Jmol to display vibrational modes

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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