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go back to [[Main Page]], [[Computational Resources]], [[Scripts]], [[Scripts for VASP]] | |||
'''IMPORTANT!!!''' You need the following file [[script.s]] in order to use ''setandsubmit.s''!! | |||
#README | #README | ||
#README | #README | ||
#README | #README | ||
# We need an INPUT folder. Inside it, it is neccesary: INCAR, KPOINTS, POTCAR (named POTCAR.Me.Molecule , POTCAR.Pt.NO , for each metal) | # We need an INPUT folder. Inside it, it is neccesary: INCAR, KPOINTS, POTCAR (named POTCAR.Me.Molecule , POTCAR.Pt.NO , for each metal) | ||
# and the converged CONTCAR, and also, a file called INPUT | # and the converged CONTCAR, and also, a file called INPUT | ||
| Line 17: | Line 21: | ||
# . . | # . . | ||
# | # | ||
#It is neccesry | #It is neccesry also the submision file "script.s": | ||
#Create the directories for all the metals, both in home and in scratch. | #Create the directories for all the metals, both in home and in scratch. | ||
#Here there is the set of metals that we are going to studie: | #Here there is the set of metals that we are going to studie: | ||
for i in Au Cu Ir Pd Pt Rh ; do | for i in Au Cu Ir Pd Pt Rh ; do | ||
#The molecules: | #The molecules: | ||
for j in CN ; do | for j in CN CO NO; do | ||
#and the states: | #and the states: | ||
for k in initial final ts ; do | for k in initial final ts ; do | ||
mkdir Me-$j | mkdir Me-$j | ||
mkdir Me-$j/$i | mkdir Me-$j/$i | ||
mkdir Me-$j/$i/$j | mkdir Me-$j/$i/$j | ||
mkdir Me-$j/$i/$j/$k | mkdir Me-$j/$i/$j/$k | ||
mkdir /gpfs/scratch/iciq08/iciq08494/Me-$j | mkdir /gpfs/scratch/iciq08/iciq08494/Me-$j | ||
mkdir /gpfs/scratch/iciq08/iciq08494/Me-$j/$i | mkdir /gpfs/scratch/iciq08/iciq08494/Me-$j/$i | ||
mkdir /gpfs/scratch/iciq08/iciq08494/Me-$j/$i/$j | mkdir /gpfs/scratch/iciq08/iciq08494/Me-$j/$i/$j | ||
mkdir /gpfs/scratch/iciq08/iciq08494/Me-$j/$i/$j/$k | mkdir /gpfs/scratch/iciq08/iciq08494/Me-$j/$i/$j/$k | ||
#Copy INCAR, KPOINTS, and POTCAR's in /scratch/ | #Copy INCAR, KPOINTS, and POTCAR's in /scratch/ | ||
cp ./INPUTS/INCAR /gpfs/scratch/iciq08/iciq08494/Me-$j/$i/$j/$k | cp ./INPUTS/INCAR /gpfs/scratch/iciq08/iciq08494/Me-$j/$i/$j/$k | ||
cp ./INPUTS/KPOINTS /gpfs/scratch/iciq08/iciq08494/Me-$j/$i/$j/$k | cp ./INPUTS/KPOINTS /gpfs/scratch/iciq08/iciq08494/Me-$j/$i/$j/$k | ||
cp ./INPUTS/POTCAR.$i.$j /gpfs/scratch/iciq08/iciq08494/Me-$j/$i/$j/$k | cp ./INPUTS/POTCAR.$i.$j /gpfs/scratch/iciq08/iciq08494/Me-$j/$i/$j/$k | ||
#CONTCAR's tunning | #CONTCAR's tunning | ||
echo $i $j > Me-$j/$i/$j/$k/POSCAR.$k | echo $i $j > Me-$j/$i/$j/$k/POSCAR.$k | ||
grep "$i" INPUTS/INPUT | awk ' {print $2}' > parameter | grep "$i" INPUTS/INPUT | awk ' {print $2}' > parameter | ||
tail parameter >> Me-$j/$i/$j/$k/POSCAR.$k | tail parameter >> Me-$j/$i/$j/$k/POSCAR.$k | ||
M=`wc -l INPUTS/CONTCAR.Pt.CN | awk '{print $1}'` | M=`wc -l INPUTS/CONTCAR.Pt.CN | awk '{print $1}'` | ||
N=`expr $M - 2` | N=`expr $M - 2` | ||
echo $N | echo $N | ||
tail -$N INPUTS/CONTCAR.Pt.CN >> Me-$j/$i/$j/$k/POSCAR.$k | tail -$N INPUTS/CONTCAR.Pt.CN >> Me-$j/$i/$j/$k/POSCAR.$k | ||
mv Me-$j/$i/$j/$k/POSCAR.$k Me-$j/$i/$j/$k/POSCAR | mv Me-$j/$i/$j/$k/POSCAR.$k Me-$j/$i/$j/$k/POSCAR | ||
cp ./INPUTS/INCAR /gpfs/scratch/iciq08/iciq08494/Me-$j/$i/$j/$k | cp ./INPUTS/INCAR /gpfs/scratch/iciq08/iciq08494/Me-$j/$i/$j/$k | ||
cp ./INPUTS/KPOINTS /gpfs/scratch/iciq08/iciq08494/Me-$j/$i/$j/$k | cp ./INPUTS/KPOINTS /gpfs/scratch/iciq08/iciq08494/Me-$j/$i/$j/$k | ||
