Gaussian

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Also search this wiki for 'g09' for a couple of more examples.

Contents

GaussView aka gview

 ssh -X sunetid@corn  # connect to corn with x11 forwarding
 module load gaussian  # load the gaussian module
 gview  # start up gview

You should see a graphical screen with a molecule on it. You can load gaussian .com files via File->Open

If you get some error about "display", likely your X11 forwarding isn't configured correctly.

There is another program called "gview" also installed on the system, so if you get the "graphical vi" text editor window, that's not the Gaussian gview. You probably forgot to load the module.

As of 2016-08-15 the GView errors out with an xcb errof with XQuartz v2.7.9 but it works fine with XQuartz 2.7.8

Gaussian

To start gaussian: 'module load gaussian', 'which g09'.

interactive example

bishopj@corn21:~$ module load gaussian
bishopj@corn21:~$ g09 az.com   
bishopj@corn21:~$ cat az.com
%chk=az
#P RB3LYP 6-31G(D) FOPT FREQ=ReadIsotopes

Azulene

0 1
C 0.0  0.0  2.7
C 0.0  0.0 -2.5
C 0.0 -1.2  1.9
C 0.0  1.2  1.9
C 0.0 -0.7  0.5
C 0.0  0.7  0.5
C 0.0 -1.6 -0.5
C 0.0  1.6 -0.5
C 0.0 -1.3 -1.9
C 0.0  1.3 -1.9
H 0.0  0.0  3.8
H 0.0  0.0 -3.6
H 0.0 -2.2  2.2
H 0.0  2.2  2.2
H 0.0 -2.7 -0.3
H 0.0  2.7 -0.3
H 0.0 -2.1 -2.6
H 0.0  2.1 -2.6

300 1.0 0.9804
12
12
12
12
12
12
12
12
12
12
1
1
1
1
1
1
1
1

bishopj@corn21:~$ ls -tlr az*
-rw------- 1 bishopj root         415 Oct 26  2006 az.com
-rw------- 1 bishopj operator  359570 Apr 15 20:06 az.log
-rw------- 1 bishopj operator 2985984 Apr 15 20:06 az.chk
bishopj@corn21:~$ 

job submission example

How to setup and run Gaussian (g09) calculation on Barley. Gaussian calculations must run on a single node.


Setup Gaussian Input (g09_example.com). Below is for O2. Make sure to specfiy %mem and %nproc. Here 4 processors and 8GB RAM (2GB/proc). %nproc must be equal or less then total number of processors on a single node (See Main Page#Technical_details). As of April 2012 max processors is 24.

%mem=8GB
%nproc=4
%chk=g09_example.chk
#t sp b3lyp/6-31g

This is an example gaussian job file

0 3
O 0.00000 0.0000 0.0000
O 1.22000 0.0000 0.0000


Setup Job Script: g09_example.script

Important parameter "#$ -pe shm 4" requests a single node with 4 processors. Change number to change number of requested processors. Match value in %nproc.

Line "#$ -N example" sets $JOB_NAME to be g09_example so only need to change name of gaussian input name in a single place.

#!/bin/bash
#$ -N g09_example
#$ -cwd
#$ -pe shm 4

module load gaussian
#set the Gaussian scratch directory to the job-specifc temp dir
export GAUSS_SCRDIR=$TMPDIR
g09 $JOB_NAME.com $JOB_NAME.log


Submit the script:

qsub g09_example.script

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