#!/bin/bash
#PBS -l walltime=24:00:00
#PBS -l select=1:ncpus=48:mem=124gb:avx=TRUE
#PBS -N FIELD_TS
#PBS -J 1-4
#PBS -j oe

module load gaussian/g09-d01

INFILE="`sed -n ${PBS_ARRAY_INDEX}p $PBS_O_WORKDIR/file_list`"

cp $PBS_O_WORKDIR/$INFILE.xyz $TMPDIR/opt.xyz
cp $PBS_O_WORKDIR/Center.f90 $TMPDIR
cp $PBS_O_WORKDIR/Element_Table_$INFILE $TMPDIR/Element_Table
cp $PBS_O_WORKDIR/HEADER.com $TMPDIR
cd $TMPDIR
echo "EXECUTION IN "$TMPDIR > FORTRANLOG
date >> FORTRANLOG
cat /dev/null > Energies
gfortran Center.f90
for i in {1..10}
do
	head -1 Element_Table > traj_$INFILE
	echo $INFILE >> traj_$INFILE
	./a.out >> FORTRANLOG
	cat HEADER.com opt.xyz > $INFILE.com
	g09 < $TMPDIR/$INFILE.com > $TMPDIR/$INFILE.log
	newzmat -ichk -oxyz opt
	cat traj_$INFILE opt.xyz >> traj_$INFILE
	grep -m 1 "E(" $INFILE.log | cut -c 26-39 >> Energies
done
date >> FORTRANLOG
mkdir $PBS_O_WORKDIR/$INFILE
mkdir $PBS_O_WORKDIR/optimized
cp $TMPDIR/$INFILE.log $PBS_O_WORKDIR/$INFILE
cp $TMPDIR/FORTRANLOG $PBS_O_WORKDIR/$INFILE
cp $TMPDIR/Energies $PBS_O_WORKDIR/$INFILE
cp $TMPDIR/traj_$INFILE $PBS_O_WORKDIR/$INFILE/traj_$INFILE.xyz
mv opt.xyz $INFILE.xyz
cp $TMPDIR/$INFILE.xyz $PBS_O_WORKDIR/optimized
cp $TMPDIR/$INFILE $PBS_O_WORKDIR/optimized/$INFILE.xyz