Metadata-Version: 2.4
Name: seamm_md_analysis
Version: 2026.10.15
Summary: Analysis of molecular dynamics output for SEAMM: time-series statistics, correlation functions, Green-Kubo and Helfand transport coefficients, and trajectory readers
Author-email: Paul Saxe <psaxe@molssi.org>
License: BSD-3-Clause
Project-URL: Source, https://github.com/molssi-seamm/seamm_md_analysis/
Project-URL: Documentation, https://molssi-seamm.github.io/seamm_md_analysis/
Classifier: License :: OSI Approved :: BSD License
Classifier: Programming Language :: Python :: 3
Requires-Python: >=3.12
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: h5py
Requires-Dist: numpy
Requires-Dist: pint
Requires-Dist: pymbar
Requires-Dist: scipy
Provides-Extra: structure
Requires-Dist: MDAnalysis; extra == "structure"
Provides-Extra: test
Requires-Dist: MDAnalysis; extra == "test"
Requires-Dist: pytest>=6.1.2; extra == "test"
Requires-Dist: pytest-cov; extra == "test"
Dynamic: license-file

seamm_md_analysis
=================
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Analysis of molecular dynamics output for SEAMM.

`seamm_md_analysis` is the shared library behind SEAMM's MD analysis steps
(Diffusivity, Thermal Conductivity, and later Viscosity, Structure and the
Dielectric constant). It holds:

- **statistics:** mean ± error over replicas, block averages, statistical
  inefficiency and equilibration detection (pymbar), and formatting of values
  with their errors;
- **correlation functions** of time series, by FFT;
- **transport coefficients:** collective and single-molecule Helfand moments
  and mean square displacements (by FFT), fits of Green–Kubo integrals and
  Helfand moments, and the Yeh–Hummer finite-size correction;
- **plots** of these for SEAMM's `.graph` files;
- **readers** for the time-series and trajectory files the LAMMPS step writes.

The design is in the SEAMM developer guide, campaign 2026-10-14 ("MD analysis:
H5MD output, a shared library and analysis steps"). This is its phase 1.

### Copyright

Copyright (c) 2026, Paul Saxe

#### Acknowledgements

Project based on the
[Computational Molecular Science Python Cookiecutter](https://github.com/molssi/cookiecutter-cms) version 1.11.
