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VASP sbatch File
VASP Postprocessing
Gaussian sbatch File

VASP sbatch File

Used to submit a VASP calculation on the Research Computing cluster Alpine.

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#!/bin/bash

## Account_info

# SBATCH --account=ucb-general

## QoS_type

# SBATCH --qos=normal

## note: this one will be empty for shas nodes

## Partition_name

# SBATCH --partition=amilan

## Job_name

# SBATCH --job-name=vasp

# SBATCH -o o.%j                 # Name of stdout output file (%j expands to jobId)

# SBATCH -e e.%j                 # name of error file

## Number_of_nodes

# SBATCH --nodes=1-1

## Number_of_processors

# SBATCH --ntasks=12

### SBATCH --ntasks-per-socket=12

## Job_Wall_Time

# SBATCH --time=0:30:00

# SBATCH --mail-user= YOUR EMAIL HERE

### SBATCH --mail-type=BEGIN     # email me when the job starts, commented out

### SBATCH --mail-type=END       # email me when the job finishes, commented out

# SBATCH --mail-type=FAIL        # email me if the job fails

# SBATCH --export=NONE                   # for modules on new nodes

# load modules required for MPI and VASP

# CHECK THAT THESE MODULES MATCH YOUR INSTALLATION

module purge; module load intel/20.2  mkl/20.2  impi/19.8

# Create ECHO option if not already present

if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi

## useful directories

VASP_DIR=/projects/$USER/programs/summit_vasp.6.3.1_O2_intel20/bin/vasp_std
SUBM_DIR=$PWD # submitting directory
SCR_DIR=/scratch/summit/$USER/${SLURM_JOB_ID}

### make SCR_DIR for this job

mkdir -p -v ${SCR_DIR}

## Record calculation to jobs_log file

printf '%s\n' "${SLURM_JOB_ID}  ${SLURM_JOB_NAME}  $(date)  $HOSTNAME    ${SBATCH_ACCOUNT}  ${SUBM_DIR}" >> ~/jobs_log

StartTime=$( date +%s.%N ) # bash timing

## this clean_up function moves output to the submitting directory and

## cleans up scratch space

clean_up () {

    StopTime=$( date +%s.%N )
    printf "Elapsed(sec):  %.3F\n" $( $ECHO  "${StopTime}-${StartTime}"|bc ) >
    VASP_${SLURM_JOB_ID}_Timed.bash

    $ECHO
    $ECHO "Moving results to head node ${SUBM_DIR}..."
    mv -v $SCR_DIR/* $SUBM_DIR
    $ECHO "...done"

    wait

    rm -r -v -f ${SCR_DIR}

    $ECHO "... done"
    $ECHO
    $ECHO "Changing directory to ${SUBM_DIR}"
    cd ${SUBM_DIR}

    mv OUTCAR OUTCAR.${SLURM_JOB_ID}
    cp POSCAR POSCAR.${SLURM_JOB_ID}
    cp INCAR INCAR.${SLURM_JOB_ID}
    mv vasprun.xml vasprun.xml.${SLURM_JOB_ID}
    mv CONTCAR POSCAR

    if [ -f PROCAR ]; then
      ## because I can't figure out FORTRAN to save my life...:
      ## this line fixes spacing in the header of the PROCAR file
        sed -i "s/ion      s     py     pz     px    dxy    dyz    dz2   dxz    dx2    tot/ions   py        pz        px       dxy       dyz       dz2       dxz       dx2      tot/g" PROCAR
    fi

    $ECHO "...done"
    $ECHO
    $ECHO "over and out"
}

set -P; shopt -s extglob

cp -v ${SUBM_DIR}/!(o.${SLURM_JOB_ID}|e.${SLURM_JOB_ID}|README) ${SCR_DIR}
rm -v ${SUBM_DIR}/!(o.${SLURM_JOB_ID}|e.${SLURM_JOB_ID}|README)
cd ${SCR_DIR}

$ECHO
$ECHO
$ECHO "running vasp program..."

