struphy 2.2.0__tar.gz → 2.3.1__tar.gz

{struphy-2.2.0 → struphy-2.3.1}/LICENSE

@@ -1,4 +1,4 @@
-Copyright (c) 2019-2023, Struphy developers, Max Planck Institute for Plasma Physics
+Copyright (c) 2019-2024, Struphy developers, Max Planck Institute for Plasma Physics
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of this software and 
 associated documentation files (the "Software"), to deal in the Software without restriction, 

{struphy-2.2.0/src/struphy.egg-info → struphy-2.3.1}/PKG-INFO

@@ -1,10 +1,10 @@
 Metadata-Version: 2.1
 Name: struphy
-Version: 2.2.0
+Version: 2.3.1
 Summary: Multi-model plasma physics package
 Author: Max Planck Institute for Plasma Physics
 Author-email: stefan.possanner@ipp.mpg.de, eric.sonnendruecker@ipp.mpg.de
-License: Copyright (c) 2019-2023, Struphy developers, Max Planck Institute for Plasma Physics
+License: Copyright (c) 2019-2024, Struphy developers, Max Planck Institute for Plasma Physics
         
         Permission is hereby granted, free of charge, to any person obtaining a copy of this software and 
         associated documentation files (the "Software"), to deal in the Software without restriction, 
@@ -27,34 +27,37 @@ Project-URL: changelog, https://gitlab.mpcdf.mpg.de/struphy/struphy/-/blob/devel
 Project-URL: Bug Tracker, https://gitlab.mpcdf.mpg.de/struphy/struphy/-/issues
 Keywords: plasma physics, fusion, numerical modeling, partial differential equations, energetic particles
 Classifier: Programming Language :: Python :: 3
-Requires-Python: <3.12,>=3.7
+Requires-Python: <3.12,>=3.10
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: PyYAML==6.0.1
-Requires-Dist: argcomplete==3.2.1
-Requires-Dist: docutils==0.20.1
-Requires-Dist: gvec-to-python==1.2.0
-Requires-Dist: h5py==3.10.0
-Requires-Dist: ipyparallel==8.6.1
+Requires-Dist: argcomplete==3.4.0
+Requires-Dist: desc-opt==0.11.1
+Requires-Dist: docutils==0.21.2
+Requires-Dist: gvec-to-python==1.2.2
+Requires-Dist: h5py==3.11.0
+Requires-Dist: ipyparallel==8.8.0
+Requires-Dist: lxml_html_clean==0.1.1
 Requires-Dist: m2r2==0.3.3.post2
-Requires-Dist: matplotlib==3.8.2
+Requires-Dist: matplotlib==3.9.0
 Requires-Dist: mistune==0.8.4
-Requires-Dist: mpi4py==3.1.5
-Requires-Dist: myst-parser==2.0.0
-Requires-Dist: nbsphinx==0.9.3
-Requires-Dist: notebook==7.0.6
+Requires-Dist: mpi4py==3.1.6
+Requires-Dist: myst-parser==3.0.1
+Requires-Dist: nbsphinx==0.9.4
+Requires-Dist: netCDF4==1.6.5
+Requires-Dist: notebook==7.2.1
 Requires-Dist: numpy==1.24.4
-Requires-Dist: pyccel==1.11.1
-Requires-Dist: pydata-sphinx-theme==0.15.1
-Requires-Dist: pytest==7.4.4
+Requires-Dist: pyccel==1.12.0
+Requires-Dist: pydata-sphinx-theme==0.15.3
+Requires-Dist: pytest==8.2.2
 Requires-Dist: pytest-monitor==1.6.6
 Requires-Dist: pytest-mpi==0.6
-Requires-Dist: scipy==1.11.4
-Requires-Dist: Sphinx==7.2.6
+Requires-Dist: scipy==1.13.1
+Requires-Dist: Sphinx==7.3.7
 Requires-Dist: sphinxcontrib-napoleon==0.7
-Requires-Dist: tqdm==4.66.1
+Requires-Dist: tqdm==4.66.4
 Requires-Dist: vtk==9.3.0
-Requires-Dist: wheel==0.42.0
+Requires-Dist: wheel==0.43.0
 
