left(\mathbf{K} \nabla p\right) \cdot \nabla q \;\mathrm{d}x, @f} and @f{equation*} @@ -139,186 +139,330 @@ that is only defined in cell interiors. Consequently, for all discrete test functions $q_h$, where @f{equation*} \mathcal{A}_h\left(p_h,q_h\right) - := \sum_{T \in \mathcal{T}_h} - \int_T \mathbf{K} \nabla_{w,d} p_h \cdot \nabla_{w,d} q_h \;\mathrm{d}x, + := \sum_{K \in \mathbb{T}} + \int_K \mathbf{K} \nabla_{w,d} p_h \cdot \nabla_{w,d} q_h \;\mathrm{d}x, @f} and @f{equation*} \mathcal{F}\left(q_h\right) - := \sum_{T \in \mathcal{T}_h} \int_T f \, q_h^\circ \;\mathrm{d}x + := \sum_{K \in \mathbb{T}} \int_K f \, q_h^\circ \;\mathrm{d}x - \sum_{\gamma \in \Gamma_h^N} \int_\gamma u_N q_h^\partial \;\mathrm{d}x, @f} The key point is that here, we have replaced the gradient $\nabla p_h$ by the -discrete weak gradient - $ \nabla_{w,d} p_h $ that is defined for our peculiarly defined approximation $p_h$. -We use FE_DGQ as the interior polynomial space, -FE_FaceQ as the face polynomial space, and Raviart-Thomas elements for the velocity -$\mathbf{u} = -{\mathbf{K}} \nabla_{w,d} p$. +discrete weak gradient operator + $ \nabla_{w,d} p_h $ that makes sense for our peculiarly defined approximation $p_h$. + +The question is then how that operator works. For this, let us first say how we +think of the discrete approximation $p_h$ of the pressure. As mentioned above, +the "function" $p_h$ actually consists of two parts: the values $p_h^\circ$ in +the interior of cells, and $p_h^\partial$ on the interfaces. We have to define +discrete (finite-dimensional) function spaces for both of these; in this +program, we will use FE_DGQ for $p_h^\circ$ as the space in the interior of +cells (defined on each cell, but in general discontinuous along interfaces), +and FE_FaceQ for $p_h^\partial$ as the space on the interfaces. -

    Assembling the linear system

    +Then let us consider just a single cell (because the integrals above are all +defined cell-wise, and because the weak discrete gradient is defined cell-by-cell). +The restriction of $p_h$ to cell $K$, $p_h|_K$ then consists +of the pair $(p_h^\circ|_K,p_h^\partial|_{\partial K})$. In essence, we can +think of $\nabla_{w,d} p_h$ of some function defined on $K$ that approximates +the gradient; in particular, if $p_h|_K$ was the restriction of a differentiable +function (to the interior and boundary of $K$ -- which would make it continuous +between the interior and boundary), then +$\nabla_{w,d} p_h$ would simply be the exact gradient $\nabla p_h$. But, since +$p_h|_K$ is not continuous between interior and boundary of $K$, we need a more +general definition; furthermore, we can not deal with arbitrary functions, and +so require that $\nabla_{w,d} p_h$ is also in a finite element space (which, since +the gradient is a vector, has to be vector-valued). + +The way this is done is to define this weak gradient operator $\nabla_{w,d}|_K : +DGQ_k(K) \times DGQ_r(\partial K) \rightarrow RT_s(K)$ (where $RT_s(K)$ is the +vector-valued Raviart-Thomas space of order $s$ on cell $K$) in the following way: +@f{equation*}{ + \int_K \mathbf v_h \cdot (\nabla_{w,d} p_h) + = + -\int_K (\nabla \cdot \mathbf v_h) p_h^\circ + +\int_{\partial K} (\mathbf v_h \cdot \mathbf n) p_h^\partial, +@f} +for all test functions $\mathbf v_h \in RT_s(K)$. +This is, in essence, simply an application of the integration-by-parts +formula. In other words, for a given $p_h=(p^\circ_h,p^\partial_h)$, +we need to think of $\nabla_{w,d} p_h|_K$ as that +Raviart-Thomas function of degree $s$ for which the left hand side and right hand side +are equal for all test functions. + +@note It may be worth pointing out that while the weak discrete + gradient is an element of the Raviart-Thomas space $RT_s(K)$ on each + cell $K$, it is discontinuous between cells. On the other hand, the + Raviart-Thomas space $RT_s=RT_s({\mathbb T})$ defined on the entire + mesh and implemented by the FE_RaviartThomas class represents + functions that have continuous normal components at interfaces + between cells. This means that globally, $\nabla_{w,d} p_h$ + is not in $RT_s$, even though it is on every cell $K$ in $RT_s(K)$. + Rather, it is in a "broken" Raviart-Thomas space that below we will + represent by the symbol $DGRT_s$. (The term "broken" here refers to + the process of "breaking something apart", and not to the synonym to + the expression "not functional".) -First, we solve for the pressure. -We collect two local spaces together in one FESystem, -the first component in this finite element system denotes -the space for interior pressure, and the second denotes -the space for face pressure. -For the interior component, we use the polynomial space FE_DGQ. -For the face component, we use FE_FaceQ. - -We use shape functions defined on spaces FE_DGQ and FE_FaceQ to -approximate pressures, i.e., $p_h = \sum a_i \phi_i,$ -where $\phi_i$ are shape functions of FESystem. -We construct the local system by using discrete weak gradients of -shape functions of FE_DGQ and FE_FaceQ. -The discrete weak gradients of shape functions $\nabla_{w,d} \phi$ are defined as -$\nabla_{w,d} \phi = \sum_{i=1}^m c_i \mathbf{w}_i,$ -where $\mathbf{w}_i$ is the basis function of $RT(k)$. - -Using integration by parts, we have a small linear system -on each element $T$, + +

    Representing the weak gradient

    + +Since $p_h$ is an element of a finite element space, we can expand it in a basis +as we always do, i.e., we can write +@f{equation*}{ + p_h(\mathbf x) = \sum_j P_j \varphi_j(\mathbf x). +@f} +Here, since $p_h$ has two components (the interior and the interface components), +the same must hold true for the basis functions $\varphi_j(\mathbf x)$, which we +can write as $\varphi_j = (\varphi_j^\circ,\varphi_j^\partial)$. If you've +followed the descriptions in step-8, step-20, and the +@ref vector_valued "documentation module on vector-valued problems", +it will be no surprise that for some values of $j$, $\varphi_j^\circ$ will be +zero, whereas for other values of $j$, $\varphi_j^\partial$ will be zero -- i.e., +shape functions will be of either one or the other kind. That is not important, +here, however. What is important is that we need to wonder how we can represent +$\nabla_{w,d} \varphi_j$ because that is clearly what will appear in the +problem when we want to implement the bilinear form @f{equation*} -\int_{T} \left(\nabla_{w,d} \phi \right) \cdot \mathbf{w} \mathrm{d}x= -\int_{T^\partial} \phi^{\partial} \left(\mathbf{w} \cdot \mathbf{n}\right) \mathrm{d}x- -\int_{T^\circ} \phi^{\circ} \left(\nabla \cdot \mathbf{w}\right) \mathrm{d}x, -\quad \forall \mathbf{w} \in RT_{[k]}(E), +\mathcal{A}_h\left(p_h,q_h\right) + = \sum_{K \in \mathbb{T}} + \int_K \mathbf{K} \nabla_{w,d} p_h \cdot \nabla_{w,d} q_h \;\mathrm{d}x, @f} +The key point is that $\nabla_{w,d} \varphi_j$ is known to be a member of the +"broken" Raviart-Thomas space $DGRT_s$. What this means is that we can +represent (on each cell $K$ separately) @f{equation*} -\sum_{i=1}^m c_i \int_T \mathbf{w}_i \cdot \mathbf{w}_j \mathrm{d}x = -\int_{T^{\partial}} \phi_i^{\partial} -\left(\mathbf{w}_j \cdot \mathbf{n} \right) \mathrm{d}x - -\int_{T^{\circ}} \phi_i^{\circ} \left (\nabla \cdot \mathbf{w}_j \right)\mathrm{d}x, +\nabla_{w,d} \varphi_j|_K + = \sum_k C_{jk}^K \mathbf v_k|_K @f} -which can be simplified to be -@f{equation*} -\mathbf{C}_{E}\mathbf{M}_{E} = \mathbf{F}_{E}, +where the functions $\mathbf v_k \in DGRT_s$, and where $C^K$ is a matrix of +dimension +@f{align*}{ + \text{dim}\left(DGQ_k(K) \times DGQ_r(K)\right) &\times \text{dim}\left(RT_s(K)\right) + \\ + &= + \left(\text{dim}(DGQ_k(K)) + \text{dim}(DGQ_r(K))\right) \times \text{dim}\left(RT_s(K)\right). @f} -where $\mathbf{C}_E$ is the matrix with unknown coefficients $c$, -$\mathbf{M}_E$ is the Gram matrix -$\left[ \int_T \mathbf{w}_i \cdot \mathbf{w}_j \right] \mathrm{d}x$, -$\mathbf{F}_E$ is the matrix of right hand side, -$\mathbf{w}$ and $\phi_i^{\circ}$ are in FEValues, -$\phi_i^{\partial}$ is in FEFaceValues. -Then we solve for $\mathbf{C}_E = \mathbf{F}_E \mathbf{M}_E^{-1}$. -Now, discrete weak gradients of shape functions are written as -linear combinations of basis functions of the $RT$ space. -In our code, we name $\mathbf{C}_E$ as cell_matrix_C, -$\mathbf{M}_E$ as cell_matrix_rt, -$\mathbf{F}_E$ as cell_matrix_F. - -The components of the local cell matrices $\mathbf{A}$ are -@f{equation*} -\mathbf{A}_{ij} = -\int_{T} \mathbf{K} \nabla_{w,d} \phi_i \cdot \nabla_{w,d} \phi_j \mathrm{d}x. +(That the weak discrete gradient can be represented as a matrix should not come +as a surprise: It is a linear operator from one finite dimensional +space to another finite dimensional space. If one chooses bases +for both of these spaces, then every linear operator can +of course be written as a matrix mapping the vector of expansion coefficients +with regards to the basis of the domain space of the operator, to +the vector of expansion coefficients with regards to the basis in the image +space.) + +Using this expansion, we can easily use the definition of the weak +discrete gradient above to define what the matrix is going to be: +@f{equation*}{ + \int_K \mathbf v_i \cdot \left(\sum_k C_{jk}^K \mathbf v_k\right) + = + -\int_K (\nabla \cdot \mathbf v_i) \varphi_j^\circ + +\int_{\partial K} (\mathbf v_i \cdot \mathbf n) \varphi_j^\partial, @f} -From previous steps, we know $\nabla_{w,d} \phi_i = \sum_{k=1}^m c_{ik} \mathbf{w}_k,$ -and $\nabla_{w,d} \phi_j = \sum_{l=1}^m c_{jl} \mathbf{w}_l.$ -Then combining the coefficients we have calculated, components of $\mathbf{A}$ are calculated as -@f{equation*} -\int_T \sum_{k,l = 1}^{m}c_{ik} c_{jl} \left(\mathbf{K} \mathbf{w}_i \cdot \mathbf{w}_j\right) \mathrm{d}x -= \sum_{k,l = 1}^{m}c_{ik} c_{jl} \int_{T} \mathbf{K} \mathbf{w}_i \cdot \mathbf{w}_j \mathrm{d}x. +for all test functions $\mathbf v_i \in DGRT_s$. + +This clearly leads to a linear system of the form +@f{equation*}{ + \sum_k M_{ik}^K C_{jk}^K + = + G_{ij}^K +@f} +with +@f{equation*}{ + M_{ik}^K = \int_K \mathbf v_i \cdot \mathbf v_k, + \qquad\qquad + G_{ij}^K = -\int_K (\nabla \cdot \mathbf v_i) \varphi_j^\circ + +\int_{\partial K} (\mathbf v_i \cdot \mathbf n) \varphi_j^\partial, +@f} +and consequently +@f{equation*}{ + \left(C^K\right)^T = \left(M^K\right)^{-1} G^K. @f} +(In this last step, we have assumed that the indices $i,j,k$ only range +over those degrees of freedom active on cell $K$, +thereby ensuring that the mass matrix on the space $RT_s(K)$ is invertible.) +Equivalently, using the symmetry of the matrix $M$, we have that +@f{equation*}{ + C^K = \left(G^K\right)^{T} \left(M^K\right)^{-1}. +@f} +Also worth pointing out is that the +matrices $C^K$ and $G^K$ are of course not square but rectangular. -Next, we use ConstraintMatrix::distribute_local_to_global to -distribute contributions from local matrices $\mathbf{A}$ to the system matrix. -In the scheme -$\mathcal{A}_h\left(p_h,q \right) = \mathcal{F} \left( q \right),$ -we have system matrix and system right hand side, -we can solve for the coefficients of the system matrix. -The solution vector of the scheme represents the pressure values in interiors and on faces. +

    Assembling the linear system

    + +Having explained how the weak discrete gradient is defined, we can now +come back to the question of how the linear system for the equation in question +should be assembled. Specifically, using the definition of the bilinear +form ${\cal A}_h$ shown above, we then need to compute the elements of the +local contribution to the global matrix, +@f{equation*}{ + A^K_{ij} = \int_K \left({\mathbf K} \nabla_{w,d} \varphi_i\right) \cdot \nabla_{w,d} \varphi_j. +@f} +As explained above, we can expand $\nabla_{w,d} \varphi_i$ in terms of the +Raviart-Thomas basis on each cell, and similarly for $\nabla_{w,d} \varphi_j$: +@f{equation*}{ + A^K_{ij} = \int_K + \left( + {\mathbf K} + \sum_k C_{ik}^K \mathbf v_k|_K + \right) + \cdot + \sum_l C_{jl}^K \mathbf v_l|_K. +@f} +By re-arranging sums, this yields the following expression: +@f{equation*}{ + A^K_{ij} = + \sum_k \sum_l C_{ik}^K C_{jl}^K + \int_K + \left( + {\mathbf K} + \mathbf v_k|_K + \right) + \cdot + \mathbf v_l|_K. +@f} +So, if we have the matrix $C^K$ for each cell $K$, then we can easily compute +the contribution $A^K$ for cell $K$ to the matrix $A$ as follows: +@f{equation*}{ + A^K_{ij} = + \sum_k \sum_l C_{ik}^K C_{jl}^K + H^K_{kl} + = + \sum_k \sum_l C_{ik}^K H^K_{kl} C_{jl}^K + = + \left(C^K H^K (C^K)^T \right)_{ij}. +@f} +Here, +@f{equation*}{ + H^K_{kl} = + \int_K + \left( + {\mathbf K} + \mathbf v_k|_K + \right) + \cdot + \mathbf v_l|_K, +@f} +which is really just the mass matrix on cell $K$ using the Raviart-Thomas +basis and weighting by the permeability tensor $\mathbf K$. The derivation +here then shows that the weak Galerkin method really just requires us +to compute these $C^K$ and $H^K$ matrices on each cell $K$, and then +$A^K = C^K H^K (C^K)^T$, which is easily computed. The code to be shown +below does exactly this. + +Having so computed the contribution $A^K$ of cell $K$ to the global +matrix, all we have to do is to "distribute" these local contributions +into the global matrix. How this is done is first shown in step-3 and +step-4. In the current program, this will be facilitated by calling +AffineConstraints::distribute_local_to_global(). + +A linear system of course also needs a right hand side. There is no difficulty +associated with computing the right hand side here other than the fact +that we only need to use the cell-interior part $\varphi_i^\circ$ for +each shape function $\varphi_i$. +

    Post-processing and $L_2$-errors

    -After we have calculated the numerical pressure $p$, -we use discrete weak gradients of $p$ to calculate the velocity on each element. +The discussions in the previous sections have given us a linear +system that we can solve for the numerical pressure $p_h$. We can use +this to compute an approximation to the variable $\mathbf u = -{\mathbf K}\nabla p$ +that corresponds to the velocity with which the medium flows in a porous +medium if this is the model we are trying to solve. This kind of +step -- computing a derived quantity from the solution of the discrete +problem -- is typically called "post-processing". -On each element the gradient of the numerical pressure $\nabla p$ can be -approximated by discrete weak gradients $ \nabla_{w,d}\phi_i$, so +Here, instead of using the exact gradient of $p_h$, let us instead +use the discrete weak gradient of $p_h$ to calculate the velocity on each element. +As discussed above, +on each element the gradient of the numerical pressure $\nabla p$ can be +approximated by discrete weak gradients $ \nabla_{w,d}\phi_i$: @f{equation*} -\nabla_{w,d} p_h = \sum_{i} a_i \nabla_{w,d}\phi_i. +\nabla_{w,d} p_h += \nabla_{w,d} \left(\sum_{i} P_i \phi_i\right) += \sum_{i} P_i \nabla_{w,d}\phi_i. @f} -The numerical velocity $ \mathbf{u}_h = -\mathbf{K} \nabla_{w,d}p_h$ can be written as -@f{equation*} -\mathbf{u}_h = -\mathbf{K} \nabla_{w,d} p = --\sum_{i} \sum_{j} a_ic_{ij}\mathbf{K}\mathbf{w}_j, +On cell $K$, +the numerical velocity $ \mathbf{u}_h = -\mathbf{K} \nabla_{w,d}p_h$ can be written as +@f{align*}{ + \mathbf{u}_h + &= -\mathbf{K} \nabla_{w,d} p + = -\mathbf{K}\sum_{i} \sum_{j} P_i C^K_{ij}\mathbf{v}_j, @f} -where $c_{ij}$ is the coefficient of Gram matrix, -$\mathbf{w}_j$ is the basis function of the $RT$ space. -$\mathbf{K} \mathbf{w}_j$ may not be in the $RT$ space. -So we need $L_2$-projection to project it back to the $RT$ space. +where $C^K$ is the expansion matrix from above, and +$\mathbf{v}_j$ is the basis function of the $RT$ space on a cell. + +Unfortunately, $\mathbf{K} \mathbf{v}_j$ may not be in the $RT$ space +(unless, of course, if $\mathbf K$ is constant times the identity matrix). +So, in order to represent it in a finite element program, we need to +project it back into a finite dimensional space we can work with. Here, +we we will use the $L_2$-projection to project it back to the (broken) $RT$ +space. We define the projection as -$ \mathbf{Q}_h \left( \mathbf{K}\mathbf{w}_j \right) = -\sum_{k} d_{jk}\mathbf{w}_k$. +$ \mathbf{Q}_h \left( \mathbf{K}\mathbf{v}_j \right) = +\sum_{k} d_{jk}\mathbf{v}_k$ on each cell $K$. For any $j$, -$\left( \mathbf{Q}_h \left( \mathbf{Kw}_j \right),\mathbf{w}_k \right)_E = -\left( \mathbf{Kw}_j,\mathbf{w}_k \right)_E.$ -So the numerical velocity becomes +$\left( \mathbf{Q}_h \left( \mathbf{Kv}_j \right),\mathbf{v}_k \right)_K = +\left( \mathbf{Kv}_j,\mathbf{v}_k \right)_K.$ +So, rather than the formula shown above, the numerical velocity on cell $K$ +instead becomes @f{equation*} \mathbf{u}_h = \mathbf{Q}_h \left( -\mathbf{K}\nabla_{w,d}p_h \right) = --\sum_{i=0}^{4} \sum_{j=1}^{4}a_ib_{ij}\mathbf{Q}_h \left( \mathbf{K}\mathbf{w}_j \right), +-\sum_i \sum_j P_i B^K_{ij}\mathbf{Q}_h \left( \mathbf{K}\mathbf{v}_j \right), @f} -and we have the following system to solve for the coefficients $d_{jk}$, +and we have the following system to solve for the coefficients $d_{jk}$: @f{equation*} - \left[ - \begin{matrix} - \left(\mathbf{w}_i,\mathbf{w}_j \right) - \end{matrix} - \right] - \left[ - \begin{matrix} + \sum_j + \left(\mathbf{v}_i,\mathbf{v}_j\right) d_{jk} - \end{matrix} - \right] = - \left[ - \begin{matrix} - \left( \mathbf{Kw}_j,\mathbf{w}_k \right) - \end{matrix} - \right]. + \left( \mathbf{Kv}_j,\mathbf{v}_k \right). @f} +In the implementation below, the matrix with elements $ - \left[ - \begin{matrix} d_{jk} - \end{matrix} - \right] $ -is named cell_matrix_D, +is called cell_matrix_D, +whereas the matrix with elements $ -\left[ - \begin{matrix} - \left( \mathbf{Kw}_j,\mathbf{w}_k \right) - \end{matrix} - \right] + \left( \mathbf{Kv}_j,\mathbf{v}_k \right) $ -is named cell_matrix_E. +is called cell_matrix_E. Then the elementwise velocity is @f{equation*} -\mathbf{u}_h = -\sum_{i} \sum_{j}a_ic_{ij}\sum_{k}d_{jk}\mathbf{w}_k = -\sum_{k}- \left(\sum_{j} \sum_{i} a_ic_{ij}d_{jk} \right)\mathbf{w}_k, +\mathbf{u}_h = -\sum_{i} \sum_{j}P_ic_{ij}\sum_{k}d_{jk}\mathbf{v}_k = +\sum_{k}- \left(\sum_{j} \sum_{i} P_ic_{ij}d_{jk} \right)\mathbf{v}_k, @f} -where $-\sum_{j} \sum_{i} a_ic_{ij}d_{jk}$ is named +where $-\sum_{j} \sum_{i} P_ic_{ij}d_{jk}$ is called beta in the code. -We calculate the $L_2$-errors of pressure, velocity and flux -by the following formulas, +Using this velocity obtained by "postprocessing" the solution, we can +define the $L_2$-errors of pressure, velocity, and flux +by the following formulas: @f{eqnarray*} \|p-p_h^\circ\|^2 - = \sum_{T \in \mathcal{T}_h} \|p-p_h^\circ\|_{L^2(E)}^2, \\ + = \sum_{K \in \mathbb{T}} \|p-p_h^\circ\|_{L_2(K)}^2, \\ \|\mathbf{u}-\mathbf{u}_h\|^2 - = \sum_{T \in \mathcal{T}_h} \|\mathbf{u}-\mathbf{u}_h\|_{L^2(E)^2}^2,\\ + = \sum_{K \in \mathbb{T}} \|\mathbf{u}-\mathbf{u}_h\|_{L_2(K)^2}^d,\\ \|(\mathbf{u}-\mathbf{u}_h) \cdot \mathbf{n}\|^2 - = \sum_{T \in \mathcal{T}_h} \sum_{\gamma \subset T^\partial} - \frac{|T|}{|\gamma|} \|\mathbf{u} \cdot \mathbf{n} - \mathbf{u}_h \cdot \mathbf{n}\|_{L^2(\gamma)}^2, + = \sum_{K \in \mathbb{T}} \sum_{\gamma \subset \partial K} + \frac{|K|}{|\gamma|} \|\mathbf{u} \cdot \mathbf{n} - \mathbf{u}_h \cdot \mathbf{n}\|_{L_2(\gamma)}^2, @f} -where $| T |$ is the area of the element, +where $| K |$ is the area of the element, $\gamma$ are faces of the element, -$\mathbf{n}$ are unit normal vectors of each face. +$\mathbf{n}$ are unit normal vectors of each face. The last of these +norms measures the accuracy of the normal component of the velocity +vectors over the interfaces between the cells of the mesh. The scaling +factor $|K|/|\gamma|$ is chosen so as to scale out the difference in +the length (or area) of the collection of interfaces as the mesh size +changes. -We will extract interior pressure solutions of each cell -from the global solution and calculate the $L_2$ error -by using function VectorTools::integrate_difference. +The first of these errors above is easily computed using +VectorTools::integrate_difference. The others require a bit more work +and are implemented in the code below. From f0c54937dbde209b95ad4dced0c903a088a563b5 Mon Sep 17 00:00:00 2001 From: Wolfgang Bangerth Date: Thu, 4 Apr 2019 14:34:40 -0600 Subject: [PATCH 370/507] Fix a misspelled word. --- include/deal.II/multigrid/mg_matrix.h | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/include/deal.II/multigrid/mg_matrix.h b/include/deal.II/multigrid/mg_matrix.h index 2463e3ca39b9..59fcf3a9c446 100644 --- a/include/deal.II/multigrid/mg_matrix.h +++ b/include/deal.II/multigrid/mg_matrix.h @@ -35,8 +35,8 @@ namespace mg { /** * Multilevel matrix. This matrix stores an MGLevelObject of - * LinearOpetors. It implements the interface defined in MGMatrixBase, so - * that it can be used as a matrix in Multigrid. + * LinearOperator objects. It implements the interface defined in + * MGMatrixBase, so that it can be used as a matrix in Multigrid. * * @author Guido Kanschat * @date 2002, 2010 From 90a81c9e4ada48a0a34cf28d464141f75ce186c9 Mon Sep 17 00:00:00 2001 From: David Wells Date: Fri, 5 Apr 2019 17:07:43 -0400 Subject: [PATCH 371/507] Silence an unused variable warning. --- source/base/hdf5.cc | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/source/base/hdf5.cc b/source/base/hdf5.cc index 75e45497230b..bd13d4adeb76 100644 --- a/source/base/hdf5.cc +++ b/source/base/hdf5.cc @@ -267,10 +267,10 @@ namespace HDF5 if (mpi) { # ifdef DEAL_II_WITH_MPI - herr_t ret; plist = H5Pcreate(H5P_DATASET_XFER); Assert(plist >= 0, ExcInternalError()); - ret = H5Pset_dxpl_mpio(plist, H5FD_MPIO_COLLECTIVE); + const herr_t ret = H5Pset_dxpl_mpio(plist, H5FD_MPIO_COLLECTIVE); + (void)ret; Assert(ret >= 0, ExcInternalError()); # else AssertThrow(false, ExcNotImplemented()); @@ -304,6 +304,7 @@ namespace HDF5 { # ifdef DEAL_II_WITH_MPI herr_t ret; + (void)ret; if (query_io_mode) { ret = H5Pget_mpio_actual_io_mode(plist, &io_mode); From 88d865167aaceba18ffeee838085c780eee40502 Mon Sep 17 00:00:00 2001 From: tcclevenger Date: Tue, 19 Feb 2019 16:15:20 -0700 Subject: [PATCH 372/507] add step-63.cc (no doc) --- examples/step-63/block_jacobi.prm | 14 + examples/step-63/block_sor.prm | 14 + examples/step-63/jacobi.prm | 14 + examples/step-63/sor.prm | 15 + examples/step-63/step-63.cc | 1082 ++++++++++++++++++++++++++++- 5 files changed, 1135 insertions(+), 4 deletions(-) create mode 100644 examples/step-63/block_jacobi.prm create mode 100644 examples/step-63/block_sor.prm create mode 100644 examples/step-63/jacobi.prm create mode 100644 examples/step-63/sor.prm diff --git a/examples/step-63/block_jacobi.prm b/examples/step-63/block_jacobi.prm new file mode 100644 index 000000000000..a8dc7f556696 --- /dev/null +++ b/examples/step-63/block_jacobi.prm @@ -0,0 +1,14 @@ +# Finite Element degree +set fe degree = 1 + +# Smoother Type: sor|jacobi|block sor|block jacobi +set smoother type = block jacobi + +# Dof renumbering: no|random|downstream|upstream +set dof renumbering = downstream + +# With streamline diffusion: true|false +set with sd = true + +# Output: true|false +set output = false diff --git a/examples/step-63/block_sor.prm b/examples/step-63/block_sor.prm new file mode 100644 index 000000000000..f5991834c4a5 --- /dev/null +++ b/examples/step-63/block_sor.prm @@ -0,0 +1,14 @@ +# Finite Element degree +set fe degree = 1 + +# Smoother Type: sor|jacobi|block sor|block jacobi +set smoother type = block sor + +# Dof renumbering: none|random|downstream|upstream +set dof renumbering = downstream + +# With streamline diffusion: true|false +set with sd = true + +# Output: true|false +set output = false diff --git a/examples/step-63/jacobi.prm b/examples/step-63/jacobi.prm new file mode 100644 index 000000000000..d6a55ff53b93 --- /dev/null +++ b/examples/step-63/jacobi.prm @@ -0,0 +1,14 @@ +# Finite Element degree +set fe degree = 1 + +# Smoother Type: sor|jacobi|block sor|block jacobi +set smoother type = jacobi + +# Dof renumbering: no|random|downstream|upstream +set dof renumbering = downstream + +# With streamline diffusion: true|false +set with sd = true + +# Output: true|false +set output = false diff --git a/examples/step-63/sor.prm b/examples/step-63/sor.prm new file mode 100644 index 000000000000..47ab13c3d5b3 --- /dev/null +++ b/examples/step-63/sor.prm @@ -0,0 +1,15 @@ +# Finite Element degree +set fe degree = 1 + +# Smoother Type: sor|jacobi|block sor|block jacobi +set smoother type = sor + +# Dof renumbering: no|random|downstream|upstream +set dof renumbering = downstream + + +# With streamline diffusion: true|false +set with sd = true + +# Output: true|false +set output = false diff --git a/examples/step-63/step-63.cc b/examples/step-63/step-63.cc index 2534596dc665..dcfcd1fa54ec 100644 --- a/examples/step-63/step-63.cc +++ b/examples/step-63/step-63.cc @@ -19,16 +19,1091 @@ // @note: This is work in progress and will be an example for block smoothers // in geometric multigrid. +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include +#include + +#include +#include +#include +#include +#include +#include +#include +#include + + + +#include #include -#include -int main() + +#include +#include + + + +namespace Step100 +{ + using namespace dealii; + + + template + struct ScratchData + { + ScratchData(const FiniteElement &fe, + const unsigned int quadrature_degree) + : fe_values(fe, + QGauss(quadrature_degree), + update_values | update_gradients | update_hessians | + update_quadrature_points | update_JxW_values) + {} + + ScratchData(const ScratchData &scratch_data) + : fe_values(scratch_data.fe_values.get_fe(), + scratch_data.fe_values.get_quadrature(), + update_values | update_gradients | update_hessians | + update_quadrature_points | update_JxW_values) + {} + + FEValues fe_values; + }; + struct CopyData + { + unsigned int level; + unsigned int dofs_per_cell; + + FullMatrix cell_matrix; + Vector cell_rhs; + std::vector local_dof_indices; + }; + + + struct Settings + { + bool try_parse(const std::string &prm_filename); + + unsigned int fe_degree; + std::string smoother_type; + std::string dof_renum; + bool with_sd; + bool output; + }; + + + bool Settings::try_parse(const std::string &prm_filename) + { + ParameterHandler prm; + + prm.declare_entry("fe degree", + "1", + Patterns::Integer(0), + "Finite Element degree"); + prm.declare_entry("smoother type", + "block sor", + Patterns::Selection("sor|jacobi|block sor|block jacobi"), + "Smoother Type: sor|jacobi|block sor|block jacobi"); + prm.declare_entry("dof renumbering", + "downstream", + Patterns::Selection("none|random|downstream|upstream"), + "Dof renumbering: none|random|downstream|upstream"); + prm.declare_entry("with sd", + "true", + Patterns::Bool(), + "With streamline diffusion: true|false"); + prm.declare_entry("output", + "true", + Patterns::Bool(), + "Generate graphical output: true|false"); + + try + { + prm.parse_input(prm_filename); + } + catch (const dealii::PathSearch::ExcFileNotFound &) + { + if (prm_filename.size() > 0) + std::cerr << "ERRROR: could not open the .prm file '" << prm_filename + << "'" << std::endl; + else + std::cerr << "Usage: please pass a .prm file as the first argument" + << std::endl; + + prm.print_parameters(std::cout, ParameterHandler::Text); + return false; + } + this->fe_degree = prm.get_integer("fe degree"); + this->smoother_type = prm.get("smoother type"); + this->dof_renum = prm.get("dof renumbering"); + this->with_sd = prm.get_bool("with sd"); + this->output = prm.get_bool("output"); + + return true; + } + + + + namespace + { + template + struct CompareDownstream + { + /** + * Constructor. + */ + CompareDownstream(const Tensor<1, dim> &dir) + : dir(dir) + {} + /** + * Return true if c1 less c2. + */ + bool operator()(const Iterator &c1, const Iterator &c2) const + { + const Tensor<1, dim> diff = c2->center() - c1->center(); + return (diff * dir > 0); + } + + private: + /** + * Flow direction. + */ + const Tensor<1, dim> dir; + }; + + // Functions for creating permutation of cells for output and Block + // smoothers + template + std::vector + create_downstream_order(const DoFHandler &dof, + const Tensor<1, dim> direction, + const unsigned int level) + { + std::vector::level_cell_iterator> ordered_cells; + ordered_cells.reserve(dof.get_triangulation().n_cells(level)); + const CompareDownstream::level_cell_iterator, + dim> + comparator(direction); + + typename DoFHandler::level_cell_iterator cell = dof.begin(level); + typename DoFHandler::level_cell_iterator endc = dof.end(level); + for (; cell != endc; ++cell) + ordered_cells.push_back(cell); + + std::sort(ordered_cells.begin(), ordered_cells.end(), comparator); + + std::vector ordered_indices; + ordered_indices.reserve(dof.get_triangulation().n_cells(level)); + + for (unsigned int i = 0; i < ordered_cells.size(); ++i) + ordered_indices.push_back(ordered_cells[i]->index()); + + return ordered_indices; + } + + template + std::vector + create_downstream_order(const DoFHandler &dof, + const Tensor<1, dim> direction) + { + std::vector::active_cell_iterator> ordered_cells; + ordered_cells.reserve(dof.get_triangulation().n_active_cells()); + const CompareDownstream::active_cell_iterator, + dim> + comparator(direction); + + typename DoFHandler::active_cell_iterator cell = dof.begin_active(); + typename DoFHandler::active_cell_iterator endc = dof.end(); + for (; cell != endc; ++cell) + ordered_cells.push_back(cell); + + std::sort(ordered_cells.begin(), ordered_cells.end(), comparator); + + std::vector ordered_indices; + ordered_indices.reserve(dof.get_triangulation().n_active_cells()); + + for (unsigned int i = 0; i < ordered_cells.size(); ++i) + ordered_indices.push_back(ordered_cells[i]->index()); + + return ordered_indices; + } + + + + template + std::vector create_random_order(const DoFHandler &dof, + const unsigned int level) + { + const unsigned int n_cells = dof.get_triangulation().n_cells(level); + + std::vector ordered_cells; + ordered_cells.reserve(n_cells); + + typename DoFHandler::cell_iterator cell = dof.begin(level); + typename DoFHandler::cell_iterator endc = dof.end(level); + for (; cell != endc; ++cell) + ordered_cells.push_back(cell->index()); + + // shuffle the elements; the following is essentially std::shuffle (which + // is new in C++11) but with a boost URNG + ::boost::mt19937 random_number_generator; + for (unsigned int i = 1; i < n_cells; ++i) + { + // get a random number between 0 and i (inclusive) + const unsigned int j = + ::boost::random::uniform_int_distribution<>(0, i)( + random_number_generator); + + // if possible, swap the elements + if (i != j) + std::swap(ordered_cells[i], ordered_cells[j]); + } + + return ordered_cells; + } + + template + std::vector create_random_order(const DoFHandler &dof) + { + const unsigned int n_cells = dof.get_triangulation().n_active_cells(); + + std::vector ordered_cells; + ordered_cells.reserve(n_cells); + + typename DoFHandler::active_cell_iterator cell = dof.begin_active(); + typename DoFHandler::active_cell_iterator endc = dof.end(); + for (; cell != endc; ++cell) + ordered_cells.push_back(cell->index()); + + // shuffle the elements; the following is essentially std::shuffle (which + // is new in C++11) but with a boost URNG + ::boost::mt19937 random_number_generator; + for (unsigned int i = 1; i < n_cells; ++i) + { + // get a random number between 0 and i (inclusive) + const unsigned int j = + ::boost::random::uniform_int_distribution<>(0, i)( + random_number_generator); + + // if possible, swap the elements + if (i != j) + std::swap(ordered_cells[i], ordered_cells[j]); + } + + return ordered_cells; + } + + } // namespace + + + + // RHS and boundary is an adaptation from one in + // Finite Elements and Fast Iterative Solvers: with Applications + // in Incompressible Fluid Dynamics + template + class RightHandSide : public Function + { + public: + RightHandSide() + : Function() + {} + + virtual double value(const Point & p, + const unsigned int component = 0) const; + + virtual void value_list(const std::vector> &points, + std::vector & values, + const unsigned int component = 0) const; + + private: + static const Point center_point; + }; + + template + double RightHandSide::value(const Point & p, + const unsigned int component) const + { + Assert(component == 0, ExcIndexRange(component, 0, 1)); + (void)component; + (void)p; + + return 0.0; + } + + + + template + void RightHandSide::value_list(const std::vector> &points, + std::vector & values, + const unsigned int component) const + { + Assert(values.size() == points.size(), + ExcDimensionMismatch(values.size(), points.size())); + + for (unsigned int i = 0; i < points.size(); ++i) + values[i] = RightHandSide::value(points[i], component); + } + + + + template + class BoundaryValues : public Function + { + public: + BoundaryValues() + : Function() + {} + + virtual double value(const Point & p, + const unsigned int component = 0) const; + + virtual void value_list(const std::vector> &points, + std::vector & values, + const unsigned int component = 0) const; + }; + + + template + double BoundaryValues::value(const Point & p, + const unsigned int component) const + { + Assert(component == 0, ExcIndexRange(component, 0, 1)); + (void)component; + + if (std::fabs(p[0] * p[0] + p[1] * p[1] - 0.3 * 0.3) < + 1e-8 // around cylinder + || std::fabs(p[0] + 1) < 1e-8 // x == -1 + || std::fabs(p[1] - 1) < 1e-8 // y == 1 + || (std::fabs(p[1] + 1) < 1e-8 && p[0] < 0.5) // y == -1, x <= 0.5 + ) + { + return 0.0; + } + else if (std::fabs(p[0] - 1) < 1e-8 // x = 1 + || (std::fabs(p[1] + 1) < 1e-8 && p[0] >= 0.5) // y == -1, x > 0.5 + ) + { + return 1.0; + } + else + { + return 0.0; + } + } + + + + template + void BoundaryValues::value_list(const std::vector> &points, + std::vector & values, + const unsigned int component) const + { + Assert(values.size() == points.size(), + ExcDimensionMismatch(values.size(), points.size())); + + for (unsigned int i = 0; i < points.size(); ++i) + values[i] = BoundaryValues::value(points[i], component); + } + + template + double delta_value(const double hk, + const double eps, + const Tensor<1, dim> dir, + const double pk) + { + // Value defined in 'On discontinuity–capturing methods for + // convection–diffusion equations' + double Peclet = dir.norm() * hk / (2.0 * eps * pk); + double coth = + (1.0 + std::exp(-2.0 * Peclet)) / (1.0 - std::exp(-2.0 * Peclet)); + + return hk / (2.0 * dir.norm() * pk) * (coth - 1.0 / Peclet); + } + + + template + class AdvectionProblem + { + public: + AdvectionProblem(Settings settings); + void run(); + + private: + void setup_system(); + + template + void assemble_cell(const IteratorType &cell, + ScratchData & scratch_data, + CopyData & copy_data); + void assemble_system_and_multigrid(); + + std::unique_ptr>> create_smoother(); + + void solve(); + void refine_grid(); + void output_results(const unsigned int cycle) const; + + Triangulation triangulation; + DoFHandler dof_handler; + + FE_Q fe; + MappingQ mapping; + unsigned int quad_degree; + + AffineConstraints constraints; + + SparsityPattern sparsity_pattern; + SparseMatrix system_matrix; + + Vector solution; + Vector system_rhs; + + MGLevelObject mg_sparsity_patterns; + MGLevelObject mg_interface_sparsity_patterns; + + MGLevelObject> mg_matrices; + MGLevelObject> mg_interface_in; + MGLevelObject> mg_interface_out; + + MGConstrainedDoFs mg_constrained_dofs; + + Settings settings; + const double epsilon; + Tensor<1, dim> advection_direction; + }; + + + + template + AdvectionProblem::AdvectionProblem(Settings settings) + : triangulation(Triangulation::limit_level_difference_at_vertices) + , dof_handler(triangulation) + , fe(settings.fe_degree) + , mapping(settings.fe_degree) + , quad_degree(2 * fe.degree + 2) + , settings(settings) + , epsilon(0.005) + { + // Set Advection direction (problem is an adaptation from one in + // Finite Elements and Fast Iterative Solvers: with Applications + // in Incompressible Fluid Dynamics) + advection_direction[0] = -std::sin(numbers::PI / 6.0); + if (dim > 1) + advection_direction[1] = std::cos(numbers::PI / 6.0); + if (dim > 2) + advection_direction[2] = std::sin(numbers::PI / 6.0); + } + + + + template + void AdvectionProblem::setup_system() + { + const unsigned int n_levels = triangulation.n_levels(); + + dof_handler.distribute_dofs(fe); + + // We could renumber the active dofs with DoFRenumbering::downstream() + // here, but the smoothers only act on multigrid levels and as such, this + // wouldn't matter. Instead, we will renumber the DoFs on each multigrid + // level below. + + solution.reinit(dof_handler.n_dofs()); + system_rhs.reinit(dof_handler.n_dofs()); + + constraints.clear(); + DoFTools::make_hanging_node_constraints(dof_handler, constraints); + + VectorTools::interpolate_boundary_values( + mapping, dof_handler, 0, BoundaryValues(), constraints); + VectorTools::interpolate_boundary_values( + mapping, dof_handler, 1, BoundaryValues(), constraints); + constraints.close(); + + DynamicSparsityPattern dsp(dof_handler.n_dofs()); + DoFTools::make_sparsity_pattern(dof_handler, + dsp, + constraints, + /*keep_constrained_dofs = */ false); + + sparsity_pattern.copy_from(dsp); + + system_matrix.reinit(sparsity_pattern); + + + // Setup GMG DoFs + dof_handler.distribute_mg_dofs(); + + // Renumber DoFs on each level in downstream or upstream direction if + // needed. This is only necessary for point smoothers (SOR and Jacobi) as + // the block smoothers operate on cells (see create_smoother()): + if (settings.smoother_type == "sor" || settings.smoother_type == "jacobi") + { + if (settings.dof_renum == "downstream" || + settings.dof_renum == "upstream") + { + const Tensor<1, dim> direction = + (settings.dof_renum == "upstream" ? -1.0 : 1.0) * + advection_direction; + + for (unsigned int level = 0; level < n_levels; ++level) + DoFRenumbering::downstream(dof_handler, + level, + direction, + /*dof_wise_renumbering = */ true); + } + else if (settings.dof_renum == "random") + { + for (unsigned int level = 0; level < n_levels; ++level) + DoFRenumbering::random(dof_handler, level); + } + else + Assert(false, ExcNotImplemented()); + } + + mg_constrained_dofs.clear(); + mg_constrained_dofs.initialize(dof_handler); + + std::set dirichlet_boundary_ids = {0, 1}; + mg_constrained_dofs.make_zero_boundary_constraints(dof_handler, + dirichlet_boundary_ids); + + mg_matrices.resize(0, n_levels - 1); + mg_matrices.clear_elements(); + mg_interface_in.resize(0, n_levels - 1); + mg_interface_in.clear_elements(); + mg_interface_out.resize(0, n_levels - 1); + mg_interface_out.clear_elements(); + mg_sparsity_patterns.resize(0, n_levels - 1); + mg_interface_sparsity_patterns.resize(0, n_levels - 1); + + for (unsigned int level = 0; level < n_levels; ++level) + { + { + DynamicSparsityPattern dsp(dof_handler.n_dofs(level), + dof_handler.n_dofs(level)); + MGTools::make_sparsity_pattern(dof_handler, dsp, level); + mg_sparsity_patterns[level].copy_from(dsp); + mg_matrices[level].reinit(mg_sparsity_patterns[level]); + } + { + DynamicSparsityPattern dsp(dof_handler.n_dofs(level), + dof_handler.n_dofs(level)); + MGTools::make_interface_sparsity_pattern(dof_handler, + mg_constrained_dofs, + dsp, + level); + mg_interface_sparsity_patterns[level].copy_from(dsp); + + // We need both interface in and out matrices since our problem is not + // symmetric + mg_interface_in[level].reinit(mg_interface_sparsity_patterns[level]); + mg_interface_out[level].reinit(mg_interface_sparsity_patterns[level]); + } + } + } + + + template + template + void AdvectionProblem::assemble_cell(const IteratorType &cell, + ScratchData & scratch_data, + CopyData & copy_data) + { + const unsigned int level = cell->level(); + copy_data.level = level; + + const unsigned int dofs_per_cell = + scratch_data.fe_values.get_fe().dofs_per_cell; + copy_data.dofs_per_cell = dofs_per_cell; + + const unsigned int n_q_points = + scratch_data.fe_values.get_quadrature().size(); + copy_data.cell_matrix.reinit(dofs_per_cell, dofs_per_cell); + + if (!cell->is_level_cell()) + copy_data.cell_rhs.reinit(dofs_per_cell); + + copy_data.local_dof_indices.resize(dofs_per_cell); + cell->get_active_or_mg_dof_indices(copy_data.local_dof_indices); + + scratch_data.fe_values.reinit(cell); + + const RightHandSide right_hand_side; + std::vector rhs_values(n_q_points); + + right_hand_side.value_list(scratch_data.fe_values.get_quadrature_points(), + rhs_values); + + const double delta = settings.with_sd ? delta_value(cell->diameter(), + epsilon, + advection_direction, + settings.fe_degree) : + 0.0; + + for (unsigned int q_point = 0; q_point < n_q_points; ++q_point) + for (unsigned int i = 0; i < dofs_per_cell; ++i) + { + for (unsigned int j = 0; j < dofs_per_cell; ++j) + { + copy_data.cell_matrix(i, j) += + (epsilon * scratch_data.fe_values.shape_grad(j, q_point) * + scratch_data.fe_values.shape_grad(i, q_point) * + scratch_data.fe_values.JxW(q_point)) + + ((advection_direction * + scratch_data.fe_values.shape_grad(j, q_point)) * + scratch_data.fe_values.shape_value(i, q_point)) * + scratch_data.fe_values.JxW(q_point); + + if (settings.with_sd) + copy_data.cell_matrix(i, j) += + delta * + (advection_direction * + scratch_data.fe_values.shape_grad(j, q_point)) * + (advection_direction * + scratch_data.fe_values.shape_grad(i, q_point)) * + scratch_data.fe_values.JxW(q_point) - + delta * epsilon * + trace(scratch_data.fe_values.shape_hessian(j, q_point)) * + (advection_direction * + scratch_data.fe_values.shape_grad(i, q_point)) * + scratch_data.fe_values.JxW(q_point); + } + if (!cell->is_level_cell()) + { + copy_data.cell_rhs(i) += + scratch_data.fe_values.shape_value(i, q_point) * + rhs_values[q_point] * scratch_data.fe_values.JxW(q_point); + if (settings.with_sd) + copy_data.cell_rhs(i) += + delta * rhs_values[q_point] * advection_direction * + scratch_data.fe_values.shape_grad(i, q_point) * + scratch_data.fe_values.JxW(q_point); + } + } + } + + + template + void AdvectionProblem::assemble_system_and_multigrid() + { + auto cell_worker_active = + [&](const decltype(dof_handler.begin_active()) &cell, + ScratchData & scratch_data, + CopyData & copy_data) { + this->assemble_cell(cell, scratch_data, copy_data); + }; + + + + auto copier_active = [&](const CopyData ©_data) { + constraints.distribute_local_to_global(copy_data.cell_matrix, + copy_data.cell_rhs, + copy_data.local_dof_indices, + system_matrix, + system_rhs); + }; + + + MeshWorker::mesh_loop(dof_handler.begin_active(), + dof_handler.end(), + cell_worker_active, + copier_active, + ScratchData(fe, quad_degree), + CopyData(), + MeshWorker::assemble_own_cells); + + + // Assemble GMG + std::vector> boundary_constraints( + triangulation.n_global_levels()); + for (unsigned int level = 0; level < triangulation.n_global_levels(); + ++level) + { + IndexSet dofset; + DoFTools::extract_locally_relevant_level_dofs(dof_handler, + level, + dofset); + boundary_constraints[level].reinit(dofset); + boundary_constraints[level].add_lines( + mg_constrained_dofs.get_refinement_edge_indices(level)); + boundary_constraints[level].add_lines( + mg_constrained_dofs.get_boundary_indices(level)); + boundary_constraints[level].close(); + } + + auto cell_worker_mg = [&](const decltype(dof_handler.begin_mg()) &cell, + ScratchData &scratch_data, + CopyData & copy_data) { + this->assemble_cell(cell, scratch_data, copy_data); + }; + + auto copier_mg = [&](const CopyData ©_data) { + boundary_constraints[copy_data.level].distribute_local_to_global( + copy_data.cell_matrix, + copy_data.local_dof_indices, + mg_matrices[copy_data.level]); + + // If (i,j) is an interface_out dof pair, then (j,i) is an interface_in + // dof pair. Note: for interface_in, we load the transpose of the + // interface entries, i.e., the entry for dof pair (j,i) is stored in + // interface_in(i,j). + for (unsigned int i = 0; i < copy_data.dofs_per_cell; ++i) + for (unsigned int j = 0; j < copy_data.dofs_per_cell; ++j) + if (mg_constrained_dofs.is_interface_matrix_entry( + copy_data.level, + copy_data.local_dof_indices[i], + copy_data.local_dof_indices[j])) + { + mg_interface_out[copy_data.level].add( + copy_data.local_dof_indices[i], + copy_data.local_dof_indices[j], + copy_data.cell_matrix(i, j)); + mg_interface_in[copy_data.level].add( + copy_data.local_dof_indices[i], + copy_data.local_dof_indices[j], + copy_data.cell_matrix(j, i)); + } + }; + + MeshWorker::mesh_loop(dof_handler.begin_mg(), + dof_handler.end_mg(), + cell_worker_mg, + copier_mg, + ScratchData(fe, quad_degree), + CopyData(), + MeshWorker::assemble_own_cells); + } + + + template + std::unique_ptr>> + AdvectionProblem::create_smoother() + { + if (settings.smoother_type == "sor") + { + typedef PreconditionSOR> Smoother; + + auto smoother = + std_cxx14::make_unique, + Smoother, + Vector>>(); + smoother->initialize(mg_matrices, + Smoother::AdditionalData(fe.degree == 1 ? 1.0 : + 0.62)); + smoother->set_steps(2); + return smoother; + } + else if (settings.smoother_type == "jacobi") + { + typedef PreconditionJacobi> Smoother; + auto smoother = + std_cxx14::make_unique, + Smoother, + Vector>>(); + smoother->initialize(mg_matrices, + Smoother::AdditionalData(fe.degree == 1 ? 0.6667 : + 0.47)); + smoother->set_steps(4); + return smoother; + } + else if (settings.smoother_type == "block sor") + { + typedef RelaxationBlockSOR, double, Vector> + Smoother; + + static MGLevelObject smoother_data; + smoother_data.resize(0, triangulation.n_levels() - 1); + + for (unsigned int level = 0; level < triangulation.n_levels(); ++level) + { + DoFTools::make_cell_patches(smoother_data[level].block_list, + dof_handler, + level); + + smoother_data[level].relaxation = 1.0; + smoother_data[level].inversion = PreconditionBlockBase::svd; + + std::vector ordered_indices; + if (settings.dof_renum == "downstream") + ordered_indices = create_downstream_order(dof_handler, + advection_direction, + level); + else if (settings.dof_renum == "upstream") + ordered_indices = + create_downstream_order(dof_handler, + -1.0 * advection_direction, + level); + else if (settings.dof_renum == "random") + ordered_indices = create_random_order(dof_handler, level); + else if (settings.dof_renum == "none") + { + // Do nothing + } + else + AssertThrow(false, ExcNotImplemented()); + + smoother_data[level].order = + std::vector>(1, ordered_indices); + } + + auto smoother = + std_cxx14::make_unique, + Smoother, + Vector>>(); + smoother->initialize(mg_matrices, smoother_data); + smoother->set_steps(1); + return smoother; + } + else if (settings.smoother_type == "block jacobi") + { + typedef RelaxationBlockJacobi, + double, + Vector> + Smoother; + + static MGLevelObject smoother_data; + smoother_data.resize(0, triangulation.n_levels() - 1); + + for (unsigned int level = 0; level < triangulation.n_levels(); ++level) + { + DoFTools::make_cell_patches(smoother_data[level].block_list, + dof_handler, + level); + + smoother_data[level].relaxation = 0.25; + smoother_data[level].inversion = PreconditionBlockBase::svd; + + std::vector ordered_indices; + if (settings.dof_renum == "downstream") + ordered_indices = create_downstream_order(dof_handler, + advection_direction, + level); + else if (settings.dof_renum == "upstream") + ordered_indices = + create_downstream_order(dof_handler, + -1.0 * advection_direction, + level); + else if (settings.dof_renum == "random") + ordered_indices = create_random_order(dof_handler, level); + else if (settings.dof_renum == "none") + { + // Do nothing + } + else + AssertThrow(false, ExcNotImplemented()); + + smoother_data[level].order = + std::vector>(1, ordered_indices); + } + + auto smoother = + std_cxx14::make_unique, + Smoother, + Vector>>(); + smoother->initialize(mg_matrices, smoother_data); + smoother->set_steps(2); + return smoother; + } + else + AssertThrow(false, ExcNotImplemented()); + } + + + template + void AdvectionProblem::solve() + { + Timer time; + + const double solve_tol = 1e-8 * system_rhs.l2_norm(); + const unsigned int max_iters = 200; + SolverControl solver_control(max_iters, solve_tol, true, true); + solver_control.enable_history_data(); + + typedef MGTransferPrebuilt> Transfer; + Transfer mg_transfer(mg_constrained_dofs); + mg_transfer.build_matrices(dof_handler); + + FullMatrix coarse_matrix; + coarse_matrix.copy_from(mg_matrices[0]); + MGCoarseGridHouseholder> coarse_grid_solver; + coarse_grid_solver.initialize(coarse_matrix); + + std::unique_ptr>> mg_smoother = create_smoother(); + + mg::Matrix> mg_matrix(mg_matrices); + mg::Matrix> mg_interface_matrix_in(mg_interface_in); + mg::Matrix> mg_interface_matrix_out(mg_interface_out); + + Multigrid> mg( + mg_matrix, coarse_grid_solver, mg_transfer, *mg_smoother, *mg_smoother); + mg.set_edge_matrices(mg_interface_matrix_out, mg_interface_matrix_in); + + PreconditionMG, Transfer> preconditioner(dof_handler, + mg, + mg_transfer); + + + std::cout << " Solving with GMRES to tol " << solve_tol << "..." + << std::endl; + SolverGMRES<> solver(solver_control); + + time.restart(); + solver.solve(system_matrix, solution, system_rhs, preconditioner); + time.stop(); + + std::cout << " converged in " << solver_control.last_step() + << " iterations" + << " in " << time.last_wall_time() << " seconds " << std::endl; + + constraints.distribute(solution); + } + + + + template + void AdvectionProblem::output_results(const unsigned int cycle) const + { + DataOut data_out; + data_out.attach_dof_handler(dof_handler); + data_out.add_data_vector(solution, "solution"); + + // Here we generate an index for each cell to visualize the ordering used + // by the smoothers. Note that we do this only for the active cells + // instead of the levels, where the smoothers are actually used. For the + // point smoothers we renumber DoFs instead of cells, so this is only an + // approximation of what happens in reality. Finally, the random ordering + // is not the random ordering we actually use (see create_smoother() for + // that). + const unsigned int n_active_cells = triangulation.n_active_cells(); + Vector cell_indices(n_active_cells); + + { + // First generate a permutation vector for the cell indices: + std::vector ordered_indices; + if (settings.dof_renum == "downstream") + { + ordered_indices = + create_downstream_order(dof_handler, advection_direction); + } + else if (settings.dof_renum == "upstream") + { + ordered_indices = + create_downstream_order(dof_handler, -1.0 * advection_direction); + } + else if (settings.dof_renum == "random") + { + ordered_indices = create_random_order(dof_handler); + } + else if (settings.dof_renum == "none") + { + ordered_indices.resize(n_active_cells); + for (unsigned int i = 0; i < n_active_cells; ++i) + ordered_indices[i] = i; + } + else + AssertThrow(false, ExcNotImplemented()); + + // Then copy the permutation in ordered_indices into an output vector: + for (unsigned int i = 0; i < n_active_cells; ++i) + cell_indices(ordered_indices[i]) = static_cast(i); + } + + data_out.add_data_vector(cell_indices, "cell_index"); + + data_out.build_patches(); + + std::string filename = + "solution-" + Utilities::int_to_string(cycle) + ".vtu"; + std::ofstream output(filename.c_str()); + data_out.write_vtu(output); + } + + + template + void AdvectionProblem::run() + { + for (unsigned int cycle = 0; cycle < (settings.fe_degree == 1 ? 7 : 5); + ++cycle) + { + std::cout << " Cycle " << cycle << ':' << std::endl; + + if (cycle == 0) + { + GridGenerator::hyper_cube_with_cylindrical_hole( + triangulation, 0.3, 1.0, 0.5, 1, false); + static const SphericalManifold manifold_description( + Point(0, 0)); + triangulation.set_manifold(1, manifold_description); + } + + triangulation.refine_global(); + + setup_system(); + + std::cout << " Number of active cells: " + << triangulation.n_active_cells() << " (" + << triangulation.n_levels() << " levels)" << std::endl; + std::cout << " Number of degrees of freedom: " + << dof_handler.n_dofs() << std::endl; + + assemble_system_and_multigrid(); + + solve(); + + if (settings.output) + output_results(cycle); + + std::cout << std::endl; + } + } +} // namespace Step100 + + +int main(int argc, char *argv[]) { try { - // do nothing. + Step100::Settings settings; + if (!settings.try_parse((argc > 1) ? (argv[1]) : "")) + return 0; + + Step100::AdvectionProblem<2> advection_problem_2d(settings); + advection_problem_2d.run(); } catch (std::exception &exc) { @@ -41,7 +1116,6 @@ int main() << "Aborting!" << std::endl << "----------------------------------------------------" << std::endl; - return 1; } catch (...) From 74fdd5139d12f8d1522cb4efe6105fe0ee42560f Mon Sep 17 00:00:00 2001 From: tcclevenger Date: Fri, 5 Apr 2019 17:09:38 -0600 Subject: [PATCH 373/507] requested changes --- examples/step-63/block_jacobi.prm | 14 +- examples/step-63/block_sor.prm | 14 +- examples/step-63/jacobi.prm | 14 +- examples/step-63/sor.prm | 15 +- examples/step-63/step-63.cc | 600 +++++++++++++++--------------- 5 files changed, 332 insertions(+), 325 deletions(-) diff --git a/examples/step-63/block_jacobi.prm b/examples/step-63/block_jacobi.prm index a8dc7f556696..9e6f98326eaa 100644 --- a/examples/step-63/block_jacobi.prm +++ b/examples/step-63/block_jacobi.prm @@ -1,14 +1,14 @@ # Finite Element degree -set fe degree = 1 +set Fe degree = 1 -# Smoother Type: sor|jacobi|block sor|block jacobi -set smoother type = block jacobi +# Smoother Type: SOR|Jacobi|block SOR|block Jacobi +set Smoother type = block Jacobi -# Dof renumbering: no|random|downstream|upstream -set dof renumbering = downstream +# DoF renumbering: no|downstream|upstream|random +set DoF renumbering = downstream # With streamline diffusion: true|false -set with sd = true +set With streamline diffusion = true # Output: true|false -set output = false +set Output = false diff --git a/examples/step-63/block_sor.prm b/examples/step-63/block_sor.prm index f5991834c4a5..375e7e63cb32 100644 --- a/examples/step-63/block_sor.prm +++ b/examples/step-63/block_sor.prm @@ -1,14 +1,14 @@ # Finite Element degree -set fe degree = 1 +set Fe degree = 1 -# Smoother Type: sor|jacobi|block sor|block jacobi -set smoother type = block sor +# Smoother Type: SOR|Jacobi|block SOR|block Jacobi +set Smoother type = block SOR -# Dof renumbering: none|random|downstream|upstream -set dof renumbering = downstream +# DoF renumbering: no|downstream|upstream|random +set DoF renumbering = downstream # With streamline diffusion: true|false -set with sd = true +set With streamline diffusion = true # Output: true|false -set output = false +set Output = false \ No newline at end of file diff --git a/examples/step-63/jacobi.prm b/examples/step-63/jacobi.prm index d6a55ff53b93..4c7365e06a7d 100644 --- a/examples/step-63/jacobi.prm +++ b/examples/step-63/jacobi.prm @@ -1,14 +1,14 @@ # Finite Element degree -set fe degree = 1 +set Fe degree = 1 -# Smoother Type: sor|jacobi|block sor|block jacobi -set smoother type = jacobi +# Smoother Type: SOR|Jacobi|block SOR|block Jacobi +set Smoother type = Jacobi -# Dof renumbering: no|random|downstream|upstream -set dof renumbering = downstream +# DoF renumbering: no|downstream|upstream|random +set DoF renumbering = downstream # With streamline diffusion: true|false -set with sd = true +set With streamline diffusion = true # Output: true|false -set output = false +set Output = false \ No newline at end of file diff --git a/examples/step-63/sor.prm b/examples/step-63/sor.prm index 47ab13c3d5b3..dbdc74c19810 100644 --- a/examples/step-63/sor.prm +++ b/examples/step-63/sor.prm @@ -1,15 +1,14 @@ # Finite Element degree -set fe degree = 1 +set Fe degree = 1 -# Smoother Type: sor|jacobi|block sor|block jacobi -set smoother type = sor - -# Dof renumbering: no|random|downstream|upstream -set dof renumbering = downstream +# Smoother Type: SOR|Jacobi|block SOR|block Jacobi +set Smoother type = SOR +# DoF renumbering: no|downstream|upstream|random +set DoF renumbering = downstream # With streamline diffusion: true|false -set with sd = true +set With streamline diffusion = true # Output: true|false -set output = false +set Output = false \ No newline at end of file diff --git a/examples/step-63/step-63.cc b/examples/step-63/step-63.cc index dcfcd1fa54ec..3f9717ec8964 100644 --- a/examples/step-63/step-63.cc +++ b/examples/step-63/step-63.cc @@ -66,19 +66,12 @@ #include #include - - #include #include +#include - -#include -#include - - - -namespace Step100 +namespace Step63 { using namespace dealii; @@ -103,8 +96,13 @@ namespace Step100 FEValues fe_values; }; + + + struct CopyData { + CopyData() = default; + unsigned int level; unsigned int dofs_per_cell; @@ -116,38 +114,51 @@ namespace Step100 struct Settings { - bool try_parse(const std::string &prm_filename); + enum DoFRenumberingStrategy + { + none, + downstream, + upstream, + random + }; - unsigned int fe_degree; - std::string smoother_type; - std::string dof_renum; - bool with_sd; - bool output; - }; + bool get_parameters(const std::string &prm_filename); + unsigned int fe_degree; + std::string smoother_type; + DoFRenumberingStrategy dof_renumbering; + bool with_streamline_diffusion; + bool output; + }; - bool Settings::try_parse(const std::string &prm_filename) + bool Settings::get_parameters(const std::string &prm_filename) { + if (prm_filename.size() == 0) + { + std::cerr << "Usage: please pass a .prm file as the first argument" + << std::endl; + return false; + } + ParameterHandler prm; - prm.declare_entry("fe degree", + prm.declare_entry("Fe degree", "1", Patterns::Integer(0), "Finite Element degree"); - prm.declare_entry("smoother type", - "block sor", - Patterns::Selection("sor|jacobi|block sor|block jacobi"), - "Smoother Type: sor|jacobi|block sor|block jacobi"); - prm.declare_entry("dof renumbering", + prm.declare_entry("Smoother type", + "block SOR", + Patterns::Selection("sor|Jacobi|block SOR|block Jacobi"), + "Smoother Type: SOR|Jacobi|block SOR|block Jacobi"); + prm.declare_entry("DoF renumbering", "downstream", - Patterns::Selection("none|random|downstream|upstream"), - "Dof renumbering: none|random|downstream|upstream"); - prm.declare_entry("with sd", + Patterns::Selection("none|downstream|upstream|random"), + "DoF renumbering: none|downstream|upstream|random"); + prm.declare_entry("With streamline diffusion", "true", Patterns::Bool(), "With streamline diffusion: true|false"); - prm.declare_entry("output", - "true", + prm.declare_entry("Output","true", Patterns::Bool(), "Generate graphical output: true|false"); @@ -157,183 +168,155 @@ namespace Step100 } catch (const dealii::PathSearch::ExcFileNotFound &) { - if (prm_filename.size() > 0) - std::cerr << "ERRROR: could not open the .prm file '" << prm_filename - << "'" << std::endl; - else - std::cerr << "Usage: please pass a .prm file as the first argument" - << std::endl; + std::cerr << "ERROR: could not parse input from given .prm file" + << prm_filename << "'" << std::endl; prm.print_parameters(std::cout, ParameterHandler::Text); return false; } - this->fe_degree = prm.get_integer("fe degree"); - this->smoother_type = prm.get("smoother type"); - this->dof_renum = prm.get("dof renumbering"); - this->with_sd = prm.get_bool("with sd"); - this->output = prm.get_bool("output"); - return true; - } + fe_degree = prm.get_integer("Fe degree"); + smoother_type = prm.get("Smoother type"); + std::string renumbering = prm.get("DoF renumbering"); + if (renumbering == "none") + dof_renumbering = DoFRenumberingStrategy::none; + else if (renumbering == "downstream") + dof_renumbering = DoFRenumberingStrategy::downstream; + else if (renumbering == "upstream") + dof_renumbering = DoFRenumberingStrategy::upstream; + else if (renumbering == "random") + dof_renumbering = DoFRenumberingStrategy::random; + with_streamline_diffusion = prm.get_bool("With streamline diffusion"); + output = prm.get_bool("Output"); - namespace - { - template - struct CompareDownstream - { - /** - * Constructor. - */ - CompareDownstream(const Tensor<1, dim> &dir) - : dir(dir) - {} - /** - * Return true if c1 less c2. - */ - bool operator()(const Iterator &c1, const Iterator &c2) const - { - const Tensor<1, dim> diff = c2->center() - c1->center(); - return (diff * dir > 0); - } + return true; + } - private: - /** - * Flow direction. - */ - const Tensor<1, dim> dir; - }; - // Functions for creating permutation of cells for output and Block - // smoothers - template - std::vector - create_downstream_order(const DoFHandler &dof, - const Tensor<1, dim> direction, - const unsigned int level) - { - std::vector::level_cell_iterator> ordered_cells; - ordered_cells.reserve(dof.get_triangulation().n_cells(level)); - const CompareDownstream::level_cell_iterator, - dim> + // Functions for creating permutation of cells for output and Block + // smoothers + template + std::vector + create_downstream_cell_ordering(const DoFHandler &dof, + const Tensor<1, dim> direction, + const unsigned int level) + { + std::vector::level_cell_iterator> ordered_cells; + ordered_cells.reserve(dof.get_triangulation().n_cells(level)); + const DoFRenumbering:: + CompareDownstream::level_cell_iterator, dim> comparator(direction); - typename DoFHandler::level_cell_iterator cell = dof.begin(level); - typename DoFHandler::level_cell_iterator endc = dof.end(level); - for (; cell != endc; ++cell) - ordered_cells.push_back(cell); + typename DoFHandler::level_cell_iterator cell = dof.begin(level); + typename DoFHandler::level_cell_iterator endc = dof.end(level); + for (; cell != endc; ++cell) + ordered_cells.push_back(cell); - std::sort(ordered_cells.begin(), ordered_cells.end(), comparator); + std::sort(ordered_cells.begin(), ordered_cells.end(), comparator); - std::vector ordered_indices; - ordered_indices.reserve(dof.get_triangulation().n_cells(level)); + std::vector ordered_indices; + ordered_indices.reserve(dof.get_triangulation().n_cells(level)); - for (unsigned int i = 0; i < ordered_cells.size(); ++i) - ordered_indices.push_back(ordered_cells[i]->index()); + for (unsigned int i = 0; i < ordered_cells.size(); ++i) + ordered_indices.push_back(ordered_cells[i]->index()); - return ordered_indices; - } + return ordered_indices; + } - template - std::vector - create_downstream_order(const DoFHandler &dof, - const Tensor<1, dim> direction) - { - std::vector::active_cell_iterator> ordered_cells; - ordered_cells.reserve(dof.get_triangulation().n_active_cells()); - const CompareDownstream::active_cell_iterator, - dim> + template + std::vector + create_downstream_cell_ordering(const DoFHandler &dof, + const Tensor<1, dim> direction) + { + std::vector::active_cell_iterator> ordered_cells; + ordered_cells.reserve(dof.get_triangulation().n_active_cells()); + const