PyMHD 0.1.0__tar.gz

pymhd-0.1.0/.gitignore

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pymhd-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2026 Yuyang HUA
+
+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
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+
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+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

pymhd-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: PyMHD
+Version: 0.1.0
+Summary: A Python package for post-processing MHD turbulence simulations
+Project-URL: Homepage, https://github.com/PlasmaHua/PyMHD
+Project-URL: Repository, https://github.com/PlasmaHua/PyMHD.git
+Project-URL: Issues, https://github.com/PlasmaHua/PyMHD/issues
+Author-email: "Yuyang Hua (华宇阳)" <yuyanghua@stu.pku.edu.cn>
+License-Expression: MIT
+License-File: LICENSE
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Requires-Python: >=3.10
+Requires-Dist: h5py>=3.10
+Requires-Dist: jax>=0.4.26
+Requires-Dist: kdepy>=1.1
+Requires-Dist: matplotlib>=3.7
+Requires-Dist: numpy>=1.26
+Requires-Dist: yt>=4.2
+Description-Content-Type: text/markdown
+
+# PyMHD
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20749062.svg)](https://doi.org/10.5281/zenodo.20749062)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://github.com/PlasmaHua/PyMHD/blob/main/LICENSE)
+
+
+A Python package for post-processing magnetohydrodynamic (MHD) turbulence simulations.
+
+## Features
+
+- [x] High-fidelity ***a posteriori* estimation of numerical dissipation** in MHD turbulence simulations;
+- [x] Computation and visualization of turbulent energy spectra;
+- [x] Visualization of 2D slices of MHD variables;
+- [x] Built-in support for simulations from the Athena family, including [Athena++](https://github.com/PrincetonUniversity/athena), [AthenaK](https://github.com/IAS-Astrophysics/athenak), and [AthenaPK](https://github.com/parthenon-hpc-lab/athenapk);
+- [x] Support for **driven MHD turbulence** (e.g., Alfvénic turbulence and small-scale dynamos), driven hydrodynamic turbulence, and **MRI-driven turbulence** (from shearing-box simulations) with triply periodic boundary conditions;
+- [ ] Support for adiabatic and isothermal equations of state (EoS); **TODO:** add support for incompressible EoS;
+- [ ] **TODO:** Computation and visualization of correlation functions;
+- [ ] **TODO:** Spectral energy transfer analysis following [Grete, Philipp, et al. Physics of Plasmas 24.9 (2017)](https://doi.org/10.1063/1.4990613).
+- [ ] **TODO:** Support JAX acceleration on GPUs and multi-node CPUs (currently, certain algorithms support parallelism on single-node, multi-core CPUs).
+
+
+## Quick Start
+
+### Installation
+
+Install **PyMHD** from [PyPI](https://pypi.org/) via:
+
+```bash
+pip install pymhd
+```
+
+This will automatically install PyMHD and its required dependencies, including:
+- [NumPy](https://github.com/numpy/numpy) for core computation;
+- [JAX](https://github.com/jax-ml/jax) for parallel acceleration on single-node, multi-core CPUs; therefore, [the CPU version of JAX](https://docs.jax.dev/en/latest/installation.html#pip-installation-cpu) is required;
+- [yt](https://github.com/yt-project/yt) and [h5py](https://github.com/h5py/h5py) for extracting data from HDF5 output files, specifically Athena++ `.athdf` files, AthenaK `.bin` files, and AthenaPK `.phdf` files;
+- [Matplotlib](https://github.com/matplotlib/matplotlib) for plotting functionality in the `pymhd.plot` modules;
+- [KDEpy](https://github.com/tommyod/KDEpy) for plotting smoothed histograms of numerical dissipation data in the `pymhd.plot.nd` module.
+
+### Built-in Examples
+
+For a quick start, clone the source repository, for example:
+
+```bash
+git clone https://github.com/PlasmaHua/PyMHD.git
+```
+
+Then navigate to the `./examples` subdirectory using `cd PyMHD/examples`, where two AthenaK simulation examples are provided.
+
+Under construction.
+
+### Analyze Your Own Athena Simulations
+
+PyMHD natively supports simulations from Athena++, AthenaK, and AthenaPK. Use the `pymhd.output2turbulence` function to extract output data and input-file metadata, then construct a PyMHD `Turbulence` object for further analysis.
+
+## API Documentation
+
+Under construction.
+
+## Citation
+
+If PyMHD contributes to your work in any way, please consider citing the package via:
+
+```bibtex
+@misc{Hua2026,
+  doi = {10.5281/zenodo.20749062},
+  url = {https://zenodo.org/doi/10.5281/zenodo.20749062},
+  author = {Hua, Yuyang},
+  title = {PyMHD: Python package for post-processing MHD turbulence simulations},
+  publisher = {Zenodo},
+  year = {2026},
+  copyright = {MIT License}
+}
+```
+
+If you specifically use the framework for numerical dissipation estimation, please cite our method paper via:
+
+```bibtex
+
+```

