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VASP.GPU.sb
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#!/bin/bash
#SBATCH --nodes=1
#SBATCH --tasks-per-node=1
#SBATCH -t 06:00:00
#SBATCH -e vasp_gpu.err
#SBATCH -p gpu-shared
#SBATCH --gres=gpu:k80:1
#SBATCH --export=ALL
module unload intel
module load vasp
module load cuda
exe=`which vasp_gpu`
processors=$(( $SLURM_NNODES * $SLURM_NTASKS_PER_NODE ))
mpirun -np $processors -genv I_MPI_FABRICS shm:ofa $exe >& vasp.log
mo_files='absolute/path/to/orbital_calculation/input/files/' # cleanup.sh INCAR(please look for file INCAR_mo for this file format) KPOINTS
bader_files='absolute/path/to/bader_calculation/input/files/' # bader chgsum.pl INCAR(please look for file INCAR_bader for this file format) (bader,chgsum.pl can be obtained from http://theory.cm.utexas.edu/henkelman/code/bader/ )
# checking last ionic loop
grep -h Iteration OUTCAR >>iter.txt
ionic=(); scf=()
while read -r line; do
if [[ "$line" =~ ([0-9]+)\(\ +([0-9]+) ]]; then
ionic+=("${BASH_REMATCH[1]}")
scf+=("${BASH_REMATCH[2]}")
fi
done < iter.txt
len=(${#scf[@]})
if [ "${scf[$len-1]}" == 60 ] # -1 bcos indexing starts at 0 1 2 ...
then
declare -i xx && xx=1 && echo $xx
while [ ${scf[$len-(60*$xx)-1]} == 60 ]
do
xx+=1
done
newNSW="${ionic[$len-(60*$xx)-1]}"
mkdir nextRelax && cp cleanup.sh INCAR KPOINTS POTCAR POSCAR nextRelax/ && cd nextRelax/ &&
cp INCAR INCAR.tmp && sed "s/NSW = 10/NSW = $newNSW/" <INCAR.tmp >INCAR && rm -f INCAR.tmp &&
mpirun -np $processors -genv I_MPI_FABRICS shm:ofa $exe >& vasp.log
cd ../ ; rm OUTCAR LOCPOT CHGCAR WAVECAR XDATCAR ; sh cleanup.sh ; cd nextRelax/ ;
mv OUTCAR LOCPOT CHGCAR WAVECAR XDATCAR CONTCAR ../ ; cd ../
##################################################### assigning HOMO and LUMO variables
x=$(awk '/E-fermi/{print NR}' OUTCAR)
echo $x>>row.txt
tr -s ' ' '\n'< row.txt > column.txt
rm row.txt ; mv column.txt temp.txt
lastElement=$( tail -n 1 temp.txt )
rm temp.txt
tail -n +$lastElement OUTCAR >>tempB.txt
sed -n '/band No. band energies occupation/,/soft charge-density along one line/p' tempB.txt >>tempC.txt
rm tempB.txt
grep 2.00000 tempC.txt | tail -1>>HOMO.txt
grep -m 1 0.00000 tempC.txt >>LUMO.txt
rm tempC.txt
tr -s ' ' '\n'< HOMO.txt > HOMO_Col.txt
mapfile -t myArray < HOMO_Col.txt
nHOMO=${myArray[1]} ; unset myArray
tr -s ' ' '\n'< LUMO.txt > LUMO_Col.txt
mapfile -t myArray < LUMO_Col.txt
nLUMO=${myArray[1]} ; unset myArray
rm HOMO.txt HOMO_Col.txt LUMO.txt LUMO_Col.txt ; unset x
##################################################### assigning HOMO and LUMO variables ends
##################################################### molecular orbital job
mkdir MO && cd MO && cp $mo_files/* ./ && cp ../CONTCAR ./ && mv CONTCAR POSCAR && cp ../POTCAR ./ && cp ../WAVECAR ./ &&
cp INCAR INCAR.tmp && sed "s/67/$nHOMO/" <INCAR.tmp >INCAR && rm -f INCAR.tmp &&
mpirun -np $processors -genv I_MPI_FABRICS shm:ofa $exe >& vasp.log &&