DoFRenumbering:: + CompareDownstream::active_cell_iterator, dim> comparator(direction); - typename DoFHandler::active_cell_iterator cell = dof.begin_active(); - typename DoFHandler::active_cell_iterator endc = dof.end(); - for (; cell != endc; ++cell) - ordered_cells.push_back(cell); + typename DoFHandler::active_cell_iterator cell = dof.begin_active(); + typename DoFHandler::active_cell_iterator endc = dof.end(); + for (; cell != endc; ++cell) + ordered_cells.push_back(cell); - std::sort(ordered_cells.begin(), ordered_cells.end(), comparator); + std::sort(ordered_cells.begin(), ordered_cells.end(), comparator); - std::vector ordered_indices; - ordered_indices.reserve(dof.get_triangulation().n_active_cells()); + std::vector ordered_indices; + ordered_indices.reserve(dof.get_triangulation().n_active_cells()); - for (unsigned int i = 0; i < ordered_cells.size(); ++i) - ordered_indices.push_back(ordered_cells[i]->index()); + for (unsigned int i = 0; i < ordered_cells.size(); ++i) + ordered_indices.push_back(ordered_cells[i]->index()); - return ordered_indices; - } + return ordered_indices; + } - template - std::vector create_random_order(const DoFHandler &dof, - const unsigned int level) - { - const unsigned int n_cells = dof.get_triangulation().n_cells(level); + template + std::vector + create_random_cell_ordering(const DoFHandler &dof, + const unsigned int level) + { + const unsigned int n_cells = dof.get_triangulation().n_cells(level); - std::vector ordered_cells; - ordered_cells.reserve(n_cells); + std::vector ordered_cells; + ordered_cells.reserve(n_cells); - typename DoFHandler::cell_iterator cell = dof.begin(level); - typename DoFHandler::cell_iterator endc = dof.end(level); - for (; cell != endc; ++cell) - ordered_cells.push_back(cell->index()); + typename DoFHandler::cell_iterator cell = dof.begin(level); + typename DoFHandler::cell_iterator endc = dof.end(level); + for (; cell != endc; ++cell) + ordered_cells.push_back(cell->index()); - // shuffle the elements; the following is essentially std::shuffle (which - // is new in C++11) but with a boost URNG - ::boost::mt19937 random_number_generator; - for (unsigned int i = 1; i < n_cells; ++i) - { - // get a random number between 0 and i (inclusive) - const unsigned int j = - ::boost::random::uniform_int_distribution<>(0, i)( - random_number_generator); - - // if possible, swap the elements - if (i != j) - std::swap(ordered_cells[i], ordered_cells[j]); - } + // shuffle the elements + std::mt19937 random_number_generator; + for (unsigned int i = 1; i < n_cells; ++i) + { + // get a random number between 0 and i (inclusive) + const unsigned int j = + std::uniform_int_distribution<>(0, i)(random_number_generator); - return ordered_cells; - } + // if possible, swap the elements + if (i != j) + std::swap(ordered_cells[i], ordered_cells[j]); + } - template - std::vector create_random_order(const DoFHandler &dof) - { - const unsigned int n_cells = dof.get_triangulation().n_active_cells(); + return ordered_cells; + } - std::vector ordered_cells; - ordered_cells.reserve(n_cells); + template + std::vector + create_random_cell_ordering(const DoFHandler &dof) + { + const unsigned int n_cells = dof.get_triangulation().n_active_cells(); - typename DoFHandler::active_cell_iterator cell = dof.begin_active(); - typename DoFHandler::active_cell_iterator endc = dof.end(); - for (; cell != endc; ++cell) - ordered_cells.push_back(cell->index()); + std::vector ordered_cells; + ordered_cells.reserve(n_cells); - // shuffle the elements; the following is essentially std::shuffle (which - // is new in C++11) but with a boost URNG - ::boost::mt19937 random_number_generator; - for (unsigned int i = 1; i < n_cells; ++i) - { - // get a random number between 0 and i (inclusive) - const unsigned int j = - ::boost::random::uniform_int_distribution<>(0, i)( - random_number_generator); - - // if possible, swap the elements - if (i != j) - std::swap(ordered_cells[i], ordered_cells[j]); - } + typename DoFHandler::active_cell_iterator cell = dof.begin_active(); + typename DoFHandler::active_cell_iterator endc = dof.end(); + for (; cell != endc; ++cell) + ordered_cells.push_back(cell->index()); - return ordered_cells; - } + // shuffle the elements + std::mt19937 random_number_generator; + for (unsigned int i = 1; i < n_cells; ++i) + { + // get a random number between 0 and i (inclusive) + const unsigned int j = + std::uniform_int_distribution<>(0, i)(random_number_generator); - } // namespace + // if possible, swap the elements + if (i != j) + std::swap(ordered_cells[i], ordered_cells[j]); + } + + return ordered_cells; + } - // RHS and boundary is an adaptation from one in - // Finite Elements and Fast Iterative Solvers: with Applications - // in Incompressible Fluid Dynamics template class RightHandSide : public Function { @@ -348,9 +331,6 @@ namespace Step100 virtual void value_list(const std::vector> &points, std::vector & values, const unsigned int component = 0) const; - - private: - static const Point center_point; }; template @@ -440,15 +420,15 @@ namespace Step100 } template - double delta_value(const double hk, - const double eps, - const Tensor<1, dim> dir, - const double pk) + double compute_stabilization_delta(const double hk, + const double eps, + const Tensor<1, dim> dir, + const double pk) { // Value defined in 'On discontinuity–capturing methods for // convection–diffusion equations' - double Peclet = dir.norm() * hk / (2.0 * eps * pk); - double coth = + const double Peclet = dir.norm() * hk / (2.0 * eps * pk); + const double coth = (1.0 + std::exp(-2.0 * Peclet)) / (1.0 - std::exp(-2.0 * Peclet)); return hk / (2.0 * dir.norm() * pk) * (coth - 1.0 / Peclet); @@ -480,9 +460,8 @@ namespace Step100 Triangulation triangulation; DoFHandler dof_handler; - FE_Q fe; - MappingQ mapping; - unsigned int quad_degree; + const FE_Q fe; + const MappingQ mapping; AffineConstraints constraints; @@ -499,11 +478,17 @@ namespace Step100 MGLevelObject> mg_interface_in; MGLevelObject> mg_interface_out; + mg::Matrix> mg_matrix; + mg::Matrix> mg_interface_matrix_in; + mg::Matrix> mg_interface_matrix_out; + + MGConstrainedDoFs mg_constrained_dofs; - Settings settings; const double epsilon; Tensor<1, dim> advection_direction; + + const Settings settings; }; @@ -514,13 +499,9 @@ namespace Step100 , dof_handler(triangulation) , fe(settings.fe_degree) , mapping(settings.fe_degree) - , quad_degree(2 * fe.degree + 2) - , settings(settings) , epsilon(0.005) + , settings(settings) { - // Set Advection direction (problem is an adaptation from one in - // Finite Elements and Fast Iterative Solvers: with Applications - // in Incompressible Fluid Dynamics) advection_direction[0] = -std::sin(numbers::PI / 6.0); if (dim > 1) advection_direction[1] = std::cos(numbers::PI / 6.0); @@ -571,13 +552,18 @@ namespace Step100 // Renumber DoFs on each level in downstream or upstream direction if // needed. This is only necessary for point smoothers (SOR and Jacobi) as // the block smoothers operate on cells (see create_smoother()): - if (settings.smoother_type == "sor" || settings.smoother_type == "jacobi") + if (settings.smoother_type == "SOR" || settings.smoother_type == "Jacobi") { - if (settings.dof_renum == "downstream" || - settings.dof_renum == "upstream") + if (settings.dof_renumbering == + Settings::DoFRenumberingStrategy::downstream || + settings.dof_renumbering == + Settings::DoFRenumberingStrategy::upstream) { const Tensor<1, dim> direction = - (settings.dof_renum == "upstream" ? -1.0 : 1.0) * + (settings.dof_renumbering == + Settings::DoFRenumberingStrategy::upstream ? + -1.0 : + 1.0) * advection_direction; for (unsigned int level = 0; level < n_levels; ++level) @@ -586,7 +572,8 @@ namespace Step100 direction, /*dof_wise_renumbering = */ true); } - else if (settings.dof_renum == "random") + else if (settings.dof_renumbering == + Settings::DoFRenumberingStrategy::random) { for (unsigned int level = 0; level < n_levels; ++level) DoFRenumbering::random(dof_handler, level); @@ -598,9 +585,7 @@ namespace Step100 mg_constrained_dofs.clear(); mg_constrained_dofs.initialize(dof_handler); - std::set dirichlet_boundary_ids = {0, 1}; - mg_constrained_dofs.make_zero_boundary_constraints(dof_handler, - dirichlet_boundary_ids); + mg_constrained_dofs.make_zero_boundary_constraints(dof_handler, {0, 1}); mg_matrices.resize(0, n_levels - 1); mg_matrices.clear_elements(); @@ -650,12 +635,12 @@ namespace Step100 const unsigned int dofs_per_cell = scratch_data.fe_values.get_fe().dofs_per_cell; copy_data.dofs_per_cell = dofs_per_cell; + copy_data.cell_matrix.reinit(dofs_per_cell, dofs_per_cell); const unsigned int n_q_points = scratch_data.fe_values.get_quadrature().size(); - copy_data.cell_matrix.reinit(dofs_per_cell, dofs_per_cell); - if (!cell->is_level_cell()) + if (cell->is_level_cell() == false) copy_data.cell_rhs.reinit(dofs_per_cell); copy_data.local_dof_indices.resize(dofs_per_cell); @@ -669,11 +654,11 @@ namespace Step100 right_hand_side.value_list(scratch_data.fe_values.get_quadrature_points(), rhs_values); - const double delta = settings.with_sd ? delta_value(cell->diameter(), - epsilon, - advection_direction, - settings.fe_degree) : - 0.0; + const double delta = settings.with_streamline_diffusion ? + compute_stabilization_delta(cell->diameter(), + epsilon, + advection_direction, + settings.fe_degree) : 0.0; for (unsigned int q_point = 0; q_point < n_q_points; ++q_point) for (unsigned int i = 0; i < dofs_per_cell; ++i) @@ -689,7 +674,7 @@ namespace Step100 scratch_data.fe_values.shape_value(i, q_point)) * scratch_data.fe_values.JxW(q_point); - if (settings.with_sd) + if (settings.with_streamline_diffusion) copy_data.cell_matrix(i, j) += delta * (advection_direction * @@ -703,12 +688,12 @@ namespace Step100 scratch_data.fe_values.shape_grad(i, q_point)) * scratch_data.fe_values.JxW(q_point); } - if (!cell->is_level_cell()) + if (cell->is_level_cell() == false) { copy_data.cell_rhs(i) += scratch_data.fe_values.shape_value(i, q_point) * rhs_values[q_point] * scratch_data.fe_values.JxW(q_point); - if (settings.with_sd) + if (settings.with_streamline_diffusion) copy_data.cell_rhs(i) += delta * rhs_values[q_point] * advection_direction * scratch_data.fe_values.shape_grad(i, q_point) * @@ -743,7 +728,7 @@ namespace Step100 dof_handler.end(), cell_worker_active, copier_active, - ScratchData(fe, quad_degree), + ScratchData(fe, fe.degree + 1), CopyData(), MeshWorker::assemble_own_cells); @@ -754,11 +739,10 @@ namespace Step100 for (unsigned int level = 0; level < triangulation.n_global_levels(); ++level) { - IndexSet dofset; - DoFTools::extract_locally_relevant_level_dofs(dof_handler, - level, - dofset); - boundary_constraints[level].reinit(dofset); + IndexSet locally_owned_level_dof_indices; + DoFTools::extract_locally_relevant_level_dofs( + dof_handler, level, locally_owned_level_dof_indices); + boundary_constraints[level].reinit(locally_owned_level_dof_indices); boundary_constraints[level].add_lines( mg_constrained_dofs.get_refinement_edge_indices(level)); boundary_constraints[level].add_lines( @@ -804,7 +788,7 @@ namespace Step100 dof_handler.end_mg(), cell_worker_mg, copier_mg, - ScratchData(fe, quad_degree), + ScratchData(fe, fe.degree + 1), CopyData(), MeshWorker::assemble_own_cells); } @@ -814,9 +798,9 @@ namespace Step100 std::unique_ptr>> AdvectionProblem::create_smoother() { - if (settings.smoother_type == "sor") + if (settings.smoother_type == "SOR") { - typedef PreconditionSOR> Smoother; + using Smoother = PreconditionSOR>; auto smoother = std_cxx14::make_unique, @@ -828,10 +812,10 @@ namespace Step100 smoother->set_steps(2); return smoother; } - else if (settings.smoother_type == "jacobi") + else if (settings.smoother_type == "Jacobi") { - typedef PreconditionJacobi> Smoother; - auto smoother = + using Smoother = PreconditionJacobi>; + auto smoother = std_cxx14::make_unique, Smoother, Vector>>(); @@ -841,11 +825,12 @@ namespace Step100 smoother->set_steps(4); return smoother; } - else if (settings.smoother_type == "block sor") + else if (settings.smoother_type == "block SOR") { - typedef RelaxationBlockSOR, double, Vector> - Smoother; + using Smoother = + RelaxationBlockSOR, double, Vector>; + // TODO: try and remove static static MGLevelObject smoother_data; smoother_data.resize(0, triangulation.n_levels() - 1); @@ -859,23 +844,34 @@ namespace Step100 smoother_data[level].inversion = PreconditionBlockBase::svd; std::vector ordered_indices; - if (settings.dof_renum == "downstream") - ordered_indices = create_downstream_order(dof_handler, - advection_direction, - level); - else if (settings.dof_renum == "upstream") - ordered_indices = - create_downstream_order(dof_handler, - -1.0 * advection_direction, - level); - else if (settings.dof_renum == "random") - ordered_indices = create_random_order(dof_handler, level); - else if (settings.dof_renum == "none") + switch (settings.dof_renumbering) { - // Do nothing + case Settings::DoFRenumberingStrategy::downstream: + ordered_indices = + create_downstream_cell_ordering(dof_handler, + advection_direction, + level); + break; + + case Settings::DoFRenumberingStrategy::upstream: + ordered_indices = + create_downstream_cell_ordering(dof_handler, + -1.0 * advection_direction, + level); + break; + + case Settings::DoFRenumberingStrategy::random: + ordered_indices = + create_random_cell_ordering(dof_handler, level); + break; + + case Settings::DoFRenumberingStrategy::none: // Do nothing + break; + + default: + AssertThrow(false, ExcNotImplemented()); + break; } - else - AssertThrow(false, ExcNotImplemented()); smoother_data[level].order = std::vector>(1, ordered_indices); @@ -889,13 +885,12 @@ namespace Step100 smoother->set_steps(1); return smoother; } - else if (settings.smoother_type == "block jacobi") + else if (settings.smoother_type == "block Jacobi") { - typedef RelaxationBlockJacobi, - double, - Vector> - Smoother; + using Smoother = + RelaxationBlockJacobi, double, Vector>; + // TODO: try and remove static static MGLevelObject smoother_data; smoother_data.resize(0, triangulation.n_levels() - 1); @@ -909,23 +904,34 @@ namespace Step100 smoother_data[level].inversion = PreconditionBlockBase::svd; std::vector ordered_indices; - if (settings.dof_renum == "downstream") - ordered_indices = create_downstream_order(dof_handler, - advection_direction, - level); - else if (settings.dof_renum == "upstream") - ordered_indices = - create_downstream_order(dof_handler, - -1.0 * advection_direction, - level); - else if (settings.dof_renum == "random") - ordered_indices = create_random_order(dof_handler, level); - else if (settings.dof_renum == "none") + switch (settings.dof_renumbering) { - // Do nothing + case Settings::DoFRenumberingStrategy::downstream: + ordered_indices = + create_downstream_cell_ordering(dof_handler, + advection_direction, + level); + break; + + case Settings::DoFRenumberingStrategy::upstream: + ordered_indices = + create_downstream_cell_ordering(dof_handler, + -1.0 * advection_direction, + level); + break; + + case Settings::DoFRenumberingStrategy::random: + ordered_indices = + create_random_cell_ordering(dof_handler, level); + break; + + case Settings::DoFRenumberingStrategy::none: // Do nothing + break; + + default: + AssertThrow(false, ExcNotImplemented()); + break; } - else - AssertThrow(false, ExcNotImplemented()); smoother_data[level].order = std::vector>(1, ordered_indices); @@ -947,15 +953,13 @@ namespace Step100 template void AdvectionProblem::solve() { - Timer time; - - const double solve_tol = 1e-8 * system_rhs.l2_norm(); - const unsigned int max_iters = 200; - SolverControl solver_control(max_iters, solve_tol, true, true); + const unsigned int max_iters = 200; + const double solve_tolerance = 1e-8 * system_rhs.l2_norm(); + SolverControl solver_control(max_iters, solve_tolerance, true, true); solver_control.enable_history_data(); - typedef MGTransferPrebuilt> Transfer; - Transfer mg_transfer(mg_constrained_dofs); + using Transfer = MGTransferPrebuilt>; + Transfer mg_transfer(mg_constrained_dofs); mg_transfer.build_matrices(dof_handler); FullMatrix coarse_matrix; @@ -963,11 +967,12 @@ namespace Step100 MGCoarseGridHouseholder> coarse_grid_solver; coarse_grid_solver.initialize(coarse_matrix); - std::unique_ptr>> mg_smoother = create_smoother(); + const std::unique_ptr>> mg_smoother = + create_smoother(); - mg::Matrix> mg_matrix(mg_matrices); - mg::Matrix> mg_interface_matrix_in(mg_interface_in); - mg::Matrix> mg_interface_matrix_out(mg_interface_out); + mg_matrix.initialize(mg_matrices); + mg_interface_matrix_in.initialize(mg_interface_in); + mg_interface_matrix_out.initialize(mg_interface_out); Multigrid> mg( mg_matrix, coarse_grid_solver, mg_transfer, *mg_smoother, *mg_smoother); @@ -977,12 +982,12 @@ namespace Step100 mg, mg_transfer); - - std::cout << " Solving with GMRES to tol " << solve_tol << "..." + std::cout << " Solving with GMRES to tol " << solve_tolerance << "..." << std::endl; SolverGMRES<> solver(solver_control); - time.restart(); + Timer time; + time.start(); solver.solve(system_matrix, solution, system_rhs, preconditioner); time.stop(); @@ -998,10 +1003,6 @@ namespace Step100 template void AdvectionProblem::output_results(const unsigned int cycle) const { - DataOut data_out; - data_out.attach_dof_handler(dof_handler); - data_out.add_data_vector(solution, "solution"); - // Here we generate an index for each cell to visualize the ordering used // by the smoothers. Note that we do this only for the active cells // instead of the levels, where the smoothers are actually used. For the @@ -1011,40 +1012,46 @@ namespace Step100 // that). const unsigned int n_active_cells = triangulation.n_active_cells(); Vector cell_indices(n_active_cells); - { // First generate a permutation vector for the cell indices: std::vector ordered_indices; - if (settings.dof_renum == "downstream") + switch (settings.dof_renumbering) { - ordered_indices = - create_downstream_order(dof_handler, advection_direction); + case Settings::DoFRenumberingStrategy::downstream: + ordered_indices = + create_downstream_cell_ordering(dof_handler, advection_direction); + break; + + case Settings::DoFRenumberingStrategy::upstream: + ordered_indices = + create_downstream_cell_ordering(dof_handler, + -1.0 * advection_direction); + break; + + case Settings::DoFRenumberingStrategy::random: + ordered_indices = create_random_cell_ordering(dof_handler); + break; + + case Settings::DoFRenumberingStrategy::none: + ordered_indices.resize(n_active_cells); + for (unsigned int i = 0; i < n_active_cells; ++i) + ordered_indices[i] = i; + break; + + default: + AssertThrow(false, ExcNotImplemented()); + break; } - else if (settings.dof_renum == "upstream") - { - ordered_indices = - create_downstream_order(dof_handler, -1.0 * advection_direction); - } - else if (settings.dof_renum == "random") - { - ordered_indices = create_random_order(dof_handler); - } - else if (settings.dof_renum == "none") - { - ordered_indices.resize(n_active_cells); - for (unsigned int i = 0; i < n_active_cells; ++i) - ordered_indices[i] = i; - } - else - AssertThrow(false, ExcNotImplemented()); // Then copy the permutation in ordered_indices into an output vector: for (unsigned int i = 0; i < n_active_cells; ++i) cell_indices(ordered_indices[i]) = static_cast(i); } + DataOut data_out; + data_out.attach_dof_handler(dof_handler); + data_out.add_data_vector(solution, "solution"); data_out.add_data_vector(cell_indices, "cell_index"); - data_out.build_patches(); std::string filename = @@ -1091,18 +1098,19 @@ namespace Step100 std::cout << std::endl; } } -} // namespace Step100 +} // namespace Step63 + int main(int argc, char *argv[]) { try { - Step100::Settings settings; - if (!settings.try_parse((argc > 1) ? (argv[1]) : "")) + Step63::Settings settings; + if (!settings.get_parameters((argc > 1) ? (argv[1]) : "")) return 0; - Step100::AdvectionProblem<2> advection_problem_2d(settings); + Step63::AdvectionProblem<2> advection_problem_2d(settings); advection_problem_2d.run(); } catch (std::exception &exc) From 085943837d1fd596249085a0343219de30ef1ed1 Mon Sep 17 00:00:00 2001 From: Luca Heltai Date: Fri, 5 Apr 2019 19:36:52 +0200 Subject: [PATCH 374/507] Fixed documentation. --- include/deal.II/algorithms/general_data_storage.h | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/include/deal.II/algorithms/general_data_storage.h b/include/deal.II/algorithms/general_data_storage.h index ed2905776161..30228b9ffa8d 100644 --- a/include/deal.II/algorithms/general_data_storage.h +++ b/include/deal.II/algorithms/general_data_storage.h @@ -98,9 +98,11 @@ class GeneralDataStorage : public Subscriptor /** * Clear all data stored in this class instance. * - * After this function is called, all copied data owned by this class will - * go out of scope. Furthermore, all scoping requirements for data referenced - * by this class instance will be lifted. + * When you call this function, it destroys all objects you asked to be stored + * as copies, and it forgets about the references to data you asked to store + * by reference. As a consequence, you are now free to destroy the objects to + * which references were stored at whatever time you want -- before or after + * the current `GeneralDataStorage` object is destroyed. * * To clarify this point, consider the following small example: * @@ -289,7 +291,7 @@ class GeneralDataStorage : public Subscriptor stores_object_with_name(const std::string &name) const; /** - * Find out if we store an object with given name. + * Remove the object with given name. */ void remove_object_with_name(const std::string &name); From d6406eedd0982dc7821c3fff5be50097f4daa441 Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Sun, 7 Apr 2019 08:40:37 +0200 Subject: [PATCH 375/507] Add alternative test output --- .../general_data_storage_01.debug.output.2 | 74 +++++++++++++++++++ 1 file changed, 74 insertions(+) create mode 100644 tests/algorithms/general_data_storage_01.debug.output.2 diff --git a/tests/algorithms/general_data_storage_01.debug.output.2 b/tests/algorithms/general_data_storage_01.debug.output.2 new file mode 100644 index 000000000000..50b2af1bbd66 --- /dev/null +++ b/tests/algorithms/general_data_storage_01.debug.output.2 @@ -0,0 +1,74 @@ + +DEAL::Add by copy +DEAL::Size: 2 +DEAL::Add by reference +DEAL::Size: 2 +DEAL::Add or construct +DEAL::Size: 1 +DEAL::Merge +DEAL::Data pre-merge: +DEAL::value double +DEAL::Size: 1 +DEAL::Data 2 pre-merge: +DEAL::value double +DEAL::value_2 double +DEAL::Size: 2 +DEAL::Data post-merge: +DEAL::value double +DEAL::value_2 double +DEAL::Size: 2 +DEAL::Try to overwrite existing entry: Copy +DEAL:: +-------------------------------------------------------- +An error occurred in file in function + void dealii::GeneralDataStorage::add_unique_copy(const string&, const Type&) [with Type = double; std::__cxx11::string = std::__cxx11::basic_string] +The violated condition was: + !stores_object_with_name(name) +Additional information: + An entry with the name value already exists. +-------------------------------------------------------- + +DEAL::Try to overwrite existing entry: Reference +DEAL:: +-------------------------------------------------------- +An error occurred in file in function + void dealii::GeneralDataStorage::add_unique_reference(const string&, Type&) [with Type = const double; std::__cxx11::string = std::__cxx11::basic_string] +The violated condition was: + !stores_object_with_name(name) +Additional information: + An entry with the name value already exists. +-------------------------------------------------------- + +DEAL::Fetch non-existing entry +DEAL:: +-------------------------------------------------------- +An error occurred in file in function + Type& dealii::GeneralDataStorage::get_object_with_name(const string&) [with Type = double; std::__cxx11::string = std::__cxx11::basic_string] +The violated condition was: + stores_object_with_name(name) +Additional information: + No entry with the name value exists. +-------------------------------------------------------- + +DEAL::Access removed entry (reference) +DEAL:: +-------------------------------------------------------- +An error occurred in file in function + Type& dealii::GeneralDataStorage::get_object_with_name(const string&) [with Type = double; std::__cxx11::string = std::__cxx11::basic_string] +The violated condition was: + stores_object_with_name(name) +Additional information: + No entry with the name value exists. +-------------------------------------------------------- + +DEAL::Access removed entry (copy) +DEAL:: +-------------------------------------------------------- +An error occurred in file in function + Type& dealii::GeneralDataStorage::get_object_with_name(const string&) [with Type = double; std::__cxx11::string = std::__cxx11::basic_string] +The violated condition was: + stores_object_with_name(name) +Additional information: + No entry with the name value exists. +-------------------------------------------------------- + From 5ddde2f9bc7638dd815ed82423ad98e053154f54 Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Sat, 30 Mar 2019 23:27:46 +0100 Subject: [PATCH 376/507] Add functions to perform symbolic math operations using SD::Expression --- .../changes/minor/20190330Jean-PaulPelteret | 4 + include/deal.II/differentiation/sd.h | 1 + .../differentiation/sd/symengine_math.h | 785 ++++++++++++++++++ source/differentiation/sd/CMakeLists.txt | 1 + source/differentiation/sd/symengine_math.cc | 339 ++++++++ 5 files changed, 1130 insertions(+) create mode 100644 doc/news/changes/minor/20190330Jean-PaulPelteret create mode 100644 include/deal.II/differentiation/sd/symengine_math.h create mode 100644 source/differentiation/sd/symengine_math.cc diff --git a/doc/news/changes/minor/20190330Jean-PaulPelteret b/doc/news/changes/minor/20190330Jean-PaulPelteret new file mode 100644 index 000000000000..22364ffafe06 --- /dev/null +++ b/doc/news/changes/minor/20190330Jean-PaulPelteret @@ -0,0 +1,4 @@ +New: The Differentiation::SD::Expression class can now be used to perform +symbolic math calculations. +
    +(Jean-Paul Pelteret, 2019/03/30) diff --git a/include/deal.II/differentiation/sd.h b/include/deal.II/differentiation/sd.h index f2707cbfc601..0366a5fbd9c8 100644 --- a/include/deal.II/differentiation/sd.h +++ b/include/deal.II/differentiation/sd.h @@ -20,6 +20,7 @@ #ifdef DEAL_II_WITH_SYMENGINE +# include # include # include # include diff --git a/include/deal.II/differentiation/sd/symengine_math.h b/include/deal.II/differentiation/sd/symengine_math.h new file mode 100644 index 000000000000..9f18c603f924 --- /dev/null +++ b/include/deal.II/differentiation/sd/symengine_math.h @@ -0,0 +1,785 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + +#ifndef dealii_differentiation_sd_symengine_math_h +#define dealii_differentiation_sd_symengine_math_h + +#include + +#ifdef DEAL_II_WITH_SYMENGINE + +# include + +# include + +DEAL_II_NAMESPACE_OPEN + +namespace Differentiation +{ + namespace SD + { + namespace SE = ::SymEngine; + + /** + * @name Mathematical functions + * + * It is necessary that all computed inputs to SymEngine functions are + * of type SE::RCP. So we instead simply offer a unified + * interface to Expression types and with other permutations of numbers + * we convert between them. + * + * For a full list of functions that we (ultimately) expect to support, see + * http://www.cplusplus.com/reference/cmath/. Those that are currently + * supported are extracted from symengine/{functions,pow}.h; + * symengine/type_codes.inc. + */ + + /** + * @name Power functions + */ + //@{ + + /** + * Return a symbolic number that represents a @p base value to the power of + * an @p exponent. + * + * Mimics the function std::pow(base,exponent) using the + * standard math library. + */ + Expression + pow(const Expression &base, const Expression &exponent); + + /** + * Return a symbolic number that represents a @p base value to the power of + * an @p exponent. + * + * Mimics the function std::pow(base,exponent) using the + * standard math library. + * + * This variant is used when the @p exponent is not a Expression. + */ + template ::value>::type> + Expression + pow(const Expression &base, const NumberType &exponent) + { + // Call other implementation + return pow(base, Expression(exponent)); + } + + /** + * Return a symbolic number that represents a @p base value to the power of + * an @p exponent. + * + * Mimics the function std::pow(base,exponent) using the + * standard math library. + * + * This variant is used when the @p base is not a Expression. + */ + template ::value>::type> + Expression + pow(const NumberType &base, const Expression &exponent) + { + // Call other implementation + return pow(Expression(base), exponent); + } + + /** + * Return a symbolic number that represents the square root of some value @p x. + * + * Mimics the function std::sqrt(x) using the standard math + * library. + */ + Expression + sqrt(const Expression &x); + + /** + * Return a symbolic number that represents the cubic root of some value @p x. + * + * Mimics the function std::cbrt(x) using the standard math + * library. + */ + Expression + cbrt(const Expression &x); + + /** + * Return a symbolic number that represents the Euler constant + * $e approx 2.71828$ raised to the given @p exponent. + * + * Mimics the function std::exp(exponent) using the standard + * math library. + */ + Expression + exp(const Expression &exponent); + + /** + * Return a symbolic number that represents the natural logarithm of a value @p x. + * + * Mimics the function std::log(x) using the standard math + * library. + */ + Expression + log(const Expression &x); + + /** + * Return a symbolic number that represents the logarithm of a value @p x with + * respect to a @p base number. + * + * Mimics the function std::log(x,base) using the standard + * math library. + */ + Expression + log(const Expression &x, const Expression &base); + + /** + * Return a symbolic number that represents the logarithm of a value @p x with + * respect to a @p base number. + * + * Mimics the function std::log(x,base) using the standard + * math library. + * + * This variant is used when the @p base is not a Expression. + */ + template ::value>::type> + Expression + log(const Expression &x, const NumberType &base) + { + // Call other implementation + return log(x, Expression(base)); + } + + /** + * Return a symbolic number that represents the logarithm of a value @p x with + * respect to a @p base number. + * + * Mimics the function std::log(x,base) using the standard + * math library. + * + * This variant is used when the @p value is not a Expression. + */ + template ::value>::type> + Expression + log(const NumberType &x, const Expression &base) + { + // Call other implementation + return log(Expression(x), base); + } + + /** + * Return a symbolic number that represents the base 10 logarithm of a value @p x. + * + * Mimics the function std::log10(x) using the standard math + * library. + */ + Expression + log10(const Expression &x); + + //@} + + /** + * @name Trignometric functions + */ + //@{ + + /** + * Return a symbolic number that represents the sine function with the + * given argument @p x. + * + * Mimics the function std::sin(x) using the standard math + * library. + */ + Expression + sin(const Expression &x); + + /** + * Return a symbolic number that represents the cosine function with the + * given argument @p x. + * + * Mimics the function std::cos(x) using the standard math + * library. + */ + Expression + cos(const Expression &x); + + /** + * Return a symbolic number that represents the tangent function with the + * given argument @p x. + * + * Mimics the function std::tan(x) using the standard math + * library. + */ + Expression + tan(const Expression &x); + + /** + * Return a symbolic number that represents the cosecant function with the + * given argument @p x. + * + * Mimics the function 1.0/std::sin(x) using the standard + * math library. + */ + Expression + csc(const Expression &x); + + /** + * Return a symbolic number that represents the secant function with the + * given argument @p x. + * + * Mimics the function 1.0/std::cos(x) using the standard + * math library. + */ + Expression + sec(const Expression &x); + + /** + * Return a symbolic number that represents the cotangent function with the + * given argument @p x. + * + * Mimics the function 1.0/std::tan(x) using the standard + * math library. + */ + Expression + cot(const Expression &x); + + /** + * Return a symbolic number that represents the inverse sine function with + * the + * given argument @p x. + * + * Mimics the function std::asin(x) using the standard math + * library. + */ + Expression + asin(const Expression &x); + + /** + * Return a symbolic number that represents the inverse cosine function + * with the + * given argument @p x. + * + * Mimics the function std::acos(x) using the standard math + * library. + */ + Expression + acos(const Expression &x); + + /** + * Return a symbolic number that represents the inverse tangent function + * with the + * given argument @p x. + * + * Mimics the function std::atan(x) using the standard math + * library. + */ + Expression + atan(const Expression &x); + + /** + * Return a symbolic number that represents the inverse tangent function + * with the + * given arguments @p x and @p y. + * + * Mimics the function std::atan2(y,x) using the standard + * math library. + */ + Expression + atan2(const Expression &y, const Expression &x); + + /** + * Return a symbolic number that represents the inverse tangent function + * with the + * given arguments @p x and @p y. + * + * Mimics the function std::atan2(y,x) using the standard + * math library. + * + * This variant is used when the numerator @p y is not a Expression. + */ + template ::value>::type> + Expression + atan2(const NumberType &y, const Expression &x) + { + // Call other implementation + return atan2(Expression(y), x); + } + + /** + * Return a symbolic number that represents the inverse tangent function + * with the + * given arguments @p x and @p y. + * + * Mimics the function std::atan2(y,x) using the standard + * math library. + * + * This variant is used when the denominator @p x is not a Expression. + */ + template ::value>::type> + Expression + atan2(const Expression &y, const NumberType &x) + { + // Call other implementation + return atan2(y, Expression(x)); + } + + /** + * Return a symbolic number that represents the inverse cosecant function + * with the + * given argument @p x. + * + * Mimics the function 1.0/std::asin(x) using the standard + * math library. + */ + Expression + acsc(const Expression &x); + + /** + * Return a symbolic number that represents the inverse secant function + * with the + * given argument @p x. + * + * Mimics the function 1.0/std::acos(x) using the standard + * math library. + */ + Expression + asec(const Expression &x); + + /** + * Return a symbolic number that represents the inverse cotangent function + * with the + * given argument @p x. + * + * Mimics the function 1.0/std::atan(x) using the standard + * math library. + */ + Expression + acot(const Expression &x); + + //@} + + /** + * @name Hyperbolic trignometric functions + */ + //@{ + + /** + * Return a symbolic number that represents the hyperbolic sine function + * with the + * given argument @p x. + * + * Mimics the function std::sinh(x) using the standard math + * library. + */ + Expression + sinh(const Expression &x); + + /** + * Return a symbolic number that represents the hyperbolic cosine function + * with the + * given argument @p x. + * + * Mimics the function std::cosh(x) using the standard math + * library. + */ + Expression + cosh(const Expression &x); + + /** + * Return a symbolic number that represents the hyperbolic tangent function + * with the + * given argument @p x. + * + * Mimics the function std::tanh(x) using the standard math + * library. + */ + Expression + tanh(const Expression &x); + + /** + * Return a symbolic number that represents the hyperbolic cosecant + * function with the + * given argument @p x. + * + * Mimics the function 1.0/std::sinh(x) using the standard + * math library. + */ + Expression + csch(const Expression &x); + + /** + * Return a symbolic number that represents the hyperbolic secant function + * with the + * given argument @p x. + * + * Mimics the function 1.0/std::cosh(x) using the standard + * math library. + */ + Expression + sech(const Expression &x); + + /** + * Return a symbolic number that represents the hyperbolic cotangent + * function with the + * given argument @p x. + * + * Mimics the function 1.0/std::tanh(x) using the standard + * math library. + */ + Expression + coth(const Expression &x); + + /** + * Return a symbolic number that represents the inverse hyperbolic sine + * function with the + * given argument @p x. + * + * Mimics the function std::asinh(x) using the standard math + * library. + */ + Expression + asinh(const Expression &x); + + /** + * Return a symbolic number that represents the inverse hyperbolic cosine + * function with the + * given argument @p x. + * + * Mimics the function std::acosh(x) using the standard math + * library. + */ + Expression + acosh(const Expression &x); + + /** + * Return a symbolic number that represents the inverse hyperbolic tangent + * function with the + * given argument @p x. + * + * Mimics the function std::atanh(x) using the standard math + * library. + */ + Expression + atanh(const Expression &x); + + /** + * Return a symbolic number that represents the inverse hyperbolic cosecant + * function with the + * given argument @p x. + * + * Mimics the function 1.0/std::asin(x) using the standard + * math library. + */ + Expression + acsch(const Expression &x); + + /** + * Return a symbolic number that represents the inverse hyperbolic secant + * function with the + * given argument @p x. + * + * Mimics the function 1.0/std::acos(x) using the standard + * math library. + */ + Expression + asech(const Expression &x); + + /** + * Return a symbolic number that represents the inverse hyperbolic + * cotangent function with the + * given argument @p x. + * + * Mimics the function 1.0/std::atan(x) using the standard + * math library. + */ + Expression + acoth(const Expression &x); + + //@} + + /** + * @name Other functions + */ + //@{ + + /** + * Return a symbolic number that represents the absolute value of value @p x. + * + * Mimics the function std::abs(x) using the standard math + * library. + */ + Expression + abs(const Expression &x); + + + /** + * Return a symbolic number that represents the absolute value of value @p x. + * + * Mimics the function std::fabs(x) using the standard math + * library. + */ + Expression + fabs(const Expression &x); + + + /** + * Return a symbolic number that represents the sign of value @p x. + * + * Although there is no such function in the standard library, it mimics + * the function boost::sign(x) using the + * boost math library. + */ + Expression + sign(const Expression &x); + + + /** + * Return a symbolic number that represents the @p value of the first + * argument that takes the @p sign of the second argument. + * + * Mimics the function std::copysign(value, sign) using + * the standard math library. + */ + Expression + copysign(const Expression &value, const Expression &sign); + + + /** + * Return a symbolic number that represents the floor of value @p x. + * + * Mimics the function std::floor(x) using the standard math + * library. + */ + Expression + floor(const Expression &x); + + + /** + * Return a symbolic number that represents the ceiling of value @p x. + * + * Mimics the function std::ceil(x) using the standard math + * library. + */ + Expression + ceil(const Expression &x); + + /** + * Return a symbolic number that represents the maximum of two + * values @p a and @p b. + * + * Mimics the function std::max(a,b) using the standard math + * library. + */ + Expression + max(const Expression &a, const Expression &b); + + /** + * Return a symbolic number that represents the maximum of two + * values @p a and @p b. + * + * Mimics the function std::max(a,b) using the standard math + * library. + * + * This variant is used when @p b is not a Expression. + */ + template ::value>::type> + Expression + max(const Expression &a, const NumberType &b) + { + // Call other implementation + return max(a, Expression(b)); + } + + /** + * Return a symbolic number that represents the maximum of two + * values @p a and @p b. + * + * Mimics the function std::max(a,b) using the standard math + * library. + * + * This variant is used when @p a is not a Expression. + */ + template ::value>::type> + Expression + max(const NumberType &a, const Expression &b) + { + // Call other implementation + return max(Expression(a), b); + } + + /** + * Return a symbolic number that represents the minimum of two + * values @p a and @p b. + * + * Mimics the function std::min(a,b) using the standard math + * library. + */ + Expression + min(const Expression &a, const Expression &b); + + /** + * Return a symbolic number that represents the minimum of two + * values @p a and @p b. + * + * Mimics the function std::min(a,b) using the standard math + * library. + * + * This variant is used when @p b is not a Expression. + */ + template ::value>::type> + Expression + min(const Expression &a, const NumberType &b) + { + // Call other implementation + return min(a, Expression(b)); + } + + /** + * Return a symbolic number that represents the minimum of two + * values @p a and @p b. + * + * Mimics the function std::min(a,b) using the standard math + * library. + * + * This variant is used when @p a is not a Expression. + */ + template ::value>::type> + Expression + min(const NumberType &a, const Expression &b) + { + // Call other implementation + return min(Expression(a), b); + } + + /** + * Return a symbolic number that represents error function with the + * given argument @p x. + * + * Mimics the function std::erf(x) using the standard math + * library. + */ + Expression + erf(const Expression &x); + + /** + * Return a symbolic number that represents complimentary error function + * with the given argument @p x. + * + * Mimics the function std::erfc(x) using the standard math + * library. + */ + Expression + erfc(const Expression &x); + + //@} + + } // namespace SD +} // namespace Differentiation + +DEAL_II_NAMESPACE_CLOSE + + +# ifndef DOXYGEN + +// Import math operations into standard namespace. +// This gives us the ability to use them within the Tensor class. +namespace std +{ + /** + * Expose SymEngine wrapper math functions + */ + +# define DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(func) \ + using dealii::Differentiation::SD::func; + +# define DEAL_II_EXPOSE_SYMENGINE_BINARY_MATH_FUNCTION(func) \ + using dealii::Differentiation::SD::func; + + DEAL_II_EXPOSE_SYMENGINE_BINARY_MATH_FUNCTION(pow) + DEAL_II_EXPOSE_SYMENGINE_BINARY_MATH_FUNCTION(max) + DEAL_II_EXPOSE_SYMENGINE_BINARY_MATH_FUNCTION(min) + DEAL_II_EXPOSE_SYMENGINE_BINARY_MATH_FUNCTION(copysign) + + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(exp) + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(log10) + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(sqrt) + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(cbrt) + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(erf) + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(erfc) + // Note: Both unary and binary versions + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(log) + + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(abs) + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(fabs) + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(sign) + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(floor) + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(ceil) + + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(sin) + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(cos) + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(tan) + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(csc) + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(sec) + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(cot) + + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(asin) + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(acos) + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(atan) + DEAL_II_EXPOSE_SYMENGINE_BINARY_MATH_FUNCTION(atan2) + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(acsc) + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(asec) + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(acot) + + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(sinh) + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(cosh) + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(tanh) + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(csch) + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(sech) + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(coth) + + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(asinh) + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(acosh) + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(atanh) + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(acsch) + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(asech) + DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION(acoth) + +# undef DEAL_II_EXPOSE_SYMENGINE_BINARY_MATH_FUNCTION +# undef DEAL_II_EXPOSE_SYMENGINE_UNARY_MATH_FUNCTION + +} // namespace std + +# endif // DOXYGEN + +#endif // DEAL_II_WITH_SYMENGINE + +#endif diff --git a/source/differentiation/sd/CMakeLists.txt b/source/differentiation/sd/CMakeLists.txt index f6730585d816..26920f47a919 100644 --- a/source/differentiation/sd/CMakeLists.txt +++ b/source/differentiation/sd/CMakeLists.txt @@ -16,6 +16,7 @@ INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_BINARY_DIR}) SET(_src + symengine_math.cc symengine_number_types.cc symengine_types.cc symengine_utilities.cc diff --git a/source/differentiation/sd/symengine_math.cc b/source/differentiation/sd/symengine_math.cc new file mode 100644 index 000000000000..0ea483a40513 --- /dev/null +++ b/source/differentiation/sd/symengine_math.cc @@ -0,0 +1,339 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + + +#include + +#ifdef DEAL_II_WITH_SYMENGINE + +DEAL_II_DISABLE_EXTRA_DIAGNOSTICS +// Number operations +# include +# include +# include +# include +DEAL_II_ENABLE_EXTRA_DIAGNOSTICS + +# include + +DEAL_II_NAMESPACE_OPEN + +namespace Differentiation +{ + namespace SD + { + namespace SE = ::SymEngine; + + /* --------------------------- Math functions ------------------------- */ + + Expression + pow(const Expression &base, const Expression &exponent) + { + return SE::pow(base.get_RCP(), exponent.get_RCP()); + } + + + Expression + sqrt(const Expression &x) + { + return SE::sqrt(x.get_RCP()); + } + + + Expression + cbrt(const Expression &x) + { + return SE::cbrt(x.get_RCP()); + } + + + Expression + exp(const Expression &exponent) + { + return SE::exp(exponent.get_RCP()); + } + + + Expression + log(const Expression &x) + { + return SE::log(x.get_RCP()); + } + + + Expression + log(const Expression &x, const Expression &base) + { + return SE::log(x.get_RCP(), base.get_RCP()); + } + + + Expression + log10(const Expression &x) + { + return log(x.get_RCP(), Expression(10.0)); + } + + + Expression + sin(const Expression &x) + { + return SE::sin(x.get_RCP()); + } + + + Expression + cos(const Expression &x) + { + return SE::cos(x.get_RCP()); + } + + + Expression + tan(const Expression &x) + { + return SE::tan(x.get_RCP()); + } + + + Expression + csc(const Expression &x) + { + return SE::csc(x.get_RCP()); + } + + + Expression + sec(const Expression &x) + { + return SE::sec(x.get_RCP()); + } + + + Expression + cot(const Expression &x) + { + return SE::cot(x.get_RCP()); + } + + + Expression + asin(const Expression &x) + { + return SE::asin(x.get_RCP()); + } + + + Expression + acos(const Expression &x) + { + return SE::acos(x.get_RCP()); + } + + + Expression + atan(const Expression &x) + { + return SE::atan(x.get_RCP()); + } + + + Expression + atan2(const Expression &y, const Expression &x) + { + return SE::atan2(y.get_RCP(), x.get_RCP()); + } + + + Expression + acsc(const Expression &x) + { + return SE::acsc(x.get_RCP()); + } + + + Expression + asec(const Expression &x) + { + return SE::asec(x.get_RCP()); + } + + + Expression + acot(const Expression &x) + { + return SE::acot(x.get_RCP()); + } + + + Expression + sinh(const Expression &x) + { + return SE::sinh(x.get_RCP()); + } + + + Expression + cosh(const Expression &x) + { + return SE::cosh(x.get_RCP()); + } + + + Expression + tanh(const Expression &x) + { + return SE::tanh(x.get_RCP()); + } + + + Expression + csch(const Expression &x) + { + return SE::csch(x.get_RCP()); + } + + + Expression + sech(const Expression &x) + { + return SE::sech(x.get_RCP()); + } + + + Expression + coth(const Expression &x) + { + return SE::coth(x.get_RCP()); + } + + + Expression + asinh(const Expression &x) + { + return SE::asinh(x.get_RCP()); + } + + + Expression + acosh(const Expression &x) + { + return SE::acosh(x.get_RCP()); + } + + + Expression + atanh(const Expression &x) + { + return SE::atanh(x.get_RCP()); + } + + + Expression + acsch(const Expression &x) + { + return SE::acsch(x.get_RCP()); + } + + + Expression + asech(const Expression &x) + { + return SE::asech(x.get_RCP()); + } + + + Expression + acoth(const Expression &x) + { + return SE::acoth(x.get_RCP()); + } + + + Expression + abs(const Expression &x) + { + return SE::abs(x.get_RCP()); + } + + + Expression + fabs(const Expression &x) + { + return SE::abs(x.get_RCP()); + } + + + Expression + sign(const Expression &x) + { + return SE::sign(x.get_RCP()); + } + + + Expression + copysign(const Expression &value, const Expression &sign) + { + return value * Expression(SE::sign(sign.get_RCP())); + } + + + Expression + floor(const Expression &x) + { + return SE::floor(x.get_RCP()); + } + + + Expression + ceil(const Expression &x) + { + return SE::ceiling(x.get_RCP()); + } + + + Expression + max(const Expression &a, const Expression &b) + { + return SE::max({a.get_RCP(), b.get_RCP()}); + } + + + Expression + min(const Expression &a, const Expression &b) + { + return SE::min({a.get_RCP(), b.get_RCP()}); + } + + + Expression + erf(const Expression &x) + { + return SE::erf(x.get_RCP()); + } + + + Expression + erfc(const Expression &x) + { + return SE::erfc(x.get_RCP()); + } + + } // namespace SD +} // namespace Differentiation + +DEAL_II_NAMESPACE_CLOSE + +#endif // DEAL_II_WITH_SYMENGINE From fe78e1db653e0ce71cc18f03bfc4cb761d2179f1 Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Sat, 30 Mar 2019 23:27:57 +0100 Subject: [PATCH 377/507] Add test for symbolic math functions --- tests/symengine/symengine_number_type_02.cc | 492 ++++++++++++++++++ .../symengine/symengine_number_type_02.output | 300 +++++++++++ 2 files changed, 792 insertions(+) create mode 100644 tests/symengine/symengine_number_type_02.cc create mode 100644 tests/symengine/symengine_number_type_02.output diff --git a/tests/symengine/symengine_number_type_02.cc b/tests/symengine/symengine_number_type_02.cc new file mode 100644 index 000000000000..a78a3e8118cb --- /dev/null +++ b/tests/symengine/symengine_number_type_02.cc @@ -0,0 +1,492 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + + +// Check that the wrapper for symengine expressions can be used within +// math functions + +#include + +#include + +#include +#include +#include + +#include "../tests.h" + +using namespace dealii; +namespace SD = Differentiation::SD; +namespace SE = SymEngine; + +template +bool +same_number(const NumberType1 &val1, + const NumberType2 &val2, + const bool print = true, + const double tol_eps = 10.0) +{ + if (print == true) + std::cout << "Diff: " << std::abs(val1 - val2) << std::endl; + const long double eps1 = std::numeric_limits::epsilon(); + const long double eps2 = std::numeric_limits::epsilon(); + return std::abs(val1 - val2) <= tol_eps * std::max(eps1, eps2); +} + +template +void +test_number_functions() +{ + typedef SD::Expression SD_number_t; + typedef SE::RCP SE_double_t; + // typedef SD_number_t result_t; + typedef NumberType result_t; + typedef double float_result_t; + + // Primitive numbers + const NumberType x_(NumberType(2.2)); + const NumberType a_(NumberType(3.3)); + const NumberType b_(NumberType(-4.4)); + const NumberType inv_a_(NumberType(1.0 / a_)); + // Raw SymEngine number pointers + const SE_double_t x__(SE::real_double(x_)); + const SE_double_t a__(SE::real_double(a_)); + const SE_double_t b__(SE::real_double(b_)); + const SE_double_t inv_a__(SE::real_double(inv_a_)); + // Our wrapped numbers + const SD_number_t x(x_); + const SD_number_t a(a_); + const SD_number_t b(b_); + const SD_number_t inv_a(inv_a_); + + // SD_number_t f; // Temporary value; Check default constructor + // SD_number_t::substitution_map_t sub_vals; + + // --- Values --- + // NOTE: The returned results from SymEngineWrapper functions are actually + // symbolic in nature, so we cast them to the number in order to evaluate + // them. + + deallog.push("Power functions"); + { + deallog << "pow(a_,x_): " << std::pow(a_, x_) << std::endl; + deallog << "pow(a__,x__): " << *SE::pow(a__, x__) << std::endl; + deallog << "pow(a,x): " << static_cast(pow(a, x)) << std::endl; + deallog << "pow(a,x_): " << static_cast(pow(a, x_)) << std::endl; + deallog << "pow(a_,x): " << static_cast(pow(a_, x)) << std::endl; + Assert(same_number(static_cast(pow(a, x)), std::pow(a_, x_)), + ExcMessage("Incorrect result from pow function")); + // -------------- + deallog << "sqrt(a_): " << std::sqrt(a_) << std::endl; + deallog << "sqrt(a__): " << *SE::sqrt(a__) << std::endl; + deallog << "sqrt(a): " << sqrt(a) << std::endl; + deallog << "sqrt(a): " << static_cast(sqrt(a)) + << std::endl; + Assert(same_number(static_cast(sqrt(a)), std::sqrt(a_)), + ExcMessage("Incorrect result from sqrt function")); + // -------------- + deallog << "cbrt(a_): " << std::cbrt(a_) << std::endl; + deallog << "cbrt(a__): " << *SE::cbrt(a__) << std::endl; + deallog << "cbrt(a): " << cbrt(a) << std::endl; + deallog << "cbrt(a): " << static_cast(cbrt(a)) + << std::endl; + Assert(same_number(static_cast(cbrt(a)), std::cbrt(a_)), + ExcMessage("Incorrect result from cbrt function")); + // -------------- + deallog << "exp(a_): " << std::exp(a_) << std::endl; + deallog << "exp(a__): " << *SE::exp(a__) << std::endl; + deallog << "exp(a): " << exp(a) + << std::endl; // Returns a SymEngine function, not a number + deallog << "exp(a): " << static_cast(exp(a)) << std::endl; + Assert(same_number(static_cast(exp(a)), std::exp(a_)), + ExcMessage("Incorrect result from exp function")); + // -------------- + deallog << "log(a_): " << std::log(a_) << std::endl; + deallog << "log(a__): " << *SE::log(a__) << std::endl; + deallog << "log(a): " << log(a) + << std::endl; // Returns a SymEngine function, not a number + deallog << "log(a): " << static_cast(log(a)) << std::endl; + Assert(same_number(static_cast(log(a)), std::log(a_)), + ExcMessage("Incorrect result from log function")); + } + deallog.pop(); + + deallog.push("Other functions"); + { + deallog << "abs(b_): " << std::abs(b_) << std::endl; + deallog << "abs(b): " << static_cast(abs(b)) << std::endl; + Assert(same_number(static_cast(abs(b)), std::abs(b_)), + ExcMessage("Incorrect result from abs function")); + // -------------- + deallog << "copysign(1.0, b_): " << std::copysign(1.0, b_) << std::endl; + deallog << "sign(b): " << static_cast(sign(b)) << std::endl; + Assert(same_number(static_cast(sign(b)), std::copysign(1.0, b_)), + ExcMessage("Incorrect result from sign function")); + // -------------- + deallog << "copysign(a_, b_): " << std::copysign(a_, b_) << std::endl; + deallog << "copysign(a, b): " << static_cast(copysign(a, b)) + << std::endl; + Assert(same_number(static_cast(copysign(a, b)), + std::copysign(a_, b_)), + ExcMessage("Incorrect result from copysign function")); + // -------------- + deallog << "floor(b_): " << std::floor(b_) << std::endl; + deallog << "floor(b): " << static_cast(floor(b)) << std::endl; + Assert(same_number(static_cast(floor(b)), std::floor(b_)), + ExcMessage("Incorrect result from floor function")); + // -------------- + deallog << "ceil(b_): " << std::ceil(b_) << std::endl; + deallog << "ceil(b): " << static_cast(ceil(b)) << std::endl; + Assert(same_number(static_cast(ceil(b)), std::ceil(b_)), + ExcMessage("Incorrect result from ceil function")); + // -------------- + deallog << "max(a_,x_): " << std::max(a_, x_) << std::endl; + deallog << "max(a__,x__): " << *SE::max({a__, x__}) << std::endl; + deallog << "max(a,x): " << static_cast(max(a, x)) << std::endl; + deallog << "max(a,x_): " << static_cast(max(a, x_)) << std::endl; + deallog << "max(a_,x): " << static_cast(max(a_, x)) << std::endl; + Assert(same_number(static_cast(max(a, x)), std::max(a_, x_)), + ExcMessage("Incorrect result from max function")); + // -------------- + deallog << "min(a_,x_): " << std::min(a_, x_) << std::endl; + deallog << "min(a__,x__): " << *SE::min({a__, x__}) << std::endl; + deallog << "min(a,x): " << static_cast(min(a, x)) << std::endl; + deallog << "min(a,x_): " << static_cast(min(a, x_)) << std::endl; + deallog << "min(a_,x): " << static_cast(min(a_, x)) << std::endl; + Assert(same_number(static_cast(min(a, x)), std::min(a_, x_)), + ExcMessage("Incorrect result from max function")); + // -------------- + deallog << "erf(a_): " << std::erf(a_) << std::endl; + deallog << "erf(a__): " << *SE::erf(a__) << std::endl; + deallog << "erf(a): " << erf(a) + << std::endl; // Returns a SymEngine function, not a number + deallog << "erf(a): " << static_cast(erf(a)) << std::endl; + Assert(same_number(static_cast(erf(a)), std::erf(a_)), + ExcMessage("Incorrect result from erf function")); + // -------------- + deallog << "erfc(a_): " << std::erfc(a_) << std::endl; + deallog << "erfc(a__): " << *SE::erfc(a__) << std::endl; + deallog << "erfc(a): " << erfc(a) + << std::endl; // Returns a SymEngine function, not a number + deallog << "erfc(a): " << static_cast(erfc(a)) + << std::endl; + Assert(same_number(static_cast(erfc(a)), std::erfc(a_)), + ExcMessage("Incorrect result from erfc function")); + } + deallog.pop(); + + // References: + // https://en.wikipedia.org/wiki/Trigonometric_functions + // https://en.wikipedia.org/wiki/Hyperbolic_function + // http://mathworld.wolfram.com/InverseCosecant.html + deallog.push("Trig functions"); + { + deallog << "sin(a_): " << std::sin(a_) << std::endl; + deallog << "sin(a__): " << *SE::sin(a__) << std::endl; + deallog << "sin(a): " << sin(a) + << std::endl; // Returns a SymEngine function, not a number + deallog << "sin(a): " << static_cast(sin(a)) << std::endl; + Assert(same_number(static_cast(sin(a)), std::sin(a_)), + ExcMessage("Incorrect result from sin function")); + // -------------- + deallog << "cos(a_): " << std::cos(a_) << std::endl; + deallog << "cos(a__): " << *SE::cos(a__) << std::endl; + deallog << "cos(a): " << cos(a) + << std::endl; // Returns a SymEngine function, not a number + deallog << "cos(a): " << static_cast(cos(a)) << std::endl; + Assert(same_number(static_cast(cos(a)), std::cos(a_)), + ExcMessage("Incorrect result from cos function")); + // -------------- + deallog << "tan(a_): " << std::tan(a_) << std::endl; + deallog << "tan(a__): " << *SE::tan(a__) << std::endl; + deallog << "tan(a): " << tan(a) + << std::endl; // Returns a SymEngine function, not a number + deallog << "tan(a): " << static_cast(tan(a)) << std::endl; + Assert(same_number(static_cast(tan(a)), std::tan(a_)), + ExcMessage("Incorrect result from tan function")); + } + deallog.pop(); + + deallog.push("Reciprocal trig functions"); + { + deallog << "csc(a_): " << (NumberType(1.0) / std::sin(a_)) << std::endl; + deallog << "csc(a__): " << *SE::csc(a__) << std::endl; + deallog << "csc(a): " << csc(a) + << std::endl; // Returns a SymEngine function, not a number + deallog << "csc(a): " << static_cast(csc(a)) << std::endl; + Assert(same_number(static_cast(csc(a)), + (NumberType(1.0) / std::sin(a_))), + ExcMessage("Incorrect result from csc function")); + // -------------- + deallog << "sec(a_): " << (NumberType(1.0) / std::cos(a_)) << std::endl; + deallog << "sec(a__): " << *SE::sec(a__) << std::endl; + deallog << "sec(a): " << sec(a) + << std::endl; // Returns a SymEngine function, not a number + deallog << "sec(a): " << static_cast(sec(a)) << std::endl; + Assert(same_number(static_cast(sec(a)), + (NumberType(1.0) / std::cos(a_))), + ExcMessage("Incorrect result from sec function")); + // -------------- + deallog << "cot(a_): " << (NumberType(1.0) / std::tan(a_)) << std::endl; + deallog << "cot(a__): " << *SE::cot(a__) << std::endl; + deallog << "cot(a): " << cot(a) + << std::endl; // Returns a SymEngine function, not a number + deallog << "cot(a): " << static_cast(cot(a)) << std::endl; + Assert(same_number(static_cast(cot(a)), + (NumberType(1.0) / std::tan(a_))), + ExcMessage("Incorrect result from cot function")); + } + deallog.pop(); + + deallog.push("Inverse trig functions"); + { + deallog << "asin(inv_a_): " << std::asin(inv_a_) << std::endl; + deallog << "asin(inv_a__): " << *SE::asin(inv_a__) << std::endl; + deallog << "asin(inv_a): " << asin(inv_a) + << std::endl; // Returns a SymEngine function, not a number + deallog << "asin(inv_a): " << static_cast(asin(inv_a)) + << std::endl; + Assert(same_number(static_cast(asin(inv_a)), + std::asin(inv_a_)), + ExcMessage("Incorrect result from asin function")); + // -------------- + deallog << "acos(inv_a_): " << std::acos(inv_a_) << std::endl; + deallog << "acos(inv_a__): " << *SE::acos(inv_a__) << std::endl; + deallog << "acos(inv_a): " << acos(inv_a) + << std::endl; // Returns a SymEngine function, not a number + deallog << "acos(inv_a): " << static_cast(acos(inv_a)) + << std::endl; + Assert(same_number(static_cast(acos(inv_a)), + std::acos(inv_a_)), + ExcMessage("Incorrect result from acos function")); + // -------------- + deallog << "atan(inv_a_): " << std::atan(inv_a_) << std::endl; + deallog << "atan(inv_a__): " << *SE::atan(inv_a__) << std::endl; + deallog << "atan(inv_a): " << atan(inv_a) + << std::endl; // Returns a SymEngine function, not a number + deallog << "atan(inv_a): " << static_cast(atan(inv_a)) + << std::endl; + Assert(same_number(static_cast(atan(inv_a)), + std::atan(inv_a_)), + ExcMessage("Incorrect result from atan function")); + // -------------- + deallog << "atan2(x_,a_): " << std::atan2(x_, a_) << std::endl; + deallog << "atan2(x__,a__): " << *SE::atan2(x__, a__) << std::endl; + deallog << "atan2(x,a): " << atan2(x, a) + << std::endl; // Returns a SymEngine function, not a number + deallog << "atan2(x,a): " << static_cast(atan2(x, a)) + << std::endl; + Assert(same_number(static_cast(atan2(x, a)), + std::atan2(x_, a_)), + ExcMessage("Incorrect result from atan2 function")); + } + deallog.pop(); + + deallog.push("Reciprocal inverse trig functions"); + { + deallog << "acsc(a_): " << std::asin(NumberType(1.0) / a_) << std::endl; + deallog << "acsc(a__): " << *SE::acsc(a__) << std::endl; + deallog << "acsc(a): " << acsc(a) + << std::endl; // Returns a SymEngine function, not a number + deallog << "acsc(a): " << static_cast(acsc(a)) + << std::endl; + Assert(same_number(static_cast(acsc(a)), + std::asin(NumberType(1.0) / a_)), + ExcMessage("Incorrect result from acsc function")); + // -------------- + deallog << "asec(a_): " << std::acos(NumberType(1.0) / a_) << std::endl; + deallog << "asec(a__): " << *SE::asec(a__) << std::endl; + deallog << "asec(a): " << asec(a) + << std::endl; // Returns a SymEngine function, not a number + deallog << "asec(a): " << static_cast(asec(a)) + << std::endl; + Assert(same_number(static_cast(asec(a)), + std::acos(NumberType(1.0) / a_)), + ExcMessage("Incorrect result from asec function")); + // -------------- + deallog << "acot(a_): " << std::atan(NumberType(1.0) / a_) << std::endl; + deallog << "acot(a__): " << *SE::acot(a__) << std::endl; + deallog << "acot(a): " << acot(a) + << std::endl; // Returns a SymEngine function, not a number + deallog << "acot(a): " << static_cast(acot(a)) + << std::endl; + Assert(same_number(static_cast(acot(a)), + std::atan(NumberType(1.0) / a_)), + ExcMessage("Incorrect result from acot function")); + } + deallog.pop(); + + deallog.push("Hyperbolic trig functions"); + { + deallog << "sinh(a_): " << std::sinh(a_) << std::endl; + deallog << "sinh(a__): " << *SE::sinh(a__) << std::endl; + deallog << "sinh(a): " << sinh(a) + << std::endl; // Returns a SymEngine function, not a number + deallog << "sinh(a): " << static_cast(sinh(a)) + << std::endl; + Assert(same_number(static_cast(sinh(inv_a)), + std::sinh(inv_a_)), + ExcMessage("Incorrect result from sinh function")); + // -------------- + deallog << "cosh(a_): " << std::cosh(a_) << std::endl; + deallog << "cosh(a__): " << *SE::cosh(a__) << std::endl; + deallog << "cosh(a): " << cosh(a) + << std::endl; // Returns a SymEngine function, not a number + deallog << "cosh(a): " << static_cast(cosh(a)) + << std::endl; + Assert(same_number(static_cast(cosh(inv_a)), + std::cosh(inv_a_)), + ExcMessage("Incorrect result from cosh function")); + // -------------- + deallog << "tanh(a_): " << std::tanh(a_) << std::endl; + deallog << "tanh(a__): " << *SE::tanh(a__) << std::endl; + deallog << "tanh(a): " << tanh(a) + << std::endl; // Returns a SymEngine function, not a number + deallog << "tanh(a): " << static_cast(tanh(a)) + << std::endl; + Assert(same_number(static_cast(tanh(inv_a)), + std::tanh(inv_a_)), + ExcMessage("Incorrect result from tanh function")); + } + deallog.pop(); + + deallog.push("Reciprocal hyperbolic trig functions"); + { + deallog << "csch(a_): " << (NumberType(1.0) / std::sinh(a_)) << std::endl; + deallog << "csch(a__): " << *SE::csch(a__) << std::endl; + deallog << "csch(a): " << csch(a) + << std::endl; // Returns a SymEngine function, not a number + deallog << "csch(a): " << static_cast(csch(a)) + << std::endl; + Assert(same_number(static_cast(csch(a)), + (NumberType(1.0) / std::sinh(a_))), + ExcMessage("Incorrect result from csch function")); + // -------------- + deallog << "sech(a_): " << (NumberType(1.0) / std::cosh(a_)) << std::endl; + deallog << "sech(a__): " << *SE::sech(a__) << std::endl; + deallog << "sech(a): " << sech(a) + << std::endl; // Returns a SymEngine function, not a number + deallog << "sech(a): " << static_cast(sech(a)) + << std::endl; + Assert(same_number(static_cast(sech(a)), + (NumberType(1.0) / std::cosh(a_))), + ExcMessage("Incorrect result from sech function")); + // -------------- + deallog << "coth(a_): " << (NumberType(1.0) / std::tanh(a_)) << std::endl; + deallog << "coth(a__): " << *SE::coth(a__) << std::endl; + deallog << "coth(a): " << coth(a) + << std::endl; // Returns a SymEngine function, not a number + deallog << "coth(a): " << static_cast(coth(a)) + << std::endl; + Assert(same_number(static_cast(coth(a)), + (NumberType(1.0) / std::tanh(a_))), + ExcMessage("Incorrect result from coth function")); + } + deallog.pop(); + + deallog.push("Inverse hyperbolic trig functions"); + { + deallog << "asinh(inv_a_): " << std::asinh(inv_a_) << std::endl; + deallog << "asinh(inv_a__): " << *SE::asinh(inv_a__) << std::endl; + deallog << "asinh(inv_a): " << asinh(inv_a) + << std::endl; // Returns a SymEngine function, not a number + deallog << "asinh(inv_a): " << static_cast(asinh(inv_a)) + << std::endl; + Assert(same_number(static_cast(asinh(inv_a)), + std::asinh(inv_a_)), + ExcMessage("Incorrect result from asinh function")); + // -------------- + deallog << "acosh(a_): " << std::acosh(a_) << std::endl; + deallog << "acosh(a__): " << *SE::acosh(a__) << std::endl; + deallog << "acosh(a): " << acosh(a) + << std::endl; // Returns a SymEngine function, not a number + deallog << "acosh(a): " << static_cast(acosh(a)) + << std::endl; + Assert(same_number(static_cast(acosh(a)), std::acosh(a_)), + ExcMessage("Incorrect result from acosh function")); + // -------------- + deallog << "atanh(inv_a_): " << std::atanh(inv_a_) << std::endl; + deallog << "atanh(inv_a__): " << *SE::atanh(inv_a__) << std::endl; + deallog << "atanh(inv_a): " << atanh(inv_a) + << std::endl; // Returns a SymEngine function, not a number + deallog << "atanh(inv_a): " << static_cast(atanh(inv_a)) + << std::endl; + Assert(same_number(static_cast(atanh(inv_a)), + std::atanh(inv_a_)), + ExcMessage("Incorrect result from atanh function")); + } + deallog.pop(); + + deallog.push("Reciprocal inverse hyperbolic trig functions"); + { + deallog << "acsch(a_): " << std::asinh(NumberType(1.0) / a_) << std::endl; + deallog << "acsch(a__): " << *SE::acsch(a__) << std::endl; + deallog << "acsch(a): " << acsch(a) + << std::endl; // Returns a SymEngine function, not a number + deallog << "acsch(a): " << static_cast(acsch(a)) + << std::endl; + Assert(same_number(static_cast(acsch(a)), + std::asinh(NumberType(1.0) / a_)), + ExcMessage("Incorrect result from acsch function")); + // -------------- + deallog << "asech(inv_a_): " << std::acosh(a_) << std::endl; + deallog << "asech(inv_a__): " << *SE::asech(inv_a__) << std::endl; + deallog << "asech(inv_a): " << asech(inv_a) + << std::endl; // Returns a SymEngine function, not a number + deallog << "asech(inv_a): " << static_cast(asech(inv_a)) + << std::endl; + Assert(same_number(static_cast(asech(inv_a)), + std::acosh(a_)), + ExcMessage("Incorrect result from asech function")); + // -------------- + deallog << "acoth(a_): " << std::atanh(NumberType(1.0) / a_) << std::endl; + deallog << "acoth(a__): " << *SE::acoth(a__) << std::endl; + deallog << "acoth(a): " << acoth(inv_a) + << std::endl; // Returns a SymEngine function, not a number + deallog << "acoth(a): " << static_cast(acoth(a)) + << std::endl; + Assert(same_number(static_cast(acoth(a)), + std::atanh(NumberType(1.0) / a_)), + ExcMessage("Incorrect result from acoth function")); + } + deallog.pop(); +} + +int +main() +{ + initlog(); + + // Most of the functions tested return irrational values. Making a test + // work for both integer and floating point values is hard! + // deallog.push("Integer"); + // test_number_functions(); + + deallog.push("Float"); + test_number_functions(); + deallog.pop(); + + deallog.push("Double"); + test_number_functions(); + deallog.pop(); + + // Not available yet + // SymEngine::SymEngineException: Invalid Format: Expected Integer or Rational + // deallog.push("Complex double"); + // test_number_functions>(); + // deallog.pop(); + + deallog << "OK" << std::endl; +} diff --git a/tests/symengine/symengine_number_type_02.output b/tests/symengine/symengine_number_type_02.output new file mode 100644 index 000000000000..61f12a229a13 --- /dev/null +++ b/tests/symengine/symengine_number_type_02.output @@ -0,0 +1,300 @@ + +DEAL:Float:Power functions::pow(a_,x_): 13.8271 +DEAL:Float:Power functions::pow(a__,x__): 13.827086465678 +DEAL:Float:Power functions::pow(a,x): 13.8271 +DEAL:Float:Power functions::pow(a,x_): 13.8271 +DEAL:Float:Power functions::pow(a_,x): 13.8271 +DEAL:Float:Power functions::sqrt(a_): 1.81659 +DEAL:Float:Power functions::sqrt(a__): 1.81659019933398 +DEAL:Float:Power functions::sqrt(a): 1.81659019933398 +DEAL:Float:Power functions::sqrt(a): 1.81659 +DEAL:Float:Power functions::cbrt(a_): 1.48881 +DEAL:Float:Power functions::cbrt(a__): 1.48880554578294 +DEAL:Float:Power functions::cbrt(a): 1.48880554578294 +DEAL:Float:Power functions::cbrt(a): 1.48881 +DEAL:Float:Power functions::exp(a_): 27.1126 +DEAL:Float:Power functions::exp(a__): 27.1126376278265 +DEAL:Float:Power functions::exp(a): 27.1126376278265 +DEAL:Float:Power functions::exp(a): 27.1126 +DEAL:Float:Power functions::log(a_): 1.19392 +DEAL:Float:Power functions::log(a__): 1.19392245402282 +DEAL:Float:Power functions::log(a): 1.19392245402282 +DEAL:Float:Power functions::log(a): 1.19392 +DEAL:Float:Other functions::abs(b_): 4.40000 +DEAL:Float:Other functions::abs(b): 4.40000 +DEAL:Float:Other functions::copysign(1.0, b_): -1.00000 +DEAL:Float:Other functions::sign(b): -1.00000 +DEAL:Float:Other functions::copysign(a_, b_): -3.30000 +DEAL:Float:Other functions::copysign(a, b): -3.30000 +DEAL:Float:Other functions::floor(b_): -5.00000 +DEAL:Float:Other functions::floor(b): -5.00000 +DEAL:Float:Other functions::ceil(b_): -4.00000 +DEAL:Float:Other functions::ceil(b): -4.00000 +DEAL:Float:Other functions::max(a_,x_): 3.30000 +DEAL:Float:Other functions::max(a__,x__): 3.29999995231628 +DEAL:Float:Other functions::max(a,x): 3.30000 +DEAL:Float:Other functions::max(a,x_): 3.30000 +DEAL:Float:Other functions::max(a_,x): 3.30000 +DEAL:Float:Other functions::min(a_,x_): 2.20000 +DEAL:Float:Other functions::min(a__,x__): 2.20000004768372 +DEAL:Float:Other functions::min(a,x): 2.20000 +DEAL:Float:Other functions::min(a,x_): 2.20000 +DEAL:Float:Other functions::min(a_,x): 2.20000 +DEAL:Float:Other functions::erf(a_): 0.999997 +DEAL:Float:Other functions::erf(a__): 0.9999969422892 +DEAL:Float:Other functions::erf(a): 0.9999969422892 +DEAL:Float:Other functions::erf(a): 0.999997 +DEAL:Float:Other functions::erfc(a_): 3.05771e-06 +DEAL:Float:Other functions::erfc(a__): 3.05771079957068e-06 +DEAL:Float:Other functions::erfc(a): 3.05771079957068e-06 +DEAL:Float:Other functions::erfc(a): 3.05771e-06 +DEAL:Float:Trig functions::sin(a_): -0.157746 +DEAL:Float:Trig functions::sin(a__): -0.157745647056543 +DEAL:Float:Trig functions::sin(a): -0.157745647056543 +DEAL:Float:Trig functions::sin(a): -0.157746 +DEAL:Float:Trig functions::cos(a_): -0.987480 +DEAL:Float:Trig functions::cos(a__): -0.987479777430765 +DEAL:Float:Trig functions::cos(a): -0.987479777430765 +DEAL:Float:Trig functions::cos(a): -0.987480 +DEAL:Float:Trig functions::tan(a_): 0.159746 +DEAL:Float:Trig functions::tan(a__): 0.15974569875949 +DEAL:Float:Trig functions::tan(a): 0.15974569875949 +DEAL:Float:Trig functions::tan(a): 0.159746 +DEAL:Float:Reciprocal trig functions::csc(a_): -6.33932 +DEAL:Float:Reciprocal trig functions::csc(a__): -6.33931914229971 +DEAL:Float:Reciprocal trig functions::csc(a): -6.33931914229971 +DEAL:Float:Reciprocal trig functions::csc(a): -6.33932 +DEAL:Float:Reciprocal trig functions::sec(a_): -1.01268 +DEAL:Float:Reciprocal trig functions::sec(a__): -1.01267896604608 +DEAL:Float:Reciprocal trig functions::sec(a): -1.01267896604608 +DEAL:Float:Reciprocal trig functions::sec(a): -1.01268 +DEAL:Float:Reciprocal trig functions::cot(a_): 6.25995 +DEAL:Float:Reciprocal trig functions::cot(a__): 6.2599494557007 +DEAL:Float:Reciprocal trig functions::cot(a): 6.2599494557007 +DEAL:Float:Reciprocal trig functions::cot(a): 6.25995 +DEAL:Float:Inverse trig functions::asin(inv_a_): 0.307871 +DEAL:Float:Inverse trig functions::asin(inv_a__): 0.30787087787464 +DEAL:Float:Inverse trig functions::asin(inv_a): 0.30787087787464 +DEAL:Float:Inverse trig functions::asin(inv_a): 0.307871 +DEAL:Float:Inverse trig functions::acos(inv_a_): 1.26293 +DEAL:Float:Inverse trig functions::acos(inv_a__): 1.26292544892026 +DEAL:Float:Inverse trig functions::acos(inv_a): 1.26292544892026 +DEAL:Float:Inverse trig functions::acos(inv_a): 1.26293 +DEAL:Float:Inverse trig functions::atan(inv_a_): 0.294235 +DEAL:Float:Inverse trig functions::atan(inv_a__): 0.294234573382648 +DEAL:Float:Inverse trig functions::atan(inv_a): 0.294234573382648 +DEAL:Float:Inverse trig functions::atan(inv_a): 0.294235 +DEAL:Float:Inverse trig functions::atan2(x_,a_): 0.588003 +DEAL:Float:Inverse trig functions::atan2(x__,a__): atan2(2.20000004768372, 3.29999995231628) +DEAL:Float:Inverse trig functions::atan2(x,a): atan2(2.20000004768372, 3.29999995231628) +DEAL:Float:Inverse trig functions::atan2(x,a): 0.588003 +DEAL:Float:Reciprocal inverse trig functions::acsc(a_): 0.307871 +DEAL:Float:Reciprocal inverse trig functions::acsc(a__): 0.307870872992762 +DEAL:Float:Reciprocal inverse trig functions::acsc(a): 0.307870872992762 +DEAL:Float:Reciprocal inverse trig functions::acsc(a): 0.307871 +DEAL:Float:Reciprocal inverse trig functions::asec(a_): 1.26293 +DEAL:Float:Reciprocal inverse trig functions::asec(a__): 1.26292545380213 +DEAL:Float:Reciprocal inverse trig functions::asec(a): 1.26292545380213 +DEAL:Float:Reciprocal inverse trig functions::asec(a): 1.26293 +DEAL:Float:Reciprocal inverse trig functions::acot(a_): 0.294235 +DEAL:Float:Reciprocal inverse trig functions::acot(a__): 0.294234569121593 +DEAL:Float:Reciprocal inverse trig functions::acot(a): 0.294234569121593 +DEAL:Float:Reciprocal inverse trig functions::acot(a): 0.294235 +DEAL:Float:Hyperbolic trig functions::sinh(a_): 13.5379 +DEAL:Float:Hyperbolic trig functions::sinh(a__): 13.5378772293333 +DEAL:Float:Hyperbolic trig functions::sinh(a): 13.5378772293333 +DEAL:Float:Hyperbolic trig functions::sinh(a): 13.5379 +DEAL:Float:Hyperbolic trig functions::cosh(a_): 13.5748 +DEAL:Float:Hyperbolic trig functions::cosh(a__): 13.5747603984933 +DEAL:Float:Hyperbolic trig functions::cosh(a): 13.5747603984933 +DEAL:Float:Hyperbolic trig functions::cosh(a): 13.5748 +DEAL:Float:Hyperbolic trig functions::tanh(a_): 0.997283 +DEAL:Float:Hyperbolic trig functions::tanh(a__): 0.997282959840377 +DEAL:Float:Hyperbolic trig functions::tanh(a): 0.997282959840377 +DEAL:Float:Hyperbolic trig functions::tanh(a): 0.997283 +DEAL:Float:Reciprocal hyperbolic trig functions::csch(a_): 0.0738668 +DEAL:Float:Reciprocal hyperbolic trig functions::csch(a__): 0.0738668243964602 +DEAL:Float:Reciprocal hyperbolic trig functions::csch(a): 0.0738668243964602 +DEAL:Float:Reciprocal hyperbolic trig functions::csch(a): 0.0738668 +DEAL:Float:Reciprocal hyperbolic trig functions::sech(a_): 0.0736661 +DEAL:Float:Reciprocal hyperbolic trig functions::sech(a__): 0.0736661252681112 +DEAL:Float:Reciprocal hyperbolic trig functions::sech(a): 0.0736661252681112 +DEAL:Float:Reciprocal hyperbolic trig functions::sech(a): 0.0736661 +DEAL:Float:Reciprocal hyperbolic trig functions::coth(a_): 1.00272 +DEAL:Float:Reciprocal hyperbolic trig functions::coth(a__): 1.00272444257952 +DEAL:Float:Reciprocal hyperbolic trig functions::coth(a): 1.00272444257952 +DEAL:Float:Reciprocal hyperbolic trig functions::coth(a): 1.00272 +DEAL:Float:Inverse hyperbolic trig functions::asinh(inv_a_): 0.298574 +DEAL:Float:Inverse hyperbolic trig functions::asinh(inv_a__): 0.298574346656372 +DEAL:Float:Inverse hyperbolic trig functions::asinh(inv_a): 0.298574346656372 +DEAL:Float:Inverse hyperbolic trig functions::asinh(inv_a): 0.298574 +DEAL:Float:Inverse hyperbolic trig functions::acosh(a_): 1.86328 +DEAL:Float:Inverse hyperbolic trig functions::acosh(a__): 1.86327933599091 +DEAL:Float:Inverse hyperbolic trig functions::acosh(a): 1.86327933599091 +DEAL:Float:Inverse hyperbolic trig functions::acosh(a): 1.86328 +DEAL:Float:Inverse hyperbolic trig functions::atanh(inv_a_): 0.312853 +DEAL:Float:Inverse hyperbolic trig functions::atanh(inv_a__): 0.312852959826358 +DEAL:Float:Inverse hyperbolic trig functions::atanh(inv_a): 0.312852959826358 +DEAL:Float:Inverse hyperbolic trig functions::atanh(inv_a): 0.312853 +DEAL:Float:Reciprocal inverse hyperbolic trig functions::acsch(a_): 0.298574 +DEAL:Float:Reciprocal inverse hyperbolic trig functions::acsch(a__): 0.298574342203972 +DEAL:Float:Reciprocal inverse hyperbolic trig functions::acsch(a): 0.298574342203972 +DEAL:Float:Reciprocal inverse hyperbolic trig functions::acsch(a): 0.298574 +DEAL:Float:Reciprocal inverse hyperbolic trig functions::asech(inv_a_): 1.86328 +DEAL:Float:Reciprocal inverse hyperbolic trig functions::asech(inv_a__): 1.86327931988071 +DEAL:Float:Reciprocal inverse hyperbolic trig functions::asech(inv_a): 1.86327931988071 +DEAL:Float:Reciprocal inverse hyperbolic trig functions::asech(inv_a): 1.86328 +DEAL:Float:Reciprocal inverse hyperbolic trig functions::acoth(a_): 0.312853 +DEAL:Float:Reciprocal inverse hyperbolic trig functions::acoth(a__): 0.312852954703614 +DEAL:Float:Reciprocal inverse hyperbolic trig functions::acoth(a): 0.312852959826358 + 1.5707963267949*I +DEAL:Float:Reciprocal inverse hyperbolic trig functions::acoth(a): 0.312853 +DEAL:Double:Power functions::pow(a_,x_): 13.8271 +DEAL:Double:Power functions::pow(a__,x__): 13.8270861180441 +DEAL:Double:Power functions::pow(a,x): 13.8271 +DEAL:Double:Power functions::pow(a,x_): 13.8271 +DEAL:Double:Power functions::pow(a_,x): 13.8271 +DEAL:Double:Power functions::sqrt(a_): 1.81659 +DEAL:Double:Power functions::sqrt(a__): 1.81659021245849 +DEAL:Double:Power functions::sqrt(a): 1.81659021245849 +DEAL:Double:Power functions::sqrt(a): 1.81659 +DEAL:Double:Power functions::cbrt(a_): 1.48881 +DEAL:Double:Power functions::cbrt(a__): 1.48880555295383 +DEAL:Double:Power functions::cbrt(a): 1.48880555295383 +DEAL:Double:Power functions::cbrt(a): 1.48881 +DEAL:Double:Power functions::exp(a_): 27.1126 +DEAL:Double:Power functions::exp(a__): 27.1126389206579 +DEAL:Double:Power functions::exp(a): 27.1126389206579 +DEAL:Double:Power functions::exp(a): 27.1126 +DEAL:Double:Power functions::log(a_): 1.19392 +DEAL:Double:Power functions::log(a__): 1.19392246847243 +DEAL:Double:Power functions::log(a): 1.19392246847243 +DEAL:Double:Power functions::log(a): 1.19392 +DEAL:Double:Other functions::abs(b_): 4.40000 +DEAL:Double:Other functions::abs(b): 4.40000 +DEAL:Double:Other functions::copysign(1.0, b_): -1.00000 +DEAL:Double:Other functions::sign(b): -1.00000 +DEAL:Double:Other functions::copysign(a_, b_): -3.30000 +DEAL:Double:Other functions::copysign(a, b): -3.30000 +DEAL:Double:Other functions::floor(b_): -5.00000 +DEAL:Double:Other functions::floor(b): -5.00000 +DEAL:Double:Other functions::ceil(b_): -4.00000 +DEAL:Double:Other functions::ceil(b): -4.00000 +DEAL:Double:Other functions::max(a_,x_): 3.30000 +DEAL:Double:Other functions::max(a__,x__): 3.3 +DEAL:Double:Other functions::max(a,x): 3.30000 +DEAL:Double:Other functions::max(a,x_): 3.30000 +DEAL:Double:Other functions::max(a_,x): 3.30000 +DEAL:Double:Other functions::min(a_,x_): 2.20000 +DEAL:Double:Other functions::min(a__,x__): 2.2 +DEAL:Double:Other functions::min(a,x): 2.20000 +DEAL:Double:Other functions::min(a,x_): 2.20000 +DEAL:Double:Other functions::min(a_,x): 2.20000 +DEAL:Double:Other functions::erf(a_): 0.999997 +DEAL:Double:Other functions::erf(a__): 0.999996942290204 +DEAL:Double:Other functions::erf(a): 0.999996942290204 +DEAL:Double:Other functions::erf(a): 0.999997 +DEAL:Double:Other functions::erfc(a_): 3.05771e-06 +DEAL:Double:Other functions::erfc(a__): 3.05770979643816e-06 +DEAL:Double:Other functions::erfc(a): 3.05770979643816e-06 +DEAL:Double:Other functions::erfc(a): 3.05771e-06 +DEAL:Double:Trig functions::sin(a_): -0.157746 +DEAL:Double:Trig functions::sin(a__): -0.157745694143248 +DEAL:Double:Trig functions::sin(a): -0.157745694143248 +DEAL:Double:Trig functions::sin(a): -0.157746 +DEAL:Double:Trig functions::cos(a_): -0.987480 +DEAL:Double:Trig functions::cos(a__): -0.987479769908865 +DEAL:Double:Trig functions::cos(a): -0.987479769908865 +DEAL:Double:Trig functions::cos(a): -0.987480 +DEAL:Double:Trig functions::tan(a_): 0.159746 +DEAL:Double:Trig functions::tan(a__): 0.159745747660032 +DEAL:Double:Trig functions::tan(a): 0.159745747660032 +DEAL:Double:Trig functions::tan(a): 0.159746 +DEAL:Double:Reciprocal trig functions::csc(a_): -6.33932 +DEAL:Double:Reciprocal trig functions::csc(a__): -6.33931725002842 +DEAL:Double:Reciprocal trig functions::csc(a): -6.33931725002842 +DEAL:Double:Reciprocal trig functions::csc(a): -6.33932 +DEAL:Double:Reciprocal trig functions::sec(a_): -1.01268 +DEAL:Double:Reciprocal trig functions::sec(a__): -1.01267897375993 +DEAL:Double:Reciprocal trig functions::sec(a): -1.01267897375993 +DEAL:Double:Reciprocal trig functions::sec(a): -1.01268 +DEAL:Double:Reciprocal trig functions::cot(a_): 6.25995 +DEAL:Double:Reciprocal trig functions::cot(a__): 6.25994753943736 +DEAL:Double:Reciprocal trig functions::cot(a): 6.25994753943736 +DEAL:Double:Reciprocal trig functions::cot(a): 6.25995 +DEAL:Double:Inverse trig functions::asin(inv_a_): 0.307871 +DEAL:Double:Inverse trig functions::asin(inv_a__): 0.307870868398053 +DEAL:Double:Inverse trig functions::asin(inv_a): 0.307870868398053 +DEAL:Double:Inverse trig functions::asin(inv_a): 0.307871 +DEAL:Double:Inverse trig functions::acos(inv_a_): 1.26293 +DEAL:Double:Inverse trig functions::acos(inv_a__): 1.26292545839684 +DEAL:Double:Inverse trig functions::acos(inv_a): 1.26292545839684 +DEAL:Double:Inverse trig functions::acos(inv_a): 1.26293 +DEAL:Double:Inverse trig functions::atan(inv_a_): 0.294235 +DEAL:Double:Inverse trig functions::atan(inv_a__): 0.294234565111188 +DEAL:Double:Inverse trig functions::atan(inv_a): 0.294234565111188 +DEAL:Double:Inverse trig functions::atan(inv_a): 0.294235 +DEAL:Double:Inverse trig functions::atan2(x_,a_): 0.588003 +DEAL:Double:Inverse trig functions::atan2(x__,a__): atan2(2.2, 3.3) +DEAL:Double:Inverse trig functions::atan2(x,a): atan2(2.2, 3.3) +DEAL:Double:Inverse trig functions::atan2(x,a): 0.588003 +DEAL:Double:Reciprocal inverse trig functions::acsc(a_): 0.307871 +DEAL:Double:Reciprocal inverse trig functions::acsc(a__): 0.307870868398053 +DEAL:Double:Reciprocal inverse trig functions::acsc(a): 0.307870868398053 +DEAL:Double:Reciprocal inverse trig functions::acsc(a): 0.307871 +DEAL:Double:Reciprocal inverse trig functions::asec(a_): 1.26293 +DEAL:Double:Reciprocal inverse trig functions::asec(a__): 1.26292545839684 +DEAL:Double:Reciprocal inverse trig functions::asec(a): 1.26292545839684 +DEAL:Double:Reciprocal inverse trig functions::asec(a): 1.26293 +DEAL:Double:Reciprocal inverse trig functions::acot(a_): 0.294235 +DEAL:Double:Reciprocal inverse trig functions::acot(a__): 0.294234565111188 +DEAL:Double:Reciprocal inverse trig functions::acot(a): 0.294234565111188 +DEAL:Double:Reciprocal inverse trig functions::acot(a): 0.294235 +DEAL:Double:Hyperbolic trig functions::sinh(a_): 13.5379 +DEAL:Double:Hyperbolic trig functions::sinh(a__): 13.5378778766283 +DEAL:Double:Hyperbolic trig functions::sinh(a): 13.5378778766283 +DEAL:Double:Hyperbolic trig functions::sinh(a): 13.5379 +DEAL:Double:Hyperbolic trig functions::cosh(a_): 13.5748 +DEAL:Double:Hyperbolic trig functions::cosh(a__): 13.5747610440296 +DEAL:Double:Hyperbolic trig functions::cosh(a): 13.5747610440296 +DEAL:Double:Hyperbolic trig functions::cosh(a): 13.5748 +DEAL:Double:Hyperbolic trig functions::tanh(a_): 0.997283 +DEAL:Double:Hyperbolic trig functions::tanh(a__): 0.997282960099142 +DEAL:Double:Hyperbolic trig functions::tanh(a): 0.997282960099142 +DEAL:Double:Hyperbolic trig functions::tanh(a): 0.997283 +DEAL:Double:Reciprocal hyperbolic trig functions::csch(a_): 0.0738668 +DEAL:Double:Reciprocal hyperbolic trig functions::csch(a__): 0.0738668208646195 +DEAL:Double:Reciprocal hyperbolic trig functions::csch(a): 0.0738668208646195 +DEAL:Double:Reciprocal hyperbolic trig functions::csch(a): 0.0738668 +DEAL:Double:Reciprocal hyperbolic trig functions::sech(a_): 0.0736661 +DEAL:Double:Reciprocal hyperbolic trig functions::sech(a__): 0.0736661217649808 +DEAL:Double:Reciprocal hyperbolic trig functions::sech(a): 0.0736661217649808 +DEAL:Double:Reciprocal hyperbolic trig functions::sech(a): 0.0736661 +DEAL:Double:Reciprocal hyperbolic trig functions::coth(a_): 1.00272 +DEAL:Double:Reciprocal hyperbolic trig functions::coth(a__): 1.00272444231935 +DEAL:Double:Reciprocal hyperbolic trig functions::coth(a): 1.00272444231935 +DEAL:Double:Reciprocal hyperbolic trig functions::coth(a): 1.00272 +DEAL:Double:Inverse hyperbolic trig functions::asinh(inv_a_): 0.298574 +DEAL:Double:Inverse hyperbolic trig functions::asinh(inv_a__): 0.298574338013478 +DEAL:Double:Inverse hyperbolic trig functions::asinh(inv_a): 0.298574338013478 +DEAL:Double:Inverse hyperbolic trig functions::asinh(inv_a): 0.298574 +DEAL:Double:Inverse hyperbolic trig functions::acosh(a_): 1.86328 +DEAL:Double:Inverse hyperbolic trig functions::acosh(a__): 1.86327935115345 +DEAL:Double:Inverse hyperbolic trig functions::acosh(a): 1.86327935115345 +DEAL:Double:Inverse hyperbolic trig functions::acosh(a): 1.86328 +DEAL:Double:Inverse hyperbolic trig functions::atanh(inv_a_): 0.312853 +DEAL:Double:Inverse hyperbolic trig functions::atanh(inv_a__): 0.312852949882206 +DEAL:Double:Inverse hyperbolic trig functions::atanh(inv_a): 0.312852949882206 +DEAL:Double:Inverse hyperbolic trig functions::atanh(inv_a): 0.312853 +DEAL:Double:Reciprocal inverse hyperbolic trig functions::acsch(a_): 0.298574 +DEAL:Double:Reciprocal inverse hyperbolic trig functions::acsch(a__): 0.298574338013478 +DEAL:Double:Reciprocal inverse hyperbolic trig functions::acsch(a): 0.298574338013478 +DEAL:Double:Reciprocal inverse hyperbolic trig functions::acsch(a): 0.298574 +DEAL:Double:Reciprocal inverse hyperbolic trig functions::asech(inv_a_): 1.86328 +DEAL:Double:Reciprocal inverse hyperbolic trig functions::asech(inv_a__): 1.86327935115345 +DEAL:Double:Reciprocal inverse hyperbolic trig functions::asech(inv_a): 1.86327935115345 +DEAL:Double:Reciprocal inverse hyperbolic trig functions::asech(inv_a): 1.86328 +DEAL:Double:Reciprocal inverse hyperbolic trig functions::acoth(a_): 0.312853 +DEAL:Double:Reciprocal inverse hyperbolic trig functions::acoth(a__): 0.312852949882206 +DEAL:Double:Reciprocal inverse hyperbolic trig functions::acoth(a): 0.312852949882206 + 1.5707963267949*I +DEAL:Double:Reciprocal inverse hyperbolic trig functions::acoth(a): 0.312853 +DEAL::OK From 6d1e3d8af4c25588c430fcddfeb2608747053614 Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Sun, 7 Apr 2019 21:47:27 +0200 Subject: [PATCH 378/507] Try to reproduce GCC tester error with ambiguous constructor --- tests/algorithms/general_data_storage_01.cc | 23 +++++++++++++++++++ .../general_data_storage_01.debug.output | 1 + .../general_data_storage_01.debug.output.2 | 1 + .../general_data_storage_01.release.output | 1 + 4 files changed, 26 insertions(+) diff --git a/tests/algorithms/general_data_storage_01.cc b/tests/algorithms/general_data_storage_01.cc index fc421e7895af..5721492f80b3 100644 --- a/tests/algorithms/general_data_storage_01.cc +++ b/tests/algorithms/general_data_storage_01.cc @@ -138,6 +138,29 @@ main() deallog << "Size: " << data.size() << std::endl; } + deallog << "Ambiguous construction" << std::endl; + { + // Pass Arguments by lvalue reference + { + const double val_1 = 1.0; + const double &val_2 = + data.get_or_add_object_with_name("value", val_1); + } + + // Pass Arguments by rvalue reference + { + double val_1 = 1.0; + const double &val_2 = + data.get_or_add_object_with_name("value", std::move(val_1)); + } + + // Pass Arguments ambiguously + { + const double &val_2 = + data.get_or_add_object_with_name("value", 1.0); + } + } + deal_II_exceptions::disable_abort_on_exception(); diff --git a/tests/algorithms/general_data_storage_01.debug.output b/tests/algorithms/general_data_storage_01.debug.output index 4583c5e2160f..0c9a8b99b98c 100644 --- a/tests/algorithms/general_data_storage_01.debug.output +++ b/tests/algorithms/general_data_storage_01.debug.output @@ -17,6 +17,7 @@ DEAL::Data post-merge: DEAL::value double DEAL::value_2 double DEAL::Size: 2 +DEAL::Ambiguous construction DEAL::Try to overwrite existing entry: Copy DEAL:: -------------------------------------------------------- diff --git a/tests/algorithms/general_data_storage_01.debug.output.2 b/tests/algorithms/general_data_storage_01.debug.output.2 index 50b2af1bbd66..f44444ad4eac 100644 --- a/tests/algorithms/general_data_storage_01.debug.output.2 +++ b/tests/algorithms/general_data_storage_01.debug.output.2 @@ -17,6 +17,7 @@ DEAL::Data post-merge: DEAL::value double DEAL::value_2 double DEAL::Size: 2 +DEAL::Ambiguous construction DEAL::Try to overwrite existing entry: Copy DEAL:: -------------------------------------------------------- diff --git a/tests/algorithms/general_data_storage_01.release.output b/tests/algorithms/general_data_storage_01.release.output index b10d09135f90..9384e0f746b8 100644 --- a/tests/algorithms/general_data_storage_01.release.output +++ b/tests/algorithms/general_data_storage_01.release.output @@ -17,6 +17,7 @@ DEAL::Data post-merge: DEAL::value double DEAL::value_2 double DEAL::Size: 2 +DEAL::Ambiguous construction DEAL::Try to overwrite existing entry: Copy DEAL::Try to overwrite existing entry: Reference DEAL::Fetch non-existing entry From 5d4698301c187af9b00387ab9b51a06128011128 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Mon, 8 Apr 2019 14:49:40 +0200 Subject: [PATCH 379/507] Require SymEngine version 0.4 --- cmake/configure/configure_symengine.cmake | 29 +++++++++++++++++++---- cmake/modules/FindSYMENGINE.cmake | 2 +- 2 files changed, 26 insertions(+), 5 deletions(-) diff --git a/cmake/configure/configure_symengine.cmake b/cmake/configure/configure_symengine.cmake index 4485401c9bec..20da3601c285 100644 --- a/cmake/configure/configure_symengine.cmake +++ b/cmake/configure/configure_symengine.cmake @@ -17,11 +17,32 @@ # Configuration for the SymEngine library: # -# -# We require at least version 0.3 of the symengine library: -# -SET(SYMENGINE_MINIMUM_REQUIRED_VERSION "0.3") +MACRO(FEATURE_SYMENGINE_FIND_EXTERNAL var) + FIND_PACKAGE(SYMENGINE) + + IF(SYMENGINE_FOUND) + SET(${var} TRUE) + + # + # We require at least version 0.4 of the symengine library: + # + SET(_version_required "0.4") + + IF(SYMENGINE_VERSION VERSION_LESS ${_version_required}) + MESSAGE(STATUS "Insufficient SymEngine installation found: " + "At least version ${_version_required} is required " + "but version ${SYMENGINE_VERSION} was found." + ) + SET(SYMENGINE_ADDITIONAL_ERROR_STRING + "Insufficient SymEngine installation found!\n" + "At least version ${_version_required} is required " + "but version ${SYMENGINE_VERSION} was found.\n" + ) + SET(${var} FALSE) + ENDIF() + ENDIF() +ENDMACRO() MACRO(FEATURE_SYMENGINE_CONFIGURE_EXTERNAL) SET(DEAL_II_SYMENGINE_WITH_LLVM ${SYMENGINE_WITH_LLVM}) diff --git a/cmake/modules/FindSYMENGINE.cmake b/cmake/modules/FindSYMENGINE.cmake index 9c9dbbba071f..20b73fa50b6e 100644 --- a/cmake/modules/FindSYMENGINE.cmake +++ b/cmake/modules/FindSYMENGINE.cmake @@ -35,7 +35,7 @@ SET (DEAL_II_CMAKE_MODULE_PATH ${CMAKE_MODULE_PATH}) # # Include the SymEngine: # -FIND_PACKAGE(SymEngine ${SYMENGINE_MINIMUM_REQUIRED_VERSION} +FIND_PACKAGE(SymEngine CONFIG QUIET HINTS ${SYMENGINE_DIR} PATH_SUFFIXES lib/cmake/symengine From b4d6601602eec04a783924dd65123543383d523e Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Mon, 8 Apr 2019 08:01:39 -0600 Subject: [PATCH 380/507] mpi quicktests fail mpirun completes about not finding the executable. This reverts part of --- tests/quick_tests/CMakeLists.txt | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/tests/quick_tests/CMakeLists.txt b/tests/quick_tests/CMakeLists.txt index ba2493fdb300..7c3023344e36 100644 --- a/tests/quick_tests/CMakeLists.txt +++ b/tests/quick_tests/CMakeLists.txt @@ -46,7 +46,11 @@ MACRO(make_quicktest test_basename build_name mpi_run) IF("${mpi_run}" STREQUAL "") SET(_command ${_target}) ELSE() - SET(_command ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${mpi_run} ${MPIEXEC_PREFLAGS} ${_target}) + IF(CMAKE_SYSTEM_NAME MATCHES "Windows") + SET(_command ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${mpi_run} ${MPIEXEC_PREFLAGS} ${_target}) + ELSE() + SET(_command ${MPIEXEC} ${MPIEXEC_NUMPROC_FLAG} ${mpi_run} ${MPIEXEC_PREFLAGS} ./${_target}) + ENDIF() ENDIF() ADD_CUSTOM_TARGET(${_target}.run DEPENDS ${_target} From 036cb4fa105161ae5caacb5b28855ea84473b622 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Mon, 8 Apr 2019 23:19:12 +0200 Subject: [PATCH 381/507] Fix ambiguous function call --- .../deal.II/algorithms/general_data_storage.h | 24 ++++++++++++------- 1 file changed, 16 insertions(+), 8 deletions(-) diff --git a/include/deal.II/algorithms/general_data_storage.h b/include/deal.II/algorithms/general_data_storage.h index 30228b9ffa8d..07d9075e60af 100644 --- a/include/deal.II/algorithms/general_data_storage.h +++ b/include/deal.II/algorithms/general_data_storage.h @@ -244,9 +244,11 @@ class GeneralDataStorage : public Subscriptor * arguments. For this function, the @p arguments are passed as * lvalue references. */ - template + template Type & - get_or_add_object_with_name(const std::string &name, Args &... arguments); + get_or_add_object_with_name(const std::string &name, + Arg & argument, + Args &... arguments); /** * Return a reference to the object with given name. If the object does @@ -258,9 +260,11 @@ class GeneralDataStorage : public Subscriptor * arguments. In contrast to the previous function of the same name, for * this function the @p arguments are passed as rvalue references. */ - template + template Type & - get_or_add_object_with_name(const std::string &name, Args &&... arguments); + get_or_add_object_with_name(const std::string &name, + Arg && argument, + Args &&... arguments); /** * Return a reference to the object with given name. @@ -443,25 +447,29 @@ GeneralDataStorage::get_object_with_name(const std::string &name) const } -template +template Type & GeneralDataStorage::get_or_add_object_with_name(const std::string &name, + Arg & argument, Args &... arguments) { if (!stores_object_with_name(name)) - add_unique_copy(name, Type(arguments...)); + add_unique_copy(name, Type(argument, arguments...)); return get_object_with_name(name); } -template +template Type & GeneralDataStorage::get_or_add_object_with_name(const std::string &name, + Arg && argument, Args &&... arguments) { if (!stores_object_with_name(name)) - add_unique_copy(name, Type(std::forward(arguments)...)); + add_unique_copy(name, + Type(std::forward(argument), + std::forward(arguments)...)); return get_object_with_name(name); } From aa543df321a53c520966486eed1483bb32da5125 Mon Sep 17 00:00:00 2001 From: Kurt Kremitzki Date: Mon, 8 Apr 2019 19:52:52 -0500 Subject: [PATCH 382/507] Update dead LICENSE link in README --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 733e289308c7..ba69add07c7f 100644 --- a/README.md +++ b/README.md @@ -45,7 +45,7 @@ on how to set this up. License: -------- -Please see the file [./LICENSE](LICENSE) for details +Please see the file [./LICENSE.md](LICENSE.md) for details Further information: -------------------- From d31a04bb005a449944114a4ec23e1e4881737e16 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Tue, 9 Apr 2019 15:03:19 +0200 Subject: [PATCH 383/507] Add overload for default constructors --- .../deal.II/algorithms/general_data_storage.h | 18 ++++++++++++++++++ tests/algorithms/general_data_storage_01.cc | 6 ++++++ 2 files changed, 24 insertions(+) diff --git a/include/deal.II/algorithms/general_data_storage.h b/include/deal.II/algorithms/general_data_storage.h index 07d9075e60af..2517b411497a 100644 --- a/include/deal.II/algorithms/general_data_storage.h +++ b/include/deal.II/algorithms/general_data_storage.h @@ -266,6 +266,13 @@ class GeneralDataStorage : public Subscriptor Arg && argument, Args &&... arguments); + /** + * Same as above for default constructors. + */ + template + Type & + get_or_add_object_with_name(const std::string &name); + /** * Return a reference to the object with given name. * @@ -475,6 +482,17 @@ GeneralDataStorage::get_or_add_object_with_name(const std::string &name, } +template +Type & +GeneralDataStorage::get_or_add_object_with_name(const std::string &name) +{ + if (!stores_object_with_name(name)) + add_unique_copy(name, Type()); + + return get_object_with_name(name); +} + + #endif // DOXYGEN diff --git a/tests/algorithms/general_data_storage_01.cc b/tests/algorithms/general_data_storage_01.cc index 5721492f80b3..483149a9b8a3 100644 --- a/tests/algorithms/general_data_storage_01.cc +++ b/tests/algorithms/general_data_storage_01.cc @@ -145,6 +145,8 @@ main() const double val_1 = 1.0; const double &val_2 = data.get_or_add_object_with_name("value", val_1); + const std::string &str = + data.get_or_add_object_with_name("empty string"); } // Pass Arguments by rvalue reference @@ -152,12 +154,16 @@ main() double val_1 = 1.0; const double &val_2 = data.get_or_add_object_with_name("value", std::move(val_1)); + const std::string &str = + data.get_or_add_object_with_name("empty string"); } // Pass Arguments ambiguously { const double &val_2 = data.get_or_add_object_with_name("value", 1.0); + const std::string &str = + data.get_or_add_object_with_name("empty string"); } } From 9c036a426574082c326a181300d71f17439cfd02 Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Mon, 8 Apr 2019 08:17:43 -0600 Subject: [PATCH 384/507] [CI]: run quicktests also execute the quicktests as part of CI --- Jenkinsfile | 2 ++ contrib/ci/Jenkinsfile.osx | 1 + 2 files changed, 3 insertions(+) diff --git a/Jenkinsfile b/Jenkinsfile index 48064a8afb4f..4f94fc4410eb 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -131,6 +131,7 @@ pipeline -D DEAL_II_UNITY_BUILD=ON \ $WORKSPACE/ time ninja -j $NP + time ninja test # quicktests time ninja setup_tests time ctest --output-on-failure -DDESCRIPTION="CI-$JOB_NAME" -j $NP --no-compress-output -T test ''' @@ -182,6 +183,7 @@ pipeline -D DEAL_II_UNITY_BUILD=OFF \ $WORKSPACE/ time ninja -j $NP + time ninja test # quicktests time ninja setup_tests time ctest -R "all-headers|multigrid/transfer" --output-on-failure -DDESCRIPTION="CI-$JOB_NAME" -j $NP --no-compress-output -T test ''' diff --git a/contrib/ci/Jenkinsfile.osx b/contrib/ci/Jenkinsfile.osx index c214ca0a8efa..8538cbdcdde7 100644 --- a/contrib/ci/Jenkinsfile.osx +++ b/contrib/ci/Jenkinsfile.osx @@ -94,6 +94,7 @@ pipeline -D DEAL_II_CXX_FLAGS='-Werror' \ -D CMAKE_BUILD_TYPE=Debug \ $WORKSPACE/ && make -j 4 + make test # quicktests ''' } } From 5ac43cff8e80725a5895ba5ec914c1bd4611b2f7 Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Mon, 8 Apr 2019 13:25:30 -0600 Subject: [PATCH 385/507] CI: catch failures --- Jenkinsfile | 2 ++ contrib/ci/Jenkinsfile.osx | 1 + 2 files changed, 3 insertions(+) diff --git a/Jenkinsfile b/Jenkinsfile index 4f94fc4410eb..2f6d440b15bd 100644 --- a/Jenkinsfile +++ b/Jenkinsfile @@ -120,6 +120,7 @@ pipeline { sh "echo \"building on node ${env.NODE_NAME}\"" sh '''#!/bin/bash + set -e export NP=`grep -c ^processor /proc/cpuinfo` export TEST_TIME_LIMIT=1200 mkdir -p /home/dealii/build @@ -173,6 +174,7 @@ pipeline { sh "echo \"building on node ${env.NODE_NAME}\"" sh '''#!/bin/bash + set -e export NP=`grep -c ^processor /proc/cpuinfo` mkdir -p /home/dealii/build cd /home/dealii/build diff --git a/contrib/ci/Jenkinsfile.osx b/contrib/ci/Jenkinsfile.osx index 8538cbdcdde7..5c0d92165ca2 100644 --- a/contrib/ci/Jenkinsfile.osx +++ b/contrib/ci/Jenkinsfile.osx @@ -88,6 +88,7 @@ pipeline { sh "echo \"building on node ${env.NODE_NAME}\"" sh '''#!/bin/bash + set -e mkdir build && cd build cmake \ -D DEAL_II_WITH_MPI=OFF \ From 05e5cb6c2269be5df9bb642f9dae8a857515fab1 Mon Sep 17 00:00:00 2001 From: Luca Heltai Date: Tue, 9 Apr 2019 23:04:16 +0200 Subject: [PATCH 386/507] CopyData --- include/deal.II/meshworker/copy_data.h | 164 +++++++++++++++++++++++++ 1 file changed, 164 insertions(+) create mode 100644 include/deal.II/meshworker/copy_data.h diff --git a/include/deal.II/meshworker/copy_data.h b/include/deal.II/meshworker/copy_data.h new file mode 100644 index 000000000000..252f4bab6e31 --- /dev/null +++ b/include/deal.II/meshworker/copy_data.h @@ -0,0 +1,164 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + +#ifndef dealii_meshworker_copy_data_h +#define dealii_meshworker_copy_data_h + +#include + +#include + +#include +#include + +#include + +DEAL_II_NAMESPACE_OPEN + +namespace MeshWorker +{ + /** + * Helper copy data struct. + * + * This class is a good default drop in CopyData object for the + * WorkStream::run() and MeshWorker::mesh_loop() functions. + * + * It arrays of (local) full matrices, vectors, and local degrees of freedom + * index vectors, with size determined by the corresponding template argument. + * + * In particular, you can specify the following template arguments + * + * - @p n_matrices: Size of the array of matrices + * - @p n_vectors: size of the array of vectors + * - @p n_dof_indices: size of the array of local dof indices + * + * @author Luca Heltai, 2019. + */ + template + struct CopyData + { + /** + * Initialize everything with the same @p size. This is usually the number + * of local degrees of freedom. + */ + CopyData(const unsigned int size); + + /** + * For every object, specify the size they should have. + */ + CopyData( + const std::array, n_matrices> &matrix_sizes, + const std::array & vector_sizes, + const std::array &dof_indices_sizes); + + /** + * Deep copy constructor. + */ + CopyData(const CopyData &other) = + default; + + /** + * Allow resetting of all elements of the struct to zero, by simply + * calling `(*this) = 0;` + * + * Notice that the only allowed number here is really `0`. Calling this + * function with any other number will trigger an assertion. + * + * The elements of the arrays of local degrees of freedom indices are + * all set to numbers::invalid_dof_index. + */ + void + operator=(const double &number); + + /** + * An array of local matrices. + */ + std::array, n_matrices> matrices; + + /** + * An array of local vectors. + */ + std::array, n_vectors> vectors; + + /** + * An array of local degrees of freedom indices. + */ + std::array, n_dof_indices> + local_dof_indices; + }; + + +#ifndef DOXYGEN + // + // Template definitions + // + template + CopyData::CopyData( + const unsigned int size) + { + for (auto &m : matrices) + m.reinit({size, size}); + for (auto &v : vectors) + v.reinit(size); + for (auto &d : local_dof_indices) + d.resize(size); + } + + + + template + CopyData::CopyData( + const std::array, n_matrices> &matrix_sizes, + const std::array & vector_sizes, + const std::array &dof_indices_sizes) + { + for (unsigned int i = 0; i < n_matrices; ++i) + matrices[i].reinit(matrix_sizes[i++]); + + for (unsigned int i = 0; i < n_vectors; ++i) + vectors[i].reinit(vector_sizes[i++]); + + for (unsigned int i = 0; i < n_dof_indices; ++i) + local_dof_indices[i].resize(dof_indices_sizes[i++]); + } + + + + template + void + CopyData:: + operator=(const double &number) + { + Assert(number == 0.0, + ExcMessage("You should only call this method with " + "argument 0.0")); + + for (auto &m : matrices) + m = number; + for (auto &v : vectors) + v = number; + for (auto &d : local_dof_indices) + for (auto &val : d) + val = numbers::invalid_dof_index; + } + +#endif // DOXYGEN +} // namespace MeshWorker + +DEAL_II_NAMESPACE_CLOSE + +#endif From 5c7445b1ca3c72c36553ab859af1e0be2876de5d Mon Sep 17 00:00:00 2001 From: Luca Heltai Date: Tue, 9 Apr 2019 23:04:36 +0200 Subject: [PATCH 387/507] ScratchData --- include/deal.II/meshworker/scratch_data.h | 1264 +++++++++++++++++++++ source/meshworker/CMakeLists.txt | 2 + source/meshworker/scratch_data.cc | 356 ++++++ source/meshworker/scratch_data.inst.in | 23 + 4 files changed, 1645 insertions(+) create mode 100644 include/deal.II/meshworker/scratch_data.h create mode 100644 source/meshworker/scratch_data.cc create mode 100644 source/meshworker/scratch_data.inst.in diff --git a/include/deal.II/meshworker/scratch_data.h b/include/deal.II/meshworker/scratch_data.h new file mode 100644 index 000000000000..c249357c0824 --- /dev/null +++ b/include/deal.II/meshworker/scratch_data.h @@ -0,0 +1,1264 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + +#ifndef dealii_meshworker_scratch_data_h +#define dealii_meshworker_scratch_data_h + +#include + +#include + +#include + +#include +#include + +#include + +#include +#include +#include + +DEAL_II_NAMESPACE_OPEN + +namespace MeshWorker +{ + namespace internal + { + /** + * Alias used to deduce the OutputType when asking for values or gradients + * of shape functions multiplied with the given @p NumberType. + */ + template + using OutputType = typename FEValuesViews::View:: + template OutputType; + } // namespace internal + + /** + * A helper class to simplify the parallel assembly of linear and non-linear + * problems, and the evaluation of finite element fields. + * + * This class is a drop in ScratchData to use with the WorkStream::run() + * function and with the MeshWorker::mesh_loop function(). + * + * The ScratchData class has three main goals: + * - to create FEValues, FEFaceValues, and FESubfaceValues for the current + * cell and for its neighbor cell *on demand* (only if they are + * necessary for the algorithm provided by the user), and to provide a + * uniform interface to access the FEValues objects when assembling cell, + * face, or subface contributions + * - to store arbitrary data types (or references to arbitrary data types), + * that can be retrieved by name (for example, when the assembly needs to + * make reference to other objects such as previous time steps' solution + * vectors, previous nonlinear iteration vectors, geometry descriptions, + * etc.) in an object of type + * - to provide a reasonable interface for those use cases where the user may + * need temporary vectors of data at quadrature points, allowing the + * construction of these temporaries *on demand*, and easy access to + * values, gradients, etc., of already computed solution vectors. + * + * The methods in @ref CurrentCellMethods initialize on demand internal FEValues, + * FEFaceValues, and FESubfaceValues objects on the current cell, allowing the + * use of this class as a single substitute for three different objects used + * to integrate and query finite element values on cells, faces, and subfaces. + * + * Similarly, the methods in @ref NeighborCellMethods initialize on demand + * (different) internal FEValues, FEFaceValues, and FESubfaceValues, on + * neighbor cells, allowing the use of this class aslo as a single substitute + * for the additional three objects you would typically need to integrate on + * the neighbor cell, and on its faces and subfaces (for example, in + * discontinuous Galerkin methods). + * + * If you need to retrieve values or gradients of finite element solution + * vectors, on the cell, face, or subface that has just beeing initialized + * with one of the functions in @ref CurrentCellMethods, you can use the + * methods in @ref CurrentCellEvaluation. + * + * An example usage for this class is given by the following snippet of code: + * + * @code + * ScratchData scratch(fe, + * cell_quadrature, + * update_values | update_gradients); + * + * FEValuesExtractors::Vector velocity(0); + * FEValuesExtractors::Scalar pressure(dim); + * + * ... + * + * for(const auto &cell : dof_handler.active_cell_iterators()) + * { + * const auto &fe_values = scratch.reinit(cell); + * scratch.extract_local_dof_values("current_solution", + * current_solution); + * + * scratch.extract_local_dof_values("previous_solution", + * previous_solution); + * + * const auto &local_solution_values = + * scratch.get_local_dof_values("current_solution", + * current_solution); + * + * const auto &local_previous_solution_values = + * scratch.get_local_dof_values("previous_solution", + * previous_solution); + * + * const auto &previous_solution_values_velocity = + * scratch.get_values("previous_solution", velocity); + * const auto &previous_solution_values_pressure = + * scratch.get_values("previous_solution", pressure); + * + * const auto &solution_values_velocity = + * scratch.get_values("solution", velocity); + * const auto &solution_values_pressure = + * scratch.get_values("solution", pressure); + * + * const auto &solution_symmetric_gradients_velocity = + * scratch.get_symmetric_gradients("solution", velocity); + * + * // Do something with the above. + * } + * @endcode + * + * The order in which you call functions of this class matters: if you call + * the ScratchData::reinit() function that takes an active cell iterator, + * then subsequent calls to methods that internally need an FEValuesBase + * object will use the internal FEValues object initialized with the given + * cell to perform their calculations. On the other hand, if you have called + * the ScratchData::reinit() method that also takes a face index, all + * subsequent calls to methods that need an FEValuesBase object, will use an + * internally stored FEFaceValues object, initialized with the cell and face + * index passed to the ScratchData::reinit() function. The same applies for + * the ScratchData::reinit() method that takes three arguments: the cell, the + * face index, and the subface index. + * + * The user code should be structured without interleaving work on cells and + * work on faces. + * + * Consider, for example, the following snippet of code: + * + * @code + * ScratchData scratch(...); + * FEValuesExtractors::Scalar temperature(0); + * + * for(const auto &cell : dof_handler.active_cell_iterators()) + * { + * const auto &fe_values = scratch.reinit(cell); + * const auto &local_dof_values = + * scratch.extract_local_dof_values("solution", solution); + * + * // This will contain all values of the temperature on the cell + * // quadrature points + * const auto &solution_values_cell = + * scratch.get_values("solution", temperature); + * + * // Do something with values on the cell + * ... + * + * // Now start working on the faces + * for(unsigned int f=0; f::faces_per_cell; ++f) + * { + * const auto &fe_face_values = scratch.reinit(cell, f); + * + * // Now we'll have access to the values of the temperature on the faces + * const auto &solution_values_face = + * scratch.get_values("solution", temperature); + * + * // Notice how the function call is the same, but the result depends + * // on what was the last reinit() function that was called. In this + * // case, we called reinit(cell, f), triggering internal work on + * // faces. + * } + * + * // At this point, we would like to go back and work on cells, + * // for example querying the values of the gradients: + * const auto &solution_gradients = + * scratch.get_gradients("solution", temperature); + * + * // This assertion would be triggered in debug mode + * AssertDimension(solution_gradients.size(), quadrature_cell.size()); + * + * // However, with the above call the content of solution_gradients is the + * // gradient of the temperature on the quadrature points of the last face + * // visited in the previous loop. + * // If you really want to have the values of the gradients on the cell, + * // at this point your only option is to call + * scratch.reinit(cell); + * + * // (again) before querying for the gradients: + * const auto &solution_gradients_cell = + * scratch.get_gradients("solution", temperature); + * + * // The call to reinit(cell), however, is an expensive one. You + * // should make sure you only call it once per cell by grouping together + * // all queries that concern cells in the same place (right after you + * // call the reinit(cell) method). + * // A similar argument holds for all calls on each face and subface. + * } + * @endcode + * + * When using this class, please cite + * @code{.bib} + * @article{SartoriGiulianiBardelloni-2018-a, + * Author = {Sartori, Alberto and Giuliani, Nicola and + * Bardelloni, Mauro and Heltai, Luca}, + * Journal = {SoftwareX}, + * Pages = {318--327}, + * Title = {{deal2lkit: A toolkit library for high performance + * programming in deal.II}}, + * Doi = {10.1016/j.softx.2018.09.004}, + * Volume = {7}, + * Year = {2018}} + * @endcode + * + * @author Luca Heltai, 2019. + */ + template + class ScratchData + { + public: + /** + * Create an empty ScratchData object. A SmartPointer pointing to + * @p mapping and @p fe is stored internally. Make sure they live longer + * than this class instance. + * + * The constructor does not initialize any of the internal FEValues objects. + * These are initialized the first time one of the reinit() functions is + * called, using the arguments passed here. + * + * @param mapping The mapping to use in the internal FEValues objects + * @param fe The finite element + * @param quadrature The cell quadrature + * @param update_flags UpdateFlags for the current cell FEValues and + * neighbor cell FEValues + * @param face_quadrature Face quadrature, used for FEFaceFvalues and + * FESubfaceValues for both the current cell and the neighbor cell + * @param face_update_flags UpdateFlags used for FEFaceFvalues and + * FESubfaceValues for both the current cell and the neighbor cell + */ + ScratchData( + const Mapping & mapping, + const FiniteElement &fe, + const Quadrature & quadrature, + const UpdateFlags & update_flags, + const Quadrature &face_quadrature = Quadrature(), + const UpdateFlags & face_update_flags = update_default); + + /** + * Similar to the other constructor, but this one allows to specify + * different flags for neighbor cells and faces. + * + * @param mapping The mapping to use in the internal FEValues objects + * @param fe The finite element + * @param quadrature The cell quadrature + * @param update_flags UpdateFlags for the current cell FEValues + * @param neighbor_update_flags UpdateFlags for the neighbor cell FEValues + * @param face_quadrature Face quadrature, used for FEFaceFvalues and + * FESubfaceValues for both the current cell and the neighbor cell + * @param face_update_flags UpdateFlags used for FEFaceFvalues and + * FESubfaceValues for the current cell + * @param neighbor_face_update_flags UpdateFlags used for FEFaceFvalues and + * FESubfaceValues for the neighbor cell + */ + ScratchData( + const Mapping & mapping, + const FiniteElement &fe, + const Quadrature & quadrature, + const UpdateFlags & update_flags, + const UpdateFlags & neighbor_update_flags, + const Quadrature &face_quadrature = Quadrature(), + const UpdateFlags & face_update_flags = update_default, + const UpdateFlags & neighbor_face_update_flags = update_default); + + /** + * Same as the other constructor, using the default MappingQ1. + * + * @param mapping The mapping to use in the internal FEValues objects + * @param fe The finite element + * @param quadrature The cell quadrature + * @param update_flags UpdateFlags for the current cell FEValues + * @param neighbor_update_flags UpdateFlags for the neighbor cell FEValues + * @param face_quadrature Face quadrature, used for FEFaceFvalues and + * FESubfaceValues for both the current cell and the neighbor cell + * @param face_update_flags UpdateFlags used for FEFaceFvalues and + * FESubfaceValues for the current cell + * @param neighbor_face_update_flags UpdateFlags used for FEFaceFvalues and + * FESubfaceValues for the neighbor cell + */ + ScratchData( + const FiniteElement &fe, + const Quadrature & quadrature, + const UpdateFlags & update_flags, + const Quadrature &face_quadrature = Quadrature(), + const UpdateFlags & face_update_flags = update_default); + + /** + * Same as the other constructor, using the default MappingQ1. + * + * @param mapping The mapping to use in the internal FEValues objects + * @param fe The finite element + * @param quadrature The cell quadrature + * @param update_flags UpdateFlags for the current cell FEValues + * @param neighbor_update_flags UpdateFlags for the neighbor cell FEValues + * @param face_quadrature Face quadrature, used for FEFaceFvalues and + * FESubfaceValues for both the current cell and the neighbor cell + * @param face_update_flags UpdateFlags used for FEFaceFvalues and + * FESubfaceValues for the current cell + * @param neighbor_face_update_flags UpdateFlags used for FEFaceFvalues and + * FESubfaceValues for the neighbor cell + */ + ScratchData( + const FiniteElement &fe, + const Quadrature & quadrature, + const UpdateFlags & update_flags, + const UpdateFlags & neighbor_update_flags, + const Quadrature &face_quadrature = Quadrature(), + const UpdateFlags & face_update_flags = update_default, + const UpdateFlags & neighbor_face_update_flags = update_default); + + /** + * Deep copy constructor. FEValues objects are not copied. + */ + ScratchData(const ScratchData &scratch); + + /** + * \defgroup CurrentCellMethos Methods to work on current cell + */ + /**@{*/ + + /** + * Initialize the internal FEValues with the given @p cell, and return + * a reference to it. + * + * After calling this function, get_current_fe_values() will return the + * same object of this method, as an FEValuesBase reference. + */ + const FEValues & + reinit( + const typename DoFHandler::active_cell_iterator &cell); + + /** + * Initialize the internal FEFaceValues to use the given @p face_no on the given + * @p cell, and return a reference to it. + * + * After calling this function, get_current_fe_values() will return the + * same object of this method, as an FEValuesBase reference. + */ + const FEFaceValues & + reinit(const typename DoFHandler::active_cell_iterator &cell, + const unsigned int face_no); + + /** + * Initialize the internal FESubfaceValues to use the given @p subface_no, + * on @p face_no, on the given @p cell, and return a reference to it. + * + * After calling this function, get_current_fe_values() will return the + * same object of this method, as an FEValuesBase reference. + * + * If @p subface_no is numbers::invalid_unsigned_int, the reinit() function + * that takes only the @p cell and the @p face_no is called. + */ + const FEFaceValuesBase & + reinit(const typename DoFHandler::active_cell_iterator &cell, + const unsigned int face_no, + const unsigned int subface_no); + + /** + * Get the currently initialized FEValues. + * + * This function will return the internal FEValues if the + * reinit(cell) function was called last. If the reinit(cell, face_no) + * function was called, then this function returns the internal + * FEFaceValues, and if the reinit(cell, face_no, subface_no) function was + * called (with a valid @p subface_no argument), it returns the internal + * FESubfaceValues object. + */ + const FEValuesBase & + get_current_fe_values() const; + + /** + * Return the quadrature points of the internal FEValues object. + */ + const std::vector> & + get_quadrature_points() const; + + /** + * Return the JxW values of the internal FEValues object. + */ + const std::vector & + get_JxW_values() const; + + /** + * Return the last computed normal vectors. + */ + const std::vector> & + get_normal_vectors() const; + + /** + * Return the local dof indices for the cell passed the last time the + * reinit() function was called. + */ + const std::vector & + get_local_dof_indices() const; + + /** @} */ // CurrentCellMethods + + /** + * @defgroup NeighborCellMethods Methods to work on neighbor cell + */ + /** @{ */ + + /** + * Initialize the internal neighbor FEValues to use the given @p cell, and + * return a reference to it. + * + * After calling this function, get_current_fe_values() will return the + * same object of this method, as an FEValuesBase reference. + */ + const FEValues & + reinit_neighbor( + const typename DoFHandler::active_cell_iterator &cell); + + /** + * Initialize the internal FEFaceValues to use the given @p face_no on the + * given @p cell, and return a reference to it. + * + * After calling this function, get_current_fe_values() will return the + * same object of this method, as an FEValuesBase reference. + */ + const FEFaceValues & + reinit_neighbor( + const typename DoFHandler::active_cell_iterator &cell, + const unsigned int face_no); + + /** + * Initialize the internal FESubfaceValues to use the given @p subface_no, + * on @p face_no, on the given @p cell, and return a reference to it. + * + * After calling this function, get_current_fe_values() will return the + * same object of this method, as an FEValuesBase reference. + * + * If @p subface_no is numbers::invalid_unsigned_int, the reinit() function + * that takes only the @p cell and the @p face_no is called. + */ + const FEFaceValuesBase & + reinit_neighbor( + const typename DoFHandler::active_cell_iterator &cell, + const unsigned int face_no, + const unsigned int subface_no); + + /** + * Get the currently initialized neighbor FEValues. + * + * This function will return the neighbor FEValues if the + * reinit_neighbor(cell) function was called last. If the + * reinit_neighbor(cell, face_no) function was called, then this function + * returns the internal neighbor FEFaceValues, and if the + * reinit_neighbor(cell, face_no, subface_no) function was + * called (with a valid @p subface_no argument), it returns the internal neighbor + * FESubfaceValues object. + */ + const FEValuesBase & + get_current_neighbor_fe_values() const; + + /** + * Return the JxW values of the neighbor FEValues object. + */ + const std::vector & + get_neighbor_JxW_values() const; + + /** + * Return the last computed normal vectors on the neighbor. + */ + const std::vector> & + get_neighbor_normal_vectors(); + + /** + * Return the local dof indices of the neighbor passed the last time the + * reinit_neighbor() function was called. + */ + const std::vector & + get_neighbor_dof_indices() const; + + /** @} */ // NeighborCellMethods + + /** + * Return a GeneralDataStorage object that can be used to store store any + * amount of data, of any type, which is then made accessible by an + * identifier string. + */ + GeneralDataStorage & + get_general_data_storage(); + + /** @defgroup CurrentCellEvaluation Evaluation of finite element fields + * and their derivatives on the current cell + * @{ + */ + + /** + * Extract the local dof values associated with the internally initialized + * cell. + * + * Before you call this function, you have to make sure you have previously + * called one of the reinit() functions. + * + * At every call of this