please send me a couple of files. Also, I just added vib reading to the
fchk reader.
On Wed, Aug 26, 2015 at 10:02 AM, Kubasik, Matthew A. <
mkuba...@fairfield.edu> wrote:
> Dear Bob,
>
> Could you and the Jmol development community consider adding the reading
> of “High Precision” modes (g09 option freq(HPModes)) to Jmol’s Gaussian
> file reader?
>
> Additionally, if the displacement vectors could be added to atom
> properties, that would be great!
>
> Currently, Jmol will reads this section of a Gaussian output file:
>
> 1 2 3
> A A A
> Frequencies -- 11.1381 12.4908 15.3386
> Red. masses -- 4.5657 4.9034 5.4670
> Frc consts -- 0.0003 0.0005 0.0008
> IR Inten -- 0.2569 0.0415 0.0019
> Atom AN X Y Z X Y Z X Y
> Z
> 1 6 0.01 0.01 0.01 0.04 0.02 0.10 0.09 -0.05
> -0.01
> 2 6 0.01 0.01 -0.02 0.00 -0.01 0.15 0.10 -0.03
> 0.01
> 3 1 0.03 0.00 -0.03 -0.02 0.00 0.17 0.08 -0.02
> 0.02
> 4 6 0.00 0.02 -0.03 0.00 -0.04 0.19 0.15 -0.02
> 0.01
> 5 1 0.01 0.02 -0.05 -0.03 -0.06 0.23 0.16 0.00
> 0.02
> 6 6 -0.02 0.03 -0.02 0.03 -0.05 0.17 0.18 -0.03
> -0.01
> …
>
> This provides atomic displacement properties, such as {model=m and
> atomno=n}.vxyz, as well as vX, vY, and VZ.
>
> The Gaussian formatting for HPModes is like this:
>
> 1 2 3 4 5
> A A A A A
> Frequencies --- 11.1381 12.4908 15.3386 18.8667 21.7801
> Reduced masses --- 4.5657 4.9034 5.4670 4.7261 4.7314
> Force constants --- 0.0003 0.0005 0.0008 0.0010 0.0013
> IR Intensities --- 0.2569 0.0415 0.0019 0.0809 0.0278
> Coord Atom Element:
> 1 1 6 0.00808 0.03641 0.08901 -0.04609 0.03999
> 2 1 6 0.00694 0.02030 -0.05281 0.01034 0.03379
> 3 1 6 0.01135 0.09711 -0.01221 -0.02791 -0.04076
> 1 2 6 0.01455 0.00394 0.10466 -0.01421 0.00668
> 2 2 6 0.00958 -0.00739 -0.03172 0.03848 0.01153
> 3 2 6 -0.01679 0.15117 0.00826 -0.07526 0.05221
> …
>
> Perhaps these data could be put into atomic properties of vHPxyz, vHPx,
> vHPy, and vHPz?
>
> I tried to extract HPmodes by using y.find() and y.replace and y.split()
> functions and for loops, etc, after loading the file into a variable, but I
> am confident that adding this feature to the native Gaussian file reader
> would be more elegant.
>
> Thoughts?
>
> Matt
>
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>
--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
Chair, Department 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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