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 .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 version 1.11.