visualize

   1 #!/bin/sh
   2
   3 #
   4 # visualization script
   5 # author: frank.zirkelbach@physik.uni-augsburg.de
   6 #
   7
   8 # help function
   9 draw_cyl() {
  10         cat >> temp.pov <<-EOF
  11 cylinder {
  12 <$1, $3, $2>, <$4, $6, $5>, 0.05
  13 pigment { color White }
  14 }
  15 EOF
  16 }
  17 draw_bond() {
  18         cat >> temp.pov <<-EOF
  19 cylinder {
  20 <$1, $3, $2>, <$4, $6, $5>, $7
  21 pigment { color Blue }
  22 }
  23 EOF
  24 }
  25
  26 directory="doesnt_exist____for_sure"
  27 width="640"
  28 height="480"
  29 radius="1.0"
  30 x0=""; y0=""; z0="";
  31 x1=""; y1=""; z1="";
  32 cx=""; cy=""; cz="";
  33 lx="0"; ly="-100"; lz="100";
  34 ortographic=""
  35 bx0=""; by0=""; bz0="";
  36 bx1=""; by1=""; bz1="";
  37 bcr="";
  38
  39 while [ "$1" ]; do
  40         case "$1" in
  41                 -d)             directory=$2;           shift 2;;
  42                 -w)             width=$2;               shift 2;;
  43                 -h)             height=$2;              shift 2;;
  44                 -r)             radius=$2;              shift 2;;
  45                 -nll)           x0=$2; y0=$3; z0=$4;    shift 4;;
  46                 -fur)           x1=$2; y1=$3; z1=$4;    shift 4;;
  47                 -c)             cx=$2; cy=$3; cz=$4;    shift 4;;
  48                 -l)             lx=$2; ly=$3; lz=$4;    shift 4;;
  49                 -o)             ortographic=1;          shift 1;;
  50                 -b)             bx0=$2; by0=$3; bz0=$4;
  51                                 bx1=$5; by1=$6; bz1=$7; shift 7;;
  52                 -B)             bcr=$2;                 shift 2;;
  53                 *)
  54                                 echo "options:"
  55                                 echo "########"
  56                                 echo "directory to progress:"
  57                                 echo "  -d <directory> (mandatory)"
  58                                 echo "png dim:"
  59                                 echo "  -w <width>"
  60                                 echo "  -h <height>"
  61                                 echo "atom size:"
  62                                 echo "  -r <radius>"
  63                                 echo "  -B <bond cylinder radius>"
  64                                 echo "visualization volume:"
  65                                 echo "  -nll <x> <y> <z> (near lower left)"
  66                                 echo "  -fur <x> <y> <z> (far upper right)"
  67                                 echo "  -o (ortographic)"
  68                                 echo "bounding box:"
  69                                 echo "  -b <x0> <y0> <z0> <x1> <y1> <z1>"
  70                                 echo "povray:"
  71                                 echo "  -c <x> <y> <z> (camera position)"
  72                                 echo "  -l <x> <y> <z> (light source)"
  73                                 exit 1;;
  74         esac
  75 done
  76
  77 if [ ! -d $directory ] ; then
  78         echo "no valid directory"
  79         exit 1
  80 fi
  81
  82 POVRAY="povray -W${width} -H${height} -d"
  83
  84 for file in $directory/atomic_conf_*.xyz; do
  85
  86         cat > temp.pov <<-EOF
  87 #include "colors.inc"
  88 #include "textures.inc"
  89 #include "shapes.inc"
  90 #include "glass.inc"
  91 #include "metals.inc"
  92 #include "woods.inc"
  93 #include "stones.inc"
  94 EOF
  95
  96         # meta info
  97         count=`grep '# \[P\]' $file | awk '{ print $3 }'`
  98         time=`grep '# \[P\]' $file | awk '{ print $4 }'`
  99         camloc=`grep '# \[P\]' $file | awk '{ print $5 }'`
 100         [ -n "$cx" -a -n "$cy" -a -n "$cz" ] && camloc="<$cx,$cz,$cy>"
 101
 102         # atoms
 103         if [ -n "$x0" ]; then
 104                 export x0 y0 z0 x1 y1 z1 radius
 105                 cat $file | grep -v '#' | awk '\
 106                 BEGIN {
 107                         x0=ENVIRON["x0"]; y0=ENVIRON["y0"]; z0=ENVIRON["z0"];
 108                         x1=ENVIRON["x1"]; y1=ENVIRON["y1"]; z1=ENVIRON["z1"];
 109                         radius=ENVIRON["radius"];
 110                 }
 111                 {
 112                         if(($2>=x0)&&($3>=y0)&&($4>=z0)&&\
 113                            ($2<=x1)&&($3<=y1)&&($4<=z1)) {
 114                                 print "sphere { <"$2","$4","$3">, "radius" ";
 115                                 print "texture { pigment { color "$5" } ";
 116                                 print "finish { phong 1 metallic } } }";
 117                         }
 118                 }' >> temp.pov
 119         else
 120                 cat $file | grep -v '#' | while read name x y z color temp; do
 121                         cat >> temp.pov <<-EOF
 122 sphere {
 123 <$x, $z, $y>, $radius
 124 texture {
 125 pigment { color $color }
 126 finish {
 127 phong 1
 128 metallic
 129 }
 130 }
 131 }
 132 EOF
 133                 done
 134         fi
 135
 136         # boundaries
 137         if [ -z "$bx0" ]; then
 138
 139         if [ -z "$x0" ]; then
 140
 141         cat $file | grep '# \[D\]' | while read foo bar x1 y1 z1 x2 y2 z2 ; do
 142                 draw_cyl $x1 $z1 $y1 $x2 $z2 $y2 0.05
 143         done
 144
 145         else
 146                 # manually drawing the 3x4 boundaries ...
