Ceci est une ancienne révision du document !
#!/bin/bash #$ -S /bin/bash #$ -N vasp_ompi_8 #$ -q E5-2667v2* #$ -pe mpi8_debian 8 #$ -V #$ -cwd # Choose the version of vasp by loading the module file accordingly export MODULEPATH=/home/tjiang/modules/lmod/:${MODULEPATH} module use ${MODULEPATH} module load vasp/5.4.1 #module load vasp/5.3.5 # for OpenMP + multithreaded MKL export OMP_NUM_THREADS=1 export MKL_NUM_THREADS=1 #ulimit -l unlimited # Where are we HOMEDIR=$SGE_O_WORKDIR # stuff for parallel computing MPIRUN=mpirun HOSTFILE=$TMPDIR/machines # save nodelist (optional) #/bin/cat $TMPDIR/machines > $HOMEDIR/tmp # Copy from home to scratch QUEUE=$QUEUE SCRATCHDIR=/scratch/$USER/$JOB_ID/ echo $SCRATCHDIR /bin/mkdir -p $SCRATCHDIR cd ${HOMEDIR} #for normal calculation /bin/cp -f INCAR KPOINTS POTCAR POSCAR WAVECAR ${SCRATCHDIR}/ #for neb calculation, numbering depends on the number of images #/bin/cp -rf INCAR KPOINTS POTCAR POSCAR WAVECAR 00 01 02 ${SCRATCHDIR}/ # If starting wavecar and chgcar exists, uncomment the following line #/bin/cp -f $HOMEDIR/CHG* $HOMEDIR/WAVECAR # go to scratch (instead of SGE workdir) cd ${SCRATCHDIR} echo ${HOMEDIR} > homedir # The line for computing mpirun -hostfile $HOSTFILE -np ${NSLOTS} vasp_std > ${HOMEDIR}/out #mpirun -hostfile $HOSTFILE -np ${NSLOTS} vasp_gam > ${HOMEDIR}/out #mpirun -hostfile $HOSTFILE -np ${NSLOTS} vasp_ncl > ${HOMEDIR}/out # Get back the results # Full copy back #cp WAVECAR CHG* OUTCAR POSCAR OSZICAR XDATCAR CONTCAR vasprun.xml $HOMEDIR/ # Minimum copy back cp -rf OUTCAR POSCAR OSZICAR XDATCAR CONTCAR $HOMEDIR/ # copy back for neb calculation, numbering depends on the number of images #cp -rf OUTCAR POSCAR OSZICAR XDATCAR CONTCAR 00 01 02 $HOMEDIR/ # Zip OUTCAR to save space cd $HOMEDIR bzip2 OUTCAR #gzip OUTCAR # Cleaning up rm -rf ${SCRATCHDIR} # The following part is only useful for users from the chemistry lab of ens-lyon. # Importing finished calculation into database if [ ! -d /home/${USER}/.chimie_db/ ]; then mkdir /home/${USER}/.chimie_db/ fi export PYTHONPATH=/home/tjiang/usr/lib/python2.7/site-package/:$PYTHONPATH export PATH=/home/tjiang/chimie4psmn/database/:$PATH import_vasp_calc -p -u ${USER} -n 1 -d /home/${USER}/.chimie_db/${USER}.db ${HOMEDIR}