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 # defaults
  27
  28 lc=5.429
  29 directory="doesnt_exist____for_sure"
  30 width="640"
  31 height="480"
  32 radius="0.6"
  33 x0="-0.6"; y0="-0.6"; z0="-0.6";
  34 x1="0.6"; y1="0.6"; z1="0.6";
  35 cx=""; cy=""; cz="";
  36 lx="0"; ly="-100"; lz="100";
  37 ortographic=""
  38 bx0=""; by0=""; bz0="";
  39 bx1=""; by1=""; bz1="";
  40 bcr="";
  41 clx="0"; cly="0"; clz="0";
  42 extra=0
  43
  44 # parse argv
  45
  46 while [ "$1" ]; do
  47         case "$1" in
  48                 -d)             directory=$2;           shift 2;;
  49                 -w)             width=$2;               shift 2;;
  50                 -h)             height=$2;              shift 2;;
  51                 -r)             radius=$2;              shift 2;;
  52                 -nll)           x0=$2; y0=$3; z0=$4;    shift 4;;
  53                 -fur)           x1=$2; y1=$3; z1=$4;    shift 4;;
  54                 -c)             cx=$2; cy=$3; cz=$4;    shift 4;;
  55                 -L)             clx=$2; cly=$3; clz=$4; shift 4;;
  56                 -l)             lx=$2; ly=$3; lz=$4;    shift 4;;
  57                 -o)             ortographic=1;          shift 1;;
  58                 -b)             bx0=$2; by0=$3; bz0=$4;
  59                                 bx1=$5; by1=$6; bz1=$7; shift 7;;
  60                 -B)             bcr=$2;                 shift 2;;
  61                 -C)             lc=$2;                  shift 2;;
  62                 -e)             extra=1;                shift 1;;
  63                 *)
  64                                 echo "options:"
  65                                 echo "########"
  66                                 echo "directory to progress:"
  67                                 echo "  -d <directory> (mandatory)"
  68                                 echo "png dim:"
  69                                 echo "  -w <width>"
  70                                 echo "  -h <height>"
  71                                 echo "atom size:"
  72                                 echo "  -r <radius>"
  73                                 echo "  -B <bond cylinder radius>"
  74                                 echo "unit cell:"
  75                                 echo "  -C <lattice constant>"
  76                                 echo "visualization volume:"
  77                                 echo "  -nll <x> <y> <z> (near lower left)"
  78                                 echo "  -fur <x> <y> <z> (far upper right)"
  79                                 echo "  -o (ortographic)"
  80                                 echo "bounding box:"
  81                                 echo "  -b <x0> <y0> <z0> <x1> <y1> <z1>"
  82                                 echo "povray:"
  83                                 echo "  -c <x> <y> <z> (camera position)"
  84                                 echo "  -L <x> <y> <z> (camera look)"
  85                                 echo "  -l <x> <y> <z> (light source)"
  86                                 exit 1;;
  87         esac
  88 done
  89
  90 # calculation from lattic eunits to angstroms
  91
  92 [ "$lc" = "sic" ] && lc=4.359
  93 [ "$lc" = "si" ] && lc=5.429
  94 [ "$lc" = "c" ] && lc=3.566
  95
  96 offset=`echo 0.125 \* $lc | bc`
  97 #offset=0.0
  98
  99 x0=`echo $x0 \* $lc + $offset | bc`
 100 y0=`echo $y0 \* $lc + $offset | bc`
 101 z0=`echo $z0 \* $lc + $offset | bc`
 102 x1=`echo $x1 \* $lc + $offset | bc`
 103 y1=`echo $y1 \* $lc + $offset | bc`
 104 z1=`echo $z1 \* $lc + $offset | bc`
 105
 106 clx=`echo $clx \* $lc + $offset | bc`
 107 cly=`echo $cly \* $lc + $offset | bc`
 108 clz=`echo $clz \* $lc + $offset | bc`
 109
 110 if [ -n "$cx" -a -n "$cy" -a -n "$cz" ]; then
 111         cx=`echo $cx \* $lc + $offset | bc`
 112         cy=`echo $cy \* $lc + $offset | bc`
 113         cz=`echo $cz \* $lc + $offset | bc`
 114 fi
 115
 116 if [ -n "$bx0" ]; then
 117         bx0=`echo $bx0 \* $lc + $offset | bc`
 118         by0=`echo $by0 \* $lc + $offset | bc`
 119         bz0=`echo $bz0 \* $lc + $offset | bc`
 120         bx1=`echo $bx1 \* $lc + $offset | bc`
 121         by1=`echo $by1 \* $lc + $offset | bc`
 122         bz1=`echo $bz1 \* $lc + $offset | bc`
 123 fi
 124
 125 # povray command
 126
 127 POVRAY="povray -W${width} -H${height} -d"
 128
 129 # convert options
 130
 131 COPTS="-font /usr/share/fonts/truetype/ttf-dejavu/DejaVuSans.ttf"
 132 COPTS="$COPTS -depth 8 -fill white -stroke blue -pointsize 24"
 133
 134 # do it ...
