Chimie Théorique » Opt'n Path

#PBS -S /bin/sh

#PBS -N VaspPara

#PBS -l nodes=8:Other

#PBS -q Para8

#PBS -o Test_Vasp_Para.batch-log

#PBS -j oe

#PBS -M Paul.Fleurat-Lessard@ens-lyon.fr

#PBS -m aeb

#!/bin/bash

home_dir=$PBS_O_WORKDIR

work_dir=$PBS_O_WORKDIR

numb=3x3_run1

######################################

#

# you might have to change the following variables

#

######################################

#

# Name of the Path Input file

#

Job=Test_Vasp_Para

#

#

# Where is Path.exe ??

#

PathExe=~/Programs/optnpath/src/Path.exe

#

# Where is VASP ?

#

export VASP=/home/dloffred/VASP_SOURCES/Intel_P4/VASP46_CINEB

#

# Whre is mpirun ?

#

export MPIRUN=/usr/local/mpich-intel-090404/bin/mpirun

#

# Some libraries... 

#

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/intel/fc/9.1.037/lib/:/opt/intel/cc/9.1.045/lib:/usr/lib:/opt/intel/mkl/8.1/lib/32

export PATH=/opt/intel/fc/9.1.037/bin/:/opt/intel/cc/9.1.045/bin/:$PATH:$HOME/bin:/usr/local/mpich-intel9/bin

export LD_RUN_PATH=$LD_RUN_PATH:/opt/intel/fc/9.1.037/lib/:/opt/intel/cc/9.1.045/lib

export MANPATH=$MANPATH:/opt/intel/fc/9.1.037/man/:/opt/intel/cc/9.1.045/man

export LANG=C

#

#Usually nothing has to be changed after this line

#

#################################################

#################################

#

# We create the machinefile

#

# even if it is not really needed for SERIAL calculations

#

#################################

nodes=`cat $PBS_NODEFILE`

nnodes=`wc $PBS_NODEFILE | awk '{print $1}'` 

confile=$home_dir/ip.$PBS_JOBID.conf

touch $confile

j="init"

for i in $nodes

do

if [ $j != $i ]

then echo "$i:1" >> $confile

else

	echo "vous calculez sur des noeuds smp"

fi

j=$i

done

###############################

#

# We go to the Work Directory

#

###############################

cd $work_dir

#! we create the 00, 01... and 0x directorires

# First we get the number of images in the INCAR file:

NbIm=`grep -i IMAGES INCAR | awk -F"=" '{n=$2*1+1; print n}' `

n=0

while [ $n -le $NbIm ]

do

ndir=`echo $n | awk '{k="00" $1; l=length(k); l=l-1; print substr(k,l,2)}'`

mkdir -p $ndir

let n=n+1

done

# A small test to see if everything matches

NbImP=` sed 's/,/^M/g' ${Job}.path | grep -i ngeomf | awk -F"=" '{n=$2*1-1; print n}' `

if [ $NbImP -ne $NbIm ]; then

 echo "WARNING WARNING WARNING WARNING WARNING WARNING"

 echo "IMAGES in INCAR and NGeomF in " ${Job}.path

 echo "Do Not Match... problems might be expected..."

 echo "Check it !!!"

 echo "WARNING WARNING WARNING WARNING WARNING WARNING"

fi

#############################

#

#  We create the 'VaspExe' file that Path will use to run the

# actual VASP calculations of E and forces

#

#############################

echo "$MPIRUN -nolocal -machinefile $confile -np $nnodes $VASP > out_$numb" >  ./RunVasp

chmod u+x ./RunVasp

###############################

#

# We launch PATH

#

###############################

ln -fs ${PathExe} .

#############################

#

#  We create the 'VaspExe' file that Path will use to run the

# actual VASP calculations of E and forces

#

#############################

echo "$MPIRUN -nolocal -machinefile $confile -np $nnodes $VASP > out_$numb" >  ./RunVasp

chmod u+x ./RunVasp

###############################

#

# We launch PATH

#

###############################

ln -fs ${PathExe} .

./Path.exe ${Job}.path &> ${Job}.out