vasp_tools/search_bonds

   1 #!/bin/bash
   2
   3 file=$1
   4 len=$2
   5 delta=$3
   6 tA=$4
   7 tB=$5
   8
   9 echo
  10 echo "usage:"
  11 echo "$0 <contcar file> <len> <delta> <type a> <type b>"
  12 echo
  13 echo "args: $@"
  14 echo
  15
  16 scale=`sed -n 2p $1`
  17
  18 X1=`sed -n 3p $file | awk '{ print $1 }'`
  19 X2=`sed -n 3p $file | awk '{ print $2 }'`
  20 X3=`sed -n 3p $file | awk '{ print $3 }'`
  21
  22 Y1=`sed -n 4p $file | awk '{ print $1 }'`
  23 Y2=`sed -n 4p $file | awk '{ print $2 }'`
  24 Y3=`sed -n 4p $file | awk '{ print $3 }'`
  25
  26 Z1=`sed -n 5p $file | awk '{ print $1 }'`
  27 Z2=`sed -n 5p $file | awk '{ print $2 }'`
  28 Z3=`sed -n 5p $file | awk '{ print $3 }'`
  29
  30 export X1 X2 X3
  31 export Y1 Y2 Y3
  32 export Z1 Z2 Z3
  33
  34 nsi=`sed -n 6p $file | awk '{ print $1 }'`
  35 nc=`sed -n 6p $file | awk '{ print $2 }'`
  36
  37 ((nt=nsi+nc))
  38
  39 ((offset=8))
  40 ((count=1))
  41
  42 echo "found $nt atoms: Si = $nsi / C = $nc"
  43 echo "scale: $scale"
  44 echo "X: $X1 $X2 $X3"
  45 echo "Y: $Y1 $Y2 $Y3"
  46 echo "Z: $Z1 $Z2 $Z3"
  47 echo
  48
  49 while [ "1" ]; do
  50
  51         if [ $count -le $nsi ]; then
  52                 typea=S
  53         else
  54                 typea=C
  55         fi
  56
  57         if [ "$tA" != "$typea" ]; then
  58                 ((count+=1))
  59                 [ $count -gt $nt ] && break
  60                 continue
  61         fi
  62
  63         ((line=count+offset))
  64
  65         temp="`sed -n ${line}p $1`"
  66         xa=`echo $temp | awk '{ print $1 }'`
  67         ya=`echo $temp | awk '{ print $2 }'`
  68         za=`echo $temp | awk '{ print $3 }'`
  69
  70         ((ic=1))
  71         while [ "1" ]; do
  72                 ((il=ic+offset))
  73                 if [ $line != $il ]; then
  74                         if [ $ic -le $nsi ] ; then
  75                                 typeb=S
  76                         else
  77                                 typeb=C
  78                         fi
  79                         if [ "$typeb" != "$tB" ]; then
  80                                 ((ic+=1))
  81                                 [ $ic -gt $nt ] && break
  82                                 continue
  83                         fi
  84                         tmpb="`sed -n ${il}p $1`"
  85                         xb=`echo $tmpb | awk '{ print $1 }'`
  86                         yb=`echo $tmpb | awk '{ print $2 }'`
  87                         zb=`echo $tmpb | awk '{ print $3 }'`
  88
  89                         echo "$xa $ya $za $xb $yb $zb $scale $len $delta" | \
  90                         awk ' \
  91                         BEGIN {
  92                         dxt=0; dyt=0; dzt=0
  93                         dx=0; dy=0; dz=0; dist=0
  94                         X=0; Y=0; Z=0
  95                         X1=ENVIRON["X1"]; X2=ENVIRON["X2"]; X3=ENVIRON["X3"]
  96                         Y1=ENVIRON["Y1"]; Y2=ENVIRON["Y2"]; Y3=ENVIRON["Y3"]
  97                         Z1=ENVIRON["Z1"]; Z2=ENVIRON["Z2"]; Z3=ENVIRON["Z3"]
  98                         }
  99                         {
 100                         X=sqrt(X1^2+X2^2+X3^2)
 101                         Y=sqrt(Y1^2+Y2^2+Y3^2)
 102                         Z=sqrt(Z1^2+Z2^2+Z3^2)
 103                         dx=$1-$4
 104                         dy=$2-$5
 105                         dz=$3-$6
 106                         if(dx>1/2)
 107                                 dx-=1
 108                         if(dx<-1/2)
 109                                 dx+=1
 110                         if(dy>1/2)
 111                                 dy-=1
 112                         if(dy<-1/2)
 113                                 dy+=1
 114                         if(dz>1/2)
 115                                 dz-=1
 116                         if(dz<-1/2)
 117                                 dz+=1
 118                         dxt=dx*X1+dy*Y1+dz*Z1
 119                         dyt=dx*X2+dy*Y2+dz*Z2
 120                         dzt=dx*X3+dy*Y3+dz*Z3
 121                         dist=sqrt(dxt^2+dyt^2+dzt^2)
 122                         dist*=$7
 123                         if((dist>=($8-$9))&&(dist<=($8+$9))) {
 124                                 print ""
 125                                 print $1 " " $2 " " $3
 126                                 print $4 " " $5 " " $6 " (" dist " - " $8 ")"
 127                                 print "displace: " dx*X " " dy*Y " " dz*Z
 128                         }
 129                         }'
 130                 fi
 131
 132                 ((ic+=1))
 133                 [ $ic -gt $nt ] && break
 134
 135         done
 136
 137         ((count+=1))
 138         [ $count -gt $nt ] && break
 139
 140 done
 141
 142 echo "done"
 143