This version of the script has been deprecated, please scroll down to New Version to find the latest version

This script uses the collection document to display an overlay of the penetrant molecules from a constant volume dynamics calculation. As such it can be used to visualize the diffusion process. The penetrant molecules are colored by time, going from white to red. A study table is provided which shows the total distance moved from the starting position. Plotting this data gives the ability to estimate jump distances as your molecules move from pore to pore within a polymer.

Path of a single penetrant oxygen molecule showing clusters of atoms representing jump diffusion

There are two scripts provided:

ColorPenetrantMolecules - Overlays and colors the penetrant molecules by time. The distance from the first frame, and the distance moved in each frame is returned in a study table for each penetrant. Distance monitors are also used to show the path from one frame to another. This requires "molecules" to be defined in the trajectory. If they are not defined, you cannot add them after the dynamics has completed and should use the script below.

ColorPenetrantAtomsBasic - Without the molecule definition, I couldn't think of an easy way to automatically define a molecule so this script just does the overlay and colors but does not provide the extra distance information. This could be developed further to work with pre-defined centroids if someone wants to extend it!

The scripts have various settings to control whether distances are returned etc but both require you to define your set of penetrant atoms and give the name of the set in the script.

Minimum version: Materials Studio 4.2
Modules: Materials Visualizer

Cheers

Stephen