struphy 1.9.8__tar.gz → 2.0.0__tar.gz

struphy-2.0.0/LICENSE

@@ -0,0 +1,23 @@
+Copyright 2019 (c) Struphy dev team | 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, 
+including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, 
+and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, 
+subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial 
+portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT 
+NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 
+IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+In addition, we ask you to cite the following reference in scientific publications which contain
+results obtained with this software and developments:
+
+F. Holderied, S. Possanner, X. Wang, 
+"MHD-kinetic hybrid code based on structure-preserving finite elements with particles-in-cell",
+J. Comp. Phys. 433 (2021) 110143

struphy-2.0.0/PKG-INFO

@@ -0,0 +1,115 @@
+Metadata-Version: 2.1
+Name: struphy
+Version: 2.0.0
+Summary: Multi-model plasma physics package
+Author: Max Planck Institute for Plasma Physics
+Author-email: stefan.possanner@ipp.mpg.de, florian.holderied@ipp.mpg.de
+License: Copyright 2019 (c) Struphy dev team | 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, 
+        including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, 
+        and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, 
+        subject to the following conditions:
+        
+        The above copyright notice and this permission notice shall be included in all copies or substantial 
+        portions of the Software.
+        
+        THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT 
+        NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. 
+        IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
+        WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+        SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+        
+        In addition, we ask you to cite the following reference in scientific publications which contain
+        results obtained with this software and developments:
+        
+        F. Holderied, S. Possanner, X. Wang, 
+        "MHD-kinetic hybrid code based on structure-preserving finite elements with particles-in-cell",
+        J. Comp. Phys. 433 (2021) 110143
+        
+Project-URL: homepage, https://struphy.pages.mpcdf.de/struphy/
+Project-URL: documentation, https://struphy.pages.mpcdf.de/struphy/
+Project-URL: repository, https://gitlab.mpcdf.mpg.de/struphy/struphy
+Project-URL: changelog, https://gitlab.mpcdf.mpg.de/struphy/struphy/-/blob/devel/CHANGELOG.md
+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: <3.11,>=3.7
+Description-Content-Type: text/markdown
+License-File: LICENSE
+
+# STRUPHY - STRUcture-Preserving HYbrid codes
+
+A Python package for energetic particles in plasma.
+
+The package is developed since 2019 at [Max Planck Institute for Plasma Physics](https://www.ipp.mpg.de/) 
+in the division [NMPP (Numerical Methods for Plasma Physics)](https://www.ipp.mpg.de/ippcms/de/for/bereiche/numerik).
+
+## What you can do with struphy
+
+* Investigate plasma physics problems with multiple [models equations](https://struphy.pages.mpcdf.de/struphy/sections/models.html) containing fluid and/or kinetic components 
+* Simulate each model on [curved domains](https://struphy.pages.mpcdf.de/struphy/sections/domains.html) 
+* Load a variety of [MHD equilibira](https://struphy.pages.mpcdf.de/struphy/sections/mhd_equils.html) and [kinetic backgrounds](https://struphy.pages.mpcdf.de/struphy/sections/kinetic_backgrounds.html)
