#!/bin/bash

file=$1
atom=$2
btom=$3

scale=`sed -n 2p $1`

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

((line1=atom+offset))
((line2=btom+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 "atom 1:"
echo $temp

temp="`sed -n ${line2}p $1`"
xb=`echo $temp | awk '{ print $1 }'`
yb=`echo $temp | awk '{ print $2 }'`
zb=`echo $temp | awk '{ print $3 }'`

echo "atom 2:"
echo $temp

echo -en "distance: "
echo "$xa $ya $za $xb $yb $zb $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)
		dx=$1-$4
		dy=$2-$5
		dz=$3-$6
		if(dx>1/2)
			dx-=1
		if(dx<-1/2)
			dx+=1
		if(dy>1/2)
			dy-=1
		if(dy<-1/2)
			dy+=1
		if(dz>1/2)
			dz-=1
		if(dz<-1/2)
			dz+=1
		dxt=dx*X1+dy*Y1+dz*Z1
		dyt=dx*X2+dy*Y2+dz*Z2
		dzt=dx*X3+dy*Y3+dz*Z3
		dist=sqrt(dxt^2+dyt^2+dzt^2)
		dist*=$7
		print dist
	}'

echo