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 clx="0"; cly="0"; clz="0";
  39
  40 while [ "$1" ]; do
  41         case "$1" in
  42                 -d)             directory=$2;           shift 2;;
  43                 -w)             width=$2;               shift 2;;
  44                 -h)             height=$2;              shift 2;;
  45                 -r)             radius=$2;              shift 2;;
  46                 -nll)           x0=$2; y0=$3; z0=$4;    shift 4;;
  47                 -fur)           x1=$2; y1=$3; z1=$4;    shift 4;;
  48                 -c)             cx=$2; cy=$3; cz=$4;    shift 4;;
  49                 -L)             clx=$2; cly=$3; clz=$4; shift 4;;
  50                 -l)             lx=$2; ly=$3; lz=$4;    shift 4;;
  51                 -o)             ortographic=1;          shift 1;;
  52                 -b)             bx0=$2; by0=$3; bz0=$4;
  53                                 bx1=$5; by1=$6; bz1=$7; shift 7;;
  54                 -B)             bcr=$2;                 shift 2;;
  55                 *)
  56                                 echo "options:"
  57                                 echo "########"
  58                                 echo "directory to progress:"
  59                                 echo "  -d <directory> (mandatory)"
  60                                 echo "png dim:"
  61                                 echo "  -w <width>"
  62                                 echo "  -h <height>"
  63                                 echo "atom size:"
  64                                 echo "  -r <radius>"
  65                                 echo "  -B <bond cylinder radius>"
  66                                 echo "visualization volume:"
  67                                 echo "  -nll <x> <y> <z> (near lower left)"
  68                                 echo "  -fur <x> <y> <z> (far upper right)"
  69                                 echo "  -o (ortographic)"
  70                                 echo "bounding box:"
  71                                 echo "  -b <x0> <y0> <z0> <x1> <y1> <z1>"
  72                                 echo "povray:"
  73                                 echo "  -c <x> <y> <z> (camera position)"
  74                                 echo "  -L <x> <y> <z> (camera look)"
  75                                 echo "  -l <x> <y> <z> (light source)"
  76                                 exit 1;;
  77         esac
  78 done
  79
  80 POVRAY="povray -W${width} -H${height} -d"
  81
  82 if [ -d $directory ]; then
  83         filesource=$directory/atomic_conf_*.xyz
  84 fi
  85
  86 if [ -f $directory ]; then
  87         filesource=$directory
  88 fi
  89
  90 for file in $filesource; do
  91
  92         cat > temp.pov <<-EOF
  93 #include "colors.inc"
  94 #include "textures.inc"
  95 #include "shapes.inc"
  96 #include "glass.inc"
  97 #include "metals.inc"
  98 #include "woods.inc"
  99 #include "stones.inc"
 100 EOF
 101
 102         # meta info
 103         count=`grep '# \[P\]' $file | awk '{ print $3 }'`
 104         time=`grep '# \[P\]' $file | awk '{ print $4 }'`
 105         camloc=`grep '# \[P\]' $file | awk '{ print $5 }'`
 106         [ -n "$cx" -a -n "$cy" -a -n "$cz" ] && camloc="<$cx,$cz,$cy>"
 107
 108         # atoms
 109         if [ -n "$x0" ]; then
 110                 export x0 y0 z0 x1 y1 z1 radius
 111                 cat $file | grep -v '#' | awk '\
 112                 BEGIN {
 113                         x0=ENVIRON["x0"]; y0=ENVIRON["y0"]; z0=ENVIRON["z0"];
 114                         x1=ENVIRON["x1"]; y1=ENVIRON["y1"]; z1=ENVIRON["z1"];
 115                         radius=ENVIRON["radius"];
 116                 }
 117                 {
 118                         if(($2>=x0)&&($3>=y0)&&($4>=z0)&&\
 119                            ($2<=x1)&&($3<=y1)&&($4<=z1)) {
 120                                 print "sphere { <"$2","$4","$3">, "radius" ";
 121                                 print "texture { pigment { color "$5" } ";
 122                                 print "finish { phong 1 metallic } } }";
 123                         }
 124                 }' >> temp.pov
 125         else
 126                 cat $file | grep -v '#' | while read name x y z color temp; do
 127                         cat >> temp.pov <<-EOF
 128 sphere {
 129 <$x, $z, $y>, $radius
 130 texture {
 131 pigment { color $color }
 132 finish {
 133 phong 1
 134 metallic
 135 }
 136 }
 137 }
 138 EOF
 139                 done
 140         fi
 141
 142         # boundaries
 143         if [ -z "$bx0" ]; then
 144
 145         if [ -z "$x0" ]; then
 146
 147         cat $file | grep '# \[D\]' | while read foo bar x1 y1 z1 x2 y2 z2 ; do
 148                 draw_cyl $x1 $z1 $y1 $x2 $z2 $y2 0.05
 149         done
 150
 151         else
 152                 # manually drawing the 3x4 boundaries ...