 # Struphy - Structure-preserving hybrid codes
 

{struphy-2.2.0 → struphy-2.3.1}/pyproject.toml

@@ -4,9 +4,9 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "struphy"
-version = "2.2.0"
+version = "2.3.1"
 readme = "README.md"
-requires-python = ">=3.7, <3.12"
+requires-python = ">=3.10, <3.12"
 license = {file = "LICENSE"}
 authors = [
   { name = "Max Planck Institute for Plasma Physics"},
@@ -20,30 +20,33 @@ classifiers = [
     ]
 dependencies = [
     'PyYAML==6.0.1',
-    'argcomplete==3.2.1',
-    'docutils==0.20.1',
-    'gvec-to-python==1.2.0',
-    'h5py==3.10.0',
-    'ipyparallel==8.6.1',
+    'argcomplete==3.4.0',
+    'desc-opt==0.11.1',
+    'docutils==0.21.2',
+    'gvec-to-python==1.2.2',
+    'h5py==3.11.0',
+    'ipyparallel==8.8.0',
+    'lxml_html_clean==0.1.1',
     'm2r2==0.3.3.post2',
-    'matplotlib==3.8.2',
+    'matplotlib==3.9.0',
     'mistune==0.8.4',
-    'mpi4py==3.1.5',
-    'myst-parser==2.0.0',
-    'nbsphinx==0.9.3',
-    'notebook==7.0.6',
+    'mpi4py==3.1.6',
+    'myst-parser==3.0.1',
+    'nbsphinx==0.9.4',
+    'netCDF4==1.6.5',
+    'notebook==7.2.1',
     'numpy==1.24.4',
-    'pyccel==1.11.1',
-    'pydata-sphinx-theme==0.15.1',
-    'pytest==7.4.4',
+    'pyccel==1.12.0',
+    'pydata-sphinx-theme==0.15.3',
+    'pytest==8.2.2',
     'pytest-monitor==1.6.6',
     'pytest-mpi==0.6',
-    'scipy==1.11.4',
-    'Sphinx==7.2.6',
+    'scipy==1.13.1',
+    'Sphinx==7.3.7',
     'sphinxcontrib-napoleon==0.7',
-    'tqdm==4.66.1',
+    'tqdm==4.66.4',
     'vtk==9.3.0',
-    'wheel==0.42.0',
+    'wheel==0.43.0',
 ]
 
 [project.urls]
@@ -79,5 +82,5 @@ struphy = "struphy.console.main:struphy"
                     ]
                     
 struphy = ['compile_struphy.mk',
-           'psydac-0.1.9-py3-none-any.whl',
+           'psydac-0.1.13-py3-none-any.whl',
            ]

{struphy-2.2.0 → struphy-2.3.1}/src/struphy/bsplines/bsplines.py

@@ -373,7 +373,7 @@ def collocation_matrix(knots, degree, xgrid, periodic, normalize=False):
 # ==============================================================================
 def histopolation_matrix(knots, degree, xgrid, periodic):
     """
-    Computes the histopolation matrix $H_ij = int_x_i^x_{i+1} D_j(x) dx$ of the M_splines.
+    Computes the histopolation matrix $H_ij = int_{x_i}^x_{i+1} D_j(x) dx$ of the M_splines.
 
     Parameters
     ----------

{struphy-2.2.0 → struphy-2.3.1}/src/struphy/console/compile.py

@@ -208,7 +208,7 @@ def struphy_compile(language, compiler, omp_pic, omp_feec, delete, status, verbo
             flags += ' --verbose'
 
         # install psydac from wheel if not there
-        current_ver = '0.1.9'
+        current_ver = '0.1.13'
         psydac_file = 'psydac-' + current_ver + '-py3-none-any.whl'
 
         try:

{struphy-2.2.0 → struphy-2.3.1}/src/struphy/console/main.py

@@ -40,7 +40,7 @@ def struphy():
 
     # version message
     version_message = f'Struphy {__version__}\n'
-    version_message += 'Copyright 2019-2023 (c) Struphy dev team | Max Planck Institute for Plasma Physics\n'
+    version_message += 'Copyright 2019-2024 (c) Struphy dev team | Max Planck Institute for Plasma Physics\n'
     version_message += 'MIT license\n'
 
