hartree2eV

#!/bin/bash
#####################################################################
#	Program :														#
#				Change the energy unit from Hartree to eV			#
#	Input :															#
#			$1 = *.txt												#
#	Output :														#
#			PES_eV.txt												#
##################################################################### 

# 2016/10/12, Grace, 1st. ver.

# Step 0. Check the existance of input file
[ "$1" == "" ] && echo 'No input argument, stop the program.' && exit
[ -f "$1" ] || echo "File is not exist" 
[ -f "$1" ] || exit
# Step 1. Get the number of grid points
#		  Get the number of state
num_pts=$(wc $1|awk '{print $1}')
num_column=$(awk -F ' ' 'NR==2{print NF}' $1)
	# fix bug, 2016/09/09, Grace. if the first row is not completed
	
num_state=$(($num_column-1))
# Step 2. Decide the energy reference, and then change the energy unit 
#		  from Hartree to kcal/mol
ref=$(awk '{print $2}' $1|head -n 1)
if [ "$ref" == '' ]
then 
	ref=$(echo 0)
fi

for energy in `awk '{print $2}' $1`
do 
	judge=`echo $ref '>' $energy | bc -l`
	if  [ $judge == 1 ]
	then
		ref=$(echo $energy)
	fi
done

rm -f tmp*.txt
for (( i=2; i<=$num_column; i++))
do
	awk "{print \$$i}" $1 > list.txt
	line=$(wc list.txt | awk '{print $1}')
	for (( j=1;j<=$line;j++))
	do 
		energy=$(head -n $j list.txt | tail -n 1)
		if [ "$energy" == "" ] 
		then
			echo "" >> tmp$i.txt
		else
			echo "( $energy - $ref ) * 27.212" | bc >> tmp$i.txt
		fi
	done
done
# Step 3. Store all information into file PES_kcal.txt
awk '{print $1}' $1 > x.txt
line=$(echo x.txt)
for (( i=2; i<=$num_column; i++))
do
	line=$(echo "$line tmp$i.txt")
done
paste `echo $line` > PES_eV.txt
rm -f x.txt list.txt tmp*.txt