calcIRCvec

#!/bin/bash
#############################################################################
#   Program : Create a serious of vectors                                   #
#                                                                           #
#   Input :                                                                 #
#       $1 = *.xyz ; a serious of structure                                 #
#       format                                                              #
#       number of atome                                                     #
#       name of structure                                                   #
#       name of atom (integer or char.) xyz coordinate                      #
#   Output :                                                                #
#       *.vec.txt ; a serious of vector                                     #
#       format                                                              #
#       number of atom                                                      #
#       name of vector                                                      #
#       xyz vector                                                          #
#                                                                           #
#   Note :                                                                  #
#   the amount of vector is less than 1 by compare to the amount of         #
#   structure                                                               #
#############################################################################

# 2016/11/14, Grace, 1st. ver.
# 2019/06/10, Grace, add the amount of digit =10 

# Step 1. Std-out instruction and check the status of input argument
	test -f $1 || echo $1 is not exist
	[ "$1" == "" ] \
	&& echo "No input argument, please key-in the name of file (.xyz)." \
	&& exit
	echo ''
	echo "--- Program $0 calculate the displacement difference, vector,"
	echo "--- between two structures, and then create a serious of vector"
	echo "--- from file $1"
	name=$(echo $1 | sed 's/.xyz//')
	echo ''
	echo "Output data: $name.vec.txt"
	echo ''
# Step 2. Calculate a serious of vector
	NAtoms=$(head -n 1 $1)
	totline=$(wc -l $1| awk '{print $1}')
	Nfiles=$(($totline/($NAtoms+2)))

	rm -f $name.vec.txt
	for (( i=1; i<=$((Nfiles-1)); i++ ))
	do
		head -n $(( $i*($NAtoms+2) )) $1 | tail -n $NAtoms \
			| awk '{print $2,$3,$4}' > struc0.txt
		head -n $(( ($i+1)*($NAtoms+2) )) $1 | tail -n $NAtoms \
			| awk '{print $2,$3,$4}' > struc1.txt
		echo $NAtoms >> $name.vec.txt
		echo $i >> $name.vec.txt
		# assign the element of arrays
		for (( j=1; j<=$NAtoms; j++ ))
		do
			struc0=($(head -n $j struc0.txt | tail -n 1))
			struc1=($(head -n $j struc1.txt | tail -n 1))
			for (( k=0; k<=2;k++ ))
			do
				vec[$k]=$(echo "scale=10; ${struc1[$k]} - ${struc0[$k]} "|bc)
			#	echo ${struc1[$k]} ${struc0[$k]} ${vec[@]}
			done
			# echo $k ${vec[@]}
			echo ${vec[@]} >> $name.vec.txt	
		done
	done

	rm -f struc0.txt struc1.txt