cp ./INPUTS/POTCAR.$i.$j /gpfs/scratch/iciq08/iciq08494/Me-$j/$i/$j/$k/POTCAR | cp ./INPUTS/POTCAR.$i.$j /gpfs/scratch/iciq08/iciq08494/Me-$j/$i/$j/$k/POTCAR | ||
cp Me-$j/$i/$j/$k/POSCAR /gpfs/scratch/iciq08/iciq08494/Me-$j/$i/$j/$k/POSCAR | cp Me-$j/$i/$j/$k/POSCAR /gpfs/scratch/iciq08/iciq08494/Me-$j/$i/$j/$k/POSCAR | ||
# | #Copy the script to the directories | ||
head -30 script.s > Me-$j/$i/$j/$k/script.$i.$j.$k.s | head -30 script.s > Me-$j/$i/$j/$k/script.$i.$j.$k.s | ||
echo "cd /gpfs/scratch/iciq08/iciq08494/Me-$j/$i/$j/$k" >> Me-$j/$i/$j/$k/script.$i.$j.$k.s | echo "cd /gpfs/scratch/iciq08/iciq08494/Me-$j/$i/$j/$k" >> Me-$j/$i/$j/$k/script.$i.$j.$k.s | ||
tail -2 script.s >> Me-$j/$i/$j/$k/script.$i.$j.$k.s | tail -2 script.s >> Me-$j/$i/$j/$k/script.$i.$j.$k.s | ||
# Now run | # Now run | ||
echo Me-$j/$i/$j/$k >> jobs | echo Me-$j/$i/$j/$k >> jobs | ||
llsubmit Me-$j/$i/$j/$k/script.$i.$j.$k.s >> jobs | llsubmit Me-$j/$i/$j/$k/script.$i.$j.$k.s >> jobs | ||
done | done | ||
done | done | ||
done | done | ||
#And move the input files to the folder | #And move the input files to the folder | ||
mv INPUTS Me-$j | mv INPUTS Me-$j | ||
mv script.s Me-$j | mv script.s Me-$j | ||
Latest revision as of 13:23, 21 September 2010
go back to Main Page, Computational Resources, Scripts, Scripts for VASP
IMPORTANT!!! You need the following file script.s in order to use setandsubmit.s!!
#README
#README
#README
# We need an INPUT folder. Inside it, it is neccesary: INCAR, KPOINTS, POTCAR (named POTCAR.Me.Molecule , POTCAR.Pt.NO , for each metal)
# and the converged CONTCAR, and also, a file called INPUT
# with the cell parameters in the following format:
#
# "Me" "cell parameter" , for example:
#
#
# Au 4.0223
# Cu 3.6267
# . .
# . .
# . .
#
#It is neccesry also the submision file "script.s":
#Create the directories for all the metals, both in home and in scratch.
#Here there is the set of metals that we are going to studie:
for i in Au Cu Ir Pd Pt Rh ; do
#The molecules:
for j in CN CO NO; do
#and the states:
for k in initial final ts ; do
mkdir Me-$j
mkdir Me-$j/$i
mkdir Me-$j/$i/$j
mkdir Me-$j/$i/$j/$k
mkdir /gpfs/scratch/iciq08/iciq08494/Me-$j
mkdir /gpfs/scratch/iciq08/iciq08494/Me-$j/$i
mkdir /gpfs/scratch/iciq08/iciq08494/Me-$j/$i/$j
mkdir /gpfs/scratch/iciq08/iciq08494/Me-$j/$i/$j/$k
#Copy INCAR, KPOINTS, and POTCAR's in /scratch/
cp ./INPUTS/INCAR /gpfs/scratch/iciq08/iciq08494/Me-$j/$i/$j/$k
cp ./INPUTS/KPOINTS /gpfs/scratch/iciq08/iciq08494/Me-$j/$i/$j/$k
cp ./INPUTS/POTCAR.$i.$j /gpfs/scratch/iciq08/iciq08494/Me-$j/$i/$j/$k
#CONTCAR's tunning
echo $i $j > Me-$j/$i/$j/$k/POSCAR.$k
grep "$i" INPUTS/INPUT | awk ' {print $2}' > parameter
tail parameter >> Me-$j/$i/$j/$k/POSCAR.$k
M=`wc -l INPUTS/CONTCAR.Pt.CN | awk '{print $1}'`
N=`expr $M - 2`
echo $N
tail -$N INPUTS/CONTCAR.Pt.CN >> Me-$j/$i/$j/$k/POSCAR.$k
mv Me-$j/$i/$j/$k/POSCAR.$k Me-$j/$i/$j/$k/POSCAR
cp ./INPUTS/INCAR /gpfs/scratch/iciq08/iciq08494/Me-$j/$i/$j/$k
cp ./INPUTS/KPOINTS /gpfs/scratch/iciq08/iciq08494/Me-$j/$i/$j/$k
cp ./INPUTS/POTCAR.$i.$j /gpfs/scratch/iciq08/iciq08494/Me-$j/$i/$j/$k/POTCAR
cp Me-$j/$i/$j/$k/POSCAR /gpfs/scratch/iciq08/iciq08494/Me-$j/$i/$j/$k/POSCAR
#Copy the script to the directories
head -30 script.s > Me-$j/$i/$j/$k/script.$i.$j.$k.s
echo "cd /gpfs/scratch/iciq08/iciq08494/Me-$j/$i/$j/$k" >> Me-$j/$i/$j/$k/script.$i.$j.$k.s
tail -2 script.s >> Me-$j/$i/$j/$k/script.$i.$j.$k.s
# Now run
echo Me-$j/$i/$j/$k >> jobs
llsubmit Me-$j/$i/$j/$k/script.$i.$j.$k.s >> jobs
done
done
done
#And move the input files to the folder
mv INPUTS Me-$j
mv script.s Me-$j