HPC/Applications/g03

Introduction

Gaussian is an electronic structure program used by chemists, chemical engineers, biochemists, physicists and others for research in established and emerging areas of chemical interest.

Starting from the basic laws of quantum mechanics, Gaussian predicts the energies, molecular structures, and vibrational frequencies of molecular systems, along with numerous molecular properties derived from these basic computation types. It can be used to study molecules and reactions under a wide range of conditions, including both stable species and compounds which are difficult or impossible to observe experimentally such as short-lived intermediates and transition structures. This article introduces several of its new and enhanced features.

Version note

The current version on Carbon is Gaussian 03: IA32L-G03RevC.02 from 12-Jun-2004. This is a 32-bit version which supports shared memory for up to 4 processors, but Linda parallelization is not supported.

The purchase of Gaussian09 with a native 64bit version is in progress and might take another few months.

Status

Available to Argonne-affiliated users only.

Modules

• module:

module load g03

Job script

• job script template:

$G03_HOME/g03.job

Usage

The template script can be used for several jobs without re-editing. Input/Output files are normally derived from the job name, which can be up to 15 characters long and should not contain unusual characters. You can set it, along with your project name and the walltime limit on the command line:

qsub -A cnm1234 -N foo [-l walltime=hhh:mm:ss]  g03.job

... or you create one or more personal versions of this script with your account name and appropriate walltime defaults filled in, and name e.g. g03-short.job and g03-long.job. You can the use them as follows:

qsub -N struc1 g03-long.job
qsub -N struc2 g03-long.job
...

Operation

Upon job execution, the script reads the input file, interprets and modifies it as follows:

• Link0-commands %NProcShared=4 and %mem=2GB are inserted automatically.
• Checkpoint-files named in %chk directives are identified and copied into the compute node's job-specifc $TMPDIR. The %chk specification will be changed to include $TMPDIR. Note that this will be echoed in the g03 output as follows:

 %chk=/tmp/12345.mds01.teamhpccluster/test420.chk

Chk-file processing will be performed only for files within the current directory; to skip processing, specify a relative or absolute path, such as %chk=./name.chk

• At the end of the job, chk-files in $TMPDIR are moved to $PBS_O_WORKDIR.