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Vera fixes on models starting with w to models starting with h. #8

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merged 4 commits into from
Mar 9, 2017
Merged

Vera fixes on models starting with w to models starting with h. #8

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c360021
Vera fixes on models starting with w to models starting with h.
stinebuu Mar 9, 2017
f9489fc
Vera fix for a model I forgot
stinebuu Mar 9, 2017
4730a50
Merge remote-tracking branch 'Plesser/fix-vera-issues' into fix_vera
stinebuu Mar 9, 2017
60eb3d8
Merge remote-tracking branch 'Plesser/fix-vera-issues' into fix_vera
stinebuu Mar 9, 2017
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12 changes: 12 additions & 0 deletions models/hh_cond_exp_traub.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -325,11 +325,17 @@ nest::hh_cond_exp_traub::~hh_cond_exp_traub()
{
// GSL structs may not have been allocated, so we need to protect destruction
if ( B_.s_ )
{
gsl_odeiv_step_free( B_.s_ );
}
if ( B_.c_ )
{
gsl_odeiv_control_free( B_.c_ );
}
if ( B_.e_ )
{
gsl_odeiv_evolve_free( B_.e_ );
}
}

/* ----------------------------------------------------------------
Expand Down Expand Up @@ -359,22 +365,28 @@ nest::hh_cond_exp_traub::init_buffers_()
B_.I_stim_ = 0.0;

if ( B_.s_ == 0 )
{
B_.s_ =
gsl_odeiv_step_alloc( gsl_odeiv_step_rkf45, State_::STATE_VEC_SIZE );
}
else
{
gsl_odeiv_step_reset( B_.s_ );
}

if ( B_.c_ == 0 )
{
B_.c_ = gsl_odeiv_control_y_new( 1e-3, 0.0 );
}
else
{
gsl_odeiv_control_init( B_.c_, 1e-3, 0.0, 1.0, 0.0 );
}

if ( B_.e_ == 0 )
{
B_.e_ = gsl_odeiv_evolve_alloc( State_::STATE_VEC_SIZE );
}
else
{
gsl_odeiv_evolve_reset( B_.e_ );
Expand Down
16 changes: 16 additions & 0 deletions models/hh_psc_alpha.cpp
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -319,11 +319,17 @@ nest::hh_psc_alpha::~hh_psc_alpha()
{
// GSL structs may not have been allocated, so we need to protect destruction
if ( B_.s_ )
{
gsl_odeiv_step_free( B_.s_ );
}
if ( B_.c_ )
{
gsl_odeiv_control_free( B_.c_ );
}
if ( B_.e_ )
{
gsl_odeiv_evolve_free( B_.e_ );
}
}

/* ----------------------------------------------------------------
Expand Down Expand Up @@ -351,22 +357,28 @@ nest::hh_psc_alpha::init_buffers_()
B_.IntegrationStep_ = B_.step_;

if ( B_.s_ == 0 )
{
B_.s_ =
gsl_odeiv_step_alloc( gsl_odeiv_step_rkf45, State_::STATE_VEC_SIZE );
}
else
{
gsl_odeiv_step_reset( B_.s_ );
}

if ( B_.c_ == 0 )
{
B_.c_ = gsl_odeiv_control_y_new( 1e-3, 0.0 );
}
else
{
gsl_odeiv_control_init( B_.c_, 1e-3, 0.0, 1.0, 0.0 );
}

if ( B_.e_ == 0 )
{
B_.e_ = gsl_odeiv_evolve_alloc( State_::STATE_VEC_SIZE );
}
else
{
gsl_odeiv_evolve_reset( B_.e_ );
Expand Down Expand Up @@ -447,7 +459,9 @@ nest::hh_psc_alpha::update( Time const& origin, const long from, const long to )
// sending spikes: crossing 0 mV, pseudo-refractoriness and local maximum...
// refractory?
if ( S_.r_ > 0 )
{
--S_.r_;
}
else
// ( threshold && maximum )
if ( S_.y_[ State_::V_M ] >= 0 && U_old > S_.y_[ State_::V_M ] )
Expand All @@ -474,9 +488,11 @@ nest::hh_psc_alpha::handle( SpikeEvent& e )
assert( e.get_delay() > 0 );

if ( e.get_weight() > 0.0 )
{
B_.spike_exc_.add_value( e.get_rel_delivery_steps(
kernel().simulation_manager.get_slice_origin() ),
e.get_weight() * e.get_multiplicity() );
}
else
{
B_.spike_inh_.add_value( e.get_rel_delivery_steps(
Expand Down
16 changes: 16 additions & 0 deletions models/hh_psc_alpha_gap.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -377,11 +377,17 @@ nest::hh_psc_alpha_gap::~hh_psc_alpha_gap()
{
// GSL structs may not have been allocated, so we need to protect destruction
if ( B_.s_ )
{
gsl_odeiv_step_free( B_.s_ );
}
if ( B_.c_ )
{
gsl_odeiv_control_free( B_.c_ );
}
if ( B_.e_ )
{
gsl_odeiv_evolve_free( B_.e_ );
}
}

