pymhd 0.1.2

A Python package for post-processing MHD turbulence simulations

PyMHD

A Python package for post-processing magnetohydrodynamic (MHD) turbulence simulations.

Features

• High-fidelity a posteriori estimation and visualization of numerical dissipation in MHD turbulence simulations
• Computation and visualization of turbulent energy spectra
• Visualization of 2D slices of MHD variables
• Built-in support for simulations from the Athena family, including Athena++, AthenaK, and AthenaPK
• 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)
• TODO: 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 with:

pip install pymhd

This command installs PyMHD and its required dependencies, including:

• NumPy for core computations
• JAX for parallel acceleration on single-node, multi-core CPUs; therefore, the CPU version of JAX is required
• yt and h5py for extracting data from HDF5 output files, specifically Athena++ .athdf files, AthenaK .bin files, and AthenaPK .phdf files
• Matplotlib for plotting functionality in the pymhd.plot modules
• 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:

git clone https://github.com/PlasmaHua/PyMHD.git

Alternatively, download the source code from the GitHub releases page. Then navigate to the ./examples subdirectory with cd PyMHD/examples, where two AthenaK simulation examples are provided.

Each directory in PyMHD/examples contains a Python script, quick.py, that demonstrates basic usage of PyMHD, including:

• Extracting a PyMHD Turbulence object from output files with the pymhd.output2turbulence function
• Calculating turbulent energy spectra with the PyMHD EnergySpectra class
• Estimating numerical dissipation a posteriori with the PyMHD NumericalDissipation class
• Visualizing turbulent spectra and numerical dissipation with the pymhd.plot module

Analyze Your Own Athena Simulations

PyMHD natively supports simulations from Athena++, AthenaK, and AthenaPK. Following the examples in PyMHD/examples, 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, please consider citing the package using the following BibTeX entry:

@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}
}