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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.


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.

Supporting a cube file has so defendencies to many g03(g94/g98) applications.

test.chk =>(by formchk) test.fchk =>(cubegen) test.cube

How Jmol reduce these defendencies ?

  1. read *.chk/*.fchk direct generation of a cube/isosurface file.
  2. read a gaussian log file that has MOs and generate cube/isosurface.
    1. with GFINPUT or with IOP option(molden use it)
    2. GFINPUT IOP(6/7=3) vs GFPRINT IOP(5/33=1)
    3. Please see also