     # state dictionary
@@ -88,7 +88,8 @@ def struphy():
             out_folders += [name]
 
     # check batch scripts in current batch path:
-    batch_files = recursive_get_files(b_path, contains=('.sh'), out=[], prefix=[])
+    batch_files = recursive_get_files(
+        b_path, contains=('.sh'), out=[], prefix=[])
 
     # collect available model, contains=('.yml', '.yaml')s
     list_fluid = []
@@ -225,11 +226,11 @@ def struphy():
     parser_compile.add_argument('-v', '--verbose',
                                 help='call pyccel with --verbose compiler option',
                                 action='store_true')
-    
+
     parser_compile.add_argument('--dependencies',
                                 help='print Struphy kernels to be compiled (.py) and their dependencies (.so) on screen',
                                 action='store_true')
-    
+
     parser_compile.add_argument('-y', '--yes',
                                 help='say yes to prompt when changing the language',
                                 action='store_true')
@@ -306,7 +307,7 @@ def struphy():
     parser_run.add_argument('--debug',
                             help='launch a Cobra debug run, see https://docs.mpcdf.mpg.de/doc/computing/cobra-user-guide.html#interactive-debug-runs',
                             action='store_true',)
-    
+
     parser_run.add_argument('--cprofile',
                             help='run with Cprofile',
                             action='store_true',)
@@ -436,20 +437,19 @@ def struphy():
                                         formatter_class=lambda prog: argparse.RawTextHelpFormatter(
                                             prog, max_help_position=30),
                                         help='run Struphy tests',
-                                        description='Run available unit tests or test Struphy models, propagators or tutorials.')
+                                        description='Run available unit tests or test Struphy models or tutorials.')
 
     parser_test.add_argument('group',
                              type=str,
                              choices=list_models +
-                             ['models'] + ['unit'] + ['propagators'] +
+                             ['models'] + ['unit'] +
                              ['tutorials'] + ['timings'],
                              metavar='GROUP',
                              help='can be either:\na) a model name (tests on 1 MPI process in "Cuboid", "HollowTorus" and "Tokamak" geometries) \
                                 \nb) "models" for quick testing of all models \
                                 \nc) "unit" for performing unit tests \
-                                \nd) "propagators" for testing all propagators \
-                                \ne) "tutorials" for notebook tutorials, see `https://struphy.pages.mpcdf.de/struphy/sections/tutorials.html`_ \
-                                \nf) "timings" for creating .html and .json files of test metrics (include --verbose to print metrics to screen)',)
+                                \nd) "tutorials" for notebook tutorials, see `https://struphy.pages.mpcdf.de/struphy/sections/tutorials.html`_ \
+                                \ne) "timings" for creating .html and .json files of test metrics (include --verbose to print metrics to screen)',)
 
     parser_test.add_argument('--mpi',
                              type=int,
@@ -464,7 +464,7 @@ def struphy():
     parser_test.add_argument('-v', '--verbose',
                              help='print timings to screen',
                              action='store_true')
-    
+
     parser_test.add_argument('--monitor',
                              help='use pytest-monitor in tests',
                              action='store_true')
@@ -473,7 +473,7 @@ def struphy():
                              type=int,
                              help='specific tutorial simulation to run (int, optional)',
                              default=None)
-    
+
     parser_test.add_argument('-T', '--Tend',
                              type=float,
                              help='if GROUP=a), simulation end time in units of the model (default=0.015 with dt=0.005), data is only saved at TEND if set',
@@ -695,11 +695,11 @@ def recursive_get_files(path, contains=('.yml', '.yaml'), out=[], prefix=[]):
                 prefix = [name]
             else:
                 prefix += [os.path.join(prefix[-1], name)]
-            recursive_get_files(os.path.join(path, name), 
-                                contains=contains, 
-                                out=out, 
+            recursive_get_files(os.path.join(path, name),
+                                contains=contains,
+                                out=out,
                                 prefix=prefix)
     if n_folders == 0 and len(prefix) != 0:
         prefix.pop()
 
-    return out
+    return out

{struphy-2.2.0 → struphy-2.3.1}/src/struphy/console/run.py

@@ -149,11 +149,12 @@ def struphy_run(model,
             command += ['-r']
             
         if cprofile:
-            print('Cprofile turned on.')
+            print('\nCprofile turned on.')
         else:
-            print('Cprofile turned off.')
+            print('\nCprofile turned off.')
 
