bugfix + should be correct now (go on to do this for viaualize and pc calc too!)

diff --git a/vasp_tools/search_bonds b/vasp_tools/search_bonds
index 9b08543..88051ee 100755 (executable)
--- 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 +86,41 @@ 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
                        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)
+                       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 "\n"
                                print $1 " " $2 " " $3
-                               print $4 " " $5 " " $6 " (" dist ")"
+                               print $4 " " $5 " " $6 " (" dist " - " $8 ")"
+                               print dx " " dy " " dz " " dxt " " dyt " " dzt
                        }
                        }'
                fi