From 0723b4e314a1885b68865086788f6d89fb2b7f13 Mon Sep 17 00:00:00 2001
From: hackbard <hackbard@sage.physik.uni-augsburg.de>
Date: Mon, 5 Oct 2009 14:18:30 +0200
Subject: [PATCH] added search bonds file ...

---
 vasp_tools/search_bonds | 123 ++++++++++++++++++++++++++++++++++++++++
 1 file changed, 123 insertions(+)
 create mode 100755 vasp_tools/search_bonds

diff --git a/vasp_tools/search_bonds b/vasp_tools/search_bonds
new file mode 100755
index 0000000..9b08543
--- /dev/null
+++ b/vasp_tools/search_bonds
@@ -0,0 +1,123 @@
+#!/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"
+
-- 
2.20.1