X-Git-Url: https://hackdaworld.org/gitweb/?a=blobdiff_plain;f=vasp_tools%2Fsearch_bonds;h=5fa2e93fc2a51e87663227c7284139c97b66c022;hb=170485f4072200994932e5675bad4e6e3d35b4e6;hp=9b085437ac371f2596447ddc3275b90472c3af48;hpb=0723b4e314a1885b68865086788f6d89fb2b7f13;p=physik%2Fposic.git

diff --git a/vasp_tools/search_bonds b/vasp_tools/search_bonds
index 9b08543..5fa2e93 100755
--- a/vasp_tools/search_bonds
+++ b/vasp_tools/search_bonds
@@ -40,6 +40,11 @@ nc=`sed -n 6p $file | awk '{ print $2 }'`
 ((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
 
@@ -81,30 +86,45 @@ while [ "1" ]; do
 			yb=`echo $tmpb | awk '{ print $2 }'`
 			zb=`echo $tmpb | awk '{ print $3 }'`
 
-			echo "$xa $ya $za $xa $yb $zb $scale $len $delta" | \
+			echo "$xa $ya $za $xb $yb $zb $scale $len $delta" | \
 			awk ' \
 			BEGIN {
-			xa=0; xb=0; 
+			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"]
 			}	
 			{
-			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)
+			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 $1 " " $2 " " $3
-				print $4 " " $5 " " $6 " (" dist ")"
+				print $4 " " $5 " " $6 " (" dist " - " $8 ")"
+				print "displace: " dx*X " " dy*Y " " dz*Z
 			}
 			}'
 		fi