/* ----------------------------------------------------------------
Expand Down Expand Up @@ -429,22 +435,28 @@ nest::hh_psc_alpha_gap::init_buffers_()
B_.IntegrationStep_ = B_.step_;

if ( B_.s_ == 0 )
{
B_.s_ =
gsl_odeiv_step_alloc( gsl_odeiv_step_rkf45, State_::STATE_VEC_SIZE );
}
else
{
gsl_odeiv_step_reset( B_.s_ );
}

if ( B_.c_ == 0 )
{
B_.c_ = gsl_odeiv_control_y_new( 1e-6, 0.0 );
}
else
{
gsl_odeiv_control_init( B_.c_, 1e-6, 0.0, 1.0, 0.0 );
}

if ( B_.e_ == 0 )
{
B_.e_ = gsl_odeiv_evolve_alloc( State_::STATE_VEC_SIZE );
}
else
{
gsl_odeiv_evolve_reset( B_.e_ );
Expand Down Expand Up @@ -560,7 +572,9 @@ nest::hh_psc_alpha_gap::update_( Time const& origin,
// maximum...
// refractory?
if ( S_.r_ > 0 )
{
--S_.r_;
}
else
// ( threshold && maximum )
if ( S_.y_[ State_::V_M ] >= 0 && U_old > S_.y_[ State_::V_M ] )
Expand Down Expand Up @@ -659,9 +673,11 @@ nest::hh_psc_alpha_gap::handle( SpikeEvent& e )
assert( e.get_delay() > 0 );

if ( e.get_weight() > 0.0 )
{
B_.spike_exc_.add_value( e.get_rel_delivery_steps(
kernel().simulation_manager.get_slice_origin() ),
e.get_weight() * e.get_multiplicity() );
}
else
{
B_.spike_inh_.add_value( e.get_rel_delivery_steps(
Expand Down
6 changes: 6 additions & 0 deletions models/ht_connection.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -237,13 +237,19 @@ HTConnection< targetidentifierT >::set_status( const DictionaryDatum& d,
updateValue< double >( d, names::P, p_ );

if ( tau_P_ <= 0.0 )
{
throw BadProperty( "tau_P > 0 required." );
}

if ( delta_P_ < 0.0 || delta_P_ > 1.0 )
{
throw BadProperty( "0 <= delta_P <= 1 required." );
}

if ( p_ < 0.0 || p_ > 1.0 )
{
throw BadProperty( "0 <= P <= 1 required." );
}
}

} // namespace
Expand Down
2 changes: 2 additions & 0 deletions models/ht_neuron.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -892,7 +892,9 @@ ht_neuron::update( Time const& origin, const long from, const long to )
}

if ( S_.ref_steps_ > 0 )
{
--S_.ref_steps_;
}

/* Add arriving spikes.
*
Expand Down
2 changes: 1 addition & 1 deletion models/ht_neuron.h
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -478,7 +478,7 @@ ht_neuron::handles_test_event( SpikeEvent&, rport receptor_type )
{
assert( B_.spike_inputs_.size() == 4 );

if ( !( INF_SPIKE_RECEPTOR < receptor_type
if ( not( INF_SPIKE_RECEPTOR < receptor_type
&& receptor_type < SUP_SPIKE_RECEPTOR ) )
{
throw UnknownReceptorType( receptor_type, get_name() );
Expand Down
4 changes: 4 additions & 0 deletions models/iaf_chs_2007.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -129,7 +129,9 @@ nest::iaf_chs_2007::Parameters_::set( const DictionaryDatum& d, State_& s )
}

if ( U_reset_ < 0 ) // sign switched above
{
throw BadProperty( "Reset potential cannot be negative." );
}
if ( tau_epsp_ <= 0 || tau_reset_ <= 0 )
{
throw BadProperty( "All time constants must be strictly positive." );
Expand Down Expand Up @@ -286,9 +288,11 @@ nest::iaf_chs_2007::handle( SpikeEvent& e )
assert( e.get_delay() > 0 );

if ( e.get_weight() >= 0.0 )
{
B_.spikes_ex_.add_value( e.get_rel_delivery_steps(
kernel().simulation_manager.get_slice_origin() ),
e.get_weight() * e.get_multiplicity() );
}
}

