Scripts

Example submission scripts for NUS HPC

atlas9 CPU node

#!/bin/bash
#PBS -j oe
#PBS -N jobname
#PBS -q parallel20
#PBS -l select=1:ncpus=20:mem=120gb
#PBS -l walltime=720:00:00
#-----------------------------------
## things you need to check
export VASPEXE="vasp_gam"
export VASP_FOLDER=/home/svu/NUSID/app/vasp/tiger2/bin/
export OMP_NUM_THREADS=1
cd ${PBS_O_WORKDIR}
source /etc/profile.d/rec_modules.sh
# geom relaxi
module load xe_2018
export LD_LIBRARY_PATH=$MKLROOT/lib/intel64:$LD_LIBRARY_PATH
cd ${PBS_O_WORKDIR}
lscpu | grep avx
if [ $? -eq 0 ]
then
export vasproot=$VASP_FOLDER/tiger2/bin/$VASPEXE
fi
lscpu | grep avx2
if [ $? -eq 0 ]
then
export vasproot=$VASP_FOLDER/atlas8/bin/$VASPEXE
fi
lscpu | grep avx512
if [ $? -eq 0 ]
then
export vasproot=$VASP_FOLDER/atlas9/bin/$VASPEXE
fi
echo `date` "Starting relaxation ..." >> status.txt
if [ ! -f vasprun.xml.relaxed.gz ]
then
if [ ! -s POSCAR.orig ]
then
  echo `date` "Backuping POSCAR to POSCAR.orig ....." >> status.txt
  cp POSCAR POSCAR.orig
fi
if [ -s CONTCAR ]
then
  echo `date` "Found CONTCAR... Copying CONTCAR to POSCAR and continuing relaxation ...." >> status.txt
  cp CONTCAR POSCAR
fi  
echo `date` "Running VASP" >> status.txt
mpirun -n 20 $vasproot >> vasp.out
echo `date` `tail -n -1 OSZICAR` >> status.txt
rel=`tail -1 OSZICAR | cut -c 1-4`

grep "Inconsistent Bravais lattice types found for crystalline" OUTCAR
if [ $? -eq 0 ]
then
  echo "SYMPREC = 1e-08" >> INCAR
fi
while [ ${rel} -gt 10 ]; do
  cp CONTCAR POSCAR
  rm WAVECAR CHG*
  echo `date` "Running VASP " >> status.txt
  mpirun -n 20 $vasproot >> vasp.out
  echo `date` `tail -n -1 OSZICAR` >> status.txt
  rel=`grep -v '^$' OSZICAR| tail -1 | cut -c 1-4`
  if [ ${rel} -gt 10 ]
  then
          echo `date` "No. of ionic steps ${rel} doesn't meet the requirement (<10), restarting ....." >> status.txt
  fi
done
if [ ${rel} -le 10 ]
then
  echo `date` "Relaxation 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  *
  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

volta GPU node

#!/bin/bash
#PBS -P volta_pilot
#PBS -j oe
#PBS -N jobname
#PBS -q volta_gpu
#PBS -l select=1:ncpus=10:mem=95gb:ngpus=2
#PBS -l walltime=72:00:00
#-----------------------------------
## things you need to check
export OMP_NUM_THREADS=4 # use omp=5 with great care! use `top -d 0.5` to see if the CPU percentage ever go above 100%. IF it >isrunning sometimes at around 400% sometimes, then it is working probably
export CONTAINER_PATH=/hpctmp/NUSNETID/container/nushpc_volta_nvhpc24.3_cuda12.3_6.4.3.sif
# change the directory to your sif container
export VASP_EXE_LOW=/opt/vasp.6.4.3/bin/vasp_gam
export VASP_EXE_HIGH=/opt/vasp.6.4.3/bin/vasp_std
#-----------------------------------
## parameters that generally don't need to change
export OMPI_MCA_hwloc_base_binding_policy=none
export OMP_STACK_SIZE=4096m
cd ${PBS_O_WORKDIR}
echo `date` "Starting relaxation ..." >> status.txt
if [ ! -f vasprun.xml.relaxed.gz ]
then
if [ ! -s POSCAR.orig ]
then
  echo `date` "Backuping POSCAR to POSCAR.orig ....." >> status.txt
  cp POSCAR POSCAR.orig
fi
if [ -s CONTCAR ]
then
  echo `date` "Found CONTCAR... Copying CONTCAR to POSCAR and continuing relaxation ...." >> status.txt
  cp CONTCAR POSCAR
fi  

