vasp_tools/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 displace=""
  44 mirror=0
  45 mx1=0; mx2=0; mx3=0;
  46 my1=0; my2=0; my3=0;
  47 mz1=0; mz2=0; mz3=0;
  48
  49 # parse argv
  50
  51 while [ "$1" ]; do
  52         case "$1" in
  53                 -d)             directory=$2;           shift 2;;
  54                 -w)             width=$2;               shift 2;;
  55                 -h)             height=$2;              shift 2;;
  56                 -r)             radius=$2;              shift 2;;
  57                 -nll)           x0=$2; y0=$3; z0=$4;    shift 4;;
  58                 -fur)           x1=$2; y1=$3; z1=$4;    shift 4;;
  59                 -c)             cx=$2; cy=$3; cz=$4;    shift 4;;
  60                 -L)             clx=$2; cly=$3; clz=$4; shift 4;;
  61                 -l)             lx=$2; ly=$3; lz=$4;    shift 4;;
  62                 -o)             ortographic=1;          shift 1;;
  63                 -b)             bx0=$2; by0=$3; bz0=$4;
  64                                 bx1=$5; by1=$6; bz1=$7; shift 7;;
  65                 -B)             bcr=$2;                 shift 2;;
  66                 -C)             lc=$2;                  shift 2;;
  67                 -e)             extra=1;                shift 1;;
  68                 -D)             displace=$2;            shift 2;;
  69                 -m)             mx1=$2; mx2=$3; mx3=$4;
  70                                 my1=$5; my2=$6; my3=$7;
  71                                 mz1=$8; mz2=$9; mz3=${10};
  72                                 mirror=1;               shift 10;;
  73
  74                 *)
  75                                 echo "options:"
  76                                 echo "########"
  77                                 echo "directory to progress:"
  78                                 echo "  -d <directory> (mandatory)"
  79                                 echo "png dim:"
  80                                 echo "  -w <width>"
  81                                 echo "  -h <height>"
  82                                 echo "atom size:"
  83                                 echo "  -r <radius>"
  84                                 echo "  -B <bond cylinder radius>"
  85                                 echo "unit cell:"
  86                                 echo "  -C <lattice constant>"
  87                                 echo "  -m <dimX> <dimY> <dimZ> (mirror atoms)"
  88                                 echo "visualization volume:"
  89                                 echo "  -nll <x> <y> <z> (near lower left)"
  90                                 echo "  -fur <x> <y> <z> (far upper right)"
  91                                 echo "  -o (ortographic)"
  92                                 echo "bounding box:"
  93                                 echo "  -b <x0> <y0> <z0> <x1> <y1> <z1>"
  94                                 echo "povray:"
  95                                 echo "  -c <x> <y> <z> (camera position)"
  96                                 echo "  -L <x> <y> <z> (camera look)"
  97                                 echo "  -l <x> <y> <z> (light source)"
  98                                 exit 1;;
  99         esac
 100 done
 101
 102 # calculation from lattic eunits to angstroms
 103
 104 [ "$lc" = "sic" ] && lc=4.359
 105 [ "$lc" = "si" ] && lc=5.480
 106 [ "$lc" = "c" ] && lc=3.566
 107
 108 #offset=`echo 0.125 \* $lc | bc`
 109 offset=0.0
 110
 111 x0=`echo $x0 \* $lc + $offset | bc`
 112 y0=`echo $y0 \* $lc + $offset | bc`
 113 z0=`echo $z0 \* $lc + $offset | bc`
 114 x1=`echo $x1 \* $lc + $offset | bc`
 115 y1=`echo $y1 \* $lc + $offset | bc`