function, a new vector of dof values is generated + * and stored internally, unless a previous vector with the same name is + * found. If this is the case, the content of that vector is overwritten. + * + * If you give a unique @p global_vector_name, then for each cell you are + * guaranteed to get a unique vector of independent dofs of the same type + * as the dummy variable. If you use an automatic differentiation number + * type (like Sacado::Fad::DFad, + * Sacado::Fad::DFad>, etc.) this method will + * also initialize the independent variables internally, allowing you + * to perform automatic differentiation. + * + * You can access the extracted local dof values by calling the method + * get_local_dof_values() with the same @p global_vector_name argument + * you passed here. + * + * Notice that using this initialization strategy renders the use of this + * ScratchData object incompatible with the AD helper classes (since they + * do their own data management). In particular, it is necessary for the + * user to manage all of the AD data themselves (both before and after this + * call). + */ + template + void + extract_local_dof_values(const std::string &global_vector_name, + const VectorType & input_vector, + const Number dummy = Number(0)); + + /** + * After calling extract_local_dof_values(), you can retrieve the stored + * information through this method. + * + * Both the argument @p global_vector_name and the type of the @p dummy + * variable should match the ones you passed to the + * extract_local_dof_values() function. + */ + template + const std::vector & + get_local_dof_values(const std::string &global_vector_name, + Number dummy = Number(0)) const; + + /** + * For the solution vector identified by @p global_vector_name, compute + * the values of the function at the quadrature points, and return a + * vector with the correct type deduced by the Extractor you passed as the + * @p variable argument. + * + * Before you can call this method, you need to call the + * extract_local_dof_values() method at least once, passing the same + * @p global_vector_name string, and the same type for the variable @p dummy. + * + * If you have not previously called the extract_local_dof_values() method, + * this function will throw an exception. + * + * For this function to work properly, the underlying FEValues, + * FEFaceValues, or FESubfaceValues object for which you called one of the + * reinit() functions, must have computed the information you are + * requesting. To do so, the update_values flag must be an element of the + * list of UpdateFlags that you passed to the constructor of this object. + * See "The interplay of UpdateFlags, Mapping, and FiniteElement" in + * the documentation of the FEValues class for more information. + */ + template + const std::vector< + typename internal::OutputType:: + value_type> & + get_values(const std::string &global_vector_name, + const Extractor & variable, + const Number dummy = Number(0)); + + /** + * For the solution vector identified by @p global_vector_name, compute + * the gradients of the function at the quadrature points, and return a + * vector with the correct type deduced by the Extractor you passed as the + * @p variable argument. + * + * Before you can call this method, you need to call the + * extract_local_dof_values() method at least once, passing the same + * @p global_vector_name string, and the same type for the variable @p dummy. + * + * If you have not previously called the extract_local_dof_values() method, + * this function will throw an exception. + * + * For this function to work properly, the underlying FEValues, + * FEFaceValues, or FESubfaceValues object for which you called one of the + * reinit() functions, must have computed the information you are + * requesting. To do so, the update_gradients flag must be an element of the + * list of UpdateFlags that you passed to the constructor of this object. + * See "The interplay of UpdateFlags, Mapping, and FiniteElement" in + * the documentation of the FEValues class for more information. + */ + template + const std::vector< + typename internal::OutputType:: + gradient_type> & + get_gradients(const std::string &global_vector_name, + const Extractor & variable, + const Number dummy = Number(0)); + + /** + * For the solution vector identified by @p global_vector_name, compute + * the symmetric gradients of the function at the quadrature points, and + * return a vector with the correct type deduced by the Extractor you passed + * as the + * @p variable argument. + * + * Before you can call this method, you need to call the + * extract_local_dof_values() method at least once, passing the same + * @p global_vector_name string, and the same type for the variable @p dummy. + * + * If you have not previously called the extract_local_dof_values() method, + * this function will throw an exception. + * + * For this function to work properly, the underlying FEValues, + * FEFaceValues, or FESubfaceValues object for which you called one of the + * reinit() functions, must have computed the information you are + * requesting. To do so, the update_gradients flag must be an element of the + * list of UpdateFlags that you passed to the constructor of this object. + * See "The interplay of UpdateFlags, Mapping, and FiniteElement" in + * the documentation of the FEValues class for more information. + */ + template + const std::vector< + typename internal::OutputType:: + symmetric_gradient_type> & + get_symmetric_gradients(const std::string &global_vector_name, + const Extractor & variable, + const Number dummy = Number(0)); + + /** + * For the solution vector identified by @p global_vector_name, compute + * the divergences of the function at the quadrature points, and return a + * vector with the correct type deduced by the Extractor you passed as the + * @p variable argument. + * + * Before you can call this method, you need to call the + * extract_local_dof_values() method at least once, passing the same + * @p global_vector_name string, and the same type for the variable @p dummy. + * + * If you have not previously called the extract_local_dof_values() method, + * this function will throw an exception. + * + * For this function to work properly, the underlying FEValues, + * FEFaceValues, or FESubfaceValues object for which you called one of the + * reinit() functions, must have computed the information you are + * requesting. To do so, the update_gradients flag must be an element of the + * list of UpdateFlags that you passed to the constructor of this object. + * See "The interplay of UpdateFlags, Mapping, and FiniteElement" in + * the documentation of the FEValues class for more information. + */ + template + const std::vector< + typename internal::OutputType:: + divergence_type> & + get_divergences(const std::string &global_vector_name, + const Extractor & variable, + const Number dummy = Number(0)); + + /** + * For the solution vector identified by @p global_vector_name, compute + * the curls of the function at the quadrature points, and return a + * vector with the correct type deduced by the Extractor you passed as the + * @p variable argument. + * + * Before you can call this method, you need to call the + * extract_local_dof_values() method at least once, passing the same + * @p global_vector_name string, and the same type for the variable @p dummy. + * + * If you have not previously called the extract_local_dof_values() method, + * this function will throw an exception. + * + * For this function to work properly, the underlying FEValues, + * FEFaceValues, or FESubfaceValues object for which you called one of the + * reinit() functions, must have computed the information you are + * requesting. To do so, the update_gradients flag must be an element of the + * list of UpdateFlags that you passed to the constructor of this object. + * See "The interplay of UpdateFlags, Mapping, and FiniteElement" in + * the documentation of the FEValues class for more information. + */ + template + const std::vector::curl_type> + & + get_curls(const std::string &global_vector_name, + const Extractor & variable, + const Number dummy = Number(0)); + + /** + * For the solution vector identified by @p global_vector_name, compute + * the hessians of the function at the quadrature points, and return a + * vector with the correct type deduced by the Extractor you passed as the + * @p variable argument. + * + * Before you can call this method, you need to call the + * extract_local_dof_values() method at least once, passing the same + * @p global_vector_name string, and the same type for the variable @p dummy. + * + * If you have not previously called the extract_local_dof_values() method, + * this function will throw an exception. + * + * For this function to work properly, the underlying FEValues, + * FEFaceValues, or FESubfaceValues object for which you called one of the + * reinit() functions, must have computed the information you are + * requesting. To do so, the update_hessians flag must be an element of the + * list of UpdateFlags that you passed to the constructor of this object. + * See "The interplay of UpdateFlags, Mapping, and FiniteElement" in + * the documentation of the FEValues class for more information. + */ + template + const std::vector< + typename internal::OutputType:: + hessian_type> & + get_hessians(const std::string &global_vector_name, + const Extractor & variable, + const Number dummy = Number(0)); + + /** + * For the solution vector identified by @p global_vector_name, compute + * the third_derivatives of the function at the quadrature points, and + * return a vector with the correct type deduced by the Extractor you passed + * as the @p variable argument. + * + * Before you can call this method, you need to call the + * extract_local_dof_values() method at least once, passing the same + * @p global_vector_name string, and the same type for the variable @p dummy. + * + * If you have not previously called the extract_local_dof_values() method, + * this function will throw an exception. + * + * For this function to work properly, the underlying FEValues, + * FEFaceValues, or FESubfaceValues object for which you called one of the + * reinit() functions, must have computed the information you are + * requesting. To do so, the update_3rd_derivatives flag must be an + * element of the list of UpdateFlags that you passed to the constructor of + * this object. See "The interplay of UpdateFlags, Mapping, and + * FiniteElement" in the documentation of the FEValues for more information. + */ + template + const std::vector< + typename internal::OutputType:: + third_derivative_type> & + get_third_derivatives(const std::string &global_vector_name, + const Extractor & variable, + const Number dummy = Number(0)); + + /** @} */ // CurrentCellEvaluation + + /** + * Return a reference to the used mapping. + */ + const Mapping & + get_mapping() const; + + private: + /** + * Construct a unique name to store vectors of values, gradients, + * divergences, etc., in the internal GeneralDataStorage object. + */ + template + std::string + get_unique_name(const std::string &global_vector_name, + const Extractor & variable, + const std::string &object_type, + const unsigned int size, + const Number & exemplar_number) const; + + /** + * Construct a unique name to store local dof values. + */ + template + std::string + get_unique_dofs_name(const std::string &global_vector_name, + const unsigned int size, + const Number & exemplar_number) const; + + /** + * The mapping used by the internal FEValues. Make sure it lives + * longer than this class. + */ + SmartPointer> mapping; + + /** + * The finite element used by the internal FEValues. Make sure it lives + * longer than this class. + */ + SmartPointer> fe; + + /** + * Quadrature formula used to integrate on the current cell, and on its + * neighbor. + */ + Quadrature cell_quadrature; + + /** + * Quadrature formula used to integrate on faces, subfaces, and neighbor + * faces and subfaces. + */ + Quadrature face_quadrature; + + /** + * UpdateFlags to use when initializing the cell FEValues object. + */ + UpdateFlags cell_update_flags; + + /** + * UpdateFlags to use when initializing the neighbor cell FEValues objects. + */ + UpdateFlags neighbor_cell_update_flags; + + /** + * UpdateFlags to use when initializing FEFaceValues and FESubfaceValues + * objects. + */ + UpdateFlags face_update_flags; + + /** + * UpdateFlags to use when initializing neighbor FEFaceValues and + * FESubfaceValues objects. + */ + UpdateFlags neighbor_face_update_flags; + + /** + * Finite element values on the current cell. + */ + std::unique_ptr> fe_values; + + /** + * Finite element values on the current face. + */ + std::unique_ptr> fe_face_values; + + /** + * Finite element values on the current subface. + */ + std::unique_ptr> fe_subface_values; + + /** + * Finite element values on the neighbor cell. + */ + std::unique_ptr> neighbor_fe_values; + + /** + * Finite element values on the neighbor face. + */ + std::unique_ptr> neighbor_fe_face_values; + + /** + * Finite element values on the neighbor subface. + */ + std::unique_ptr> neighbor_fe_subface_values; + + /** + * Dof indices on the current cell. + */ + std::vector local_dof_indices; + + /** + * Dof indices on the neighbor cell. + */ + std::vector neighbor_dof_indices; + + /** + * User data storage. + */ + GeneralDataStorage user_data_storage; + + /** + * Internal data storage. + */ + GeneralDataStorage internal_data_storage; + + /** + * A pointer to the last used FEValues/FEFaceValues, or FESubfaceValues + * object on this cell. + */ + SmartPointer> current_fe_values; + + /** + * A pointer to the last used FEValues/FEFaceValues, or FESubfaceValues + * object on the neighbor cell. + */ + SmartPointer> current_neighbor_fe_values; + }; + +#ifndef DOXYGEN + template + template + std::string + ScratchData::get_unique_name( + const std::string &global_vector_name, + const Extractor & variable, + const std::string &object_type, + const unsigned int size, + const Number & exemplar_number) const + { + return global_vector_name + "_" + variable.get_name() + "_" + object_type + + "_" + Utilities::int_to_string(size) + "_" + + Utilities::type_to_string(exemplar_number); + } + + + + template + template + std::string + ScratchData::get_unique_dofs_name( + const std::string &global_vector_name, + const unsigned int size, + const Number & exemplar_number) const + { + return global_vector_name + "_independent_local_dofs_" + + Utilities::int_to_string(size) + "_" + + Utilities::type_to_string(exemplar_number); + } + + + + template + template + void + ScratchData::extract_local_dof_values( + const std::string &global_vector_name, + const VectorType & input_vector, + const Number dummy) + { + const unsigned int n_dofs = get_current_fe_values().get_fe().dofs_per_cell; + + const std::string name = + get_unique_dofs_name(global_vector_name, n_dofs, dummy); + + auto &independent_local_dofs = + internal_data_storage + .template get_or_add_object_with_name>(name, + n_dofs); + + AssertDimension(independent_local_dofs.size(), n_dofs); + + if (Differentiation::AD::is_tapeless_ad_number::value == true) + for (unsigned int i = 0; i < n_dofs; ++i) + Differentiation::AD::internal::Marking::independent_variable( + input_vector(local_dof_indices[i]), + i, + n_dofs, + independent_local_dofs[i]); + else + for (unsigned int i = 0; i < n_dofs; ++i) + independent_local_dofs[i] = input_vector(local_dof_indices[i]); + } + + + + template + template + const std::vector & + ScratchData::get_local_dof_values( + const std::string &global_vector_name, + Number dummy) const + { + const unsigned int n_dofs = get_current_fe_values().get_fe().dofs_per_cell; + + const std::string dofs_name = + get_unique_dofs_name(global_vector_name, n_dofs, dummy); + + Assert( + internal_data_storage.stores_object_with_name(dofs_name), + ExcMessage( + "You did not call yet extract_local_dof_values with the right types!")); + + return internal_data_storage + .template get_object_with_name>(dofs_name); + } + + + + template + template + const std::vector< + typename internal::OutputType::value_type> + & + ScratchData::get_values( + const std::string &global_vector_name, + const Extractor & variable, + const Number dummy) + { + const std::vector &independent_local_dofs = + get_local_dof_values(global_vector_name, dummy); + + const FEValuesBase &fev = get_current_fe_values(); + + const unsigned int n_q_points = fev.n_quadrature_points; + + const std::string name = get_unique_name( + global_vector_name, variable, "_values_q", n_q_points, dummy); + + // Now build the return type + using RetType = + std::vector::value_type>; + + RetType &ret = + internal_data_storage.template get_or_add_object_with_name( + name, n_q_points); + + AssertDimension(ret.size(), n_q_points); + + fev[variable].get_function_values_from_local_dof_values( + independent_local_dofs, ret); + return ret; + } + + + + template + template + const std::vector< + typename internal::OutputType:: + gradient_type> & + ScratchData::get_gradients( + const std::string &global_vector_name, + const Extractor & variable, + const Number dummy) + { + const std::vector &independent_local_dofs = + get_local_dof_values(global_vector_name, dummy); + + const FEValuesBase &fev = get_current_fe_values(); + + const unsigned int n_q_points = fev.n_quadrature_points; + + const std::string name = get_unique_name( + global_vector_name, variable, "_gradients_q", n_q_points, dummy); + + // Now build the return type + using RetType = std::vector< + typename internal::OutputType:: + gradient_type>; + + RetType &ret = + internal_data_storage.template get_or_add_object_with_name( + name, n_q_points); + + AssertDimension(ret.size(), n_q_points); + + fev[variable].get_function_gradients_from_local_dof_values( + independent_local_dofs, ret); + return ret; + } + + + + template + template + const std::vector< + typename internal::OutputType:: + hessian_type> & + ScratchData::get_hessians( + const std::string &global_vector_name, + const Extractor & variable, + const Number dummy) + { + const std::vector &independent_local_dofs = + get_local_dof_values(global_vector_name, dummy); + + const FEValuesBase &fev = get_current_fe_values(); + + const unsigned int n_q_points = fev.n_quadrature_points; + + const std::string name = get_unique_name( + global_vector_name, variable, "_hessians_q", n_q_points, dummy); + + // Now build the return type + using RetType = + std::vector::hessian_type>; + + RetType &ret = + internal_data_storage.template get_or_add_object_with_name( + name, n_q_points); + + + AssertDimension(ret.size(), n_q_points); + + fev[variable].get_function_hessians_from_local_dof_values( + independent_local_dofs, ret); + return ret; + } + + + + template + template + const std::vector< + typename internal::OutputType:: + third_derivative_type> & + ScratchData::get_third_derivatives( + const std::string &global_vector_name, + const Extractor & variable, + const Number dummy) + { + const std::vector &independent_local_dofs = + get_local_dof_values(global_vector_name, dummy); + + const FEValuesBase &fev = get_current_fe_values(); + + const unsigned int n_q_points = fev.n_quadrature_points; + + const std::string name = get_unique_name( + global_vector_name, variable, "_third_derivatives_q", n_q_points, dummy); + + // Now build the return type + using RetType = std::vector< + typename internal::OutputType:: + third_derivative_type>; + + RetType &ret = + internal_data_storage.template get_or_add_object_with_name( + name, n_q_points); + + + AssertDimension(ret.size(), n_q_points); + + fev[variable].get_function_third_derivatives_from_local_dof_values( + independent_local_dofs, ret); + return ret; + } + + + + template + template + const std::vector< + typename internal::OutputType:: + symmetric_gradient_type> & + ScratchData::get_symmetric_gradients( + const std::string &global_vector_name, + const Extractor & variable, + const Number dummy) + { + const std::vector &independent_local_dofs = + get_local_dof_values(global_vector_name, dummy); + + const FEValuesBase &fev = get_current_fe_values(); + + const unsigned int n_q_points = fev.n_quadrature_points; + + const std::string name = get_unique_name( + global_vector_name, variable, "_symmetric_gradient_q", n_q_points, dummy); + + + // Now build the return type + using RetType = std::vector< + typename internal::OutputType:: + symmetric_gradient_type>; + + RetType &ret = + internal_data_storage.template get_or_add_object_with_name( + name, n_q_points); + + + AssertDimension(ret.size(), n_q_points); + + fev[variable].get_function_symmetric_gradients_from_local_dof_values( + independent_local_dofs, ret); + return ret; + } + + + template + template + const std::vector< + typename internal::OutputType:: + divergence_type> & + ScratchData::get_divergences( + const std::string &global_vector_name, + const Extractor & variable, + const Number dummy) + { + const std::vector &independent_local_dofs = + get_local_dof_values(global_vector_name, dummy); + + const FEValuesBase &fev = get_current_fe_values(); + + const unsigned int n_q_points = fev.n_quadrature_points; + + const std::string name = get_unique_name( + global_vector_name, variable, "_divergence_q", n_q_points, dummy); + + // Now build the return type + using RetType = std::vector< + typename internal::OutputType:: + divergence_type>; + + RetType &ret = + internal_data_storage.template get_or_add_object_with_name( + name, n_q_points); + + + AssertDimension(ret.size(), n_q_points); + + fev[variable].get_function_divergences_from_local_dof_values( + independent_local_dofs, ret); + return ret; + } + + + + template + template + const std::vector< + typename internal::OutputType::curl_type> + & + ScratchData::get_curls(const std::string &global_vector_name, + const Extractor & variable, + const Number dummy) + { + const std::vector &independent_local_dofs = + get_local_dof_values(global_vector_name, dummy); + + const FEValuesBase &fev = get_current_fe_values(); + + const unsigned int n_q_points = fev.n_quadrature_points; + + const std::string name = get_unique_name( + global_vector_name, variable, "_curl_q", n_q_points, dummy); + + // Now build the return type + using RetType = + std::vector::curl_type>; + + RetType &ret = + internal_data_storage.template get_or_add_object_with_name( + name, n_q_points); + + AssertDimension(ret.size(), n_q_points); + + fev[variable].get_function_curls_from_local_dof_values( + independent_local_dofs, ret); + return ret; + } + +#endif + +} // namespace MeshWorker + +DEAL_II_NAMESPACE_CLOSE + +#endif diff --git a/source/meshworker/CMakeLists.txt b/source/meshworker/CMakeLists.txt index 557829dbadff..f939da489433 100644 --- a/source/meshworker/CMakeLists.txt +++ b/source/meshworker/CMakeLists.txt @@ -19,11 +19,13 @@ SET(_src mesh_worker.cc mesh_worker_info.cc mesh_worker_vector_selector.cc + scratch_data.cc ) SET(_inst mesh_worker_info.inst.in mesh_worker_vector_selector.inst.in + scratch_data.inst.in ) FILE(GLOB _header diff --git a/source/meshworker/scratch_data.cc b/source/meshworker/scratch_data.cc new file mode 100644 index 000000000000..8e6e8708c8fe --- /dev/null +++ b/source/meshworker/scratch_data.cc @@ -0,0 +1,356 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + +#include + +DEAL_II_NAMESPACE_OPEN + +namespace MeshWorker +{ + template + ScratchData::ScratchData( + const Mapping & mapping, + const FiniteElement &fe, + const Quadrature & quadrature, + const UpdateFlags & update_flags, + const Quadrature & face_quadrature, + const UpdateFlags & face_update_flags) + : mapping(&mapping) + , fe(&fe) + , cell_quadrature(quadrature) + , face_quadrature(face_quadrature) + , cell_update_flags(update_flags) + , neighbor_cell_update_flags(update_flags) + , face_update_flags(face_update_flags) + , neighbor_face_update_flags(face_update_flags) + , local_dof_indices(fe.dofs_per_cell) + , neighbor_dof_indices(fe.dofs_per_cell) + {} + + + + template + ScratchData::ScratchData( + const Mapping & mapping, + const FiniteElement &fe, + const Quadrature & quadrature, + const UpdateFlags & update_flags, + const UpdateFlags & neighbor_update_flags, + const Quadrature & face_quadrature, + const UpdateFlags & face_update_flags, + const UpdateFlags & neighbor_face_update_flags) + : mapping(&mapping) + , fe(&fe) + , cell_quadrature(quadrature) + , face_quadrature(face_quadrature) + , cell_update_flags(update_flags) + , neighbor_cell_update_flags(neighbor_update_flags) + , face_update_flags(face_update_flags) + , neighbor_face_update_flags(neighbor_face_update_flags) + , local_dof_indices(fe.dofs_per_cell) + , neighbor_dof_indices(fe.dofs_per_cell) + {} + + + + template + ScratchData::ScratchData( + const FiniteElement &fe, + const Quadrature & quadrature, + const UpdateFlags & update_flags, + const Quadrature & face_quadrature, + const UpdateFlags & face_update_flags) + : ScratchData(StaticMappingQ1::mapping, + fe, + quadrature, + update_flags, + face_quadrature, + face_update_flags) + {} + + + + template + ScratchData::ScratchData( + const FiniteElement &fe, + const Quadrature & quadrature, + const UpdateFlags & update_flags, + const UpdateFlags & neighbor_update_flags, + const Quadrature & face_quadrature, + const UpdateFlags & face_update_flags, + const UpdateFlags & neighbor_face_update_flags) + : ScratchData(StaticMappingQ1::mapping, + fe, + quadrature, + update_flags, + neighbor_update_flags, + face_quadrature, + face_update_flags, + neighbor_face_update_flags) + {} + + + + template + ScratchData::ScratchData( + const ScratchData &scratch) + : mapping(scratch.mapping) + , fe(scratch.fe) + , cell_quadrature(scratch.cell_quadrature) + , face_quadrature(scratch.face_quadrature) + , cell_update_flags(scratch.cell_update_flags) + , neighbor_cell_update_flags(scratch.neighbor_cell_update_flags) + , face_update_flags(scratch.face_update_flags) + , neighbor_face_update_flags(scratch.neighbor_face_update_flags) + , local_dof_indices(scratch.local_dof_indices) + , neighbor_dof_indices(scratch.neighbor_dof_indices) + , user_data_storage(scratch.user_data_storage) + , internal_data_storage(scratch.internal_data_storage) + {} + + + + template + const FEValues & + ScratchData::reinit( + const typename DoFHandler::active_cell_iterator &cell) + { + if (!fe_values) + fe_values = std::make_unique>(*mapping, + *fe, + cell_quadrature, + cell_update_flags); + + fe_values->reinit(cell); + cell->get_dof_indices(local_dof_indices); + current_fe_values = fe_values.get(); + return *fe_values; + } + + + + template + const FEFaceValues & + ScratchData::reinit( + const typename DoFHandler::active_cell_iterator &cell, + const unsigned int face_no) + { + if (!fe_face_values) + fe_face_values = std::make_unique>( + *mapping, *fe, face_quadrature, face_update_flags); + + fe_face_values->reinit(cell, face_no); + cell->get_dof_indices(local_dof_indices); + current_fe_values = fe_face_values.get(); + return *fe_face_values; + } + + + + template + const FEFaceValuesBase & + ScratchData::reinit( + const typename DoFHandler::active_cell_iterator &cell, + const unsigned int face_no, + const unsigned int subface_no) + { + if (subface_no != numbers::invalid_unsigned_int) + { + if (!fe_subface_values) + fe_subface_values = std::make_unique>( + *mapping, *fe, face_quadrature, face_update_flags); + fe_subface_values->reinit(cell, face_no, subface_no); + cell->get_dof_indices(local_dof_indices); + + current_fe_values = fe_subface_values.get(); + return *fe_subface_values; + } + else + return reinit(cell, face_no); + } + + + + template + const FEValues & + ScratchData::reinit_neighbor( + const typename DoFHandler::active_cell_iterator &cell) + { + if (!neighbor_fe_values) + neighbor_fe_values = std::make_unique>( + *mapping, *fe, cell_quadrature, neighbor_cell_update_flags); + + neighbor_fe_values->reinit(cell); + cell->get_dof_indices(neighbor_dof_indices); + current_neighbor_fe_values = neighbor_fe_values.get(); + return *neighbor_fe_values; + } + + + + template + const FEFaceValues & + ScratchData::reinit_neighbor( + const typename DoFHandler::active_cell_iterator &cell, + const unsigned int face_no) + { + if (!neighbor_fe_face_values) + neighbor_fe_face_values = std::make_unique>( + *mapping, *fe, face_quadrature, neighbor_face_update_flags); + neighbor_fe_face_values->reinit(cell, face_no); + cell->get_dof_indices(neighbor_dof_indices); + current_neighbor_fe_values = neighbor_fe_face_values.get(); + return *neighbor_fe_face_values; + } + + + + template + const FEFaceValuesBase & + ScratchData::reinit_neighbor( + const typename DoFHandler::active_cell_iterator &cell, + const unsigned int face_no, + const unsigned int subface_no) + { + if (subface_no != numbers::invalid_unsigned_int) + { + if (!neighbor_fe_subface_values) + neighbor_fe_subface_values = + std::make_unique>( + *mapping, *fe, face_quadrature, neighbor_face_update_flags); + neighbor_fe_subface_values->reinit(cell, face_no, subface_no); + cell->get_dof_indices(neighbor_dof_indices); + current_neighbor_fe_values = neighbor_fe_subface_values.get(); + return *neighbor_fe_subface_values; + } + else + return reinit_neighbor(cell, face_no); + } + + + + template + const FEValuesBase & + ScratchData::get_current_fe_values() const + { + Assert(current_fe_values != nullptr, + ExcMessage("You have to initialize the cache using one of the " + "reinit functions first!")); + return *current_fe_values; + } + + + + template + const FEValuesBase & + ScratchData::get_current_neighbor_fe_values() const + { + Assert(current_neighbor_fe_values != nullptr, + ExcMessage("You have to initialize the cache using one of the " + "reinit functions first!")); + return *current_neighbor_fe_values; + } + + + + template + const std::vector> & + ScratchData::get_quadrature_points() const + { + return get_current_fe_values().get_quadrature_points(); + } + + + + template + const std::vector & + ScratchData::get_JxW_values() const + { + return get_current_fe_values().get_JxW_values(); + } + + + + template + const std::vector & + ScratchData::get_neighbor_JxW_values() const + { + return get_current_neighbor_fe_values().get_JxW_values(); + } + + + + template + const std::vector> & + ScratchData::get_normal_vectors() const + { + return get_current_fe_values().get_normal_vectors(); + } + + + + template + const std::vector> & + ScratchData::get_neighbor_normal_vectors() + { + return get_current_neighbor_fe_values().get_normal_vectors(); + } + + + + template + const std::vector & + ScratchData::get_local_dof_indices() const + { + return local_dof_indices; + } + + + + template + const std::vector & + ScratchData::get_neighbor_dof_indices() const + { + return neighbor_dof_indices; + } + + + + template + GeneralDataStorage & + ScratchData::get_general_data_storage() + { + return user_data_storage; + } + + + + template + const Mapping & + ScratchData::get_mapping() const + { + return *mapping; + } + +} // namespace MeshWorker +DEAL_II_NAMESPACE_CLOSE + +// Explicit instantiations +DEAL_II_NAMESPACE_OPEN +namespace MeshWorker +{ +#include "scratch_data.inst" +} +DEAL_II_NAMESPACE_CLOSE \ No newline at end of file diff --git a/source/meshworker/scratch_data.inst.in b/source/meshworker/scratch_data.inst.in new file mode 100644 index 000000000000..96eb79e413d1 --- /dev/null +++ b/source/meshworker/scratch_data.inst.in @@ -0,0 +1,23 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + +for (deal_II_dimension : DIMENSIONS; deal_II_space_dimension : SPACE_DIMENSIONS) + { +#if deal_II_dimension <= deal_II_space_dimension + template class ScratchData; + +#endif + } From 6081ccfebeedef8ee769fb45ef46d3cff966b3fd Mon Sep 17 00:00:00 2001 From: Luca Heltai Date: Tue, 9 Apr 2019 23:04:47 +0200 Subject: [PATCH 388/507] Test ScratchData on simple volume computation --- tests/meshworker/scratch_data_01.cc | 141 ++++++++++++++++++++++++ tests/meshworker/scratch_data_01.output | 13 +++ 2 files changed, 154 insertions(+) create mode 100644 tests/meshworker/scratch_data_01.cc create mode 100644 tests/meshworker/scratch_data_01.output diff --git a/tests/meshworker/scratch_data_01.cc b/tests/meshworker/scratch_data_01.cc new file mode 100644 index 000000000000..52dec187939e --- /dev/null +++ b/tests/meshworker/scratch_data_01.cc @@ -0,0 +1,141 @@ +/* --------------------------------------------------------------------- + * + * Copyright (C) 2019 by the deal.II authors + * + * This file is part of the deal.II library. + * + * The deal.II library is free software; you can use it, redistribute + * it, and/or modify it under the terms of the GNU Lesser General + * Public License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * The full text of the license can be found in the file LICENSE.md at + * the top level directory of deal.II. + * + * --------------------------------------------------------------------- + */ + +// Test ScratchData on simple volume computation + +#include +#include +#include +#include + +#include +#include +#include + +#include +#include +#include +#include + +#include "../tests.h" + +using namespace MeshWorker; + +template +void +test() +{ + Triangulation tria; + FE_Q fe(1); + DoFHandler dh(tria); + GridGenerator::hyper_cube(tria); + tria.refine_global(1); + tria.begin_active()->set_refine_flag(); + tria.execute_coarsening_and_refinement(); + dh.distribute_dofs(fe); + + QGauss quad(3); + QGauss face_quad(3); + + UpdateFlags cell_flags = update_JxW_values; + UpdateFlags face_flags = update_JxW_values; + + using ScratchData = MeshWorker::ScratchData; + using CopyData = MeshWorker::CopyData<0, 1, 0>; + + ScratchData scratch(fe, quad, cell_flags, face_quad, face_flags); + CopyData copy(3); // store measures + + auto cell = dh.begin_active(); + auto endc = dh.end(); + + typedef decltype(cell) Iterator; + + auto measures = std::make_tuple(0.0, 0.0, 0.0); + + + auto cell_worker = [](const Iterator &cell, ScratchData &s, CopyData &c) { + const auto &fev = s.reinit(cell); + const auto &JxW = s.get_JxW_values(); + c = 0; + for (auto w : JxW) + c.vectors[0][0] += w; + }; + + auto boundary_worker = [](const Iterator & cell, + const unsigned int &f, + ScratchData & s, + CopyData & c) { + const auto &fev = s.reinit(cell, f); + const auto &JxW = s.get_JxW_values(); + for (auto w : JxW) + c.vectors[0][1] += w; + }; + + auto face_worker = [](const Iterator & cell, + const unsigned int &f, + const unsigned int &sf, + const Iterator & ncell, + const unsigned int &nf, + const unsigned int &nsf, + ScratchData & s, + CopyData & c) { + const auto &fev = s.reinit(cell, f, sf); + const auto &nfev = s.reinit_neighbor(ncell, nf, nsf); + + const auto &JxW = s.get_JxW_values(); + const auto &nJxW = s.get_neighbor_JxW_values(); + for (auto w : JxW) + c.vectors[0][2] += w; + }; + + auto copier = [&measures](const CopyData &c) { + std::get<0>(measures) += c.vectors[0][0]; + std::get<1>(measures) += c.vectors[0][1]; + std::get<2>(measures) += c.vectors[0][2]; + }; + + mesh_loop(cell, + endc, + cell_worker, + copier, + scratch, + copy, + assemble_own_cells | assemble_boundary_faces | + assemble_own_interior_faces_once, + boundary_worker, + face_worker); + + deallog << "Testing <" << dim << "," << spacedim << ">" << std::endl; + + deallog << "Volume: " << std::get<0>(measures) << std::endl; + + deallog << "Boundary surface: " << std::get<1>(measures) << std::endl; + + deallog << "Interior surface: " << std::get<2>(measures) << std::endl; +} + + + +int +main() +{ + initlog(); + + test<2, 2>(); + test<2, 3>(); + test<3, 3>(); +} diff --git a/tests/meshworker/scratch_data_01.output b/tests/meshworker/scratch_data_01.output new file mode 100644 index 000000000000..b9c1ecd3d347 --- /dev/null +++ b/tests/meshworker/scratch_data_01.output @@ -0,0 +1,13 @@ + +DEAL::Testing <2,2> +DEAL::Volume: 1.00000 +DEAL::Boundary surface: 4.00000 +DEAL::Interior surface: 3.00000 +DEAL::Testing <2,3> +DEAL::Volume: 1.00000 +DEAL::Boundary surface: 4.00000 +DEAL::Interior surface: 3.00000 +DEAL::Testing <3,3> +DEAL::Volume: 1.00000 +DEAL::Boundary surface: 6.00000 +DEAL::Interior surface: 3.75000 From ccfcc960d721d97b3f790cb8da342c46b3868eca Mon Sep 17 00:00:00 2001 From: Luca Heltai Date: Tue, 9 Apr 2019 23:04:56 +0200 Subject: [PATCH 389/507] Test ScratchData for Laplacian (conforming) --- tests/meshworker/scratch_data_02.cc | 159 ++++++++++++++++++ ...02.with_muparser=on.with_umfpack=on.output | 2 + 2 files changed, 161 insertions(+) create mode 100644 tests/meshworker/scratch_data_02.cc create mode 100644 tests/meshworker/scratch_data_02.with_muparser=on.with_umfpack=on.output diff --git a/tests/meshworker/scratch_data_02.cc b/tests/meshworker/scratch_data_02.cc new file mode 100644 index 000000000000..d74bc90b0579 --- /dev/null +++ b/tests/meshworker/scratch_data_02.cc @@ -0,0 +1,159 @@ +/* --------------------------------------------------------------------- + * + * Copyright (C) 2018 by the deal.II authors + * + * This file is part of the deal.II library. + * + * The deal.II library is free software; you can use it, redistribute + * it, and/or modify it under the terms of the GNU Lesser General + * Public License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * The full text of the license can be found in the file LICENSE.md at + * the top level directory of deal.II. + * + * --------------------------------------------------------------------- + */ + +// Check mesh_loop + ScratchData for Laplacian (conforming) + +#include +#include +#include + +#include + +#include + +#include +#include +#include +#include +#include +#include +#include + +#include +#include + +#include +#include +#include + +#include +#include + +#include +#include +#include +#include + +#include "../tests.h" + +using namespace MeshWorker; + +template +void +test() +{ + Triangulation tria; + FE_Q fe(1); + DoFHandler dh(tria); + + FunctionParser rhs_function("1"); + FunctionParser boundary_function("0"); + + AffineConstraints constraints; + + GridGenerator::hyper_cube(tria); + tria.refine_global(5); + tria.execute_coarsening_and_refinement(); + dh.distribute_dofs(fe); + + + DoFTools::make_hanging_node_constraints(dh, constraints); + VectorTools::interpolate_boundary_values(dh, + 0, + boundary_function, + constraints); + + constraints.close(); + + SparsityPattern sparsity; + + { + DynamicSparsityPattern dsp(dh.n_dofs(), dh.n_dofs()); + DoFTools::make_flux_sparsity_pattern(dh, dsp); + sparsity.copy_from(dsp); + } + + SparseMatrix matrix; + matrix.reinit(sparsity); + + Vector solution(dh.n_dofs()); + Vector rhs(dh.n_dofs()); + + QGauss quad(3); + QGauss face_quad(3); + + UpdateFlags cell_flags = update_values | update_gradients | + update_quadrature_points | update_JxW_values; + UpdateFlags face_flags = update_JxW_values; + + using ScratchData = MeshWorker::ScratchData; + using CopyData = MeshWorker::CopyData<1, 1, 1>; + + ScratchData scratch(fe, quad, cell_flags, face_quad, face_flags); + CopyData copy(fe.dofs_per_cell); + + auto cell = dh.begin_active(); + auto endc = dh.end(); + + typedef decltype(cell) Iterator; + + auto cell_worker = + [&rhs_function](const Iterator &cell, ScratchData &s, CopyData &c) { + const auto &fev = s.reinit(cell); + const auto &JxW = s.get_JxW_values(); + const auto &p = s.get_quadrature_points(); + + c = 0; + + c.local_dof_indices[0] = s.get_local_dof_indices(); + + for (unsigned int q = 0; q < p.size(); ++q) + for (unsigned int i = 0; i < fev.dofs_per_cell; ++i) + { + for (unsigned int j = 0; j < fev.dofs_per_cell; ++j) + { + c.matrices[0](i, j) += + fev.shape_grad(i, q) * fev.shape_grad(j, q) * JxW[q]; + } + c.vectors[0](i) += + fev.shape_value(i, q) * rhs_function.value(p[q]) * JxW[q]; + } + }; + + auto copier = [&constraints, &matrix, &rhs](const CopyData &c) { + constraints.distribute_local_to_global( + c.matrices[0], c.vectors[0], c.local_dof_indices[0], matrix, rhs); + }; + + mesh_loop(cell, endc, cell_worker, copier, scratch, copy, assemble_own_cells); + + SparseDirectUMFPACK inv; + inv.initialize(matrix); + + inv.vmult(solution, rhs); + constraints.distribute(solution); + + deallog << "Linfty norm of solution: " << solution.linfty_norm() << std::endl; +} + + +int +main() +{ + initlog(); + + test<2, 2>(); +} diff --git a/tests/meshworker/scratch_data_02.with_muparser=on.with_umfpack=on.output b/tests/meshworker/scratch_data_02.with_muparser=on.with_umfpack=on.output new file mode 100644 index 000000000000..b5ad838ee801 --- /dev/null +++ b/tests/meshworker/scratch_data_02.with_muparser=on.with_umfpack=on.output @@ -0,0 +1,2 @@ + +DEAL::Linfty norm of solution: 0.0737281 From 7d6357304090cccb8407443d95cf90be94012eed Mon Sep 17 00:00:00 2001 From: Luca Heltai Date: Tue, 9 Apr 2019 23:05:08 +0200 Subject: [PATCH 390/507] Test ScratchData for Laplacian (SIPDG) --- tests/meshworker/scratch_data_03.cc | 240 ++++++++++++++++++ ...03.with_muparser=on.with_umfpack=on.output | 2 + 2 files changed, 242 insertions(+) create mode 100644 tests/meshworker/scratch_data_03.cc create mode 100644 tests/meshworker/scratch_data_03.with_muparser=on.with_umfpack=on.output diff --git a/tests/meshworker/scratch_data_03.cc b/tests/meshworker/scratch_data_03.cc new file mode 100644 index 000000000000..c8dd6ebf9a52 --- /dev/null +++ b/tests/meshworker/scratch_data_03.cc @@ -0,0 +1,240 @@ +/* --------------------------------------------------------------------- + * + * Copyright (C) 2018 by the deal.II authors + * + * This file is part of the deal.II library. + * + * The deal.II library is free software; you can use it, redistribute + * it, and/or modify it under the terms of the GNU Lesser General + * Public License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * The full text of the license can be found in the file LICENSE.md at + * the top level directory of deal.II. + * + * --------------------------------------------------------------------- + */ + +// Solve Laplacian using SIPG + mesh_loop + ScratchData + +#include +#include +#include + +#include + +#include + +#include +#include +#include +#include +#include +#include +#include + +#include +#include + +#include +#include +#include + +#include +#include + +#include +#include +#include +#include + +#include "../tests.h" + +using namespace MeshWorker; + +template +void +test() +{ + Triangulation tria; + FE_DGQ fe(1); + DoFHandler dh(tria); + + FunctionParser rhs_function("1"); + FunctionParser boundary_function("0"); + + AffineConstraints constraints; + constraints.close(); + + GridGenerator::hyper_cube(tria); + tria.refine_global(5); + tria.execute_coarsening_and_refinement(); + dh.distribute_dofs(fe); + + + SparsityPattern sparsity; + + { + DynamicSparsityPattern dsp(dh.n_dofs(), dh.n_dofs()); + DoFTools::make_flux_sparsity_pattern(dh, dsp); + sparsity.copy_from(dsp); + } + + SparseMatrix matrix; + matrix.reinit(sparsity); + + Vector solution(dh.n_dofs()); + Vector rhs(dh.n_dofs()); + + QGauss quad(3); + QGauss face_quad(3); + + UpdateFlags cell_flags = update_values | update_gradients | + update_quadrature_points | update_JxW_values; + UpdateFlags face_flags = update_values | update_gradients | + update_quadrature_points | + update_face_normal_vectors | update_JxW_values; + + // Stabilization for SIPG + double gamma = 100; + + using ScratchData = MeshWorker::ScratchData; + using CopyData = MeshWorker::CopyData<1 + GeometryInfo::faces_per_cell, + 1, + 1 + GeometryInfo::faces_per_cell>; + + ScratchData scratch(fe, quad, cell_flags, face_quad, face_flags); + CopyData copy(fe.dofs_per_cell); + + auto cell = dh.begin_active(); + auto endc = dh.end(); + + typedef decltype(cell) Iterator; + + auto cell_worker = + [&rhs_function](const Iterator &cell, ScratchData &s, CopyData &c) { + const auto &fev = s.reinit(cell); + const auto &JxW = s.get_JxW_values(); + const auto &p = s.get_quadrature_points(); + + c = 0; + + c.local_dof_indices[0] = s.get_local_dof_indices(); + + for (unsigned int q = 0; q < p.size(); ++q) + for (unsigned int i = 0; i < fev.dofs_per_cell; ++i) + { + for (unsigned int j = 0; j < fev.dofs_per_cell; ++j) + { + c.matrices[0](i, j) += + fev.shape_grad(i, q) * fev.shape_grad(j, q) * JxW[q]; + } + c.vectors[0](i) += + fev.shape_value(i, q) * rhs_function.value(p[q]) * JxW[q]; + } + }; + + auto boundary_worker = [gamma, &boundary_function](const Iterator & cell, + const unsigned int &f, + ScratchData & s, + CopyData & c) { + const auto &fev = s.reinit(cell, f); + const auto &JxW = s.get_JxW_values(); + const auto &p = s.get_quadrature_points(); + const auto &n = s.get_normal_vectors(); + + for (unsigned int q = 0; q < p.size(); ++q) + for (unsigned int i = 0; i < fev.dofs_per_cell; ++i) + { + for (unsigned int j = 0; j < fev.dofs_per_cell; ++j) + { + c.matrices[0](i, j) += + (-fev.shape_grad(i, q) * n[q] * fev.shape_value(j, q) + + -fev.shape_grad(j, q) * n[q] * fev.shape_value(i, q) + + gamma / cell->face(f)->diameter() * fev.shape_value(i, q) * + fev.shape_value(j, q)) * + JxW[q]; + } + c.vectors[0](i) += + ((gamma / cell->face(f)->diameter() * fev.shape_value(i, q) - + fev.shape_grad(i, q) * n[q]) * + boundary_function.value(p[q])) * + JxW[q]; + } + }; + + auto face_worker = [gamma](const Iterator & cell, + const unsigned int &f, + const unsigned int &sf, + const Iterator & ncell, + const unsigned int &nf, + const unsigned int &nsf, + ScratchData & s, + CopyData & c) { + const auto &fev = s.reinit(cell, f, sf); + const auto &JxW = s.get_JxW_values(); + const auto &nfev = s.reinit_neighbor(ncell, nf, nsf); + + c.local_dof_indices[f + 1] = s.get_neighbor_dof_indices(); + + const auto &p = s.get_quadrature_points(); + const auto &n = s.get_normal_vectors(); + const auto &nn = s.get_neighbor_normal_vectors(); + + const double gh = gamma / cell->face(f)->diameter(); + + for (unsigned int q = 0; q < p.size(); ++q) + for (unsigned int i = 0; i < fev.dofs_per_cell; ++i) + for (unsigned int j = 0; j < fev.dofs_per_cell; ++j) + { + c.matrices[0](i, j) += + (-.5 * fev.shape_grad(i, q) * n[q] * fev.shape_value(j, q) + + -.5 * fev.shape_value(i, q) * n[q] * fev.shape_grad(j, q) + + gh * fev.shape_value(i, q) * fev.shape_value(j, q)) * + JxW[q]; + + c.matrices[f + 1](i, j) += + (-.5 * fev.shape_grad(i, q) * nn[q] * nfev.shape_value(j, q) + + -.5 * fev.shape_value(i, q) * n[q] * nfev.shape_grad(j, q) - + gh * fev.shape_value(i, q) * nfev.shape_value(j, q)) * + JxW[q]; + } + }; + + auto copier = [&constraints, &matrix, &rhs](const CopyData &c) { + constraints.distribute_local_to_global( + c.matrices[0], c.vectors[0], c.local_dof_indices[0], matrix, rhs); + + for (unsigned int f = 0; f < GeometryInfo::faces_per_cell; ++f) + constraints.distribute_local_to_global(c.matrices[1 + f], + c.local_dof_indices[0], + c.local_dof_indices[1 + f], + matrix); + }; + + mesh_loop(cell, + endc, + cell_worker, + copier, + scratch, + copy, + assemble_own_cells | assemble_boundary_faces | + assemble_own_interior_faces_both, + boundary_worker, + face_worker); + + SparseDirectUMFPACK inv; + inv.initialize(matrix); + + inv.vmult(solution, rhs); + constraints.distribute(solution); + + deallog << "Linfty norm of solution " << solution.linfty_norm() << std::endl; +} + + +int +main() +{ + initlog(); + test<2, 2>(); +} diff --git a/tests/meshworker/scratch_data_03.with_muparser=on.with_umfpack=on.output b/tests/meshworker/scratch_data_03.with_muparser=on.with_umfpack=on.output new file mode 100644 index 000000000000..1b2777af1658 --- /dev/null +++ b/tests/meshworker/scratch_data_03.with_muparser=on.with_umfpack=on.output @@ -0,0 +1,2 @@ + +DEAL::Linfty norm of solution 0.0737281 From c4a8e9cadee0a4e53eeca593bddc52265189d636 Mon Sep 17 00:00:00 2001 From: Luca Heltai Date: Tue, 9 Apr 2019 23:05:17 +0200 Subject: [PATCH 391/507] Test ScratchData get_values --- tests/meshworker/scratch_data_04.cc | 131 ++++++++++++++++++ .../scratch_data_04.with_muparser=on.output | 2 + 2 files changed, 133 insertions(+) create mode 100644 tests/meshworker/scratch_data_04.cc create mode 100644 tests/meshworker/scratch_data_04.with_muparser=on.output diff --git a/tests/meshworker/scratch_data_04.cc b/tests/meshworker/scratch_data_04.cc new file mode 100644 index 000000000000..48877551557f --- /dev/null +++ b/tests/meshworker/scratch_data_04.cc @@ -0,0 +1,131 @@ +/* --------------------------------------------------------------------- + * + * Copyright (C) 2018 by the deal.II authors + * + * This file is part of the deal.II library. + * + * The deal.II library is free software; you can use it, redistribute + * it, and/or modify it under the terms of the GNU Lesser General + * Public License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * The full text of the license can be found in the file LICENSE.md at + * the top level directory of deal.II. + * + * --------------------------------------------------------------------- + */ + +// Compute integral of known function using mesh_loop and ScratchData + +#include +#include +#include + +#include + +#include +#include + +#include +#include +#include +#include +#include +#include +#include + +#include +#include + +#include +#include +#include + +#include +#include + +#include +#include +#include +#include + +#include "../tests.h" + +using namespace MeshWorker; + +template +void +test() +{ + Triangulation tria; + FE_Q fe(1); + DoFHandler dh(tria); + + FunctionParser integral_function("x"); + GridGenerator::hyper_cube(tria); + tria.refine_global(5); + tria.execute_coarsening_and_refinement(); + dh.distribute_dofs(fe); + + Vector solution(dh.n_dofs()); + + VectorTools::interpolate(dh, integral_function, solution); + + QGauss quad(3); + + UpdateFlags cell_flags = update_values | update_gradients | + update_quadrature_points | update_JxW_values; + + using ScratchData = ScratchData; + struct CopyData + {}; + + + double H1_norm = 0; + FEValuesExtractors::Scalar scalar(0); + + ScratchData scratch(fe, quad, cell_flags); + CopyData copy; + + auto cell = dh.begin_active(); + auto endc = dh.end(); + + typedef decltype(cell) Iterator; + + + auto cell_integrator = [&H1_norm, &solution, &scalar](const Iterator &cell, + ScratchData & s, + CopyData & c) { + const auto &fev = s.reinit(cell); + const auto &JxW = s.get_JxW_values(); + + s.extract_local_dof_values("solution", solution); + + const auto &u = s.get_values("solution", scalar); + const auto &grad_u = s.get_gradients("solution", scalar); + + for (unsigned int q = 0; q < u.size(); ++q) + H1_norm += (u[q] * u[q] + grad_u[q] * grad_u[q]) * JxW[q]; + }; + + const auto empty_copyer = [](const CopyData &) {}; + + mesh_loop(cell, + endc, + cell_integrator, + empty_copyer, + scratch, + copy, + assemble_own_cells); + + deallog << "H1 norm: " << std::sqrt(H1_norm) << std::endl; +} + + +int +main() +{ + initlog(1); + MultithreadInfo::set_thread_limit(1); // to make output deterministic + + test<2, 2>(); +} diff --git a/tests/meshworker/scratch_data_04.with_muparser=on.output b/tests/meshworker/scratch_data_04.with_muparser=on.output new file mode 100644 index 000000000000..b906801d0d6e --- /dev/null +++ b/tests/meshworker/scratch_data_04.with_muparser=on.output @@ -0,0 +1,2 @@ + +DEAL::H1 norm: 1.15470 From da5071eb97fb2c287e666f7da846ac0f61d18421 Mon Sep 17 00:00:00 2001 From: Luca Heltai Date: Tue, 9 Apr 2019 23:05:28 +0200 Subject: [PATCH 392/507] ScratchData with Sacado applied to Residual --- tests/meshworker/scratch_data_05.cc | 178 ++++++++++++++++++ ...on.with_muparser=on.with_umfpack=on.output | 2 + 2 files changed, 180 insertions(+) create mode 100644 tests/meshworker/scratch_data_05.cc create mode 100644 tests/meshworker/scratch_data_05.with_trilinos=on.with_muparser=on.with_umfpack=on.output diff --git a/tests/meshworker/scratch_data_05.cc b/tests/meshworker/scratch_data_05.cc new file mode 100644 index 000000000000..1d72bead03b8 --- /dev/null +++ b/tests/meshworker/scratch_data_05.cc @@ -0,0 +1,178 @@ +/* --------------------------------------------------------------------- + * + * Copyright (C) 2018 by the deal.II authors + * + * This file is part of the deal.II library. + * + * The deal.II library is free software; you can use it, redistribute + * it, and/or modify it under the terms of the GNU Lesser General + * Public License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * The full text of the license can be found in the file LICENSE.md at + * the top level directory of deal.II. + * + * --------------------------------------------------------------------- + */ + +// Compute Laplacian using mesh_loop, sacado, and ScratchData + +#include +#include +#include + +#include + +#include +#include + +#include +#include +#include +#include +#include +#include +#include + +#include +#include + +#include +#include +#include + +#include +#include + +#include + +#include +#include +#include +#include + +#include "../tests.h" + +using namespace MeshWorker; + +typedef Sacado::Fad::DFad Sdouble; +typedef Sacado::Fad::DFad SSdouble; + +template +void +test() +{ + Triangulation tria; + FE_Q fe(1); + DoFHandler dh(tria); + + FunctionParser rhs_function("1"); + FunctionParser boundary_function("0"); + + AffineConstraints constraints; + + GridGenerator::hyper_cube(tria); + tria.refine_global(5); + tria.execute_coarsening_and_refinement(); + dh.distribute_dofs(fe); + + + DoFTools::make_hanging_node_constraints(dh, constraints); + VectorTools::interpolate_boundary_values(dh, + 0, + boundary_function, + constraints); + + constraints.close(); + + SparsityPattern sparsity; + + { + DynamicSparsityPattern dsp(dh.n_dofs(), dh.n_dofs()); + DoFTools::make_flux_sparsity_pattern(dh, dsp); + sparsity.copy_from(dsp); + } + + SparseMatrix matrix; + matrix.reinit(sparsity); + + Vector solution(dh.n_dofs()); + Vector rhs(dh.n_dofs()); + + QGauss quad(3); + + UpdateFlags cell_flags = update_values | update_gradients | + update_quadrature_points | update_JxW_values; + + using ScratchData = MeshWorker::ScratchData; + using CopyData = MeshWorker::CopyData<1, 1, 1>; + + ScratchData scratch(fe, quad, cell_flags); + CopyData copy(fe.dofs_per_cell); + + auto cell = dh.begin_active(); + auto endc = dh.end(); + + typedef decltype(cell) Iterator; + + FEValuesExtractors::Scalar scalar(0); + + auto cell_worker = [&rhs_function, &solution, &scalar](const Iterator &cell, + ScratchData & s, + CopyData & c) { + const auto &fev = s.reinit(cell); + const auto &JxW = s.get_JxW_values(); + const auto &p = s.get_quadrature_points(); + + Sdouble dummy; + std::vector residual(fev.dofs_per_cell, Sdouble(0)); + + s.extract_local_dof_values("solution", solution, dummy); + const auto &u = s.get_values("solution", scalar, dummy); + const auto &grad_u = s.get_gradients("solution", scalar, dummy); + + c = 0; + + c.local_dof_indices[0] = s.get_local_dof_indices(); + + for (unsigned int i = 0; i < fev.dofs_per_cell; ++i) + for (unsigned int q = 0; q < p.size(); ++q) + { + residual[i] += (fev.shape_grad(i, q) * grad_u[q] - + rhs_function.value(p[q]) * fev.shape_value(i, q)) * + JxW[q]; + } + + // Copy from Sacado to normal vectors + for (unsigned int i = 0; i < fev.dofs_per_cell; ++i) + { + c.vectors[0][i] = -residual[i].val(); + for (unsigned int j = 0; j < fev.dofs_per_cell; ++j) + c.matrices[0](i, j) = residual[i].dx(j); + } + }; + + auto copier = [&constraints, &matrix, &rhs](const CopyData &c) { + constraints.distribute_local_to_global( + c.matrices[0], c.vectors[0], c.local_dof_indices[0], matrix, rhs); + }; + + mesh_loop(cell, endc, cell_worker, copier, scratch, copy, assemble_own_cells); + + SparseDirectUMFPACK inv; + inv.initialize(matrix); + + inv.vmult(solution, rhs); + constraints.distribute(solution); + + deallog << "Linfty norm of solution: " << solution.linfty_norm() << std::endl; +} + + +int +main() +{ + initlog(1); + MultithreadInfo::set_thread_limit(1); // to make output deterministic + + test<2, 2>(); +} diff --git a/tests/meshworker/scratch_data_05.with_trilinos=on.with_muparser=on.with_umfpack=on.output b/tests/meshworker/scratch_data_05.with_trilinos=on.with_muparser=on.with_umfpack=on.output new file mode 100644 index 000000000000..b5ad838ee801 --- /dev/null +++ b/tests/meshworker/scratch_data_05.with_trilinos=on.with_muparser=on.with_umfpack=on.output @@ -0,0 +1,2 @@ + +DEAL::Linfty norm of solution: 0.0737281 From 07af92a315cbe64494ecc6e38912d74c846fde10 Mon Sep 17 00:00:00 2001 From: Luca Heltai Date: Tue, 9 Apr 2019 23:05:35 +0200 Subject: [PATCH 393/507] ScratchData + Sacado applied to energies --- tests/meshworker/scratch_data_06.cc | 177 ++++++++++++++++++ ...on.with_muparser=on.with_umfpack=on.output | 2 + 2 files changed, 179 insertions(+) create mode 100644 tests/meshworker/scratch_data_06.cc create mode 100644 tests/meshworker/scratch_data_06.with_trilinos=on.with_muparser=on.with_umfpack=on.output diff --git a/tests/meshworker/scratch_data_06.cc b/tests/meshworker/scratch_data_06.cc new file mode 100644 index 000000000000..9dd081d08264 --- /dev/null +++ b/tests/meshworker/scratch_data_06.cc @@ -0,0 +1,177 @@ +/* --------------------------------------------------------------------- + * + * Copyright (C) 2018 by the deal.II authors + * + * This file is part of the deal.II library. + * + * The deal.II library is free software; you can use it, redistribute + * it, and/or modify it under the terms of the GNU Lesser General + * Public License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * The full text of the license can be found in the file LICENSE.md at + * the top level directory of deal.II. + * + * --------------------------------------------------------------------- + */ + +// Compute Laplacian using mesh_loop, sacado, ScratchData, with +// second derivatives. + +#include +#include +#include + +#include + +#include +#include + +#include +#include +#include +#include +#include +#include +#include + +#include +#include + +#include +#include +#include + +#include +#include + +#include + +#include +#include +#include +#include + +#include "../tests.h" + +using namespace MeshWorker; + +typedef Sacado::Fad::DFad Sdouble; +typedef Sacado::Fad::DFad SSdouble; + +template +void +test() +{ + Triangulation tria; + FE_Q fe(1); + DoFHandler dh(tria); + + FunctionParser rhs_function("1"); + FunctionParser boundary_function("0"); + + AffineConstraints constraints; + + GridGenerator::hyper_cube(tria); + tria.refine_global(5); + tria.execute_coarsening_and_refinement(); + dh.distribute_dofs(fe); + + + DoFTools::make_hanging_node_constraints(dh, constraints); + VectorTools::interpolate_boundary_values(dh, + 0, + boundary_function, + constraints); + + constraints.close(); + + SparsityPattern sparsity; + + { + DynamicSparsityPattern dsp(dh.n_dofs(), dh.n_dofs()); + DoFTools::make_flux_sparsity_pattern(dh, dsp); + sparsity.copy_from(dsp); + } + + SparseMatrix matrix; + matrix.reinit(sparsity); + + Vector solution(dh.n_dofs()); + Vector rhs(dh.n_dofs()); + + QGauss quad(3); + + UpdateFlags cell_flags = update_values | update_gradients | + update_quadrature_points | update_JxW_values; + + using ScratchData = MeshWorker::ScratchData; + using CopyData = MeshWorker::CopyData<1, 1, 1>; + + ScratchData scratch(fe, quad, cell_flags); + CopyData copy(fe.dofs_per_cell); + + auto cell = dh.begin_active(); + auto endc = dh.end(); + + typedef decltype(cell) Iterator; + + FEValuesExtractors::Scalar scalar(0); + + auto cell_worker = [&rhs_function, &solution, &scalar](const Iterator &cell, + ScratchData & s, + CopyData & c) { + const auto &fev = s.reinit(cell); + const auto &JxW = s.get_JxW_values(); + const auto &p = s.get_quadrature_points(); + + SSdouble energy(0); + + s.extract_local_dof_values("solution", solution, energy); + const auto &u = s.get_values("solution", scalar, energy); + const auto &grad_u = s.get_gradients("solution", scalar, energy); + + c = 0; + + c.local_dof_indices[0] = s.get_local_dof_indices(); + + for (unsigned int q = 0; q < p.size(); ++q) + { + energy += + (.5 * grad_u[q] * grad_u[q] - rhs_function.value(p[q]) * u[q]) * + JxW[q]; + } + + // Copy from Sacado to normal vectors + for (unsigned int i = 0; i < fev.dofs_per_cell; ++i) + { + c.vectors[0][i] = -energy.dx(i).val(); + for (unsigned int j = 0; j < fev.dofs_per_cell; ++j) + c.matrices[0](i, j) = energy.dx(i).dx(j); + } + }; + + auto copier = [&constraints, &matrix, &rhs](const CopyData &c) { + constraints.distribute_local_to_global( + c.matrices[0], c.vectors[0], c.local_dof_indices[0], matrix, rhs); + }; + + mesh_loop(cell, endc, cell_worker, copier, scratch, copy, assemble_own_cells); + + SparseDirectUMFPACK inv; + inv.initialize(matrix); + + inv.vmult(solution, rhs); + constraints.distribute(solution); + + deallog << "Linfty norm of solution: " << solution.linfty_norm() << std::endl; +} + + +int +main() +{ + initlog(1); + MultithreadInfo::set_thread_limit(1); // to make output deterministic + + test<2, 2>(); +} diff --git a/tests/meshworker/scratch_data_06.with_trilinos=on.with_muparser=on.with_umfpack=on.output b/tests/meshworker/scratch_data_06.with_trilinos=on.with_muparser=on.with_umfpack=on.output new file mode 100644 index 000000000000..b5ad838ee801 --- /dev/null +++ b/tests/meshworker/scratch_data_06.with_trilinos=on.with_muparser=on.with_umfpack=on.output @@ -0,0 +1,2 @@ + +DEAL::Linfty norm of solution: 0.0737281 From f9f9254334e929bfa5cc6ddc92452610eb8efdcf Mon Sep 17 00:00:00 2001 From: Luca Heltai Date: Tue, 9 Apr 2019 23:05:47 +0200 Subject: [PATCH 394/507] ScratchData + Sacado FD+RD applied to energies --- tests/meshworker/scratch_data_07.cc | 185 ++++++++++++++++++ ...on.with_muparser=on.with_umfpack=on.output | 2 + 2 files changed, 187 insertions(+) create mode 100644 tests/meshworker/scratch_data_07.cc create mode 100644 tests/meshworker/scratch_data_07.with_trilinos=on.with_muparser=on.with_umfpack=on.output diff --git a/tests/meshworker/scratch_data_07.cc b/tests/meshworker/scratch_data_07.cc new file mode 100644 index 000000000000..a1a4b13aee4f --- /dev/null +++ b/tests/meshworker/scratch_data_07.cc @@ -0,0 +1,185 @@ +/* --------------------------------------------------------------------- + * + * Copyright (C) 2018 by the deal.II authors + * + * This file is part of the deal.II library. + * + * The deal.II library is free software; you can use it, redistribute + * it, and/or modify it under the terms of the GNU Lesser General + * Public License as published by the Free Software Foundation; either + * version 2.1 of the License, or (at your option) any later version. + * The full text of the license can be found in the file LICENSE.md at + * the top level directory of deal.II. + * + * --------------------------------------------------------------------- + */ + +// Compute Laplacian using mesh_loop, sacado, ScratchData, with +// second derivatives, using forward and backward derivatives. + +#include +#include +#include + +#include + +#include +#include + +#include +#include +#include +#include +#include +#include +#include + +#include +#include + +#include +#include +#include + +#include +#include + +#include + +#include +#include +#include +#include + +#include "../tests.h" + +using namespace MeshWorker; + +typedef Sacado::Fad::DFad Sdouble; +typedef Sacado::Fad::DFad SSdouble; +typedef Sacado::Rad::ADvar RSdouble; + +template +void +test() +{ + Triangulation tria; + FE_Q fe(1); + DoFHandler dh(tria); + + FunctionParser rhs_function("1"); + FunctionParser boundary_function("0"); + + AffineConstraints constraints; + + GridGenerator::hyper_cube(tria); + tria.refine_global(5); + tria.execute_coarsening_and_refinement(); + dh.distribute_dofs(fe); + + + DoFTools::make_hanging_node_constraints(dh, constraints); + VectorTools::interpolate_boundary_values(dh, + 0, + boundary_function, + constraints); + + constraints.close(); + + SparsityPattern sparsity; + + { + DynamicSparsityPattern dsp(dh.n_dofs(), dh.n_dofs()); + DoFTools::make_flux_sparsity_pattern(dh, dsp); + sparsity.copy_from(dsp); + } + + SparseMatrix matrix; + matrix.reinit(sparsity); + + Vector solution(dh.n_dofs()); + Vector rhs(dh.n_dofs()); + + QGauss quad(3); + + UpdateFlags cell_flags = update_values | update_gradients | + update_quadrature_points | update_JxW_values; + + using ScratchData = MeshWorker::ScratchData; + using CopyData = MeshWorker::CopyData<1, 1, 1>; + + ScratchData scratch(fe, quad, cell_flags); + CopyData copy(fe.dofs_per_cell); + + auto cell = dh.begin_active(); + auto endc = dh.end(); + + typedef decltype(cell) Iterator; + + FEValuesExtractors::Scalar scalar(0); + + auto cell_worker = [&rhs_function, &solution, &scalar](const Iterator &cell, + ScratchData & s, + CopyData & c) { + const auto &fev = s.reinit(cell); + const auto &JxW = s.get_JxW_values(); + const auto &p = s.get_quadrature_points(); + + RSdouble energy(0); + + s.extract_local_dof_values("solution", solution, energy); + const auto &local_dof_values = s.get_local_dof_values("solution", energy); + const auto &u = s.get_values("solution", scalar, energy); + const auto &grad_u = s.get_gradients("solution", scalar, energy); + + c = 0; + + c.local_dof_indices[0] = s.get_local_dof_indices(); + + for (unsigned int q = 0; q < p.size(); ++q) + { + energy += + (.5 * grad_u[q] * grad_u[q] - rhs_function.value(p[q]) * u[q]) * + JxW[q]; + } + + // Compute derivatives of reverse-mode AD variables + RSdouble::Gradcomp(); + // Copy from Sacado to normal vectors + for (unsigned int i = 0; i < fev.dofs_per_cell; ++i) + { + // Compute the residual + const auto res_i = local_dof_values[i].adj(); + c.vectors[0][i] = -res_i.val(); + + // And the matrix + for (unsigned int j = 0; j < fev.dofs_per_cell; ++j) + c.matrices[0](i, j) = res_i.dx(j); + } + }; + + auto copier = [&constraints, &matrix, &rhs](const CopyData &c) { + constraints.distribute_local_to_global( + c.matrices[0], c.vectors[0], c.local_dof_indices[0], matrix, rhs); + }; + + mesh_loop(cell, endc, cell_worker, copier, scratch, copy, assemble_own_cells); + + SparseDirectUMFPACK inv; + inv.initialize(matrix); + + inv.vmult(solution, rhs); + constraints.distribute(solution); + + deallog << "Linfty norm of solution: " << solution.linfty_norm() << std::endl; +} + + +int +main() +{ + initlog(1); + MultithreadInfo::set_thread_limit(1); // to make output deterministic + + test<2, 2>(); +} diff --git a/tests/meshworker/scratch_data_07.with_trilinos=on.with_muparser=on.with_umfpack=on.output b/tests/meshworker/scratch_data_07.with_trilinos=on.with_muparser=on.with_umfpack=on.output new file mode 100644 index 000000000000..b5ad838ee801 --- /dev/null +++ b/tests/meshworker/scratch_data_07.with_trilinos=on.with_muparser=on.with_umfpack=on.output @@ -0,0 +1,2 @@ + +DEAL::Linfty norm of solution: 0.0737281 From 48301cc2693e7ce5ff3f2eb1e2b152bb1e2b1d8f Mon Sep 17 00:00:00 2001 From: Luca Heltai Date: Tue, 9 Apr 2019 23:05:59 +0200 Subject: [PATCH 395/507] ChangeLog --- doc/news/changes/minor/20190313LucaHeltai | 6 ++++++ 1 file changed, 6 insertions(+) create mode 100644 doc/news/changes/minor/20190313LucaHeltai diff --git a/doc/news/changes/minor/20190313LucaHeltai b/doc/news/changes/minor/20190313LucaHeltai new file mode 100644 index 000000000000..b3f47d11a631 --- /dev/null +++ b/doc/news/changes/minor/20190313LucaHeltai @@ -0,0 +1,6 @@ +New: Added two new classes to the MeshWorker namespace: MeshWorker::ScratchData and +MeshWorker::CopyData, that can be used as good default classes with the +WorkStream::run() and MeshWorker::mesh_loop() functions. +
