struphy 2.3.0__tar.gz → 2.3.1__tar.gz

{struphy-2.3.0/src/struphy.egg-info → struphy-2.3.1}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: struphy
-Version: 2.3.0
+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
@@ -27,33 +27,35 @@ 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==3.2.3
-Requires-Dist: docutils==0.20.1
-Requires-Dist: gvec-to-python==1.2.1
-Requires-Dist: h5py==3.10.0
-Requires-Dist: ipyparallel==8.7.0
-Requires-Dist: lxml_html_clean==0.1.0
+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==3.8.3
+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==7.1.2
+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==1.11.2
-Requires-Dist: pydata-sphinx-theme==0.15.2
-Requires-Dist: pytest==8.1.1
+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==1.12.0
-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==4.66.2
+Requires-Dist: tqdm==4.66.4
 Requires-Dist: vtk==9.3.0
 Requires-Dist: wheel==0.43.0
 

{struphy-2.3.0 → struphy-2.3.1}/pyproject.toml

@@ -4,9 +4,9 @@ build-backend = "setuptools.build_meta"
 
 [project]
 name = "struphy"
-version = "2.3.0"
+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"},
@@ -20,29 +20,31 @@ classifiers = [
     ]
 dependencies = [
     'PyYAML==6.0.1',
-    'argcomplete==3.2.3',
-    'docutils==0.20.1',
-    'gvec-to-python==1.2.1',
-    'h5py==3.10.0',
-    'ipyparallel==8.7.0',
-    'lxml_html_clean==0.1.0',
+    '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==3.8.3',
+    'matplotlib==3.9.0',
     'mistune==0.8.4',
-    'mpi4py==3.1.5',
-    'myst-parser==2.0.0',
-    'nbsphinx==0.9.3',
-    'notebook==7.1.2',
+    '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==1.11.2',
-    'pydata-sphinx-theme==0.15.2',
-    'pytest==8.1.1',
+    'pyccel==1.12.0',
+    'pydata-sphinx-theme==0.15.3',
+    'pytest==8.2.2',
     'pytest-monitor==1.6.6',
     'pytest-mpi==0.6',
-    'scipy==1.12.0',
-    'Sphinx==7.2.6',
+    'scipy==1.13.1',
+    'Sphinx==7.3.7',
     'sphinxcontrib-napoleon==0.7',
-    'tqdm==4.66.2',
+    'tqdm==4.66.4',
     'vtk==9.3.0',
     'wheel==0.43.0',
 ]
@@ -80,5 +82,5 @@ struphy = "struphy.console.main:struphy"
                     ]
                     
 struphy = ['compile_struphy.mk',
-           'psydac-0.1.12-py3-none-any.whl',
+           'psydac-0.1.13-py3-none-any.whl',
            ]

{struphy-2.3.0 → 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 = '0.1.12'
+        current_ver = '0.1.13'
         psydac_file = 'psydac-' + current_ver + '-py3-none-any.whl'
 
         try:

{struphy-2.3.0 → 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/')

{struphy-2.3.0 → struphy-2.3.1}/src/struphy/diagnostics/console_diagn.py

@@ -8,7 +8,7 @@ import h5py
 import yaml
 
 import struphy
-from struphy.diagnostics.diagn_tools import plot_scalars, plot_distr_fun
+from struphy.diagnostics.diagn_tools import plot_scalars, plot_distr_fun, phase_space_video
 
 
 def main():
@@ -19,13 +19,31 @@ def main():
                         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                  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='in which folder the simulation data has been stored')
+                        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],
@@ -41,16 +59,29 @@ def main():
     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)
@@ -59,8 +90,10 @@ def main():
 
     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]}
+    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')
@@ -78,14 +111,14 @@ def main():
                 model_name = line.split(':')[1].strip()
 
     if 'plot_scalars' in actions:
-        plot_scalars(saved_time,
-                     saved_scalars,
-                     scalars_plot=scalars_plot,
-                     do_log=do_log,
-                     save_plot=True,
-                     savedir=path)
-
-    if 'plot_distr' 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
@@ -102,15 +135,19 @@ def main():
 
             # Get default background of particles class
             from struphy.pic import particles
-            default_bckgr_type = getattr(particles, particles_class_name).default_bckgr_params()['type']
+            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()
+            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 params['kinetic'][species]['markers']['type'] == 'full_f':
+            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']
@@ -119,35 +156,59 @@ def main():
                             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 params['kinetic'][species]['markers']['type'] == 'delta_f' \
-                    or params['kinetic'][species]['markers']['type'] == 'control_variate':
+            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']
-                        bckgr_param = params['kinetic'][species]['background'][bckgr_type]['u' + str(
-                            k)]
+
+                        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
-
-            # 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,
-            )
+            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()