Jmol to display vibrational modes

Jmol is a free, open souce software package that allows users to visualise atomic structures. This can be done using various different DFT, semi-empirical and molecular dynamics input files.

Jmol: http://jmol.sourceforge.net/

Known supported structure files

• VASP

POSCAR

CONTCAR

OUTCAR

• CRYSTAL

INPUT

Known supported vibrational mode files

• VASP

OUTCAR

vasprun.xml

Animate

Instructions of how to view and animate vibrational modes using Jmol.

• load <FILEPATH> {[int] [int] [int]}

FILEPATH - location of the file on your filespace.

{[int] [int] [int]} - supercell expansion of the input structure (e.g. {3 3 2}).

NOTE: Supercell expansions only appears to be possible when loading the file.

• Go to the toolbar->Tools->Vibrate->Start vibration

The vibrations can then cycled over by pressing the arrow buttons below the toolbar or in the Tools->Vibrate submenu.

Capture

Instructions of how to capture vibrational modes as images and then convert them to gifs

• Open the console in Jmol my going to the toolbar File->Console.
• Follow the instructions in the previous section to animate the vibrational mode you intend to capture.
• Run the following command in the console:

write VIBRATION n "IMAGE_FILENAME"

Here, n denotes the number of vibrational cycles to be captured.

IMAGE_FILENAME denote the prefix and suffix of the image files generated. For example, "test.gif" will generate a set of image files labelled test0000.gif, with the number incrementing for each image generated.

• In a terminal window, go to where these images have been generated.
• Run the following command:

convert -delay 5 -loop 0 PREFIX*.SUFFIX OUT_FILENAME

Here, your original IMAGE_FILENAME=PREFIX.SUFFIX.

OUT_FILENAME is the name of the output gif file you are generating from those images.

• Follow the link below for further information on capturing vibrational modes using Jmol:

https://chemapps.stolaf.edu/jmol/docs/index.htm?search=PNGT#writeimagesandframes

OLD METHOD BELOW

• To capture the animation as a gif, you can use the following commands.

To enter the commands go to File->Console in the toolbar.

Start the capture with the first command, stop it with the second.

capture "FILENAME" LOOP DELAY

CAPTURE END