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#!/bin/bash

CHARGE_STRING="Neutral Cation"
OMEGA_VALUE="0.1 0.2 0.4"

template_file=BdPC0058.inp
input_file=BdPC0058_CHARGE_STRING_wOMEGA_VALUE.inp

for i in $CHARGE_STRING ; do
    work_dir=CHARGE_STRING${i}_OMEGA_VALUE${j}
    for j in $OMEGA_VALUE ; do
        work_dir=CHARGE_STRING${i}OMEGA_VALUE${j}
        if [ ! -d $work_dir ] ; then
            mkdir $work_dir
        else
            rm -r $work_dir/*
        fi
        sed -e "s/CHARGE_STRING/${i}/g" \
            -e "s/CHARGE_VALUE/${???}/g" \
            -e "s/MULTIPLICITY_VALUE/${???}/g" \
            -e "s/OMEGA_VALUE/${j}/g" \
            -e "s/checkpoint/BdPC0058_CHARGE_STRING${i}_wOMEGA_VALUE${jj}/g" \
            if CHARGE_STRING{i}="Neutral"
                CHARGE_VALUE+="0"
                MULTIPLICITY_VALUE+="1"
            else
                CHARGE_VALUE+="+1"
                MULTIPLICITY_VALUE+="2"
            fi
            $template_file > $work_dir/$input_file
done
done