Useful tools written for Gaussian (an electronic structure program for computational chemistry)
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README.md Add title Jun 4, 2015
g09-cartesians.py Initial commit Mar 11, 2014
g09-check-point-file-name.zsh Ensure that a filename with spaces will work Aug 19, 2014
g09-converged-point-group.zsh
g09-data-test.zsh Initial commit Mar 11, 2014
g09-electronic-energy-after-SDF-is-done.zsh Fixed GAUSSIAN_TOOLS_DIRECTORY env variable Apr 14, 2014
g09-generate-supporting-information.zsh Update supporting information file to accept files Jul 29, 2014
g09-lowest-imaginary-frequency.zsh Ensure that a filename with spaces will work Aug 19, 2014
g09-make-data.zsh Don't move files by default after making data Jul 29, 2014
g09-mean-of-alpha-and-beta-electrons.zsh
g09-mm-sanity-check--sum-of-all-charges.zsh Ensure that a filename with spaces will work Aug 19, 2014
g09-mm-sanity-check--sum-of-atom-charges.zsh Ensure that a filename with spaces will work Aug 19, 2014
g09-mulliken-charges.zsh Use BSD tail Sep 9, 2014
g09-mulliken-data.zsh Add mulliken-data Sep 9, 2014
g09-number-of-basis-functions.zsh Ensure that a filename with spaces will work Aug 19, 2014
g09-number-of-imaginary-frequencies.zsh Ensure that a filename with spaces will work Aug 19, 2014
g09-oniom-extrapolated-energy.zsh Ensure that a filename with spaces will work Aug 19, 2014
g09-organize-data.zsh Unarchive didn't work... Just do it manually. Apr 4, 2014
g09-revision.zsh Grab the revision of Gaussian used to run the job Aug 19, 2014
g09-route-section.zsh Grab the route section of a job Aug 19, 2014
g09-spin-contamination-after-annihilation.zsh Ensure that a filename with spaces will work Aug 19, 2014
g09-spin-contamination-before-annihilation.zsh
g09-stoichiometry.zsh Ensure that a filename with spaces will work Aug 19, 2014
g09-sum-of-electronic-and-thermal-energies.zsh
g09-sum-of-electronic-and-thermal-enthalpies.zsh Ensure that a filename with spaces will work Aug 19, 2014
g09-sum-of-electronic-and-thermal-free-energies.zsh
g09-sum-of-electronic-and-zero-point-energies.zsh Ensure that a filename with spaces will work Aug 19, 2014
g09-title-card.zsh

README.md

Gaussian Tools

These tools were written for Gaussian. They work well for me; they may not work for you depending on your current Gaussian version and shell configuration. Since using this scripts can have a HUGE impact on your research, please have a look at each of them to fully understand the implications of utilizing them in your work flow. That being said, I use them personally and have tested them to the best of my ability/experience. Of course, if you find a better way to do things then by all means share by opening an issue! I currently use them to extract data from output files and to tweak input files of larger jobs.

These scripts may be used individually or with one another. For example, if you are interested in the lowest imaginary frequency, you would run

g09-lowest-imaginary-frequency.zsh "foo.out"

and the pertinent data point would be output to the command line. Alternatively, if you wish to aggregate data into a csv file for further analysis with a spreadsheet program you could utilize several of the scripts together (for an example of how to integrate the individual scripts with one another, see g09-make-data and g09-generate-supporting-information). All scripts generally work in format of

g09-foo.zsh "bar.out"

with the exception of g09-mulliken-charges.zsh, which can take a second argument of the atom whose Mulliken charge you wish to obtain.

Tools

Command Description
g09-cartesians XYZ cartesian coordinates of converged geometry
g09-check-point-file-name Check point file name
g09-converged-point-group Full point group
g09-data-test Used to format the null result of each of these tests
g09-electronic-energy-after-SDF-is-done Electronic energy after SDF is done
g09-generate-supporting-information Generation of supporting information into a hybrid HTML/MultMarkdown document
g09-lowest-imaginary-frequency Lowest converged imaginary frequency
g09-make-data Generation of all of this information into a csv file for further analysis
g09-mean-of-alpha-and-beta-electrons Mean of the alpha and beta electrons
g09-mulliken-charges Grab the Mulliken charges of a molecule
g09-mm-sanity-check--sum-of-all-charges Molecular Mechanics sanity Check: sum of all charges
g09-mm-sanity-check--sum-of-atom-charges Molecular Mechanics sanity Check: sum of all atom charges
g09-number-of-basis-functions Number of basis functions
g09-number-of-imaginary-frequencies Number of imaginary frequencies in converged geometry
g09-oniom-extrapolated-energy ONIOM extrapolated energy
g09-organize-data Organize the completed jobs on a server into those that terminated correctly and those that haven't
g09-revision Grab the revision of Gaussian used to run the job
g09-route-section Route information of input file
g09-spin-contamination-after-annihilation Spin contamination after annihilation
g09-spin-contamination-before-annihilation Spin contamination before annihilation
g09-stoichiometry Stoichiometry
g09-sum-of-electronic-and-thermal-energies Sum of electronic and thermal energies
g09-sum-of-electronic-and-thermal-enthalpies Sum of electronic and thermal enthalpies
g09-sum-of-electronic-and-thermal-free-energies Sum of electronic and thermal free energies
g09-sum-of-electronic-and-zero-point-energies Sum of electronic and zero-point energies
g09-title-card Title Card of input file

Compatibility

I typically stay on the bleeding edge of computing. I created these on OS X 10.9 and have tested them using the following:

Program Version
zsh >= 5.0.2
python == 2.7.5
GNU awk >= 4.1.0
Gaussian == Gaussian 09, Revision C.01 (there is β support for Rev. D.01)

Future work

There are currently plans to incorporate the above abilities to output from the formchk utility Gaussian provides. The rationale is that the output from that utility will not change between revisions of Gaussian, making the scripts far more reliable, faster to use and easier to maintain.

Like it?

Add it to your toolbox; If not, open an issue!

Author(s)

The author(s) of this toolset should be contacted via the issue tracker.