Gaussian
From FarmShare
Also search this wiki for 'g09' for a couple of more examples.
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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
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 g09 $JOB_NAME.com $JOB_NAME.log
Submit the script:
qsub g09_example.script
