AViz is an atomistic simulation visualization softwareยน. It was developed in the Technion, IIT, Haifa. It accepts text files as input with a simple format of
<atom name> <x coordinate> <y coordinate> <z coordinate>and renders the files (usually representing crystals or other ordered structures) as a pseudo 3D image. The user can configure how to show the different atoms and bonds, and there also options for displaying the atom's spin (or other properties). Explicit examples of AViz files are available to download throughout the catalog.
AViz has a function for automatically capturing (auto-snap) an image of the rendering anytime any parameter changes (such as the point-of-view angle), thus making it easy to create movies (or .gif files) of looking around the structure. I used ffmpeg to transform the generated images (.png files) to a lightweight .mp4 file with the following command:
ffmpeg -i amorphous0%03d.png -c:v libx264 out.mp4assuming the names of the files follow the pattern amorphous0XXX.png. Since by default AViz divides the point-of-view angle to 360 parts (as in degrees), usually only 359 images are needed to create this kind of "surrounding" view.
Another important feature that used to generate animations of changing crystals is the file-list option of AViz. The program can accept a simple text file containing a list of .xyz files, and then show them (with the same rendering configurations) one by one. Which, in combination with the auto-snap, produces a list of images that can be combined to create the animated visualization. This used, for example, in the split-interstitial formation page in the catalog.