SEAMM Viscosity Plug-in
A SEAMM plug-in for the shear viscosity of liquids from equilibrium molecular dynamics.
Free software: BSD-3-Clause
Documentation: https://molssi-seamm.github.io/viscosity_step/index.html
Features
The shear viscosity by Green-Kubo and from the Helfand moments, averaging the five independent shear components of the pressure tensor.
Runs its own MD several times, or analyzes MD run earlier in the flowchart or in other jobs, from the md.h5md files the LAMMPS step writes.
Checks before the job runs that the MD samples the pressure tensor often enough.
Passes its result to a later Diffusivity step for the Yeh-Hummer correction.
Acknowledgements
This package was created with the molssi-seamm/cookiecutter-seamm-plugin tool, which is based on the excellent Cookiecutter.
Developed by the Molecular Sciences Software Institute (MolSSI), which receives funding from the National Science Foundation under award CHE-2136142.
History
- 2026.10.15 – First release: the shear viscosity from MD
Calculates the shear viscosity of a liquid from equilibrium MD by Green-Kubo and from the Helfand moments, averaging the five independent shear components of the pressure tensor.
Runs its own MD several times, or analyzes MD run earlier in the flowchart, in each iteration of a loop, or in other jobs, from the md.h5md files the LAMMPS step writes. A single run is divided into blocks to estimate the errors.
Checks before the job runs that the MD samples the pressure tensor at least every 5 fs, and turns it on when it runs its own MD.
The result is stored as a property, can be saved in variables and tables, and is used by a following Diffusivity step for its finite-size correction.
1 maintainer
Metadata
1 maintainer
Release files for viscosity-step 2026.10.15
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| viscosity_step-2026.10.15.tar.gz | 316.6 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| viscosity_step-2026.10.15-py2.py3-none-any.whl | Python 2, Python 3 | none | any | Details |
Total release size: 339.3 kB
Release files / viscosity_step-2026.10.15.tar.gz
| Download URL | viscosity_step-2026.10.15.tar.gz |
|---|---|
| Size | 316.6 kB |
| Tags | Source |
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SHA-256 checksum How to use checksums |
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Release files / viscosity_step-2026.10.15-py2.py3-none-any.whl
| Download URL | viscosity_step-2026.10.15-py2.py3-none-any.whl |
|---|---|
| Size | 22.7 kB |
| Tags | Python 2 Python 3 |
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