#!/bin/bash
#PBS -lwalltime=_TIMELIMIT_:00:00
#PBS -S /bin/bash
#PBS -lnodes=1:ppn=_NCORES_
#PBS -N _JOBNAME_

ulimit -s unlimited

# workdirectory
WORKDIR=$PBS_O_WORKDIR

#vasp exe
VASP="/home/nick/VASP-LIBXC/vasp.5.3.5/vasp-LIBXC"

# scratch directory
SCRATCH=/scratch/${USER}/${PBS_JOBID}

# copy files from one to other
scp -r ${WORKDIR}/* ${SCRATCH}/.
cd ${SCRATCH}

# prepare inputs

egrep -v '_nsw_' INCAR_		>  INCAR
echo "   NSW  = _SUBSTEPS_ "	>> INCAR

# run checker in background and determine its pid
./checker >& /dev/null &
checkerpid=$!

# execute vasp
mpirun ${VASP} >> vasp.out

# kill checker 
kill ${checkerpid}

# run check.py one last time
./check-CHD3.py

# check the number of runs

check=0
while [ -e "XDATCAR_${check}" ]
do 
	let check++
done

# get timing
grep Elapsed OUTCAR >> time.dat

# update imporant outputs
mv POSCAR POSCAR_${check}
mv OSZICAR OSZICAR_${check}
mv XDATCAR XDATCAR_${check}
mv CONTCAR CONTCAR_${check}

grep -A 51 "TOTAL-FORCE" OUTCAR > Forces_${check}.dat

rm CHG* DO* E* IB* PC* W* vasprun* OUTCAR vdw*

#Copy files back
scp -r  ${SCRATCH}/* ${WORKDIR}/.
# clean up
rm -r ${SCRATCH}/*