AVIz - Atomistic Simulation Vizualization software - is a projet aimed to help the vizualization process after numercial calculations. It was developed by Dan Peled, Joan Adler and Amihai Silverman from the Technion.
See publication here.
For AViz to be able to visualize simple systems of atoms, one should provide it with atom positions in space. An example of such input is in the form of an XYZ. This XYZ input file for AViz should inclue the number of atoms, the type (whether there is 1 atom type or more) and the (x,y,z) values of each atom.
In order to visualize the dynamics of a system i.e. movement of atoms- the user should provide AViz with more than 1 XYZ file. For example, LAMMPS outputs many XYZ files with the position of each atom in each timestep (according to the simulation specifications). This tracks the trajectory of each atom. AViz can then read these files consecutively, to visualize the dynamics of the system.
1) First the user should group all XYZ files and serialize them numerically (file names should be 001.xyz, 002.xyz etc. - NOTICE the leading zeros or else AViz won't read them in the right order).
2) Next step is to create a text file with the names of these XYZ files in the right order. This is called a file list, and this is the file AViz will open in order to iterate over all XYZ files.
3) Open AViz. Go to File>Open>>Open File List.
4) The File Control window will open. Here you can cycle through the files, and with the AutoSnap option, create a PNG file of each step. These PNG files will be a single frame if the user would like to create a short video of the simulation.