Script for BigDFT code for extract data generated by Bader analysis

Bader_analysis

#!/bin/bash -e

echo "     ------------------------"
echo "          Bader analysis     "
echo "     ------------------------"
echo "     Reading "free-Atoms/Bonds.csv/txt" from Mercury software file !!!"
echo "     Reading "dipole.yaml" from bader output file"

if [[ -e charges.dat ]] ; then
      rm -r charges.dat
fi

echo " Extracting ... "
echo " Reading number of atoms in the system"
n=`cat posinp.xyz | awk '{printf "%s\n", $1}' | tail -n +3 | sed '/^\s*$/d' | wc -l`
n=`cat posinp.xyz | awk '{printf "%s\n", $1}' | tail -n +3 | sed '/^\s*$/d' | wc -l`
awk 'BEGIN{FS=","; OFS="\t"}{print $1,$2}' free-Atoms.csv | awk '{printf "%s%d\n", $2, $1}' | tail -n +2 > ".sym"
#cat posinp.xyz | awk '{printf "%s\n", $1}' | tail -n +3 | sed '/^\s*$/d' > ".sym"
grep 'Charge core' dipole.yaml | cut -d':' -f2   | awk '{printf "%10.6f\n", $1}' | sed '/^\s*$/d' | tail -$n > ".core"
awk 'BEGIN{FS="Charge elec.:"; OFS="\t"}{print $2}' dipole.yaml | sed '/^\s*$/d' | awk '{printf "%12.6f\n", $1}' | tail -$n > ".elec" 
awk 'BEGIN{FS="Charge net:"; OFS="\t"}{print $2}'   dipole.yaml | sed '/^\s*$/d' | awk '{printf "%12.6f\n", $1}' | tail -$n > ".net"

echo " Writing to a file ... "

echo "                       Charges     " >> charges.dat
echo "        _____________________________________"  >> charges.dat
echo "Atom" "Core" "Elec" "Net"     | awk '{printf "%5s %12s %12s %12s\n", $1, $2, $3, $4}'  >> charges.dat
paste ".sym" ".core" ".elec" ".net" | awk '{printf "%5s %12.6f %12.6f %12.6f\n", $1, $2, $3, $4}'  >> charges.dat

rm -r .sym .core .elec .net

# Parsing the file separated by "," and reverse the columns
#awk 'BEGIN{FS=","; OFS="\t"}{print $1,$2}' free-Atoms.csv | awk '{printf "%s%d\n", $2, $1}'
#
# Bond extrction from a file and display in a standard way.
#awk 'BEGIN{FS=","; OFS="\t"}{print $1,$2,$3,$4}' free-Bonds.csv | awk '{printf "%5d %5s %5s %10.6f\n", $1, $2, $3, $4}'