 135
 136 if [ -d $directory ]; then
 137         filesource=$directory/atomic_conf_*.xyz
 138 fi
 139
 140 if [ -f $directory ]; then
 141         filesource=$directory
 142 fi
 143
 144 for file in $filesource; do
 145
 146         cat > temp.pov <<-EOF
 147 #include "colors.inc"
 148 #include "textures.inc"
 149 #include "shapes.inc"
 150 #include "glass.inc"
 151 #include "metals.inc"
 152 #include "woods.inc"
 153 #include "stones.inc"
 154 EOF
 155
 156         # meta info
 157         count=`grep '# \[P\]' $file | awk '{ print $3 }'`
 158         time=`grep '# \[P\]' $file | awk '{ print $4 }'`
 159         camloc=`grep '# \[P\]' $file | awk '{ print $5 }'`
 160         [ -n "$cx" -a -n "$cy" -a -n "$cz" ] && camloc="<$cx,$cz,$cy>"
 161
 162         # atoms
 163         if [ -n "$x0" ]; then
 164                 export x0 y0 z0 x1 y1 z1 radius extra
 165                 cat $file | grep -v '#' | awk '\
 166                 BEGIN {
 167                         x0=ENVIRON["x0"]; y0=ENVIRON["y0"]; z0=ENVIRON["z0"];
 168                         x1=ENVIRON["x1"]; y1=ENVIRON["y1"]; z1=ENVIRON["z1"];
 169                         radius=ENVIRON["radius"]; extra=ENVIRON["extra"];
 170                 }
 171                 {
 172                         if(($2>=x0)&&($3>=y0)&&($4>=z0)&&\
 173                            ($2<=x1)&&($3<=y1)&&($4<=z1)) {
 174                                 print "sphere { <"$2","$4","$3">, "radius" ";
 175                                 if(extra)
 176                 print "texture { pigment { color rgb<"$6/4.4",0,"1-$6/4.4"> } ";
 177                                 else
 178                 print "texture { pigment { color "$5" } ";
 179                                 print "finish { phong 1 metallic } } }";
 180                         }
 181                 }' >> temp.pov
 182         else
 183                 cat $file | grep -v '#' | while read name x y z color temp; do
 184                         cat >> temp.pov <<-EOF
 185 sphere {
 186 <$x, $z, $y>, $radius
 187 texture {
 188 pigment { color $color }
 189 finish {
 190 phong 1
 191 metallic
 192 }
 193 }
 194 }
 195 EOF
 196                 done
 197         fi
 198
 199         # boundaries
 200         if [ -z "$bx0" ]; then
 201
 202         #if [ -z "$x0" ]; then
 203
 204         cat $file | grep '# \[D\]' | while read foo bar x1 y1 z1 x2 y2 z2 ; do
 205                 draw_cyl $x1 $y1 $z1 $x2 $y2 $z2 0.05
 206         done
 207
 208         #else
 209
 210                 # manually drawing the 3x4 boundaries ...