mkdir HOMO/ && mv PARCHG INCAR vasp.log OUTCAR HOMO/ && sh cleanup.sh &&
cp $mo_files/INCAR ./ && cp INCAR INCAR.tmp && sed "s/67/$nLUMO/" <INCAR.tmp >INCAR && rm -f INCAR.tmp &&
mpirun -np $processors -genv I_MPI_FABRICS shm:ofa $exe >& vasp.log &&
mkdir LUMO/ && mv PARCHG INCAR vasp.log OUTCAR LUMO/ && sh cleanup.sh && rm WAVECAR ; unset nHOMO ; unset nLUMO
cd ../ # for bader calculations
##################################################### molecular orbital job ends
############## BADER job
mkdir BADER && cd BADER/ && cp $bader_files/* ./ && cp ../WAVECAR ./ && cp ../KPOINTS ./ && cp ../PO* ./ &&
# Step 2
mpirun -np $processors -genv I_MPI_FABRICS shm:ofa $exe >& vasp.log
# Step 3
./chgsum.pl AECCAR0 AECCAR2
# step 4
chmod +x bader && ./bader CHGCAR -ref CHGCAR_sum
# step 5
elements=() ;
awk 'NR==6' POSCAR>>POSCAR_temp
tr -s ' ' '\n'< POSCAR_temp > POSCAR_temp2
rm POSCAR_temp && mv POSCAR_temp2 POSCAR_temp
mapfile -t elements < POSCAR_temp
echo ${elements[@]}
ele_quant=() ; rm POSCAR_temp ;
awk 'NR==7' POSCAR>>POSCAR_temp
tr -s ' ' '\n'< POSCAR_temp > POSCAR_temp2
rm POSCAR_temp && mv POSCAR_temp2 POSCAR_temp
mapfile -t ele_quant < POSCAR_temp
echo ${ele_quant[@]} && rm POSCAR_temp
rm ACF_tmp
sed -e '1,2d' < ACF.dat>>ACF_tmp && head -n -4 ACF_tmp>>ACF_tmp2 && rm ACF_tmp
mv ACF_tmp2 ACF_tmp
readarray -t charge < <(cat ACF_tmp | tr -s ' ' | cut -d' ' -f6) # array name is charge
rm ACF_tmp
echo ${charge[@]}
declare -i N ; declare -i C ; declare -i O ; declare -i H ; declare -i F ; declare -i S ;
N=5 ; C=4 ; O=6 ; H=1 ; F=7 ; S=6
ZVAL=()
for (( i=0; i<=$(( ${#elements[*]} -1 )) ; i++ ))
do
if [[ ${elements[$i]} == N ]]
then
ZVAL+=("$N")
elif [[ ${elements[$i]} == C ]]
then
ZVAL+=("$C")
elif [[ ${elements[$i]} == O ]]
then
ZVAL+=("$O")
elif [[ ${elements[$i]} == H ]]
then
ZVAL+=("$H")
elif [[ ${elements[$i]} == F ]]
then
ZVAL+=("$F")
else
ZVAL+=("$S")
fi
done
echo ${#ZVAL[*]} ; echo ${ZVAL[@]} ;
temp=0 ; array=() ; declare -i yy ; yy=0
for value in "${ele_quant[@]}"
do
for (( i=0+$temp; i<$value+$temp; i++ ))
do
array+=("$i")
#charge[$i]=$(bc<<<"${charge[$i]} - ${ZVAL[$yy]}")
charge[$i]=$(bc<<<"${ZVAL[$yy]} - ${charge[$i]}")
done
temp=${#array[*]}
yy+=1
done
echo ${charge[@]}>>mod_charge.txt && unset yy
rm AECCAR* CHG* WAVECAR
############## BADER job ends
else
# checking last ionic loop end
##################################################### assigning HOMO and LUMO variables
x=$(awk '/E-fermi/{print NR}' OUTCAR)
echo $x>>row.txt
tr -s ' ' '\n'< row.txt > column.txt
rm row.txt ; mv column.txt temp.txt
lastElement=$( tail -n 1 temp.txt )
rm temp.txt
tail -n +$lastElement OUTCAR >>tempB.txt
sed -n '/band No. band energies occupation/,/soft charge-density along one line/p' tempB.txt >>tempC.txt
rm tempB.txt
grep 2.00000 tempC.txt | tail -1>>HOMO.txt
grep -m 1 0.00000 tempC.txt >>LUMO.txt
rm tempC.txt
tr -s ' ' '\n'< HOMO.txt > HOMO_Col.txt
mapfile -t myArray < HOMO_Col.txt
