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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