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