         # run command as subprocess
+        print(f"\nRunning the following command:\n{' '.join(command)}")
         subprocess.run(command, check=True, cwd=libpath)
 
     # run in batch mode

{struphy-2.2.0 → struphy-2.3.1}/src/struphy/console/test.py

@@ -31,8 +31,6 @@ def struphy_test(group, mpi=2, fast=False, verbose=False, monitor=False, n=None,
         If group is a model name, simulation end time in units of the model (default=0.015 with dt=0.005). Data is only saved at Tend if set.
     """
 
-    assert mpi >= 2, 'Tests require at least 2 MPI processes.'
-
     libpath = struphy.__path__[0]
 
     pymon_abs = os.path.join(libpath, '_pymon/')
@@ -53,7 +51,7 @@ def struphy_test(group, mpi=2, fast=False, verbose=False, monitor=False, n=None,
                         'pytest',
                         '--no-monitor'*(not monitor),
                         '-k',
-                        'not _models and not _propagators and not _tutorial and not pproc',
+                        'not _models and not _tutorial and not pproc',
                         '--with-mpi',
                         '--restrict-scope-to',
                         'module',
@@ -127,31 +125,6 @@ def struphy_test(group, mpi=2, fast=False, verbose=False, monitor=False, n=None,
                         '--no-monitor',],
                        check=True, cwd=libpath)
 
-    elif 'propagators' in group:
-        pymon_file = os.path.join(pymon_abs, '.pymon_propagators')
-        if os.path.isfile(pymon_file):
-            os.remove(pymon_file)
-
-        subprocess.run(['mpirun',
-                        '-n',
-                        str(mpi),
-                        'pytest',
-                        '--no-monitor'*(not monitor),
-                        '-k',
-                        '_propagators',
-                        '--with-mpi',
-                        '--restrict-scope-to',
-                        'module',
-                        '--db',
-                        '_pymon/.pymon_propagators',
-                        '--description',
-                        f'language={state["last_used_language"]}, compiler={state["last_used_compiler"]}, omp_pic={state["last_used_omp_pic"]}, omp_feec={state["last_used_omp_feec"]}',
-                        '--tag',
-                        f'struphy={importlib.metadata.version("struphy")}',
-                        '--tag',
-                        f'pyccel={pyccel.__version__}',],
-                       check=True, cwd=libpath)
-
     elif 'tutorials' in group:
         pymon_file = os.path.join(pymon_abs, '.pymon_tutorials')
         if os.path.isfile(pymon_file):
@@ -204,7 +177,7 @@ def struphy_test(group, mpi=2, fast=False, verbose=False, monitor=False, n=None,
 
     elif 'timings' in group:
 
-        for gr in ['unit', 'models', 'propagators', 'tutorials']:
+        for gr in ['unit', 'models', 'tutorials']:
             _file = os.path.join(pymon_abs, '.pymon_' + gr)
             if os.path.isfile(_file):
                 pymon_html_json(gr, verbose=verbose)
@@ -238,7 +211,7 @@ def pymon_html_json(group, verbose=False):
     Parameters
     ----------
     group : str
-        One of "unit", "models", "propagators", "tutorials" or "pproc".
+        One of "unit", "models", "tutorials" or "pproc".
     '''
 
     libpath = struphy.__path__[0]

