struphy 2.2.0__tar.gz → 2.3.0__tar.gz

{struphy-2.2.0 → struphy-2.3.0}/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-2.3.0}/PKG-INFO

@@ -1,10 +1,10 @@
 Metadata-Version: 2.1
 Name: struphy
-Version: 2.2.0
+Version: 2.3.0
 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, 
@@ -31,30 +31,31 @@ Requires-Python: <3.12,>=3.7
 Description-Content-Type: text/markdown
 License-File: LICENSE
 Requires-Dist: PyYAML==6.0.1
-Requires-Dist: argcomplete==3.2.1
+Requires-Dist: argcomplete==3.2.3
 Requires-Dist: docutils==0.20.1
-Requires-Dist: gvec-to-python==1.2.0
+Requires-Dist: gvec-to-python==1.2.1
 Requires-Dist: h5py==3.10.0
-Requires-Dist: ipyparallel==8.6.1
+Requires-Dist: ipyparallel==8.7.0
+Requires-Dist: lxml_html_clean==0.1.0
 Requires-Dist: m2r2==0.3.3.post2
-Requires-Dist: matplotlib==3.8.2
+Requires-Dist: matplotlib==3.8.3
 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: notebook==7.1.2
 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==1.11.2
+Requires-Dist: pydata-sphinx-theme==0.15.2
+Requires-Dist: pytest==8.1.1
 Requires-Dist: pytest-monitor==1.6.6
 Requires-Dist: pytest-mpi==0.6
-Requires-Dist: scipy==1.11.4
+Requires-Dist: scipy==1.12.0
 Requires-Dist: Sphinx==7.2.6
 Requires-Dist: sphinxcontrib-napoleon==0.7
-Requires-Dist: tqdm==4.66.1
+Requires-Dist: tqdm==4.66.2
 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-2.3.0}/pyproject.toml

@@ -4,7 +4,7 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "struphy"
-version = "2.2.0"
+version = "2.3.0"
 readme = "README.md"
 requires-python = ">=3.7, <3.12"
 license = {file = "LICENSE"}
@@ -20,30 +20,31 @@ classifiers = [
     ]
 dependencies = [
     'PyYAML==6.0.1',
-    'argcomplete==3.2.1',
+    'argcomplete==3.2.3',
     'docutils==0.20.1',
-    'gvec-to-python==1.2.0',
+    'gvec-to-python==1.2.1',
     'h5py==3.10.0',
-    'ipyparallel==8.6.1',
+    'ipyparallel==8.7.0',
+    'lxml_html_clean==0.1.0',
     'm2r2==0.3.3.post2',
-    'matplotlib==3.8.2',
+    'matplotlib==3.8.3',
     'mistune==0.8.4',
     'mpi4py==3.1.5',
     'myst-parser==2.0.0',
     'nbsphinx==0.9.3',
-    'notebook==7.0.6',
+    'notebook==7.1.2',
     'numpy==1.24.4',
-    'pyccel==1.11.1',
-    'pydata-sphinx-theme==0.15.1',
-    'pytest==7.4.4',
+    'pyccel==1.11.2',
+    'pydata-sphinx-theme==0.15.2',
+    'pytest==8.1.1',
     'pytest-monitor==1.6.6',
     'pytest-mpi==0.6',
-    'scipy==1.11.4',
+    'scipy==1.12.0',
     'Sphinx==7.2.6',
     'sphinxcontrib-napoleon==0.7',
-    'tqdm==4.66.1',
+    'tqdm==4.66.2',
     'vtk==9.3.0',
-    'wheel==0.42.0',
+    'wheel==0.43.0',
 ]
 
 [project.urls]
@@ -79,5 +80,5 @@ struphy = "struphy.console.main:struphy"
                     ]
                     
 struphy = ['compile_struphy.mk',
-           'psydac-0.1.9-py3-none-any.whl',
+           'psydac-0.1.12-py3-none-any.whl',
            ]

{struphy-2.2.0 → struphy-2.3.0}/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-2.3.0}/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 = '0.1.12'
         psydac_file = 'psydac-' + current_ver + '-py3-none-any.whl'
 
         try:

