Re: [Jmol-users] Help on vibrations needed

[Bob H. <ha...@st...>]

> 
> 2. -my biggest problem: I had my output from another MD-program  
> converted into something similar to a g98 file, and it worked nicely 
> with jmol9, including the vibrations, but now with jmol10 it fails to 
> load in both the application and the applet.  So, what is the minimum 
> requirement for a gaussian.out file to be acknowledged by jmol. However, 
> the application does not show vibrations with the file above  
> (ch3oh_g94.out) either!

There were definitely some changes in the Jmol reading of Gaussian files that 
occurred recently, and yes, it broke just this sort of application. You have to 
understand that the Gaussian reader is sort of a fake. (No offense.) It's taking 
log output from Gaussian and pretending that's some real format. Of course, who 
knows how the next Gaussian version will change this. So I, too, was creating 
fake Gaussian files, and it broke my reader. (So for that application I'm just 
using the old applet for now.

Take a look at http://www.stolaf.edu/people/hansonr/jmol/inline/

The second example there involves a vibration in XYZ format. And the third 
example shows a multiple model version of the XYZ format. Combining those two 
ideas you should be all set. WAY easier than faking Gaussian output!

For example, if you clip the following into the XYZ format box and then "Use 
.loadInline()", you will see the first vibration going.

3
A    x y z  charge dx  dy dz
S -1.5 0 0   0     0  .10  0
C    0 0 0   0     0 -.10  0
S  1.5 0 0   0     0  .10  0
3
A    x y z  charge dx  dy dz
S -1.5 0 0   0     x .10 -.10  0
S  1.5 0 0   0     0  .10  0
3
A    x y z  charge dx  dy dz
S -1.5 0 0   0     0  .10  0
C    0 0 0   0     0 -.10  .10
S  1.5 0 0   0     0  .10  0

Then at the Script box below the third example, type

  model 2

and press "run"

similarly,

  model 3

  model 0





Bob Hanson





-- 

Robert M. Hanson, ha...@st..., 507-646-3107
Professor of Chemistry, St. Olaf College
1520 St. Olaf Ave., Northfield, MN 55057
mailto:ha...@st...
http://www.stolaf.edu/people/hansonr

"Imagination is more important than knowledge."  - Albert Einstein