struphy-2.3.1/src/struphy/diagnostics/console_diagn.py

@@ -0,0 +1,217 @@
+""" An executable for quick access to the diagnostic tools in diagn_tools.py """
+
+#!/usr/bin/env python3
+import numpy as np
+import argparse
+import os
+import h5py
+import yaml
+
+import struphy
+from struphy.diagnostics.diagn_tools import plot_scalars, plot_distr_fun, phase_space_video
+
+
+def main():
+    parser = argparse.ArgumentParser(
+        formatter_class=argparse.RawTextHelpFormatter)
+
+    parser.add_argument('actions', nargs='+', type=str, default=[None],
+                        help='''which actions to perform:\
+                            \n - plot_scalars : plots the scalar quantities that were saved during the simulation\
+                            \n - plot_distr   : plots the distribution function and delta-f (if available)\
+                            \n                  set points for slicing with options below (default is middle of the space)\
+                            \n - phase_space  : make a video of the distribution function (minus the background) in a 2D slice of phase space
+                        ''')
+    parser.add_argument('-f', nargs=1, type=str, default=['sim_1'],
+                        help='name of the folder for the simulation data (in io/out)')
+    parser.add_argument('-scalars', nargs='+', action='append', default=[],
+                        help='(for plot_scalars) which quantities to plot')
+    parser.add_argument('--log', action='store_true',
+                        help='(for plot_scalars) if logarithmic y-axis should be used')
+    parser.add_argument('--show', action='store_true',
+                        help='(for plot_scalars) if the plot should be shown')
+    parser.add_argument('--nosave', action='store_true',
+                        help='(for plot_scalars) if the plot should not be displayed')
+    parser.add_argument('--fit', action='store_true',
+                        help='(for plot_scalars) if a fit should be done (using maxima)')
+    parser.add_argument('--minfit', action='store_true',
+                        help='(for plot_scalars) if a fit should be done using minima')
+    parser.add_argument('-degree', nargs=1, type=int, default=[1],
+                        help='(for plot_scalars --fit) the degree of the fit curve')
+    parser.add_argument('-extrema', nargs=1, type=int, default=[4],
+                        help='(for plot_scalars --fit) how many extrema should be used for the fit')
+    parser.add_argument('-startextr', nargs=1, type=int, default=[0],
+                        help='(for plot_scalars --fit) which extremum should be used first for the fit (0 = first)')
+    parser.add_argument('-order', nargs=1, type=int, default=[4],
+                        help='(for plot_scalars --fit) how many neighbouring points should be used for determining the extrema')
+    parser.add_argument('-t', nargs=1, type=float, default=[0.],
+                        help='(for plot_distr) at which time to plot the distribution function')
+    parser.add_argument('-e1', nargs=1, type=float, default=[0.5],
+                        help='(for plot_distr) at which position in eta1 direction to plot')
+    parser.add_argument('-e2', nargs=1, type=float, default=[0.5],
+                        help='(for plot_distr) at which position in eta2 direction to plot')
+    parser.add_argument('-e3', nargs=1, type=float, default=[0.5],
+                        help='(for plot_distr) at which position in eta3 direction to plot')
+    parser.add_argument('-v1', nargs=1, type=float, default=[None],
+                        help='(for plot_distr) at which point in v1 direction to plot')
+    parser.add_argument('-v2', nargs=1, type=float, default=[None],
+                        help='(for plot_distr) at which point in v2 direction to plot')
+    parser.add_argument('-v3', nargs=1, type=float, default=[None],
+                        help='(for plot_distr) at which point in v3 direction to plot')
+
+    # Parse the arguments
+    args = parser.parse_args()
+    actions = args.actions
+    foldername = args.f[0]
+    time = args.t[0]
+    do_log = args.log
+    show = args.show
+    nosave = args.nosave
+    if len(args.scalars) != 0:
+        scalars_plot = args.scalars[0]
+    else:
+        scalars_plot = args.scalars
+
+    # Arguments for fitting
+    do_fit = args.fit
+    fit_minima = args.minfit
+    if fit_minima and do_fit:
+        do_fit = False
+    no_extrema = args.extrema[0]
+    order = args.order[0]
+    degree = args.degree[0]
+    start_extremum = args.startextr[0]
+
+    libpath = struphy.__path__[0]
+    with open(os.path.join(libpath, 'state.yml')) as f:
+        state = yaml.load(f, Loader=yaml.FullLoader)
+
+    o_path = state['o_path']
+
+    path = os.path.join(o_path, foldername)
+
+    grid_slices = {
+        'e1': args.e1[0], 'e2': args.e2[0], 'e3': args.e3[0],
+        'v1': args.v1[0], 'v2': args.v2[0], 'v3': args.v3[0]
+    }
+
+    # Get fields
+    file = h5py.File(os.path.join(path, 'data/', 'data_proc0.hdf5'), 'r')
+    saved_scalars = file['scalar']
