Editing Setandsubmit.s

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'''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