Gaussian Example
Author: Sina G. Lewis
To help familiarize the user with Gaussian, I have put together a page with all of the knowledge needed to run a simple calculation for anthracene.
Gaussian is installed as a module on the university’s high performance computing (HPC) system, Alpine. See the CURC page if you are new to HPC. There are two files that are important for getting started: the input file and the sbatch file.
Although Gaussian can be run entirely within an interactive session (via the command ‘acompile’ followed by ‘module load gaussian’), for multiple or longer jobs we want to submit it through a sbatch script. An example sbatch script has been uploaded for reference. The majority of the file handles telling Slurm the requested details for running the calculation (length of time, account to use, number of nodes…) or moving files around to places convenient for running the calculation (e.g. so we don’t run out of space in our project or home directory due to intermediate files). The most important lines specific to a Gaussian calculation are
module purge
module load gaussian
g16 <${JOBNAME}.in >${JOBNAME}.log
these lines, in order, clear any extraneous modules loaded on the CPUs to avoid any strange behaviour, load Gaussian so we can run the program, and then run the program with the details specified in our input file while printing the output to a sensibly named log file.
The ${JOBNAME}.in file we feed into Gaussian has a somewhat straightforward structure, as long as what you want to do isn’t too complex. For our anthracene example, let’s say we want to simply relax the geometry to find the ground state structure. The file begins with some optional lines starting with % indicating if we’re going to read in from any previous calculations or want to save some intermediate files. Most frequently you will specify the name of the checkpoint file via %Chk=chkpointName so that you can start a new calculation from the old one. The immediate next line begins with a # and is called the route section. For all calculations, this line should specify the desired density functional method and basis set. If no basis set is specified, Gaussian will default to STO-3G for most calculations. There does not seem to be a specified default density functional. This section is ‘blank line terminated’ meaning you can break it up between lines and MUST have a blank line before the next section. Following the blank line is our title section. As the name suggests, you should put a short line here that gets printed in various output files to help you identify the calculation that the file came from. The title is also blank line terminated and is followed by information about the molecule you are interested in calculating. The molecule section is again blank line terminated, so most of your calculations should end with a blank line or the calculation will crash. The first line of the molecule section should specify the charge (typically 0) and the multiplicity (typically 1). The following lines are xyz file format style information about the molecule.
Our example input file, following the instructions above, looks like this
%Chk=opt
#p B3LYP/aug-cc-pVDZ Opt
Optimize an anthracene molecule using the hybrid density functional B3LYP
and the basis set cc-pVDZ (correlation consistent double zeta) that has been *aug*mented with diffuse functions.
0 1
C 10.78830 5.60957 26.31730
C 9.92421 6.47424 25.63038
C 12.00347 5.21621 25.73742
C 10.27019 6.93771 24.33700
C 11.47751 6.53025 23.74973
C 12.35030 5.68044 24.44474
C 12.88610 4.37527 26.43378
C 14.10475 4.00577 25.85792
C 14.44717 4.46338 24.58321
C 13.57402 5.29381 23.87450
C 8.72180 6.89549 26.21979
C 7.87542 7.77343 25.53757
C 8.21584 8.23016 24.26138
C 9.40604 7.81226 23.65865
H 8.44182 6.55450 27.20957
H 6.95432 8.10375 26.00104
H 7.55741 8.91257 23.73981
H 9.65406 8.17971 22.66967
H 10.52354 5.25562 27.30812
H 13.85852 5.64034 22.88784
H 15.39452 4.17703 24.14417
H 12.63870 4.01237 27.42454
H 14.78634 3.36575 26.40315
H 11.74398 6.88702 22.76106
To use the checkpoint file that we saved, and demonstrate another feature of Gaussian, we can take our new anthracene structure and ask to obtain information needed for calculating the absorption spectra. We can use the same sbatch file, just changing the JOBNAME variable if you wish, and the following input file
%OldChk=opt
%Chk=TD-root0
#p B3LYP/aug-cc-pVDZ Freq(HPModes,SaveNM) TD(NStates=20,Root=0) Guess=Check Geom=AllCheck
Because we have used the keyword/option combo Geom=AllCheck, Gaussian will look in the file opt.chk for all the information it needs about the geometry. To highlight some of the other options, we have asked Gaussian to perform a frequency calculation, saving the normal modes and keeping the values of the modes to high precision. We want to solve for 20 excited states with TD-DFT, specifying the ground state as the state of interest. And we want to pull the initial guess for the Hartree-Fock wavefunction from the checkpoint file.
Running this again, specifying state 1 as the state of interest gives us everything we need for a rudimentary absorption spectra calculation. To use the output files (i.e the *.chk files) with other programs, we need to ask Gaussian to format them. I typically wait for the calculations to finish after submitting them with the sbatch file and then load up Gaussian in an acompile session. We use the formchk command to get the formatted checkpoint file, if no output filename is given the default is the name of the checkpoint file with the extension .fchk.
acompile
module load gaussian
formchk CHECKPOINT
These files can be given to the tools packaged with FCClasses3 to calculate a one-photon absorption spectra using the vertical gradient method (see the FCClasses3 tutorial).