diffusivity-step 2026.1.8

A SEAMM plug-in for Diffusivity

SEAMM Diffusivity Plug-in

A SEAMM plug-in for Diffusivity

• Free software: BSD-3-Clause

• Documentation: https://molssi-seamm.github.io/diffusivity_step/index.html

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

Features

• Please edit this section!

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

2026.1.8 – Enhancement to use atomic position and velocity trajectories

• Add support for the atomic position and velocity trajectories for forcefields/potentials such as EAM/MEAM where there are no bonds, and hence the center-of-mass trajectories used from molecules are not allowed by LAMMPS.

2025.9.23 – Bugfix: Fixed error storing diffusion constants as properties

2024.7.30.1 – Bugfix: Reinitialization of data in loops

• Fixed a bug where the data was not being correctly initialized if the step was in a loop. This caused the timing results to be incorrect.

• Added actual number of samples for the MSD and length of the Helfand integral to the results.

2024.7.30 – Added optional correction for cell size

• Added an option to use the Yeh-Hummer hydrostatic correction for the effects of the finite cell size. The viscosity is required as an input, but the correction eliminates the need to extrapolate to 1/L = 0.

• Added control parameters and timings to the available results.

2024.7.21 – Significant improvements!

• Simplified error analysis to safe approach of analyzing the diffusion constants over runs.

• Improved fitting of the curves to focus on the central linear portion. There are reasonable defaults but the user can adjust as needed.

• Provided a combined average and error bars when both the MSF approach and Helfand moments are used.

• Capture temperature, pressure, and cell size from the MD step, providing 1/L as a result since the true diffusion constants are found by extrapolating to 1/L = 0.

• Provided control over the number of steps for the expensive numerical integration in the Helfand moments, providing a reasonable default of 1000.

2024.7.15 – Bugfix: Significant error in Helfand Moment approach

• Now fixed and seems to be working.

2024.7.4 – Improved fitting of curves

• Removed weighting of the fit by the stdev since it is too biased to the beginning

• Added control over the portion of the data to fit in order to avoid the initial curvature and poor data towards the end.

2024.6.3 – Bugfix: handling of options for subflowchart

• Fixed a bug where the options for the subflowchart were not being parsed correctly.

2024.5.26 – Updated for new task handling

• The new handling of running tasks such as LAMMPS required a small change in the code.

2023.9.5 – Changed default to using only MSD

• The Helfand moments approach seems give incorrect results if the sampling time is too long. It is not dramatic, but gives increasingly incorrect results as the sampling time is increased. Thus using the Helfand moments is dangerous because the results may be wrong, but not obviously so.

2023.8.30 – Initial working version

• A working version that has been tested somewhat. Further testing and documentation will follow

2023.5.8 – Initial development version created

• Plug-in created using the SEAMM plug-in cookiecutter.