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Merge pull request #15 from pabloprf/development_mitim
Latest developments, breaks back-compatibility, changes flag names, significant restructuring of code, getting ready for MITIM 2.0.0
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‎config/config_user_example.json

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@@ -1,18 +1,19 @@
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{
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"preferences": {
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"verbose_level": "1",
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"dpi_notebook": "100",
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"trxpl": "mfews",
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"profiles_gen": "engaging",
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"tgyro": "engaging",
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"tglf": "engaging",
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"cgyro": "engaging",
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"astra": "engaging",
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"eq": "mfews",
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"scruncher": "mfews",
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"ntcc": "mfews",
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"get_fbm": "mfews",
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"transp": "globus",
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"idl": "mfews",
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"verbose_level": "1",
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"dpi_notebook": "100"
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"idl": "mfews"
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},
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"local": {
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"machine": "local",

‎config/machines_sources/aliases.bashrc

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# mitim_tools interfaces: read, run, plot
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7-
alias mitim_plot_gacode="ipython3 -i -- $MITIM_PATH/src/mitim_tools/gacode_tools/exe/read_gacode.py $1"
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alias mitim_plot_tgyro="ipython3 -i -- $MITIM_PATH/src/mitim_tools/gacode_tools/exe/read_tgyro.py $1"
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alias mitim_plot_tglf="ipython3 -i -- $MITIM_PATH/src/mitim_tools/gacode_tools/exe/read_tglf.py $1" # [--suffix _0.55] [--gacode input.gacode]
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alias mitim_plot_cgyro="ipython3 -i -- $MITIM_PATH/src/mitim_tools/gacode_tools/exe/read_cgyro.py $1"
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alias mitim_plot_eq="ipython3 -i -- $MITIM_PATH/src/mitim_tools/gs_tools/exe/read_eq.py $1"
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alias mitim_plot_transp="ipython3 -i -- $MITIM_PATH/src/mitim_tools/transp_tools/exe/read_transp.py $1"
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alias mitim_plot_gacode="ipython3 -i -- $MITIM_PATH/src/mitim_tools/gacode_tools/scripts/read_gacode.py $1"
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alias mitim_plot_tgyro="ipython3 -i -- $MITIM_PATH/src/mitim_tools/gacode_tools/scripts/read_tgyro.py $1"
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alias mitim_plot_tglf="ipython3 -i -- $MITIM_PATH/src/mitim_tools/gacode_tools/scripts/read_tglf.py $1" # [--suffix _0.55] [--gacode input.gacode]
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alias mitim_plot_cgyro="ipython3 -i -- $MITIM_PATH/src/mitim_tools/gacode_tools/scripts/read_cgyro.py $1"
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alias mitim_plot_eq="ipython3 -i -- $MITIM_PATH/src/mitim_tools/gs_tools/scripts/read_eq.py $1"
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alias mitim_plot_transp="ipython3 -i -- $MITIM_PATH/src/mitim_tools/transp_tools/scripts/read_transp.py $1"
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alias mitim_run_tglf="ipython3 -i -- $MITIM_PATH/src/mitim_tools/gacode_tools/exe/run_tglf.py $1 $2" # (folder input.tglf) [--gacode input.gacode] [--scan RLTS_2] [--drives True]
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alias mitim_run_tglf="ipython3 -i -- $MITIM_PATH/src/mitim_tools/gacode_tools/scripts/run_tglf.py $1 $2" # (folder input.tglf) [--gacode input.gacode] [--scan RLTS_2] [--drives True]
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# Optimizations
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alias mitim_plot_opt="ipython3 -i -- $MITIM_PATH/src/mitim_tools/opt_tools/exe/read.py --type 4 --resolution 20 $1"
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alias mitim_plot_portals="ipython3 -i -- $MITIM_PATH/src/mitim_modules/portals/exe/readMetrics.py $1"
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alias mitim_slurm="python3 $MITIM_PATH/src/mitim_tools/opt_tools/exe/slurm.py $1"
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alias mitim_plot_opt="ipython3 -i -- $MITIM_PATH/src/mitim_tools/opt_tools/scripts/read.py --type 4 --resolution 20 $1"
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alias mitim_plot_portals="ipython3 -i -- $MITIM_PATH/src/mitim_modules/portals/scripts/read_portals.py $1"
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alias mitim_slurm="python3 $MITIM_PATH/src/mitim_tools/opt_tools/scripts/slurm.py $1"
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# TRANSP
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alias mitim_trcheck="python3 $MITIM_PATH/src/mitim_tools/transp_tools/exe/run_check.py $1" # mitim_trcheck pablorf
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alias mitim_trcheck_p="python3 $MITIM_PATH/src/mitim_tools/transp_tools/exe/run_check_periodic.py $1" # mitim_trcheck_p pablorf
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alias mitim_trclean="python3 $MITIM_PATH/src/mitim_tools/transp_tools/exe/run_clean.py $1" # mitim_trclean 88664P CMOD --numbers 1,2,3
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alias mitim_trlook="ipython3 -i -- $MITIM_PATH/src/mitim_tools/transp_tools/exe/run_look.py $1" # mitim_trlook 152895P01 CMOD --nofull --plot --remove
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alias mitim_trcheck="python3 $MITIM_PATH/src/mitim_tools/transp_tools/scripts/run_check.py $1" # mitim_trcheck pablorf
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alias mitim_trcheck_p="python3 $MITIM_PATH/src/mitim_tools/transp_tools/scripts/run_check_periodic.py $1" # mitim_trcheck_p pablorf
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alias mitim_trclean="python3 $MITIM_PATH/src/mitim_tools/transp_tools/scripts/run_clean.py $1" # mitim_trclean 88664P CMOD --numbers 1,2,3
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alias mitim_trlook="ipython3 -i -- $MITIM_PATH/src/mitim_tools/transp_tools/scripts/run_look.py $1" # mitim_trlook 152895P01 CMOD --nofull --plot --remove
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# To run TRANSP (in folder with required files): transp 88664 P01 CMOD --version tshare --trmpi 32 --toricmpi 32 --ptrmpi 32
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alias transp="python3 $MITIM_PATH/src/mitim_tools/transp_tools/exe/run_transp.py"
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alias transp="python3 $MITIM_PATH/src/mitim_tools/transp_tools/scripts/run_transp.py"
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# IM Aliases
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alias runim="python3 $MITIM_PATH/src/mitim_tools/im_tools/exe/run_im.py ./" # To run complete IM evaluation: runim 7 [DebugOption: --debug 0]
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alias runmitim="python3 $MITIM_PATH/mitim_opt/scenarios_tools/routines/runMITIM_BO.py" # To peform scenario optimization
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alias runim="python3 $MITIM_PATH/src/mitim_tools/im_tools/scripts/run_im.py ./" # To run complete IM evaluation: runim 7 [DebugOption: --debug 0]
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alias runmitim="python3 $MITIM_PATH/mitim_opt/scenarios_tools/scripts/runMITIM_BO.py" # To peform scenario optimization
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# Others
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alias compare_nml="python3 $MITIM_PATH/src/mitim_tools/transp_tools/routines/compareNML.py $1"
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alias compare_nml="python3 $MITIM_PATH/src/mitim_tools/misc_tools/scripts/compare_namelist.py $1"
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alias eff_job="python3 $MITIM_PATH/src/mitim_tools/misc_tools/PARALLELtools.py $1" # Give mitim.out or slurm_output.dat