pymhd-0.1.0/README.md

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+# PyMHD
+
+[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.20749062.svg)](https://doi.org/10.5281/zenodo.20749062)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://github.com/PlasmaHua/PyMHD/blob/main/LICENSE)
+
+
+A Python package for post-processing magnetohydrodynamic (MHD) turbulence simulations.
+
+## Features
+
+- [x] High-fidelity ***a posteriori* estimation of numerical dissipation** in MHD turbulence simulations;
+- [x] Computation and visualization of turbulent energy spectra;
+- [x] Visualization of 2D slices of MHD variables;
+- [x] Built-in support for simulations from the Athena family, including [Athena++](https://github.com/PrincetonUniversity/athena), [AthenaK](https://github.com/IAS-Astrophysics/athenak), and [AthenaPK](https://github.com/parthenon-hpc-lab/athenapk);
+- [x] Support for **driven MHD turbulence** (e.g., Alfvénic turbulence and small-scale dynamos), driven hydrodynamic turbulence, and **MRI-driven turbulence** (from shearing-box simulations) with triply periodic boundary conditions;
+- [ ] Support for adiabatic and isothermal equations of state (EoS); **TODO:** add support for incompressible EoS;
+- [ ] **TODO:** Computation and visualization of correlation functions;
+- [ ] **TODO:** Spectral energy transfer analysis following [Grete, Philipp, et al. Physics of Plasmas 24.9 (2017)](https://doi.org/10.1063/1.4990613).
+- [ ] **TODO:** Support JAX acceleration on GPUs and multi-node CPUs (currently, certain algorithms support parallelism on single-node, multi-core CPUs).
+
+
+## Quick Start
+
+### Installation
+
+Install **PyMHD** from [PyPI](https://pypi.org/) via:
+
+```bash
+pip install pymhd
+```
+
+This will automatically install PyMHD and its required dependencies, including:
+- [NumPy](https://github.com/numpy/numpy) for core computation;
+- [JAX](https://github.com/jax-ml/jax) for parallel acceleration on single-node, multi-core CPUs; therefore, [the CPU version of JAX](https://docs.jax.dev/en/latest/installation.html#pip-installation-cpu) is required;
+- [yt](https://github.com/yt-project/yt) and [h5py](https://github.com/h5py/h5py) for extracting data from HDF5 output files, specifically Athena++ `.athdf` files, AthenaK `.bin` files, and AthenaPK `.phdf` files;
+- [Matplotlib](https://github.com/matplotlib/matplotlib) for plotting functionality in the `pymhd.plot` modules;
+- [KDEpy](https://github.com/tommyod/KDEpy) for plotting smoothed histograms of numerical dissipation data in the `pymhd.plot.nd` module.
+
+### Built-in Examples
+
+For a quick start, clone the source repository, for example:
+
+```bash
+git clone https://github.com/PlasmaHua/PyMHD.git
+```
+
+Then navigate to the `./examples` subdirectory using `cd PyMHD/examples`, where two AthenaK simulation examples are provided.
+
+Under construction.
+
+### Analyze Your Own Athena Simulations
+
+PyMHD natively supports simulations from Athena++, AthenaK, and AthenaPK. Use the `pymhd.output2turbulence` function to extract output data and input-file metadata, then construct a PyMHD `Turbulence` object for further analysis.
+
+## API Documentation
+
+Under construction.
+
+## Citation
+
+If PyMHD contributes to your work in any way, please consider citing the package via:
+
+```bibtex
+@misc{Hua2026,
+  doi = {10.5281/zenodo.20749062},
+  url = {https://zenodo.org/doi/10.5281/zenodo.20749062},
+  author = {Hua, Yuyang},
+  title = {PyMHD: Python package for post-processing MHD turbulence simulations},
+  publisher = {Zenodo},
+  year = {2026},
+  copyright = {MIT License}
+}
+```
+
+If you specifically use the framework for numerical dissipation estimation, please cite our method paper via:
+
+```bibtex
+
+```

pymhd-0.1.0/pymhd/__init__.py

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+# PyMHD: Python for Magnetohydrodynamic Turbulence.
+# Copyright (c) 2026 Yuyang Hua (华宇阳)
+# License: MIT
+
+"""
+pymhd/__init__.py
+-----------------
+
+Unified interface for PyMHD.
+"""
+
+from .turbulence import Scalar, Vector, ScalarField, VectorField, Turbulence, avg, std
+from .derivatives.derivative import Dx, Dy, Dz, grad, div, curl, laplacian, Algorithm
+
+from .spectra import Spectrum, Spectrum1D, EnergySpectra
+from .numdiss import NumericalDissipation
+from .preprocess import output2turbulence
+
+from .plot import plot
+
+__all__ = [
+    "Scalar", "Vector",
+    "ScalarField", "VectorField", "avg", "std", "Turbulence",
+    "Algorithm",
+    "Dx", "Dy", "Dz", "grad", "div", "curl", "laplacian",
+    "Spectrum", "Spectrum1D",
+    "EnergySpectra",
+    "NumericalDissipation",
+    "output2turbulence",
+    "plot",
+]