Skip to main content

Job submission

Submit a job on Fornax​

Prepare inputs​

  • Submission script: PBS Pro (job scheduling system) for the relaxations of initial and final images
#!/bin/sh --login
#PBS -N Relaxation #job name
#PBS -l walltime=72:00:00 #time request hr:min:sec
#PBS -q largemem #queue, can be checked using qstat -q
#PBS -j oe # generate standard output (*.o[JOBID]) and error (*.e[JOBID])
#PBS -l select=16:ncpus=8:mpiprocs=8 #resource to be requested
#PBS -l place=excl # occupy the node exclusively

module load vasp/vasp.6.3.2 # load VASP to environment; module avail; module purge

#! DO NOT CHANGE THIS UNLESS YOU KNOW WHAT YOU'RE DOING
#export OMP_NUM_THREADS=1

cd ${PBS_O_WORKDIR} # $ means variable; ${PBS_O_WORKDIR} is your submission directory

# Recursive relaxation to get rid of pulay stress
echo `date` "Starting job ..." > status.txt
if [ ! -f vasprun.xml.relaxed.gz ]
then
  cp INCAR INCAR.orig
  cp POSCAR POSCAR.orig
  cp KPOINTS KPOINTS.orig
  echo `date` "Running VASP using 1 nodes..." >> status.txt
  mpiexec vasp_std  >& ${PBS_O_WORKDIR}/vasp.out # mpiexec execute VASP using MPI
  echo `date` `tail -n -1 OSZICAR` >> status.txt

  rel=`tail -1 OSZICAR | cut -c 1-4` # OSZICAR stores energies
  while [ ${rel} -ne 1 ]; do
    cp CONTCAR POSCAR
    rm WAVECAR CHG*
    echo `date` "Running VASP using 1 nodes..." >> status.txt
    mpiexec vasp_std  >& ${PBS_O_WORKDIR}/vasp.out
    echo `date` `tail -n -1 OSZICAR` >> status.txt
    rel=`grep -v '^$' OSZICAR| tail -1 | cut -c 1-4`
    if [ ${rel} -ne 1 ]
    then
	    echo `date` "No. of ionic steps ${rel} doesn't meet the requirement (=1), restarting ....." >> status.txt
    fi
  done

  if [ ${rel} -eq 1 ]
  then
    echo `date` "Calculation finished!" >> status.txt
    mv CONTCAR CONTCAR.relaxed
    mv DOSCAR DOSCAR.relaxed
    mv EIGENVAL EIGENVAL.relaxed
    mv IBZKPT IBZKPT.relaxed
    mv INCAR INCAR.relaxed
    mv KPOINTS KPOINTS.relaxed
    mv OSZICAR OSZICAR.relaxed
    mv OUTCAR OUTCAR.relaxed
    mv POSCAR POSCAR.relaxed
    mv PROCAR PROCAR.relaxed
    mv vasprun.xml vasprun.xml.relaxed
    mv vasp.out vasp.out.relaxed
    rm WAVECAR CHG*
    echo `date` "Ending job ..." >> status.txt
    gzip -f  * # compuress all files
    exit 0

  else
    echo `date` "Error or unfinished job!" >> status.txt
    exit 1
  fi

else
  echo `date` "vasprun.xml.relaxed.gz exist, skip this calculation ....." >> status.txt
  exit 0
fi

NEB Job (after relaxation of initial and final images)​

Difference compared to a regular VASP calculation​

  • You should use a different VASP binary in script folder

Directory​

  • NEB_ROOT- initial / final: relaxations of initial and final images
  • 00 01 02 ... N_images-1 : NEB images to be created by interpola3.py
  • submission_script for NEB : this should be put in the NEB_ROOT directory
  • INCAR POTCAR KPOINTS are put in the NEB_ROOT directory while POSCARs are put in image folder
  • standard outputs for each image can be found in each image folder
#!/bin/sh --login
#PBS -N NEB #job name
#PBS -l walltime=24:00:00 #time request hr:min:sec, for NSCC 24hrs maximum
#PBS -P [PROJECT_CODE] # Project code
#PBS -l select=[N_image*Resource_each_image]:ncpus=24:mpiprocs=24 #resource to be requested

#! DO NOT CHANGE THIS UNLESS YOU KNOW WHAT YOU'RE DOING
#export OMP_NUM_THREADS=1
VASP=xxxx # the place for VASP binary (NEB version) vasp_std
cd ${PBS_O_WORKDIR} # $ means variable; ${PBS_O_WORKDIR} is your submission directory

mpirun ${VASP}  >& ${PBS_O_WORKDIR}/vasp.out # run VASP-NEB

To do​

  • Use scp command upload initial and final folders to fornax or just use git clone on fornax
  • Be careful, you should remove CHG CHGCAR WAVECAR before commit and push to git repository
  • Relax initial and final images in test on fornax
  • Use interpola3.0.py to get interpolation