‎config/machines_sources/eofe.bashrc

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# GPU
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alias nvi='nvidia-smi pmon -i 0'
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alias slgpu='python3 $MITIM_PATH/mitim_opt/opt_tools/exe/slurm.py $1 --partition sched_mit_psfc_gpu_r8 $2'
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alias slgpu='python3 $MITIM_PATH/mitim_opt/opt_tools/scripts/slurm.py $1 --partition sched_mit_psfc_gpu_r8 $2'
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alias sagpu='salloc --partition sched_mit_psfc_gpu_r8 --nodes=1 --exclusive --time=8:00:00'
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# --------------------------------------------------------------------------------
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! [ -z "$PS1" ] && echo " * ASTRA modules loaded"
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fi
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# --------------------------------------------------------------------------------
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# TRANSP
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# --------------------------------------------------------------------------------
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module load singularity
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fi
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# --------------------------------------------------------------------------------

‎config/machines_sources/iris.bashrc

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export GACODE_PLATFORM=IRIS
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export GACODE_ROOT=/home/$USER/gacode
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. ${GACODE_ROOT}/shared/bin/gacode_setup
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module load ntcc
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module load ntcc-dev
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#. ${GACODE_ROOT}/platform/env/env.${GACODE_PLATFORM} # IMPORTANT to not do this, otherwise it will then point to atom
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‎config/machines_sources/slurm_aliases.bashrc