+* Use [diagnostic tools](https://struphy.pages.mpcdf.de/struphy/sections/diagnostics.html) to visualize results
+* Compare simulations to analytic [dispersion relations](https://struphy.pages.mpcdf.de/struphy/sections/diagnostics.html#module-struphy.dispersion_relations.analytic)
+* Solve the [MHD eigenvalue problem](https://struphy.pages.mpcdf.de/struphy/index.html) in axisymmetric toroidal geometries
+* [Improve Struphy](https://struphy.pages.mpcdf.de/struphy/sections/developers.html) by adding
+    * model equations
+    * domains (geometry)
+    * MHD equilibria
+    * kinetic backgrounds
+    * diagnostic tools
+    * dispersion relations
+    * other physics features (e.g. collision operators etc.)
+
+## Algorithmic features
+
+* Particle-in-cell method for kinetic species
+* Discrete differential forms based on high-order B-spline finite elements ([Psydac library](https://github.com/pyccel/psydac)) for fields/fluids
+* Exact conservation laws
+* Polar splines to treat a polar singularity 
+* Kernels are pre-compiled with [Pyccel](https://github.com/pyccel/pyccel) to achieve near-Fortran performance
+* MPI/OpenMP hybrid parallelization  
+
+## Installation
+
+See the [struphy documentation](https://struphy.pages.mpcdf.de/struphy/index.html).
+
+## Tutorials
+
+* [Turorial 01](https://gitlab.mpcdf.mpg.de/struphy/struphy/-/blob/devel/notebooks/tutorial_01_units_run_main.ipynb): Learn about Struphy model's normalization (units), simulation parameters and the Struphy main execution file.
+
+* [Tutorial 02](https://gitlab.mpcdf.mpg.de/struphy/struphy/-/blob/devel/notebooks/tutorial_02_postproc_standard_plotting.ipynb): Learn about the data generated by Struphy simulations, data post processing and simple plotting 
+of field/fluid and kinetic variables.
+
+* [Tutorial 03](https://gitlab.mpcdf.mpg.de/struphy/struphy/-/blob/devel/notebooks/tutorial_03_plot_poloidal_planes.ipynb): Learn about plotting field/fluid variables in toroidal geometry.
+
+## Key references
+
+* F. Holderied, S. Possanner, X. Wang, "MHD-kinetic hybrid code based on structure-preserving finite elements with particles-in-cell", [J. Comp. Phys. 433 (2021) 110143](https://www.sciencedirect.com/science/article/pii/S0021999121000358?via%3Dihub)
+
+* F. Holderied, S. Possanner, "Magneto-hydrodynamic eigenvalue solver for axis-symmetric equilibria based on smooth polar splines", [J. Comp. Phys. 464 (2022) 111329](https://www.sciencedirect.com/science/article/pii/S0021999122003916?via%3Dihub)
+
+* F. Holderied, "STRUPHY: a structure-preserving hybrid MHD-kinetic code for the interaction of energetic particles with Alfvén waves in magnetized plasmas", [PhD thesis (2022)](https://mediatum.ub.tum.de/?id=1656539)
+
+## License
+
+Copyright 2019 (c) Struphy dev team | 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, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+In addition, we ask you to cite the following reference in scientific publications which contain results obtained with
+this software and developments:
+
+F. Holderied, S. Possanner, X. Wang, "MHD-kinetic hybrid code based on structure-preserving finite elements with particles-in-cell", J. Comp. Phys. 433 (2021) 110143
+
+## Contact
+
+* Florian Holderied [floho@ipp.mpg.de](floho@ipp.mpg.de)
+* Stefan Possanner [spossann@ipp.mpg.de](spossann@ipp.mpg.de)
+* Xin Wang [xin.wang@ipp.mpg.de](xin.wang@ipp.mpg.de)