+    saved_time = file['time']['value'][:]
+
+    # read in parameters
+    with open(path + '/parameters.yml') as file:
+        params = yaml.load(file, Loader=yaml.FullLoader)
+
+    # Get model name
+    with open(path + '/meta.txt', 'r') as file:
+        for line in file.readlines():
+            if line[0:10] == 'model_name':
+                model_name = line.split(':')[1].strip()
+
+    if 'plot_scalars' in actions:
+        plot_scalars(
+            time=saved_time, scalar_quantities=saved_scalars, scalars_plot=scalars_plot,
+            do_log=do_log, do_fit=do_fit, fit_minima=fit_minima, order=order,
+            no_extrema=no_extrema, degree=degree, show_plot=show, start_extremum=start_extremum,
+            save_plot=not nosave, savedir=path
+        )
+
+    if 'plot_distr' or 'phase_space' in actions:
+        for species in params['kinetic'].keys():
+            # Get model class
+            from struphy.models import fluid, kinetic, hybrid, toy
+            objs = [fluid, kinetic, hybrid, toy]
+            for obj in objs:
+                try:
+                    model_class = getattr(obj, model_name)
+                except AttributeError:
+                    pass
+
+            # get particles class name
+            species_dict = model_class.species()
+            particles_class_name = species_dict['kinetic'][species]
+
+            # Get default background of particles class
+            from struphy.pic import particles
+            default_bckgr_type = getattr(
+                particles, particles_class_name).default_bckgr_params()['type']
+
+            # Get default background parameters
+            from struphy.kinetic_background import maxwellians
+            default_bckgr_params = getattr(
+                maxwellians, default_bckgr_type).default_maxw_params()
+
+            marker_type = params['kinetic'][species]['markers']['type']
+            # Set velocity point of evaluation to v_shift of background params if not given by input
+            if marker_type == 'full_f':
+                for k in range(1, 4):
+
+                    if grid_slices['v' + str(k)] is None:
+                        key = 'u' + str(k)
+                        bckgr_type = params['kinetic'][species]['background']['type']
+
+                        if key not in params['kinetic'][species]['background'][bckgr_type].keys():
+                            bckgr_param = default_bckgr_params[key]
+                        else:
+                            bckgr_param = params['kinetic'][species]['background'][bckgr_type][key]
+
+                        if isinstance(bckgr_param, dict):
+                            grid_slices['v' + str(k)] = \
+                                bckgr_param['u0' + str(k)]
+                        else:
+                            grid_slices['v' + str(k)] = bckgr_param
+            elif marker_type in ['delta_f', 'control_variate']:
+                for k in range(1, 4):
+
+                    if grid_slices['v' + str(k)] is None:
+                        key = 'u' + str(k)
+                        bckgr_type = params['kinetic'][species]['background']['type']
+
+                        if key not in params['kinetic'][species]['background'][bckgr_type].keys():
+                            bckgr_param = default_bckgr_params[key]
+                        else:
+                            bckgr_param = params['kinetic'][species]['background'][bckgr_type][key]
+
+                        if isinstance(bckgr_param, dict):
+                            grid_slices['v' + str(k)] = \
+                                bckgr_param['u0' + str(k)]
+                        else:
+                            grid_slices['v' + str(k)] = bckgr_param
+            else:
+                raise NotImplementedError(
+                    f"Diagnostics for markers of type {marker_type} are not implemented!")
+
+            if 'plot_distr' in actions:
+                # Get index of where to plot in time
+                time_idx = np.argmin(np.abs(time - saved_time))
+
+                plot_distr_fun(
+                    path=os.path.join(
+                        path, 'post_processing', 'kinetic_data', species
+                    ),
+                    time_idx=time_idx,
+                    grid_slices=grid_slices,
+                    save_plot=True, savepath=path,
+                )
+
+            if 'phase_space' in actions:
+                for slice_name in os.listdir(os.path.join(
+                    path, 'post_processing', 'kinetic_data', species, 'distribution_function'
+                )):
+                    phase_space_video(
+                        t_grid=saved_time, grid_slices=grid_slices,
+                        slice_name=slice_name,
+                        marker_type=params['kinetic'][species]['markers']['type'],
+                        species=species,
+                        path=path,
+                        model_name=model_name,
+                        background_params=params['kinetic'][species]['background']
+                    )
+
+    file.close()
+
+
+if __name__ == '__main__':
+    main()