## run program

export OMP_NUM_THREADS=1
mpirun -np ${SLURM_NTASKS} ${VASP_DIR} > screen.${SLURM_JOB_ID}

$ECHO "vasp done... over and out"
 clean_up

if [ -s POSCAR ]; then
        : # do nothing
else
        cp POSCAR POSCAR.empty
        cp POSCAR.${SLURM_JOB_ID} POSCAR
fi

## sometimes, jobs aren't recorded into ~/jobs_log; check if this happens and append to

## end of file if so

vijID=$( grep "${SLURM_JOB_ID}" ~/jobs_log | cut -f1 -d' ' )
if [[ $vijID == ${SLURM_JOB_ID} ]]; then
        exit 0
else
        ## Record calculation to jobs_log file
        printf '\%s{\textbackslash}n' "${SLURM_JOB_ID}  ${SLURM_JOB_NAME}  $(date)  $HOSTNAME}
        ${SBATCH_ACCOUNT}  ${SUBM_DIR}" >> ~/jobs_log
fi

VASP Postprocessing

See the GitHub package VASP_postprocessing.jl for Julia and MATLAB code to assist in convergence and efficiency testing as well as various postprocessing code.

Gaussian sbatch File

Used to submit a Gaussian calculation on the Research Computing cluster Alpine.

View Contents

#!/bin/bash

# !/bin/bash

## Account_info

# SBATCH --account=ucb-general

## QoS_type

# SBATCH --qos=normal

## note: this one will be empty for shas nodes

## Partition_name

# SBATCH --partition=amilan # alpine

# SBATCH --constraint=ib    # use the infiniband

## Job_name

# SBATCH --job-name=g16

# SBATCH -o o.%j          # Name of stdout output file (%j expands to jobId)

# SBATCH -e e.%j    # name of error file

## Number_of_nodes

# SBATCH --nodes=1

## Number_of_processors

# SBATCH --ntasks=32

### SBATCH --ntasks-per-socket=16

## Job_Wall_Time

# SBATCH --time=04:00:00

# SBATCH --mail-user= YOUR EMAIL HERE

### SBATCH --mail-type=BEGIN               # email me when the job starts

### SBATCH --mail-type=END        # email me when the job finishes

# SBATCH --mail-type=FAIL     # email me if the job fails

# SBATCH --export=NONE                   # for modules on new nodes

# load modules required for MPI and VASP

module purge
module load gaussian/16_avx2

# Create ECHO option if not already present

if test "`echo -e`" = "-e" ; then ECHO=echo ; else ECHO="echo -e" ; fi

## useful directories

SUBM_DIR=$PWD # submitting directory
SCR_DIR=/scratch/alpine/$USER/${SLURM_JOB_ID}
JOBNAME=planar-root0-optGS  ## CHANGE TO MATCH YOUR INPUT FILE NAME

## Record calculation to jobs_log file

printf '%s\n' "${SLURM_JOB_ID}  ${SLURM_JOB_NAME}  $(date)  $HOSTNAME  ${SBATCH_ACCOUNT}  ${SUBM_DIR}" >> ~/jobs_log

StartTime=$( date +%s.%N ) # bash timing

## this clean_up function moves output to the submitting directory and cleans up scratch space

clean_up () {

 StopTime=$( date +%s.%N )
 printf "Elapsed(sec):  %.3F\n" $( $ECHO  "${StopTime}-${StartTime}"|bc ) > ${SLURM_JOB_ID}_Timed.bash

        $ECHO
 $ECHO "Moving results to head node ${SUBM_DIR}..."
 $ECHO "...done"

 wait

 $ECHO "... done"
 $ECHO
 $ECHO "Changing directory to ${SUBM_DIR}"

 $ECHO "...done"
 $ECHO
 $ECHO "over and out"
}

set -P; shopt -s extglob

$ECHO
$ECHO
$ECHO "running gaussian program..."

## run program

export OMP_NUM_THREADS=1
g16 <${JOBNAME}.in >${JOBNAME}.log

$ECHO "gaussian done... over and out"

clean_up

## sometimes, jobs aren't recorded into ~/jobs_log; check if this happens and append to end of file if so

vijID=$( grep "${SLURM_JOB_ID}" ~/jobs_log | cut -f1 -d' ' )
if [[ $vijID == ${SLURM_JOB_ID} ]]; then
        exit 0
else
        ## Record calculation to jobs_log file
        printf '%s\n' "${SLURM_JOB_ID}  ${SLURM_JOB_NAME}  $(date)  $HOSTNAME  ${SBATCH_ACCOUNT}  ${SUBM_DIR}" >> ~/jobs_log
fi