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 2026.10.17.1
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| seamm_md_analysis-2026.10.17.1.tar.gz | 106.2 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| seamm_md_analysis-2026.10.17.1-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 148.4 kB
Release files / seamm_md_analysis-2026.10.17.1.tar.gz
| Download URL | seamm_md_analysis-2026.10.17.1.tar.gz |
|---|---|
| Size | 106.2 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
3bce27477812832afed23199fdae4cede2939fd00a0be04d0d9e1f0b13539f94
|
|
BLAKE2b-256 checksum How to use checksums |
d313e92d65fdaffc524eec3c688e6296067d1cd0f7edc1680011bccc4027a9e5
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
Release files / seamm_md_analysis-2026.10.17.1-py3-none-any.whl
| Download URL | seamm_md_analysis-2026.10.17.1-py3-none-any.whl |
|---|---|
| Size | 42.2 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
49e96e1ebc3277bf36d7f1146dc9846b0a28bee851aa6512e2324b719873c44f
|
|
BLAKE2b-256 checksum How to use checksums |
96f8c07493147dac12f9973cdb16a91e2d93f004fa5e095459434b3ac7ed6c68
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
