#!/bin/bash
#PBS -lwalltime=_TIMELIMIT_:00:00
##PBS -q small
#PBS -S /bin/bash
#PBS -lmem=4gb
#PBS -N _NAME_-_FIRSTJOB_-_LASTJOB_
#PBS -lnodes=1:ppn=1

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

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

# workdirectory
WORKDIR=nick@z6r4u40:$PBS_O_WORKDIR

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

# copy files from one to other
scp -r ${WORKDIR}/Genlammps_AIMD.py ${SCRATCH}/.
scp -r ${WORKDIR}/sim.lmp ${SCRATCH}/.
scp -r ${WORKDIR}/check-HCl-NN.py ${SCRATCH}/.
scp -r ${WORKDIR}/RuNNer ${SCRATCH}/.
scp -r ${WORKDIR}/energytransfer.py ${SCRATCH}/.
scp -r ${WORKDIR}/create_poscar_scratch_.py ${SCRATCH}/.
scp -r ${WORKDIR}/DynamicsINPUTS/ ${SCRATCH}/.

cd ${SCRATCH}

sed -e "s|xFIRSTJOBx|$(echo '_FIRSTJOB_' | sed 's/^0*//')|g" create_poscar_scratch_.py > create_poscar_scratch.py
sed -i "s|xLASTJOBx|$(echo '_LASTJOB_' | sed 's/^0*//')|g" create_poscar_scratch.py
python create_poscar_scratch.py

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}

	python ../Genlammps_AIMD.py

	rm EW.txt
	../lmp_serial -in ../sim.lmp > kkk
	python ../check-HCl-NN.py

	tail -n38 states.xyz > states_temp.xyz
	mv states_temp.xyz states.xyz

	cp ../RuNNer/weights* .
	cp ../RuNNer/scaling.data .
	cp ../RuNNer/input.nn .
	python ../energytransfer.py
	rm weights* scaling.data input.nn

	rm log.lammps cfg_lammps.RuN.config ET.profile

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

	cd ..
#	scp -r ${i} ${WORKDIR}/.
done
cd ${SCRATCH}
rsync -rz {_FIRSTJOB_.._LASTJOB_} ${WORKDIR}/.

# clean up
rm -r ${SCRATCH}

# ready