struphy-2.0.0/README.md

@@ -0,0 +1,74 @@
+# STRUPHY - STRUcture-Preserving HYbrid codes
+
+A Python package for energetic particles in plasma.
+
+The package is developed since 2019 at [Max Planck Institute for Plasma Physics](https://www.ipp.mpg.de/) 
+in the division [NMPP (Numerical Methods for Plasma Physics)](https://www.ipp.mpg.de/ippcms/de/for/bereiche/numerik).
+
+## What you can do with struphy
+
+* Investigate plasma physics problems with multiple [models equations](https://struphy.pages.mpcdf.de/struphy/sections/models.html) containing fluid and/or kinetic components 
+* Simulate each model on [curved domains](https://struphy.pages.mpcdf.de/struphy/sections/domains.html) 
+* Load a variety of [MHD equilibira](https://struphy.pages.mpcdf.de/struphy/sections/mhd_equils.html) and [kinetic backgrounds](https://struphy.pages.mpcdf.de/struphy/sections/kinetic_backgrounds.html)
+* Use [diagnostic tools](https://struphy.pages.mpcdf.de/struphy/sections/diagnostics.html) to visualize results
+* Compare simulations to analytic [dispersion relations](https://struphy.pages.mpcdf.de/struphy/sections/diagnostics.html#module-struphy.dispersion_relations.analytic)
+* Solve the [MHD eigenvalue problem](https://struphy.pages.mpcdf.de/struphy/index.html) in axisymmetric toroidal geometries
+* [Improve Struphy](https://struphy.pages.mpcdf.de/struphy/sections/developers.html) by adding
+    * model equations
+    * domains (geometry)
+    * MHD equilibria
+    * kinetic backgrounds
+    * diagnostic tools
+    * dispersion relations
+    * other physics features (e.g. collision operators etc.)
+
+## Algorithmic features
+
+* Particle-in-cell method for kinetic species
+* Discrete differential forms based on high-order B-spline finite elements ([Psydac library](https://github.com/pyccel/psydac)) for fields/fluids
+* Exact conservation laws
+* Polar splines to treat a polar singularity 
+* Kernels are pre-compiled with [Pyccel](https://github.com/pyccel/pyccel) to achieve near-Fortran performance
+* MPI/OpenMP hybrid parallelization  
+
+## Installation
+
+See the [struphy documentation](https://struphy.pages.mpcdf.de/struphy/index.html).
+
+## Tutorials
+
+* [Turorial 01](https://gitlab.mpcdf.mpg.de/struphy/struphy/-/blob/devel/notebooks/tutorial_01_units_run_main.ipynb): Learn about Struphy model's normalization (units), simulation parameters and the Struphy main execution file.
+
+* [Tutorial 02](https://gitlab.mpcdf.mpg.de/struphy/struphy/-/blob/devel/notebooks/tutorial_02_postproc_standard_plotting.ipynb): Learn about the data generated by Struphy simulations, data post processing and simple plotting 
+of field/fluid and kinetic variables.
+
+* [Tutorial 03](https://gitlab.mpcdf.mpg.de/struphy/struphy/-/blob/devel/notebooks/tutorial_03_plot_poloidal_planes.ipynb): Learn about plotting field/fluid variables in toroidal geometry.
+
+## Key references
+
+* F. Holderied, S. Possanner, X. Wang, "MHD-kinetic hybrid code based on structure-preserving finite elements with particles-in-cell", [J. Comp. Phys. 433 (2021) 110143](https://www.sciencedirect.com/science/article/pii/S0021999121000358?via%3Dihub)
+
+* F. Holderied, S. Possanner, "Magneto-hydrodynamic eigenvalue solver for axis-symmetric equilibria based on smooth polar splines", [J. Comp. Phys. 464 (2022) 111329](https://www.sciencedirect.com/science/article/pii/S0021999122003916?via%3Dihub)
+
+* F. Holderied, "STRUPHY: a structure-preserving hybrid MHD-kinetic code for the interaction of energetic particles with Alfvén waves in magnetized plasmas", [PhD thesis (2022)](https://mediatum.ub.tum.de/?id=1656539)
+
+## License
+
+Copyright 2019 (c) Struphy dev team | 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, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+
+In addition, we ask you to cite the following reference in scientific publications which contain results obtained with
+this software and developments:
+
+F. Holderied, S. Possanner, X. Wang, "MHD-kinetic hybrid code based on structure-preserving finite elements with particles-in-cell", J. Comp. Phys. 433 (2021) 110143
+
+## Contact
+
+* Florian Holderied [floho@ipp.mpg.de](floho@ipp.mpg.de)
+* Stefan Possanner [spossann@ipp.mpg.de](spossann@ipp.mpg.de)
+* Xin Wang [xin.wang@ipp.mpg.de](xin.wang@ipp.mpg.de)

