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:

figure opening_list.png
we can edit the figure's appearance - change the atom color, bond length and more:
figure edit.jpg
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.
figure gen_png.jpg
After all the png files are made we generate GIF file by the comand - convert *.png name.gif
CdSe QD simulation