An advantage of simulating materials is that we can learn, not only about how a material will settle given, for example, the number of particles, density, and temperature, but also how the system evolved at every step from beginning to end. With every atom's position tracked throughout the course of the simulation, the first investigation into the nature of the system is often to the play the "movie" of where the atoms went and who they fraternized with along the way.
The cmelab is currently utilizing two distinct resources for this purpose. They both have their pros/cons.
- VMD is an open source software package. The interface may be unintuitive to begin, but our lab has more expertise with this tool at present. VMD is highly configurable! An example .vmdrc file
for doing so can be found here. This file tells
VMD how to look and react to a specific user. You can get this file locally by running
makein the root directory of this repository (this'll copy all the config files into your home directory) or by copying the files individually. Once copied, you can view or edit this file by runningvim ~/.vmdrcin your command line. VMD requires a plugin to read the output from most of the simulations run in this lab (gsd files). Installation instructions can be found here under the "Installing Visual Molecular Dynamics (VMD)" header. - Ovito is a propreitary software package with a free basic version availaible for download. Getting off the ground may be faster with Ovito, but if we outgrow the basic version's functionality, someone will have to pay for an upgrade! A notable advantage of Ovito is the ability to view the output from a simulation remotely.