BADER.sb

#!/bin/bash
#SBATCH --nodes=1
#SBATCH --tasks-per-node=1
#SBATCH -t 02:00:00
#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 ))

bader_files='/oasis/scratch/comet/jkashyap/temp_project/covid19/amber/paper_sim/CORE_OPT/DFT/BADER/FILES'
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 ${charge[@]}
declare -i N ; declare -i C ; declare -i O ; declare -i H ; declare -i F ; declare -i S ;
N=5 ; C=4 ; O=6 ; H=1 ; F=7 ; S=6   # updating this line/variables with the ZVAL from POTCAR files that you are using 
ZVAL=()
for (( i=0; i<=$(( ${#elements[*]} -1 )) ; i++ ))
do
if   [[ ${elements[$i]} == N ]]       # update this loop depending upon elements in your system (consider the system having max element types, if it works for it, it will work for any other system in your project)
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