grep "NSW = 400" INCAR
if [ $? -eq 0 ]  
then
  echo `date` "Copying CONTCAR to POSCAR and continuing relaxation with ENCUT=400" >> status.txt
  singularity exec ${CONTAINER_PATH} mpirun -n 2 $VASP_EXE_LOW >> vasp.out
  echo `date` `tail -n -1 OSZICAR` >> status.txt
  rel=`tail -1 OSZICAR | cut -c 1-4`
  while [ ${rel} -gt 10 ]; do
  echo `date` "Copying CONTCAR to POSCAR and continuing relaxation with ENCUT=400" >> status.txt
  cp CONTCAR POSCAR

  echo `date` "Running VASP with low precision: ENCUT=400 and KPOINTS=4, this aims for a fast relaxation. Will be switching to >higher precision" >> status.txt

  grep "Inconsistent Bravais lattice types found for crystalline" OUTCAR
  if [ $? -eq 0 ]
  then
      echo "Inconsistent lattice types error, add SYMPREC=1e-08" >> status.txt
      echo "SYMPREC = 1e-08" >> INCAR
  fi
  singularity exec ${CONTAINER_PATH} mpirun -n 2 $VASP_EXE_LOW >> vasp.out
  echo `date` `tail -n -1 OSZICAR` >> status.txt
  rel=`tail -1 OSZICAR | cut -c 1-4`
  if [ ${rel} -gt 10 ]
  then
      echo `date` "No. of ionic steps ${rel} doesn't meet the requirement (<10), restarting ....." >> status.txt
  fi
  done
  if [ ${rel} -le 10 ]
  then
  echo `date` "the ionic steps take less than 10 steps to converge. Now switch to high precision mode."
  sed 's/ENCUT = 400/ENCUT = 520/g' INCAR > INCAR.tmp
  cp INCAR.tmp INCAR
  cp ../KPOINTS.precise KPOINTS
  else
  echo `date` "Error or unfinished job!" >> status.txt
  exit 1
  fi
fi  
echo `date` "Running VASP with high precision" >> status.txt
singularity exec ${CONTAINER_PATH} mpirun -n 2 $VASP_EXE_HIGH >> vasp.out
echo `date` `tail -n -1 OSZICAR` >> status.txt
rel=`tail -1 OSZICAR | cut -c 1-4`
grep "Inconsistent Bravais lattice types found for crystalline" OUTCAR
if [ $? -eq 0 ]
then
  echo "Inconsistent lattice types error, add SYMPREC=1e-08" >> status.txt
  echo "SYMPREC = 1e-08" >> INCAR
fi
while [ ${rel} -gt 10 ]; do
  cp CONTCAR POSCAR
  rm WAVECAR CHG*
  echo `date` "Running VASP " >> status.txt
  singularity exec ${CONTAINER_PATH} mpirun -n 2 $VASP_EXE_HIGH >> vasp.out
  echo `date` `tail -n -1 OSZICAR` >> status.txt
  rel=`grep -v '^$' OSZICAR| tail -1 | cut -c 1-4`
  grep "Inconsistent Bravais lattice types found for crystalline" OUTCAR
  if [ $? -eq 0 ]
  then
  echo "Inconsistent lattice types error, add SYMPREC=1e-08" >> status.txt
  echo "SYMPREC = 1e-08" >> INCAR
  fi
  if [ ${rel} -gt 10 ]
  then
      echo `date` "No. of ionic steps ${rel} doesn't meet the requirement (<10), restarting ....." >> status.txt
  fi
done
if [ ${rel} -le 10 ]
then
  echo `date` "Relaxation 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  *
  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

