AViz

Visualization was essential for development of this project. Our computational physics group developed the Atomic Visualization package AViz [78]. This is a very powerful visualization tool which helps to enhance 3D perception. It includes various options, which let one to rotate the still sample, change relative sizes of atoms, create animations and movies, add and remove the bonds and borders of the sample, use color coding, slice the sample and much more.

The Atomic Visualization package (AViz) was used extensively in all stages of this work. A visualization of our amorphous carbon samples with color coding for different atomic bonding helped indentify clusters of either $sp^2$ or $sp^3$ coordinated atoms, rings, graphite-like planes. The animated vizualizations were created to keep track of the processes occuring inside the damaged region.