LAMMPS

#!/bin/bash
#
#$ -S /bin/bash
#$ -N C6_equilibration3
##$ -q E5-2670deb128B
#$ -q E5_test
#$ -pe test_debian  2
#$ -cwd
#$ -V
#$ -m be
 
module purge
module use /home/tjiang/modules/lmod
module load lammps/trunk
 
# donné par le système de batch
HOSTFILE=${TMPDIR}/machines
 
 
if [[ -d "/scratch" ]]
then
    ### for Lake scratch / CLG* SLG* queues
    if [[ -e "/scratch/Lake/lake-gfs-scratch" ]]
    then
    	SCRATCHDIR=/scratch/Lake/$USER/$JOB_ID/
    ### for E5N scratch / E5* queues
    elif [[ -e "/scratch/E5N/E5N-gfs-scratch" ]]
    then
    	SCRATCHDIR=/scratch/E5N/$USER/$JOB_ID/
    ### for Chimie scratch
    elif [[ -e "/scratch/Chimie/chimie-gfs-scratch" ]]
    then
    	SCRATCHDIR=/scratch/Chimie/$USER/$JOB_ID/
    else
    	echo "/scratch not found, cannot create ${SCRATCHDIR}"
    	exit 1
    fi
else
    echo "/scratch not found, cannot create ${SCRATCHDIR}"
    exit 1
fi
 
# Using /tmp as scratch instead
# SCRATCHDIR=/tmp/$USER/$JOB_ID/
 
echo $SCRATCHDIR
/bin/mkdir -p $SCRATCHDIR
 
# modifier les noms des fichiers
cd ${SGE_O_WORKDIR}
cp -f in*.lmp data*.lmp ${SCRATCHDIR}/
#cp -f in*.lmp data*.lmp pair*.lmp ${SCRATCHDIR}/
 
 
# modifier noms des fichiers
cd ${SCRATCHDIR}
mpirun -v -hostfile ${HOSTFILE} -np ${NSLOTS} lammps.sse -in in.eq.lmp > out.lmp
cp -rpf *  ${SGE_O_WORKDIR}/
rm -f ${SCRATCHDIR}/