User Guide#
The diffusivity step in SEAMM calculates the diffusion coefficients using molecular dynamics. You will need to setup an appropriate molecular dynamics run in the subflowchart and ensure that it produces the center-of-mass positions and/or velocities of the particles/molecules.
The positions are used to calculate the diffusion coefficient from the mean-sqaure-displacement (MSD) of the molecules. The velocities are needed for the approach using Helfand moments, which is related to the more traditional Green-Kubo method.