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 2026.10.18
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-2026.10.18.tar.gz | 124.9 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| seamm_md_analysis-2026.10.18-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 179.0 kB
Release files / seamm_md_analysis-2026.10.18.tar.gz
| Download URL | seamm_md_analysis-2026.10.18.tar.gz |
|---|---|
| Size | 124.9 kB |
| Tags | Source |
|
SHA-256 checksum How to use checksums |
898a545e6f44a505e8b51dd7e3c22eaad4f63a0dded836483ba7e5fc0e466df0
|
|
BLAKE2b-256 checksum How to use checksums |
36b1db29b509f33df33be252a2491542046cced523c99cf498a2f55864c97773
|
| 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-2026.10.18-py3-none-any.whl
| Download URL | seamm_md_analysis-2026.10.18-py3-none-any.whl |
|---|---|
| Size | 54.2 kB |
| Tags | Python 3 |
|
SHA-256 checksum How to use checksums |
b5320b5abcb5f125efc4d5a2f71fe88bf116b7040b795e14b99162662d5e1f7c
|
|
BLAKE2b-256 checksum How to use checksums |
c4c0e197233c409f9bf6dced133bb46505aade1b9e50eab9dce663d62946fddb
|
| Upload date | |
|
Uploaded using Trusted Publishing? What is trusted publishing? |
No |
| Uploaded via |
twine/7.0.0 CPython/3.13.14
|