 211 #               draw_cyl $x0 $y0 $z0 $x1 $y0 $z0
 212 #               draw_cyl $x0 $y0 $z0 $x0 $y1 $z0
 213 #               draw_cyl $x1 $y1 $z0 $x1 $y0 $z0
 214 #               draw_cyl $x0 $y1 $z0 $x1 $y1 $z0
 215
 216 #               draw_cyl $x0 $y0 $z1 $x1 $y0 $z1
 217 #               draw_cyl $x0 $y0 $z1 $x0 $y1 $z1
 218 #               draw_cyl $x1 $y1 $z1 $x1 $y0 $z1
 219 #               draw_cyl $x0 $y1 $z1 $x1 $y1 $z1
 220
 221 #               draw_cyl $x0 $y0 $z1 $x0 $y0 $z0
 222 #               draw_cyl $x0 $y1 $z1 $x0 $y1 $z0
 223 #               draw_cyl $x1 $y0 $z1 $x1 $y0 $z0
 224 #               draw_cyl $x1 $y1 $z1 $x1 $y1 $z0
 225 #       fi
 226
 227         else
 228
 229                 # manually drawing the 3x4 boundaries specified by argv ...
 230                 draw_cyl $bx0 $by0 $bz0 $bx1 $by0 $bz0
 231                 draw_cyl $bx0 $by0 $bz0 $bx0 $by1 $bz0
 232                 draw_cyl $bx1 $by1 $bz0 $bx1 $by0 $bz0
 233                 draw_cyl $bx0 $by1 $bz0 $bx1 $by1 $bz0
 234
 235                 draw_cyl $bx0 $by0 $bz1 $bx1 $by0 $bz1
 236                 draw_cyl $bx0 $by0 $bz1 $bx0 $by1 $bz1
 237                 draw_cyl $bx1 $by1 $bz1 $bx1 $by0 $bz1
 238                 draw_cyl $bx0 $by1 $bz1 $bx1 $by1 $bz1
 239
 240                 draw_cyl $bx0 $by0 $bz1 $bx0 $by0 $bz0
 241                 draw_cyl $bx0 $by1 $bz1 $bx0 $by1 $bz0
 242                 draw_cyl $bx1 $by0 $bz1 $bx1 $by0 $bz0
 243                 draw_cyl $bx1 $by1 $bz1 $bx1 $by1 $bz0
 244
 245         fi
 246
 247         # bonds
 248         if [ -n "$bcr" ]; then
 249
 250                 if [ -z "$x0" ]; then
 251
 252         cat $file | grep '# \[B\]' | while read foo bar x1 y1 z1 x2 y2 z2 ; do
 253                 draw_bond $x1 $z1 $y1 $x2 $z2 $y2 $bcr
 254         done
 255
 256                 else
 257
 258                 export x0 y0 z0 x1 y1 z1 bcr
 259                 cat $file | grep '# \[B\]' | awk '\
 260                 BEGIN {
 261                         x0=ENVIRON["x0"]; y0=ENVIRON["y0"]; z0=ENVIRON["z0"];
 262                         x1=ENVIRON["x1"]; y1=ENVIRON["y1"]; z1=ENVIRON["z1"];
 263                         bcr=ENVIRON["bcr"];
 264                 }
 265                 {
 266                         if(($3>=x0)&&($4>=y0)&&($5>=z0)&&\
 267                            ($3<=x1)&&($4<=y1)&&($5<=z1)) {
 268                                 print "cylinder {";
 269                                 print "<"$3","$5","$4">,";
 270                                 print "<"$6","$8","$7">, "bcr;
 271                                 print "pigment { color Blue }";
 272                                 print "}";
 273                         }
 274                 }' >> temp.pov
 275
 276                 fi
 277         fi
 278
 279         # add camera and light source
 280         cat >> temp.pov <<-EOF
 281 camera {
 282 EOF
 283         if [ -n "$ortographic" ]; then  cat >> temp.pov <<-EOF
 284 orthographic
 285 EOF
 286         fi
 287         cat >> temp.pov <<-EOF
 288 location $camloc
 289 look_at <$clx,$clz,$clz>
 290 }
 291 light_source { <0,100,-100> color White shadowless }
 292 EOF
 293
 294         # mv png
 295         $POVRAY temp.pov > /dev/null 2>&1
 296         time=`basename $file | awk -F. '{ print $1 }' | awk -F_ '{ print $3 }'`
 297         convert $COPTS -draw "text 5,20 't = $time fs'" temp.png temp.png
 298         mv temp.png `echo $file | sed 's/\.xyz/\.png/'`
 299
 300 done
 301
 302 echo "done"