 153                 draw_cyl $x0 $y0 $z0 $x1 $y0 $z0
 154                 draw_cyl $x0 $y0 $z0 $x0 $y1 $z0
 155                 draw_cyl $x1 $y1 $z0 $x1 $y0 $z0
 156                 draw_cyl $x0 $y1 $z0 $x1 $y1 $z0
 157
 158                 draw_cyl $x0 $y0 $z1 $x1 $y0 $z1
 159                 draw_cyl $x0 $y0 $z1 $x0 $y1 $z1
 160                 draw_cyl $x1 $y1 $z1 $x1 $y0 $z1
 161                 draw_cyl $x0 $y1 $z1 $x1 $y1 $z1
 162
 163                 draw_cyl $x0 $y0 $z1 $x0 $y0 $z0
 164                 draw_cyl $x0 $y1 $z1 $x0 $y1 $z0
 165                 draw_cyl $x1 $y0 $z1 $x1 $y0 $z0
 166                 draw_cyl $x1 $y1 $z1 $x1 $y1 $z0
 167         fi
 168
 169         else
 170
 171                 # manually drawing the 3x4 boundaries specified by argv ...
 172                 draw_cyl $bx0 $by0 $bz0 $bx1 $by0 $bz0
 173                 draw_cyl $bx0 $by0 $bz0 $bx0 $by1 $bz0
 174                 draw_cyl $bx1 $by1 $bz0 $bx1 $by0 $bz0
 175                 draw_cyl $bx0 $by1 $bz0 $bx1 $by1 $bz0
 176
 177                 draw_cyl $bx0 $by0 $bz1 $bx1 $by0 $bz1
 178                 draw_cyl $bx0 $by0 $bz1 $bx0 $by1 $bz1
 179                 draw_cyl $bx1 $by1 $bz1 $bx1 $by0 $bz1
 180                 draw_cyl $bx0 $by1 $bz1 $bx1 $by1 $bz1
 181
 182                 draw_cyl $bx0 $by0 $bz1 $bx0 $by0 $bz0
 183                 draw_cyl $bx0 $by1 $bz1 $bx0 $by1 $bz0
 184                 draw_cyl $bx1 $by0 $bz1 $bx1 $by0 $bz0
 185                 draw_cyl $bx1 $by1 $bz1 $bx1 $by1 $bz0
 186
 187         fi
 188
 189         # bonds
 190         if [ -n "$bcr" ]; then
 191
 192                 if [ -z "$x0" ]; then
 193
 194         cat $file | grep '# \[B\]' | while read foo bar x1 y1 z1 x2 y2 z2 ; do
 195                 draw_bond $x1 $z1 $y1 $x2 $z2 $y2 $bcr
 196         done
 197
 198                 else
 199
 200                 export x0 y0 z0 x1 y1 z1 bcr
 201                 cat $file | grep '# \[B\]' | awk '\
 202                 BEGIN {
 203                         x0=ENVIRON["x0"]; y0=ENVIRON["y0"]; z0=ENVIRON["z0"];
 204                         x1=ENVIRON["x1"]; y1=ENVIRON["y1"]; z1=ENVIRON["z1"];
 205                         bcr=ENVIRON["bcr"];
 206                 }
 207                 {
 208                         if(($3>=x0)&&($4>=y0)&&($5>=z0)&&\
 209                            ($3<=x1)&&($4<=y1)&&($5<=z1)) {
 210                                 print "cylinder {";
 211                                 print "<"$3","$5","$4">,";
 212                                 print "<"$6","$8","$7">, "bcr;
 213                                 print "pigment { color Blue }";
 214                                 print "}";
 215                         }
 216                 }' >> temp.pov
 217
 218                 fi
 219         fi
 220
 221         # add camera and light source
 222         cat >> temp.pov <<-EOF
 223 camera {
 224 EOF
 225         if [ -n "$ortographic" ]; then  cat >> temp.pov <<-EOF
 226 orthographic
 227 EOF
 228         fi
 229         cat >> temp.pov <<-EOF
 230 location $camloc
 231 look_at <$clx,$clz,$clz>
 232 }
 233 light_source { <0,100,-100> color White shadowless }
 234 EOF
 235
 236         # mv png
 237         $POVRAY temp.pov > /dev/null 2>&1
 238         mv temp.png `echo $file | sed 's/\.xyz/\.png/'`
 239
 240 done
 241
 242 echo "done"