#!/bin/bash

file=$1
init=$2
atom=$3

if [ -n "$4" ]; then
ref=$4
else
ref=$atom
fi
echo "atom number $ref is used as a reference ..."
echo

scale=`sed -n 2p $file`

X1=`sed -n 3p $file | awk '{ print $1 }'`
X2=`sed -n 3p $file | awk '{ print $2 }'`
X3=`sed -n 3p $file | awk '{ print $3 }'`

Y1=`sed -n 4p $file | awk '{ print $1 }'`
Y2=`sed -n 4p $file | awk '{ print $2 }'`
Y3=`sed -n 4p $file | awk '{ print $3 }'`

Z1=`sed -n 5p $file | awk '{ print $1 }'`
Z2=`sed -n 5p $file | awk '{ print $2 }'`
Z3=`sed -n 5p $file | awk '{ print $3 }'`

export X1 X2 X3
export Y1 Y2 Y3
export Z1 Z2 Z3

((offset=8))

echo "final:"
echo "scale: $scale"
echo "X: $X1 $X2 $X3"
echo "Y: $Y1 $Y2 $Y3"
echo "Z: $Z1 $Z2 $Z3"

((line1=atom+offset))

temp="`sed -n ${line1}p $1`"
xa=`echo $temp | awk '{ print $1 }'`
ya=`echo $temp | awk '{ print $2 }'`
za=`echo $temp | awk '{ print $3 }'`
echo "(x,y,z) = $xa $ya $za $scale"

results=`echo "$xa $ya $za $scale" | \
	awk ' \
	BEGIN {
		X1=ENVIRON["X1"]; X2=ENVIRON["X2"]; X3=ENVIRON["X3"]
		Y1=ENVIRON["Y1"]; Y2=ENVIRON["Y2"]; Y3=ENVIRON["Y3"]
		Z1=ENVIRON["Z1"]; Z2=ENVIRON["Z2"]; Z3=ENVIRON["Z3"]
	}	
	{
		X=sqrt(X1^2+X2^2+X3^2)
		Y=sqrt(Y1^2+Y2^2+Y3^2)
		Z=sqrt(Z1^2+Z2^2+Z3^2)
		x=$1*X
		if(x>1.0)
			x-=1.0;
		if(x<-1.0)
			x+=1.0;
		y=$2*Y
		if(y>1.0)
			y-=1.0;
		if(y<-1.0)
			y+=1.0;
		z=$3*Z
		if(z>1.0)
			z-=1.0;
		if(z<-1.0)
			z+=1.0;

		print x*$4 " " y*$4 " " z*$4
	}'`

xf=`echo $results | awk '{ print $1 }'`
yf=`echo $results | awk '{ print $2 }'`
zf=`echo $results | awk '{ print $3 }'`
echo "---> $xf $yf $zf"

file=$init

scale=`sed -n 2p $file`

X1=`sed -n 3p $file | awk '{ print $1 }'`
X2=`sed -n 3p $file | awk '{ print $2 }'`
X3=`sed -n 3p $file | awk '{ print $3 }'`

Y1=`sed -n 4p $file | awk '{ print $1 }'`
Y2=`sed -n 4p $file | awk '{ print $2 }'`
Y3=`sed -n 4p $file | awk '{ print $3 }'`

Z1=`sed -n 5p $file | awk '{ print $1 }'`
Z2=`sed -n 5p $file | awk '{ print $2 }'`
Z3=`sed -n 5p $file | awk '{ print $3 }'`

export X1 X2 X3
export Y1 Y2 Y3
export Z1 Z2 Z3

((offset=8))

echo
echo "initial:"
echo "scale: $scale"
echo "X: $X1 $X2 $X3"
echo "Y: $Y1 $Y2 $Y3"
echo "Z: $Z1 $Z2 $Z3"

((line1=ref+offset))

temp="`sed -n ${line1}p $file`"
xa=`echo $temp | awk '{ print $1 }'`
ya=`echo $temp | awk '{ print $2 }'`
za=`echo $temp | awk '{ print $3 }'`
echo "(x,y,z) = $xa $ya $za $scale"

results=`echo "$xa $ya $za $scale" | \
	awk ' \
	BEGIN {
		X1=ENVIRON["X1"]; X2=ENVIRON["X2"]; X3=ENVIRON["X3"]
		Y1=ENVIRON["Y1"]; Y2=ENVIRON["Y2"]; Y3=ENVIRON["Y3"]
		Z1=ENVIRON["Z1"]; Z2=ENVIRON["Z2"]; Z3=ENVIRON["Z3"]
	}	
	{
		X=sqrt(X1^2+X2^2+X3^2)
		Y=sqrt(Y1^2+Y2^2+Y3^2)
		Z=sqrt(Z1^2+Z2^2+Z3^2)
		x=$1*X
		if(x>1.0)
			x-=1.0;
		if(x<-1.0)
			x+=1.0;
		y=$2*Y
		if(y>1.0)
			y-=1.0;
		if(y<-1.0)
			y+=1.0;
		z=$3*Z
		if(z>1.0)
			z-=1.0;
		if(z<-1.0)
			z+=1.0;

		print x*$4 " " y*$4 " " z*$4
	}'`

xi=`echo $results | awk '{ print $1 }'`
yi=`echo $results | awk '{ print $2 }'`
zi=`echo $results | awk '{ print $3 }'`
echo "---> $xi $yi $zi"

echo
echo -en "displacement: "
echo $xf $yf $zf $xi $yi $zi | awk '{ print $1-$4 " " $2-$5 " " $3-$6 }'
echo