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

• Code: https://github.com/molssi-seamm/viscosity_step

History

2026.10.15.1 – Internal: a regression test against SPC/E water

• regression/spce holds a flowchart computing the viscosity and diffusion coefficient of rigid SPC/E water, and a script checking them against published values. It is run by hand after changes that could affect the results; the new “Regression” page in the developer guide describes it and records its results.

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.