    +(Luca Heltai, 2019/03/13) + From b69e909c2a8c1c4f5425c286b5404100e79aab8e Mon Sep 17 00:00:00 2001 From: Reza Rastak Date: Tue, 9 Apr 2019 22:38:14 -0700 Subject: [PATCH 396/507] Fixed documentation error in filtered_iterator.h --- include/deal.II/grid/filtered_iterator.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/include/deal.II/grid/filtered_iterator.h b/include/deal.II/grid/filtered_iterator.h index 88f47c7a3bfb..0ee727aee79b 100644 --- a/include/deal.II/grid/filtered_iterator.h +++ b/include/deal.II/grid/filtered_iterator.h @@ -849,7 +849,7 @@ namespace internal * ... * const auto filtered_iterators_range = * filter_iterators(dof_handler.active_cell_iterators(), - * IteratorFilters::LocallyOwned()); + * IteratorFilters::LocallyOwnedCell()); * for (const auto &cell : filtered_iterators_range) * { * fe_values.reinit (cell); From 431cc648927fc59e1173b7791e7655d591759835 Mon Sep 17 00:00:00 2001 From: Luca Heltai Date: Wed, 10 Apr 2019 18:50:34 +0200 Subject: [PATCH 397/507] Comments. --- include/deal.II/meshworker/copy_data.h | 6 +++--- include/deal.II/meshworker/scratch_data.h | 14 +++++++------- 2 files changed, 10 insertions(+), 10 deletions(-) diff --git a/include/deal.II/meshworker/copy_data.h b/include/deal.II/meshworker/copy_data.h index 252f4bab6e31..d3c1549e3f17 100644 --- a/include/deal.II/meshworker/copy_data.h +++ b/include/deal.II/meshworker/copy_data.h @@ -40,9 +40,9 @@ namespace MeshWorker * * In particular, you can specify the following template arguments * - * - @p n_matrices: Size of the array of matrices - * - @p n_vectors: size of the array of vectors - * - @p n_dof_indices: size of the array of local dof indices + * - @tparam n_matrices: Size of the array of matrices + * - @tparam n_vectors: size of the array of vectors + * - @tparam n_dof_indices: size of the array of local dof indices * * @author Luca Heltai, 2019. */ diff --git a/include/deal.II/meshworker/scratch_data.h b/include/deal.II/meshworker/scratch_data.h index c249357c0824..6b466286164e 100644 --- a/include/deal.II/meshworker/scratch_data.h +++ b/include/deal.II/meshworker/scratch_data.h @@ -212,15 +212,15 @@ namespace MeshWorker * When using this class, please cite * @code{.bib} * @article{SartoriGiulianiBardelloni-2018-a, - * Author = {Sartori, Alberto and Giuliani, Nicola and + * Author = {Sartori, Alberto and Giuliani, Nicola and * Bardelloni, Mauro and Heltai, Luca}, * Journal = {SoftwareX}, - * Pages = {318--327}, - * Title = {{deal2lkit: A toolkit library for high performance - * programming in deal.II}}, - * Doi = {10.1016/j.softx.2018.09.004}, - * Volume = {7}, - * Year = {2018}} + * Pages = {318--327}, + * Title = {{deal2lkit: A toolkit library for high performance + * programming in deal.II}}, + * Doi = {10.1016/j.softx.2018.09.004}, + * Volume = {7}, + * Year = {2018}} * @endcode * * @author Luca Heltai, 2019. From c6e49c5d7f5604eef01433c9a4263c9512edd62b Mon Sep 17 00:00:00 2001 From: Luca Heltai Date: Wed, 10 Apr 2019 22:35:20 +0200 Subject: [PATCH 398/507] defgroup -> name --- include/deal.II/meshworker/scratch_data.h | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/include/deal.II/meshworker/scratch_data.h b/include/deal.II/meshworker/scratch_data.h index 6b466286164e..5c4088d5baaa 100644 --- a/include/deal.II/meshworker/scratch_data.h +++ b/include/deal.II/meshworker/scratch_data.h @@ -334,7 +334,7 @@ namespace MeshWorker ScratchData(const ScratchData &scratch); /** - * \defgroup CurrentCellMethos Methods to work on current cell + * @name CurrentCellMethos Methods to work on current cell */ /**@{*/ @@ -416,7 +416,7 @@ namespace MeshWorker /** @} */ // CurrentCellMethods /** - * @defgroup NeighborCellMethods Methods to work on neighbor cell + * @name NeighborCellMethods Methods to work on neighbor cell */ /** @{ */ @@ -502,7 +502,7 @@ namespace MeshWorker GeneralDataStorage & get_general_data_storage(); - /** @defgroup CurrentCellEvaluation Evaluation of finite element fields + /** @name CurrentCellEvaluation Evaluation of finite element fields * and their derivatives on the current cell * @{ */ From f9178378db4981fd64446b8b4202f6c0b2cdc2f0 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Thu, 11 Apr 2019 14:54:15 +0200 Subject: [PATCH 399/507] Replace std::make_unique by std_cxx14::make_unique --- source/meshworker/scratch_data.cc | 24 ++++++++++++------------ 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/source/meshworker/scratch_data.cc b/source/meshworker/scratch_data.cc index 8e6e8708c8fe..c55c72e77e64 100644 --- a/source/meshworker/scratch_data.cc +++ b/source/meshworker/scratch_data.cc @@ -128,10 +128,8 @@ namespace MeshWorker const typename DoFHandler::active_cell_iterator &cell) { if (!fe_values) - fe_values = std::make_unique>(*mapping, - *fe, - cell_quadrature, - cell_update_flags); + fe_values = std_cxx14::make_unique>( + *mapping, *fe, cell_quadrature, cell_update_flags); fe_values->reinit(cell); cell->get_dof_indices(local_dof_indices); @@ -148,7 +146,7 @@ namespace MeshWorker const unsigned int face_no) { if (!fe_face_values) - fe_face_values = std::make_unique>( + fe_face_values = std_cxx14::make_unique>( *mapping, *fe, face_quadrature, face_update_flags); fe_face_values->reinit(cell, face_no); @@ -169,8 +167,9 @@ namespace MeshWorker if (subface_no != numbers::invalid_unsigned_int) { if (!fe_subface_values) - fe_subface_values = std::make_unique>( - *mapping, *fe, face_quadrature, face_update_flags); + fe_subface_values = + std_cxx14::make_unique>( + *mapping, *fe, face_quadrature, face_update_flags); fe_subface_values->reinit(cell, face_no, subface_no); cell->get_dof_indices(local_dof_indices); @@ -189,7 +188,7 @@ namespace MeshWorker const typename DoFHandler::active_cell_iterator &cell) { if (!neighbor_fe_values) - neighbor_fe_values = std::make_unique>( + neighbor_fe_values = std_cxx14::make_unique>( *mapping, *fe, cell_quadrature, neighbor_cell_update_flags); neighbor_fe_values->reinit(cell); @@ -207,8 +206,9 @@ namespace MeshWorker const unsigned int face_no) { if (!neighbor_fe_face_values) - neighbor_fe_face_values = std::make_unique>( - *mapping, *fe, face_quadrature, neighbor_face_update_flags); + neighbor_fe_face_values = + std_cxx14::make_unique>( + *mapping, *fe, face_quadrature, neighbor_face_update_flags); neighbor_fe_face_values->reinit(cell, face_no); cell->get_dof_indices(neighbor_dof_indices); current_neighbor_fe_values = neighbor_fe_face_values.get(); @@ -228,7 +228,7 @@ namespace MeshWorker { if (!neighbor_fe_subface_values) neighbor_fe_subface_values = - std::make_unique>( + std_cxx14::make_unique>( *mapping, *fe, face_quadrature, neighbor_face_update_flags); neighbor_fe_subface_values->reinit(cell, face_no, subface_no); cell->get_dof_indices(neighbor_dof_indices); @@ -353,4 +353,4 @@ namespace MeshWorker { #include "scratch_data.inst" } -DEAL_II_NAMESPACE_CLOSE \ No newline at end of file +DEAL_II_NAMESPACE_CLOSE From 69a1d048aa702a5ca320f9de22a6b859960b07be Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Tue, 9 Apr 2019 04:26:59 +0200 Subject: [PATCH 400/507] Use std::string in SmartPointer and Subscriptor interface --- doc/news/changes/minor/20190408Arndt | 4 ++ include/deal.II/base/smartpointer.h | 6 +-- include/deal.II/base/subscriptor.h | 38 ++----------------- source/base/subscriptor.cc | 11 +++--- .../base/unsubscribe_subscriptor.debug.output | 4 +- ...subscribe_subscriptor.debug.output.clang-6 | 4 +- ...unsubscribe_subscriptor.debug.output.intel | 4 +- 7 files changed, 22 insertions(+), 49 deletions(-) create mode 100644 doc/news/changes/minor/20190408Arndt diff --git a/doc/news/changes/minor/20190408Arndt b/doc/news/changes/minor/20190408Arndt new file mode 100644 index 000000000000..eaf8cc5e3f71 --- /dev/null +++ b/doc/news/changes/minor/20190408Arndt @@ -0,0 +1,4 @@ +Changed: SmartPointer and Subscriptor use a std::string +instead of a const char * as identifier. +
    +(Daniel Arndt, 2019/04/08) diff --git a/include/deal.II/base/smartpointer.h b/include/deal.II/base/smartpointer.h index 82066b872a94..a27fce37afa3 100644 --- a/include/deal.II/base/smartpointer.h +++ b/include/deal.II/base/smartpointer.h @@ -95,7 +95,7 @@ class SmartPointer * The id is used in the call to Subscriptor::subscribe(id) and by * ~SmartPointer() in the call to Subscriptor::unsubscribe(). */ - SmartPointer(T *t, const char *id); + SmartPointer(T *t, const std::string &id); /** * Constructor taking a normal pointer. If possible, i.e. if the pointer is @@ -200,7 +200,7 @@ class SmartPointer /** * The identification for the subscriptor. */ - const char *const id; + const std::string id; /** * The Smartpointer is invalidated when the object pointed to is destroyed @@ -235,7 +235,7 @@ inline SmartPointer::SmartPointer(T *t) template -inline SmartPointer::SmartPointer(T *t, const char *id) +inline SmartPointer::SmartPointer(T *t, const std::string &id) : t(t) , id(id) , pointed_to_object_is_alive(false) diff --git a/include/deal.II/base/subscriptor.h b/include/deal.II/base/subscriptor.h index aae53ff17d17..cd07834741d2 100644 --- a/include/deal.II/base/subscriptor.h +++ b/include/deal.II/base/subscriptor.h @@ -105,23 +105,11 @@ class Subscriptor /** * Subscribes a user of the object by storing the pointer @p validity. The - * subscriber may be identified by text supplied as @p identifier. The latter - * variable must not be a temporary and its type must decay to - * const char *. In particular, calling this function with a rvalue reference - * is not allowed. - */ - template - typename std::enable_if< - std::is_same::value>::type - subscribe(std::atomic *const validity, - ConstCharStar identifier = nullptr) const; - - /** - * Calling subscribe() with a rvalue reference as identifier is not allowed. + * subscriber may be identified by text supplied as @p identifier. */ void subscribe(std::atomic *const validity, - const char *&& identifier) const = delete; + const std::string & identifier = "") const; /** * Unsubscribes a user from the object. @@ -131,7 +119,7 @@ class Subscriptor */ void unsubscribe(std::atomic *const validity, - const char * identifier = nullptr) const; + const std::string & identifier = "") const; /** * Return the present number of subscriptions to this object. This allows to @@ -222,24 +210,11 @@ class Subscriptor */ mutable std::atomic counter; - /* - * Functor struct used for key comparison in #counter_map. - * Not the memory location but the actual C-string content is compared. - */ - struct MapCompare - { - bool - operator()(const char *lhs, const char *rhs) const - { - return std::strcmp(lhs, rhs) > 0; - } - }; - /** * In this map, we count subscriptions for each different identification * string supplied to subscribe(). */ - mutable std::map counter_map; + mutable std::map counter_map; /** * The data type used in #counter_map. @@ -340,11 +315,6 @@ Subscriptor::list_subscribers(StreamType &stream) const << it.first << '\"' << std::endl; } -// forward declare template specialization -template <> -void -Subscriptor::subscribe(std::atomic *const validity, - const char * id) const; DEAL_II_NAMESPACE_CLOSE #endif diff --git a/source/base/subscriptor.cc b/source/base/subscriptor.cc index 669f71b9092b..3aa98f2d5f7e 100644 --- a/source/base/subscriptor.cc +++ b/source/base/subscriptor.cc @@ -126,10 +126,9 @@ Subscriptor::operator=(Subscriptor &&s) noexcept -template <> void -Subscriptor::subscribe(std::atomic *const validity, - const char * id) const +Subscriptor::subscribe(std::atomic *const validity, + const std::string & id) const { std::lock_guard lock(mutex); @@ -137,7 +136,7 @@ Subscriptor::subscribe(std::atomic *const validity, object_info = &typeid(*this); ++counter; - const char *const name = (id != nullptr) ? id : unknown_subscriber; + const std::string name = (id != "") ? id : unknown_subscriber; map_iterator it = counter_map.find(name); if (it == counter_map.end()) @@ -153,9 +152,9 @@ Subscriptor::subscribe(std::atomic *const validity, void Subscriptor::unsubscribe(std::atomic *const validity, - const char * id) const + const std::string & id) const { - const char *name = (id != nullptr) ? id : unknown_subscriber; + const std::string name = (id != "") ? id : unknown_subscriber; if (counter == 0) { AssertNothrow(counter > 0, ExcNoSubscriber(object_info->name(), name)); diff --git a/tests/base/unsubscribe_subscriptor.debug.output b/tests/base/unsubscribe_subscriptor.debug.output index e0f38759735b..03bd8c6462bf 100644 --- a/tests/base/unsubscribe_subscriptor.debug.output +++ b/tests/base/unsubscribe_subscriptor.debug.output @@ -3,7 +3,7 @@ DEAL::Exception: ExcNoSubscriber(object_info->name(), name) DEAL:: -------------------------------------------------------- An error occurred in file in function - void dealii::Subscriptor::unsubscribe(std::atomic*, const char*) const + void dealii::Subscriptor::unsubscribe(std::atomic*, const string&) const The violated condition was: it != counter_map.end() Additional information: @@ -14,7 +14,7 @@ DEAL::Exception: ExcMessage( "This Subscriptor object does not know anything abo DEAL:: -------------------------------------------------------- An error occurred in file in function - void dealii::Subscriptor::unsubscribe(std::atomic*, const char*) const + void dealii::Subscriptor::unsubscribe(std::atomic*, const string&) const The violated condition was: validity_ptr_it != validity_pointers.end() Additional information: diff --git a/tests/base/unsubscribe_subscriptor.debug.output.clang-6 b/tests/base/unsubscribe_subscriptor.debug.output.clang-6 index 5c2e16e2dafb..41313921d204 100644 --- a/tests/base/unsubscribe_subscriptor.debug.output.clang-6 +++ b/tests/base/unsubscribe_subscriptor.debug.output.clang-6 @@ -3,7 +3,7 @@ DEAL::Exception: ExcNoSubscriber(object_info->name(), name) DEAL:: -------------------------------------------------------- An error occurred in file in function - void dealii::Subscriptor::unsubscribe(std::atomic *const, const char *) const + void dealii::Subscriptor::unsubscribe(std::atomic *const, const std::string &) const The violated condition was: it != counter_map.end() Additional information: @@ -14,7 +14,7 @@ DEAL::Exception: ExcMessage( "This Subscriptor object does not know anything abo DEAL:: -------------------------------------------------------- An error occurred in file in function - void dealii::Subscriptor::unsubscribe(std::atomic *const, const char *) const + void dealii::Subscriptor::unsubscribe(std::atomic *const, const std::string &) const The violated condition was: validity_ptr_it != validity_pointers.end() Additional information: diff --git a/tests/base/unsubscribe_subscriptor.debug.output.intel b/tests/base/unsubscribe_subscriptor.debug.output.intel index 76846bd70c11..4817452f841b 100644 --- a/tests/base/unsubscribe_subscriptor.debug.output.intel +++ b/tests/base/unsubscribe_subscriptor.debug.output.intel @@ -3,7 +3,7 @@ DEAL::Exception: ExcNoSubscriber(object_info->name(), name) DEAL:: -------------------------------------------------------- An error occurred in file in function - void dealii::Subscriptor::unsubscribe(std::atomic *, const char *) const + void dealii::Subscriptor::unsubscribe(std::atomic *, const std::__cxx11::basic_string, std::allocator> &) const The violated condition was: it != counter_map.end() Additional information: @@ -14,7 +14,7 @@ DEAL::Exception: ExcMessage( "This Subscriptor object does not know anything abo DEAL:: -------------------------------------------------------- An error occurred in file in function - void dealii::Subscriptor::unsubscribe(std::atomic *, const char *) const + void dealii::Subscriptor::unsubscribe(std::atomic *, const std::__cxx11::basic_string, std::allocator> &) const The violated condition was: validity_ptr_it != validity_pointers.end() Additional information: From dafa99c41eaa2baac2259159c4f738109be2a234 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Tue, 9 Apr 2019 14:11:48 +0200 Subject: [PATCH 401/507] Replace empty string comparison --- include/deal.II/lac/block_matrix_array.h | 2 +- include/deal.II/lac/swappable_vector.templates.h | 12 ++++++------ source/base/data_out_base.cc | 14 +++++++------- source/base/exceptions.cc | 2 +- source/base/parameter_acceptor.cc | 8 ++++---- source/base/parameter_handler.cc | 6 +++--- source/base/path_search.cc | 2 +- source/base/subscriptor.cc | 6 +++--- source/base/table_handler.cc | 4 ++-- source/base/timer.cc | 4 ++-- source/gmsh/utilities.cc | 2 +- source/grid/grid_in.cc | 2 +- 12 files changed, 32 insertions(+), 32 deletions(-) diff --git a/include/deal.II/lac/block_matrix_array.h b/include/deal.II/lac/block_matrix_array.h index 75fd70b812bd..3f8a10223769 100644 --- a/include/deal.II/lac/block_matrix_array.h +++ b/include/deal.II/lac/block_matrix_array.h @@ -609,7 +609,7 @@ BlockMatrixArray::print_latex(StreamType &out) const std::ostringstream stream; - if (array(m->row, m->col) != "" && m->prefix >= 0) + if (!array(m->row, m->col).empty() && m->prefix >= 0) stream << "+"; if (m->prefix != 1.) stream << m->prefix << 'x'; diff --git a/include/deal.II/lac/swappable_vector.templates.h b/include/deal.II/lac/swappable_vector.templates.h index 54963f8920f5..74b39b7b722f 100644 --- a/include/deal.II/lac/swappable_vector.templates.h +++ b/include/deal.II/lac/swappable_vector.templates.h @@ -39,7 +39,7 @@ SwappableVector::SwappableVector(const SwappableVector &v) , filename() , data_is_preloaded(false) { - Assert(v.filename == "", ExcInvalidCopyOperation()); + Assert(v.filename.empty(), ExcInvalidCopyOperation()); } @@ -54,7 +54,7 @@ SwappableVector::~SwappableVector() // first, before killing the vector // itself - if (filename != "") + if (!filename.empty()) { try { @@ -72,7 +72,7 @@ SwappableVector & SwappableVector::operator=(const SwappableVector &v) { // if necessary, first delete data - if (filename != "") + if (!filename.empty()) kill_file(); // if in MT mode, block all other @@ -97,7 +97,7 @@ SwappableVector::swap_out(const std::string &name) // that has not been deleted in the // meantime, then we kill that file // first - if (filename != "") + if (!filename.empty()) kill_file(); filename = name; @@ -197,7 +197,7 @@ SwappableVector::reload_vector(const bool set_flag) { (void)set_flag; - Assert(filename != "", ExcInvalidFilename(filename)); + Assert(!filename.empty(), ExcInvalidFilename(filename)); Assert(this->size() == 0, ExcSizeNonzero()); std::ifstream tmp_in(filename.c_str()); @@ -233,7 +233,7 @@ SwappableVector::kill_file() // is most probably an error, not? Assert(data_is_preloaded == false, ExcInternalError()); - if (filename != "") + if (!filename.empty()) { int status = std::remove(filename.c_str()); (void)status; diff --git a/source/base/data_out_base.cc b/source/base/data_out_base.cc index 939c0c905042..719909c3dbd2 100644 --- a/source/base/data_out_base.cc +++ b/source/base/data_out_base.cc @@ -5345,7 +5345,7 @@ namespace DataOutBase // underscores unless a vector name has been specified out << "VECTORS "; - if (std::get<2>(nonscalar_data_range) != "") + if (!std::get<2>(nonscalar_data_range).empty()) out << std::get<2>(nonscalar_data_range); else { @@ -5580,7 +5580,7 @@ namespace DataOutBase // underscores unless a vector name has been specified out << " (nonscalar_data_range) != "") + if (!std::get<2>(nonscalar_data_range).empty()) out << std::get<2>(nonscalar_data_range); else { @@ -5811,7 +5811,7 @@ namespace DataOutBase // underscores unless a vector name has been specified out << " (nonscalar_data_range) != "") + if (!std::get<2>(nonscalar_data_range).empty()) out << std::get<2>(nonscalar_data_range); else { @@ -7820,7 +7820,7 @@ DataOutBase::write_filtered_data( // Determine the vector name. Concatenate all the component names with // double underscores unless a vector name has been specified - if (std::get<2>(nonscalar_data_ranges[n_th_vector]) != "") + if (!std::get<2>(nonscalar_data_ranges[n_th_vector]).empty()) { vector_name = std::get<2>(nonscalar_data_ranges[n_th_vector]); } @@ -8565,7 +8565,7 @@ DataOutInterface::validate_dataset_names() const for (const auto &range : ranges) { const std::string &name = std::get<2>(range); - if (name != "") + if (!name.empty()) { Assert(all_names.find(name) == all_names.end(), ExcMessage( @@ -9013,7 +9013,7 @@ namespace DataOutBase while ((header.size() != 0) && (header[header.size() - 1] == ' ')) header.erase(header.size() - 1); } - while ((header == "") && in); + while ((header.empty()) && in); std::ostringstream s; s << "[deal.II intermediate Patch<" << dim << ',' << spacedim << ">]"; diff --git a/source/base/exceptions.cc b/source/base/exceptions.cc index 412b3b008cc9..9d743306cbaf 100644 --- a/source/base/exceptions.cc +++ b/source/base/exceptions.cc @@ -147,7 +147,7 @@ const char * ExceptionBase::what() const noexcept { // If no error c_string was generated so far, do it now: - if (what_str == "") + if (what_str.empty()) { #ifdef DEAL_II_HAVE_GLIBC_STACKTRACE // We have deferred the symbol lookup to this point to avoid costly diff --git a/source/base/parameter_acceptor.cc b/source/base/parameter_acceptor.cc index b239541c403f..da217ac3ca97 100644 --- a/source/base/parameter_acceptor.cc +++ b/source/base/parameter_acceptor.cc @@ -47,8 +47,8 @@ ParameterAcceptor::~ParameterAcceptor() std::string ParameterAcceptor::get_section_name() const { - return (section_name != "" ? section_name : - boost::core::demangle(typeid(*this).name())); + return (!section_name.empty() ? section_name : + boost::core::demangle(typeid(*this).name())); } @@ -60,7 +60,7 @@ ParameterAcceptor::initialize( ParameterHandler & prm) { declare_all_parameters(prm); - if (filename != "") + if (!filename.empty()) { // check the extension of input file if (filename.substr(filename.find_last_of('.') + 1) == "prm") @@ -106,7 +106,7 @@ ParameterAcceptor::initialize( "Invalid extension of parameter file. Please use .prm or .xml")); } - if (output_filename != "") + if (!output_filename.empty()) { std::ofstream outfile(output_filename.c_str()); Assert(outfile, ExcIO()); diff --git a/source/base/parameter_handler.cc b/source/base/parameter_handler.cc index 68e828c745a5..3e9f4b3e2be1 100644 --- a/source/base/parameter_handler.cc +++ b/source/base/parameter_handler.cc @@ -494,8 +494,8 @@ namespace // make sure we have a corresponding entry in the destination // object as well const std::string full_path = - (current_path == "" ? p->first : - current_path + path_separator + p->first); + (current_path.empty() ? p->first : + current_path + path_separator + p->first); const std::string new_value = p->second.get("value"); AssertThrow(destination.get_optional(full_path) && @@ -533,7 +533,7 @@ namespace { // it must be a subsection read_xml_recursively(p->second, - (current_path == "" ? + (current_path.empty() ? p->first : current_path + path_separator + p->first), path_separator, diff --git a/source/base/path_search.cc b/source/base/path_search.cc index 4faee0bd51c8..cf53ddb59030 100644 --- a/source/base/path_search.cc +++ b/source/base/path_search.cc @@ -146,7 +146,7 @@ PathSearch::find(const std::string &filename, // try again with the suffix appended, unless there is // no suffix - if (suffix != "") + if (!suffix.empty()) { real_name = *path + filename + suffix; if (debug > 1) diff --git a/source/base/subscriptor.cc b/source/base/subscriptor.cc index 3aa98f2d5f7e..973e5d2e1f37 100644 --- a/source/base/subscriptor.cc +++ b/source/base/subscriptor.cc @@ -84,7 +84,7 @@ Subscriptor::check_no_subscribers() const noexcept std::string(map_entry.first); } - if (infostring == "") + if (infostring.empty()) infostring = ""; AssertNothrow(counter == 0, @@ -136,7 +136,7 @@ Subscriptor::subscribe(std::atomic *const validity, object_info = &typeid(*this); ++counter; - const std::string name = (id != "") ? id : unknown_subscriber; + const std::string name = (!id.empty()) ? id : unknown_subscriber; map_iterator it = counter_map.find(name); if (it == counter_map.end()) @@ -154,7 +154,7 @@ void Subscriptor::unsubscribe(std::atomic *const validity, const std::string & id) const { - const std::string name = (id != "") ? id : unknown_subscriber; + const std::string name = (!id.empty()) ? id : unknown_subscriber; if (counter == 0) { AssertNothrow(counter > 0, ExcNoSubscriber(object_info->name(), name)); diff --git a/source/base/table_handler.cc b/source/base/table_handler.cc index 6ae95c51ce2d..6342e4f57fc2 100644 --- a/source/base/table_handler.cc +++ b/source/base/table_handler.cc @@ -722,9 +722,9 @@ TableHandler::write_tex(std::ostream &out, const bool with_header) const } out << "\\end{tabular}" << std::endl << "\\end{center}" << std::endl; - if (tex_table_caption != "") + if (!tex_table_caption.empty()) out << "\\caption{" << tex_table_caption << "}" << std::endl; - if (tex_table_label != "") + if (!tex_table_label.empty()) out << "\\label{" << tex_table_label << "}" << std::endl; out << "\\end{table}" << std::endl; if (with_header) diff --git a/source/base/timer.cc b/source/base/timer.cc index 13ee1aa8f70d..119ae4d477bb 100644 --- a/source/base/timer.cc +++ b/source/base/timer.cc @@ -459,7 +459,7 @@ TimerOutput::leave_subsection(const std::string §ion_name) std::lock_guard lock(mutex); - if (section_name != "") + if (!section_name.empty()) { Assert(sections.find(section_name) != sections.end(), ExcMessage("Cannot delete a section that was never created.")); @@ -472,7 +472,7 @@ TimerOutput::leave_subsection(const std::string §ion_name) // if no string is given, exit the last // active section. const std::string actual_section_name = - (section_name == "" ? active_sections.back() : section_name); + (section_name.empty() ? active_sections.back() : section_name); sections[actual_section_name].timer.stop(); sections[actual_section_name].total_wall_time += diff --git a/source/gmsh/utilities.cc b/source/gmsh/utilities.cc index 456e4fe6f845..512196010eef 100644 --- a/source/gmsh/utilities.cc +++ b/source/gmsh/utilities.cc @@ -59,7 +59,7 @@ namespace Gmsh { std::string base_name = prm.output_base_name; char dir_template[] = "ctfbc-XXXXXX"; - if (base_name == "") + if (base_name.empty()) { const char *temp = mkdtemp(dir_template); AssertThrow(temp != nullptr, diff --git a/source/grid/grid_in.cc b/source/grid/grid_in.cc index 28f2907258f8..addc9a384cb5 100644 --- a/source/grid/grid_in.cc +++ b/source/grid/grid_in.cc @@ -382,7 +382,7 @@ GridIn::read_vtk(std::istream &in) set = keyword; break; } - if (set == "") + if (set.empty()) // keep ignoring everything until the next SCALARS // keyword continue; From 0216e3c95260ce37f7a360505ea56cd8434a78db Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Tue, 9 Apr 2019 13:50:51 -0400 Subject: [PATCH 402/507] Use references and clean up a bit --- source/base/subscriptor.cc | 11 ++++------- 1 file changed, 4 insertions(+), 7 deletions(-) diff --git a/source/base/subscriptor.cc b/source/base/subscriptor.cc index 973e5d2e1f37..9aa36568458e 100644 --- a/source/base/subscriptor.cc +++ b/source/base/subscriptor.cc @@ -136,13 +136,9 @@ Subscriptor::subscribe(std::atomic *const validity, object_info = &typeid(*this); ++counter; - const std::string name = (!id.empty()) ? id : unknown_subscriber; + const std::string &name = id.empty() ? unknown_subscriber : id; - map_iterator it = counter_map.find(name); - if (it == counter_map.end()) - counter_map.insert(map_value_type(name, 1U)); - else - it->second++; + ++counter_map[name]; *validity = true; validity_pointers.push_back(validity); @@ -154,7 +150,8 @@ void Subscriptor::unsubscribe(std::atomic *const validity, const std::string & id) const { - const std::string name = (!id.empty()) ? id : unknown_subscriber; + const std::string &name = id.empty() ? unknown_subscriber : id; + if (counter == 0) { AssertNothrow(counter > 0, ExcNoSubscriber(object_info->name(), name)); From 77fb2394f658eac51d0be277f583ede16b6c2993 Mon Sep 17 00:00:00 2001 From: Luca Heltai Date: Thu, 11 Apr 2019 15:53:58 +0200 Subject: [PATCH 403/507] Make sure rtree works with mappings that do not preserve vertices. --- doc/news/changes/minor/20190411LucaHeltai-c | 3 + source/grid/grid_tools_cache.cc | 29 +++++-- tests/grid/grid_tools_cache_05.cc | 83 +++++++++++++++++++++ tests/grid/grid_tools_cache_05.output | 10 +++ 4 files changed, 120 insertions(+), 5 deletions(-) create mode 100644 doc/news/changes/minor/20190411LucaHeltai-c create mode 100644 tests/grid/grid_tools_cache_05.cc create mode 100644 tests/grid/grid_tools_cache_05.output diff --git a/doc/news/changes/minor/20190411LucaHeltai-c b/doc/news/changes/minor/20190411LucaHeltai-c new file mode 100644 index 000000000000..e8a86eb0ffb6 --- /dev/null +++ b/doc/news/changes/minor/20190411LucaHeltai-c @@ -0,0 +1,3 @@ +Fixed: Make sure that GridTools::Cache::get_cell_bounding_boxes_rtree() honors mappings. +
    +(Luca Heltai, 2019/04/11) diff --git a/source/grid/grid_tools_cache.cc b/source/grid/grid_tools_cache.cc index d1098c69862d..b0e1be61cf35 100644 --- a/source/grid/grid_tools_cache.cc +++ b/source/grid/grid_tools_cache.cc @@ -131,17 +131,36 @@ namespace GridTools std::vector, typename Triangulation::active_cell_iterator>> - boxes(tria->n_active_cells()); - unsigned int i = 0; - for (const auto &cell : tria->active_cell_iterators()) - boxes[i++] = std::make_pair(cell->bounding_box(), cell); + boxes(tria->n_active_cells()); + if (mapping->preserves_vertex_locations()) + { + unsigned int i = 0; + for (const auto &cell : tria->active_cell_iterators()) + boxes[i++] = std::make_pair(cell->bounding_box(), cell); + } + else + { + unsigned int i = 0; + for (const auto &cell : tria->active_cell_iterators()) + { + const auto vertices = mapping->get_vertices(cell); + Point p0 = vertices[0], p1 = vertices[0]; + for (unsigned int j = 1; j < vertices.size(); ++j) + for (unsigned int d = 0; d < spacedim; ++d) + { + p0[d] = std::min(p0[d], vertices[j][d]); + p1[d] = std::max(p1[d], vertices[j][d]); + } + boxes[i++] = + std::make_pair(BoundingBox({p0, p1}), cell); + } + } cell_bounding_boxes_rtree = pack_rtree(boxes); } return cell_bounding_boxes_rtree; } - #ifdef DEAL_II_WITH_NANOFLANN template const KDTree & diff --git a/tests/grid/grid_tools_cache_05.cc b/tests/grid/grid_tools_cache_05.cc new file mode 100644 index 000000000000..c4aef6710636 --- /dev/null +++ b/tests/grid/grid_tools_cache_05.cc @@ -0,0 +1,83 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + +// test that GridTools::Cache::get_cell_bounding_boxes_rtree() +// works in conjunction with MappingQEulerian + +#include +#include +#include + +#include +#include +#include + +#include +#include +#include + +#include +#include + +#include "../tests.h" + +using namespace dealii; + + +template +void +test() +{ + deallog << "dim=" << dim << std::endl; + + Triangulation triangulation; + GridGenerator::hyper_cube(triangulation, -1, 1); + + FESystem fe(FE_Q(2), dim); + DoFHandler dof_handler(triangulation); + dof_handler.distribute_dofs(fe); + + Vector displacements(dof_handler.n_dofs()); + + displacements = 2.0; + + MappingQEulerian euler(2, dof_handler, displacements); + + GridTools::Cache cache0(triangulation); + GridTools::Cache cache1(triangulation, euler); + + auto &tree0 = cache0.get_cell_bounding_boxes_rtree(); + auto &tree1 = cache1.get_cell_bounding_boxes_rtree(); + + const auto box0 = tree0.begin()->first; + const auto box1 = tree1.begin()->first; + + deallog << "No Mapping : " << box0.get_boundary_points().first << ", " + << box0.get_boundary_points().second << std::endl + << "MappingQEulerian: " << box1.get_boundary_points().first << ", " + << box1.get_boundary_points().second << std::endl; +} + + + +int +main() +{ + initlog(); + + test<1>(); + test<2>(); + test<3>(); +} diff --git a/tests/grid/grid_tools_cache_05.output b/tests/grid/grid_tools_cache_05.output new file mode 100644 index 000000000000..a12320a83c3a --- /dev/null +++ b/tests/grid/grid_tools_cache_05.output @@ -0,0 +1,10 @@ + +DEAL::dim=1 +DEAL::No Mapping : -1.00000, 1.00000 +DEAL::MappingQEulerian: 1.00000, 3.00000 +DEAL::dim=2 +DEAL::No Mapping : -1.00000 -1.00000, 1.00000 1.00000 +DEAL::MappingQEulerian: 1.00000 1.00000, 3.00000 3.00000 +DEAL::dim=3 +DEAL::No Mapping : -1.00000 -1.00000 -1.00000, 1.00000 1.00000 1.00000 +DEAL::MappingQEulerian: 1.00000 1.00000 1.00000, 3.00000 3.00000 3.00000 From 026b280c76c9136610d189fc918f69fb77ff3755 Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Thu, 11 Apr 2019 16:47:35 -0600 Subject: [PATCH 404/507] clang-tidy: only debug mode I don't think it makes sense to also compile in release mode for the tidy checks. This change should speed up the CI tester as well. --- contrib/utilities/run_clang_tidy.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/contrib/utilities/run_clang_tidy.sh b/contrib/utilities/run_clang_tidy.sh index d013f5663947..70dc612c6621 100755 --- a/contrib/utilities/run_clang_tidy.sh +++ b/contrib/utilities/run_clang_tidy.sh @@ -43,7 +43,7 @@ echo "SRC-DIR=$SRC" # enable MPI (to get MPI warnings) # export compile commands (so that run-clang-tidy.py works) -ARGS=("-D" "DEAL_II_WITH_MPI=ON" "-D" "CMAKE_EXPORT_COMPILE_COMMANDS=ON" "$@") +ARGS=("-D" "DEAL_II_WITH_MPI=ON" "-D" "CMAKE_EXPORT_COMPILE_COMMANDS=ON" "-D" "CMAKE_BUILD_TYPE=Debug" "$@") # for a list of checks, see /.clang-tidy cat "$SRC/.clang-tidy" From 6b040506829cf9336ced4c3aa43fc53eaeb6faf4 Mon Sep 17 00:00:00 2001 From: Luca Heltai Date: Thu, 11 Apr 2019 15:52:36 +0200 Subject: [PATCH 405/507] Enlarge BoundingBox --- doc/news/changes/minor/20190411LucaHeltai-b | 3 ++ include/deal.II/base/bounding_box.h | 24 +++++++++ tests/base/bounding_box_5.cc | 60 +++++++++++++++++++++ tests/base/bounding_box_5.output | 7 +++ 4 files changed, 94 insertions(+) create mode 100644 doc/news/changes/minor/20190411LucaHeltai-b create mode 100644 tests/base/bounding_box_5.cc create mode 100644 tests/base/bounding_box_5.output diff --git a/doc/news/changes/minor/20190411LucaHeltai-b b/doc/news/changes/minor/20190411LucaHeltai-b new file mode 100644 index 000000000000..70e55832071a --- /dev/null +++ b/doc/news/changes/minor/20190411LucaHeltai-b @@ -0,0 +1,3 @@ +New: Added BoundingBox::extend() that allows extending and shrinking of BoundingBox objects. +
    +(Luca Heltai, 2019/04/11) diff --git a/include/deal.II/base/bounding_box.h b/include/deal.II/base/bounding_box.h index d4c594c55a63..97acdb873d78 100644 --- a/include/deal.II/base/bounding_box.h +++ b/include/deal.II/base/bounding_box.h @@ -140,6 +140,16 @@ class BoundingBox bool point_inside(const Point &p) const; + /** + * Increase (or decrease) the size of the bounding box by the given amount. + * + * If you call this method with a negative number, and one of the axes of the + * original bounding box is smaller than amount/2, the method will trigger + * an assertion. + */ + void + extend(const Number &amount); + /** * Compute the volume (i.e. the dim-dimensional measure) of the BoundingBox. */ @@ -176,6 +186,20 @@ inline BoundingBox::BoundingBox( this->boundary_points = boundary_points; } +template +inline void +BoundingBox::extend(const Number &amount) +{ + for (unsigned int d = 0; d < spacedim; ++d) + { + boundary_points.first[d] -= amount; + boundary_points.second[d] += amount; + Assert(boundary_points.first[d] <= boundary_points.second[d], + ExcMessage("Bounding Box can't be shrinked this much: the points' " + "order should remain bottom left, top right.")); + } +} + template template diff --git a/tests/base/bounding_box_5.cc b/tests/base/bounding_box_5.cc new file mode 100644 index 000000000000..8f9790337d90 --- /dev/null +++ b/tests/base/bounding_box_5.cc @@ -0,0 +1,60 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + +// test BoundingBox::extend + +#include + +#include +#include + +#include "../tests.h" + +using namespace dealii; + + +template +void +test() +{ + Point p0, p1; + for (unsigned int d = 0; d < dim; ++d) + p1[d] = 1; + + BoundingBox box({p0, p1}); + + box.extend(.5); + + deallog << "New points: " << box.get_boundary_points().first << ", " + << box.get_boundary_points().second << std::endl; + + + box.extend(-.8); + + deallog << "New points: " << box.get_boundary_points().first << ", " + << box.get_boundary_points().second << std::endl; +} + + + +int +main() +{ + initlog(); + + test<1>(); + test<2>(); + test<3>(); +} diff --git a/tests/base/bounding_box_5.output b/tests/base/bounding_box_5.output new file mode 100644 index 000000000000..837b1d9bd95b --- /dev/null +++ b/tests/base/bounding_box_5.output @@ -0,0 +1,7 @@ + +DEAL::New points: -0.500000, 1.50000 +DEAL::New points: 0.300000, 0.700000 +DEAL::New points: -0.500000 -0.500000, 1.50000 1.50000 +DEAL::New points: 0.300000 0.300000, 0.700000 0.700000 +DEAL::New points: -0.500000 -0.500000 -0.500000, 1.50000 1.50000 1.50000 +DEAL::New points: 0.300000 0.300000 0.300000, 0.700000 0.700000 0.700000 From 9929cda885091f83176c67c214f8be325263fc47 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Fri, 12 Apr 2019 13:51:10 +0200 Subject: [PATCH 406/507] Avoid floating point exception in symengine_number_type_01 --- tests/symengine/symengine_number_type_01.cc | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/tests/symengine/symengine_number_type_01.cc b/tests/symengine/symengine_number_type_01.cc index 4b26361e1f57..d67bf54cb7c0 100644 --- a/tests/symengine/symengine_number_type_01.cc +++ b/tests/symengine/symengine_number_type_01.cc @@ -1125,6 +1125,10 @@ main() // No condition is met { +#if defined(DEAL_II_HAVE_FP_EXCEPTIONS) + fedisableexcept(FE_INVALID); +#endif + const double x_val = -1.0; SD::types::substitution_map sub_map; sub_map[x] = SD_number_t(x_val); From a2322195ef5bd9835c804ea60dbd127e47c9fe61 Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Fri, 12 Apr 2019 15:07:03 -0600 Subject: [PATCH 407/507] indent --- examples/step-63/step-63.cc | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/examples/step-63/step-63.cc b/examples/step-63/step-63.cc index 3f9717ec8964..06781b27425e 100644 --- a/examples/step-63/step-63.cc +++ b/examples/step-63/step-63.cc @@ -158,7 +158,8 @@ namespace Step63 "true", Patterns::Bool(), "With streamline diffusion: true|false"); - prm.declare_entry("Output","true", + prm.declare_entry("Output", + "true", Patterns::Bool(), "Generate graphical output: true|false"); @@ -658,7 +659,8 @@ namespace Step63 compute_stabilization_delta(cell->diameter(), epsilon, advection_direction, - settings.fe_degree) : 0.0; + settings.fe_degree) : + 0.0; for (unsigned int q_point = 0; q_point < n_q_points; ++q_point) for (unsigned int i = 0; i < dofs_per_cell; ++i) From 94a34b46dfbb216a878984b8600ad63b73514440 Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Fri, 12 Apr 2019 15:07:36 -0600 Subject: [PATCH 408/507] get rid of static smoother data --- examples/step-63/step-63.cc | 28 +++++++++++++++------------- 1 file changed, 15 insertions(+), 13 deletions(-) diff --git a/examples/step-63/step-63.cc b/examples/step-63/step-63.cc index 06781b27425e..c23896f4f53b 100644 --- a/examples/step-63/step-63.cc +++ b/examples/step-63/step-63.cc @@ -452,7 +452,7 @@ namespace Step63 CopyData & copy_data); void assemble_system_and_multigrid(); - std::unique_ptr>> create_smoother(); + void setup_smoother(); void solve(); void refine_grid(); @@ -483,6 +483,12 @@ namespace Step63 mg::Matrix> mg_interface_matrix_in; mg::Matrix> mg_interface_matrix_out; + using SmootherType = + RelaxationBlock, double, Vector>; + using SmootherAdditionalDataType = SmootherType::AdditionalData; + std::unique_ptr>> mg_smoother; + + MGLevelObject smoother_data; MGConstrainedDoFs mg_constrained_dofs; @@ -797,8 +803,7 @@ namespace Step63 template - std::unique_ptr>> - AdvectionProblem::create_smoother() + void AdvectionProblem::setup_smoother() { if (settings.smoother_type == "SOR") { @@ -812,7 +817,7 @@ namespace Step63 Smoother::AdditionalData(fe.degree == 1 ? 1.0 : 0.62)); smoother->set_steps(2); - return smoother; + mg_smoother = std::move(smoother); } else if (settings.smoother_type == "Jacobi") { @@ -825,15 +830,13 @@ namespace Step63 Smoother::AdditionalData(fe.degree == 1 ? 0.6667 : 0.47)); smoother->set_steps(4); - return smoother; + mg_smoother = std::move(smoother); } else if (settings.smoother_type == "block SOR") { using Smoother = RelaxationBlockSOR, double, Vector>; - // TODO: try and remove static - static MGLevelObject smoother_data; smoother_data.resize(0, triangulation.n_levels() - 1); for (unsigned int level = 0; level < triangulation.n_levels(); ++level) @@ -885,15 +888,13 @@ namespace Step63 Vector>>(); smoother->initialize(mg_matrices, smoother_data); smoother->set_steps(1); - return smoother; + mg_smoother = std::move(smoother); } else if (settings.smoother_type == "block Jacobi") { using Smoother = RelaxationBlockJacobi, double, Vector>; - // TODO: try and remove static - static MGLevelObject smoother_data; smoother_data.resize(0, triangulation.n_levels() - 1); for (unsigned int level = 0; level < triangulation.n_levels(); ++level) @@ -945,7 +946,7 @@ namespace Step63 Vector>>(); smoother->initialize(mg_matrices, smoother_data); smoother->set_steps(2); - return smoother; + mg_smoother = std::move(smoother); } else AssertThrow(false, ExcNotImplemented()); @@ -969,8 +970,7 @@ namespace Step63 MGCoarseGridHouseholder> coarse_grid_solver; coarse_grid_solver.initialize(coarse_matrix); - const std::unique_ptr>> mg_smoother = - create_smoother(); + setup_smoother(); mg_matrix.initialize(mg_matrices); mg_interface_matrix_in.initialize(mg_interface_in); @@ -998,6 +998,8 @@ namespace Step63 << " in " << time.last_wall_time() << " seconds " << std::endl; constraints.distribute(solution); + + mg_smoother.release(); } From 5babb4fcb7adaeeacf258811a97a35ff3c54f43c Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Fri, 12 Apr 2019 15:19:23 -0600 Subject: [PATCH 409/507] change parse_parameter logic --- examples/step-63/step-63.cc | 30 ++++++++---------------------- 1 file changed, 8 insertions(+), 22 deletions(-) diff --git a/examples/step-63/step-63.cc b/examples/step-63/step-63.cc index c23896f4f53b..6bc23c5e79f2 100644 --- a/examples/step-63/step-63.cc +++ b/examples/step-63/step-63.cc @@ -122,7 +122,7 @@ namespace Step63 random }; - bool get_parameters(const std::string &prm_filename); + void get_parameters(const std::string &prm_filename); unsigned int fe_degree; std::string smoother_type; @@ -131,15 +131,8 @@ namespace Step63 bool output; }; - bool Settings::get_parameters(const std::string &prm_filename) + void Settings::get_parameters(const std::string &prm_filename) { - if (prm_filename.size() == 0) - { - std::cerr << "Usage: please pass a .prm file as the first argument" - << std::endl; - return false; - } - ParameterHandler prm; prm.declare_entry("Fe degree", @@ -163,19 +156,15 @@ namespace Step63 Patterns::Bool(), "Generate graphical output: true|false"); - try - { - prm.parse_input(prm_filename); - } - catch (const dealii::PathSearch::ExcFileNotFound &) + if (prm_filename.size() == 0) { - std::cerr << "ERROR: could not parse input from given .prm file" - << prm_filename << "'" << std::endl; - prm.print_parameters(std::cout, ParameterHandler::Text); - return false; + AssertThrow( + false, ExcMessage("please pass a .prm file as the first argument!")); } + prm.parse_input(prm_filename); + fe_degree = prm.get_integer("Fe degree"); smoother_type = prm.get("Smoother type"); @@ -191,8 +180,6 @@ namespace Step63 with_streamline_diffusion = prm.get_bool("With streamline diffusion"); output = prm.get_bool("Output"); - - return true; } @@ -1111,8 +1098,7 @@ int main(int argc, char *argv[]) try { Step63::Settings settings; - if (!settings.get_parameters((argc > 1) ? (argv[1]) : "")) - return 0; + settings.get_parameters((argc > 1) ? (argv[1]) : ""); Step63::AdvectionProblem<2> advection_problem_2d(settings); advection_problem_2d.run(); From 8b17cbc4026bce1105f540e8b1dba7d21e7e1c74 Mon Sep 17 00:00:00 2001 From: Timo Heister Date: Fri, 12 Apr 2019 15:25:23 -0600 Subject: [PATCH 410/507] edit intro --- examples/step-63/doc/intro.dox | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/examples/step-63/doc/intro.dox b/examples/step-63/doc/intro.dox index b8535c110b50..4b90b10a306e 100644 --- a/examples/step-63/doc/intro.dox +++ b/examples/step-63/doc/intro.dox @@ -6,4 +6,4 @@

    Introduction

    Please note: This is work in progress and will be an example for block -smoothers in geometric multigrid. For now, this is just step-16. +smoothers in geometric multigrid. From 8cf6bb0e095132f5244630c7d803461e28c2860f Mon Sep 17 00:00:00 2001 From: David Wells Date: Fri, 12 Apr 2019 22:42:36 -0400 Subject: [PATCH 411/507] Add missing '@ingroup functions' annotations. --- include/deal.II/base/function.h | 3 +++ include/deal.II/base/function_bessel.h | 1 + include/deal.II/base/function_cspline.h | 1 + include/deal.II/base/function_lib.h | 4 ++++ include/deal.II/base/function_spherical.h | 1 + 5 files changed, 10 insertions(+) diff --git a/include/deal.II/base/function.h b/include/deal.II/base/function.h index cb5789440959..49c42d623b8a 100644 --- a/include/deal.II/base/function.h +++ b/include/deal.II/base/function.h @@ -704,6 +704,7 @@ class ComponentSelectFunction : public ConstantFunction * @endcode * The savings in work to write this are apparent. * + * @ingroup functions * @author Wolfgang Bangerth, 2011 */ template @@ -770,6 +771,7 @@ class ScalarFunctionFromFunctionObject : public Function * obviously easily extended to functions that are non-constant in their one * component. * + * @ingroup functions * @author Wolfgang Bangerth, 2011 */ template @@ -858,6 +860,7 @@ class VectorFunctionFromScalarFunctionObject * where the dim components of the tensor function are placed * into the first dim components of the function object. * + * @ingroup functions * @author Spencer Patty, 2013 */ template diff --git a/include/deal.II/base/function_bessel.h b/include/deal.II/base/function_bessel.h index eb8824b6816d..6597f0a69fae 100644 --- a/include/deal.II/base/function_bessel.h +++ b/include/deal.II/base/function_bessel.h @@ -29,6 +29,7 @@ namespace Functions /** * The Bessel functions of first kind or positive integer order. * + * @ingroup functions * @author Guido Kanschat * @date 2010 */ diff --git a/include/deal.II/base/function_cspline.h b/include/deal.II/base/function_cspline.h index 2442827db7fd..9d6d99ce0d05 100644 --- a/include/deal.II/base/function_cspline.h +++ b/include/deal.II/base/function_cspline.h @@ -68,6 +68,7 @@ namespace Functions * * @note This function is only implemented for dim==1 . * + * @ingroup functions * @author Denis Davydov * @date 2016 */ diff --git a/include/deal.II/base/function_lib.h b/include/deal.II/base/function_lib.h index 30a49f3d0481..665cef4b3c8d 100644 --- a/include/deal.II/base/function_lib.h +++ b/include/deal.II/base/function_lib.h @@ -1133,6 +1133,7 @@ namespace Functions * exponents are of course equally valid. Exponents can't be real when the * bases are negative numbers. * + * @ingroup functions * @author Wolfgang Bangerth, 2006 */ template @@ -1217,6 +1218,7 @@ namespace Functions * @note The use of the related class InterpolatedUniformGridData is * discussed in step-53. * + * @ingroup functions * @author Wolfgang Bangerth, 2013 */ template @@ -1320,6 +1322,7 @@ namespace Functions * * @note The use of this class is discussed in step-53. * + * @ingroup functions * @author Wolfgang Bangerth, 2013 */ template @@ -1386,6 +1389,7 @@ namespace Functions * takes a Table<2,double> to describe the set of exponents and a * Vector to describe the set of coefficients. * + * @ingroup functions * @author Ángel Rodríguez, 2015 */ template diff --git a/include/deal.II/base/function_spherical.h b/include/deal.II/base/function_spherical.h index 9c1b9ee7d21a..9a78f60f0444 100644 --- a/include/deal.II/base/function_spherical.h +++ b/include/deal.II/base/function_spherical.h @@ -38,6 +38,7 @@ namespace Functions * * @note This function is currently only implemented for dim==3 . * + * @ingroup functions * @author Denis Davydov, 2017 */ template From e3109ce2d1e75db170b255b736b044e712830514 Mon Sep 17 00:00:00 2001 From: Wolfgang Bangerth Date: Sun, 14 Apr 2019 18:08:40 -0600 Subject: [PATCH 412/507] Enclose everything in step-61 into its own namespace. --- examples/step-61/step-61.cc | 1600 ++++++++++++++++++----------------- 1 file changed, 809 insertions(+), 791 deletions(-) diff --git a/examples/step-61/step-61.cc b/examples/step-61/step-61.cc index d62b125a7b8c..331876650fb4 100644 --- a/examples/step-61/step-61.cc +++ b/examples/step-61/step-61.cc @@ -13,12 +13,13 @@ * * --------------------------------------------------------------------- - * Author: Zhuoran Wang + * Author: Zhuoran Wang, Colorado State University, 2018 */ // @sect3{Include files} // This program is based on step-7, step-20 and step-51, -// we add these include files. +// so most of the following header files are familiar. We +// need the following: #include #include #include @@ -58,854 +59,870 @@ #include #include -using namespace dealii; -// @sect3{The WGDarcyEquation class template} - -// We will solve for the numerical pressure in the interior and on faces and -// calculate its $L_2$ error of pressure. In the post-processing step, we will -// calculate $L_2$-errors of velocity and flux. -template -class WGDarcyEquation -{ -public: - WGDarcyEquation(); - void run(); - -private: - void make_grid(); - void setup_system(); - void assemble_system(); - void solve(); - void postprocess(); - void process_solution(); - void output_results() const; - - Triangulation triangulation; - - AffineConstraints constraints; - - FE_RaviartThomas fe_rt; - DoFHandler dof_handler_rt; - - // The finite element system is used for interior and face solutions. - FESystem fe; - DoFHandler dof_handler; - - SparsityPattern sparsity_pattern; - SparseMatrix system_matrix; - - Vector solution; - Vector system_rhs; -}; - -// @sect3{Right hand side, boundary values, and exact solution} - -// Next, we define the coefficient matrix $\mathbf{K}$, -// Dirichlet boundary conditions, the right-hand side $f = 2\pi^2 \sin(\pi x) -// \sin(\pi y)$, and the reference solutions $p = \sin(\pi x) \sin(\pi y) $. -// -// The coefficient matrix $\mathbf{K}$ is the identity matrix as a test example. -template -class Coefficient : public TensorFunction<2, dim> -{ -public: - Coefficient() - : TensorFunction<2, dim>() - {} - - virtual void value_list(const std::vector> &points, - std::vector> & values) const override; -}; - -template -void Coefficient::value_list(const std::vector> &points, - std::vector> & values) const -{ - Assert(points.size() == values.size(), - ExcDimensionMismatch(points.size(), values.size())); - for (unsigned int p = 0; p < points.size(); ++p) - { - values[p].clear(); - for (unsigned int d = 0; d < dim; ++d) - values[p][d][d] = 1; - } -} - -template -class BoundaryValues : public Function -{ -public: - BoundaryValues() - : Function(2) - {} - - virtual double value(const Point & p, - const unsigned int component = 0) const override; -}; - -template -double BoundaryValues::value(const Point & /*p*/, - const unsigned int /*component*/) const +// Our first step, as always, is to put everything related to this tutorial +// program into its own namespace: +namespace Step61 { - return 0; -} - -template -class RightHandSide : public Function -{ -public: - RightHandSide() - : Function() - {} - - virtual double value(const Point & p, - const unsigned int component = 0) const override; -}; + using namespace dealii; -template -double RightHandSide::value(const Point &p, - const unsigned int /*component*/) const -{ - double return_value = 0.0; - return_value = 2 * M_PI * M_PI * sin(M_PI * p[0]) * sin(M_PI * p[1]); - return return_value; -} + // @sect3{The WGDarcyEquation class template} -template -class Solution : public Function -{ -public: - Solution() - : Function(1) - {} - - virtual double value(const Point &p, const unsigned int) const override; -}; + // We will solve for the numerical pressure in the interior and on faces and + // calculate its $L_2$ error of pressure. In the post-processing step, we will + // calculate $L_2$-errors of velocity and flux. + template + class WGDarcyEquation + { + public: + WGDarcyEquation(); + void run(); + + private: + void make_grid(); + void setup_system(); + void assemble_system(); + void solve(); + void postprocess(); + void process_solution(); + void output_results() const; + + Triangulation triangulation; + + AffineConstraints constraints; + + FE_RaviartThomas fe_rt; + DoFHandler dof_handler_rt; + + // The finite element system is used for interior and face solutions. + FESystem fe; + DoFHandler dof_handler; + + SparsityPattern sparsity_pattern; + SparseMatrix system_matrix; + + Vector solution; + Vector system_rhs; + }; + + // @sect3{Right hand side, boundary values, and exact solution} + + // Next, we define the coefficient matrix $\mathbf{K}$, + // Dirichlet boundary conditions, the right-hand side $f = 2\pi^2 \sin(\pi x) + // \sin(\pi y)$, and the reference solutions $p = \sin(\pi x) \sin(\pi y) $. + // + // The coefficient matrix $\mathbf{K}$ is the identity matrix as a test + // example. + template + class Coefficient : public TensorFunction<2, dim> + { + public: + Coefficient() + : TensorFunction<2, dim>() + {} + + virtual void value_list(const std::vector> &points, + std::vector> &values) const override; + }; + + template + void Coefficient::value_list(const std::vector> &points, + std::vector> & values) const + { + Assert(points.size() == values.size(), + ExcDimensionMismatch(points.size(), values.size())); + for (unsigned int p = 0; p < points.size(); ++p) + { + values[p].clear(); + for (unsigned int d = 0; d < dim; ++d) + values[p][d][d] = 1; + } + } -template -double Solution::value(const Point &p, const unsigned int) const -{ - double return_value = 0; - return_value = sin(M_PI * p[0]) * sin(M_PI * p[1]); - return return_value; -} + template + class BoundaryValues : public Function + { + public: + BoundaryValues() + : Function(2) + {} + + virtual double value(const Point & p, + const unsigned int component = 0) const override; + }; + + template + double BoundaryValues::value(const Point & /*p*/, + const unsigned int /*component*/) const + { + return 0; + } -template -class Velocity : public TensorFunction<1, dim> -{ -public: - Velocity() - : TensorFunction<1, dim>() - {} + template + class RightHandSide : public Function + { + public: + RightHandSide() + : Function() + {} + + virtual double value(const Point & p, + const unsigned int component = 0) const override; + }; + + template + double RightHandSide::value(const Point &p, + const unsigned int /*component*/) const + { + double return_value = 0.0; + return_value = 2 * M_PI * M_PI * sin(M_PI * p[0]) * sin(M_PI * p[1]); + return return_value; + } - virtual Tensor<1, dim> value(const Point &p) const override; -}; + template + class Solution : public Function + { + public: + Solution() + : Function(1) + {} -template -Tensor<1, dim> Velocity::value(const Point &p) const -{ - Tensor<1, dim> return_value; - return_value[0] = -M_PI * cos(M_PI * p[0]) * sin(M_PI * p[1]); - return_value[1] = -M_PI * sin(M_PI * p[0]) * cos(M_PI * p[1]); - return return_value; -} + virtual double value(const Point &p, + const unsigned int) const override; + }; -// @sect3{WGDarcyEquation class implementation} + template + double Solution::value(const Point &p, const unsigned int) const + { + double return_value = 0; + return_value = sin(M_PI * p[0]) * sin(M_PI * p[1]); + return return_value; + } -// @sect4{WGDarcyEquation::WGDarcyEquation} + template + class Velocity : public TensorFunction<1, dim> + { + public: + Velocity() + : TensorFunction<1, dim>() + {} -// In this constructor, we create a finite element space for vector valued -// functions, FE_RaviartThomas. We will need shape functions in -// this space to approximate discrete weak gradients. + virtual Tensor<1, dim> value(const Point &p) const override; + }; -// FESystem defines finite element spaces in the interior and on -// edges of elements. Each of them gets an individual component. Others are the -// same as previous tutorial programs. -template -WGDarcyEquation::WGDarcyEquation() - : fe_rt(0) - , dof_handler_rt(triangulation) - , + template + Tensor<1, dim> Velocity::value(const Point &p) const + { + Tensor<1, dim> return_value; + return_value[0] = -M_PI * cos(M_PI * p[0]) * sin(M_PI * p[1]); + return_value[1] = -M_PI * sin(M_PI * p[0]) * cos(M_PI * p[1]); + return return_value; + } - fe(FE_DGQ(0), 1, FE_FaceQ(0), 1) - , dof_handler(triangulation) + // @sect3{WGDarcyEquation class implementation} -{} + // @sect4{WGDarcyEquation::WGDarcyEquation} -// @sect4{WGDarcyEquation::make_grid} + // In this constructor, we create a finite element space for vector valued + // functions, FE_RaviartThomas. We will need shape functions in + // this space to approximate discrete weak gradients. -// We generate a mesh on the unit square domain and refine it. + // FESystem defines finite element spaces in the interior and on + // edges of elements. Each of them gets an individual component. Others are + // the same as previous tutorial programs. + template + WGDarcyEquation::WGDarcyEquation() + : fe_rt(0) + , dof_handler_rt(triangulation) + , -template -void WGDarcyEquation::make_grid() -{ - GridGenerator::hyper_cube(triangulation, 0, 1); - triangulation.refine_global(1); + fe(FE_DGQ(0), 1, FE_FaceQ(0), 1) + , dof_handler(triangulation) - std::cout << " Number of active cells: " << triangulation.n_active_cells() - << std::endl - << " Total number of cells: " << triangulation.n_cells() - << std::endl; -} + {} -// @sect4{WGDarcyEquation::setup_system} + // @sect4{WGDarcyEquation::make_grid} -// After we create the mesh, we distribute degrees of freedom for the two -// DoFHandler objects. + // We generate a mesh on the unit square domain and refine it. -template -void WGDarcyEquation::setup_system() -{ - dof_handler_rt.distribute_dofs(fe_rt); - dof_handler.distribute_dofs(fe); + template + void WGDarcyEquation::make_grid() + { + GridGenerator::hyper_cube(triangulation, 0, 1); + triangulation.refine_global(1); - std::cout << " Number of flux degrees of freedom: " - << dof_handler_rt.n_dofs() << std::endl; + std::cout << " Number of active cells: " << triangulation.n_active_cells() + << std::endl + << " Total number of cells: " << triangulation.n_cells() + << std::endl; + } - std::cout << " Number of pressure degrees of freedom: " - << dof_handler.n_dofs() << std::endl; + // @sect4{WGDarcyEquation::setup_system} - solution.reinit(dof_handler.n_dofs()); - system_rhs.reinit(dof_handler.n_dofs()); + // After we create the mesh, we distribute degrees of freedom for the two + // DoFHandler objects. + template + void WGDarcyEquation::setup_system() { - constraints.clear(); - FEValuesExtractors::Scalar face(1); - ComponentMask face_pressure_mask = fe.component_mask(face); - VectorTools::interpolate_boundary_values( - dof_handler, 0, BoundaryValues(), constraints, face_pressure_mask); - constraints.close(); - } - - - // In the bilinear form, there is no integration term over faces - // between two neighboring cells, so we can just use - // DoFTools::make_sparsity_pattern to calculate the sparse - // matrix. - DynamicSparsityPattern dsp(dof_handler.n_dofs()); - DoFTools::make_sparsity_pattern(dof_handler, dsp, constraints); - sparsity_pattern.copy_from(dsp); + dof_handler_rt.distribute_dofs(fe_rt); + dof_handler.distribute_dofs(fe); - system_matrix.reinit(sparsity_pattern); + std::cout << " Number of flux degrees of freedom: " + << dof_handler_rt.n_dofs() << std::endl; - // solution.reinit(dof_handler.n_dofs()); - // system_rhs.reinit(dof_handler.n_dofs()); -} + std::cout << " Number of pressure degrees of freedom: " + << dof_handler.n_dofs() << std::endl; -// @sect4{WGDarcyEquation::assemble_system} + solution.reinit(dof_handler.n_dofs()); + system_rhs.reinit(dof_handler.n_dofs()); -// First, we create quadrature points and FEValue objects for cells -// and faces. Then we allocate space for all cell matrices and the right-hand -// side vector. The following definitions have been explained in previous -// tutorials. -template -void WGDarcyEquation::assemble_system() -{ - QGauss quadrature_formula(fe_rt.degree + 1); - QGauss face_quadrature_formula(fe_rt.degree + 1); - const RightHandSide right_hand_side; - - // We define objects to evaluate values and - // gradients of shape functions at the quadrature points. - // Since we need shape functions and normal vectors on faces, we need - // FEFaceValues. - FEValues fe_values_rt(fe_rt, - quadrature_formula, - update_values | update_gradients | - update_quadrature_points | update_JxW_values); - - FEValues fe_values(fe, - quadrature_formula, - update_values | update_quadrature_points | - update_JxW_values); - - FEFaceValues fe_face_values(fe, - face_quadrature_formula, - update_values | update_normal_vectors | - update_quadrature_points | - update_JxW_values); - - FEFaceValues fe_face_values_rt(fe_rt, - face_quadrature_formula, - update_values | update_normal_vectors | - update_quadrature_points | - update_JxW_values); - - - const unsigned int dofs_per_cell_rt = fe_rt.dofs_per_cell; - const unsigned int dofs_per_cell = fe.dofs_per_cell; - - const unsigned int n_q_points = fe_values.get_quadrature().size(); - const unsigned int n_q_points_rt = fe_values_rt.get_quadrature().size(); - const unsigned int n_face_q_points = fe_face_values.get_quadrature().size(); - - std::vector local_dof_indices(dofs_per_cell); - - // We will construct these cell matrices to solve for the pressure. - FullMatrix cell_matrix_rt(dofs_per_cell_rt, dofs_per_cell_rt); - FullMatrix cell_matrix_F(dofs_per_cell, dofs_per_cell_rt); - FullMatrix cell_matrix_C(dofs_per_cell, dofs_per_cell_rt); - FullMatrix local_matrix(dofs_per_cell, dofs_per_cell); - Vector cell_rhs(dofs_per_cell); - Vector cell_solution(dofs_per_cell); - - const Coefficient coefficient; - std::vector> coefficient_values(n_q_points_rt); - - // We need FEValuesExtractors to access the @p interior and - // @p face component of the FESystem shape functions. - const FEValuesExtractors::Vector velocities(0); - const FEValuesExtractors::Scalar interior(0); - const FEValuesExtractors::Scalar face(1); - - typename DoFHandler::active_cell_iterator cell = - dof_handler.begin_active(), - endc = dof_handler.end(); - typename DoFHandler::active_cell_iterator cell_rt = - dof_handler_rt.begin_active(); - - // Here, we will calculate cell matrices used to construct the local matrix on - // each cell. We need shape functions for the Raviart-Thomas space as well, so - // we also loop over the corresponding velocity cell iterators. - for (; cell != endc; ++cell, ++cell_rt) { - // On each cell, cell matrices are different, so in every loop, they need - // to be re-computed. - fe_values_rt.reinit(cell_rt); - fe_values.reinit(cell); - coefficient.value_list(fe_values_rt.get_quadrature_points(), - coefficient_values); - - // This cell matrix is the mass matrix for the Raviart-Thomas space. - // Hence, we need to loop over all the quadrature points - // for the velocity FEValues object. - cell_matrix_rt = 0; - for (unsigned int q = 0; q < n_q_points_rt; ++q) - { - for (unsigned int i = 0; i < dofs_per_cell_rt; ++i) - { - const Tensor<1, dim> phi_i_u = - fe_values_rt[velocities].value(i, q); - for (unsigned int j = 0; j < dofs_per_cell_rt; ++j) - { - const Tensor<1, dim> phi_j_u = - fe_values_rt[velocities].value(j, q); - cell_matrix_rt(i, j) += - (phi_i_u * phi_j_u * fe_values_rt.JxW(q)); - } - } - } - // Next we take the inverse of this matrix by using - // gauss_jordan(). It will be used to calculate the - // coefficient matrix later. - cell_matrix_rt.gauss_jordan(); - - // From the introduction, we know that the right hand side - // is the difference between a face integral and a cell integral. - // Here, we approximate the negative of the contribution in the interior. - // Each component of this matrix is the integral of a product between a - // basis function of the polynomial space and the divergence of a basis - // function of the Raviart-Thomas space. These basis functions are defined - // in the interior. - cell_matrix_F = 0; - for (unsigned int q = 0; q < n_q_points; ++q) - { - for (unsigned int i = 0; i < dofs_per_cell; ++i) - { - for (unsigned int k = 0; k < dofs_per_cell_rt; ++k) - { - const double phi_k_u_div = - fe_values_rt[velocities].divergence(k, q); - cell_matrix_F(i, k) -= (fe_values[interior].value(i, q) * - phi_k_u_div * fe_values.JxW(q)); - } - } - } - - // Now, we approximate the integral on faces. - // Each component is the integral of a product between a basis function of - // the polynomial space and the dot product of a basis function of the - // Raviart-Thomas space and the normal vector. So we loop over all the - // faces of the element and obtain the normal vector. - for (unsigned int face_n = 0; face_n < GeometryInfo::faces_per_cell; - ++face_n) - { - fe_face_values.reinit(cell, face_n); - fe_face_values_rt.reinit(cell_rt, face_n); - for (unsigned int q = 0; q < n_face_q_points; ++q) - { - const Tensor<1, dim> normal = fe_face_values.normal_vector(q); - for (unsigned int i = 0; i < dofs_per_cell; ++i) - { - for (unsigned int k = 0; k < dofs_per_cell_rt; ++k) - { - const Tensor<1, dim> phi_k_u = - fe_face_values_rt[velocities].value(k, q); - cell_matrix_F(i, k) += - (fe_face_values[face].value(i, q) * (phi_k_u * normal) * - fe_face_values.JxW(q)); - } - } - } - } - - // @p cell_matrix_C is matrix product between the inverse of mass matrix @p cell_matrix_rt and @p cell_matrix_F. - cell_matrix_C = 0; - cell_matrix_F.mmult(cell_matrix_C, cell_matrix_rt); - - // Element $a_{ij}$ of the local cell matrix $A$ is given by - // $\int_{E} \sum_{k,l} c_{ik} c_{jl} (\mathbf{K} \mathbf{w}_k) \cdot - // \mathbf{w}_l \mathrm{d}x.