Animate Modes

Animate the Vibrational Modes.

The orca_pltvib module is used in conjunction with gOpenMol, wxMacmolplt or Chemcraft to produce animations or plots of vibrational modes following a frequency run. The usage is simple and produce a 20 frames of animation.

Remember that there are 3N-1 vibrational modes, so to check the number of the frequency you want to animate, search in the output the VIBRATIONAL FREQUENCIES tag, and inspect the number of the frequency.

Isoprene molecule has 13 atoms so 39-1 vibrational modes.
grep -A 38 'IR ' isoprene.out #This will display in your screen all the vibrations.

orca_pltvib file.hess #freq #Generates the .xyz to see de vibration mode.

These are the output files from the numerical frequency analisis.

[emma@pople]$ ls
isoprene.gbw isoprene.out isoprene.xyz isoprene.hess isoprene.inp orca-4.2.0.pbs

Then let's check the vibration modes.

[emma@pople]$ grep -A32 'IR' isoprene.out
IR SPECTRUM
-------------
Mode freq(cm**-1)
-------------
6: 151.83 cm**-1
.
.
17: 935.31 cm**-1
.
19: 980.39 cm**-1

Generate the 17 mode of vibration.

[emma@pople]$ orca_pltvib isoprene.hess 17
This file is being recognized as a valid
Will plot 1 vibrations:
17
Creating: isoprene.hess.v017.xyz
[emma@pople]$ ls
isoprene.gbw isoprene.out isoprene.xyz isoprene.hess isoprene.inp orca-4.2.0.pbs isoprene.hess.v017.xyz

Visulize the vibration with wxmacmolplt

[emma@pople]$wxmacmolplt *hess.v017.xyz