Appendix: How to use V_Sim
V_Sim is a visualization software for periodic systems, which can be
used to nicely visualize phonons. In this tutorial we will only discuss
the most important settings, for more information please visit
Open V_Sim by typing:
ANIMATION_FILE is one of your
files. Then you should see the following two windows:
Now you can see one unit cell, where the two Si atoms are shown as two large green spheres. In the visualization window (first) you can rotate the cell by using the left mouse button and zoom by using the mouse wheel. First, you should reduce the size of the spheres for Si atoms and show also bonds between Si atoms.
The most important elements of the initial setting window are marked in the Figure below and are explained in the follwoing.
(a) Here you can change the tool. After starting V_Sim you will always see the tool set element characteristics.
(b) Here you can specify for which element you want to modify the appearance. In our case we only have Si atoms, so you do not need to change something here.
(c) Here you can change the color of the spheres.
(d) Here you can change the radius of the spheres.
(e) Click on that checkbox to activate the visualization of bonds.
(f) Here you can open the settings window for bonds between atoms. This window is shown in the next figure. You can specify the range of Si-Si distances for which a bond is shown (h, i), the color (j) and the thickness (k) of the bonds.
(g) Here you can quit the whole program.
Next, you should not only visualize the unit cell but a larger supercell. Therefore, you first have to switch to the tool geometry operations (see next two figures). Then, click on the checkbox expand nodes (l) and increase the numbers of dx, dy, and dz to 1 (m-o).
Now, switch to the tool phonons. You can select a phonon mode by clicking in the respective line, i.e., you can show phonon mode 3 by clicking at q. To play the animation of the selected phonon mode click the button at t. If you want to see also arrows for the atomic displacements, click on the checkbox at p. In addition, you can also change the frequency (r) and the amplitude (s) of the animation.