Submission scripts for ALF project on NUS HPC

Submission script for running VASP single point calculation using GPU

#!/bin/bash
#PBS -P volta_pilot
#PBS -j oe
#PBS -N jobname
#PBS -q volta_gpu
#PBS -l select=1:ncpus=10:mem=95gb:ngpus=1
#PBS -l walltime=72:00:00

export OMPI_MCA_hwloc_base_binding_policy=none
export OMP_STACK_SIZE=4096m

source /etc/profile.d/rec_modules.sh
module add singularity/3.8.3

export vasp_gam=/opt/vasp/bin/vasp_gam
export vasp_std=/opt/vasp/bin/vasp_std
export OMP_NUM_THREADS=4 # use omp=5 with great care! use `top -d 0.5` to see if the CPU >percentage ever go above >100%. IF it is running sometimes at around 400% sometimes, then it >is working probably
export singularity_exec="singularity exec --nv /home/svu/msedz/nushpc_volta_nvhpc24.3_cuda12.3_6.4.3.sif  mpirun -n 1" #change this line to your own directory

cd ${PBS_O_WORKDIR}

$singularity_exec $vasp_std > vasp.out

Submission script for running VASP relaxation using 2 GPUs

#!/bin/bash
#PBS -P volta_pilot
#PBS -j oe
#PBS -N jobname
#PBS -q volta_gpu
#PBS -l select=1:ncpus=10:mem=95gb:ngpus=2
#PBS -l walltime=72:00:00
#-----------------------------------
## things you need to check
export OMP_NUM_THREADS=4 # use omp=5 with great care! use `top -d 0.5` to see if the CPU >percentage ever go above 100%. IF it is running sometimes at around 400% sometimes, then it >is working probably
export vasp_gam=/opt/vasp/bin/vasp_gam
export vasp_std=/opt/vasp/bin/vasp_std
export singularity_exec="singularity exec --nv /home/svu/msedz/nushpc_volta_nvhpc24.3_cuda12.3_6.4.3.sif mpirun -n 2" #change this line to your own directory
#-----------------------------------
source /etc/profile.d/rec_modules.sh
module add singularity/3.8.3
export OMPI_MCA_hwloc_base_binding_policy=none
export OMP_STACK_SIZE=4096m

cd ${PBS_O_WORKDIR}

echo `date` "Running VASP ..." >> status.txt
$singularity_exec $vasp_std >> vasp.out
echo `date` `tail -n -1 OSZICAR` >> status.txt
rel=`tail -1 OSZICAR | cut -c 1-4`
grep "Inconsistent Bravais lattice types found for crystalline" OUTCAR
if [ $? -eq 0 ]
then
  echo "Inconsistent lattice types error, add SYMPREC=1e-08" >> status.txt
  echo "SYMPREC = 1e-08" >> INCAR
fi

while [ ${rel} -gt 10 ]; do
  cp CONTCAR POSCAR
  rm WAVECAR CHG*
  echo `date` "Running VASP " >> status.txt
  $singularity_exec $vasp_std >> vasp.out
  echo `date` `tail -n -1 OSZICAR` >> status.txt
  rel=`grep -v '^$' OSZICAR| tail -1 | cut -c 1-4`
  grep "Inconsistent Bravais lattice types found for crystalline" OUTCAR
  if [ $? -eq 0 ]
  then
  echo "Inconsistent lattice types error, add SYMPREC=1e-08" >> status.txt
  echo "SYMPREC = 1e-08" >> INCAR
  fi
  if [ ${rel} -gt 10 ]
  then
      echo `date` "No. of ionic steps ${rel} doesn't meet the requirement (<10), >restarting ....." >> status.txt
  fi
done


if [ ${rel} -le 10 ]
then
  echo `date` "Relaxation 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  *
  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