$ We have calculated coefficients $c$ in the - // previous step. - local_matrix = 0; - for (unsigned int q = 0; q < n_q_points_rt; ++q) - { - for (unsigned int i = 0; i < dofs_per_cell; ++i) - { - for (unsigned int j = 0; j < dofs_per_cell; ++j) - { - for (unsigned int k = 0; k < dofs_per_cell_rt; ++k) - { - const Tensor<1, dim> phi_k_u = - fe_values_rt[velocities].value(k, q); - for (unsigned int l = 0; l < dofs_per_cell_rt; ++l) - { - const Tensor<1, dim> phi_l_u = - fe_values_rt[velocities].value(l, q); - local_matrix(i, j) += coefficient_values[q] * - cell_matrix_C[i][k] * phi_k_u * - cell_matrix_C[j][l] * phi_l_u * - fe_values_rt.JxW(q); - } - } - } - } - } + constraints.clear(); + FEValuesExtractors::Scalar face(1); + ComponentMask face_pressure_mask = fe.component_mask(face); + VectorTools::interpolate_boundary_values( + dof_handler, 0, BoundaryValues(), constraints, face_pressure_mask); + constraints.close(); + } - // Next, we calculate the right hand side, $\int_{E} f q \mathrm{d}x$. - cell_rhs = 0; - for (unsigned int q = 0; q < n_q_points; ++q) - { - for (unsigned int i = 0; i < dofs_per_cell; ++i) - { - cell_rhs(i) += - (fe_values[interior].value(i, q) * - right_hand_side.value(fe_values.quadrature_point(q)) * - fe_values.JxW(q)); - } - } - // In this part, we distribute components of this local matrix into the - // system matrix and transfer components of the cell right-hand side into - // the system right hand side. - cell->get_dof_indices(local_dof_indices); - constraints.distribute_local_to_global( - local_matrix, cell_rhs, local_dof_indices, system_matrix, system_rhs); - } -} + // In the bilinear form, there is no integration term over faces + // between two neighboring cells, so we can just use + // DoFTools::make_sparsity_pattern to calculate the sparse + // matrix. + DynamicSparsityPattern dsp(dof_handler.n_dofs()); + DoFTools::make_sparsity_pattern(dof_handler, dsp, constraints); + sparsity_pattern.copy_from(dsp); -// @sect4{WGDarcyEquation::solve} + system_matrix.reinit(sparsity_pattern); -// Solving the system of the Darcy equation. Now, we have pressures in the -// interior and on the faces of all the cells. -template -void WGDarcyEquation::solve() -{ - SolverControl solver_control(1000, 1e-8 * system_rhs.l2_norm()); - SolverCG<> solver(solver_control); - solver.solve(system_matrix, solution, system_rhs, PreconditionIdentity()); - constraints.distribute(solution); -} + // solution.reinit(dof_handler.n_dofs()); + // system_rhs.reinit(dof_handler.n_dofs()); + } -// @sect4{WGDarcyEquation::process_solution} + // @sect4{WGDarcyEquation::assemble_system} -// This part is to calculate the $L_2$ error of the pressure. -template -void WGDarcyEquation::process_solution() -{ - // Since we have two different spaces for finite elements in interior and on - // faces, if we want to calculate $L_2$ errors in interior, we need degrees of - // freedom only defined in cells. In FESystem, we have two - // components, the first one is for interior, the second one is for skeletons. - // fe.base_element(0) shows we only need degrees of freedom - // defined in cells. - DoFHandler interior_dof_handler(triangulation); - interior_dof_handler.distribute_dofs(fe.base_element(0)); - // We define a vector to extract pressures in cells. - // The size of the vector is the collective number of all degrees of freedom - // in the interior of all the elements. - Vector interior_solution(interior_dof_handler.n_dofs()); + // First, we create quadrature points and FEValue objects for + // cells and faces. Then we allocate space for all cell matrices and the + // right-hand side vector. The following definitions have been explained in + // previous tutorials. + template + void WGDarcyEquation::assemble_system() { - // types::global_dof_index is used to know the global indices - // of degrees of freedom. So here, we get the global indices of local - // degrees of freedom and the global indices of interior degrees of freedom. - std::vector local_dof_indices(fe.dofs_per_cell); - std::vector interior_local_dof_indices( - fe.base_element(0).dofs_per_cell); - typename DoFHandler::active_cell_iterator - cell = dof_handler.begin_active(), - endc = dof_handler.end(), - interior_cell = interior_dof_handler.begin_active(); - - // In the loop of all cells and interior of the cell, - // we extract interior solutions from the global solution. - for (; cell != endc; ++cell, ++interior_cell) + QGauss quadrature_formula(fe_rt.degree + 1); + QGauss face_quadrature_formula(fe_rt.degree + 1); + const RightHandSide right_hand_side; + + // We define objects to evaluate values and + // gradients of shape functions at the quadrature points. + // Since we need shape functions and normal vectors on faces, we need + // FEFaceValues. + FEValues fe_values_rt(fe_rt, + quadrature_formula, + update_values | update_gradients | + update_quadrature_points | update_JxW_values); + + FEValues fe_values(fe, + quadrature_formula, + update_values | update_quadrature_points | + update_JxW_values); + + FEFaceValues fe_face_values(fe, + face_quadrature_formula, + update_values | update_normal_vectors | + update_quadrature_points | + update_JxW_values); + + FEFaceValues fe_face_values_rt(fe_rt, + face_quadrature_formula, + update_values | update_normal_vectors | + update_quadrature_points | + update_JxW_values); + + + const unsigned int dofs_per_cell_rt = fe_rt.dofs_per_cell; + const unsigned int dofs_per_cell = fe.dofs_per_cell; + + const unsigned int n_q_points = fe_values.get_quadrature().size(); + const unsigned int n_q_points_rt = fe_values_rt.get_quadrature().size(); + const unsigned int n_face_q_points = fe_face_values.get_quadrature().size(); + + std::vector local_dof_indices(dofs_per_cell); + + // We will construct these cell matrices to solve for the pressure. + FullMatrix cell_matrix_rt(dofs_per_cell_rt, dofs_per_cell_rt); + FullMatrix cell_matrix_F(dofs_per_cell, dofs_per_cell_rt); + FullMatrix cell_matrix_C(dofs_per_cell, dofs_per_cell_rt); + FullMatrix local_matrix(dofs_per_cell, dofs_per_cell); + Vector cell_rhs(dofs_per_cell); + Vector cell_solution(dofs_per_cell); + + const Coefficient coefficient; + std::vector> coefficient_values(n_q_points_rt); + + // We need FEValuesExtractors to access the @p interior and + // @p face component of the FESystem shape functions. + const FEValuesExtractors::Vector velocities(0); + const FEValuesExtractors::Scalar interior(0); + const FEValuesExtractors::Scalar face(1); + + typename DoFHandler::active_cell_iterator cell = + dof_handler.begin_active(), + endc = dof_handler.end(); + typename DoFHandler::active_cell_iterator cell_rt = + dof_handler_rt.begin_active(); + + // Here, we will calculate cell matrices used to construct the local matrix + // on each cell. We need shape functions for the Raviart-Thomas space as + // well, so we also loop over the corresponding velocity cell iterators. + for (; cell != endc; ++cell, ++cell_rt) { + // On each cell, cell matrices are different, so in every loop, they + // need to be re-computed. + fe_values_rt.reinit(cell_rt); + fe_values.reinit(cell); + coefficient.value_list(fe_values_rt.get_quadrature_points(), + coefficient_values); + + // This cell matrix is the mass matrix for the Raviart-Thomas space. + // Hence, we need to loop over all the quadrature points + // for the velocity FEValues object. + cell_matrix_rt = 0; + for (unsigned int q = 0; q < n_q_points_rt; ++q) + { + for (unsigned int i = 0; i < dofs_per_cell_rt; ++i) + { + const Tensor<1, dim> phi_i_u = + fe_values_rt[velocities].value(i, q); + for (unsigned int j = 0; j < dofs_per_cell_rt; ++j) + { + const Tensor<1, dim> phi_j_u = + fe_values_rt[velocities].value(j, q); + cell_matrix_rt(i, j) += + (phi_i_u * phi_j_u * fe_values_rt.JxW(q)); + } + } + } + // Next we take the inverse of this matrix by using + // gauss_jordan(). It will be used to calculate the + // coefficient matrix later. + cell_matrix_rt.gauss_jordan(); + + // From the introduction, we know that the right hand side + // is the difference between a face integral and a cell integral. + // Here, we approximate the negative of the contribution in the + // interior. Each component of this matrix is the integral of a product + // between a basis function of the polynomial space and the divergence + // of a basis function of the Raviart-Thomas space. These basis + // functions are defined in the interior. + cell_matrix_F = 0; + for (unsigned int q = 0; q < n_q_points; ++q) + { + for (unsigned int i = 0; i < dofs_per_cell; ++i) + { + for (unsigned int k = 0; k < dofs_per_cell_rt; ++k) + { + const double phi_k_u_div = + fe_values_rt[velocities].divergence(k, q); + cell_matrix_F(i, k) -= (fe_values[interior].value(i, q) * + phi_k_u_div * fe_values.JxW(q)); + } + } + } + + // Now, we approximate the integral on faces. + // Each component is the integral of a product between a basis function + // of the polynomial space and the dot product of a basis function of + // the Raviart-Thomas space and the normal vector. So we loop over all + // the faces of the element and obtain the normal vector. + for (unsigned int face_n = 0; + face_n < GeometryInfo::faces_per_cell; + ++face_n) + { + fe_face_values.reinit(cell, face_n); + fe_face_values_rt.reinit(cell_rt, face_n); + for (unsigned int q = 0; q < n_face_q_points; ++q) + { + const Tensor<1, dim> normal = fe_face_values.normal_vector(q); + for (unsigned int i = 0; i < dofs_per_cell; ++i) + { + for (unsigned int k = 0; k < dofs_per_cell_rt; ++k) + { + const Tensor<1, dim> phi_k_u = + fe_face_values_rt[velocities].value(k, q); + cell_matrix_F(i, k) += + (fe_face_values[face].value(i, q) * + (phi_k_u * normal) * fe_face_values.JxW(q)); + } + } + } + } + + // @p cell_matrix_C is matrix product between the inverse of mass matrix @p cell_matrix_rt and @p cell_matrix_F. + cell_matrix_C = 0; + cell_matrix_F.mmult(cell_matrix_C, cell_matrix_rt); + + // Element $a_{ij}$ of the local cell matrix $A$ is given by + // $\int_{E} \sum_{k,l} c_{ik} c_{jl} (\mathbf{K} \mathbf{w}_k) \cdot + // \mathbf{w}_l \mathrm{d}x.$ We have calculated coefficients $c$ in the + // previous step. + local_matrix = 0; + for (unsigned int q = 0; q < n_q_points_rt; ++q) + { + for (unsigned int i = 0; i < dofs_per_cell; ++i) + { + for (unsigned int j = 0; j < dofs_per_cell; ++j) + { + for (unsigned int k = 0; k < dofs_per_cell_rt; ++k) + { + const Tensor<1, dim> phi_k_u = + fe_values_rt[velocities].value(k, q); + for (unsigned int l = 0; l < dofs_per_cell_rt; ++l) + { + const Tensor<1, dim> phi_l_u = + fe_values_rt[velocities].value(l, q); + local_matrix(i, j) += + coefficient_values[q] * cell_matrix_C[i][k] * + phi_k_u * cell_matrix_C[j][l] * phi_l_u * + fe_values_rt.JxW(q); + } + } + } + } + } + + // Next, we calculate the right hand side, $\int_{E} f q \mathrm{d}x$. + cell_rhs = 0; + for (unsigned int q = 0; q < n_q_points; ++q) + { + for (unsigned int i = 0; i < dofs_per_cell; ++i) + { + cell_rhs(i) += + (fe_values[interior].value(i, q) * + right_hand_side.value(fe_values.quadrature_point(q)) * + fe_values.JxW(q)); + } + } + + // In this part, we distribute components of this local matrix into the + // system matrix and transfer components of the cell right-hand side + // into the system right hand side. cell->get_dof_indices(local_dof_indices); - interior_cell->get_dof_indices(interior_local_dof_indices); - - for (unsigned int i = 0; i < fe.base_element(0).dofs_per_cell; ++i) - interior_solution(interior_local_dof_indices[i]) = - solution(local_dof_indices[fe.component_to_system_index(0, i)]); + constraints.distribute_local_to_global( + local_matrix, cell_rhs, local_dof_indices, system_matrix, system_rhs); } } - // We define a vector that holds the norm of the error on each cell. - // Next, we use VectorTool::integrate_difference - // to compute the error in the $L_2$ norm on each cell. - // Finally, we get the global $L_2$ norm. - Vector difference_per_cell(triangulation.n_active_cells()); - VectorTools::integrate_difference(interior_dof_handler, - interior_solution, - Solution(), - difference_per_cell, - QGauss(fe.degree + 2), - VectorTools::L2_norm); - - const double L2_error = difference_per_cell.l2_norm(); - std::cout << "L2_error_pressure " << L2_error << std::endl; -} - -// @sect4{WGDarcyEquation::postprocess} + // @sect4{WGDarcyEquation::solve} -// After we calculated the numerical pressure, we evaluate $L_2$ errors for the -// velocity on each cell and $L_2$ errors for the flux on faces. + // Solving the system of the Darcy equation. Now, we have pressures in the + // interior and on the faces of all the cells. + template + void WGDarcyEquation::solve() + { + SolverControl solver_control(1000, 1e-8 * system_rhs.l2_norm()); + SolverCG<> solver(solver_control); + solver.solve(system_matrix, solution, system_rhs, PreconditionIdentity()); + constraints.distribute(solution); + } -// We are going to evaluate velocities on each cell and calculate the difference -// between numerical and exact velocities. To calculate velocities, we need -// interior and face pressure values of each element, and some other cell -// matrices. + // @sect4{WGDarcyEquation::process_solution} -template -void WGDarcyEquation::postprocess() -{ - QGauss quadrature_formula(fe_rt.degree + 1); - QGauss face_quadrature_formula(fe_rt.degree + 1); - - FEValues fe_values_rt(fe_rt, - quadrature_formula, - update_values | update_gradients | - update_quadrature_points | update_JxW_values); - - FEValues fe_values(fe, - quadrature_formula, - update_values | update_quadrature_points | - update_JxW_values); - - FEFaceValues fe_face_values(fe, - face_quadrature_formula, - update_values | update_normal_vectors | - update_quadrature_points | - update_JxW_values); - - FEFaceValues fe_face_values_rt(fe_rt, - face_quadrature_formula, - update_values | update_normal_vectors | - update_quadrature_points | - update_JxW_values); - - const unsigned int dofs_per_cell_rt = fe_rt.dofs_per_cell; - const unsigned int dofs_per_cell = fe.dofs_per_cell; - - const unsigned int n_q_points_rt = fe_values_rt.get_quadrature().size(); - const unsigned int n_q_points = fe_values.get_quadrature().size(); - const unsigned int n_face_q_points = fe_face_values.get_quadrature().size(); - const unsigned int n_face_q_points_rt = - fe_face_values_rt.get_quadrature().size(); - - - std::vector local_dof_indices(dofs_per_cell); - FullMatrix cell_matrix_rt(dofs_per_cell_rt, dofs_per_cell_rt); - FullMatrix cell_matrix_F(dofs_per_cell, dofs_per_cell_rt); - FullMatrix cell_matrix_C(dofs_per_cell, dofs_per_cell_rt); - FullMatrix local_matrix(dofs_per_cell, dofs_per_cell); - FullMatrix cell_matrix_D(dofs_per_cell_rt, dofs_per_cell_rt); - FullMatrix cell_matrix_E(dofs_per_cell_rt, dofs_per_cell_rt); - Vector cell_rhs(dofs_per_cell); - Vector cell_solution(dofs_per_cell); - Tensor<1, dim> velocity_cell; - Tensor<1, dim> velocity_face; - Tensor<1, dim> exact_velocity_face; - double L2_err_velocity_cell_sqr_global; - L2_err_velocity_cell_sqr_global = 0; - double L2_err_flux_sqr; - L2_err_flux_sqr = 0; - - typename DoFHandler::active_cell_iterator cell = - dof_handler.begin_active(), - endc = dof_handler.end(); - - typename DoFHandler::active_cell_iterator cell_rt = - dof_handler_rt.begin_active(); - - const Coefficient coefficient; - std::vector> coefficient_values(n_q_points_rt); - const FEValuesExtractors::Vector velocities(0); - const FEValuesExtractors::Scalar pressure(dim); - const FEValuesExtractors::Scalar interior(0); - const FEValuesExtractors::Scalar face(1); - - Velocity exact_velocity; - - // In the loop over all cells, we will calculate $L_2$ errors of velocity and - // flux. - - // First, we calculate the $L_2$ velocity error. - // In the introduction, we explained how to calculate the numerical velocity - // on the cell. We need the pressure solution values on each cell, - // coefficients of the Gram matrix and coefficients of the $L_2$ projection. - // We have already calculated the global solution, so we will extract the cell - // solution from the global solution. The coefficients of the Gram matrix have - // been calculated when we assembled the system matrix for the pressures. We - // will do the same way here. For the coefficients of the projection, we do - // matrix multiplication, i.e., the inverse of the Gram matrix times the - // matrix with $(\mathbf{K} \mathbf{w}, \mathbf{w})$ as components. Then, we - // multiply all these coefficients and call them beta. The numerical velocity - // is the product of beta and the basis functions of the Raviart-Thomas space. - for (; cell != endc; ++cell, ++cell_rt) + // This part is to calculate the $L_2$ error of the pressure. + template + void WGDarcyEquation::process_solution() + { + // Since we have two different spaces for finite elements in interior and on + // faces, if we want to calculate $L_2$ errors in interior, we need degrees + // of freedom only defined in cells. In FESystem, we have two + // components, the first one is for interior, the second one is for + // skeletons. fe.base_element(0) shows we only need degrees of + // freedom defined in cells. + DoFHandler interior_dof_handler(triangulation); + interior_dof_handler.distribute_dofs(fe.base_element(0)); + // We define a vector to extract pressures in cells. + // The size of the vector is the collective number of all degrees of freedom + // in the interior of all the elements. + Vector interior_solution(interior_dof_handler.n_dofs()); { - fe_values_rt.reinit(cell_rt); - fe_values.reinit(cell); - coefficient.value_list(fe_values_rt.get_quadrature_points(), - coefficient_values); - - // The component of this cell_matrix_E is the integral of - // $(\mathbf{K} \mathbf{w}, \mathbf{w})$. cell_matrix_rt is - // the Gram matrix. - cell_matrix_E = 0; - cell_matrix_rt = 0; - for (unsigned int q = 0; q < n_q_points_rt; ++q) + // types::global_dof_index is used to know the global indices + // of degrees of freedom. So here, we get the global indices of local + // degrees of freedom and the global indices of interior degrees of + // freedom. + std::vector local_dof_indices(fe.dofs_per_cell); + std::vector interior_local_dof_indices( + fe.base_element(0).dofs_per_cell); + typename DoFHandler::active_cell_iterator + cell = dof_handler.begin_active(), + endc = dof_handler.end(), + interior_cell = interior_dof_handler.begin_active(); + + // In the loop of all cells and interior of the cell, + // we extract interior solutions from the global solution. + for (; cell != endc; ++cell, ++interior_cell) { - for (unsigned int i = 0; i < dofs_per_cell_rt; ++i) - { - const Tensor<1, dim> phi_i_u = - fe_values_rt[velocities].value(i, q); - - for (unsigned int j = 0; j < dofs_per_cell_rt; ++j) - { - const Tensor<1, dim> phi_j_u = - fe_values_rt[velocities].value(j, q); - - cell_matrix_E(i, j) += (coefficient_values[q] * phi_j_u * - phi_i_u * fe_values_rt.JxW(q)); - cell_matrix_rt(i, j) += - (phi_i_u * phi_j_u * fe_values_rt.JxW(q)); - } - } + cell->get_dof_indices(local_dof_indices); + interior_cell->get_dof_indices(interior_local_dof_indices); + + for (unsigned int i = 0; i < fe.base_element(0).dofs_per_cell; ++i) + interior_solution(interior_local_dof_indices[i]) = + solution(local_dof_indices[fe.component_to_system_index(0, i)]); } + } - // We take the inverse of the Gram matrix, take matrix multiplication and - // get the matrix with coefficients of projection. - cell_matrix_D = 0; - cell_matrix_rt.gauss_jordan(); - cell_matrix_rt.mmult(cell_matrix_D, cell_matrix_E); + // We define a vector that holds the norm of the error on each cell. + // Next, we use VectorTool::integrate_difference + // to compute the error in the $L_2$ norm on each cell. + // Finally, we get the global $L_2$ norm. + Vector difference_per_cell(triangulation.n_active_cells()); + VectorTools::integrate_difference(interior_dof_handler, + interior_solution, + Solution(), + difference_per_cell, + QGauss(fe.degree + 2), + VectorTools::L2_norm); + + const double L2_error = difference_per_cell.l2_norm(); + std::cout << "L2_error_pressure " << L2_error << std::endl; + } - // This cell matrix will be used to calculate the coefficients of the Gram - // matrix. This part is the same as the part in evaluating pressure. - cell_matrix_F = 0; - for (unsigned int q = 0; q < n_q_points; ++q) - { - for (unsigned int i = 0; i < dofs_per_cell; ++i) - { - for (unsigned int k = 0; k < dofs_per_cell_rt; ++k) - { - const double phi_k_u_div = - fe_values_rt[velocities].divergence(k, q); - cell_matrix_F(i, k) -= (fe_values[interior].value(i, q) * - phi_k_u_div * fe_values.JxW(q)); - } - } - } + // @sect4{WGDarcyEquation::postprocess} - for (unsigned int face_n = 0; face_n < GeometryInfo::faces_per_cell; - ++face_n) - { - fe_face_values.reinit(cell, face_n); - fe_face_values_rt.reinit(cell_rt, face_n); - for (unsigned int q = 0; q < n_face_q_points; ++q) - { - const Tensor<1, dim> normal = fe_face_values.normal_vector(q); - for (unsigned int i = 0; i < dofs_per_cell; ++i) - { - for (unsigned int k = 0; k < dofs_per_cell_rt; ++k) - { - const Tensor<1, dim> phi_k_u = - fe_face_values_rt[velocities].value(k, q); - cell_matrix_F(i, k) += - (fe_face_values[face].value(i, q) * (phi_k_u * normal) * - fe_face_values.JxW(q)); - } - } - } - } - cell_matrix_C = 0; - cell_matrix_F.mmult(cell_matrix_C, cell_matrix_rt); + // After we calculated the numerical pressure, we evaluate $L_2$ errors for + // the velocity on each cell and $L_2$ errors for the flux on faces. - // This is to extract pressure values of the element. - cell->get_dof_indices(local_dof_indices); - cell_solution = 0; - for (unsigned int i = 0; i < dofs_per_cell; ++i) - { - cell_solution(i) = solution(local_dof_indices[i]); - } + // We are going to evaluate velocities on each cell and calculate the + // difference between numerical and exact velocities. To calculate velocities, + // we need interior and face pressure values of each element, and some other + // cell matrices. - // From previous calculations we obtained all the coefficients needed to - // calculate beta. - Vector beta(dofs_per_cell_rt); - beta = 0; - for (unsigned int k = 0; k < dofs_per_cell_rt; ++k) - { - for (unsigned int j = 0; j < dofs_per_cell_rt; ++j) - { - for (unsigned int i = 0; i < dofs_per_cell; ++i) - { - beta(k) += -(cell_solution(i) * cell_matrix_C(i, j) * - cell_matrix_D(k, j)); - } - } - } + template + void WGDarcyEquation::postprocess() + { + QGauss quadrature_formula(fe_rt.degree + 1); + QGauss face_quadrature_formula(fe_rt.degree + 1); + + FEValues fe_values_rt(fe_rt, + quadrature_formula, + update_values | update_gradients | + update_quadrature_points | update_JxW_values); + + FEValues fe_values(fe, + quadrature_formula, + update_values | update_quadrature_points | + update_JxW_values); + + FEFaceValues fe_face_values(fe, + face_quadrature_formula, + update_values | update_normal_vectors | + update_quadrature_points | + update_JxW_values); + + FEFaceValues fe_face_values_rt(fe_rt, + face_quadrature_formula, + update_values | update_normal_vectors | + update_quadrature_points | + update_JxW_values); + + const unsigned int dofs_per_cell_rt = fe_rt.dofs_per_cell; + const unsigned int dofs_per_cell = fe.dofs_per_cell; + + const unsigned int n_q_points_rt = fe_values_rt.get_quadrature().size(); + const unsigned int n_q_points = fe_values.get_quadrature().size(); + const unsigned int n_face_q_points = fe_face_values.get_quadrature().size(); + const unsigned int n_face_q_points_rt = + fe_face_values_rt.get_quadrature().size(); + + + std::vector local_dof_indices(dofs_per_cell); + FullMatrix cell_matrix_rt(dofs_per_cell_rt, dofs_per_cell_rt); + FullMatrix cell_matrix_F(dofs_per_cell, dofs_per_cell_rt); + FullMatrix cell_matrix_C(dofs_per_cell, dofs_per_cell_rt); + FullMatrix local_matrix(dofs_per_cell, dofs_per_cell); + FullMatrix cell_matrix_D(dofs_per_cell_rt, dofs_per_cell_rt); + FullMatrix cell_matrix_E(dofs_per_cell_rt, dofs_per_cell_rt); + Vector cell_rhs(dofs_per_cell); + Vector cell_solution(dofs_per_cell); + Tensor<1, dim> velocity_cell; + Tensor<1, dim> velocity_face; + Tensor<1, dim> exact_velocity_face; + double L2_err_velocity_cell_sqr_global; + L2_err_velocity_cell_sqr_global = 0; + double L2_err_flux_sqr; + L2_err_flux_sqr = 0; + + typename DoFHandler::active_cell_iterator cell = + dof_handler.begin_active(), + endc = dof_handler.end(); + + typename DoFHandler::active_cell_iterator cell_rt = + dof_handler_rt.begin_active(); + + const Coefficient coefficient; + std::vector> coefficient_values(n_q_points_rt); + const FEValuesExtractors::Vector velocities(0); + const FEValuesExtractors::Scalar pressure(dim); + const FEValuesExtractors::Scalar interior(0); + const FEValuesExtractors::Scalar face(1); + + Velocity exact_velocity; + + // In the loop over all cells, we will calculate $L_2$ errors of velocity + // and flux. + + // First, we calculate the $L_2$ velocity error. + // In the introduction, we explained how to calculate the numerical velocity + // on the cell. We need the pressure solution values on each cell, + // coefficients of the Gram matrix and coefficients of the $L_2$ projection. + // We have already calculated the global solution, so we will extract the + // cell solution from the global solution. The coefficients of the Gram + // matrix have been calculated when we assembled the system matrix for the + // pressures. We will do the same way here. For the coefficients of the + // projection, we do matrix multiplication, i.e., the inverse of the Gram + // matrix times the matrix with $(\mathbf{K} \mathbf{w}, \mathbf{w})$ as + // components. Then, we multiply all these coefficients and call them beta. + // The numerical velocity is the product of beta and the basis functions of + // the Raviart-Thomas space. + for (; cell != endc; ++cell, ++cell_rt) + { + fe_values_rt.reinit(cell_rt); + fe_values.reinit(cell); + coefficient.value_list(fe_values_rt.get_quadrature_points(), + coefficient_values); + + // The component of this cell_matrix_E is the integral of + // $(\mathbf{K} \mathbf{w}, \mathbf{w})$. cell_matrix_rt is + // the Gram matrix. + cell_matrix_E = 0; + cell_matrix_rt = 0; + for (unsigned int q = 0; q < n_q_points_rt; ++q) + { + for (unsigned int i = 0; i < dofs_per_cell_rt; ++i) + { + const Tensor<1, dim> phi_i_u = + fe_values_rt[velocities].value(i, q); + + for (unsigned int j = 0; j < dofs_per_cell_rt; ++j) + { + const Tensor<1, dim> phi_j_u = + fe_values_rt[velocities].value(j, q); + + cell_matrix_E(i, j) += (coefficient_values[q] * phi_j_u * + phi_i_u * fe_values_rt.JxW(q)); + cell_matrix_rt(i, j) += + (phi_i_u * phi_j_u * fe_values_rt.JxW(q)); + } + } + } + + // We take the inverse of the Gram matrix, take matrix multiplication + // and get the matrix with coefficients of projection. + cell_matrix_D = 0; + cell_matrix_rt.gauss_jordan(); + cell_matrix_rt.mmult(cell_matrix_D, cell_matrix_E); + + // This cell matrix will be used to calculate the coefficients of the + // Gram matrix. This part is the same as the part in evaluating + // pressure. + cell_matrix_F = 0; + for (unsigned int q = 0; q < n_q_points; ++q) + { + for (unsigned int i = 0; i < dofs_per_cell; ++i) + { + for (unsigned int k = 0; k < dofs_per_cell_rt; ++k) + { + const double phi_k_u_div = + fe_values_rt[velocities].divergence(k, q); + cell_matrix_F(i, k) -= (fe_values[interior].value(i, q) * + phi_k_u_div * fe_values.JxW(q)); + } + } + } + + for (unsigned int face_n = 0; + face_n < GeometryInfo::faces_per_cell; + ++face_n) + { + fe_face_values.reinit(cell, face_n); + fe_face_values_rt.reinit(cell_rt, face_n); + for (unsigned int q = 0; q < n_face_q_points; ++q) + { + const Tensor<1, dim> normal = fe_face_values.normal_vector(q); + for (unsigned int i = 0; i < dofs_per_cell; ++i) + { + for (unsigned int k = 0; k < dofs_per_cell_rt; ++k) + { + const Tensor<1, dim> phi_k_u = + fe_face_values_rt[velocities].value(k, q); + cell_matrix_F(i, k) += + (fe_face_values[face].value(i, q) * + (phi_k_u * normal) * fe_face_values.JxW(q)); + } + } + } + } + cell_matrix_C = 0; + cell_matrix_F.mmult(cell_matrix_C, cell_matrix_rt); + + // This is to extract pressure values of the element. + cell->get_dof_indices(local_dof_indices); + cell_solution = 0; + for (unsigned int i = 0; i < dofs_per_cell; ++i) + { + cell_solution(i) = solution(local_dof_indices[i]); + } + + // From previous calculations we obtained all the coefficients needed to + // calculate beta. + Vector beta(dofs_per_cell_rt); + beta = 0; + for (unsigned int k = 0; k < dofs_per_cell_rt; ++k) + { + for (unsigned int j = 0; j < dofs_per_cell_rt; ++j) + { + for (unsigned int i = 0; i < dofs_per_cell; ++i) + { + beta(k) += -(cell_solution(i) * cell_matrix_C(i, j) * + cell_matrix_D(k, j)); + } + } + } + + // Now, we can calculate the numerical velocity at each quadrature point + // and compute the $L_2$ error on each cell. + double L2_err_velocity_cell_sqr_local; + double difference_velocity_cell_sqr; + L2_err_velocity_cell_sqr_local = 0; + velocity_cell = 0; + for (unsigned int q = 0; q < n_q_points_rt; ++q) + { + difference_velocity_cell_sqr = 0; + velocity_cell = 0; + for (unsigned int k = 0; k < dofs_per_cell_rt; ++k) + { + const Tensor<1, dim> phi_k_u = + fe_values_rt[velocities].value(k, q); + velocity_cell += beta(k) * phi_k_u; + } + difference_velocity_cell_sqr = + (velocity_cell - + exact_velocity.value(fe_values_rt.quadrature_point(q))) * + (velocity_cell - + exact_velocity.value(fe_values_rt.quadrature_point(q))); + L2_err_velocity_cell_sqr_local += + difference_velocity_cell_sqr * fe_values_rt.JxW(q); + } + + L2_err_velocity_cell_sqr_global += L2_err_velocity_cell_sqr_local; + + // For reconstructing the flux we need the size of cells and faces. + // Since fluxes are calculated on faces, we have the loop over all four + // faces of each cell. To calculate face velocity, we use the + // coefficient beta we have calculated previously. Then, we calculate + // the squared velocity error in normal direction. Finally, we calculate + // $L_2$ flux error on the cell and add it to the global error. + double difference_velocity_face_sqr; + double L2_err_flux_face_sqr_local; + double err_flux_each_face; + double err_flux_face; + L2_err_flux_face_sqr_local = 0; + err_flux_face = 0; + const double cell_area = cell->measure(); + for (unsigned int face_n = 0; + face_n < GeometryInfo::faces_per_cell; + ++face_n) + { + const double face_length = cell->face(face_n)->measure(); + fe_face_values.reinit(cell, face_n); + fe_face_values_rt.reinit(cell_rt, face_n); + L2_err_flux_face_sqr_local = 0; + err_flux_each_face = 0; + for (unsigned int q = 0; q < n_face_q_points_rt; ++q) + { + difference_velocity_face_sqr = 0; + velocity_face = 0; + const Tensor<1, dim> normal = fe_face_values.normal_vector(q); + for (unsigned int k = 0; k < dofs_per_cell_rt; ++k) + { + const Tensor<1, dim> phi_k_u = + fe_face_values_rt[velocities].value(k, q); + velocity_face += beta(k) * phi_k_u; + } + exact_velocity_face = + exact_velocity.value(fe_face_values_rt.quadrature_point(q)); + difference_velocity_face_sqr = + (velocity_face * normal - exact_velocity_face * normal) * + (velocity_face * normal - exact_velocity_face * normal); + L2_err_flux_face_sqr_local += + difference_velocity_face_sqr * fe_face_values_rt.JxW(q); + } + err_flux_each_face = + L2_err_flux_face_sqr_local / (face_length) * (cell_area); + err_flux_face += err_flux_each_face; + } + L2_err_flux_sqr += err_flux_face; + } - // Now, we can calculate the numerical velocity at each quadrature point - // and compute the $L_2$ error on each cell. - double L2_err_velocity_cell_sqr_local; - double difference_velocity_cell_sqr; - L2_err_velocity_cell_sqr_local = 0; - velocity_cell = 0; - for (unsigned int q = 0; q < n_q_points_rt; ++q) - { - difference_velocity_cell_sqr = 0; - velocity_cell = 0; - for (unsigned int k = 0; k < dofs_per_cell_rt; ++k) - { - const Tensor<1, dim> phi_k_u = - fe_values_rt[velocities].value(k, q); - velocity_cell += beta(k) * phi_k_u; - } - difference_velocity_cell_sqr = - (velocity_cell - - exact_velocity.value(fe_values_rt.quadrature_point(q))) * - (velocity_cell - - exact_velocity.value(fe_values_rt.quadrature_point(q))); - L2_err_velocity_cell_sqr_local += - difference_velocity_cell_sqr * fe_values_rt.JxW(q); - } + // After adding up errors over all cells, we take square root and get the + // $L_2$ errors of velocity and flux. + const double L2_err_velocity_cell = + std::sqrt(L2_err_velocity_cell_sqr_global); + std::cout << "L2_error_vel " << L2_err_velocity_cell << std::endl; + const double L2_err_flux_face = std::sqrt(L2_err_flux_sqr); + std::cout << "L2_error_flux " << L2_err_flux_face << std::endl; + } - L2_err_velocity_cell_sqr_global += L2_err_velocity_cell_sqr_local; - - // For reconstructing the flux we need the size of cells and faces. Since - // fluxes are calculated on faces, we have the loop over all four faces of - // each cell. To calculate face velocity, we use the coefficient beta we - // have calculated previously. Then, we calculate the squared velocity - // error in normal direction. Finally, we calculate $L_2$ flux error on - // the cell and add it to the global error. - double difference_velocity_face_sqr; - double L2_err_flux_face_sqr_local; - double err_flux_each_face; - double err_flux_face; - L2_err_flux_face_sqr_local = 0; - err_flux_face = 0; - const double cell_area = cell->measure(); - for (unsigned int face_n = 0; face_n < GeometryInfo::faces_per_cell; - ++face_n) - { - const double face_length = cell->face(face_n)->measure(); - fe_face_values.reinit(cell, face_n); - fe_face_values_rt.reinit(cell_rt, face_n); - L2_err_flux_face_sqr_local = 0; - err_flux_each_face = 0; - for (unsigned int q = 0; q < n_face_q_points_rt; ++q) - { - difference_velocity_face_sqr = 0; - velocity_face = 0; - const Tensor<1, dim> normal = fe_face_values.normal_vector(q); - for (unsigned int k = 0; k < dofs_per_cell_rt; ++k) - { - const Tensor<1, dim> phi_k_u = - fe_face_values_rt[velocities].value(k, q); - velocity_face += beta(k) * phi_k_u; - } - exact_velocity_face = - exact_velocity.value(fe_face_values_rt.quadrature_point(q)); - difference_velocity_face_sqr = - (velocity_face * normal - exact_velocity_face * normal) * - (velocity_face * normal - exact_velocity_face * normal); - L2_err_flux_face_sqr_local += - difference_velocity_face_sqr * fe_face_values_rt.JxW(q); - } - err_flux_each_face = - L2_err_flux_face_sqr_local / (face_length) * (cell_area); - err_flux_face += err_flux_each_face; - } - L2_err_flux_sqr += err_flux_face; - } - // After adding up errors over all cells, we take square root and get the - // $L_2$ errors of velocity and flux. - const double L2_err_velocity_cell = - std::sqrt(L2_err_velocity_cell_sqr_global); - std::cout << "L2_error_vel " << L2_err_velocity_cell << std::endl; - const double L2_err_flux_face = std::sqrt(L2_err_flux_sqr); - std::cout << "L2_error_flux " << L2_err_flux_face << std::endl; -} + // @sect4{WGDarcyEquation::output_results} + // We have 2 sets of results to output: the interior solution + // and the skeleton solution. We use DataOut to visualize + // interior results. The graphical output for the skeleton results is done by + // using the DataOutFaces class. + template + void WGDarcyEquation::output_results() const + { + DataOut data_out; + data_out.attach_dof_handler(dof_handler); + data_out.add_data_vector(solution, "Pressure_Interior"); + data_out.build_patches(fe.degree); + std::ofstream output("Pressure_Interior.vtk"); + data_out.write_vtk(output); + + DataOutFaces data_out_face(false); + std::vector + face_component_type(2, DataComponentInterpretation::component_is_scalar); + data_out_face.add_data_vector(dof_handler, + solution, + "Pressure_Edge", + face_component_type); + data_out_face.build_patches(fe.degree); + std::ofstream face_output("Pressure_Edge.vtk"); + data_out_face.write_vtk(face_output); + } -// @sect4{WGDarcyEquation::output_results} -// We have 2 sets of results to output: the interior solution -// and the skeleton solution. We use DataOut to visualize interior -// results. The graphical output for the skeleton results is done by using the -// DataOutFaces class. -template -void WGDarcyEquation::output_results() const -{ - DataOut data_out; - data_out.attach_dof_handler(dof_handler); - data_out.add_data_vector(solution, "Pressure_Interior"); - data_out.build_patches(fe.degree); - std::ofstream output("Pressure_Interior.vtk"); - data_out.write_vtk(output); - - DataOutFaces data_out_face(false); - std::vector - face_component_type(2, DataComponentInterpretation::component_is_scalar); - data_out_face.add_data_vector(dof_handler, - solution, - "Pressure_Edge", - face_component_type); - data_out_face.build_patches(fe.degree); - std::ofstream face_output("Pressure_Edge.vtk"); - data_out_face.write_vtk(face_output); -} + // @sect4{WGDarcyEquation::run} + // This is the final function of the main class. It calls the other functions + // of our class. + template + void WGDarcyEquation::run() + { + std::cout << "Solving problem in " << dim << " space dimensions." + << std::endl; + make_grid(); + setup_system(); + assemble_system(); + solve(); + process_solution(); + postprocess(); + output_results(); + } -// @sect4{WGDarcyEquation::run} +} // namespace Step61 -// This is the final function of the main class. It calls the other functions of -// our class. -template -void WGDarcyEquation::run() -{ - std::cout << "Solving problem in " << dim << " space dimensions." - << std::endl; - make_grid(); - setup_system(); - assemble_system(); - solve(); - process_solution(); - postprocess(); - output_results(); -} // @sect3{The main function} @@ -914,9 +931,9 @@ int main() { try { - deallog.depth_console(2); - WGDarcyEquation<2> WGDarcyEquationTest; - WGDarcyEquationTest.run(); + dealii::deallog.depth_console(2); + Step61::WGDarcyEquation<2> wg_darcy; + wg_darcy.run(); } catch (std::exception &exc) { @@ -929,6 +946,7 @@ int main() << "Aborting!" << std::endl << "----------------------------------------------------" << std::endl; + return 1; } catch (...) { @@ -940,7 +958,7 @@ int main() << "Aborting!" << std::endl << "----------------------------------------------------" << std::endl; - throw; + return 1; } return 0; From 81f145ea4b679bf549198244e62f64ea14e9d7fb Mon Sep 17 00:00:00 2001 From: Wolfgang Bangerth Date: Sun, 14 Apr 2019 18:16:58 -0600 Subject: [PATCH 413/507] Update requirements for step-61. --- examples/step-61/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/examples/step-61/CMakeLists.txt b/examples/step-61/CMakeLists.txt index 83a33d091ac2..438736f4746b 100644 --- a/examples/step-61/CMakeLists.txt +++ b/examples/step-61/CMakeLists.txt @@ -23,7 +23,7 @@ SET(TARGET_SRC CMAKE_MINIMUM_REQUIRED(VERSION 2.8.12) -FIND_PACKAGE(deal.II 9.0.0 QUIET +FIND_PACKAGE(deal.II 9.1.0 QUIET HINTS ${deal.II_DIR} ${DEAL_II_DIR} ../ ../../ $ENV{DEAL_II_DIR} ) IF(NOT ${deal.II_FOUND}) From 0cfc5f917ebd3de5974453392ff471f4a1ed6ffc Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Mon, 15 Apr 2019 16:00:58 +0200 Subject: [PATCH 414/507] Fix symengine_number_type_01 in Release mode --- tests/symengine/symengine_number_type_01.cc | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/symengine/symengine_number_type_01.cc b/tests/symengine/symengine_number_type_01.cc index d67bf54cb7c0..074e8e86a740 100644 --- a/tests/symengine/symengine_number_type_01.cc +++ b/tests/symengine/symengine_number_type_01.cc @@ -1125,7 +1125,7 @@ main() // No condition is met { -#if defined(DEAL_II_HAVE_FP_EXCEPTIONS) +#if defined(DEBUG) && defined(DEAL_II_HAVE_FP_EXCEPTIONS) fedisableexcept(FE_INVALID); #endif From 32b1158be54c7f493fe7924bb3fe0519a258433f Mon Sep 17 00:00:00 2001 From: tcclevenger Date: Mon, 15 Apr 2019 09:24:06 -0600 Subject: [PATCH 415/507] requested changes --- examples/step-63/step-63.cc | 110 +++++++++--------------------------- 1 file changed, 27 insertions(+), 83 deletions(-) diff --git a/examples/step-63/step-63.cc b/examples/step-63/step-63.cc index 6bc23c5e79f2..5b906c97ff31 100644 --- a/examples/step-63/step-63.cc +++ b/examples/step-63/step-63.cc @@ -372,17 +372,8 @@ namespace Step63 Assert(component == 0, ExcIndexRange(component, 0, 1)); (void)component; - if (std::fabs(p[0] * p[0] + p[1] * p[1] - 0.3 * 0.3) < - 1e-8 // around cylinder - || std::fabs(p[0] + 1) < 1e-8 // x == -1 - || std::fabs(p[1] - 1) < 1e-8 // y == 1 - || (std::fabs(p[1] + 1) < 1e-8 && p[0] < 0.5) // y == -1, x <= 0.5 - ) - { - return 0.0; - } - else if (std::fabs(p[0] - 1) < 1e-8 // x = 1 - || (std::fabs(p[1] + 1) < 1e-8 && p[0] >= 0.5) // y == -1, x > 0.5 + if (std::fabs(p[0] - 1) < 1e-8 // x == 1 + || (std::fabs(p[1] + 1) < 1e-8 && p[0] >= 0.5) // y == -1, x > 0.5 ) { return 1.0; @@ -623,8 +614,7 @@ namespace Step63 ScratchData & scratch_data, CopyData & copy_data) { - const unsigned int level = cell->level(); - copy_data.level = level; + copy_data.level = cell->level(); const unsigned int dofs_per_cell = scratch_data.fe_values.get_fe().dofs_per_cell; @@ -727,8 +717,6 @@ namespace Step63 CopyData(), MeshWorker::assemble_own_cells); - - // Assemble GMG std::vector> boundary_constraints( triangulation.n_global_levels()); for (unsigned int level = 0; level < triangulation.n_global_levels(); @@ -819,11 +807,9 @@ namespace Step63 smoother->set_steps(4); mg_smoother = std::move(smoother); } - else if (settings.smoother_type == "block SOR") + else if (settings.smoother_type == "block SOR" || + settings.smoother_type == "block Jacobi") { - using Smoother = - RelaxationBlockSOR, double, Vector>; - smoother_data.resize(0, triangulation.n_levels() - 1); for (unsigned int level = 0; level < triangulation.n_levels(); ++level) @@ -832,7 +818,8 @@ namespace Step63 dof_handler, level); - smoother_data[level].relaxation = 1.0; + smoother_data[level].relaxation = + (settings.smoother_type == "block SOR" ? 1.0 : 0.25); smoother_data[level].inversion = PreconditionBlockBase::svd; std::vector ordered_indices; @@ -869,71 +856,28 @@ namespace Step63 std::vector>(1, ordered_indices); } - auto smoother = - std_cxx14::make_unique, - Smoother, - Vector>>(); - smoother->initialize(mg_matrices, smoother_data); - smoother->set_steps(1); - mg_smoother = std::move(smoother); - } - else if (settings.smoother_type == "block Jacobi") - { - using Smoother = - RelaxationBlockJacobi, double, Vector>; - - smoother_data.resize(0, triangulation.n_levels() - 1); - - for (unsigned int level = 0; level < triangulation.n_levels(); ++level) + if (settings.smoother_type == "block SOR") { - DoFTools::make_cell_patches(smoother_data[level].block_list, - dof_handler, - level); - - smoother_data[level].relaxation = 0.25; - smoother_data[level].inversion = PreconditionBlockBase::svd; - - std::vector ordered_indices; - switch (settings.dof_renumbering) - { - case Settings::DoFRenumberingStrategy::downstream: - ordered_indices = - create_downstream_cell_ordering(dof_handler, - advection_direction, - level); - break; - - case Settings::DoFRenumberingStrategy::upstream: - ordered_indices = - create_downstream_cell_ordering(dof_handler, - -1.0 * advection_direction, - level); - break; - - case Settings::DoFRenumberingStrategy::random: - ordered_indices = - create_random_cell_ordering(dof_handler, level); - break; - - case Settings::DoFRenumberingStrategy::none: // Do nothing - break; - - default: - AssertThrow(false, ExcNotImplemented()); - break; - } - - smoother_data[level].order = - std::vector>(1, ordered_indices); + auto smoother = std_cxx14::make_unique, + RelaxationBlockSOR, double, Vector>, + Vector>>(); + smoother->initialize(mg_matrices, smoother_data); + smoother->set_steps(1); + mg_smoother = std::move(smoother); + } + else if (settings.smoother_type == "block Jacobi") + { + auto smoother = std_cxx14::make_unique< + MGSmootherPrecondition, + RelaxationBlockJacobi, + double, + Vector>, + Vector>>(); + smoother->initialize(mg_matrices, smoother_data); + smoother->set_steps(2); + mg_smoother = std::move(smoother); } - - auto smoother = - std_cxx14::make_unique, - Smoother, - Vector>>(); - smoother->initialize(mg_matrices, smoother_data); - smoother->set_steps(2); - mg_smoother = std::move(smoother); } else AssertThrow(false, ExcNotImplemented()); From 5cc659cc45992d01dfe56578de879845c0e6a4a5 Mon Sep 17 00:00:00 2001 From: Bruno Turcksin Date: Mon, 15 Apr 2019 21:34:46 +0000 Subject: [PATCH 416/507] Remove unused variables --- include/deal.II/matrix_free/cuda_matrix_free.templates.h | 5 ----- 1 file changed, 5 deletions(-) diff --git a/include/deal.II/matrix_free/cuda_matrix_free.templates.h b/include/deal.II/matrix_free/cuda_matrix_free.templates.h index 86da1001383d..67720c10edd2 100644 --- a/include/deal.II/matrix_free/cuda_matrix_free.templates.h +++ b/include/deal.II/matrix_free/cuda_matrix_free.templates.h @@ -514,11 +514,6 @@ namespace CUDAWrappers constexpr unsigned int cells_per_block = cells_per_block_shmem(dim, Functor::n_dofs_1d - 1); - constexpr unsigned int n_dofs_per_block = - cells_per_block * Functor::n_local_dofs; - constexpr unsigned int n_q_points_per_block = - cells_per_block * Functor::n_q_points; - const unsigned int local_cell = threadIdx.x / Functor::n_dofs_1d; const unsigned int cell = local_cell + cells_per_block * (blockIdx.x + gridDim.x * blockIdx.y); From e2e647c09d14727d2cc5b12949806f59522761b6 Mon Sep 17 00:00:00 2001 From: Bruno Turcksin Date: Mon, 15 Apr 2019 21:35:00 +0000 Subject: [PATCH 417/507] Add missing instantiations --- source/lac/read_write_vector.cc | 27 +++++++++++++++++++++++++++ 1 file changed, 27 insertions(+) diff --git a/source/lac/read_write_vector.cc b/source/lac/read_write_vector.cc index 9d17935bba39..0baf5cd8b4ee 100644 --- a/source/lac/read_write_vector.cc +++ b/source/lac/read_write_vector.cc @@ -39,6 +39,33 @@ namespace LinearAlgebra #endif #undef TEMPL_COPY_CONSTRUCTOR + + template void + ReadWriteVector::import( + const distributed::Vector &, + VectorOperation::values, + const std::shared_ptr &); + + template void + ReadWriteVector::import( + const distributed::Vector &, + VectorOperation::values, + const std::shared_ptr &); +#ifdef DEAL_II_WITH_COMPLEX_VALUES + template void + ReadWriteVector>::import( + const distributed::Vector, ::dealii::MemorySpace::Host> + &, + VectorOperation::values, + const std::shared_ptr &); + + template void + ReadWriteVector>::import( + const distributed::Vector, ::dealii::MemorySpace::Host> + &, + VectorOperation::values, + const std::shared_ptr &); +#endif } // namespace LinearAlgebra DEAL_II_NAMESPACE_CLOSE From d1ed71376b9d7faca6e1321ea745f0e2d848df00 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Thu, 18 Apr 2019 21:01:36 +0200 Subject: [PATCH 418/507] Fix configuring with external Boost-1.70.0 --- cmake/modules/FindBOOST.cmake | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/cmake/modules/FindBOOST.cmake b/cmake/modules/FindBOOST.cmake index 423dcd047ee8..f640f49e8564 100644 --- a/cmake/modules/FindBOOST.cmake +++ b/cmake/modules/FindBOOST.cmake @@ -50,6 +50,10 @@ ENDIF() # temporarily disable ${CMAKE_SOURCE_DIR}/cmake/modules for module lookup LIST(REMOVE_ITEM CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/cmake/modules/) + +# Workaround a CMake compatibility issue with boost-1.70.0 +SET(Boost_NO_BOOST_CMAKE ON) + IF(DEAL_II_WITH_ZLIB) FIND_PACKAGE(Boost ${BOOST_VERSION_REQUIRED} COMPONENTS iostreams serialization system thread @@ -77,7 +81,7 @@ IF(NOT Boost_FOUND AND Boost_USE_STATIC_LIBS) LIST(APPEND CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/cmake/modules/) ENDIF() - +UNSET(Boost_NO_BOOST_CMAKE) IF(Boost_FOUND) # From ffac3a27160d751fa757d27b7ac9102984d12e03 Mon Sep 17 00:00:00 2001 From: Daniel Arndt Date: Thu, 18 Apr 2019 21:32:20 +0200 Subject: [PATCH 419/507] Add links --- cmake/modules/FindBOOST.cmake | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/cmake/modules/FindBOOST.cmake b/cmake/modules/FindBOOST.cmake index f640f49e8564..8274a3613ee7 100644 --- a/cmake/modules/FindBOOST.cmake +++ b/cmake/modules/FindBOOST.cmake @@ -51,7 +51,9 @@ ENDIF() # temporarily disable ${CMAKE_SOURCE_DIR}/cmake/modules for module lookup LIST(REMOVE_ITEM CMAKE_MODULE_PATH ${CMAKE_SOURCE_DIR}/cmake/modules/) -# Workaround a CMake compatibility issue with boost-1.70.0 +# Work around a CMake compatibility issue with boost-1.70.0 +# compare https://gitlab.kitware.com/cmake/cmake/issues/18865 +# and https://lists.boost.org/Archives/boost/2019/02/245016.php SET(Boost_NO_BOOST_CMAKE ON) IF(DEAL_II_WITH_ZLIB) From 1a7b598b7a80955c120b51a696367fbb2c9c3dbf Mon Sep 17 00:00:00 2001 From: Benjamin Brands Date: Thu, 18 Apr 2019 22:25:21 +0200 Subject: [PATCH 420/507] add explicit instantiations for shared::Triangulation --- source/grid/grid_tools_dof_handlers.inst.in | 48 +++++++++++++++++++++ 1 file changed, 48 insertions(+) diff --git a/source/grid/grid_tools_dof_handlers.inst.in b/source/grid/grid_tools_dof_handlers.inst.in index 9ef81e67af5d..39c7284ad50d 100644 --- a/source/grid/grid_tools_dof_handlers.inst.in +++ b/source/grid/grid_tools_dof_handlers.inst.in @@ -337,3 +337,51 @@ for (deal_II_dimension : DIMENSIONS; deal_II_space_dimension : SPACE_DIMENSIONS) # endif #endif } + +// TODO the text above the last instantiation block implies that this should not +// be necessary... is it? +for (deal_II_dimension : DIMENSIONS; deal_II_space_dimension : SPACE_DIMENSIONS) + { +#if deal_II_dimension <= deal_II_space_dimension +# if deal_II_dimension >= 2 + + namespace GridTools + \{ + template void + collect_periodic_faces< + parallel::shared::Triangulation>( + const parallel::shared::Triangulation &, + const types::boundary_id, + const types::boundary_id, + const int, + std::vector::cell_iterator>> &, + const Tensor<1, + parallel::shared::Triangulation< + deal_II_dimension, + deal_II_space_dimension>::space_dimension> &, + const FullMatrix &); + + template void + collect_periodic_faces< + parallel::shared::Triangulation>( + const parallel::shared::Triangulation &, + const types::boundary_id, + const int, + std::vector::cell_iterator>> &, + const Tensor<1, + parallel::shared::Triangulation< + deal_II_dimension, + deal_II_space_dimension>::space_dimension> &, + const FullMatrix &); + \} +# endif +#endif + } From 0bd307516917cd804b26a7302a4608cfee3ce524 Mon Sep 17 00:00:00 2001 From: Isuru Fernando Date: Thu, 18 Apr 2019 19:35:43 -0500 Subject: [PATCH 421/507] CMake: Clear CMAKE_REQUIRED_FLAGS before calling FindLAPACK CMAKE_REQUIRED_FLAGS is populated by dealii with CXXFLAGS and this should be cleared before calling any function that calls try_compile on a C file. FindLAPACK calls FindTHREADS.cmake which uses try_compile on a C file. --- cmake/configure/configure_1_lapack.cmake | 1 + 1 file changed, 1 insertion(+) diff --git a/cmake/configure/configure_1_lapack.cmake b/cmake/configure/configure_1_lapack.cmake index 2eb4519a15db..b773ccbb8d1e 100644 --- a/cmake/configure/configure_1_lapack.cmake +++ b/cmake/configure/configure_1_lapack.cmake @@ -18,6 +18,7 @@ # MACRO(FEATURE_LAPACK_FIND_EXTERNAL var) + CLEAR_CMAKE_REQUIRED() FIND_PACKAGE(LAPACK) # From 01c49cb26b25082af43cdb0ffc7183acf40c4e7c Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Sun, 14 Apr 2019 10:56:15 +0200 Subject: [PATCH 422/507] Add some SD-related utility functions --- include/deal.II/differentiation/sd.h | 1 + .../differentiation/sd/symengine_utilities.h | 85 +++++++++++++++++++ .../differentiation/sd/symengine_utilities.cc | 16 ++++ tests/symengine/symengine_utilities_01.cc | 57 +++++++++++++ tests/symengine/symengine_utilities_01.output | 10 +++ 5 files changed, 169 insertions(+) create mode 100644 tests/symengine/symengine_utilities_01.cc create mode 100644 tests/symengine/symengine_utilities_01.output diff --git a/include/deal.II/differentiation/sd.h b/include/deal.II/differentiation/sd.h index 0366a5fbd9c8..e618da464616 100644 --- a/include/deal.II/differentiation/sd.h +++ b/include/deal.II/differentiation/sd.h @@ -24,6 +24,7 @@ # include # include # include +# include DEAL_II_NAMESPACE_OPEN diff --git a/include/deal.II/differentiation/sd/symengine_utilities.h b/include/deal.II/differentiation/sd/symengine_utilities.h index e9f64c57162d..69188a863442 100644 --- a/include/deal.II/differentiation/sd/symengine_utilities.h +++ b/include/deal.II/differentiation/sd/symengine_utilities.h @@ -49,12 +49,97 @@ namespace Differentiation convert_expression_vector_to_basic_vector( const SD::types::symbol_vector &symbol_vector); + /** + * Extract the symbols (key entries) from a substitution map. + * + * @note It is guarenteed that the order of extraction of data into the + * output vector is the same as that for extract_values(). + * That is to say that the unzipped key and value pairs as given by + * extract_symbols() and extract_values() always have a 1:1 + * correspondence. + */ + SD::types::symbol_vector + extract_symbols(const SD::types::substitution_map &substitution_values); + + /** + * Extract the values from a substitution map. + * The value entries will be converted into the @p NumberType given + * as a template parameter to this function via the @p ExpressionType. + * + * @note It is guarenteed that the order of extraction of data into the + * output vector is the same as that for extract_symbols(). + * That is to say that the unzipped key and value pairs as given by + * extract_symbols() and extract_values() always have a 1:1 + * correspondence. + */ + template + std::vector + extract_values(const SD::types::substitution_map &substitution_values); + + /** + * Print the key and value pairs stored in a substitution map. + */ + template + StreamType & + print_substitution_map( + StreamType & stream, + const SD::types::substitution_map &symbol_value_map); + } // namespace Utilities } // namespace SD } // namespace Differentiation +/* -------------------- inline and template functions ------------------ */ + + +# ifndef DOXYGEN + + +namespace Differentiation +{ + namespace SD + { + namespace Utilities + { + template + std::vector + extract_values(const SD::types::substitution_map &substitution_values) + { + std::vector values; + values.reserve(substitution_values.size()); + + for (const auto &entry : substitution_values) + values.push_back( + static_cast(ExpressionType(entry.second))); + + return values; + } + + + template + StreamType & + print_substitution_map( + StreamType & stream, + const SD::types::substitution_map &symbol_value_map) + { + for (const auto &entry : symbol_value_map) + stream << entry.first << " = " << entry.second << "\n"; + + stream << std::flush; + return stream; + } + + } // namespace Utilities + + } // namespace SD +} // namespace Differentiation + + +# endif // DOXYGEN + + DEAL_II_NAMESPACE_CLOSE #endif // DEAL_II_WITH_SYMENGINE diff --git a/source/differentiation/sd/symengine_utilities.cc b/source/differentiation/sd/symengine_utilities.cc index 9697316831f8..3d499a9e4aad 100644 --- a/source/differentiation/sd/symengine_utilities.cc +++ b/source/differentiation/sd/symengine_utilities.cc @@ -52,6 +52,22 @@ namespace Differentiation return symb_vec; } + + SD::types::symbol_vector + extract_symbols(const