Gaussian

If you want your jobs to run faster in the queue

#SBATCH -A mendoza_q

#SBATCH --exclude=amr-163,amr-178,amr-179

this should submit to our queue, exclude your buyin nodes and flip the jobs to run in the general partition, avoiding incurring cpu.

Submission files for the HPCC

Here is a script made to facilitate the submission of files into the supercomputers via SSH. Be aware that this script only works with files with the .gjf extension and is for the only purpose of submitting a job in Gaussian 16. 

if [ $# -eq 1 ]

then

filename=`basename $1 .gjf`

echo "#!/bin/bash --login

#SBATCH --time=120:00:00              # limit of wall clock time - how long the job will run (same as -t)

#SBATCH --nodes=1                     # number of different nodes - could be an exact number or a range of nodes                                        # (same as -N)

#SBATCH --ntasks=16                   # number of tasks - how many tasks (nodes) that you require (same as -n)

#SBATCH --cpus-per-task=2             # number of CPUs (or cores) per task (same as -c)

#SBATCH --mem-per-cpu=2G              # memory required per allocated CPU (or core) - amount of memory (in bytes)

#SBATCH --job-name \"$filename\"      # you can give your job a name for easier identification (same as -J)

module purge

module load Gaussian/16.C.01-AVX

g16<$filename.gjf>$filename.out" > $filename.slurm

sbatch $filename.slurm

exit 0

fi

Gaussian sample input file

This is an example of an input file with the method, basis set, and atomic coordinates inside.

%mem=48GB

%nprocshared=24

#p opt freq wb97xd/6-31+g(d,p)

int=(grid=ultrafine,acc2e=12) symm=veryloose

3-chloro-1,2-propylene oxide

0 1

 C                  2.14716100    0.31002500   -0.01534700

 H                  2.30058600    0.96110300   -0.87503900

 H                  2.98944200    0.22531700    0.66786000

 C                  0.78622300    0.07703500    0.48468500

 H                  0.65286800   -0.19089500    1.53225700

 C                 -0.37969000    0.76703200   -0.15991300

 H                 -0.19998500    0.90774200   -1.22654600

 H                 -0.56780400    1.73136800    0.31552400

 Cl                -1.89127900   -0.19637600    0.00342800

 O                  1.45680800   -0.90259900   -0.29110900

Gaussian sample input file for TS search 

An example input file with the method, basis set, and cartesian coordinates of guess transition state geometry.

%mem=48GB

%nprocshared=24

#p opt=(calcfc,ts,noeigentest) freq=noraman b3lyp/6-311+g(d,p)

int=(grid=ultrafine,acc2e=12) scf=(xqc,maxcycles=900)

CH3Cl and F- (as a nucleophile), SN2 reaction

-1 1

 C                 -0.20562177    0.11434441    0.03372112

 H                 -0.25495316   -0.95277573    0.09472169

 H                 -0.23654344    0.70325755    0.92653977

 H                 -0.12536850    0.59255073   -0.92010178

 Cl                -2.83805538    0.22659490   -0.13148507

 F                  1.81357399    0.02824485    0.16045052

Gaussian sample input file for IRC calculation

An example input file with the method, basis set, and cartesian coordinates of optimized transition state geometry (input for IRC calculation).

%mem=48GB

%nprocshared=24

#p irc=(calcall,maxpoints=1000) freq=noraman b3lyp/6-311+g(d,p)

int=(grid=ultrafine,acc2e=12) scf=(xqc,maxcycles=900)

SN2 reaction

-1 1

 C                 -0.20562177    0.11434441    0.03372112

 H                 -0.25495316   -0.95277573    0.09472169

 H                 -0.23654344    0.70325755    0.92653977

 H                 -0.12536850    0.59255073   -0.92010178

 Cl                -2.83805538    0.22659490   -0.13148507

 F                  1.81357399    0.02824485    0.16045052

Please follow the below DropBox link to get Hessian Matrix 

https://www.dropbox.com/s/9n8uatn7kintjkd/Hessian.pptx?dl=0

Run Gaussian through GaussView in a Desktop or Laptop:

A useful tutorial to learn the basics of GaussView and Gaussian can be found at https://barrett-group.mcgill.ca/tutorials/Gaussian%20tutorial.pdf 

Both GaussView and Gaussian should be installed in the same computer to run the calculations by this method. GaussView is a useful molecule building tool. It can be used to build molecules/materials, visualize the Gaussian files (input, output, checkpoint, MOs, cubes, etc.), and create input files (.gjf or .com extension) for running calculations. Highly recommended method for learning the basics quickly and effectively. There are many YouTube tutorials available on creating input files and running calculations using GaussView. This is a fairly straightforward approach. 

Run Gaussian through the High Performance Computing (HPC) Clusters

If only GaussView is installed in the Laptop/Desktop and the cluster/supercomputer (referred to as HPC) is used for running calculations, then follow this tutorial. 

One could run the calculations using the following steps. 

(1) Build the structure using GaussView, ChemCraft (we have license), or any opensource molecular builder. Save the structure as .gjf or .com file. 

(2) Transfer the input file to the HPC. Create a directory in HPC for the project and then create several sub-directories for running calculations. Only one Gaussian job can run at a time in any directory. 

(3) Run the calculation using the slurm file attached. Rename the input, output, job names in the slurm accordingly before running the calculations. Also, remember to allocate sufficient number of nodes (typically single node is used for Gaussian), number of processors, time, etc. 

(under construction. Will be updated soon).