nHOMO=${myArray[1]} ; unset myArray
tr -s ' ' '\n'< LUMO.txt > LUMO_Col.txt
mapfile -t myArray < LUMO_Col.txt
nLUMO=${myArray[1]} ; unset myArray
rm HOMO.txt HOMO_Col.txt LUMO.txt LUMO_Col.txt ; unset x
##################################################### assigning HOMO and LUMO variables ends
##################################################### molecular orbital job
mkdir MO && cd MO && cp $mo_files/* ./ && cp ../CONTCAR ./ && mv CONTCAR POSCAR && cp ../POTCAR ./ && cp ../WAVECAR ./ &&
cp INCAR INCAR.tmp && sed "s/67/$nHOMO/" <INCAR.tmp >INCAR && rm -f INCAR.tmp &&
mpirun -np $processors -genv I_MPI_FABRICS shm:ofa $exe >& vasp.log &&
mkdir HOMO/ && mv PARCHG INCAR vasp.log OUTCAR HOMO/ && sh cleanup.sh &&
cp $mo_files/INCAR ./ && cp INCAR INCAR.tmp && sed "s/67/$nLUMO/" <INCAR.tmp >INCAR && rm -f INCAR.tmp &&
mpirun -np $processors -genv I_MPI_FABRICS shm:ofa $exe >& vasp.log &&
mkdir LUMO/ && mv PARCHG INCAR vasp.log OUTCAR LUMO/ && sh cleanup.sh && rm WAVECAR ; unset nHOMO ; unset nLUMO
cd ../ # for bader calculations
##################################################### molecular orbital job ends
############## BADER job
mkdir BADER && cd BADER/ && cp $bader_files/* ./ && cp ../WAVECAR ./ && cp ../KPOINTS ./ && cp ../PO* ./ &&
# Step 2
mpirun -np $processors -genv I_MPI_FABRICS shm:ofa $exe >& vasp.log
# Step 3
./chgsum.pl AECCAR0 AECCAR2
# step 4
chmod +x bader && ./bader CHGCAR -ref CHGCAR_sum
# step 5
elements=() ;
awk 'NR==6' POSCAR>>POSCAR_temp
tr -s ' ' '\n'< POSCAR_temp > POSCAR_temp2
rm POSCAR_temp && mv POSCAR_temp2 POSCAR_temp
mapfile -t elements < POSCAR_temp
echo ${elements[@]}
ele_quant=() ; rm POSCAR_temp ;
awk 'NR==7' POSCAR>>POSCAR_temp
tr -s ' ' '\n'< POSCAR_temp > POSCAR_temp2
rm POSCAR_temp && mv POSCAR_temp2 POSCAR_temp
mapfile -t ele_quant < POSCAR_temp
echo ${ele_quant[@]} && rm POSCAR_temp
rm ACF_tmp
sed -e '1,2d' < ACF.dat>>ACF_tmp && head -n -4 ACF_tmp>>ACF_tmp2 && rm ACF_tmp
mv ACF_tmp2 ACF_tmp
readarray -t charge < <(cat ACF_tmp | tr -s ' ' | cut -d' ' -f6) # array name is charge
rm ACF_tmp
echo ${charge[@]}
declare -i N ; declare -i C ; declare -i O ; declare -i H ; declare -i F ; declare -i S ;
N=5 ; C=4 ; O=6 ; H=1 ; F=7 ; S=6
ZVAL=()
for (( i=0; i<=$(( ${#elements[*]} -1 )) ; i++ ))
do
if [[ ${elements[$i]} == N ]]
then
ZVAL+=("$N")
elif [[ ${elements[$i]} == C ]]
then
ZVAL+=("$C")
elif [[ ${elements[$i]} == O ]]
then
ZVAL+=("$O")
elif [[ ${elements[$i]} == H ]]
then
ZVAL+=("$H")
elif [[ ${elements[$i]} == F ]]
then
ZVAL+=("$F")
else
ZVAL+=("$S")
fi
done
echo ${#ZVAL[*]} ; echo ${ZVAL[@]} ;
temp=0 ; array=() ; declare -i yy ; yy=0
for value in "${ele_quant[@]}"
do
for (( i=0+$temp; i<$value+$temp; i++ ))
do
array+=("$i")
#charge[$i]=$(bc<<<"${charge[$i]} - ${ZVAL[$yy]}")
charge[$i]=$(bc<<<"${ZVAL[$yy]} - ${charge[$i]}")
done
temp=${#array[*]}
yy+=1
done
echo ${charge[@]}>>mod_charge.txt && unset yy
rm AECCAR* CHG* WAVECAR
############## BADER job ends
fi