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
  44 while [ "1" ]; do
  45
  46         if [ $count -le $nsi ]; then
  47                 typea=S
  48         else
  49                 typea=C
  50         fi
  51
  52         if [ "$tA" != "$typea" ]; then
  53                 ((count+=1))
  54                 [ $count -gt $nt ] && break
  55                 continue
  56         fi
  57
  58         ((line=count+offset))
  59
  60         temp="`sed -n ${line}p $1`"
  61         xa=`echo $temp | awk '{ print $1 }'`
  62         ya=`echo $temp | awk '{ print $2 }'`
  63         za=`echo $temp | awk '{ print $3 }'`
  64
  65         ((ic=1))
  66         while [ "1" ]; do
  67                 ((il=ic+offset))
  68                 if [ $line != $il ]; then
  69                         if [ $ic -le $nsi ] ; then
  70                                 typeb=S
  71                         else
  72                                 typeb=C
  73                         fi
  74                         if [ "$typeb" != "$tB" ]; then
  75                                 ((ic+=1))
  76                                 [ $ic -gt $nt ] && break
  77                                 continue
  78                         fi
  79                         tmpb="`sed -n ${il}p $1`"
  80                         xb=`echo $tmpb | awk '{ print $1 }'`
  81                         yb=`echo $tmpb | awk '{ print $2 }'`
  82                         zb=`echo $tmpb | awk '{ print $3 }'`
  83
  84                         echo "$xa $ya $za $xa $yb $zb $scale $len $delta" | \
  85                         awk ' \
  86                         BEGIN {
  87                         xa=0; xb=0;
  88                         dx=0; dy=0; dz=0; dist=0
  89                         X1=ENVIRON["X1"]; X2=ENVIRON["X2"]; X3=ENVIRON["X3"]
  90                         Y1=ENVIRON["Y1"]; Y2=ENVIRON["Y2"]; Y3=ENVIRON["Y3"]
  91                         Z1=ENVIRON["Z1"]; Z2=ENVIRON["Z2"]; Z3=ENVIRON["Z3"]
  92                         }
  93                         {
  94                         xa=$1*X1+$2*Y1+$3*Z1
  95                         ya=$1*X2+$2*Y2+$3*Z2
  96                         za=$1*X3+$2*Y3+$3*Z3
  97                         xb=$4*X1+$5*Y1+$6*Z1
  98                         yb=$4*X2+$5*Y2+$6*Z2
  99                         zb=$4*X3+$5*Y3+$6*Z3
 100                         dx=xa-xb
 101                         dy=ya-yb
 102                         dz=za-zb
 103                         dist=sqrt(dx^2+dy^2+dz^2)
 104                         dist*=$7
 105                         if((dist>=($8-$9))&&(dist<=($8+$9))) {
 106                                 print $1 " " $2 " " $3
 107                                 print $4 " " $5 " " $6 " (" dist ")"
 108                         }
 109                         }'
 110                 fi
 111
 112                 ((ic+=1))
 113                 [ $ic -gt $nt ] && break
 114
 115         done
 116
 117         ((count+=1))
 118         [ $count -gt $nt ] && break
 119
 120 done
 121
 122 echo "done"
 123