Virtualization with AViz
This page is adapted from Yahel Barak's class project website.
Some more explanations and language editing have been made.
The results of the LAMMPS simulation is xyz files that describe the locations
of each of the sample atoms. To understend what happend to the
sample we need to see it so we virtualized it using AViz
virtualization software. First we need to make a list of all the .xyz files
from the code - ls -1 *.xyz | sort -n > filelist.dat. After that we run AViz by the aviz comand and load the file list:
we can edit the figure's appearance - change the atom color, bond length and more:
A good way to illustrate the results is a GIF animation. To do that we
first need to make a .png file for every .xyz, We click on the AutoSnap
button and then on Cycle button, as shown in the screen shot below. When
the file names start to end at 2, stop by reclicking the Cycle button.
After all the png files are made we generate GIF file by the comand - convert *.png name.gif