void
Expand Down
16 changes: 16 additions & 0 deletions models/iaf_chxk_2008.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -172,7 +172,9 @@ nest::iaf_chxk_2008::State_& nest::iaf_chxk_2008::State_::operator=(
const State_& s )
{
if ( this == &s ) // avoid assignment to self
{
return *this;
}
for ( size_t i = 0; i < STATE_VEC_SIZE; ++i )
{
y[ i ] = s.y[ i ];
Expand Down Expand Up @@ -287,11 +289,17 @@ nest::iaf_chxk_2008::~iaf_chxk_2008()
{
// GSL structs may not have been allocated, so we need to protect destruction
if ( B_.s_ )
{
gsl_odeiv_step_free( B_.s_ );
}
if ( B_.c_ )
{
gsl_odeiv_control_free( B_.c_ );
}
if ( B_.e_ )
{
gsl_odeiv_evolve_free( B_.e_ );
}
}

/* ----------------------------------------------------------------
Expand Down Expand Up @@ -320,22 +328,28 @@ nest::iaf_chxk_2008::init_buffers_()
B_.IntegrationStep_ = B_.step_;

if ( B_.s_ == 0 )
{
B_.s_ =
gsl_odeiv_step_alloc( gsl_odeiv_step_rkf45, State_::STATE_VEC_SIZE );
}
else
{
gsl_odeiv_step_reset( B_.s_ );
}

if ( B_.c_ == 0 )
{
B_.c_ = gsl_odeiv_control_y_new( 1e-3, 0.0 );
}
else
{
gsl_odeiv_control_init( B_.c_, 1e-3, 0.0, 1.0, 0.0 );
}

if ( B_.e_ == 0 )
{
B_.e_ = gsl_odeiv_evolve_alloc( State_::STATE_VEC_SIZE );
}
else
{
gsl_odeiv_evolve_reset( B_.e_ );
Expand Down Expand Up @@ -462,9 +476,11 @@ nest::iaf_chxk_2008::handle( SpikeEvent& e )
assert( e.get_delay() > 0 );

if ( e.get_weight() > 0.0 )
{
B_.spike_exc_.add_value( e.get_rel_delivery_steps(
kernel().simulation_manager.get_slice_origin() ),
e.get_weight() * e.get_multiplicity() );
}
else
{
B_.spike_inh_.add_value( e.get_rel_delivery_steps(
Expand Down
16 changes: 16 additions & 0 deletions models/iaf_cond_alpha.cpp
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -158,7 +158,9 @@ nest::iaf_cond_alpha::State_& nest::iaf_cond_alpha::State_::operator=(
const State_& s )
{
if ( this == &s ) // avoid assignment to self
{
return *this;
}
for ( size_t i = 0; i < STATE_VEC_SIZE; ++i )
{
y[ i ] = s.y[ i ];
Expand Down Expand Up @@ -284,11 +286,17 @@ nest::iaf_cond_alpha::~iaf_cond_alpha()
{
// GSL structs may not have been allocated, so we need to protect destruction
if ( B_.s_ )
{
gsl_odeiv_step_free( B_.s_ );
}
if ( B_.c_ )
{
gsl_odeiv_control_free( B_.c_ );
}
if ( B_.e_ )
{
gsl_odeiv_evolve_free( B_.e_ );
}
}

/* ----------------------------------------------------------------
Expand Down Expand Up @@ -317,22 +325,28 @@ nest::iaf_cond_alpha::init_buffers_()
B_.IntegrationStep_ = B_.step_;

if ( B_.s_ == 0 )
{
B_.s_ =
gsl_odeiv_step_alloc( gsl_odeiv_step_rkf45, State_::STATE_VEC_SIZE );
}
else
{
gsl_odeiv_step_reset( B_.s_ );
}

if ( B_.c_ == 0 )
{
B_.c_ = gsl_odeiv_control_y_new( 1e-3, 0.0 );
}
else
{
gsl_odeiv_control_init( B_.c_, 1e-3, 0.0, 1.0, 0.0 );
}

if ( B_.e_ == 0 )
{
B_.e_ = gsl_odeiv_evolve_alloc( State_::STATE_VEC_SIZE );
}
else
{
gsl_odeiv_evolve_reset( B_.e_ );
Expand Down Expand Up @@ -445,9 +459,11 @@ nest::iaf_cond_alpha::handle( SpikeEvent& e )
assert( e.get_delay() > 0 );

if ( e.get_weight() > 0.0 )
{
B_.spike_exc_.add_value( e.get_rel_delivery_steps(
kernel().simulation_manager.get_slice_origin() ),
e.get_weight() * e.get_multiplicity() );
}
else
{
B_.spike_inh_.add_value( e.get_rel_delivery_steps(
Expand Down
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