hartree2kcal

#!/bin/bash
#####################################################################
#	Program :														#
#				Change the energy unit from Hartree to kcal/mol		#
#	Input :															#
#			$1 = *													#
#	Output :														#
#			* (User defined)										#
##################################################################### 

# 2016/09/15, Grace, 1st. ver.
# 2016/11/16, Grace, 2nd. ver. 
# 2017/04/28, Grace, 3rd. ver.
# 2017/12/28, Grace, tmp. ver. close stdin
# Step 0. Check the existance of input file
[ "$1" == "" ] && echo 'No 1st. input argument, stop the program.' && exit
[ -f "$1" ] || echo "$1 is not exist" 
[ -f "$1" ] || exit
[ "$2" == "" ] && echo 'No 2nd. input argument, stop the program.' && exit
# Step 1. Get the number of grid points
#		  Get the number of state
num_pts=$(wc $1|awk '{print $1}')
num_column=$(cat $1 | sort -n -k 2 | head -n 1 | awk '{FS = " "} ; {print NF}')
	# fix bug, 2017/11/27, Grace. remove fail jobs
num_state=$(($num_column-1))
# Step 2. Decide the energy reference, and then change the energy unit 
#		  from Hartree to kcal/mol
read -p 'Use the smallest energy as the reference (yes/no): ' judge
#judge='yes'
case $judge in 
	"yes") # smallest one as ref.
		ref=$(awk '{print $2}' $1|sed '/^$/d' | sort -nr  | tail -n 1)
	;;
	"no")
		read -p 'Key-in the energy of reference: ' ref
	;;
	"*")
		echo "Wrong type! exit" 
		exit
esac

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 - $ref ) * 627.5095" | bc >> tmp$i.txt
		fi
	done
done
# Step 3. Store all information into file $2
echo "output file : $2"
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` > $2
rm -f x.txt list.txt tmp*.txt