 147                 draw_cyl $x0 $y0 $z0 $x1 $y0 $z0
 148                 draw_cyl $x0 $y0 $z0 $x0 $y1 $z0
 149                 draw_cyl $x1 $y1 $z0 $x1 $y0 $z0
 150                 draw_cyl $x0 $y1 $z0 $x1 $y1 $z0
 151
 152                 draw_cyl $x0 $y0 $z1 $x1 $y0 $z1
 153                 draw_cyl $x0 $y0 $z1 $x0 $y1 $z1
 154                 draw_cyl $x1 $y1 $z1 $x1 $y0 $z1
 155                 draw_cyl $x0 $y1 $z1 $x1 $y1 $z1
 156
 157                 draw_cyl $x0 $y0 $z1 $x0 $y0 $z0
 158                 draw_cyl $x0 $y1 $z1 $x0 $y1 $z0
 159                 draw_cyl $x1 $y0 $z1 $x1 $y0 $z0
 160                 draw_cyl $x1 $y1 $z1 $x1 $y1 $z0
 161         fi
 162
 163         else
 164
 165                 # manually drawing the 3x4 boundaries specified by argv ...
 166                 draw_cyl $bx0 $by0 $bz0 $bx1 $by0 $bz0
 167                 draw_cyl $bx0 $by0 $bz0 $bx0 $by1 $bz0
 168                 draw_cyl $bx1 $by1 $bz0 $bx1 $by0 $bz0
 169                 draw_cyl $bx0 $by1 $bz0 $bx1 $by1 $bz0
 170
 171                 draw_cyl $bx0 $by0 $bz1 $bx1 $by0 $bz1
 172                 draw_cyl $bx0 $by0 $bz1 $bx0 $by1 $bz1
 173                 draw_cyl $bx1 $by1 $bz1 $bx1 $by0 $bz1
 174                 draw_cyl $bx0 $by1 $bz1 $bx1 $by1 $bz1
 175
 176                 draw_cyl $bx0 $by0 $bz1 $bx0 $by0 $bz0
 177                 draw_cyl $bx0 $by1 $bz1 $bx0 $by1 $bz0
 178                 draw_cyl $bx1 $by0 $bz1 $bx1 $by0 $bz0
 179                 draw_cyl $bx1 $by1 $bz1 $bx1 $by1 $bz0
 180
 181         fi
 182
 183         # bonds
 184         if [ -n "$bcr" ]; then
 185
 186                 if [ -z "$x0" ]; then
 187
 188         cat $file | grep '# \[B\]' | while read foo bar x1 y1 z1 x2 y2 z2 ; do
 189                 draw_bond $x1 $z1 $y1 $x2 $z2 $y2 $bcr
 190         done
 191
 192                 else
 193
 194                 export x0 y0 z0 x1 y1 z1 bcr
 195                 cat $file | grep '# \[B\]' | awk '\
 196                 BEGIN {
 197                         x0=ENVIRON["x0"]; y0=ENVIRON["y0"]; z0=ENVIRON["z0"];
 198                         x1=ENVIRON["x1"]; y1=ENVIRON["y1"]; z1=ENVIRON["z1"];
 199                         bcr=ENVIRON["bcr"];
 200                 }
 201                 {
 202                         if(($3>=x0)&&($4>=y0)&&($5>=z0)&&\
 203                            ($3<=x1)&&($4<=y1)&&($5<=z1)) {
 204                                 print "cylinder {";
 205                                 print "<"$3","$5","$4">,";
 206                                 print "<"$6","$8","$7">, "bcr;
 207                                 print "pigment { color Blue }";
 208                                 print "}";
 209                         }
 210                 }' >> temp.pov
 211
 212                 fi
 213         fi
 214
 215         # add camera and light source
 216         cat >> temp.pov <<-EOF
 217 camera {
 218 EOF
 219         if [ -n "$ortographic" ]; then  cat >> temp.pov <<-EOF
 220 orthographic
 221 EOF
 222         fi
 223         cat >> temp.pov <<-EOF
 224 location $camloc
 225 look_at <0,0,0>
 226 }
 227 light_source { <0,100,-100> color White shadowless }
 228 EOF
 229
 230         # mv png
 231         $POVRAY temp.pov > /dev/null 2>&1
 232         mv temp.png `echo $file | sed 's/\.xyz/\.png/'`
 233
 234 done
 235
 236 echo "done"