 116 z1=`echo $z1 \* $lc + $offset | bc`
 117
 118 mx1=`echo $mx1 \* $lc + $offset | bc`
 119 my1=`echo $my1 \* $lc + $offset | bc`
 120 mz1=`echo $mz1 \* $lc + $offset | bc`
 121 mx2=`echo $mx2 \* $lc + $offset | bc`
 122 my2=`echo $my2 \* $lc + $offset | bc`
 123 mz2=`echo $mz2 \* $lc + $offset | bc`
 124 mx3=`echo $mx3 \* $lc + $offset | bc`
 125 my3=`echo $my3 \* $lc + $offset | bc`
 126 mz3=`echo $mz3 \* $lc + $offset | bc`
 127
 128 clx=`echo $clx \* $lc + $offset | bc`
 129 cly=`echo $cly \* $lc + $offset | bc`
 130 clz=`echo $clz \* $lc + $offset | bc`
 131
 132 if [ -n "$cx" -a -n "$cy" -a -n "$cz" ]; then
 133         cx=`echo $cx \* $lc + $offset | bc`
 134         cy=`echo $cy \* $lc + $offset | bc`
 135         cz=`echo $cz \* $lc + $offset | bc`
 136 fi
 137
 138 if [ -n "$bx0" ]; then
 139         bx0=`echo $bx0 \* $lc + $offset | bc`
 140         by0=`echo $by0 \* $lc + $offset | bc`
 141         bz0=`echo $bz0 \* $lc + $offset | bc`
 142         bx1=`echo $bx1 \* $lc + $offset | bc`
 143         by1=`echo $by1 \* $lc + $offset | bc`
 144         bz1=`echo $bz1 \* $lc + $offset | bc`
 145 fi
 146
 147 # povray command
 148
 149 POVRAY="povray -W${width} -H${height} -d"
 150
 151 # convert options
 152
 153 COPTS="-font /usr/share/fonts/truetype/ttf-dejavu/DejaVuSans.ttf"
 154 COPTS="$COPTS -depth 8 -fill white -stroke blue -pointsize 24"
 155
 156 # do it ...
 157
 158 if [ -d $directory ]; then
 159         filesource=$directory/atomic_conf_*.xyz
 160 fi
 161
 162 if [ -f $directory ]; then
 163         filesource=$directory
 164 fi
 165
 166 for file in $filesource; do
 167
 168         cat > temp.pov <<-EOF
 169 #include "colors.inc"
 170 #include "textures.inc"
 171 #include "shapes.inc"
 172 #include "glass.inc"
 173 #include "metals.inc"
 174 #include "woods.inc"
 175 #include "stones.inc"
 176 EOF
 177
 178         # meta info
 179         count=`grep '# \[P\]' $file | awk '{ print $3 }'`
 180         time=`grep '# \[P\]' $file | awk '{ print $4 }'`
 181         camloc=`grep '# \[P\]' $file | awk '{ print $5 }'`
 182         [ -n "$cx" -a -n "$cy" -a -n "$cz" ] && camloc="<$cx,$cz,$cy>"
 183
 184         # atoms
 185 #echo "-----> $x0 $y0 $z0 $x1 $y1 $z1 <-----"
 186         if [ -n "$x0" ]; then
 187                 export x0 y0 z0 x1 y1 z1 radius extra
 188                 export mx1 mx2 mx3
 189                 export my1 my2 my3
 190                 export mz1 mz2 mz3
 191                 export mirror
 192                 cat $file | grep -v '#' | awk '\
 193                 BEGIN {
 194                         x0=ENVIRON["x0"]; y0=ENVIRON["y0"]; z0=ENVIRON["z0"];
 195                         x1=ENVIRON["x1"]; y1=ENVIRON["y1"]; z1=ENVIRON["z1"];
 196                         mx1=ENVIRON["mx1"]; my1=ENVIRON["my1"];
 197                         mz1=ENVIRON["mz1"]; mx2=ENVIRON["mx2"];
 198                         my2=ENVIRON["my2"]; mz2=ENVIRON["mz2"];
 199                         mx3=ENVIRON["mx3"]; my3=ENVIRON["my3"];
 200                         mz3=ENVIRON["mz3"]; mirror=ENVIRON["mirror"];
 201                         radius=ENVIRON["radius"]; extra=ENVIRON["extra"];
 202                         nx=0; ny=0; nz=0;
 203                 }
 204                 {
 205                         if(($2>=x0)&&($3>=y0)&&($4>=z0)&&\
 206                            ($2<=x1)&&($3<=y1)&&($4<=z1)) {
 207                                 print "sphere { <"$2","$4","$3">, "radius" ";
 208                                 if(extra)
 209                 print "texture { pigment { color rgb<"$6/4.4",0,"1-$6/4.4"> } ";
 210                                 else
 211                 print "texture { pigment { color "$5" } ";