{struphy-2.2.0 → struphy-2.3.0}/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-2.3.0}/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-2.3.0}/src/struphy/console/test.py

@@ -53,7 +53,7 @@ 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 +127,6 @@ 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 +179,7 @@ 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 +213,7 @@ 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-2.2.0 → struphy-2.3.0}/src/struphy/diagnostics/console_diagn.py

@@ -71,6 +71,12 @@ def main():
     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(saved_time,
                      saved_scalars,
@@ -81,13 +87,38 @@ def main():
 
     if 'plot_distr' 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_bckgr_params()
+
             # Set velocity point of evaluation to v_shift of background params if not given by input
             if params['kinetic'][species]['markers']['type'] == 'full_f':
                 for k in range(1, 4):
                     if grid_slices['v' + str(k)] is None:
-                        bckgr_type = params['kinetic'][species]['init']['type']
-                        bckgr_param = params['kinetic'][species]['init'][bckgr_type]['u' + str(
-                            k)]
+                        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)]
@@ -109,10 +140,14 @@ def main():
             # 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)
+            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,
+            )
 
     file.close()
 

{struphy-2.2.0 → struphy-2.3.0}/src/struphy/diagnostics/diagn_tools.py

@@ -12,8 +12,7 @@ def power_spectrum_2d(values, name, code, grids,
                grids_mapped=None, component=0, slice_at=[None, 0, 0],
                do_plot=False, disp_name=None, disp_params={},
                save_plot=False, save_name=None, file_format='png'):
-    """
-    Perform fft in space-time, (t, x) -> (omega, k), where x can be a logical or physical coordinate.
+    """ Perform fft in space-time, (t, x) -> (omega, k), where x can be a logical or physical coordinate.
     Returns values if plot=False.
 
     Parameters
@@ -176,8 +175,7 @@ def power_spectrum_2d(values, name, code, grids,
 
 
 def plot_scalars(time, scalar_quantities, scalars_plot=[], do_log=False, save_plot=False, savedir=None, file_format='png'):
-    """
-    Plot the scalar quantities and the relative error in the total energy for a simulation.
+    """ Plot the scalar quantities and the relative error in the total energy for a simulation.
 
     Parameters
     ----------
@@ -251,8 +249,7 @@ def plot_scalars(time, scalar_quantities, scalars_plot=[], do_log=False, save_pl
 
 
 def plot_distr_fun(path, time_idx, grid_slices, save_plot=False, savepath=None, file_format='png'):
-    """
-    Plot the binned distribution function at given slices of the phase space.
+    """ Plot the binned distribution function at given slices of the phase space.
 
     Parameters
     ----------

{struphy-2.2.0 → struphy-2.3.0}/src/struphy/examples/_draw_parallel.py

@@ -40,7 +40,7 @@ def main():
 
     # create particles
     particles = Particles6D(
-        'energetic_ions', **marker_params, derham=derham)
+        'energetic_ions', **marker_params, derham=derham, bckgr_params=None)
 
     comm.Barrier()
     print('Number of particles w/wo holes on each process before sorting : ')

{struphy-2.2.0 → struphy-2.3.0}/src/struphy/feec/basis_projection_ops.py

@@ -41,7 +41,7 @@ class BasisProjectionOperators:
         if np.any([p == 1 and Nel > 1 for p, Nel in zip(derham.p, derham.Nel)]):
             if derham.comm.Get_rank() == 0:
                 print(
-                    f'\nWARNING: Class "BasisProjectionOperators" called with p={derham.p} (interpolation of piece-wise constants should be avoided).\n')
+                    f'\nWARNING: Class "BasisProjectionOperators" called with p={derham.p} (interpolation of piece-wise constants should be avoided).')
 
         self._derham = derham
         self._domain = domain
@@ -1285,35 +1285,39 @@ def get_span_and_basis(pts, space):
 
 class CoordinateProjector(LinearOperator):
     r"""
-    Class of projectors on one component of a ProductFemSpace. Represent the projection on the i-th component :
+    Class of projectors on one component of a ProductFemSpace. 
+    Represent the projection on the :math:`\mu`-th component :
 
     .. math::
-        P_i : X = V_1 \times V_2 \times ... \times V_n \longrightarrow V_i \\
-        \mathbf{x} = (x_1,...,x_n) \mapsto x_i
-
+    
+        \begin{align}
+        P_\mu : \ & V_1 \times \ldots \times V_\mu \times \ldots \times V_n \longrightarrow V_\mu \,,
+        \\[2mm]    
+        &\vec{x} = (x_1,\ldots,x_\mu,\ldots ,x_n) \mapsto x_\mu \,.
+        \end{align}
 
     Parameters
     ----------
-    i : int
-        The component on which to project
+    mu : int
+        The component on which to project.
 