struphy-2.0.0/pyproject.toml

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+[build-system]
+requires = ["setuptools>=61.0"]
+build-backend = "setuptools.build_meta"
+
+[project]
+name = "struphy"
+version = "2.0.0"
+readme = "README.md"
+requires-python = ">=3.7, <3.11"
+license = {file = "LICENSE"}
+authors = [
+  { name = "Max Planck Institute for Plasma Physics"},
+  { email = "stefan.possanner@ipp.mpg.de"},
+  { email = "florian.holderied@ipp.mpg.de"}
+]
+description = "Multi-model plasma physics package"
+keywords = ["plasma physics, fusion, numerical modeling, partial differential equations, energetic particles"]
+classifiers = [
+    "Programming Language :: Python :: 3",
+    ]
+dependencies = [
+    'h5py',
+    'matplotlib',
+    'mpi4py',
+    'numpy',
+    'pyccel',
+    'PyYAML',
+    'scipy',
+    'pytest',
+    'pytest-mpi',
+    'mistune<2',
+    'sphinx==4.2.0',
+    'sphinxcontrib-napoleon',
+    'sphinx-rtd-theme',
+    'm2r2==0.3.1',
+    'vtk',
+    'docutils==0.15',
+    'wheel',
+    'tqdm',
+    'gvec-to-python>=1.1.0',
+]
+
+[project.urls]
+homepage = "https://struphy.pages.mpcdf.de/struphy/"
+documentation = "https://struphy.pages.mpcdf.de/struphy/"
+repository = "https://gitlab.mpcdf.mpg.de/struphy/struphy"
+changelog = "https://gitlab.mpcdf.mpg.de/struphy/struphy/-/blob/devel/CHANGELOG.md"
+"Bug Tracker" = "https://gitlab.mpcdf.mpg.de/struphy/struphy/-/issues"
+
+[project.scripts]
+struphy = "struphy.console.main:struphy"
+
+[tool.setuptools.package-data]
+'struphy.fields_background.mhd_equil.eqdsk' = [
+            'data/*.high',
+        ]
+
+'struphy.fields_background.mhd_equil.gvec' = [
+            'ellipstell_v2/newBC_E1D6_M6N6/*.dat',
+            'ellipstell_v2/newBC_E1D6_M6N6/*.ini',
+            'ellipstell_v2/newBC_E4D6_M6N6/*.dat',
+            'ellipstell_v2/newBC_E4D6_M6N6/*.ini',
+            'ellipstell_v2/oldBC_E40D5M6N6/*.dat',
+            'ellipstell_v2/oldBC_E40D5M6N6/*.ini',
+        ]
+
+'struphy.io' = ['batch/*.sh']
+
+'struphy.io.inp' = ['parameters.yml',
+                    'tests/*.yml',
+                    'examples/*.yml',
+                    ]
+                    
+struphy = ['compile_struphy.mk',
+           'psydac-0.1-py3-none-any.whl',
+           'io_path.txt',
+           ]

struphy-2.0.0/src/struphy/console/compile.py

@@ -0,0 +1,68 @@
+def struphy_compile(no_openmp=False, delete=False, verbose=False):
+    """
+    Compile Struphy kernels.
+
+    Parameters
+    ----------
+    no_openmp : bool, optional
+        Whether to compile kernels with (no_openmp=False) or without (no_openmp=True).
+
+    delete : bool, optional
+        If True, deletes generated Fortran and .so files.
+
+    verbose : bool, optional
+        Call pyccel in verbose mode.
+    """
+
+    import subprocess
+    import struphy
+    import os
+
+    libpath = struphy.__path__[0]
+
+    if delete:
+
+        # (change dir not to be in source path)
+        print('\nDeleting .f90 and .so files ...')
+        subprocess.run(['make',
+                        'clean',
+                        '-f',
+                        'compile_struphy.mk',
+                        ], check=True, cwd=libpath)
+        print('Done.')
+
+    else:
+
+        # struphy and psydac (change dir not to be in source path)
+        flag_omp_pic = '--openmp'
+        flag_omp_mhd = ''
+        if no_openmp:
+            flag_omp_pic = ''
+
+        flag_verb = ''
+        if verbose:
+            flag_verb = '--verbose'
+
+        try:
+            import psydac.api
+        except:
+            print('\nInstalling Psydac ...')
+            subprocess.run(['pip',
+                            'install',
+                            os.path.join(
+                                libpath, 'psydac-0.1-py3-none-any.whl'),
+                            ], check=True)
+            print('Done.')
+
+        # gvec_to_python (change dir not to be in source path)
+        subprocess.run(['compile-gvec-tp'], check=True, cwd=libpath)
+
+        print('\nCompiling Struphy and Psydac kernels ...')
+        subprocess.run(['make',
+                        '-f',
+                        'compile_struphy.mk',
+                        'flags=' + flag_verb,
+                        'flags_openmp_pic=' + flag_omp_pic,
+                        'flags_openmp_mhd=' + flag_omp_mhd,
+                        ], check=True, cwd=libpath)
+        print('Done.')

struphy-2.0.0/src/struphy/console/example.py

@@ -0,0 +1,30 @@
+def struphy_example(case, diagnostics, mpi=1):
+    """
+    Run a Struphy example.
+
+    Parameters
+    ----------
+    case : str
+        Name of the example case to run.
+
+    diagnostics : bool
+        Wether to do diagnostics and plot only, if example has already been run before, and the output folder still exists.
+
+    mpi : int
+        Number of MPI processes used to run the example.
+    """
+
+    import subprocess
+    import struphy
+
+    libpath = struphy.__path__[0]
+
+    command = ['python3',
+               'examples/' + case + '.py',
+               '--mpi',
+               str(mpi)]
+
+    if diagnostics:
+        command += ['--diagnostics']
+
+    subprocess.run(command, check=True, cwd=libpath)