seamm_md_analysis
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
.graphfiles; - 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 version 1.11.
1 maintainer
Metadata
1 maintainer
Release files for seamm-md-analysis 2026.10.19
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