Python scripts for ALF project

Pymatgen to generate input files of VASP

from pymatgen.core import Structure
from pymatgen.io.vasp.sets import MITRelaxSet
incar_dict = { 'EDIFFG': -1e-2, 'IVDW': 11, 'ISYM':2,'NSW':1500, 'ENCUT':520}
structure = Structure.from_file("Al_empty.cif")
inputset = MITRelaxSet(structure = structure,user_incar_settings=incar_dict, 
                     user_kpoints_settings={'length':25})
inputset.write_input(output_dir='./DFT_calc',include_cif=True)

Script to gather VASP output data

#!/usr/bin/env python
'''
This code is used for gathering DFT data as extxyz format using ASE >and pymatgen

Zeyu Deng
dengzeyu@gmail.com
'''

from ase.io import read
import os
from pymatgen.io.vasp import Vasprun
from pymatgen.io.vasp import Outcar
import logging

def gather_data(fname_output:str='data.extxyz',
              calc_dir:str='./',
              exclude:str='quickrelax',
              read_magmom:bool=False,
              outcar_name:str='OUTCAR.gz',
              vasprun_name:str='vasprun.xml.gz')->None:

  '''Gather DFT data as extxyz format using ASE and pymatgen
  Parameters:
      fname_output (str): The name of the output file in extxyz >format. Default is 'data.extxyz'.
      calc_dir (str): The directory where the calculations are >stored. Default is './'.
      exclude (str): The string to exclude certain files from >gathering. Default is 'quickrelax'.
      read_magmom (bool): Whether to read magnetic moments from >OUTCAR file. Default is False.
      outcar_name (str): The name of the OUTCAR file. Default is >'OUTCAR.gz'.
      vasprun_name (str): The name of the vasprun.xml file. Default >is 'vasprun.xml.gz'.
  Returns:
      None
  '''
  vasprun_filenames = []
  for path, subdirs, files in os.walk(calc_dir):
      for name in files:
          if vasprun_name in name and exclude not in name:
              vasprun_filenames.append(os.path.join(path, name))

  for vasprun_fname in vasprun_filenames:
      try:
          logger.info(f"Reading {vasprun_fname}")
          vasprun = Vasprun(vasprun_fname)
      except:
          logger.exception(f"Error while reading {vasprun_fname}!")
          continue

      path_name = os.path.dirname(vasprun_fname)
      structure_name = vasprun_fname.strip().split('/')[-2]

      logger.info('checking {}'.format(structure_name))
      if vasprun.converged:
          atoms=read(vasprun_fname, format='vasp-xml')
          atoms.info['name']=structure_name
          atoms.info['path_name']=path_name                
          if not read_magmom:
              try:
                  atoms.write(fname_output,format='extxyz',>append='a')
              except:
                  logger.exception('Error while reading {}, skip..'.>format(outcar_name))
                  pass
          else:
              try:
                  logger.info(f"Reading {os.path.join(path_name,>outcar_name)}")
                  magnetization = [mag['tot'] for mag in Outcar(os.>path.join(path_name,outcar_name)).magnetization]
                  atoms.set_initial_magnetic_moments(magmoms = >magnetization)
                  atoms.write(fname_output,format='extxyz',>append='a')
              except:
                  logger.exception('Error while reading {}, skip..'.>format(outcar_name))
                  pass
      else:
          logger.exception("-> {} not converged!".format>(structure_name))

logger = logging.getLogger()
logging.basicConfig(
  format='%(asctime)s %(levelname)-8s %(message)s',
  level=logging.INFO,
  datefmt='%Y-%m-%d %H:%M:%S')

gather_data(fname_output='data.extxyz',
          calc_dir='/path/to/data',
          exclude='quickrelax',
          read_magmom=True,
          outcar_name='OUTCAR.relaxed.gz',
          vasprun_name='vasprun.xml.relaxed.gz')