Seeing a normal mode
Vibrations in a perfect crystal are relatively easy to picture as organized waves. In amorphous materials, the atomic motions can be much less intuitive.
I developed a Python script that interfaces with OVITO to animate the motion associated with a vibrational mode, given particle positions and the mode’s displacement pattern. The visualization helps connect mathematical eigenvectors with the physical motion of the atoms.
The original example below shows a vibrational mode in amorphous silicon. The motion is periodic even though it is less spatially organized than a simple wave in a crystal.
Show the original vibrational-mode animation
