#!/bin/bash

file=$1
len=$2
delta=$3
tA=$4
tB=$5

echo
echo "usage:"
echo "$0 <contcar file> <len> <delta> <type a> <type b>"
echo
echo "args: $@"
echo

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

nsi=`sed -n 6p $file | awk '{ print $1 }'`
nc=`sed -n 6p $file | awk '{ print $2 }'`

((nt=nsi+nc))

((offset=8))
((count=1))

echo "found $nt atoms: Si = $nsi / C = $nc"

while [ "1" ]; do

	if [ $count -le $nsi ]; then
		typea=S
	else
		typea=C
	fi

	if [ "$tA" != "$typea" ]; then
		((count+=1))
		[ $count -gt $nt ] && break
		continue
	fi

	((line=count+offset))

	temp="`sed -n ${line}p $1`"
	xa=`echo $temp | awk '{ print $1 }'`
	ya=`echo $temp | awk '{ print $2 }'`
	za=`echo $temp | awk '{ print $3 }'`

	((ic=1))
	while [ "1" ]; do
		((il=ic+offset))
		if [ $line != $il ]; then
			if [ $ic -le $nsi ] ; then
				typeb=S
			else
				typeb=C
			fi
			if [ "$typeb" != "$tB" ]; then
				((ic+=1))
				[ $ic -gt $nt ] && break
				continue
			fi
			tmpb="`sed -n ${il}p $1`"
			xb=`echo $tmpb | awk '{ print $1 }'`
			yb=`echo $tmpb | awk '{ print $2 }'`
			zb=`echo $tmpb | awk '{ print $3 }'`

			echo "$xa $ya $za $xa $yb $zb $scale $len $delta" | \
			awk ' \
			BEGIN {
			xa=0; xb=0; 
			dx=0; dy=0; dz=0; dist=0
			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"]
			}	
			{
			xa=$1*X1+$2*Y1+$3*Z1
			ya=$1*X2+$2*Y2+$3*Z2
			za=$1*X3+$2*Y3+$3*Z3
			xb=$4*X1+$5*Y1+$6*Z1
			yb=$4*X2+$5*Y2+$6*Z2
			zb=$4*X3+$5*Y3+$6*Z3
			dx=xa-xb
			dy=ya-yb
			dz=za-zb
			dist=sqrt(dx^2+dy^2+dz^2)
			dist*=$7
			if((dist>=($8-$9))&&(dist<=($8+$9))) {
				print $1 " " $2 " " $3
				print $4 " " $5 " " $6 " (" dist ")"
			}
			}'
		fi

		((ic+=1))
		[ $ic -gt $nt ] && break

	done

	((count+=1))
	[ $count -gt $nt ] && break

done

echo "done"