 212                                 print "finish { phong 1 metallic } } }";
 213                         }
 214
 215                         if(mirror) {
 216
 217                         nx=$2-mx1; ny=$3-mx2; nz=$4-mx3;
 218                         if((nx>=x0)&&(ny>=y0)&&(nz>=z0)&&\
 219                            (nx<=x1)&&(ny<=y1)&&(nz<=z1)) {
 220 print "// translation: "$2/5.480" "$3/5.480" "$4/5.480" -> "nx/5.480" "ny/5.480" "nz/5.480" ...";
 221                                 print "sphere { <"nx","nz","ny">, "radius" ";
 222                                 if(extra)
 223                 print "texture { pigment { color rgb<"$6/4.4",0,"1-$6/4.4"> } ";
 224                                 else
 225                 print "texture { pigment { color "$5" } ";
 226                                 print "finish { phong 1 metallic } } }";
 227                         }
 228                         nx=$2-my1; ny=$3-my2; nz=$4-my3;
 229                         if((nx>=x0)&&(ny>=y0)&&(nz>=z0)&&\
 230                            (nx<=x1)&&(ny<=y1)&&(nz<=z1)) {
 231                                 print "sphere { <"nx","nz","ny">, "radius" ";
 232                                 if(extra)
 233                 print "texture { pigment { color rgb<"$6/4.4",0,"1-$6/4.4"> } ";
 234                                 else
 235                 print "texture { pigment { color "$5" } ";
 236                                 print "finish { phong 1 metallic } } }";
 237                         }
 238                         nx=$2-mz1; ny=$3-mz2; nz=$4-mz3;
 239                         if((nx>=x0)&&(ny>=y0)&&(nz>=z0)&&\
 240                            (nx<=x1)&&(ny<=y1)&&(nz<=z1)) {
 241                                 print "sphere { <"nx","nz","ny">, "radius" ";
 242                                 if(extra)
 243                 print "texture { pigment { color rgb<"$6/4.4",0,"1-$6/4.4"> } ";
 244                                 else
 245                 print "texture { pigment { color "$5" } ";
 246                                 print "finish { phong 1 metallic } } }";
 247                         }
 248
 249                         }
 250
 251                 }' >> temp.pov
 252         else
 253                 cat $file | grep -v '#' | while read name x y z color temp; do
 254                         cat >> temp.pov <<-EOF
 255 sphere {
 256 <$x, $z, $y>, $radius
 257 texture {
 258 pigment { color $color }
 259 finish {
 260 phong 1
 261 metallic
 262 }
 263 }
 264 }
 265 EOF
 266                 done
 267         fi
 268
 269         # boundaries
 270         if [ -z "$bx0" ]; then
 271
 272         #if [ -z "$x0" ]; then
 273
 274         cat $file | grep '# \[D\]' | while read foo bar x1 y1 z1 x2 y2 z2 ; do
 275                 draw_cyl $x1 $y1 $z1 $x2 $y2 $z2 0.05
 276         done
 277
 278         #else
 279
 280                 # manually drawing the 3x4 boundaries ...
 281 #               draw_cyl $x0 $y0 $z0 $x1 $y0 $z0
 282 #               draw_cyl $x0 $y0 $z0 $x0 $y1 $z0
 283 #               draw_cyl $x1 $y1 $z0 $x1 $y0 $z0
 284 #               draw_cyl $x0 $y1 $z0 $x1 $y1 $z0
 285
 286 #               draw_cyl $x0 $y0 $z1 $x1 $y0 $z1
 287 #               draw_cyl $x0 $y0 $z1 $x0 $y1 $z1
 288 #               draw_cyl $x1 $y1 $z1 $x1 $y0 $z1
 289 #               draw_cyl $x0 $y1 $z1 $x1 $y1 $z1
 290
 291 #               draw_cyl $x0 $y0 $z1 $x0 $y0 $z0
 292 #               draw_cyl $x0 $y1 $z1 $x0 $y1 $z0
 293 #               draw_cyl $x1 $y0 $z1 $x1 $y0 $z0
 294 #               draw_cyl $x1 $y1 $z1 $x1 $y1 $z0
 295 #       fi
 296
 297         else
 298
 299                 # manually drawing the 3x4 boundaries specified by argv ...
