Some preliminary work related to this was done. For Mopac and Spartan
files, vibration information is available via Jmol.js using the
jmolGetPropertyAsArray() function:
VibrationData = jmolGetPropertyAsArray("auxiliaryInfo").vibration
Then VibrationData[0] is the data for the first vibrational mode,
VibrationData[1] is the data for the second vibrational mode, etc.
Within each of those, [0] is for the first atom, [1] is for the second
atom, etc.
Within each of those, [0] is for x, [1] is for y, and [2] is for z
So the vibration vector for the 3rd vibrational mode, atomno=2 is
VibrationData[2][1][0],VibrationData[2][1][1],VibrationData[2][1][2]
Then you can do with that whatever you want. Similarly,
FrequencyData = jmolGetPropertyAsArray("auxiliaryInfo").VibFreqs
This could be expanded to the other model types easily enough if desired.
What file type are you using?
Bob
Sebastian Schwieger wrote:
>Dear jmol users and developers,
>
>can I write xyz coordinates of a molecule corresponding to a
>displacement along a vibrational mode?
>I can animate the vibration, but did not figure out how to export the
>animated structure. Actually, I don't need the animation, but the two
>structures corresponding to the largest amplitude.
>
>Any help is appreciated.
>
>Sebastian Schwieger
>
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--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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