Job submission

Submit a job on Fornax

Prepare inputs

• Submission script: PBS Pro (job scheduling system) for the relaxations of initial and final images

Submission Script for Relaxation

#!/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

• Inputs: INCAR, POSCAR, POTCAR, KPOINTS
• Anything about VASP input can be found at: https://www.vasp.at/wiki/index.php/The_VASP_Manual
• submission: qsub [SUBMISSION_SCRIPT]
• monitor status: qstat -u [USERID]
• job details: qstat -f [JOBID]

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

Submission Script for NEB Calculation

#!/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