#!/bin/bash
#PBS -l walltime=48:00:00
#PBS -S /bin/bash
#PBS -l nodes=1:ppn=28
#PBS -N 0500-RPMD-surface

module load i-PI/2.3.0-intel-2020a-Python-3.8.3

# workdirectory
WORKDIR=$PBS_O_WORKDIR
cd ${WORKDIR}

# scratch directory
SCRATCH=${VSC_SCRATCH_NODE}/${PBS_JOBID}
mkdir -p ${SCRATCH}
cd ${SCRATCH}

# copy files from the workdir to the scratch
scp -r ${WORKDIR}/* ${SCRATCH}/.
scp -r ${WORKDIR}/../../RuNNer ${SCRATCH}/.

# lammps location
#lammps=${VSC_DATA}/Programs/lammps-29Oct20/src/lmp_mpi
lammps=${VSC_DATA}/Programs/lammps-29Oct20/src/lmp_serial

# A few times this error has popped up; simple fix
if compgen -G "/tmp/ipi_*" > /dev/null; then
	rm /tmp/ipi_*
fi

sed -e "s|_SEED_|${RANDOM}|g" input.xml_ > input.xml

# start i-PI
i-pi input.xml &

# The sleep is necessary, otherwise LAMMPS won't be able to connect and will crash since i-PI hasn't started up yet
sleep 10

# Start multiple instances of LAMMPS
#${lammps} -in sim.lmp &
for idx in `seq 24`;
	do
	
	#mpirun -np 7 ${lammps} -in sim.lmp &
	${lammps} -in sim.lmp &
	
done

wait

for i in $(seq -w 00 23); do
	tail -n52000 simulation.pos_bead_${i}.xyz > tmp
	mv tmp simulation.pos_bead_${i}.xyz
	tail -n52000 simulation.vel_bead_${i}.xyz > tmp
	mv tmp simulation.vel_bead_${i}.xyz
done

tail -n52000 simulation.pos_centroid.xyz > tmp
mv tmp simulation.pos_centroid.xyz
tail -n52000 simulation.vel_centroid.xyz > tmp
mv tmp simulation.vel_centroid.xyz

rm RESTART log.lammps
rm -r RuNNer

# copy files back
scp -r ${SCRATCH}/* ${WORKDIR}/.

# clean up
rm -r ${SCRATCH}

# ready