View source for Gaussian

=== Jmol for Gaussian ===

Most Gaussian releases are supported (94, 98, 03), and the IO reads the all structures, sequentially, and some additional information.

Since this can result in a large amount of structures, they are collected into groups of atom sets, most easily selected using the [[AtomSetChooser]].

=== Multiple Link Calculations ===

Every calculation is collected in its own branch in the [[AtomSetChooser]].

=== Geometry Optimizations ===

In case of a geometry optimization, all structures associated with the optimization trajectory are read.

This gives rise to one branch per the type of orientation encountered. Each step in the trajectory will be represented in all branches.

Additional information interpreted per step:
* Energy
* S**2
* Convergence
* -V/T

=== Geometry Scans ===

In case of a geometry scan, the initialization orientation(s) are in their own branch as are the results of each scan point. The scan point branches are similar to those of a regular geometry optimization.

Because Gaussian outputs the orientation(s) of the last scan point after it is done, one ends up with one branch more than expected. No SCF output information is given after that calculation, so I gave it the name "Last read atomset."

=== IR Calculations ===

When frequencies are encountered the orientations are stored in their sub branches, and a new branch containing all the frequencies is generated.

Depending on how the calculation was set up, one or more frames may be present before the first vibration is encountered. Again, maneuvering through all this is most easily done using the [[AtomSetChooser]].

Additional information interpreted with each vibration:
* Frequency
* IR Intensity
* Reduced Mass
* Force Constant
* Energy

=== Partial Charges ===

When partial charges are encountered, they are assigned to the last atom set. So if more than one orientation was associated with the calculation, only the last one will show the charges.

=== Orbitals ===

Orbital information written in a cube file will be read and displayed by Jmol.
The normal procedure is to use a keyword like Pop=Full and have a checkpoint file written: %chk=file.chk
Then use the Gaussian utility to convert the chk file into a formatted file: formchk file.chk file.fchk
From this file a cube file is generated for a particular orbital: cubegen 0 mo=5 file.fchk file5.cube
The latter is read by Jmol, optionally gzipped.
The contour level is included in the Jmol instruction:
load file5.cube;
isosurface posname 0.05 "file5.cube";
isosurface negname -0.05 "file5.cube";
to display both phases of the MO.