MOPAC

In this section:

Description
Available Versions
Serial Job Submission
OpenMP Job Submission
Example Input File (.mop)
Main MOPAC Keywords
Thermodynamic Properties Calculation
Job Array for Conformational Scan
Molecular Orbital Calculation
Results Analysis
References

Description 

According to the page of MOPAC, MOPAC (Molecular Orbital PACkage) is a semi-empirical quantum chemistry program based on the NDDO approximation of Dewar and Thiel.

Available Versions 

mopac/17.162 (default)

Serial Job Submission 

submit_mopac_serial.sh

#!/bin/bash
#SBATCH -J mopac_serial
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -t 24:00:00
#SBATCH --mem=8G

export INPUT="benzene.mop"
export OUTPUT="benzene.out"

module load mopac

job-nanny MOPAC2012.exe benzene.mop

OpenMP Job Submission 

submit_mopac_omp.sh

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

export INPUT="large.mop"
export OUTPUT="large.out"

module load mopac

# MOPAC automatically uses threads
export OMP_NUM_THREADS=$SLURM_CPUS_PER_TASK

job-nanny MOPAC2012.exe large.mop

Example Input File (.mop)

benzene.mop

PM7 XYZ T=2H PRECISE
Benzene optimization

C     0.000000  1.396000  0.000000
C     1.209000  0.698000  0.000000
C     1.209000 -0.698000  0.000000
C     0.000000 -1.396000  0.000000
C    -1.209000 -0.698000  0.000000
C    -1.209000  0.698000  0.000000
H     0.000000  2.478000  0.000000
H     2.146000  1.239000  0.000000
H     2.146000 -1.239000  0.000000
H     0.000000 -2.478000  0.000000
H    -2.146000 -1.239000  0.000000
H    -2.146000  1.239000  0.000000

Main MOPAC Keywords 

Common keywords
Keyword	Description
`PM6`, `PM7`	Semi-empirical method
`AM1`	Austin Model 1
`MNDO`	Modified Neglect of Diatomic Overlap
`XYZ`	Coordinates in XYZ format
`OPT`	Geometry optimization
`FORCE`	Vibrational frequency calculation
`THERMO`	Thermodynamic property calculation
`T=2H`	Time limit (2 hours)
`PRECISE`	Stricter convergence criteria
`1SCF`	Single SCF calculation (no optimization)

Thermodynamic Properties Calculation 

submit_mopac_thermo.sh

#!/bin/bash
#SBATCH -J mopac_thermo
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -t 12:00:00
#SBATCH --mem=8G

export INPUT="ethanol.mop"
export OUTPUT="ethanol.out"

module load mopac

job-nanny MOPAC2012.exe ethanol.mop

ethanol.mop

PM7 OPT FREQ THERMO XYZ T=1H
Ethanol thermochemistry

C     0.000000  0.000000  0.000000
C     1.528000  0.000000  0.000000
O     2.000000  1.320000  0.000000
H    -0.400000  1.010000  0.000000
H    -0.400000 -0.510000  0.890000
H    -0.400000 -0.510000 -0.890000
H     1.928000 -0.520000  0.880000
H     1.928000 -0.520000 -0.880000
H     2.970000  1.370000  0.000000

Job Array for Conformational Scan 

submit_mopac_array.sh

#!/bin/bash
#SBATCH -J mopac_array
#SBATCH --array=1-10
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -t 06:00:00
#SBATCH --mem=4G

ANGLES=$(seq 0 36 324)
ANGLE_ARRAY=($ANGLES)
ANGLE=${ANGLE_ARRAY[$SLURM_ARRAY_TASK_ID-1]}

export INPUT="template.mop"
export OUTPUT="angle_${ANGLE}/"

module load mopac

mkdir -p angle_${ANGLE}
cd angle_${ANGLE}

# Modify torsion angle
sed "s/DIHEDRAL_ANGLE/$ANGLE/g" ../template.mop > input.mop

job-nanny MOPAC2012.exe input.mop

template.mop

PM7 XYZ OPT T=1H
Dihedral scan at DIHEDRAL_ANGLE degrees

C   0.000000  0.000000  0.000000
C   1.540000  0.000000  0.000000
C   2.080000  1.430000  0.000000
H  -0.400000  1.030000  0.000000
H  -0.400000 -0.510000  0.890000
H  -0.400000 -0.510000 -0.890000
H   1.940000 -0.510000  0.890000
H   1.940000 -0.510000 -0.890000
H   2.080000  1.930000  0.890000
H   2.080000  1.930000 -0.890000
C   3.620000  1.430000  0.000000 DIHEDRAL_ANGLE

Molecular Orbital Calculation 

submit_mopac_orbitals.sh

#!/bin/bash
#SBATCH -J mopac_orbitals
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -t 04:00:00
#SBATCH --mem=4G

export INPUT="orbitals.mop"
export OUTPUT="orbitals.out"

module load mopac

job-nanny MOPAC2012.exe orbitals.mop

orbitals.mop

PM7 XYZ VECTORS ENPART
Molecular orbitals of benzene

C     0.000000  1.396000  0.000000
C     1.209000  0.698000  0.000000
C     1.209000 -0.698000  0.000000
C     0.000000 -1.396000  0.000000
C    -1.209000 -0.698000  0.000000
C    -1.209000  0.698000  0.000000
H     0.000000  2.478000  0.000000
H     2.146000  1.239000  0.000000
H     2.146000 -1.239000  0.000000
H     0.000000 -2.478000  0.000000
H    -2.146000 -1.239000  0.000000
H    -2.146000  1.239000  0.000000

Results Analysis 

analyze_mopac.sh

#!/bin/bash
#SBATCH -J analyze_mopac
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -t 00:30:00
#SBATCH --mem=2G

# Extract final energy
grep "FINAL HEAT OF FORMATION" *.out | awk '{print $6}' > energies.txt

# Extract optimized geometry
for out in *.out; do
    echo "Optimized geometry for $out:" >> optimized_geometries.txt
    awk '/CARTESIAN COORDINATES/,/CARTESIAN COORDINATES/ {
        if(NF==4 && $1!="CARTESIAN") print $0
    }' $out >> optimized_geometries.txt
    echo "" >> optimized_geometries.txt
done

# Extract frequencies
grep "FREQUENCY:" *.out > frequencies.txt

# Extract HOMO/LUMO orbitals
grep "HOMO LUMO" *.out | awk '{print $4, $6}' > homo_lumo.txt

References 

Documentation: http://openmopac.net/manual/
Tutorials: http://openmopac.net/manual/tutorials.html
Forum: http://openmopac.net/forum/