#!/bin/bash
#SBATCH -t _TIMELIMIT_:00:00
#SBATCH -J _FIRSTJOB_-_LASTJOB_-_NAME_
#SBATCH -n _NCORES_
#SBATCH --tasks-per-node=_NCORES_
#SBATCH --threads-per-core 1
#SBATCH -o std_out
#SBATCH -e std_err

export LD_LIBRARY_PATH=~/sharedlibs/:${LD_LIBRARY_PATH}

#source directory
srcdir=/home/nick/lammps-16Mar18/src/

# workdirectory
WORKDIR=${SLURM_SUBMIT_DIR}

# scratch directory
SCRATCH=/scratch/${SLURM_JOB_USER}/${SLURM_JOB_ID}

# copy files from one to other
scp -r ${WORKDIR}/sim.lmp ${SCRATCH}/.
scp -r ${WORKDIR}/check-H2-NN.py ${SCRATCH}/.
scp -r ${WORKDIR}/RuNNer ${SCRATCH}/.
cd ${SCRATCH}

#ln  -s $srcdir/lmp_mpi .
ln  -s $srcdir/lmp_serial .

rsync -rz ${WORKDIR}/{_FIRSTJOB_.._LASTJOB_} ${SCRATCH}/.
for i in $(seq -w _FIRSTJOB_ _LASTJOB_)
	do

#	scp -r ${WORKDIR}/${i} ${SCRATCH}/.

	cd ${i}

	if [ -f "EW.txt" ]; then
		rm EW.txt
	fi

#	srun ../lmp_mpi -in ../sim.lmp > kkk
	../lmp_serial -in ../sim.lmp > kkk
	../check-H2-NN.py

        rm log.lammps cfg_lammps.RuN.config states.xyz

        outcome=$(cat outcome)
        if [[ ! "$outcome" == *"UNCLEAR"* ]]; then
                rm analysis_rcom.dat angles.dat kkk EW.txt
        fi


	cd ..
#	scp -r ${i} ${WORKDIR}/.
done
rsync -rz $(seq -w _FIRSTJOB_ _LASTJOB_) ${WORKDIR}/.

# clean up
rm -r ${SCRATCH}

# ready