X-Git-Url: https://hackdaworld.org/gitweb/?p=physik%2Fposic.git;a=blobdiff_plain;f=vasp_tools%2Fsearch_bonds;fp=vasp_tools%2Fsearch_bonds;h=29b6d1c5c1200612581fb937aa382f9cd7cd8425;hp=0000000000000000000000000000000000000000;hb=6e6d7126ea9a845f11637d8e1b8eb2b570ac4dc9;hpb=97dc63eb6a519b8e1f4fbfaa9760dd94539436b0

diff --git a/vasp_tools/search_bonds b/vasp_tools/search_bonds
new file mode 100755
index 0000000..29b6d1c
--- /dev/null
+++ b/vasp_tools/search_bonds
@@ -0,0 +1,144 @@
+#!/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"
+echo "scale: $scale"
+echo "X: $X1 $X2 $X3"
+echo "Y: $Y1 $Y2 $Y3"
+echo "Z: $Z1 $Z2 $Z3"
+echo
+
+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 $xb $yb $zb $scale $len $delta $count $ic" | \
+			awk ' \
+			BEGIN {
+			dxt=0; dyt=0; dzt=0
+			dx=0; dy=0; dz=0; dist=0
+			X=0; Y=0; Z=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"]
+			}	
+			{
+			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
+			if((dist>=($8-$9))&&(dist<=($8+$9))) {
+				print ""
+				print "atoms: " $10 " - " $11
+				print $1 " " $2 " " $3
+				print $4 " " $5 " " $6 " (" dist " - " $8 ")"
+				print "displace: " dx*X " " dy*Y " " dz*Z
+			}
+			}'
+		fi
+
+		((ic+=1))
+		[ $ic -gt $nt ] && break
+
+	done
+
+	((count+=1))
+	[ $count -gt $nt ] && break
+
+done
+
+echo "done"
+