Useful input/output tools
These tools were written for Gaussian.1 They work for me; they may not work for you. 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
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-generate-supporting-information). All scripts generally work in format of
with the exception of
g09-mulliken-charges.zsh, which can take a second argument of the atom whose Mulliken charge you wish to obtain.
|XYZ cartesian coordinates of converged geometry|
|Check point file name|
|Full point group|
|Used to format the null result of each of these tests|
|Electronic energy after SDF is done|
|Generation of supporting information into a hybrid HTML/MultMarkdown document|
|Lowest converged imaginary frequency|
|Generation of all of this information into a |
|Mean of the alpha and beta electrons|
|Grab the Mulliken charges of a molecule|
|Molecular Mechanics sanity Check: sum of all charges|
|Molecular Mechanics sanity Check: sum of all atom charges|
|Number of basis functions|
|Number of imaginary frequencies in converged geometry|
|ONIOM extrapolated energy|
|Organize the completed jobs on a server into those that terminated correctly and those that haven’t|
|Grab the revision of Gaussian used to run the job|
|Route information of input file|
|Spin contamination after annihilation|
|Spin contamination before annihilation|
|Sum of electronic and thermal energies|
|Sum of electronic and thermal enthalpies|
|Sum of electronic and thermal free energies|
|Sum of electronic and zero-point energies|
|Title Card of input file|
I typically stay on the bleeding edge of computing. I created these on OS X 10.9 and have tested them using the following:
|GNU awk||>= 4.1.0|
|Gaussian||== Gaussian 09, Revision C.01 (there is β support for Rev. D.01)|
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.
Add it to your toolbox; If not, open an issue!
The author(s) of this toolset should be contacted via the issue tracker.
an electronic structure program for computational chemistry ↩