Gaussian

Description

According to the documentation of Gaussian, Gaussian 09 is a series of connected programs for performing semi-empirical molecular orbital, density functional, and ab initio calculations. It predicts energies, molecular structures, vibrational frequencies, and molecular properties.

Available Versions

  • gaussian/09 (default)

  • gaussian/09.lsm (license for the “lsm” group)

Serial Job Submission

submit_gaussian_serial.sh
#!/bin/bash
#SBATCH -J gaussian_serial
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -t 05:00:00
#SBATCH --mem=8G

export INPUT="water.com"
export OUTPUT="water.log"

module load gaussian
job-nanny g09 water.com

SMP (OpenMP) Job Submission

submit_gaussian_smp.sh
#!/bin/bash
#SBATCH -J gaussian_smp
#SBATCH -N 1
#SBATCH -c 8
#SBATCH -t 12:00:00
#SBATCH --mem=32G

export INPUT="benzene.com"
export OUTPUT="benzene.log"

module load gaussian

# %NProcShared controls number of threads
sed -i "s/%NProcShared=[0-9]*/%NProcShared=$SLURM_CPUS_PER_TASK/" benzene.com

job-nanny g09 benzene.com

Job Submission with Linda (Distributed Parallel)

submit_gaussian_linda.sh
#!/bin/bash
#SBATCH -J gaussian_linda
#SBATCH -N 2
#SBATCH --ntasks-per-node=14
#SBATCH -t 48:00:00
#SBATCH --mem-per-cpu=4G

export INPUT="large.com"
export OUTPUT="large.log"

module load gaussian

# Configure Linda environment
. linda_set_env

# %NProcLinda controls total number of processes
sed -i "s/%NProcLinda=[0-9]*/%NProcLinda=$SLURM_NTASKS/" large.com

job-nanny g09 large.com

Example Input File (.com)

water.com
%Chk=water.chk
%Mem=8GB
%NProcShared=8
#P B3LYP/6-31G(d) Opt Freq

Water molecule optimization

0 1
O
H  1  0.96
H  1  0.96  2  104.5

water.com

--Link1--
%Chk=water.chk
#P B3LYP/6-311+G(2d,2p) Geom=Check Guess=Read

Single point with larger basis

0 1

Specific Properties Calculation

submit_gaussian_props.sh
#!/bin/bash
#SBATCH -J gaussian_props
#SBATCH -N 1
#SBATCH -c 8
#SBATCH -t 24:00:00
#SBATCH --mem=16G

export INPUT="nmr.com"
export OUTPUT="nmr.log"

module load gaussian
job-nanny g09 nmr.com
nmr.com
%Chk=nmr.chk
%Mem=16GB
%NProcShared=8
#P B3LYP/6-311+G(2d,p) NMR GIAO

NMR calculation

0 1
C   0.000   0.000   0.000
H   1.089   0.000   0.000
H  -0.363   1.026   0.000
H  -0.363  -0.513  -0.889
H  -0.363  -0.513   0.889

nmr.com

Job Array for Parameter Scan

submit_gaussian_array.sh
#!/bin/bash
#SBATCH -J gaussian_array
#SBATCH --array=1-5
#SBATCH -N 1
#SBATCH -c 8
#SBATCH -t 24:00:00
#SBATCH --mem=16G

# Different bond distances
DISTANCES=(1.0 1.2 1.4 1.6 1.8)
DIST=${DISTANCES[$SLURM_ARRAY_TASK_ID-1]}

export INPUT="template.com"
export OUTPUT="dist_${DIST}/"

module load gaussian

mkdir -p dist_${DIST}
cd dist_${DIST}

# Modify distance in input file
sed "s/DIST_VALUE/$DIST/g" ../template.com > input.com

job-nanny g09 input.com

Excited States Calculation (TD-DFT)

submit_gaussian_tddft.sh
#!/bin/bash
#SBATCH -J gaussian_tddft
#SBATCH -N 1
#SBATCH -c 8
#SBATCH -t 36:00:00
#SBATCH --mem=32G

export INPUT="tddft.com"
export OUTPUT="tddft.log"

module load gaussian
job-nanny g09 tddft.com
tddft.com
%Chk=tddft.chk
%Mem=32GB
%NProcShared=8
#P B3LYP/6-31+G(d) TD=(NStates=10,Root=1) Freq

TD-DFT calculation

0 1
C   0.000   0.000   0.000
C   1.400   0.000   0.000
H  -0.550   0.940   0.000
H  -0.550  -0.940   0.000
H   1.950   0.940   0.000
H   1.950  -0.940   0.000

tddft.com

References

See also