     V : psydac.fem.basic.(Product)FemSpace
         Finite element spline space (domain, input space).
 
-    Vi : psydac.fem.basic.FemSpace
-        Finite element spline space (codomain, out space), must be V i-th space
+    Vmu : psydac.fem.basic.FemSpace
+        Finite element spline space (codomain, out space), must be :math:`\mu`-th space of V.
     """
 
-    def __init__(self, i, V, Vi):
+    def __init__(self, mu, V, Vmu):
         assert isinstance(V, FemSpace)
-        assert isinstance(i, int)
-        assert V.spaces[i] == Vi
+        assert isinstance(mu, int)
+        assert V.spaces[mu] == Vmu
 
         self.full_space = V
-        self.sub_space = Vi
-        self.dir = i
+        self.sub_space = Vmu
+        self.dir = mu
         self._domain = V.vector_space
-        self._codomain = Vi.vector_space
+        self._codomain = Vmu.vector_space
         self._dtype = V.vector_space.dtype
 
     @property
@@ -1364,34 +1368,39 @@ class CoordinateProjector(LinearOperator):
 
 class CoordinateInclusion(LinearOperator):
     r"""
-    Class of inclusion operator from one component of a ProductFemSpace. Represent the canonical inclusion on the i-th component :
+    Class of inclusion operator from one component of a ProductFemSpace. 
+    Represent the canonical inclusion on the :math:`\mu`-th component :
 
     .. math::
-        I_i : V_i \longrightarrow X = V_1 \times V_2 \times ... \times V_n \\
-        x_i \mapsto \mathbf{x} = (0,...,x_i,...,0)
+
+        \begin{align}
+        I_\mu : \ &V_\mu \longrightarrow V_1 \times \ldots \times V_\mu \times \ldots \times V_n \,,
+        \\[2mm]
+        &x_\mu \mapsto \vec{x} = (0,\ldots,x_\mu,\ldots , 0) \,.
+        \end{align}
 
 
     Parameters
     ----------
-    i : int
-        The component on which to project
+    mu : int
+        The component on which to project.
 
     V : psydac.fem.basic.(Product)FemSpace
         Finite element spline space (codomain, out space).
 
-    Vi : psydac.fem.basic.FemSpace
-        Finite element spline space (domain, in space), must be V i-th space
+    Vmu : psydac.fem.basic.FemSpace
+        Finite element spline space (domain, in space), must be :math:`\mu`-th space of V.
     """
 
-    def __init__(self, i, V, Vi):
+    def __init__(self, mu, V, Vmu):
         assert isinstance(V, FemSpace)
-        assert isinstance(i, int)
-        assert V.spaces[i] == Vi
+        assert isinstance(mu, int)
+        assert V.spaces[mu] == Vmu
 
         self.full_space = V
-        self.sub_space = Vi
-        self.dir = i
-        self._domain = Vi.vector_space
+        self.sub_space = Vmu
+        self.dir = mu
+        self._domain = Vmu.vector_space
         self._codomain = V.vector_space
         self._dtype = V.vector_space.dtype
 
@@ -1430,7 +1439,6 @@ class CoordinateInclusion(LinearOperator):
             assert out.space == self._codomain
             out *= 0.
             out._blocks[self.dir] += v
-
         else:
             blocks = [sspace.zeros() for sspace in self.codomain.spaces]
             blocks[self.dir] = v.copy()

{struphy-2.2.0 → struphy-2.3.0}/src/struphy/feec/linear_operators.py

@@ -509,3 +509,4 @@ class BoundaryOperator(LinOpWithTransp):
         Returns the transposed operator.
         """
         return BoundaryOperator(self._domain, self._space_id, self.bc)
+