SD::types::substitution_map &substitution_values) + { + SD::types::symbol_vector symbols; + symbols.reserve(substitution_values.size()); + + for (typename SD::types::substitution_map::const_iterator it = + substitution_values.begin(); + it != substitution_values.end(); + ++it) + symbols.push_back(it->first); + + return symbols; + } + } // namespace Utilities } // namespace SD diff --git a/tests/symengine/symengine_utilities_01.cc b/tests/symengine/symengine_utilities_01.cc new file mode 100644 index 000000000000..00d6efe9c529 --- /dev/null +++ b/tests/symengine/symengine_utilities_01.cc @@ -0,0 +1,57 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + + +// Check that substitution map decomposition and printing work as expected + +#include + +#include "../tests.h" + +using namespace dealii; +namespace SD = Differentiation::SD; + + +int +main() +{ + initlog(); + + using SD_number_t = SD::Expression; + + const SD::types::substitution_map sub_map{ + {SD_number_t("c"), SD_number_t(1.0)}, + {SD_number_t("b"), SD_number_t(2)}, + {SD_number_t("a"), SD_number_t(3.0f)}}; + + const SD::types::symbol_vector symbols = + SD::Utilities::extract_symbols(sub_map); + const std::vector values = + SD::Utilities::extract_values(sub_map); + Assert(values.size() == symbols.size(), + ExcDimensionMismatch(values.size(), symbols.size())); + + // Print the map itself (this should be dictionary ordered) + deallog << "Print substitution map" << std::endl; + SD::Utilities::print_substitution_map(deallog, sub_map); + + // Print the extracted symbol-value pairs (the ordering should match that of + // the map) + deallog << "Print extracted symbol-value pairs" << std::endl; + for (unsigned int i = 0; i < symbols.size(); ++i) + deallog << symbols[i] << " = " << values[i] << std::endl; + + deallog << "OK" << std::endl; +} diff --git a/tests/symengine/symengine_utilities_01.output b/tests/symengine/symengine_utilities_01.output new file mode 100644 index 000000000000..ddbe32bbc1aa --- /dev/null +++ b/tests/symengine/symengine_utilities_01.output @@ -0,0 +1,10 @@ + +DEAL::Print substitution map +DEAL::a = 3.0 +b = 2 +c = 1.0 +Print extracted symbol-value pairs +DEAL::a = 3.00000 +DEAL::b = 2.00000 +DEAL::c = 1.00000 +DEAL::OK From 1556051a5cf11199aa5000bc62a04b4da7b984fd Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Sun, 14 Apr 2019 10:57:52 +0200 Subject: [PATCH 423/507] Add some SD-related convenience functions for scalar operations. Specifically, these can be used to create a scalar symbol and symbolic function. --- include/deal.II/differentiation/sd.h | 1 + .../sd/symengine_scalar_operations.h | 119 ++++++++++++++++++ source/differentiation/sd/CMakeLists.txt | 1 + .../sd/symengine_scalar_operations.cc | 64 ++++++++++ .../symengine_scalar_operations_01.cc | 55 ++++++++ .../symengine_scalar_operations_01.output | 5 + 6 files changed, 245 insertions(+) create mode 100644 include/deal.II/differentiation/sd/symengine_scalar_operations.h create mode 100644 source/differentiation/sd/symengine_scalar_operations.cc create mode 100644 tests/symengine/symengine_scalar_operations_01.cc create mode 100644 tests/symengine/symengine_scalar_operations_01.output diff --git a/include/deal.II/differentiation/sd.h b/include/deal.II/differentiation/sd.h index e618da464616..2050e6a509df 100644 --- a/include/deal.II/differentiation/sd.h +++ b/include/deal.II/differentiation/sd.h @@ -23,6 +23,7 @@ # include # include # include +# include # include # include diff --git a/include/deal.II/differentiation/sd/symengine_scalar_operations.h b/include/deal.II/differentiation/sd/symengine_scalar_operations.h new file mode 100644 index 000000000000..c920cd7de1b7 --- /dev/null +++ b/include/deal.II/differentiation/sd/symengine_scalar_operations.h @@ -0,0 +1,119 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + +#ifndef dealii_differentiation_sd_symengine_scalar_operations_h +#define dealii_differentiation_sd_symengine_scalar_operations_h + +#include + +#ifdef DEAL_II_WITH_SYMENGINE + +# include + +# include +# include + +# include +# include +# include +# include + +DEAL_II_NAMESPACE_OPEN + +namespace Differentiation +{ + namespace SD + { + /** + * @name Symbolic variable creation + */ + //@{ + + /** + * Return an Expression representing a scalar symbolic variable + * with the identifier specified by @p symbol. + * + * For example, if the @p symbol is the string `"x"` then the scalar + * symbolic variable that is returned represents the scalar $x$. + * + * @param[in] symbol An indentifier (or name) for the returned symbolic + * variable. + * @return A scalar symbolic variable with the name @p symbol. + * + * @warning It is up to the user to ensure that there is no ambiguity in the + * symbols used within a section of code. + */ + Expression + make_symbol(const std::string &symbol); + + /** + * Return an Expression representing a scalar symbolic function + * with the identifier specified by @p symbol. The function's symbolic + * dependencies are specified by the input @p arguments. + * + * For example, if the @p symbol is the string `"f"`, and the + * arguments to the function that is generated are the + * symbolic variable `x` and the symbolic expression `y+z`, then the + * generic symbolic function that is returned represents $f(x, y+z)$. + * + * @param[in] symbol An indentifier (or name) for the returned symbolic + * function. + * @param[in] arguments A vector of input arguments to the returned + * symbolic function. + * @return A generic symbolic function with the identifier @p symbolic and + * the number of input arguments equal to the length of @p arguments. + * + * @warning It is up to the user to ensure that there is no ambiguity in the + * symbols used within a section of code. + */ + Expression + make_symbolic_function(const std::string & symbol, + const types::symbol_vector &arguments); + + /** + * Return an Expression representing a scalar symbolic function + * with the identifier specified by @p symbol. The function's symbolic + * dependencies are specified by the keys to the input @p arguments map; + * the values stored in the map are ignored. + * + * For example, if the @p symbol is the string `"f"`, and the + * arguments to the function that is generated are the + * symbolic variable `x` and the symbolic expression `y+z`, then the + * generic symbolic function that is returned represents $f(x, y+z)$. + * + * @param[in] symbol An indentifier (or name) for the returned symbolic + * function. + * @param[in] arguments A map of input arguments to the returned + * symbolic function. + * @return A generic symbolic function with the identifier @p symbolic and + * the number of input arguments equal to the length of @p arguments. + * + * @warning It is up to the user to ensure that there is no ambiguity in the + * symbols used within a section of code. + */ + Expression + make_symbolic_function(const std::string & symbol, + const types::substitution_map &arguments); + + //@} + + } // namespace SD +} // namespace Differentiation + +DEAL_II_NAMESPACE_CLOSE + +#endif // DEAL_II_WITH_SYMENGINE + +#endif diff --git a/source/differentiation/sd/CMakeLists.txt b/source/differentiation/sd/CMakeLists.txt index 26920f47a919..0cb7b56a5e7e 100644 --- a/source/differentiation/sd/CMakeLists.txt +++ b/source/differentiation/sd/CMakeLists.txt @@ -18,6 +18,7 @@ INCLUDE_DIRECTORIES(BEFORE ${CMAKE_CURRENT_BINARY_DIR}) SET(_src symengine_math.cc symengine_number_types.cc + symengine_scalar_operations.cc symengine_types.cc symengine_utilities.cc ) diff --git a/source/differentiation/sd/symengine_scalar_operations.cc b/source/differentiation/sd/symengine_scalar_operations.cc new file mode 100644 index 000000000000..1757f0dca15a --- /dev/null +++ b/source/differentiation/sd/symengine_scalar_operations.cc @@ -0,0 +1,64 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + + +#include + +#ifdef DEAL_II_WITH_SYMENGINE + +# include +# include +# include +# include + +DEAL_II_NAMESPACE_OPEN + +namespace Differentiation +{ + namespace SD + { + /* ------------------------- Symbol creation -----------------------*/ + + + Expression + make_symbol(const std::string &symbol) + { + return Expression(symbol); + } + + + Expression + make_symbolic_function(const std::string & symbol, + const SD::types::symbol_vector &arguments) + { + return Expression(symbol, arguments); + } + + + Expression + make_symbolic_function(const std::string & symbol, + const SD::types::substitution_map &arguments) + { + return make_symbolic_function(symbol, + SD::Utilities::extract_symbols(arguments)); + } + + + } // namespace SD +} // namespace Differentiation + +DEAL_II_NAMESPACE_CLOSE + +#endif // DEAL_II_WITH_SYMENGINE diff --git a/tests/symengine/symengine_scalar_operations_01.cc b/tests/symengine/symengine_scalar_operations_01.cc new file mode 100644 index 000000000000..666be3079ecf --- /dev/null +++ b/tests/symengine/symengine_scalar_operations_01.cc @@ -0,0 +1,55 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + + +// Check that symbols and symbolic functions can be created using the +// utility functions + +#include + +#include "../tests.h" + +using namespace dealii; +namespace SD = Differentiation::SD; + + +int +main() +{ + initlog(); + + using SD_number_t = SD::Expression; + + const SD::types::substitution_map sub_map{ + {SD_number_t("c"), SD_number_t(1.0)}, + {SD_number_t("b"), SD_number_t(2)}, + {SD_number_t("a"), SD_number_t(3.0f)}}; + + const SD::types::symbol_vector symbols{SD_number_t("c"), + SD_number_t("b"), + SD_number_t("a")}; + + const SD_number_t symb = SD::make_symbol("d"); + const SD_number_t symb_func_1 = SD::make_symbolic_function("f", symbols); + const SD_number_t symb_func_2 = SD::make_symbolic_function("g", sub_map); + + deallog << "Symbol: " << symb << std::endl; + deallog << "Symbolic function (vector of arguments): " << symb_func_1 + << std::endl; + deallog << "Symbolic function (map of arguments): " << symb_func_2 + << std::endl; + + deallog << "OK" << std::endl; +} diff --git a/tests/symengine/symengine_scalar_operations_01.output b/tests/symengine/symengine_scalar_operations_01.output new file mode 100644 index 000000000000..b81239fe9ad9 --- /dev/null +++ b/tests/symengine/symengine_scalar_operations_01.output @@ -0,0 +1,5 @@ + +DEAL::Symbol: d +DEAL::Symbolic function (vector of arguments): f(c, b, a) +DEAL::Symbolic function (map of arguments): g(a, b, c) +DEAL::OK From c74e7b6cede8a01f94ab4ac1b7002b5961b66303 Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Sun, 14 Apr 2019 13:09:07 +0200 Subject: [PATCH 424/507] Add some SD-related convenience functions for scalar operations. Specifically, a non-member function for scalar differentiation of an Expression has been added. --- .../sd/symengine_scalar_operations.h | 21 +++++++++ .../sd/symengine_scalar_operations.cc | 9 ++++ .../symengine_scalar_operations_02.cc | 44 +++++++++++++++++++ .../symengine_scalar_operations_02.output | 5 +++ 4 files changed, 79 insertions(+) create mode 100644 tests/symengine/symengine_scalar_operations_02.cc create mode 100644 tests/symengine/symengine_scalar_operations_02.output diff --git a/include/deal.II/differentiation/sd/symengine_scalar_operations.h b/include/deal.II/differentiation/sd/symengine_scalar_operations.h index c920cd7de1b7..15b9dc752922 100644 --- a/include/deal.II/differentiation/sd/symengine_scalar_operations.h +++ b/include/deal.II/differentiation/sd/symengine_scalar_operations.h @@ -109,6 +109,27 @@ namespace Differentiation //@} + /** + * @name Symbolic differentiation + */ + //@{ + + /** + * Return the symbolic result of computing the partial derivative of the + * scalar @p f with respect to the scalar @p x. + * In most use cases the function or variable @f would be called the + * dependent variable, and @p x the independent variable. + * + * @param[in] f A scalar symbolic function or (dependent) variable. + * @param[in] x A scalar symbolic (independent) variable. + * @return The symbolic function or variable representing the result + * $\frac{\partial f}{\partial x}$. + */ + Expression + differentiate(const Expression &f, const Expression &x); + + //@} + } // namespace SD } // namespace Differentiation diff --git a/source/differentiation/sd/symengine_scalar_operations.cc b/source/differentiation/sd/symengine_scalar_operations.cc index 1757f0dca15a..7df4e22cc07a 100644 --- a/source/differentiation/sd/symengine_scalar_operations.cc +++ b/source/differentiation/sd/symengine_scalar_operations.cc @@ -56,6 +56,15 @@ namespace Differentiation } + /* --------------------------- Differentiation ------------------------- */ + + + Expression + differentiate(const Expression &func, const Expression &op) + { + return func.differentiate(op); + } + } // namespace SD } // namespace Differentiation diff --git a/tests/symengine/symengine_scalar_operations_02.cc b/tests/symengine/symengine_scalar_operations_02.cc new file mode 100644 index 000000000000..db2e61af517a --- /dev/null +++ b/tests/symengine/symengine_scalar_operations_02.cc @@ -0,0 +1,44 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + + +// Check that scalar differentiation can be performed using the utility +// functions + +#include + +#include "../tests.h" + +using namespace dealii; +namespace SD = Differentiation::SD; + + +int +main() +{ + initlog(); + + using SD_number_t = SD::Expression; + + const SD_number_t x = SD::make_symbol("x"); + const SD_number_t f = 2 * x * x; + const SD_number_t df_dx = SD::differentiate(f, x); + + deallog << "x: " << x << std::endl; + deallog << "f: " << f << std::endl; + deallog << "df_dx: " << df_dx << std::endl; + + deallog << "OK" << std::endl; +} diff --git a/tests/symengine/symengine_scalar_operations_02.output b/tests/symengine/symengine_scalar_operations_02.output new file mode 100644 index 000000000000..91cad5cafa5a --- /dev/null +++ b/tests/symengine/symengine_scalar_operations_02.output @@ -0,0 +1,5 @@ + +DEAL::x: x +DEAL::f: 2*x**2 +DEAL::df_dx: 4*x +DEAL::OK From 0a91cd1a9f9439c7795b1a543ffbc05999525b4c Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Wed, 17 Apr 2019 22:08:09 +0200 Subject: [PATCH 425/507] Add template arguments for symmetric tensor ranks --- cmake/config/template-arguments.in | 3 +++ 1 file changed, 3 insertions(+) diff --git a/cmake/config/template-arguments.in b/cmake/config/template-arguments.in index 2e1a69bd7618..3370a92a6cbd 100644 --- a/cmake/config/template-arguments.in +++ b/cmake/config/template-arguments.in @@ -266,6 +266,9 @@ SPACE_DIMENSIONS := { 1; 2; 3 } // all ranks used for instantiating tensors RANKS := { 1; 2; 3; 4 } +// all ranks used for instantiating symmetric tensors +SYM_RANKS := { 2; 4 } + // Flags that are allowed in DataOutInterface::set_flags OUTPUT_FLAG_TYPES := { DXFlags; UcdFlags; GnuplotFlags; PovrayFlags; EpsFlags; GmvFlags; TecplotFlags; VtkFlags; SvgFlags; From ab67ed22932f45e353b2c71ad4080e83e85f10d8 Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Wed, 17 Apr 2019 22:27:00 +0200 Subject: [PATCH 426/507] Add ProductType for SD::Expression class. This is the first step towards support of SD::Expression within the Tensor and SymmetricTensor classes. --- include/deal.II/differentiation/sd.h | 1 + .../sd/symengine_product_types.h | 121 ++++++++++++++++++ 2 files changed, 122 insertions(+) create mode 100644 include/deal.II/differentiation/sd/symengine_product_types.h diff --git a/include/deal.II/differentiation/sd.h b/include/deal.II/differentiation/sd.h index 2050e6a509df..5039e8a4a2b5 100644 --- a/include/deal.II/differentiation/sd.h +++ b/include/deal.II/differentiation/sd.h @@ -23,6 +23,7 @@ # include # include # include +# include # include # include # include diff --git a/include/deal.II/differentiation/sd/symengine_product_types.h b/include/deal.II/differentiation/sd/symengine_product_types.h new file mode 100644 index 000000000000..06d78aa6c5d2 --- /dev/null +++ b/include/deal.II/differentiation/sd/symengine_product_types.h @@ -0,0 +1,121 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + +#ifndef dealii_differentiation_sd_symengine_product_types_h +#define dealii_differentiation_sd_symengine_product_types_h + +#include + +#ifdef DEAL_II_WITH_SYMENGINE + + +# include + +# include + +# include + +# include + + +DEAL_II_NAMESPACE_OPEN + + +template <> +struct EnableIfScalar +{ + typedef Differentiation::SD::Expression type; +}; + + +namespace internal +{ + namespace SD + { + /** + * A more general implementation of product types. + * There are so many permutation of admissible operations + * that getting the compiler to determine the valid + * combinations using template metaprogramming makes + * more sense than manually maintaining the list by + * hand. + * + * This class is a workaround for issue of non-deduction + * of types in template partial specializations that + * would otherwise occur if trying to directly implement + * these as specializations of the ProductTypeImpl class + * itself. + * + * @author Jean-Paul Pelteret, 2019 + */ + template + struct GeneralProductTypeImpl; + + template + struct GeneralProductTypeImpl< + T, + Differentiation::SD::Expression, + typename std::enable_if::value>::type> + { + typedef Differentiation::SD::Expression type; + }; + + template + struct GeneralProductTypeImpl< + T, + Differentiation::SD::Expression, + typename std::enable_if< + boost::is_complex::value && + std::is_arithmetic::value>::type> + { + typedef Differentiation::SD::Expression type; + }; + + } // namespace SD + + + template <> + struct ProductTypeImpl + { + typedef Differentiation::SD::Expression type; + }; + + + template + struct ProductTypeImpl + { + typedef + typename SD::GeneralProductTypeImpl::type + type; + }; + + template + struct ProductTypeImpl + { + typedef + typename SD::GeneralProductTypeImpl::type + type; + }; + +} // namespace internal + +DEAL_II_NAMESPACE_CLOSE + +#endif // DEAL_II_WITH_SYMENGINE + +#endif From 606ecdce1d341da8fa2a784c364beb57db346b07 Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Wed, 17 Apr 2019 22:28:16 +0200 Subject: [PATCH 427/507] Specialize some functions in the numbers namespace for SD::Expression. Also required for support of SD::Expression within the Tensor and SymmetricTensor classes. --- .../sd/symengine_number_types.h | 37 +++++++++++++++++++ 1 file changed, 37 insertions(+) diff --git a/include/deal.II/differentiation/sd/symengine_number_types.h b/include/deal.II/differentiation/sd/symengine_number_types.h index b3a487dcb2c6..23db60cd6ec9 100644 --- a/include/deal.II/differentiation/sd/symengine_number_types.h +++ b/include/deal.II/differentiation/sd/symengine_number_types.h @@ -30,6 +30,7 @@ # include # include # include +# include # include // Number operations @@ -1292,6 +1293,42 @@ namespace Differentiation } // namespace Differentiation +// Specializations from numbers.h +// These are required in order to make the SD::Expression class a compatible +// number for the Tensor and SymmetricTensor classes +namespace numbers +{ + template <> + inline bool + value_is_zero(const Differentiation::SD::Expression &value) + { + if (SymEngine::is_a_Number(value.get_value())) + { + const SymEngine::RCP number_rcp = + SymEngine::rcp_static_cast(value.get_RCP()); + return number_rcp->is_zero(); + } + + return false; + } + + template <> + inline bool + values_are_equal(const Differentiation::SD::Expression &value_1, + const Differentiation::SD::Expression &value_2) + { + return (value_1.get_value().__cmp__(value_2.get_value()) == 0); + } + + template <> + inline bool + value_is_less_than(const Differentiation::SD::Expression &value_1, + const Differentiation::SD::Expression &value_2) + { + return (value_1.get_value().__cmp__(value_2.get_value()) == -1); + } +} // namespace numbers + DEAL_II_NAMESPACE_CLOSE From 50d4e6c1c09ab607fca528aabb8c67cb2592efc4 Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Wed, 17 Apr 2019 22:29:31 +0200 Subject: [PATCH 428/507] Add some SD-related convenience functions for tensor operations. Specifically, these can be used to create a tensor symbol and symbolic function. --- include/deal.II/differentiation/sd.h | 1 + .../sd/symengine_number_types.h | 65 +++- .../sd/symengine_tensor_operations.h | 196 +++++++++++ source/differentiation/sd/CMakeLists.txt | 2 + .../sd/symengine_tensor_operations.cc | 313 ++++++++++++++++++ .../sd/symengine_tensor_operations.inst.in | 85 +++++ .../symengine_tensor_operations_01.cc | 112 +++++++ .../symengine_tensor_operations_01.output | 53 +++ 8 files changed, 825 insertions(+), 2 deletions(-) create mode 100644 include/deal.II/differentiation/sd/symengine_tensor_operations.h create mode 100644 source/differentiation/sd/symengine_tensor_operations.cc create mode 100644 source/differentiation/sd/symengine_tensor_operations.inst.in create mode 100644 tests/symengine/symengine_tensor_operations_01.cc create mode 100644 tests/symengine/symengine_tensor_operations_01.output diff --git a/include/deal.II/differentiation/sd.h b/include/deal.II/differentiation/sd.h index 5039e8a4a2b5..44dca06e9e2f 100644 --- a/include/deal.II/differentiation/sd.h +++ b/include/deal.II/differentiation/sd.h @@ -25,6 +25,7 @@ # include # include # include +# include # include # include diff --git a/include/deal.II/differentiation/sd/symengine_number_types.h b/include/deal.II/differentiation/sd/symengine_number_types.h index 23db60cd6ec9..2b4c65330874 100644 --- a/include/deal.II/differentiation/sd/symengine_number_types.h +++ b/include/deal.II/differentiation/sd/symengine_number_types.h @@ -46,6 +46,7 @@ // Differentiation # include +# include # include # include @@ -1296,6 +1297,66 @@ namespace Differentiation // Specializations from numbers.h // These are required in order to make the SD::Expression class a compatible // number for the Tensor and SymmetricTensor classes + +// Forward declarations: +template +class Tensor; + +namespace internal +{ + template <> + struct NumberType + { + static const Differentiation::SD::Expression & + value(const Differentiation::SD::Expression &t) + { + return t; + } + + template < + typename T, + typename = typename std::enable_if::value>::type> + static Differentiation::SD::Expression + value(const T &t) + { + return Differentiation::SD::Expression(t); + } + + template < + typename T, + typename = typename std::enable_if::value>::type> + static Differentiation::SD::Expression + value(T &&t) + { + return Differentiation::SD::Expression(t); + } + + template < + typename T, + typename = typename std::enable_if::value>::type> + static Differentiation::SD::Expression + value(const std::complex &t) + { + return Differentiation::SD::Expression(t); + } + + template + static Differentiation::SD::Expression + value(const Tensor<0, dim, T> &t) + { + return Differentiation::SD::Expression(static_cast(t)); + } + + template + static Differentiation::SD::Expression + value(const Tensor<0, dim, std::complex> &t) + { + return Differentiation::SD::Expression(static_cast>(t)); + } + }; +} // namespace internal + + namespace numbers { template <> @@ -1329,11 +1390,11 @@ namespace numbers } } // namespace numbers -DEAL_II_NAMESPACE_CLOSE - # endif // DOXYGEN +DEAL_II_NAMESPACE_CLOSE + #endif // DEAL_II_WITH_SYMENGINE #endif // dealii_differentiation_sd_symengine_number_types_h diff --git a/include/deal.II/differentiation/sd/symengine_tensor_operations.h b/include/deal.II/differentiation/sd/symengine_tensor_operations.h new file mode 100644 index 000000000000..d8ba72018094 --- /dev/null +++ b/include/deal.II/differentiation/sd/symengine_tensor_operations.h @@ -0,0 +1,196 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + +#ifndef dealii_differentiation_sd_symengine_tensor_operations_h +#define dealii_differentiation_sd_symengine_tensor_operations_h + +#include + +#ifdef DEAL_II_WITH_SYMENGINE + +# include +# include + +# include +# include + +# include +# include + +DEAL_II_NAMESPACE_OPEN + +namespace Differentiation +{ + namespace SD + { + /** + * @name Symbolic variable creation + */ + //@{ + + /** + * Return a vector of Expressions representing a vectorial symbolic + * variable with the identifier specified by @p symbol. + * + * For example, if the @p symbol is the string `"v"` then the vectorial + * symbolic variable that is returned represents the vector $v$. Each + * component of $v$ is prefixed by the given @p symbol, and has a suffix that + * indicates its component index. + * + * @tparam dim The dimension of the returned tensor. + * @param[in] symbol An indentifier (or name) for the vector of returned + * symbolic variables. + * @return A vector (a rank-1 tensor) of symbolic variables with the name of + * each individual component prefixed by @p symbol. + * + * @warning It is up to the user to ensure that there is no ambiguity in the + * symbols used within a section of code. + */ + template + Tensor<1, dim, Expression> + make_vector_of_symbols(const std::string &symbol); + + /** + * Return a tensor of Expressions representing a tensorial symbolic + * variable with the identifier specified by @p symbol. + * + * For example, if the @p symbol is the string `"T"` then the tensorial + * symbolic variable that is returned represents the vector $T$. Each + * component of $T$ is prefixed by the given @p symbol, and has a suffix that + * indicates its component indices. + * + * @tparam rank The rank of the returned tensor. + * @tparam dim The dimension of the returned tensor. + * @param[in] symbol An indentifier (or name) for the tensor of returned + * symbolic variables. + * @return A tensor of symbolic variables with the name of each individual + * component prefixed by @p symbol. + * + * @warning It is up to the user to ensure that there is no ambiguity in the + * symbols used within a section of code. + */ + template + Tensor + make_tensor_of_symbols(const std::string &symbol); + + /** + * Return a symmetric tensor of Expressions representing a tensorial + * symbolic variable with the identifier specified by @p symbol. + * + * For example, if the @p symbol is the string `"S"` then the tensorial + * symbolic variable that is returned represents the vector $S$. Each + * component of $S$ is prefixed by the given @p symbol, and has a suffix that + * indicates its component indices. + * + * @tparam rank The rank of the returned tensor. + * @tparam dim The dimension of the returned tensor. + * @param[in] symbol An indentifier (or name) for the tensor of returned + * symbolic variables. + * @return A tensor of symbolic variables with the name of each individual + * component prefixed by @p symbol. + * + * @warning It is up to the user to ensure that there is no ambiguity in the + * symbols used within a section of code. + */ + template + SymmetricTensor + make_symmetric_tensor_of_symbols(const std::string &symbol); + + /** + * Return a vector of Expression representing a vectorial symbolic + * function with the identifier specified by @p symbol. The functions' + * symbolic dependencies are specified by the keys to the input + * @p arguments map; the values stored in the map are ignored. + * + * @tparam dim The dimension of the returned tensor. + * @param[in] symbol An indentifier (or name) for the vector of returned + * symbolic functions. + * @param[in] arguments A map of input arguments to the returned + * symbolic functions. + * @return A vector (a rank-1 tensor) of generic symbolic functions with the + * name of each individual component prefixed by @p symbol, a suffix + * that indicates its component index, and the number of input + * arguments equal to the length of @p arguments. + * + * @warning It is up to the user to ensure that there is no ambiguity in the + * symbols used within a section of code. + */ + template + Tensor<1, dim, Expression> + make_vector_of_symbolic_functions(const std::string & symbol, + const types::substitution_map &arguments); + + /** + * Return a tensor of Expression representing a tensorial symbolic + * function with the identifier specified by @p symbol. The functions' + * symbolic dependencies are specified by the keys to the input + * @p arguments map; the values stored in the map are ignored. + * + * @tparam rank The rank of the returned tensor. + * @tparam dim The dimension of the returned tensor. + * @param[in] symbol An indentifier (or name) for the tensor of returned + * symbolic functions. + * @param[in] arguments A map of input arguments to the returned + * symbolic functions. + * @return A tensor of generic symbolic functions with the name of each + * individual component prefixed by @p symbol, a suffix that + * indicates its component indeices, and the number of input + * arguments equal to the length of @p arguments. + * + * @warning It is up to the user to ensure that there is no ambiguity in the + * symbols used within a section of code. + */ + template + Tensor + make_tensor_of_symbolic_functions(const std::string & symbol, + const types::substitution_map &arguments); + + /** + * Return a symmetric tensor of Expression representing a tensorial + * symbolic function with the identifier specified by @p symbol. The + * functions' symbolic dependencies are specified by the keys to the input + * @p arguments map; the values stored in the map are ignored. + * + * @tparam rank The rank of the returned tensor. + * @tparam dim The dimension of the returned tensor. + * @param[in] symbol An indentifier (or name) for the tensor of returned + * symbolic functions. + * @param[in] arguments A map of input arguments to the returned + * symbolic functions. + * @return A symmetric tensor of generic symbolic functions with the name of + * each individual component prefixed by @p symbol, a suffix that + * indicates its component indeices, and the number of input + * arguments equal to the length of @p arguments. + * + * @warning It is up to the user to ensure that there is no ambiguity in the + * symbols used within a section of code. + */ + template + SymmetricTensor + make_symmetric_tensor_of_symbolic_functions( + const std::string & symbol, + const types::substitution_map &arguments); + + //@} + + } // namespace SD +} // namespace Differentiation + + +DEAL_II_NAMESPACE_CLOSE + +#endif // DEAL_II_WITH_SYMENGINE + +#endif diff --git a/source/differentiation/sd/CMakeLists.txt b/source/differentiation/sd/CMakeLists.txt index 0cb7b56a5e7e..a0de87e090d6 100644 --- a/source/differentiation/sd/CMakeLists.txt +++ b/source/differentiation/sd/CMakeLists.txt @@ -19,11 +19,13 @@ SET(_src symengine_math.cc symengine_number_types.cc symengine_scalar_operations.cc + symengine_tensor_operations.cc symengine_types.cc symengine_utilities.cc ) SET(_inst + symengine_tensor_operations.inst.in ) FILE(GLOB _header diff --git a/source/differentiation/sd/symengine_tensor_operations.cc b/source/differentiation/sd/symengine_tensor_operations.cc new file mode 100644 index 000000000000..bd2e743623f9 --- /dev/null +++ b/source/differentiation/sd/symengine_tensor_operations.cc @@ -0,0 +1,313 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2016 - 2017 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + + +#include + +#ifdef DEAL_II_WITH_SYMENGINE + +# include +# include +# include + +# include +# include +# include +# include +# include + +DEAL_II_NAMESPACE_OPEN + +namespace Differentiation +{ + namespace SD + { + // --- Symbolic variable creation --- + + namespace internal + { + namespace + { + template + TableIndices<4> + make_rank_4_tensor_indices(const unsigned int &idx_i, + const unsigned int &idx_j) + { + const TableIndices<2> indices_i( + SymmetricTensor<2, dim>::unrolled_to_component_indices(idx_i)); + const TableIndices<2> indices_j( + SymmetricTensor<2, dim>::unrolled_to_component_indices(idx_j)); + return TableIndices<4>(indices_i[0], + indices_i[1], + indices_j[0], + indices_j[1]); + } + + + template + std::string + make_index_string(const TableIndices &indices) + { + std::string out; + for (unsigned int i = 0; i < rank; ++i) + out += dealii::Utilities::to_string(indices[i]); + return out; + } + + + template + struct Symbol_Tensor; + + + template + struct Symbol_Tensor + { + static Tensor + create(const std::string &sym) + { + Tensor out; + for (unsigned int i = 0; i < out.n_independent_components; ++i) + { + const TableIndices indices( + out.unrolled_to_component_indices(i)); + out[indices] = Expression(sym + std::string("_") + + internal::make_index_string(indices)); + } + return out; + } + }; + + + template + struct Symbol_Tensor<0, dim> + { + static Tensor<0, dim, Expression> + create(const std::string &sym) + { + return make_symbol(sym); + } + }; + + + template + struct Symbol_SymmetricTensor; + + + template + struct Symbol_SymmetricTensor + { + static SymmetricTensor<2, dim, Expression> + create(const std::string &sym) + { + SymmetricTensor out; + for (unsigned int i = 0; i < out.n_independent_components; ++i) + { + const TableIndices indices( + out.unrolled_to_component_indices(i)); + out[indices] = Expression(sym + std::string("_") + + internal::make_index_string(indices)); + } + return out; + } + }; + + + template + struct Symbol_SymmetricTensor<4, dim> + { + static SymmetricTensor<4, dim, Expression> + create(const std::string &sym) + { + SymmetricTensor<4, dim, Expression> out; + for (unsigned int i = 0; + i < SymmetricTensor<2, dim>::n_independent_components; + ++i) + for (unsigned int j = 0; + j < SymmetricTensor<2, dim>::n_independent_components; + ++j) + { + const TableIndices<4> indices = + make_rank_4_tensor_indices(i, j); + out[indices] = + Expression(sym + std::string("_") + + internal::make_index_string(indices)); + } + return out; + } + }; + + + template + struct Symbol_Function_Tensor; + + + template + struct Symbol_Function_Tensor + { + static Tensor + create(const std::string & sym, + const types::substitution_map &arguments) + { + Tensor out; + const types::symbol_vector args = + Utilities::extract_symbols(arguments); + for (unsigned int i = 0; i < out.n_independent_components; ++i) + { + const TableIndices indices( + out.unrolled_to_component_indices(i)); + out[indices] = + Expression(sym + std::string("_") + + internal::make_index_string(indices), + args); + } + return out; + } + }; + + + template + struct Symbol_Function_Tensor<0, dim> + { + static Tensor<0, dim, Expression> + create(const std::string & sym, + const types::substitution_map &arguments) + { + return make_symbolic_function(sym, arguments); + } + }; + + + template + struct Symbol_Function_SymmetricTensor; + + + template + struct Symbol_Function_SymmetricTensor + { + static SymmetricTensor<2, dim, Expression> + create(const std::string & sym, + const types::substitution_map &arguments) + { + SymmetricTensor out; + const types::symbol_vector args = + Utilities::extract_symbols(arguments); + for (unsigned int i = 0; i < out.n_independent_components; ++i) + { + const TableIndices indices( + out.unrolled_to_component_indices(i)); + out[indices] = + Expression(sym + std::string("_") + + internal::make_index_string(indices), + args); + } + return out; + } + }; + + + template + struct Symbol_Function_SymmetricTensor<4, dim> + { + static SymmetricTensor<4, dim, Expression> + create(const std::string & sym, + const types::substitution_map &arguments) + { + SymmetricTensor<4, dim, Expression> out; + const types::symbol_vector args = + Utilities::extract_symbols(arguments); + for (unsigned int i = 0; + i < SymmetricTensor<2, dim>::n_independent_components; + ++i) + for (unsigned int j = 0; + j < SymmetricTensor<2, dim>::n_independent_components; + ++j) + { + const TableIndices<4> indices = + make_rank_4_tensor_indices(i, j); + out[indices] = + Expression(sym + std::string("_") + + internal::make_index_string(indices), + args); + } + return out; + } + }; + } // namespace + } // namespace internal + + + template + Tensor<1, dim, Expression> + make_vector_of_symbols(const std::string &sym) + { + return internal::Symbol_Tensor<1, dim>::create(sym); + } + + + template + Tensor<1, dim, Expression> + make_vector_of_symbolic_functions(const std::string & sym, + const types::substitution_map &arguments) + { + return internal::Symbol_Function_Tensor<1, dim>::create(sym, arguments); + } + + + template + Tensor + make_tensor_of_symbols(const std::string &sym) + { + return internal::Symbol_Tensor::create(sym); + } + + + template + SymmetricTensor + make_symmetric_tensor_of_symbols(const std::string &sym) + { + return internal::Symbol_SymmetricTensor::create(sym); + } + + + template + Tensor + make_tensor_of_symbolic_functions(const std::string & sym, + const types::substitution_map &arguments) + { + return internal::Symbol_Function_Tensor::create(sym, + arguments); + } + + + template + SymmetricTensor + make_symmetric_tensor_of_symbolic_functions( + const std::string & sym, + const types::substitution_map &arguments) + { + return internal::Symbol_Function_SymmetricTensor::create( + sym, arguments); + } + + } // namespace SD +} // namespace Differentiation + +/* --- Explicit instantiations --- */ + +# include "symengine_tensor_operations.inst" + +DEAL_II_NAMESPACE_CLOSE + +#endif // DEAL_II_WITH_SYMENGINE diff --git a/source/differentiation/sd/symengine_tensor_operations.inst.in b/source/differentiation/sd/symengine_tensor_operations.inst.in new file mode 100644 index 000000000000..1a4a80204cbd --- /dev/null +++ b/source/differentiation/sd/symengine_tensor_operations.inst.in @@ -0,0 +1,85 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + + +for (deal_II_dimension : DIMENSIONS) + { + namespace Differentiation + \{ + namespace SD + \{ + + template Tensor<1, deal_II_dimension, Expression> + make_vector_of_symbols(const std::string &symbol); + + template Tensor<1, deal_II_dimension, Expression> + make_vector_of_symbolic_functions( + const std::string & symbol, + const types::substitution_map &arguments); + + /*--- Rank-0 definitions ---*/ + + template Tensor<0, deal_II_dimension, Expression> + make_tensor_of_symbols<0, deal_II_dimension>(const std::string &symbol); + + template Tensor<0, deal_II_dimension, Expression> + make_tensor_of_symbolic_functions<0, deal_II_dimension>( + const std::string & symbol, + const types::substitution_map &arguments); + \} + \} + } + + +for (rank : RANKS; deal_II_dimension : DIMENSIONS) + { + namespace Differentiation + \{ + namespace SD + \{ + + template Tensor + make_tensor_of_symbols( + const std::string &symbol); + + template Tensor + make_tensor_of_symbolic_functions( + const std::string & symbol, + const types::substitution_map &arguments); + + \} + \} + } + + +for (rank : SYM_RANKS; deal_II_dimension : DIMENSIONS) + { + namespace Differentiation + \{ + namespace SD + \{ + + template SymmetricTensor + make_symmetric_tensor_of_symbols( + const std::string &symbol); + + template SymmetricTensor + make_symmetric_tensor_of_symbolic_functions( + const std::string & symbol, + const types::substitution_map &arguments); + + \} + \} + } diff --git a/tests/symengine/symengine_tensor_operations_01.cc b/tests/symengine/symengine_tensor_operations_01.cc new file mode 100644 index 000000000000..b750d40dbcef --- /dev/null +++ b/tests/symengine/symengine_tensor_operations_01.cc @@ -0,0 +1,112 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + + +// Check that symbol tensors and symbolic function tensors can be created +// using the utility functions + +#include + +#include "../tests.h" + +using namespace dealii; +namespace SD = Differentiation::SD; + + +template +void +test() +{ + deallog.push("dim " + Utilities::to_string(dim)); + + using SD_number_t = SD::Expression; + + const Tensor<1, dim, SD_number_t> symb_v = + SD::make_vector_of_symbols("v"); + const Tensor<0, dim, SD_number_t> symb_T0 = + SD::make_tensor_of_symbols<0, dim>("T0"); + const Tensor<1, dim, SD_number_t> symb_T1 = + SD::make_tensor_of_symbols<1, dim>("T1"); + const Tensor<2, dim, SD_number_t> symb_T2 = + SD::make_tensor_of_symbols<2, dim>("T2"); + const Tensor<3, dim, SD_number_t> symb_T3 = + SD::make_tensor_of_symbols<3, dim>("T3"); + const Tensor<4, dim, SD_number_t> symb_T4 = + SD::make_tensor_of_symbols<4, dim>("T4"); + const SymmetricTensor<2, dim, SD_number_t> symb_ST2 = + SD::make_symmetric_tensor_of_symbols<2, dim>("ST2"); + const SymmetricTensor<4, dim, SD_number_t> symb_ST4 = + SD::make_symmetric_tensor_of_symbols<4, dim>("ST4"); + + deallog << "Symbol vector: " << symb_v << std::endl; + deallog << "Symbol tensor (rank-0): " << symb_T0 << std::endl; + deallog << "Symbol tensor (rank-1): " << symb_T1 << std::endl; + deallog << "Symbol tensor (rank-2): " << symb_T2 << std::endl; + deallog << "Symbol tensor (rank-3): " << symb_T3 << std::endl; + deallog << "Symbol tensor (rank-4): " << symb_T4 << std::endl; + deallog << "Symbol symmetric tensor (rank-2): " << symb_ST2 << std::endl; + deallog << "Symbol symmetric tensor (rank-4): " << symb_ST4 << std::endl; + + SD::types::substitution_map sub_map; + sub_map[symb_T0] = 0.0; + for (unsigned int i = 0; i < dim; ++i) + { + sub_map[symb_v[i]] = 0.0; + } + + const Tensor<1, dim, SD_number_t> symb_func_v = + SD::make_vector_of_symbolic_functions("f_v", sub_map); + const Tensor<0, dim, SD_number_t> symb_func_T0 = + SD::make_tensor_of_symbolic_functions<0, dim>("f_T0", sub_map); + const Tensor<1, dim, SD_number_t> symb_func_T1 = + SD::make_tensor_of_symbolic_functions<1, dim>("f_T1", sub_map); + const Tensor<2, dim, SD_number_t> symb_func_T2 = + SD::make_tensor_of_symbolic_functions<2, dim>("f_T2", sub_map); + const Tensor<3, dim, SD_number_t> symb_func_T3 = + SD::make_tensor_of_symbolic_functions<3, dim>("f_T3", sub_map); + const Tensor<4, dim, SD_number_t> symb_func_T4 = + SD::make_tensor_of_symbolic_functions<4, dim>("f_T4", sub_map); + const SymmetricTensor<2, dim, SD_number_t> symb_func_ST2 = + SD::make_symmetric_tensor_of_symbolic_functions<2, dim>("f_ST2", sub_map); + const SymmetricTensor<4, dim, SD_number_t> symb_func_ST4 = + SD::make_symmetric_tensor_of_symbolic_functions<4, dim>("f_ST4", sub_map); + + deallog << "Symbol function vector: " << symb_func_v << std::endl; + deallog << "Symbol function tensor (rank-0): " << symb_func_T0 << std::endl; + deallog << "Symbol function tensor (rank-1): " << symb_func_T1 << std::endl; + deallog << "Symbol function tensor (rank-2): " << symb_func_T2 << std::endl; + deallog << "Symbol function tensor (rank-3): " << symb_func_T3 << std::endl; + deallog << "Symbol function tensor (rank-4): " << symb_func_T4 << std::endl; + deallog << "Symbol function symmetric tensor (rank-2): " << symb_func_ST2 + << std::endl; + deallog << "Symbol function symmetric tensor (rank-4): " << symb_func_ST4 + << std::endl; + + deallog << "OK" << std::endl; + deallog.pop(); +} + + +int +main() +{ + initlog(); + + test<1>(); + test<2>(); + test<3>(); + + deallog << "OK" << std::endl; +} diff --git a/tests/symengine/symengine_tensor_operations_01.output b/tests/symengine/symengine_tensor_operations_01.output new file mode 100644 index 000000000000..ee6a9771745f --- /dev/null +++ b/tests/symengine/symengine_tensor_operations_01.output @@ -0,0 +1,53 @@ + +DEAL:dim 1::Symbol vector: v_0 +DEAL:dim 1::Symbol tensor (rank-0): T0 +DEAL:dim 1::Symbol tensor (rank-1): T1_0 +DEAL:dim 1::Symbol tensor (rank-2): T2_00 +DEAL:dim 1::Symbol tensor (rank-3): T3_000 +DEAL:dim 1::Symbol tensor (rank-4): T4_0000 +DEAL:dim 1::Symbol symmetric tensor (rank-2): ST2_00 +DEAL:dim 1::Symbol symmetric tensor (rank-4): ST4_0000 +DEAL:dim 1::Symbol function vector: f_v_0(T0, v_0) +DEAL:dim 1::Symbol function tensor (rank-0): f_T0(T0, v_0) +DEAL:dim 1::Symbol function tensor (rank-1): f_T1_0(T0, v_0) +DEAL:dim 1::Symbol function tensor (rank-2): f_T2_00(T0, v_0) +DEAL:dim 1::Symbol function tensor (rank-3): f_T3_000(T0, v_0) +DEAL:dim 1::Symbol function tensor (rank-4): f_T4_0000(T0, v_0) +DEAL:dim 1::Symbol function symmetric tensor (rank-2): f_ST2_00(T0, v_0) +DEAL:dim 1::Symbol function symmetric tensor (rank-4): f_ST4_0000(T0, v_0) +DEAL:dim 1::OK +DEAL:dim 2::Symbol vector: v_0 v_1 +DEAL:dim 2::Symbol tensor (rank-0): T0 +DEAL:dim 2::Symbol tensor (rank-1): T1_0 T1_1 +DEAL:dim 2::Symbol tensor (rank-2): T2_00 T2_01 T2_10 T2_11 +DEAL:dim 2::Symbol tensor (rank-3): T3_000 T3_001 T3_010 T3_011 T3_100 T3_101 T3_110 T3_111 +DEAL:dim 2::Symbol tensor (rank-4): T4_0000 T4_0001 T4_0010 T4_0011 T4_0100 T4_0101 T4_0110 T4_0111 T4_1000 T4_1001 T4_1010 T4_1011 T4_1100 T4_1101 T4_1110 T4_1111 +DEAL:dim 2::Symbol symmetric tensor (rank-2): ST2_00 ST2_01 ST2_01 ST2_11 +DEAL:dim 2::Symbol symmetric tensor (rank-4): ST4_0000 ST4_0001 ST4_0001 ST4_0011 ST4_0100 ST4_0101 ST4_0101 ST4_0111 ST4_0100 ST4_0101 ST4_0101 ST4_0111 ST4_1100 ST4_1101 ST4_1101 ST4_1111 +DEAL:dim 2::Symbol function vector: f_v_0(T0, v_0, v_1) f_v_1(T0, v_0, v_1) +DEAL:dim 2::Symbol function tensor (rank-0): f_T0(T0, v_0, v_1) +DEAL:dim 2::Symbol function tensor (rank-1): f_T1_0(T0, v_0, v_1) f_T1_1(T0, v_0, v_1) +DEAL:dim 2::Symbol function tensor (rank-2): f_T2_00(T0, v_0, v_1) f_T2_01(T0, v_0, v_1) f_T2_10(T0, v_0, v_1) f_T2_11(T0, v_0, v_1) +DEAL:dim 2::Symbol function tensor (rank-3): f_T3_000(T0, v_0, v_1) f_T3_001(T0, v_0, v_1) f_T3_010(T0, v_0, v_1) f_T3_011(T0, v_0, v_1) f_T3_100(T0, v_0, v_1) f_T3_101(T0, v_0, v_1) f_T3_110(T0, v_0, v_1) f_T3_111(T0, v_0, v_1) +DEAL:dim 2::Symbol function tensor (rank-4): f_T4_0000(T0, v_0, v_1) f_T4_0001(T0, v_0, v_1) f_T4_0010(T0, v_0, v_1) f_T4_0011(T0, v_0, v_1) f_T4_0100(T0, v_0, v_1) f_T4_0101(T0, v_0, v_1) f_T4_0110(T0, v_0, v_1) f_T4_0111(T0, v_0, v_1) f_T4_1000(T0, v_0, v_1) f_T4_1001(T0, v_0, v_1) f_T4_1010(T0, v_0, v_1) f_T4_1011(T0, v_0, v_1) f_T4_1100(T0, v_0, v_1) f_T4_1101(T0, v_0, v_1) f_T4_1110(T0, v_0, v_1) f_T4_1111(T0, v_0, v_1) +DEAL:dim 2::Symbol function symmetric tensor (rank-2): f_ST2_00(T0, v_0, v_1) f_ST2_01(T0, v_0, v_1) f_ST2_01(T0, v_0, v_1) f_ST2_11(T0, v_0, v_1) +DEAL:dim 2::Symbol function symmetric tensor (rank-4): f_ST4_0000(T0, v_0, v_1) f_ST4_0001(T0, v_0, v_1) f_ST4_0001(T0, v_0, v_1) f_ST4_0011(T0, v_0, v_1) f_ST4_0100(T0, v_0, v_1) f_ST4_0101(T0, v_0, v_1) f_ST4_0101(T0, v_0, v_1) f_ST4_0111(T0, v_0, v_1) f_ST4_0100(T0, v_0, v_1) f_ST4_0101(T0, v_0, v_1) f_ST4_0101(T0, v_0, v_1) f_ST4_0111(T0, v_0, v_1) f_ST4_1100(T0, v_0, v_1) f_ST4_1101(T0, v_0, v_1) f_ST4_1101(T0, v_0, v_1) f_ST4_1111(T0, v_0, v_1) +DEAL:dim 2::OK +DEAL:dim 3::Symbol vector: v_0 v_1 v_2 +DEAL:dim 3::Symbol tensor (rank-0): T0 +DEAL:dim 3::Symbol tensor (rank-1): T1_0 T1_1 T1_2 +DEAL:dim 3::Symbol tensor (rank-2): T2_00 T2_01 T2_02 T2_10 T2_11 T2_12 T2_20 T2_21 T2_22 +DEAL:dim 3::Symbol tensor (rank-3): T3_000 T3_001 T3_002 T3_010 T3_011 T3_012 T3_020 T3_021 T3_022 T3_100 T3_101 T3_102 T3_110 T3_111 T3_112 T3_120 T3_121 T3_122 T3_200 T3_201 T3_202 T3_210 T3_211 T3_212 T3_220 T3_221 T3_222 +DEAL:dim 3::Symbol tensor (rank-4): T4_0000 T4_0001 T4_0002 T4_0010 T4_0011 T4_0012 T4_0020 T4_0021 T4_0022 T4_0100 T4_0101 T4_0102 T4_0110 T4_0111 T4_0112 T4_0120 T4_0121 T4_0122 T4_0200 T4_0201 T4_0202 T4_0210 T4_0211 T4_0212 T4_0220 T4_0221 T4_0222 T4_1000 T4_1001 T4_1002 T4_1010 T4_1011 T4_1012 T4_1020 T4_1021 T4_1022 T4_1100 T4_1101 T4_1102 T4_1110 T4_1111 T4_1112 T4_1120 T4_1121 T4_1122 T4_1200 T4_1201 T4_1202 T4_1210 T4_1211 T4_1212 T4_1220 T4_1221 T4_1222 T4_2000 T4_2001 T4_2002 T4_2010 T4_2011 T4_2012 T4_2020 T4_2021 T4_2022 T4_2100 T4_2101 T4_2102 T4_2110 T4_2111 T4_2112 T4_2120 T4_2121 T4_2122 T4_2200 T4_2201 T4_2202 T4_2210 T4_2211 T4_2212 T4_2220 T4_2221 T4_2222 +DEAL:dim 3::Symbol symmetric tensor (rank-2): ST2_00 ST2_01 ST2_02 ST2_01 ST2_11 ST2_12 ST2_02 ST2_12 ST2_22 +DEAL:dim 3::Symbol symmetric tensor (rank-4): ST4_0000 ST4_0001 ST4_0002 ST4_0001 ST4_0011 ST4_0012 ST4_0002 ST4_0012 ST4_0022 ST4_0100 ST4_0101 ST4_0102 ST4_0101 ST4_0111 ST4_0112 ST4_0102 ST4_0112 ST4_0122 ST4_0200 ST4_0201 ST4_0202 ST4_0201 ST4_0211 ST4_0212 ST4_0202 ST4_0212 ST4_0222 ST4_0100 ST4_0101 ST4_0102 ST4_0101 ST4_0111 ST4_0112 ST4_0102 ST4_0112 ST4_0122 ST4_1100 ST4_1101 ST4_1102 ST4_1101 ST4_1111 ST4_1112 ST4_1102 ST4_1112 ST4_1122 ST4_1200 ST4_1201 ST4_1202 ST4_1201 ST4_1211 ST4_1212 ST4_1202 ST4_1212 ST4_1222 ST4_0200 ST4_0201 ST4_0202 ST4_0201 ST4_0211 ST4_0212 ST4_0202 ST4_0212 ST4_0222 ST4_1200 ST4_1201 ST4_1202 ST4_1201 ST4_1211 ST4_1212 ST4_1202 ST4_1212 ST4_1222 ST4_2200 ST4_2201 ST4_2202 ST4_2201 ST4_2211 ST4_2212 ST4_2202 ST4_2212 ST4_2222 +DEAL:dim 3::Symbol function vector: f_v_0(T0, v_0, v_1, v_2) f_v_1(T0, v_0, v_1, v_2) f_v_2(T0, v_0, v_1, v_2) +DEAL:dim 3::Symbol function tensor (rank-0): f_T0(T0, v_0, v_1, v_2) +DEAL:dim 3::Symbol function tensor (rank-1): f_T1_0(T0, v_0, v_1, v_2) f_T1_1(T0, v_0, v_1, v_2) f_T1_2(T0, v_0, v_1, v_2) +DEAL:dim 3::Symbol function tensor (rank-2): f_T2_00(T0, v_0, v_1, v_2) f_T2_01(T0, v_0, v_1, v_2) f_T2_02(T0, v_0, v_1, v_2) f_T2_10(T0, v_0, v_1, v_2) f_T2_11(T0, v_0, v_1, v_2) f_T2_12(T0, v_0, v_1, v_2) f_T2_20(T0, v_0, v_1, v_2) f_T2_21(T0, v_0, v_1, v_2) f_T2_22(T0, v_0, v_1, v_2) +DEAL:dim 3::Symbol function tensor (rank-3): f_T3_000(T0, v_0, v_1, v_2) f_T3_001(T0, v_0, v_1, v_2) f_T3_002(T0, v_0, v_1, v_2) f_T3_010(T0, v_0, v_1, v_2) f_T3_011(T0, v_0, v_1, v_2) f_T3_012(T0, v_0, v_1, v_2) f_T3_020(T0, v_0, v_1, v_2) f_T3_021(T0, v_0, v_1, v_2) f_T3_022(T0, v_0, v_1, v_2) f_T3_100(T0, v_0, v_1, v_2) f_T3_101(T0, v_0, v_1, v_2) f_T3_102(T0, v_0, v_1, v_2) f_T3_110(T0, v_0, v_1, v_2) f_T3_111(T0, v_0, v_1, v_2) f_T3_112(T0, v_0, v_1, v_2) f_T3_120(T0, v_0, v_1, v_2) f_T3_121(T0, v_0, v_1, v_2) f_T3_122(T0, v_0, v_1, v_2) f_T3_200(T0, v_0, v_1, v_2) f_T3_201(T0, v_0, v_1, v_2) f_T3_202(T0, v_0, v_1, v_2) f_T3_210(T0, v_0, v_1, v_2) f_T3_211(T0, v_0, v_1, v_2) f_T3_212(T0, v_0, v_1, v_2) f_T3_220(T0, v_0, v_1, v_2) f_T3_221(T0, v_0, v_1, v_2) f_T3_222(T0, v_0, v_1, v_2) +DEAL:dim 3::Symbol function tensor (rank-4): f_T4_0000(T0, v_0, v_1, v_2) f_T4_0001(T0, v_0, v_1, v_2) f_T4_0002(T0, v_0, v_1, v_2) f_T4_0010(T0, v_0, v_1, v_2) f_T4_0011(T0, v_0, v_1, v_2) f_T4_0012(T0, v_0, v_1, v_2) f_T4_0020(T0, v_0, v_1, v_2) f_T4_0021(T0, v_0, v_1, v_2) f_T4_0022(T0, v_0, v_1, v_2) f_T4_0100(T0, v_0, v_1, v_2) f_T4_0101(T0, v_0, v_1, v_2) f_T4_0102(T0, v_0, v_1, v_2) f_T4_0110(T0, v_0, v_1, v_2) f_T4_0111(T0, v_0, v_1, v_2) f_T4_0112(T0, v_0, v_1, v_2) f_T4_0120(T0, v_0, v_1, v_2) f_T4_0121(T0, v_0, v_1, v_2) f_T4_0122(T0, v_0, v_1, v_2) f_T4_0200(T0, v_0, v_1, v_2) f_T4_0201(T0, v_0, v_1, v_2) f_T4_0202(T0, v_0, v_1, v_2) f_T4_0210(T0, v_0, v_1, v_2) f_T4_0211(T0, v_0, v_1, v_2) f_T4_0212(T0, v_0, v_1, v_2) f_T4_0220(T0, v_0, v_1, v_2) f_T4_0221(T0, v_0, v_1, v_2) f_T4_0222(T0, v_0, v_1, v_2) f_T4_1000(T0, v_0, v_1, v_2) f_T4_1001(T0, v_0, v_1, v_2) f_T4_1002(T0, v_0, v_1, v_2) f_T4_1010(T0, v_0, v_1, v_2) f_T4_1011(T0, v_0, v_1, v_2) f_T4_1012(T0, v_0, v_1, v_2) f_T4_1020(T0, v_0, v_1, v_2) f_T4_1021(T0, v_0, v_1, v_2) f_T4_1022(T0, v_0, v_1, v_2) f_T4_1100(T0, v_0, v_1, v_2) f_T4_1101(T0, v_0, v_1, v_2) f_T4_1102(T0, v_0, v_1, v_2) f_T4_1110(T0, v_0, v_1, v_2) f_T4_1111(T0, v_0, v_1, v_2) f_T4_1112(T0, v_0, v_1, v_2) f_T4_1120(T0, v_0, v_1, v_2) f_T4_1121(T0, v_0, v_1, v_2) f_T4_1122(T0, v_0, v_1, v_2) f_T4_1200(T0, v_0, v_1, v_2) f_T4_1201(T0, v_0, v_1, v_2) f_T4_1202(T0, v_0, v_1, v_2) f_T4_1210(T0, v_0, v_1, v_2) f_T4_1211(T0, v_0, v_1, v_2) f_T4_1212(T0, v_0, v_1, v_2) f_T4_1220(T0, v_0, v_1, v_2) f_T4_1221(T0, v_0, v_1, v_2) f_T4_1222(T0, v_0, v_1, v_2) f_T4_2000(T0, v_0, v_1, v_2) f_T4_2001(T0, v_0, v_1, v_2) f_T4_2002(T0, v_0, v_1, v_2) f_T4_2010(T0, v_0, v_1, v_2) f_T4_2011(T0, v_0, v_1, v_2) f_T4_2012(T0, v_0, v_1, v_2) f_T4_2020(T0, v_0, v_1, v_2) f_T4_2021(T0, v_0, v_1, v_2) f_T4_2022(T0, v_0, v_1, v_2) f_T4_2100(T0, v_0, v_1, v_2) f_T4_2101(T0, v_0, v_1, v_2) f_T4_2102(T0, v_0, v_1, v_2) f_T4_2110(T0, v_0, v_1, v_2) f_T4_2111(T0, v_0, v_1, v_2) f_T4_2112(T0, v_0, v_1, v_2) f_T4_2120(T0, v_0, v_1, v_2) f_T4_2121(T0, v_0, v_1, v_2) f_T4_2122(T0, v_0, v_1, v_2) f_T4_2200(T0, v_0, v_1, v_2) f_T4_2201(T0, v_0, v_1, v_2) f_T4_2202(T0, v_0, v_1, v_2) f_T4_2210(T0, v_0, v_1, v_2) f_T4_2211(T0, v_0, v_1, v_2) f_T4_2212(T0, v_0, v_1, v_2) f_T4_2220(T0, v_0, v_1, v_2) f_T4_2221(T0, v_0, v_1, v_2) f_T4_2222(T0, v_0, v_1, v_2) +DEAL:dim 3::Symbol function symmetric tensor (rank-2): f_ST2_00(T0, v_0, v_1, v_2) f_ST2_01(T0, v_0, v_1, v_2) f_ST2_02(T0, v_0, v_1, v_2) f_ST2_01(T0, v_0, v_1, v_2) f_ST2_11(T0, v_0, v_1, v_2) f_ST2_12(T0, v_0, v_1, v_2) f_ST2_02(T0, v_0, v_1, v_2) f_ST2_12(T0, v_0, v_1, v_2) f_ST2_22(T0, v_0, v_1, v_2) +DEAL:dim 3::Symbol function symmetric tensor (rank-4): f_ST4_0000(T0, v_0, v_1, v_2) f_ST4_0001(T0, v_0, v_1, v_2) f_ST4_0002(T0, v_0, v_1, v_2) f_ST4_0001(T0, v_0, v_1, v_2) f_ST4_0011(T0, v_0, v_1, v_2) f_ST4_0012(T0, v_0, v_1, v_2) f_ST4_0002(T0, v_0, v_1, v_2) f_ST4_0012(T0, v_0, v_1, v_2) f_ST4_0022(T0, v_0, v_1, v_2) f_ST4_0100(T0, v_0, v_1, v_2) f_ST4_0101(T0, v_0, v_1, v_2) f_ST4_0102(T0, v_0, v_1, v_2) f_ST4_0101(T0, v_0, v_1, v_2) f_ST4_0111(T0, v_0, v_1, v_2) f_ST4_0112(T0, v_0, v_1, v_2) f_ST4_0102(T0, v_0, v_1, v_2) f_ST4_0112(T0, v_0, v_1, v_2) f_ST4_0122(T0, v_0, v_1, v_2) f_ST4_0200(T0, v_0, v_1, v_2) f_ST4_0201(T0, v_0, v_1, v_2) f_ST4_0202(T0, v_0, v_1, v_2) f_ST4_0201(T0, v_0, v_1, v_2) f_ST4_0211(T0, v_0, v_1, v_2) f_ST4_0212(T0, v_0, v_1, v_2) f_ST4_0202(T0, v_0, v_1, v_2) f_ST4_0212(T0, v_0, v_1, v_2) f_ST4_0222(T0, v_0, v_1, v_2) f_ST4_0100(T0, v_0, v_1, v_2) f_ST4_0101(T0, v_0, v_1, v_2) f_ST4_0102(T0, v_0, v_1, v_2) f_ST4_0101(T0, v_0, v_1, v_2) f_ST4_0111(T0, v_0, v_1, v_2) f_ST4_0112(T0, v_0, v_1, v_2) f_ST4_0102(T0, v_0, v_1, v_2) f_ST4_0112(T0, v_0, v_1, v_2) f_ST4_0122(T0, v_0, v_1, v_2) f_ST4_1100(T0, v_0, v_1, v_2) f_ST4_1101(T0, v_0, v_1, v_2) f_ST4_1102(T0, v_0, v_1, v_2) f_ST4_1101(T0, v_0, v_1, v_2) f_ST4_1111(T0, v_0, v_1, v_2) f_ST4_1112(T0, v_0, v_1, v_2) f_ST4_1102(T0, v_0, v_1, v_2) f_ST4_1112(T0, v_0, v_1, v_2) f_ST4_1122(T0, v_0, v_1, v_2) f_ST4_1200(T0, v_0, v_1, v_2) f_ST4_1201(T0, v_0, v_1, v_2) f_ST4_1202(T0, v_0, v_1, v_2) f_ST4_1201(T0, v_0, v_1, v_2) f_ST4_1211(T0, v_0, v_1, v_2) f_ST4_1212(T0, v_0, v_1, v_2) f_ST4_1202(T0, v_0, v_1, v_2) f_ST4_1212(T0, v_0, v_1, v_2) f_ST4_1222(T0, v_0, v_1, v_2) f_ST4_0200(T0, v_0, v_1, v_2) f_ST4_0201(T0, v_0, v_1, v_2) f_ST4_0202(T0, v_0, v_1, v_2) f_ST4_0201(T0, v_0, v_1, v_2) f_ST4_0211(T0, v_0, v_1, v_2) f_ST4_0212(T0, v_0, v_1, v_2) f_ST4_0202(T0, v_0, v_1, v_2) f_ST4_0212(T0, v_0, v_1, v_2) f_ST4_0222(T0, v_0, v_1, v_2) f_ST4_1200(T0, v_0, v_1, v_2) f_ST4_1201(T0, v_0, v_1, v_2) f_ST4_1202(T0, v_0, v_1, v_2) f_ST4_1201(T0, v_0, v_1, v_2) f_ST4_1211(T0, v_0, v_1, v_2) f_ST4_1212(T0, v_0, v_1, v_2) f_ST4_1202(T0, v_0, v_1, v_2) f_ST4_1212(T0, v_0, v_1, v_2) f_ST4_1222(T0, v_0, v_1, v_2) f_ST4_2200(T0, v_0, v_1, v_2) f_ST4_2201(T0, v_0, v_1, v_2) f_ST4_2202(T0, v_0, v_1, v_2) f_ST4_2201(T0, v_0, v_1, v_2) f_ST4_2211(T0, v_0, v_1, v_2) f_ST4_2212(T0, v_0, v_1, v_2) f_ST4_2202(T0, v_0, v_1, v_2) f_ST4_2212(T0, v_0, v_1, v_2) f_ST4_2222(T0, v_0, v_1, v_2) +DEAL:dim 3::OK +DEAL::OK From 8ec9f0051b8a39428a10de13b9147374f1ea7861 Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Thu, 18 Apr 2019 15:49:59 +0200 Subject: [PATCH 429/507] Add a test to check std::copy and std::swap with vector of Expressions --- tests/symengine/symengine_number_type_03.cc | 56 +++++++++++++++++++ .../symengine/symengine_number_type_03.output | 12 ++++ 2 files changed, 68 insertions(+) create mode 100644 tests/symengine/symengine_number_type_03.cc create mode 100644 tests/symengine/symengine_number_type_03.output diff --git a/tests/symengine/symengine_number_type_03.cc b/tests/symengine/symengine_number_type_03.cc new file mode 100644 index 000000000000..743745db2303 --- /dev/null +++ b/tests/symengine/symengine_number_type_03.cc @@ -0,0 +1,56 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + + +// Check that the wrapper for symengine expressions can be use with some +// of the algorithms defined in the standard namespace + +#include + +#include + +#include "../tests.h" + +using namespace dealii; +namespace SD = Differentiation::SD; + +int +main() +{ + initlog(); + + const SD::types::symbol_vector copy_from{SD::Expression(1), + SD::Expression(true), + SD::Expression(2.5), + SD::Expression("a")}; + SD::types::symbol_vector copy_to(copy_from.size()); + + // Mimics Tensor operator= + std::copy(copy_from.begin(), copy_from.end(), copy_to.begin()); + + deallog << "Copy" << std::endl; + for (unsigned int i = 0; i < copy_from.size(); ++i) + deallog << i << ": " << copy_from[i] << " -> " << copy_to[i] << std::endl; + + + SD::types::symbol_vector swap_to; + std::swap(copy_to, swap_to); + + deallog << "Swap" << std::endl; + for (unsigned int i = 0; i < swap_to.size(); ++i) + deallog << i << ": " << swap_to[i] << std::endl; + + deallog << "OK" << std::endl; +} diff --git a/tests/symengine/symengine_number_type_03.output b/tests/symengine/symengine_number_type_03.output new file mode 100644 index 000000000000..acf7106b08f3 --- /dev/null +++ b/tests/symengine/symengine_number_type_03.output @@ -0,0 +1,12 @@ + +DEAL::Copy +DEAL::0: 1 -> 1 +DEAL::1: True -> True +DEAL::2: 2.5 -> 2.5 +DEAL::3: a -> a +DEAL::Swap +DEAL::0: 1 +DEAL::1: True +DEAL::2: 2.5 +DEAL::3: a +DEAL::OK From f6e60230dcc3a6cca62746a38f3c421db7db1345 Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Thu, 18 Apr 2019 21:37:26 +0200 Subject: [PATCH 430/507] Add test for operations using symbolic and expressional tensors --- .../symengine_tensor_operations_02.cc | 219 +++++++++++++++ .../symengine_tensor_operations_02.output | 253 ++++++++++++++++++ 2 files changed, 472 insertions(+) create mode 100644 tests/symengine/symengine_tensor_operations_02.cc create mode 100644 tests/symengine/symengine_tensor_operations_02.output diff --git a/tests/symengine/symengine_tensor_operations_02.cc b/tests/symengine/symengine_tensor_operations_02.cc new file mode 100644 index 000000000000..c9e075a8a16d --- /dev/null +++ b/tests/symengine/symengine_tensor_operations_02.cc @@ -0,0 +1,219 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE at +// the top level of the deal.II distribution. +// +// --------------------------------------------------------------------- + + +// Check that some of the common tensor operations can be performed with +// tensors of expressions + +#include + +#include + +#include "../tests.h" + +using namespace dealii; +namespace SD = Differentiation::SD; + +template +Tensor<2, dim, NumberType> +make_tensor(const NumberType &val) +{ + Tensor<2, dim, NumberType> out; + for (unsigned int i = 0; i < out.n_independent_components; ++i) + out[out.unrolled_to_component_indices(i)] = NumberType(i) + val; + return out; +} + +template +SymmetricTensor<2, dim, NumberType> +make_symm_tensor(const NumberType &val) +{ + SymmetricTensor<2, dim, NumberType> out; + for (unsigned int i = 0; i < out.n_independent_components; ++i) + out[out.unrolled_to_component_indices(i)] = NumberType(i) + val; + return out; +} + +template +void +test_tensor() +{ + typedef SD::Expression SD_number_t; + typedef Tensor<2, dim, SD_number_t> SD_tensor_t; + typedef SymmetricTensor<2, dim, SD_number_t> SD_symm_tensor_t; + + // --- Values --- + deallog.push("Initialize"); + SD_tensor_t a(make_tensor(NumberType(10))); + SD_tensor_t b(make_tensor(NumberType(10))); + SD_symm_tensor_t as(make_symm_tensor(NumberType(10))); + SD_symm_tensor_t bs(make_symm_tensor(NumberType(10))); + deallog << "a: " << a << std::endl; + deallog << "b: " << b << std::endl; + deallog << "as: " << as << std::endl; + deallog << "bs: " << bs << std::endl; + deallog.pop(); + + deallog.push("Relational operators 1"); + deallog << "a == b: " << (a == b) << std::endl; + deallog << "a != b: " << (a != b) << std::endl; + if (numbers::NumberTraits::is_complex == false) + deallog << "a.norm() < b.norm(): " << (a.norm() < b.norm()) << std::endl; + deallog.pop(); + + deallog.push("Set new values"); + a = make_tensor(NumberType(5)); + b = make_tensor(NumberType(9)); + as = make_symm_tensor(NumberType(5)); + bs = make_symm_tensor(NumberType(7)); + deallog << "a: " << a << std::endl; + deallog << "b: " << b << std::endl; + deallog << "as: " << as << std::endl; + deallog << "bs: " << bs << std::endl; + deallog.pop(); + // + deallog.push("Relational operators 2"); + deallog << "a == b: " << (a == b) << std::endl; + deallog << "a != b: " << (a != b) << std::endl; + if (numbers::NumberTraits::is_complex == false) + deallog << "a.norm() < b.norm(): " << (a.norm() < b.norm()) << std::endl; + deallog.pop(); + + deallog.push("Math operators"); + deallog.push("Tensor"); + deallog << "a+b: " << (a + b) << std::endl; + deallog << "a-b: " << (a - b) << std::endl; + deallog << "a*b: " << (a * b) << std::endl; + deallog.pop(); + deallog.push("SymmetricTensor"); + deallog << "as+bs: " << (as + bs) << std::endl; + deallog << "as-bs: " << (as - bs) << std::endl; + deallog << "as*bs: " << (as * bs) << std::endl; + const SD_tensor_t as_ns = as; + deallog << "as: " << as << std::endl; + deallog << "as_ns: " << as_ns << std::endl; + const SD_tensor_t as_ns2(as); + deallog << "as+b: " << (as + b) << std::endl; + deallog << "as-b: " << (as - b) << std::endl; + deallog << "as*b: " << (static_cast(as) * b) << std::endl; + deallog.pop(); + deallog.pop(); + + // --- Normal numbers --- + deallog.push("Copy constructor"); + SD_tensor_t c(a); // Copy constructor + SD_symm_tensor_t cs(as); // Copy constructor + deallog << "c: " << c << std::endl; + deallog << "cs: " << cs << std::endl; + deallog.pop(); + + deallog.push("Math operators"); // including those with arithmetic numbers + const NumberType s(2); + deallog.push("Tensor"); + c += b; + deallog << "c+=b: " << c << std::endl; + c *= s; + deallog << "c*=s: " << c << std::endl; + c -= b; + deallog << "c-=b: " << c << std::endl; + c /= s; + deallog << "c/=s: " << c << std::endl; + deallog.pop(); + deallog.push("SymmetricTensor"); + cs += bs; + deallog << "cs+=bs: " << cs << std::endl; + cs *= s; + deallog << "cs*=s: " << cs << std::endl; + cs -= bs; + deallog << "cs-=bs: " << cs << std::endl; + cs /= s; + deallog << "cs/=s: " << cs << std::endl; + deallog.pop(); + deallog.pop(); + + // --- Symbols --- + deallog.push("Symbols"); + const SD_number_t y("y"); + const SD_tensor_t x(SD::make_tensor_of_symbols<2, dim>("x")); + const SD_symm_tensor_t z(SD::make_symmetric_tensor_of_symbols<2, dim>("z")); + deallog << "x: " << x << std::endl; + deallog << "y: " << y << std::endl; + deallog << "z: " << z << std::endl; + deallog.pop(); + + deallog.push("Math operators"); // including those with arithmetic numbers + deallog.push("Tensor"); + c += x; + deallog << "c+=x: " << c << std::endl; + c *= y; + deallog << "c*=y: " << c << std::endl; + c *= s; + deallog << "c*=s: " << c << std::endl; + c -= x; + deallog << "c-=x: " << c << std::endl; + c /= y; + deallog << "c/=y: " << c << std::endl; + c /= s; + deallog << "c/=s: " << c << std::endl; + deallog.pop(); + deallog.push("SymmetricTensor"); + cs += z; + deallog << "cs+=z: " << cs << std::endl; + cs *= y; + deallog << "cs*=y: " << cs << std::endl; + cs *= s; + deallog << "cs*=s: " << cs << std::endl; + cs -= z; + deallog << "cs-=z: " << cs << std::endl; + cs /= y; + deallog << "cs/=y: " << cs << std::endl; + cs /= s; + deallog << "cs/=s: " << cs << std::endl; + deallog.pop(); + deallog.pop(); + + deallog << "OK" << std::endl; +} + + +int +main() +{ + initlog(); + + const int dim = 2; + + deallog.push("Integer"); + test_tensor(); + deallog.pop(); + + deallog.push("Float"); + test_tensor(); + deallog.pop(); + + deallog.push("Double"); + test_tensor(); + deallog.pop(); + + deallog.push("Complex float"); + test_tensor>(); + deallog.pop(); + + deallog.push("Complex double"); + test_tensor>(); + deallog.pop(); + + deallog << "OK" << std::endl; +} diff --git a/tests/symengine/symengine_tensor_operations_02.output b/tests/symengine/symengine_tensor_operations_02.output new file mode 100644 index 000000000000..03cfc71826c6 --- /dev/null +++ b/tests/symengine/symengine_tensor_operations_02.output @@ -0,0 +1,253 @@ + +DEAL:Integer:Initialize::a: 10 11 12 13 +DEAL:Integer:Initialize::b: 10 11 12 13 +DEAL:Integer:Initialize::as: 10 12 12 11 +DEAL:Integer:Initialize::bs: 10 12 12 11 +DEAL:Integer:Relational operators 1::a == b: 1 +DEAL:Integer:Relational operators 1::a != b: 0 +DEAL:Integer:Relational operators 1::a.norm() < b.norm(): False +DEAL:Integer:Set new values::a: 5 6 7 8 +DEAL:Integer:Set new values::b: 9 10 11 12 +DEAL:Integer:Set new values::as: 5 7 7 6 +DEAL:Integer:Set new values::bs: 7 9 9 8 +DEAL:Integer:Relational operators 2::a == b: 0 +DEAL:Integer:Relational operators 2::a != b: 1 +DEAL:Integer:Relational operators 2::a.norm() < b.norm(): sqrt(174) < sqrt(446) +DEAL:Integer:Math operators:Tensor::a+b: 14 16 18 20 +DEAL:Integer:Math operators:Tensor::a-b: -4 -4 -4 -4 +DEAL:Integer:Math operators:Tensor::a*b: 111 122 151 166 +DEAL:Integer:Math operators:SymmetricTensor::as+bs: 12 16 16 14 +DEAL:Integer:Math operators:SymmetricTensor::as-bs: -2 -2 -2 -2 +DEAL:Integer:Math operators:SymmetricTensor::as*bs: 209 +DEAL:Integer:Math operators:SymmetricTensor::as: 5 7 7 6 +DEAL:Integer:Math operators:SymmetricTensor::as_ns: 5 7 7 6 +DEAL:Integer:Math operators:SymmetricTensor::as+b: 14 17 18 18 +DEAL:Integer:Math operators:SymmetricTensor::as-b: -4 -3 -4 -6 +DEAL:Integer:Math operators:SymmetricTensor::as*b: 122 134 129 142 +DEAL:Integer:Copy constructor::c: 5 6 7 8 +DEAL:Integer:Copy constructor::cs: 5 7 7 6 +DEAL:Integer:Math operators:Tensor::c+=b: 14 16 18 20 +DEAL:Integer:Math operators:Tensor::c*=s: 28 32 36 40 +DEAL:Integer:Math operators:Tensor::c-=b: 19 22 25 28 +DEAL:Integer:Math operators:Tensor::c/=s: 19/2 11 25/2 14 +DEAL:Integer:Math operators:SymmetricTensor::cs+=bs: 12 16 16 14 +DEAL:Integer:Math operators:SymmetricTensor::cs*=s: 24 32 32 28 +DEAL:Integer:Math operators:SymmetricTensor::cs-=bs: 17 23 23 20 +DEAL:Integer:Math operators:SymmetricTensor::cs/=s: 17/2 23/2 23/2 10 +DEAL:Integer:Symbols::x: x_00 x_01 x_10 x_11 +DEAL:Integer:Symbols::y: y +DEAL:Integer:Symbols::z: z_00 z_01 z_01 z_11 +DEAL:Integer:Math operators:Tensor::c+=x: 19/2 + x_00 11 + x_01 25/2 + x_10 14 + x_11 +DEAL:Integer:Math operators:Tensor::c*=y: y*(19/2 + x_00) y*(11 + x_01) y*(25/2 + x_10) y*(14 + x_11) +DEAL:Integer:Math operators:Tensor::c*=s: 2*y*(19/2 + x_00) 2*y*(11 + x_01) 2*y*(25/2 + x_10) 2*y*(14 + x_11) +DEAL:Integer:Math operators:Tensor::c-=x: -x_00 + 2*y*(19/2 + x_00) -x_01 + 2*y*(11 + x_01) -x_10 + 2*y*(25/2 + x_10) -x_11 + 2*y*(14 + x_11) +DEAL:Integer:Math operators:Tensor::c/=y: (-x_00 + 2*y*(19/2 + x_00))/y (-x_01 + 2*y*(11 + x_01))/y (-x_10 + 2*y*(25/2 + x_10))/y (-x_11 + 2*y*(14 + x_11))/y +DEAL:Integer:Math operators:Tensor::c/=s: (1/2)*(-x_00 + 2*y*(19/2 + x_00))/y (1/2)*(-x_01 + 2*y*(11 + x_01))/y (1/2)*(-x_10 + 2*y*(25/2 + x_10))/y (1/2)*(-x_11 + 2*y*(14 + x_11))/y +DEAL:Integer:Math operators:SymmetricTensor::cs+=z: 17/2 + z_00 23/2 + z_01 23/2 + z_01 10 + z_11 +DEAL:Integer:Math operators:SymmetricTensor::cs*=y: y*(17/2 + z_00) y*(23/2 + z_01) y*(23/2 + z_01) y*(10 + z_11) +DEAL:Integer:Math operators:SymmetricTensor::cs*=s: 2*y*(17/2 + z_00) 2*y*(23/2 + z_01) 2*y*(23/2 + z_01) 2*y*(10 + z_11) +DEAL:Integer:Math operators:SymmetricTensor::cs-=z: -z_00 + 2*y*(17/2 + z_00) -z_01 + 2*y*(23/2 + z_01) -z_01 + 2*y*(23/2 + z_01) -z_11 + 2*y*(10 + z_11) +DEAL:Integer:Math operators:SymmetricTensor::cs/=y: (-z_00 + 2*y*(17/2 + z_00))/y (-z_01 + 2*y*(23/2 + z_01))/y (-z_01 + 2*y*(23/2 + z_01))/y (-z_11 + 2*y*(10 + z_11))/y +DEAL:Integer:Math operators:SymmetricTensor::cs/=s: (1/2)*(-z_00 + 2*y*(17/2 + z_00))/y (1/2)*(-z_01 + 2*y*(23/2 + z_01))/y (1/2)*(-z_01 + 2*y*(23/2 + z_01))/y (1/2)*(-z_11 + 2*y*(10 + z_11))/y +DEAL:Integer::OK +DEAL:Float:Initialize::a: 10.0 11.0 12.0 13.0 +DEAL:Float:Initialize::b: 10.0 11.0 12.0 13.0 +DEAL:Float:Initialize::as: 10.0 12.0 12.0 11.0 +DEAL:Float:Initialize::bs: 10.0 12.0 12.0 11.0 +DEAL:Float:Relational operators 1::a == b: 1 +DEAL:Float:Relational operators 1::a != b: 0 +DEAL:Float:Relational operators 1::a.norm() < b.norm(): False +DEAL:Float:Set new values::a: 5.0 6.0 7.0 8.0 +DEAL:Float:Set new values::b: 9.0 10.0 11.0 12.0 +DEAL:Float:Set new values::as: 5.0 7.0 7.0 6.0 +DEAL:Float:Set new values::bs: 7.0 9.0 9.0 8.0 +DEAL:Float:Relational operators 2::a == b: 0 +DEAL:Float:Relational operators 2::a != b: 1 +DEAL:Float:Relational operators 2::a.norm() < b.norm(): True +DEAL:Float:Math operators:Tensor::a+b: 14.0 16.0 18.0 20.0 +DEAL:Float:Math operators:Tensor::a-b: -4.0 -4.0 -4.0 -4.0 +DEAL:Float:Math operators:Tensor::a*b: 111.0 122.0 151.0 166.0 +DEAL:Float:Math operators:SymmetricTensor::as+bs: 12.0 16.0 16.0 14.0 +DEAL:Float:Math operators:SymmetricTensor::as-bs: -2.0 -2.0 -2.0 -2.0 +DEAL:Float:Math operators:SymmetricTensor::as*bs: 209.0 +DEAL:Float:Math operators:SymmetricTensor::as: 5.0 7.0 7.0 6.0 +DEAL:Float:Math operators:SymmetricTensor::as_ns: 5.0 7.0 7.0 6.0 +DEAL:Float:Math operators:SymmetricTensor::as+b: 14.0 17.0 18.0 18.0 +DEAL:Float:Math operators:SymmetricTensor::as-b: -4.0 -3.0 -4.0 -6.0 +DEAL:Float:Math operators:SymmetricTensor::as*b: 122.0 134.0 129.0 142.0 +DEAL:Float:Copy constructor::c: 5.0 6.0 7.0 8.0 +DEAL:Float:Copy constructor::cs: 5.0 7.0 7.0 6.0 +DEAL:Float:Math operators:Tensor::c+=b: 14.0 16.0 18.0 20.0 +DEAL:Float:Math operators:Tensor::c*=s: 28.0 32.0 36.0 40.0 +DEAL:Float:Math operators:Tensor::c-=b: 19.0 22.0 25.0 28.0 +DEAL:Float:Math operators:Tensor::c/=s: 9.5 11.0 12.5 14.0 +DEAL:Float:Math operators:SymmetricTensor::cs+=bs: 12.0 16.0 16.0 14.0 +DEAL:Float:Math operators:SymmetricTensor::cs*=s: 24.0 32.0 32.0 28.0 +DEAL:Float:Math operators:SymmetricTensor::cs-=bs: 17.0 23.0 23.0 20.0 +DEAL:Float:Math operators:SymmetricTensor::cs/=s: 8.5 11.5 11.5 10.0 +DEAL:Float:Symbols::x: x_00 x_01 x_10 x_11 +DEAL:Float:Symbols::y: y +DEAL:Float:Symbols::z: z_00 z_01 z_01 z_11 +DEAL:Float:Math operators:Tensor::c+=x: 9.5 + x_00 11.0 + x_01 12.5 + x_10 14.0 + x_11 +DEAL:Float:Math operators:Tensor::c*=y: y*(9.5 + x_00) y*(11.0 + x_01) y*(12.5 + x_10) y*(14.0 + x_11) +DEAL:Float:Math operators:Tensor::c*=s: 2.0*y*(9.5 + x_00) 2.0*y*(11.0 + x_01) 2.0*y*(12.5 + x_10) 2.0*y*(14.0 + x_11) +DEAL:Float:Math operators:Tensor::c-=x: -x_00 + 2.0*y*(9.5 + x_00) -x_01 + 2.0*y*(11.0 + x_01) -x_10 + 2.0*y*(12.5 + x_10) -x_11 + 2.0*y*(14.0 + x_11) +DEAL:Float:Math operators:Tensor::c/=y: (-x_00 + 2.0*y*(9.5 + x_00))/y (-x_01 + 2.0*y*(11.0 + x_01))/y (-x_10 + 2.0*y*(12.5 + x_10))/y (-x_11 + 2.0*y*(14.0 + x_11))/y +DEAL:Float:Math operators:Tensor::c/=s: 0.5*(-x_00 + 2.0*y*(9.5 + x_00))/y 0.5*(-x_01 + 2.0*y*(11.0 + x_01))/y 0.5*(-x_10 + 2.0*y*(12.5 + x_10))/y 0.5*(-x_11 + 2.0*y*(14.0 + x_11))/y +DEAL:Float:Math operators:SymmetricTensor::cs+=z: 8.5 + z_00 11.5 + z_01 11.5 + z_01 10.0 + z_11 +DEAL:Float:Math operators:SymmetricTensor::cs*=y: y*(8.5 + z_00) y*(11.5 + z_01) y*(11.5 + z_01) y*(10.0 + z_11) +DEAL:Float:Math operators:SymmetricTensor::cs*=s: 2.0*y*(8.5 + z_00) 2.0*y*(11.5 + z_01) 2.0*y*(11.5 + z_01) 2.0*y*(10.0 + z_11) +DEAL:Float:Math operators:SymmetricTensor::cs-=z: -z_00 + 2.0*y*(8.5 + z_00) -z_01 + 2.0*y*(11.5 + z_01) -z_01 + 2.0*y*(11.5 + z_01) -z_11 + 2.0*y*(10.0 + z_11) +DEAL:Float:Math operators:SymmetricTensor::cs/=y: (-z_00 + 2.0*y*(8.5 + z_00))/y (-z_01 + 2.0*y*(11.5 + z_01))/y (-z_01 + 2.0*y*(11.5 + z_01))/y (-z_11 + 2.0*y*(10.0 + z_11))/y +DEAL:Float:Math operators:SymmetricTensor::cs/=s: 0.5*(-z_00 + 2.0*y*(8.5 + z_00))/y 0.5*(-z_01 + 2.0*y*(11.5 + z_01))/y 0.5*(-z_01 + 2.0*y*(11.5 + z_01))/y 0.5*(-z_11 + 2.0*y*(10.0 + z_11))/y +DEAL:Float::OK +DEAL:Double:Initialize::a: 10.0 11.0 12.0 13.0 +DEAL:Double:Initialize::b: 10.0 11.0 12.0 13.0 +DEAL:Double:Initialize::as: 10.0 12.0 12.0 11.0 +DEAL:Double:Initialize::bs: 10.0 12.0 12.0 11.0 +DEAL:Double:Relational operators 1::a == b: 1 +DEAL:Double:Relational operators 1::a != b: 0 +DEAL:Double:Relational operators 1::a.norm() < b.norm(): False +DEAL:Double:Set new values::a: 5.0 6.0 7.0 8.0 +DEAL:Double:Set new values::b: 9.0 10.0 11.0 12.0 +DEAL:Double:Set new values::as: 5.0 7.0 7.0 6.0 +DEAL:Double:Set new values::bs: 7.0 9.0 9.0 8.0 +DEAL:Double:Relational operators 2::a == b: 0 +DEAL:Double:Relational operators 2::a != b: 1 +DEAL:Double:Relational operators 2::a.norm() < b.norm(): True +DEAL:Double:Math operators:Tensor::a+b: 14.0 16.0 18.0 20.0 +DEAL:Double:Math operators:Tensor::a-b: -4.0 -4.0 -4.0 -4.0 +DEAL:Double:Math operators:Tensor::a*b: 111.0 122.0 151.0 166.0 +DEAL:Double:Math operators:SymmetricTensor::as+bs: 12.0 16.0 16.0 14.0 +DEAL:Double:Math operators:SymmetricTensor::as-bs: -2.0 -2.0 -2.0 -2.0 +DEAL:Double:Math operators:SymmetricTensor::as*bs: 209.0 +DEAL:Double:Math operators:SymmetricTensor::as: 5.0 7.0 7.0 6.0 +DEAL:Double:Math operators:SymmetricTensor::as_ns: 5.0 7.0 7.0 6.0 +DEAL:Double:Math operators:SymmetricTensor::as+b: 14.0 17.0 18.0 18.0 +DEAL:Double:Math operators:SymmetricTensor::as-b: -4.0 -3.0 -4.0 -6.0 +DEAL:Double:Math operators:SymmetricTensor::as*b: 122.0 134.0 129.0 142.0 +DEAL:Double:Copy constructor::c: 5.0 6.0 7.0 8.0 +DEAL:Double:Copy constructor::cs: 5.0 7.0 7.0 6.0 +DEAL:Double:Math operators:Tensor::c+=b: 14.0 16.0 18.0 20.0 +DEAL:Double:Math operators:Tensor::c*=s: 28.0 32.0 36.0 40.0 +DEAL:Double:Math operators:Tensor::c-=b: 19.0 22.0 25.0 28.0 +DEAL:Double:Math operators:Tensor::c/=s: 9.5 11.0 12.5 14.0 +DEAL:Double:Math operators:SymmetricTensor::cs+=bs: 12.0 16.0 16.0 14.0 +DEAL:Double:Math operators:SymmetricTensor::cs*=s: 24.0 32.0 32.0 28.0 +DEAL:Double:Math operators:SymmetricTensor::cs-=bs: 17.0 23.0 23.0 20.0 +DEAL:Double:Math operators:SymmetricTensor::cs/=s: 8.5 11.5 11.5 10.0 +DEAL:Double:Symbols::x: x_00 x_01 x_10 x_11 +DEAL:Double:Symbols::y: y +DEAL:Double:Symbols::z: z_00 z_01 z_01 z_11 +DEAL:Double:Math operators:Tensor::c+=x: 9.5 + x_00 11.0 + x_01 12.5 + x_10 14.0 + x_11 +DEAL:Double:Math operators:Tensor::c*=y: y*(9.5 + x_00) y*(11.0 + x_01) y*(12.5 + x_10) y*(14.0 + x_11) +DEAL:Double:Math operators:Tensor::c*=s: 2.0*y*(9.5 + x_00) 2.0*y*(11.0 + x_01) 2.0*y*(12.5 + x_10) 2.0*y*(14.0 + x_11) +DEAL:Double:Math operators:Tensor::c-=x: -x_00 + 2.0*y*(9.5 + x_00) -x_01 + 2.0*y*(11.0 + x_01) -x_10 + 2.0*y*(12.5 + x_10) -x_11 + 2.0*y*(14.0 + x_11) +DEAL:Double:Math operators:Tensor::c/=y: (-x_00 + 2.0*y*(9.5 + x_00))/y (-x_01 + 2.0*y*(11.0 + x_01))/y (-x_10 + 2.0*y*(12.5 + x_10))/y (-x_11 + 2.0*y*(14.0 + x_11))/y +DEAL:Double:Math operators:Tensor::c/=s: 0.5*(-x_00 + 2.0*y*(9.5 + x_00))/y 0.5*(-x_01 + 2.0*y*(11.0 + x_01))/y 0.5*(-x_10 + 2.0*y*(12.5 + x_10))/y 0.5*(-x_11 + 2.0*y*(14.0 + x_11))/y +DEAL:Double:Math operators:SymmetricTensor::cs+=z: 8.5 + z_00 11.5 + z_01 11.5 + z_01 10.0 + z_11 +DEAL:Double:Math operators:SymmetricTensor::cs*=y: y*(8.5 + z_00) y*(11.5 + z_01) y*(11.5 + z_01) y*(10.0 + z_11) +DEAL:Double:Math operators:SymmetricTensor::cs*=s: 2.0*y*(8.5 + z_00) 2.0*y*(11.5 + z_01) 2.0*y*(11.5 + z_01) 2.0*y*(10.0 + z_11) +DEAL:Double:Math operators:SymmetricTensor::cs-=z: -z_00 + 2.0*y*(8.5 + z_00) -z_01 + 2.0*y*(11.5 + z_01) -z_01 + 2.0*y*(11.5 + z_01) -z_11 + 2.0*y*(10.0 + z_11) +DEAL:Double:Math operators:SymmetricTensor::cs/=y: (-z_00 + 2.0*y*(8.5 + z_00))/y (-z_01 + 2.0*y*(11.5 + z_01))/y (-z_01 + 2.0*y*(11.5 + z_01))/y (-z_11 + 2.0*y*(10.0 + z_11))/y +DEAL:Double:Math operators:SymmetricTensor::cs/=s: 0.5*(-z_00 + 2.0*y*(8.5 + z_00))/y 0.5*(-z_01 + 2.0*y*(11.5 + z_01))/y 0.5*(-z_01 + 2.0*y*(11.5 + z_01))/y 0.5*(-z_11 + 2.0*y*(10.0 + z_11))/y +DEAL:Double::OK +DEAL:Complex float:Initialize::a: 10.0 + 0.0*I 11.0 + 0.0*I 12.0 + 0.0*I 13.0 + 0.0*I +DEAL:Complex float:Initialize::b: 10.0 + 0.0*I 11.0 + 0.0*I 12.0 + 0.0*I 13.0 + 0.0*I +DEAL:Complex float:Initialize::as: 10.0 + 0.0*I 12.0 + 0.0*I 12.0 + 0.0*I 11.0 + 0.0*I +DEAL:Complex float:Initialize::bs: 10.0 + 0.0*I 12.0 + 0.0*I 12.0 + 0.0*I 11.0 + 0.0*I +DEAL:Complex float:Relational operators 1::a == b: 1 +DEAL:Complex float:Relational operators 1::a != b: 0 +DEAL:Complex float:Set new values::a: 5.0 + 0.0*I 6.0 + 0.0*I 7.0 + 0.0*I 8.0 + 0.0*I +DEAL:Complex float:Set new values::b: 9.0 + 0.0*I 10.0 + 0.0*I 11.0 + 0.0*I 12.0 + 0.0*I +DEAL:Complex float:Set new values::as: 5.0 + 0.0*I 7.0 + 0.0*I 7.0 + 0.0*I 6.0 + 0.0*I +DEAL:Complex float:Set new values::bs: 7.0 + 0.0*I 9.0 + 0.0*I 9.0 + 0.0*I 8.0 + 0.0*I +DEAL:Complex float:Relational operators 2::a == b: 0 +DEAL:Complex float:Relational operators 2::a != b: 1 +DEAL:Complex float:Math operators:Tensor::a+b: 14.0 + 0.0*I 16.0 + 0.0*I 18.0 + 0.0*I 20.0 + 0.0*I +DEAL:Complex float:Math operators:Tensor::a-b: -4.0 + 0.0*I -4.0 + 0.0*I -4.0 + 0.0*I -4.0 + 0.0*I +DEAL:Complex float:Math operators:Tensor::a*b: 111.0 + 0.0*I 122.0 + 0.0*I 151.0 + 0.0*I 166.0 + 0.0*I +DEAL:Complex float:Math operators:SymmetricTensor::as+bs: 12.0 + 0.0*I 16.0 + 0.0*I 16.0 + 0.0*I 14.0 + 0.0*I +DEAL:Complex float:Math operators:SymmetricTensor::as-bs: -2.0 + 0.0*I -2.0 + 0.0*I -2.0 + 0.0*I -2.0 + 0.0*I +DEAL:Complex float:Math operators:SymmetricTensor::as*bs: 209.0 + 0.0*I +DEAL:Complex float:Math operators:SymmetricTensor::as: 5.0 + 0.0*I 7.0 + 0.0*I 7.0 + 0.0*I 6.0 + 0.0*I +DEAL:Complex float:Math operators:SymmetricTensor::as_ns: 5.0 + 0.0*I 7.0 + 0.0*I 7.0 + 0.0*I 6.0 + 0.0*I +DEAL:Complex float:Math operators:SymmetricTensor::as+b: 14.0 + 0.0*I 17.0 + 0.0*I 18.0 + 0.0*I 18.0 + 0.0*I +DEAL:Complex float:Math operators:SymmetricTensor::as-b: -4.0 + 0.0*I -3.0 + 0.0*I -4.0 + 0.0*I -6.0 + 0.0*I +DEAL:Complex float:Math operators:SymmetricTensor::as*b: 122.0 + 0.0*I 134.0 + 0.0*I 129.0 + 0.0*I 142.0 + 0.0*I +DEAL:Complex float:Copy constructor::c: 5.0 + 0.0*I 6.0 + 0.0*I 7.0 + 0.0*I 8.0 + 0.0*I +DEAL:Complex float:Copy constructor::cs: 5.0 + 0.0*I 7.0 + 0.0*I 7.0 + 0.0*I 6.0 + 0.0*I +DEAL:Complex float:Math operators:Tensor::c+=b: 14.0 + 0.0*I 16.0 + 0.0*I 18.0 + 0.0*I 20.0 + 0.0*I +DEAL:Complex float:Math operators:Tensor::c*=s: 28.0 + 0.0*I 32.0 + 0.0*I 36.0 + 0.0*I 40.0 + 0.0*I +DEAL:Complex float:Math operators:Tensor::c-=b: 19.0 + 0.0*I 22.0 + 0.0*I 25.0 + 0.0*I 28.0 + 0.0*I +DEAL:Complex float:Math operators:Tensor::c/=s: 9.5 + 0.0*I 11.0 + 0.0*I 12.5 + 0.0*I 14.0 + 0.0*I +DEAL:Complex float:Math operators:SymmetricTensor::cs+=bs: 12.0 + 0.0*I 16.0 + 0.0*I 16.0 + 0.0*I 14.0 + 0.0*I +DEAL:Complex float:Math operators:SymmetricTensor::cs*=s: 24.0 + 0.0*I 32.0 + 0.0*I 32.0 + 0.0*I 28.0 + 0.0*I +DEAL:Complex float:Math operators:SymmetricTensor::cs-=bs: 17.0 + 0.0*I 23.0 + 0.0*I 23.0 + 0.0*I 20.0 + 0.0*I +DEAL:Complex float:Math operators:SymmetricTensor::cs/=s: 8.5 + 0.0*I 11.5 + 0.0*I 11.5 + 0.0*I 10.0 + 0.0*I +DEAL:Complex float:Symbols::x: x_00 x_01 x_10 x_11 +DEAL:Complex float:Symbols::y: y +DEAL:Complex float:Symbols::z: z_00 z_01 z_01 z_11 +DEAL:Complex float:Math operators:Tensor::c+=x: 9.5 + 0.0*I + x_00 11.0 + 0.0*I + x_01 12.5 + 0.0*I + x_10 14.0 + 0.0*I + x_11 +DEAL:Complex float:Math operators:Tensor::c*=y: y*(9.5 + 0.0*I + x_00) y*(11.0 + 0.0*I + x_01) y*(12.5 + 0.0*I + x_10) y*(14.0 + 0.0*I + x_11) +DEAL:Complex float:Math operators:Tensor::c*=s: (2.0 + 0.0*I)*y*(9.5 + 0.0*I + x_00) (2.0 + 0.0*I)*y*(11.0 + 0.0*I + x_01) (2.0 + 0.0*I)*y*(12.5 + 0.0*I + x_10) (2.0 + 0.0*I)*y*(14.0 + 0.0*I + x_11) +DEAL:Complex float:Math operators:Tensor::c-=x: -x_00 + (2.0 + 0.0*I)*y*(9.5 + 0.0*I + x_00) -x_01 + (2.0 + 0.0*I)*y*(11.0 + 0.0*I + x_01) -x_10 + (2.0 + 0.0*I)*y*(12.5 + 0.0*I + x_10) -x_11 + (2.0 + 0.0*I)*y*(14.0 + 0.0*I + x_11) +DEAL:Complex float:Math operators:Tensor::c/=y: (-x_00 + (2.0 + 0.0*I)*y*(9.5 + 0.0*I + x_00))/y (-x_01 + (2.0 + 0.0*I)*y*(11.0 + 0.0*I + x_01))/y (-x_10 + (2.0 + 0.0*I)*y*(12.5 + 0.0*I + x_10))/y (-x_11 + (2.0 + 0.0*I)*y*(14.0 + 0.0*I + x_11))/y +DEAL:Complex float:Math operators:Tensor::c/=s: (0.5 + 0.0*I)*(-x_00 + (2.0 + 0.0*I)*y*(9.5 + 0.0*I + x_00))/y (0.5 + 0.0*I)*(-x_01 + (2.0 + 0.0*I)*y*(11.0 + 0.0*I + x_01))/y (0.5 + 0.0*I)*(-x_10 + (2.0 + 0.0*I)*y*(12.5 + 0.0*I + x_10))/y (0.5 + 0.0*I)*(-x_11 + (2.0 + 0.0*I)*y*(14.0 + 0.0*I + x_11))/y +DEAL:Complex float:Math operators:SymmetricTensor::cs+=z: 8.5 + 0.0*I + z_00 11.5 + 0.0*I + z_01 11.5 + 0.0*I + z_01 10.0 + 0.0*I + z_11 +DEAL:Complex float:Math operators:SymmetricTensor::cs*=y: y*(8.5 + 0.0*I + z_00) y*(11.5 + 0.0*I + z_01) y*(11.5 + 0.0*I + z_01) y*(10.0 + 0.0*I + z_11) +DEAL:Complex float:Math operators:SymmetricTensor::cs*=s: (2.0 + 0.0*I)*y*(8.5 + 0.0*I + z_00) (2.0 + 0.0*I)*y*(11.5 + 0.0*I + z_01) (2.0 + 0.0*I)*y*(11.5 + 0.0*I + z_01) (2.0 + 0.0*I)*y*(10.0 + 0.0*I + z_11) +DEAL:Complex float:Math operators:SymmetricTensor::cs-=z: -z_00 + (2.0 + 0.0*I)*y*(8.5 + 0.0*I + z_00) -z_01 + (2.0 + 0.0*I)*y*(11.5 + 0.0*I + z_01) -z_01 + (2.0 + 0.0*I)*y*(11.5 + 0.0*I + z_01) -z_11 + (2.0 + 0.0*I)*y*(10.0 + 0.0*I + z_11) +DEAL:Complex float:Math operators:SymmetricTensor::cs/=y: (-z_00 + (2.0 + 0.0*I)*y*(8.5 + 0.0*I + z_00))/y (-z_01 + (2.0 + 0.0*I)*y*(11.5 + 0.0*I + z_01))/y (-z_01 + (2.0 + 0.0*I)*y*(11.5 + 0.0*I + z_01))/y (-z_11 + (2.0 + 0.0*I)*y*(10.0 + 0.0*I + z_11))/y +DEAL:Complex float:Math operators:SymmetricTensor::cs/=s: (0.5 + 0.0*I)*(-z_00 + (2.0 + 0.0*I)*y*(8.5 + 0.0*I + z_00))/y (0.5 + 0.0*I)*(-z_01 + (2.0 + 0.0*I)*y*(11.5 + 0.0*I + z_01))/y (0.5 + 0.0*I)*(-z_01 + (2.0 + 0.0*I)*y*(11.5 + 0.0*I + z_01))/y (0.5 + 0.0*I)*(-z_11 + (2.0 + 0.0*I)*y*(10.0 + 0.0*I + z_11))/y +DEAL:Complex float::OK +DEAL:Complex double:Initialize::a: 10.0 + 0.0*I 11.0 + 0.0*I 12.0 + 0.0*I 13.0 + 0.0*I +DEAL:Complex double:Initialize::b: 10.0 + 0.0*I 11.0 + 0.0*I 12.0 + 0.0*I 13.0 + 0.0*I +DEAL:Complex double:Initialize::as: 10.0 + 0.0*I 12.0 + 0.0*I 12.0 + 0.0*I 11.0 + 0.0*I +DEAL:Complex double:Initialize::bs: 10.0 + 0.0*I 12.0 + 0.0*I 12.0 + 0.0*I 11.0 + 0.0*I +DEAL:Complex double:Relational operators 1::a == b: 1 +DEAL:Complex double:Relational operators 1::a != b: 0 +DEAL:Complex double:Set new values::a: 5.0 + 0.0*I 6.0 + 0.0*I 7.0 + 0.0*I 8.0 + 0.0*I +DEAL:Complex double:Set new values::b: 9.0 + 0.0*I 10.0 + 0.0*I 11.0 + 0.0*I 12.0 + 0.0*I +DEAL:Complex double:Set new values::as: 5.0 + 0.0*I 7.0 + 0.0*I 7.0 + 0.0*I 6.0 + 0.0*I +DEAL:Complex double:Set new values::bs: 7.0 + 0.0*I 9.0 + 0.0*I 9.0 + 0.0*I 8.0 + 0.0*I +DEAL:Complex double:Relational operators 2::a == b: 0 +DEAL:Complex double:Relational operators 2::a != b: 1 +DEAL:Complex double:Math operators:Tensor::a+b: 14.0 + 0.0*I 16.0 + 0.0*I 18.0 + 0.0*I 20.0 + 0.0*I +DEAL:Complex double:Math operators:Tensor::a-b: -4.0 + 0.0*I -4.0 + 0.0*I -4.0 + 0.0*I -4.0 + 0.0*I +DEAL:Complex double:Math operators:Tensor::a*b: 111.0 + 0.0*I 122.0 + 0.0*I 151.0 + 0.0*I 166.0 + 0.0*I +DEAL:Complex double:Math operators:SymmetricTensor::as+bs: 12.0 + 0.0*I 16.0 + 0.0*I 16.0 + 0.0*I 14.0 + 0.0*I +DEAL:Complex double:Math operators:SymmetricTensor::as-bs: -2.0 + 0.0*I -2.0 + 0.0*I -2.0 + 0.0*I -2.0 + 0.0*I +DEAL:Complex double:Math operators:SymmetricTensor::as*bs: 209.0 + 0.0*I +DEAL:Complex double:Math operators:SymmetricTensor::as: 5.0 + 0.0*I 7.0 + 0.0*I 7.0 + 0.0*I 6.0 + 0.0*I +DEAL:Complex double:Math operators:SymmetricTensor::as_ns: 5.0 + 0.0*I 7.0 + 0.0*I 7.0 + 0.0*I 6.0 + 0.0*I +DEAL:Complex double:Math operators:SymmetricTensor::as+b: 14.0 + 0.0*I 17.0 + 0.0*I 18.0 + 0.0*I 18.0 + 0.0*I +DEAL:Complex double:Math operators:SymmetricTensor::as-b: -4.0 + 0.0*I -3.0 + 0.0*I -4.0 + 0.0*I -6.0 + 0.0*I +DEAL:Complex double:Math operators:SymmetricTensor::as*b: 122.0 + 0.0*I 134.0 + 0.0*I 129.0 + 0.0*I 142.0 + 0.0*I +DEAL:Complex double:Copy constructor::c: 5.0 + 0.0*I 6.0 + 0.0*I 7.0 + 0.0*I 8.0 + 0.0*I +DEAL:Complex double:Copy constructor::cs: 5.0 + 0.0*I 7.0 + 0.0*I 7.0 + 0.0*I 6.0 + 0.0*I +DEAL:Complex double:Math operators:Tensor::c+=b: 14.0 + 0.0*I 16.0 + 0.0*I 18.0 + 0.0*I 20.0 + 0.0*I +DEAL:Complex double:Math operators:Tensor::c*=s: 28.0 + 0.0*I 32.0 + 0.0*I 36.0 + 0.0*I 40.0 + 0.0*I +DEAL:Complex double:Math operators:Tensor::c-=b: 19.0 + 0.0*I 22.0 + 0.0*I 25.0 + 0.0*I 28.0 + 0.0*I +DEAL:Complex double:Math operators:Tensor::c/=s: 9.5 + 0.0*I 11.0 + 0.0*I 12.5 + 0.0*I 14.0 + 0.0*I +DEAL:Complex double:Math operators:SymmetricTensor::cs+=bs: 12.0 + 0.0*I 16.0 + 0.0*I 16.0 + 0.0*I 14.0 + 0.0*I +DEAL:Complex double:Math operators:SymmetricTensor::cs*=s: 24.0 + 0.0*I 32.0 + 0.0*I 32.0 + 0.0*I 28.0 + 0.0*I +DEAL:Complex double:Math operators:SymmetricTensor::cs-=bs: 17.0 + 0.0*I 23.0 + 0.0*I 23.0 + 0.0*I 20.0 + 0.0*I +DEAL:Complex double:Math operators:SymmetricTensor::cs/=s: 8.5 + 0.0*I 11.5 + 0.0*I 11.5 + 0.0*I 10.0 + 0.0*I +DEAL:Complex double:Symbols::x: x_00 x_01 x_10 x_11 +DEAL:Complex double:Symbols::y: y +DEAL:Complex double:Symbols::z: z_00 z_01 z_01 z_11 +DEAL:Complex double:Math operators:Tensor::c+=x: 9.5 + 0.0*I + x_00 11.0 + 0.0*I + x_01 12.5 + 0.0*I + x_10 14.0 + 0.0*I + x_11 +DEAL:Complex double:Math operators:Tensor::c*=y: y*(9.5 + 0.0*I + x_00) y*(11.0 + 0.0*I + x_01) y*(12.5 + 0.0*I + x_10) y*(14.0 + 0.0*I + x_11) +DEAL:Complex double:Math operators:Tensor::c*=s: (2.0 + 0.0*I)*y*(9.5 + 0.0*I + x_00) (2.0 + 0.0*I)*y*(11.0 + 0.0*I + x_01) (2.0 + 0.0*I)*y*(12.5 + 0.0*I + x_10) (2.0 + 0.0*I)*y*(14.0 + 0.0*I + x_11) +DEAL:Complex double:Math operators:Tensor::c-=x: -x_00 + (2.0 + 0.0*I)*y*(9.5 + 0.0*I + x_00) -x_01 + (2.0 + 0.0*I)*y*(11.0 + 0.0*I + x_01) -x_10 + (2.0 + 0.0*I)*y*(12.5 + 0.0*I + x_10) -x_11 + (2.0 + 0.0*I)*y*(14.0 + 0.0*I + x_11) +DEAL:Complex double:Math operators:Tensor::c/=y: (-x_00 + (2.0 + 0.0*I)*y*(9.5 + 0.0*I + x_00))/y (-x_01 + (2.0 + 0.0*I)*y*(11.0 + 0.0*I + x_01))/y (-x_10 + (2.0 + 0.0*I)*y*(12.5 + 0.0*I + x_10))/y (-x_11 + (2.0 + 0.0*I)*y*(14.0 + 0.0*I + x_11))/y +DEAL:Complex double:Math operators:Tensor::c/=s: (0.5 + 0.0*I)*(-x_00 + (2.0 + 0.0*I)*y*(9.5 + 0.0*I + x_00))/y (0.5 + 0.0*I)*(-x_01 + (2.0 + 0.0*I)*y*(11.0 + 0.0*I + x_01))/y (0.5 + 0.0*I)*(-x_10 + (2.0 + 0.0*I)*y*(12.5 + 0.0*I + x_10))/y (0.5 + 0.0*I)*(-x_11 + (2.0 + 0.0*I)*y*(14.0 + 0.0*I + x_11))/y +DEAL:Complex double:Math operators:SymmetricTensor::cs+=z: 8.5 + 0.0*I + z_00 11.5 + 0.0*I + z_01 11.5 + 0.0*I + z_01 10.0 + 0.0*I + z_11 +DEAL:Complex double:Math operators:SymmetricTensor::cs*=y: y*(8.5 + 0.0*I + z_00) y*(11.5 + 0.0*I + z_01) y*(11.5 + 0.0*I + z_01) y*(10.0 + 0.0*I + z_11) +DEAL:Complex double:Math operators:SymmetricTensor::cs*=s: (2.0 + 0.0*I)*y*(8.5 + 0.0*I + z_00) (2.0 + 0.0*I)*y*(11.5 + 0.0*I + z_01) (2.0 + 0.0*I)*y*(11.5 + 0.0*I + z_01) (2.0 + 0.0*I)*y*(10.0 + 0.0*I + z_11) +DEAL:Complex double:Math operators:SymmetricTensor::cs-=z: -z_00 + (2.0 + 0.0*I)*y*(8.5 + 0.0*I + z_00) -z_01 + (2.0 + 0.0*I)*y*(11.5 + 0.0*I + z_01) -z_01 + (2.0 + 0.0*I)*y*(11.5 + 0.0*I + z_01) -z_11 + (2.0 + 0.0*I)*y*(10.0 + 0.0*I + z_11) +DEAL:Complex double:Math operators:SymmetricTensor::cs/=y: (-z_00 + (2.0 + 0.0*I)*y*(8.5 + 0.0*I + z_00))/y (-z_01 + (2.0 + 0.0*I)*y*(11.5 + 0.0*I + z_01))/y (-z_01 + (2.0 + 0.0*I)*y*(11.5 + 0.0*I + z_01))/y (-z_11 + (2.0 + 0.0*I)*y*(10.0 + 0.0*I + z_11))/y +DEAL:Complex double:Math operators:SymmetricTensor::cs/=s: (0.5 + 0.0*I)*(-z_00 + (2.0 + 0.0*I)*y*(8.5 + 0.0*I + z_00))/y (0.5 + 0.0*I)*(-z_01 + (2.0 + 0.0*I)*y*(11.5 + 0.0*I + z_01))/y (0.5 + 0.0*I)*(-z_01 + (2.0 + 0.0*I)*y*(11.5 + 0.0*I + z_01))/y (0.5 + 0.0*I)*(-z_11 + (2.0 + 0.0*I)*y*(10.0 + 0.0*I + z_11))/y +DEAL:Complex double::OK +DEAL::OK From 6b4ecb1b86adb780c6ef54819f97304ce3635923 Mon Sep 17 00:00:00 2001 From: Wolfgang Bangerth Date: Sun, 21 Apr 2019 21:38:04 -0600 Subject: [PATCH 431/507] Mark two function references better. --- include/deal.II/distributed/tria.h | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/include/deal.II/distributed/tria.h b/include/deal.II/distributed/tria.h index 04b212427be6..f373f7145f7c 100644 --- a/include/deal.II/distributed/tria.h +++ b/include/deal.II/distributed/tria.h @@ -1177,7 +1177,7 @@ namespace parallel * @return A vector of unsigned integers representing the weight or * computational load of every cell after the refinement/coarsening/ * repartition cycle. Note that the number of entries does not need to - * be equal to either n_active_cells or n_locally_owned_active_cells, + * be equal to either n_active_cells() or n_locally_owned_active_cells(), * because the triangulation is not updated yet. The weights are sorted * in the order that p4est will encounter them while iterating over * them. From daad233e194283efa1a980d7b9acef537cdad821 Mon Sep 17 00:00:00 2001 From: Wolfgang Bangerth Date: Mon, 22 Apr 2019 08:32:49 -0600 Subject: [PATCH 432/507] Clarify a piece of documentation. --- include/deal.II/numerics/error_estimator.h | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/include/deal.II/numerics/error_estimator.h b/include/deal.II/numerics/error_estimator.h index a9b3fa4a6087..44f767ccfe7d 100644 --- a/include/deal.II/numerics/error_estimator.h +++ b/include/deal.II/numerics/error_estimator.h @@ -117,10 +117,12 @@ namespace hp * contributions of the faces (which are the integrated square of the jumps * times some factor) of each cell and take the square root. * - * The integration is done using a quadrature formula on the face. For linear - * trial functions (FEQ1), QGauss (with two points) or even the QMidpoint rule - * will suffice. For higher order elements, it is necessary to utilize higher - * order quadrature formulae as well. + * The integration is done using a quadrature formula on the face + * provided by the caller of the estimate() functions declared by this + * class. For linear trial functions (FE_Q(1)), QGauss with two points + * or even the QMidpoint rule might actually suffice. For higher order + * elements, it is necessary to utilize higher order quadrature + * formulae with `fe.degree+1` Gauss points. * * We store the contribution of each face in a @p map, as provided by the C++ * standard library, with the iterator pointing to that face being the key From 34e5510daf3021aa1601a0946faaa14eba197617 Mon Sep 17 00:00:00 2001 From: Matthias Maier Date: Mon, 22 Apr 2019 14:16:05 -0500 Subject: [PATCH 433/507] SparsityPattern: Fix copy from DynamicSparsityPattern --- source/lac/sparsity_pattern.cc | 36 +++++++++++++++++++++++++++++----- 1 file changed, 31 insertions(+), 5 deletions(-) diff --git a/source/lac/sparsity_pattern.cc b/source/lac/sparsity_pattern.cc index 7a084e8c5b55..0f46463aed06 100644 --- a/source/lac/sparsity_pattern.cc +++ b/source/lac/sparsity_pattern.cc @@ -489,13 +489,39 @@ SparsityPattern::copy_from(const SparsityPattern &sp) void SparsityPattern::copy_from(const DynamicSparsityPattern &dsp) { - const bool do_diag_optimize = (dsp.n_rows() == dsp.n_cols()); + const bool do_diag_optimize = (dsp.n_rows() == dsp.n_cols()); + const auto &row_index_set = dsp.row_index_set(); + std::vector row_lengths(dsp.n_rows()); - for (size_type i = 0; i < dsp.n_rows(); ++i) + + if (row_index_set.size() == 0) { - row_lengths[i] = dsp.row_length(i); - if (do_diag_optimize && !dsp.exists(i, i)) - ++row_lengths[i]; + for (size_type i = 0; i < dsp.n_rows(); ++i) + { + row_lengths[i] = dsp.row_length(i); + if (do_diag_optimize && !dsp.exists(i, i)) + ++row_lengths[i]; + } + } + else + { + for (size_type i = 0; i < dsp.n_rows(); ++i) + { + if (row_index_set.is_element(i)) + { + row_lengths[i] = dsp.row_length(i); + if (do_diag_optimize && !dsp.exists(i, i)) + ++row_lengths[i]; + } + else + { + // If the row i is not stored in the DynamicSparsityPattern we + // nevertheless need to allocate 1 entry per row for the + // "diagonal optimization". (We store a pointer to the next row + // in place of the repeated index i for the diagonal element.) + row_lengths[i] = do_diag_optimize ? 1 : 0; + } + } } reinit(dsp.n_rows(), dsp.n_cols(), row_lengths); From 09e3944c6e653dbed77210ec8842dba96de27f1a Mon Sep 17 00:00:00 2001 From: Matthias Maier Date: Mon, 15 Apr 2019 11:30:30 -0500 Subject: [PATCH 434/507] add a test --- tests/sparsity/dynamic_sparsity_pattern_21.cc | 40 +++++++++++++++++++ .../dynamic_sparsity_pattern_21.output | 2 + 2 files changed, 42 insertions(+) create mode 100644 tests/sparsity/dynamic_sparsity_pattern_21.cc create mode 100644 tests/sparsity/dynamic_sparsity_pattern_21.output diff --git a/tests/sparsity/dynamic_sparsity_pattern_21.cc b/tests/sparsity/dynamic_sparsity_pattern_21.cc new file mode 100644 index 000000000000..cd217ae249da --- /dev/null +++ b/tests/sparsity/dynamic_sparsity_pattern_21.cc @@ -0,0 +1,40 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2004 - 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + +// Check DynamicSparsityPattern::exists() with supplied rowindex by copying +// to a static SparsityPattern. + +#include +#include + +#include "../tests.h" + +int +main() +{ + initlog(); + + const unsigned int n_dofs = 2; + IndexSet index_set(n_dofs); + index_set.add_index(1); + + DynamicSparsityPattern dsp(n_dofs, n_dofs, index_set); + SparsityPattern sp; + sp.copy_from(dsp); + + deallog << "OK" << std::endl; + + return 0; +} diff --git a/tests/sparsity/dynamic_sparsity_pattern_21.output b/tests/sparsity/dynamic_sparsity_pattern_21.output new file mode 100644 index 000000000000..0fd8fc12f0b4 --- /dev/null +++ b/tests/sparsity/dynamic_sparsity_pattern_21.output @@ -0,0 +1,2 @@ + +DEAL::OK From aae1a0580b896086c557856b9eafa6d5534d5351 Mon Sep 17 00:00:00 2001 From: Matthias Maier Date: Mon, 22 Apr 2019 14:18:45 -0500 Subject: [PATCH 435/507] avoid a segmentation fault --- source/lac/dynamic_sparsity_pattern.cc | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/source/lac/dynamic_sparsity_pattern.cc b/source/lac/dynamic_sparsity_pattern.cc index cb93d1a37d08..b96163570f1b 100644 --- a/source/lac/dynamic_sparsity_pattern.cc +++ b/source/lac/dynamic_sparsity_pattern.cc @@ -360,6 +360,11 @@ DynamicSparsityPattern::exists(const size_type i, const size_type j) const Assert(j < cols, ExcIndexRange(j, 0, cols)); Assert(rowset.size() == 0 || rowset.is_element(i), ExcInternalError()); + // Avoid a segmentation fault in below code if the row index happens to + // not be present in the IndexSet rowset: + if (!(rowset.size() == 0 || rowset.is_element(i))) + return false; + if (!have_entries) return false; From 1cbb7e8d5ae8d8b1b72e57eea4b1604027d44d9e Mon Sep 17 00:00:00 2001 From: Matthias Maier Date: Mon, 22 Apr 2019 14:32:19 -0500 Subject: [PATCH 436/507] improve error message --- source/lac/dynamic_sparsity_pattern.cc | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/source/lac/dynamic_sparsity_pattern.cc b/source/lac/dynamic_sparsity_pattern.cc index b96163570f1b..5631edc66191 100644 --- a/source/lac/dynamic_sparsity_pattern.cc +++ b/source/lac/dynamic_sparsity_pattern.cc @@ -358,7 +358,11 @@ DynamicSparsityPattern::exists(const size_type i, const size_type j) const { Assert(i < rows, ExcIndexRange(i, 0, rows)); Assert(j < cols, ExcIndexRange(j, 0, cols)); - Assert(rowset.size() == 0 || rowset.is_element(i), ExcInternalError()); + Assert( + rowset.size() == 0 || rowset.is_element(i), + ExcMessage( + "The row IndexSet does not contain the index i. This sparsity pattern " + "object cannot know whether the entry (i, j) exists or not.")); // Avoid a segmentation fault in below code if the row index happens to // not be present in the IndexSet rowset: From 08182a4b05e9107dba58fef96ec892eeffb6c889 Mon Sep 17 00:00:00 2001 From: Luca Heltai Date: Fri, 19 Apr 2019 10:17:13 +0200 Subject: [PATCH 437/507] Mapping::get_center() --- doc/news/changes/minor/20190411LucaHeltai | 4 + include/deal.II/fe/mapping.h | 26 ++++++ source/fe/mapping.cc | 25 ++++++ tests/mappings/mapping_q_eulerian_12.cc | 96 +++++++++++++++++++++ tests/mappings/mapping_q_eulerian_12.output | 10 +++ 5 files changed, 161 insertions(+) create mode 100644 doc/news/changes/minor/20190411LucaHeltai create mode 100644 tests/mappings/mapping_q_eulerian_12.cc create mode 100644 tests/mappings/mapping_q_eulerian_12.output diff --git a/doc/news/changes/minor/20190411LucaHeltai b/doc/news/changes/minor/20190411LucaHeltai new file mode 100644 index 000000000000..ad5ad6c43737 --- /dev/null +++ b/doc/news/changes/minor/20190411LucaHeltai @@ -0,0 +1,4 @@ +New: The method Mapping::get_center() allows one to retrieve the cell center of a cell when the +mapping object does not preserve vertex locations. +
    +(Luca Heltai, 2019/04/11) diff --git a/include/deal.II/fe/mapping.h b/include/deal.II/fe/mapping.h index 21bec9ebc2a3..c1c60aac8ba7 100644 --- a/include/deal.II/fe/mapping.h +++ b/include/deal.II/fe/mapping.h @@ -336,6 +336,32 @@ class Mapping : public Subscriptor get_vertices( const typename Triangulation::cell_iterator &cell) const; + /** + * Return the mapped center of a cell. + * + * If you are using a (bi-,tri-)linear mapping that preserves vertex + * locations, this function simply returns the value also produced by + * `cell->center()`. However, there are also mappings that add displacements + * or choose completely different locations, e.g., MappingQEulerian, + * MappingQ1Eulerian, or MappingFEField. + * + * By default, this function returns the average of the vertex locations + * returned by the the get_vertices() method. If the parameter + * @p map_center_of_reference_cell is set to true, than a more expensive + * algorithm is used, that returns the mapped center of the reference cell, + * obtained by the transform_unit_to_real_cell() method. + * + * @param[in] cell The cell for which you want to compute the center + * @param[in] map_center_of_reference_cell A flag that switches the algorithm + * for the computation of the cell center from vertex averages to + * transform_unit_to_real_cell() applied to the center of the reference cell + * + * @author Luca Heltai, 2019. + */ + virtual Point + get_center(const typename Triangulation::cell_iterator &cell, + const bool map_center_of_reference_cell = false) const; + /** * Return whether the mapping preserves vertex locations. In other words, * this function returns whether the mapped location of the reference cell diff --git a/source/fe/mapping.cc b/source/fe/mapping.cc index 60d57958000e..97a7a38f2364 100644 --- a/source/fe/mapping.cc +++ b/source/fe/mapping.cc @@ -36,6 +36,31 @@ Mapping::get_vertices( +template +Point +Mapping::get_center( + const typename Triangulation::cell_iterator &cell, + const bool map_center_of_reference_cell) const +{ + if (map_center_of_reference_cell) + { + Point reference_center; + for (unsigned int d = 0; d < dim; ++d) + reference_center[d] = .5; + return transform_unit_to_real_cell(cell, reference_center); + } + else + { + const auto vertices = get_vertices(cell); + Point center; + for (const auto &v : vertices) + center += v; + return center / GeometryInfo::vertices_per_cell; + } +} + + + template Point Mapping::project_real_point_to_unit_point_on_face( diff --git a/tests/mappings/mapping_q_eulerian_12.cc b/tests/mappings/mapping_q_eulerian_12.cc new file mode 100644 index 000000000000..e8626585c506 --- /dev/null +++ b/tests/mappings/mapping_q_eulerian_12.cc @@ -0,0 +1,96 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + +// test that MappingQEulerian knows how to compute centers of cells + +#include + +#include +#include +#include + +#include +#include +#include + +#include +#include + +#include + +#include +#include + +#include "../tests.h" + +using namespace dealii; + + +template +class Displacement : public Function +{ +public: + Displacement() + : Function(dim) + {} + + double + value(const Point &p, const unsigned int component) const + { + return p[component] * p[0] / 2; + } +}; + + +template +void +test() +{ + deallog << "dim=" << dim << std::endl; + + Triangulation triangulation; + GridGenerator::hyper_cube(triangulation, -1, 1); + + FESystem fe(FE_Q(2), dim); + DoFHandler dof_handler(triangulation); + dof_handler.distribute_dofs(fe); + + Vector displacements(dof_handler.n_dofs()); + + VectorTools::interpolate(dof_handler, Displacement(), displacements); + + MappingQEulerian euler(2, dof_handler, displacements); + + // now the actual test + for (const auto &cell : dof_handler.active_cell_iterators()) + { + deallog << "Center: [" << cell->center() << "], with mapping [" + << euler.get_center(cell) << "]" << std::endl; + deallog << "Center: [" << cell->center() << "], with mapping + flag [" + << euler.get_center(cell, true) << "]" << std::endl; + } +} + + + +int +main() +{ + initlog(1); + + test<1>(); + test<2>(); + test<3>(); +} diff --git a/tests/mappings/mapping_q_eulerian_12.output b/tests/mappings/mapping_q_eulerian_12.output new file mode 100644 index 000000000000..eb04a22389ae --- /dev/null +++ b/tests/mappings/mapping_q_eulerian_12.output @@ -0,0 +1,10 @@ + +DEAL::dim=1 +DEAL::Center: [0.00000], with mapping [0.500000] +DEAL::Center: [0.00000], with mapping + flag [0.00000] +DEAL::dim=2 +DEAL::Center: [0.00000 0.00000], with mapping [0.500000 0.00000] +DEAL::Center: [0.00000 0.00000], with mapping + flag [0.00000 0.00000] +DEAL::dim=3 +DEAL::Center: [0.00000 0.00000 0.00000], with mapping [0.500000 0.00000 0.00000] +DEAL::Center: [0.00000 0.00000 0.00000], with mapping + flag [0.00000 0.00000 0.00000] From 440455f0d9a13cff2a67735a3b418192d9e111f4 Mon Sep 17 00:00:00 2001 From: Luca Heltai Date: Tue, 23 Apr 2019 11:22:12 +0200 Subject: [PATCH 438/507] Fix documentation of extend + spelling. --- include/deal.II/base/bounding_box.h | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/include/deal.II/base/bounding_box.h b/include/deal.II/base/bounding_box.h index 97acdb873d78..bfb85c5e79ee 100644 --- a/include/deal.II/base/bounding_box.h +++ b/include/deal.II/base/bounding_box.h @@ -141,7 +141,8 @@ class BoundingBox point_inside(const Point &p) const; /** - * Increase (or decrease) the size of the bounding box by the given amount. + * Increase (or decrease) the size of the bounding box by the given amount, + * in both directions in all coordinate directions. * * If you call this method with a negative number, and one of the axes of the * original bounding box is smaller than amount/2, the method will trigger @@ -195,7 +196,7 @@ BoundingBox::extend(const Number &amount) boundary_points.first[d] -= amount; boundary_points.second[d] += amount; Assert(boundary_points.first[d] <= boundary_points.second[d], - ExcMessage("Bounding Box can't be shrinked this much: the points' " + ExcMessage("Bounding Box can't be shrunk this much: the points' " "order should remain bottom left, top right.")); } } From 92003f37ac757ffbb8ebb002519975fe6cb08428 Mon Sep 17 00:00:00 2001 From: Luca Heltai Date: Tue, 23 Apr 2019 14:46:08 +0200 Subject: [PATCH 439/507] Improved documentation. --- include/deal.II/base/bounding_box.h | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/include/deal.II/base/bounding_box.h b/include/deal.II/base/bounding_box.h index bfb85c5e79ee..8922fa6b3676 100644 --- a/include/deal.II/base/bounding_box.h +++ b/include/deal.II/base/bounding_box.h @@ -141,8 +141,10 @@ class BoundingBox point_inside(const Point &p) const; /** - * Increase (or decrease) the size of the bounding box by the given amount, - * in both directions in all coordinate directions. + * Increase (or decrease) the size of the bounding box by the given amount. + * After calling this method, the lower left corner of the bounding box will + * have each coordinate decreased by @p amount, and the upper right corner + * of the bounding box will have each coordinate increased by @p amount. * * If you call this method with a negative number, and one of the axes of the * original bounding box is smaller than amount/2, the method will trigger From 772651e912cf3caf2394fddbef1cabb58ad2f832 Mon Sep 17 00:00:00 2001 From: Luca Heltai Date: Thu, 18 Apr 2019 09:31:50 +0200 Subject: [PATCH 440/507] Modify FunctionCutOff to support integration to one. --- doc/news/changes/minor/20190418LucaHeltai | 3 + include/deal.II/base/function_lib.h | 50 ++++++++- source/base/function_lib_cutoff.cc | 131 ++++++++++++++++++---- tests/function_cutoff_01.cc | 120 ++++++++++++++++++++ tests/function_cutoff_01.output | 64 +++++++++++ 5 files changed, 339 insertions(+), 29 deletions(-) create mode 100644 doc/news/changes/minor/20190418LucaHeltai create mode 100644 tests/function_cutoff_01.cc create mode 100644 tests/function_cutoff_01.output diff --git a/doc/news/changes/minor/20190418LucaHeltai b/doc/news/changes/minor/20190418LucaHeltai new file mode 100644 index 000000000000..a0b5e6a83b34 --- /dev/null +++ b/doc/news/changes/minor/20190418LucaHeltai @@ -0,0 +1,3 @@ +New: Functions::CutOffFunctionBase now supports rescaling the function to keep its integral equal to one. +
    +(Luca Heltai, 2019/04/18) diff --git a/include/deal.II/base/function_lib.h b/include/deal.II/base/function_lib.h index 665cef4b3c8d..3769444c3e74 100644 --- a/include/deal.II/base/function_lib.h +++ b/include/deal.II/base/function_lib.h @@ -912,8 +912,12 @@ namespace Functions * radius of the supporting ball of a cut-off function. It also stores the * number of the non-zero component, if the function is vector-valued. * + * This class can also be used for approximated Dirac delta functions. These + * are special cut-off functions whose integral is always equal to one, + * independently on the radius of the supporting ball. + * * @ingroup functions - * @author Guido Kanschat, 2002 + * @author Guido Kanschat, 2002, Luca Heltai, 2019. */ template class CutOffFunctionBase : public Function @@ -930,12 +934,17 @@ namespace Functions * * If an argument select is given and not -1, the cut-off * function will be non-zero for this component only. + * + * If the argument @p integrate_to_one is set to true, then the value of + * the function is rescaled whenever a new radius is set. */ CutOffFunctionBase( const double radius = 1., const Point = Point(), const unsigned int n_components = 1, - const unsigned int select = CutOffFunctionBase::no_component); + const unsigned int select = CutOffFunctionBase::no_component, + const bool integrate_to_one = false, + const double unitary_integral_value = 1.0); /** * Move the center of the ball to new point p. @@ -949,6 +958,18 @@ namespace Functions void new_radius(const double r); + /** + * Return the center stored in this object. + */ + const Point & + get_center() const; + + /** + * Return the radius stored in this object. + */ + double + get_radius() const; + protected: /** * Center of the integration ball. @@ -965,6 +986,22 @@ namespace Functions * in all components. */ const unsigned int selected; + + /** + * Flag that controls wether we rescale the value when the radius changes. + */ + const bool integrate_to_one; + + /** + * The reference integral value. Derived classes should specify what their + * integral is when @p radius = 1.0. + */ + const double unitary_integral_value; + + /** + * Current rescaling to apply the the cut-off function. + */ + double rescaling; }; @@ -992,7 +1029,8 @@ namespace Functions const double radius = 1., const Point = Point(), const unsigned int n_components = 1, - const unsigned int select = CutOffFunctionBase::no_component); + const unsigned int select = CutOffFunctionBase::no_component, + const bool integrate_to_one = false); /** * Function value at one point. @@ -1040,7 +1078,8 @@ namespace Functions const double radius = 1., const Point = Point(), const unsigned int n_components = 1, - const unsigned int select = CutOffFunctionBase::no_component); + const unsigned int select = CutOffFunctionBase::no_component, + const bool integrate_to_one = false); /** * Function value at one point. @@ -1089,7 +1128,8 @@ namespace Functions const double radius = 1., const Point = Point(), const unsigned int n_components = 1, - const unsigned int select = CutOffFunctionBase::no_component); + const unsigned int select = CutOffFunctionBase::no_component, + bool integrate_to_one = false); /** * Function value at one point. diff --git a/source/base/function_lib_cutoff.cc b/source/base/function_lib_cutoff.cc index b35fcc42d9ec..71ba7b7834fc 100644 --- a/source/base/function_lib_cutoff.cc +++ b/source/base/function_lib_cutoff.cc @@ -27,15 +27,25 @@ DEAL_II_NAMESPACE_OPEN namespace Functions { template - CutOffFunctionBase::CutOffFunctionBase(const double r, - const Point p, - const unsigned int n_components, - const unsigned int select) + CutOffFunctionBase::CutOffFunctionBase( + const double r, + const Point p, + const unsigned int n_components, + const unsigned int select, + const bool integrate_to_one, + const double unitary_integral_value) : Function(n_components) , center(p) , radius(r) , selected(select) - {} + , integrate_to_one(integrate_to_one) + , unitary_integral_value(unitary_integral_value) + , rescaling(integrate_to_one ? 1. / (unitary_integral_value * + Utilities::fixed_power(radius)) : + 1.0) + { + Assert(r > 0, ExcMessage("You must specify a radius > 0.")); + } template @@ -46,22 +56,68 @@ namespace Functions } + + template + const Point & + CutOffFunctionBase::get_center() const + { + return center; + } + + + template void CutOffFunctionBase::new_radius(const double r) { radius = r; + Assert(r > 0, ExcMessage("You must specify a radius > 0.")); + if (integrate_to_one) + rescaling = + 1. / (unitary_integral_value * Utilities::fixed_power(radius)); + else + rescaling = 1.0; + } + + + + template + double + CutOffFunctionBase::get_radius() const + { + return radius; } + ////////////////////////////////////////////////////////////////////// + namespace + { + double integral_Linfty[] = {2.0, + 3.14159265358979323846264338328, + 4.18879020478639098461685784437}; + double integral_W1[] = {1.0, + 1.04719755119659774615421446109, + 1.04719755119659774615421446109}; + + double integral_Cinfty[] = {1.20690032243787617533623799633, + 1.26811216112759608094632335664, + 1.1990039070192139033798473858}; + } // namespace + template CutOffFunctionLinfty::CutOffFunctionLinfty( const double r, const Point p, const unsigned int n_components, - const unsigned int select) - : CutOffFunctionBase(r, p, n_components, select) + const unsigned int select, + const bool integrate_to_one) + : CutOffFunctionBase(r, + p, + n_components, + select, + integrate_to_one, + integral_Linfty[dim - 1]) {} @@ -72,7 +128,7 @@ namespace Functions { if (this->selected == CutOffFunctionBase::no_component || component == this->selected) - return ((this->center.distance(p) < this->radius) ? 1. : 0.); + return ((this->center.distance(p) < this->radius) ? this->rescaling : 0.); return 0.; } @@ -92,7 +148,9 @@ namespace Functions if (this->selected == CutOffFunctionBase::no_component || component == this->selected) for (unsigned int k = 0; k < values.size(); ++k) - values[k] = (this->center.distance(points[k]) < this->radius) ? 1. : 0.; + values[k] = (this->center.distance(points[k]) < this->radius) ? + this->rescaling : + 0.; else std::fill(values.begin(), values.end(), 0.); } @@ -109,8 +167,9 @@ namespace Functions for (unsigned int k = 0; k < values.size(); ++k) { - const double val = - (this->center.distance(points[k]) < this->radius) ? 1. : 0.; + const double val = (this->center.distance(points[k]) < this->radius) ? + this->rescaling : + 0.; if (this->selected == CutOffFunctionBase::no_component) values[k] = val; else @@ -121,13 +180,18 @@ namespace Functions } } - template CutOffFunctionW1::CutOffFunctionW1(const double r, const Point p, const unsigned int n_components, - const unsigned int select) - : CutOffFunctionBase(r, p, n_components, select) + const unsigned int select, + const bool integrate_to_one) + : CutOffFunctionBase(r, + p, + n_components, + select, + integrate_to_one, + integral_W1[dim - 1]) {} @@ -140,7 +204,9 @@ namespace Functions component == this->selected) { const double d = this->center.distance(p); - return ((d < this->radius) ? (this->radius - d) : 0.); + return ((d < this->radius) ? + (this->radius - d) / this->radius * this->rescaling : + 0.); } return 0.; } @@ -160,7 +226,9 @@ namespace Functions for (unsigned int i = 0; i < values.size(); ++i) { const double d = this->center.distance(points[i]); - values[i] = ((d < this->radius) ? (this->radius - d) : 0.); + values[i] = ((d < this->radius) ? + (this->radius - d) / this->radius * this->rescaling : + 0.); } else std::fill(values.begin(), values.end(), 0.); @@ -179,8 +247,11 @@ namespace Functions for (unsigned int k = 0; k < values.size(); ++k) { - const double d = this->center.distance(points[k]); - const double val = (d < this->radius) ? (this->radius - d) : 0.; + const double d = this->center.distance(points[k]); + const double val = + (d < this->radius) ? + (this->radius - d) / this->radius * this->rescaling : + 0.; if (this->selected == CutOffFunctionBase::no_component) values[k] = val; else @@ -197,8 +268,14 @@ namespace Functions const double r, const Point p, const unsigned int n_components, - const unsigned int select) - : CutOffFunctionBase(r, p, n_components, select) + const unsigned int select, + bool integrate_to_one) + : CutOffFunctionBase(r, + p, + n_components, + select, + integrate_to_one, + integral_Cinfty[dim - 1]) {} @@ -215,7 +292,7 @@ namespace Functions if (d >= r) return 0.; const double e = -r * r / (r * r - d * d); - return ((e < -50) ? 0. : numbers::E * std::exp(e)); + return ((e < -50) ? 0. : numbers::E * std::exp(e) * this->rescaling); } return 0.; } @@ -244,7 +321,8 @@ namespace Functions else { const double e = -r * r / (r * r - d * d); - values[i] = (e < -50) ? 0. : numbers::E * std::exp(e); + values[i] = + (e < -50) ? 0. : numbers::E * std::exp(e) * this->rescaling; } } else @@ -270,7 +348,7 @@ namespace Functions { const double e = -r * r / (r * r - d * d); if (e > -50) - val = numbers::E * std::exp(e); + val = numbers::E * std::exp(e) * this->rescaling; } if (this->selected == CutOffFunctionBase::no_component) @@ -298,11 +376,16 @@ namespace Functions return ((e < -50) ? Point() : (p - this->center) / d * (-2.0 * r * r / std::pow(-r * r + d * d, 2.0) * d * - std::exp(e))); + std::exp(e)) * + this->rescaling); } // explicit instantiations + template class CutOffFunctionBase<1>; + template class CutOffFunctionBase<2>; + template class CutOffFunctionBase<3>; + template class CutOffFunctionLinfty<1>; template class CutOffFunctionLinfty<2>; template class CutOffFunctionLinfty<3>; diff --git a/tests/function_cutoff_01.cc b/tests/function_cutoff_01.cc new file mode 100644 index 000000000000..428660863091 --- /dev/null +++ b/tests/function_cutoff_01.cc @@ -0,0 +1,120 @@ +// --------------------------------------------------------------------- +// +// Copyright (C) 2019 by the deal.II authors +// +// This file is part of the deal.II library. +// +// The deal.II library is free software; you can use it, redistribute +// it, and/or modify it under the terms of the GNU Lesser General +// Public License as published by the Free Software Foundation; either +// version 2.1 of the License, or (at your option) any later version. +// The full text of the license can be found in the file LICENSE.md at +// the top level directory of deal.II. +// +// --------------------------------------------------------------------- + +// Test the functionality of the CutOffFunction with integrate_to_one = true + +#include +#include +#include + +#include +#include + +#include + +#include + +#include + +#include "../tests.h" + +using namespace Functions; + +template +struct Domain +{ + Domain() + : fe(1) + , dh(tria) + , quad(5) + { + deallog << "Testing dim = " << dim << std::endl; + GridGenerator::hyper_cube(tria, -2, 2); + tria.refine_global(5 - dim); + dh.distribute_dofs(fe); + zero.reinit(dh.n_dofs()); + cell_integral.reinit(tria.n_active_cells()); + } + + template + void + integrate(const Function &fun) + { + deallog << "Integrating " << Utilities::type_to_string(fun) + << " -2,2 cube: "; + + VectorTools::integrate_difference( + dh, zero, fun, cell_integral, quad, VectorTools::L1_norm); + const double integral = + VectorTools::compute_global_error(tria, + cell_integral, + VectorTools::L1_norm); + + deallog << integral << std::endl; + } + + Triangulation tria; + FE_Q fe; + DoFHandler dh; + Vector zero; + Vector cell_integral; + QGauss quad; +}; + +template class TestCutOffFunction> +void +test() +{ + static Domain domain; + TestCutOffFunction fun(1., + Point(), + 1, + Functions::CutOffFunctionBase::no_component, + /*integrate_to_one = */ true); + deallog << "Center: " << fun.get_center() << std::endl + << "Radius: " << fun.get_radius() << std::endl; + + domain.integrate(fun); + + Point new_center; + for (unsigned int i = 0; i < dim; ++i) + new_center[i] = .5; + + fun.new_center(new_center); + fun.new_radius(.5); + + deallog << "Center: " << fun.get_center() << std::endl + << "Radius: " << fun.get_radius() << std::endl; + + domain.integrate(fun); +} + +int +main() +{ + initlog(1); + + test<1, Functions::CutOffFunctionLinfty>(); + test<2, Functions::CutOffFunctionLinfty>(); + test<3, Functions::CutOffFunctionLinfty>(); + + test<1, Functions::CutOffFunctionW1>(); + test<2, Functions::CutOffFunctionW1>(); + test<3, Functions::CutOffFunctionW1>(); + + test<1, Functions::CutOffFunctionCinfty>(); + test<2, Functions::CutOffFunctionCinfty>(); + test<3, Functions::CutOffFunctionCinfty>(); +} diff --git a/tests/function_cutoff_01.output b/tests/function_cutoff_01.output new file mode 100644 index 000000000000..2554c237b72e --- /dev/null +++ b/tests/function_cutoff_01.output @@ -0,0 +1,64 @@ + +DEAL::Testing dim = 1 +DEAL::Center: 0.00000 +DEAL::Radius: 1.00000 +DEAL::Integrating dealii::Functions::CutOffFunctionLinfty<1> -2,2 cube: 1.00000 +DEAL::Center: 0.500000 +DEAL::Radius: 0.500000 +DEAL::Integrating dealii::Functions::CutOffFunctionLinfty<1> -2,2 cube: 1.00000 +DEAL::Testing dim = 2 +DEAL::Center: 0.00000 0.00000 +DEAL::Radius: 1.00000 +DEAL::Integrating dealii::Functions::CutOffFunctionLinfty<2> -2,2 cube: 0.993980 +DEAL::Center: 0.500000 0.500000 +DEAL::Radius: 0.500000 +DEAL::Integrating dealii::Functions::CutOffFunctionLinfty<2> -2,2 cube: 1.02445 +DEAL::Testing dim = 3 +DEAL::Center: 0.00000 0.00000 0.00000 +DEAL::Radius: 1.00000 +DEAL::Integrating dealii::Functions::CutOffFunctionLinfty<3> -2,2 cube: 1.00850 +DEAL::Center: 0.500000 0.500000 0.500000 +DEAL::Radius: 0.500000 +DEAL::Integrating dealii::Functions::CutOffFunctionLinfty<3> -2,2 cube: 0.958427 +DEAL::Testing dim = 1 +DEAL::Center: 0.00000 +DEAL::Radius: 1.00000 +DEAL::Integrating dealii::Functions::CutOffFunctionW1<1> -2,2 cube: 1.00000 +DEAL::Center: 0.500000 +DEAL::Radius: 0.500000 +DEAL::Integrating dealii::Functions::CutOffFunctionW1<1> -2,2 cube: 1.00000 +DEAL::Testing dim = 2 +DEAL::Center: 0.00000 0.00000 +DEAL::Radius: 1.00000 +DEAL::Integrating dealii::Functions::CutOffFunctionW1<2> -2,2 cube: 1.00030 +DEAL::Center: 0.500000 0.500000 +DEAL::Radius: 0.500000 +DEAL::Integrating dealii::Functions::CutOffFunctionW1<2> -2,2 cube: 1.00316 +DEAL::Testing dim = 3 +DEAL::Center: 0.00000 0.00000 0.00000 +DEAL::Radius: 1.00000 +DEAL::Integrating dealii::Functions::CutOffFunctionW1<3> -2,2 cube: 1.00445 +DEAL::Center: 0.500000 0.500000 0.500000 +DEAL::Radius: 0.500000 +DEAL::Integrating dealii::Functions::CutOffFunctionW1<3> -2,2 cube: 1.03922 +DEAL::Testing dim = 1 +DEAL::Center: 0.00000 +DEAL::Radius: 1.00000 +DEAL::Integrating dealii::Functions::CutOffFunctionCinfty<1> -2,2 cube: 1.00002 +DEAL::Center: 0.500000 +DEAL::Radius: 0.500000 +DEAL::Integrating dealii::Functions::CutOffFunctionCinfty<1> -2,2 cube: 0.999735 +DEAL::Testing dim = 2 +DEAL::Center: 0.00000 0.00000 +DEAL::Radius: 1.00000 +DEAL::Integrating dealii::Functions::CutOffFunctionCinfty<2> -2,2 cube: 0.999958 +DEAL::Center: 0.500000 0.500000 +DEAL::Radius: 0.500000 +DEAL::Integrating dealii::Functions::CutOffFunctionCinfty<2> -2,2 cube: 0.998842 +DEAL::Testing dim = 3 +DEAL::Center: 0.00000 0.00000 0.00000 +DEAL::Radius: 1.00000 +DEAL::Integrating dealii::Functions::CutOffFunctionCinfty<3> -2,2 cube: 0.999614 +DEAL::Center: 0.500000 0.500000 0.500000 +DEAL::Radius: 0.500000 +DEAL::Integrating dealii::Functions::CutOffFunctionCinfty<3> -2,2 cube: 1.00165 From 96c4a2a8b98e10a20be9336e7df7e45e32792ae4 Mon Sep 17 00:00:00 2001 From: Luca Heltai Date: Thu, 18 Apr 2019 15:48:51 +0200 Subject: [PATCH 441/507] Deprecate new_* in favour of set_* --- include/deal.II/base/function_lib.h | 22 ++++++++++++++++++++-- source/base/function_lib_cutoff.cc | 18 ++++++++++++++++++ tests/{ => base}/function_cutoff_01.cc | 4 ++-- tests/{ => base}/function_cutoff_01.output | 0 4 files changed, 40 insertions(+), 4 deletions(-) rename tests/{ => base}/function_cutoff_01.cc (98%) rename tests/{ => base}/function_cutoff_01.output (100%) diff --git a/include/deal.II/base/function_lib.h b/include/deal.II/base/function_lib.h index 3769444c3e74..0b36b2d4e32d 100644 --- a/include/deal.II/base/function_lib.h +++ b/include/deal.II/base/function_lib.h @@ -948,16 +948,34 @@ namespace Functions /** * Move the center of the ball to new point p. + * + * @deprecated Use set_center() instead. */ - void + DEAL_II_DEPRECATED void new_center(const Point &p); /** * Set the radius of the ball to r. + * + * @deprecated Use set_radius() instead. */ - void + DEAL_II_DEPRECATED void new_radius(const double r); + /** + * Set the center of the ball to the point @p p. + */ + void + set_center(const Point &p); + + /** + * Set the radius of the ball to @p r + * + * @deprecated Use set_radius() instead. + */ + void + set_radius(const double r); + /** * Return the center stored in this object. */ diff --git a/source/base/function_lib_cutoff.cc b/source/base/function_lib_cutoff.cc index 71ba7b7834fc..e1fa60fc532b 100644 --- a/source/base/function_lib_cutoff.cc +++ b/source/base/function_lib_cutoff.cc @@ -51,6 +51,15 @@ namespace Functions template void CutOffFunctionBase::new_center(const Point &p) + { + set_center(p); + } + + + + template + void + CutOffFunctionBase::set_center(const Point &p) { center = p; } @@ -69,6 +78,15 @@ namespace Functions template void CutOffFunctionBase::new_radius(const double r) + { + set_radius(r); + } + + + + template + void + CutOffFunctionBase::set_radius(const double r) { radius = r; Assert(r > 0, ExcMessage("You must specify a radius > 0.")); diff --git a/tests/function_cutoff_01.cc b/tests/base/function_cutoff_01.cc similarity index 98% rename from tests/function_cutoff_01.cc rename to tests/base/function_cutoff_01.cc index 428660863091..c51ac0f79747 100644 --- a/tests/function_cutoff_01.cc +++ b/tests/base/function_cutoff_01.cc @@ -92,8 +92,8 @@ test() for (unsigned int i = 0; i < dim; ++i) new_center[i] = .5; - fun.new_center(new_center); - fun.new_radius(.5); + fun.set_center(new_center); + fun.set_radius(.5); deallog << "Center: " << fun.get_center() << std::endl << "Radius: " << fun.get_radius() << std::endl; diff --git a/tests/function_cutoff_01.output b/tests/base/function_cutoff_01.output similarity index 100% rename from tests/function_cutoff_01.output rename to tests/base/function_cutoff_01.output From 454a08167dbc5d67dc43a6d91e1993e7b8405c07 Mon Sep 17 00:00:00 2001 From: Luca Heltai Date: Thu, 18 Apr 2019 19:57:37 +0200 Subject: [PATCH 442/507] Added FunctionCutOffTensorProduct. --- include/deal.II/base/function_lib.h | 109 +++++++++++++++++++++++- source/base/function_lib_cutoff.cc | 79 ++++++++++++++++++ tests/base/function_cutoff_02.cc | 120 +++++++++++++++++++++++++++ tests/base/function_cutoff_02.output | 64 ++++++++++++++ 4 files changed, 369 insertions(+), 3 deletions(-) create mode 100644 tests/base/function_cutoff_02.cc create mode 100644 tests/base/function_cutoff_02.output diff --git a/include/deal.II/base/function_lib.h b/include/deal.II/base/function_lib.h index 0b36b2d4e32d..ff38a07bc863 100644 --- a/include/deal.II/base/function_lib.h +++ b/include/deal.II/base/function_lib.h @@ -21,6 +21,7 @@ #include #include +#include #include #include @@ -946,6 +947,11 @@ namespace Functions const bool integrate_to_one = false, const double unitary_integral_value = 1.0); + /** + * Virtual destructor. + */ + virtual ~CutOffFunctionBase() = default; + /** * Move the center of the ball to new point p. * @@ -965,7 +971,7 @@ namespace Functions /** * Set the center of the ball to the point @p p. */ - void + virtual void set_center(const Point &p); /** @@ -973,7 +979,7 @@ namespace Functions * * @deprecated Use set_radius() instead. */ - void + virtual void set_radius(const double r); /** @@ -988,6 +994,12 @@ namespace Functions double get_radius() const; + /** + * Return a boolean indicating if this function integrates to one. + */ + bool + integrates_to_one() const; + protected: /** * Center of the integration ball. @@ -1008,7 +1020,7 @@ namespace Functions /** * Flag that controls wether we rescale the value when the radius changes. */ - const bool integrate_to_one; + bool integrate_to_one; /** * The reference integral value. Derived classes should specify what their @@ -1023,6 +1035,76 @@ namespace Functions }; + /** + * Tensor product of CutOffFunctionBase objects. + * + * Instead of using the distance to compute the cut-off function, this class + * performs a tensor product of the same CutOffFunctionBase object in each + * coordinate direction. + * + * @ingroup functions + * @author Luca Heltai, 2019. + */ + template + class CutOffFunctionTensorProduct : public CutOffFunctionBase + { + public: + /** + * Construct an empty CutOffFunctionTensorProduct object. + * + * Before you can use this class, you have to call the set_base() method + * with a class derived from the CutOffFunctionBase object. + * + * If you try to use this class before you call the set_base() method, + * and exception will be triggered. + */ + CutOffFunctionTensorProduct( + double radius = 1.0, + const Point & center = Point(), + const unsigned int n_components = 1, + const unsigned int select = CutOffFunctionBase::no_component, + const bool integrate_to_one = false); + + /** + * Initialize the class with an objet of type + * @tparam CutOffFunctionBaseType<1>. + */ + template