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# Submission
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# --------------------------------------------------------------------------------
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alias sl='python3 $MITIM_PATH/mitim_opt/opt_tools/exe/slurm.py $1 --partition $MITIM_PARTITION $2'
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alias sl='python3 $MITIM_PATH/mitim_opt/opt_tools/scripts/slurm.py $1 --partition $MITIM_PARTITION $2'
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# --------------------------------------------------------------------------------
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# Information

‎docs/capabilities/optimization.rst

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.. code-block:: python
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folder = IOtools.expandPath('$MITIM_PATH/tests/scratch/mitim_tut/')
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namelist = IOtools.expandPath('$MITIM_PATH/templates/main.namelist')
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namelist = IOtools.expandPath('$MITIM_PATH/templates/main.namelist.json')
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Then create your custom optimization object as a child of the parent ``STRATEGYtools.FUNmain`` class.
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Then create your custom optimization object as a child of the parent ``STRATEGYtools.opt_evaluator`` class.
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You only need to modify what operations need to occur inside the ``run()`` (where operations/simulations happen) and ``scalarized_objective()`` (to define what is the target to maximize) methods.
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In this example, we are using ``x**2`` as our function with a 2% evaluation error, to find ``x`` such that ``x**2=15``:
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.. code-block:: python
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class opt_class(STRATEGYtools.FUNmain):
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class opt_class(STRATEGYtools.opt_evaluator):
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def __init__(self, folder, namelist):
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# Store folder, namelist. Read namelist
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super().__init__(folder, namelist=namelist)
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# ----------------------------------------
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# Problem description (rest of problem parameters are taken from namelist)
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self.Optim["dvs"] = ["x"]
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self.Optim["dvs_min"] = [0.0]
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self.Optim["dvs_max"] = [20.0]
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self.optimization_options["dvs"] = ["x"]
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self.optimization_options["dvs_min"] = [0.0]
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self.optimization_options["dvs_max"] = [20.0]
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self.Optim["ofs"] = ["z", "zval"]
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self.optimization_options["ofs"] = ["z", "zval"]
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self.name_objectives = ["zval_match"]
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def run(self, paramsfile, resultsfile):
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self.write(dictOFs, resultsfile)
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def scalarized_objective(self, Y):
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ofs_ordered_names = np.array(self.Optim["ofs"])
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ofs_ordered_names = np.array(self.optimization_options["ofs"])
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of = Y[..., ofs_ordered_names == "z"]
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cal = Y[..., ofs_ordered_names == "zval"]
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Understanding the MITIM namelist
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~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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Checkout file ``$MITIM_PATH/templates/main.namelist``, which has comprehensive comments.
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Checkout file ``$MITIM_PATH/templates/main.namelist.json``, which has comprehensive comments.
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*Under development*
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‎docs/capabilities/tgyro_capabilities.rst

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'tgyro_method': 6,
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'relax_param': 0.1 }
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physics_options = { 'TargetType':2 } # 2: Only evolve exchange, 3: Reactor
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physics_options = { 'TypeTarget':2 } # 2: Only evolve exchange, 3: Reactor
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PredictionSet = [1,1,0] # Profiles to predict: [Te, Ti, ne]
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iterations = 5 # Number of TGYRO iterations
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TGLFsettings = 5 # TGLF pre-sets
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PredictionSet = PredictionSet,
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TGLFsettings = TGLFsettings,
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TGYRO_solver_options = solver,
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TGYRO_physics_options = physics_options)
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Physics_options = physics_options)
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Read:
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‎docs/capabilities/vitals_capabilities.rst

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# Option 1: Provide the complete namelist yourself
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vitals_fun = VITALSmain.evaluateVITALS( folder, namelist = path_to_namelist )
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vitals_fun = VITALSmain.vitals( folder, namelist = path_to_namelist )
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# Option 2: Use a curated VITALS namelist and only modify some requested values
117-
vitals_fun = VITALSmain.evaluateVITALS( folder )
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vitals_fun.Optim['BOiterations'] = 5
117+
vitals_fun = VITALSmain.vitals( folder )
118+
vitals_fun.optimization_options['BO_iterations'] = 5
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Once the VITALS object has been created, parameters such as the TGLF control inputs can be chosen:
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