 300                 draw_cyl $bx0 $by0 $bz0 $bx1 $by0 $bz0
 301                 draw_cyl $bx0 $by0 $bz0 $bx0 $by1 $bz0
 302                 draw_cyl $bx1 $by1 $bz0 $bx1 $by0 $bz0
 303                 draw_cyl $bx0 $by1 $bz0 $bx1 $by1 $bz0
 304
 305                 draw_cyl $bx0 $by0 $bz1 $bx1 $by0 $bz1
 306                 draw_cyl $bx0 $by0 $bz1 $bx0 $by1 $bz1
 307                 draw_cyl $bx1 $by1 $bz1 $bx1 $by0 $bz1
 308                 draw_cyl $bx0 $by1 $bz1 $bx1 $by1 $bz1
 309
 310                 draw_cyl $bx0 $by0 $bz1 $bx0 $by0 $bz0
 311                 draw_cyl $bx0 $by1 $bz1 $bx0 $by1 $bz0
 312                 draw_cyl $bx1 $by0 $bz1 $bx1 $by0 $bz0
 313                 draw_cyl $bx1 $by1 $bz1 $bx1 $by1 $bz0
 314
 315         fi
 316
 317         # bonds
 318         if [ -n "$bcr" ]; then
 319
 320                 if [ -z "$x0" ]; then
 321
 322         cat $file | grep '# \[B\]' | while read foo bar x1 y1 z1 x2 y2 z2 ; do
 323                 draw_bond $x1 $z1 $y1 $x2 $z2 $y2 $bcr
 324         done
 325
 326                 else
 327
 328                 export x0 y0 z0 x1 y1 z1 bcr
 329                 cat $file | grep '# \[B\]' | awk '\
 330                 BEGIN {
 331                         x0=ENVIRON["x0"]; y0=ENVIRON["y0"]; z0=ENVIRON["z0"];
 332                         x1=ENVIRON["x1"]; y1=ENVIRON["y1"]; z1=ENVIRON["z1"];
 333                         bcr=ENVIRON["bcr"];
 334                 }
 335                 {
 336                         if(($3>=x0)&&($4>=y0)&&($5>=z0)&&\
 337                            ($3<=x1)&&($4<=y1)&&($5<=z1)) {
 338                                 print "cylinder {";
 339                                 print "<"$3","$5","$4">,";
 340                                 print "<"$6","$8","$7">, "bcr;
 341                                 print "pigment { color Blue }";
 342                                 print "}";
 343                         }
 344                 }' >> temp.pov
 345
 346                 fi
 347         fi
 348
 349         # add camera and light source
 350         cat >> temp.pov <<-EOF
 351 camera {
 352 EOF
 353         if [ -n "$ortographic" ]; then  cat >> temp.pov <<-EOF
 354 orthographic
 355 EOF
 356         fi
 357         cat >> temp.pov <<-EOF
 358 location $camloc
 359 look_at <$clx,$clz,$clz>
 360 }
 361 light_source { <0,100,-100> color White shadowless }
 362 EOF
 363
 364         # mv png
 365         $POVRAY temp.pov > /dev/null 2>&1
 366         time=`basename $file | awk -F. '{ print $1 }' | awk -F_ '{ print $3 }'`
 367         if [ ! -z $displace ]; then
 368         convert $COPTS -draw "text 5,20 'd = $displace %'" temp.png temp.png
 369         else
 370         convert $COPTS -draw "text 5,20 't = $time fs'" temp.png temp.png
 371         fi
 372         mv temp.png `echo $file | sed 's/\.xyz/\.png/'`
 373
 374 done
 375
 376 echo "done"