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="0.1";
  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 ab=0
  49
  50 # parse argv
  51
  52 while [ "$1" ]; do
  53         case "$1" in
  54                 -d)             directory=$2;           shift 2;;
  55                 -w)             width=$2;               shift 2;;
  56                 -h)             height=$2;              shift 2;;
  57                 -r)             radius=$2;              shift 2;;
  58                 -nll)           x0=$2; y0=$3; z0=$4;    shift 4;;
  59                 -fur)           x1=$2; y1=$3; z1=$4;    shift 4;;
  60                 -c)             cx=$2; cy=$3; cz=$4;    shift 4;;
  61                 -L)             clx=$2; cly=$3; clz=$4; shift 4;;
  62                 -l)             lx=$2; ly=$3; lz=$4;    shift 4;;
  63                 -o)             ortographic=1;          shift 1;;
  64                 -b)             bx0=$2; by0=$3; bz0=$4;
  65                                 bx1=$5; by1=$6; bz1=$7; shift 7;;
  66                 -B)             bcr=$2;                 shift 2;;
  67                 -C)             lc=$2;                  shift 2;;
  68                 -e)             extra=1;                shift 1;;
  69                 -D)             displace=$2;            shift 2;;
  70                 -m)             mx1=$2; mx2=$3; mx3=$4;
  71                                 my1=$5; my2=$6; my3=$7;
  72                                 mz1=$8; mz2=$9; mz3=${10};
  73                                 mirror=1;               shift 10;;
  74                 -A)             ab=1;
  75                                 anr=$2; cutoff=$3;      shift 3;;
  76                 *)
  77                                 echo "options:"
  78                                 echo "########"
  79                                 echo "directory to progress:"
  80                                 echo "  -d <directory> (mandatory)"
  81                                 echo "png dim:"
  82                                 echo "  -w <width>"
  83                                 echo "  -h <height>"
  84                                 echo "atom size:"
  85                                 echo "  -r <radius>"
  86                                 echo "  -B <bond cylinder radius>"
  87                                 echo "unit cell:"
  88                                 echo "  -C <lattice constant>"
  89                                 echo "  -m <dimX> <dimY> <dimZ> (mirror atoms)"
  90                                 echo "visualization volume:"
  91                                 echo "  -nll <x> <y> <z> (near lower left)"
  92                                 echo "  -fur <x> <y> <z> (far upper right)"
  93                                 echo "  -o (ortographic)"
  94                                 echo "bounding box:"
  95                                 echo "  -b <x0> <y0> <z0> <x1> <y1> <z1>"
  96                                 echo "povray:"
  97                                 echo "  -c <x> <y> <z> (camera position)"
  98                                 echo "  -L <x> <y> <z> (camera look)"
  99                                 echo "  -l <x> <y> <z> (light source)"
 100                                 echo "bonds:"
 101                                 echo "  -ab <atom number> <cutoff> (auto bonds)"
 102                                 exit 1;;
 103         esac
 104 done
 105
 106 # calculation from lattic eunits to angstroms
 107
 108 [ "$lc" = "sic" ] && lc=4.359
 109 [ "$lc" = "si" ] && lc=5.480
 110 [ "$lc" = "c" ] && lc=3.566
 111
 112 #offset=`echo 0.125 \* $lc | bc`
 113 offset=0.0
 114
 115 x0=`echo $x0 \* $lc + $offset | bc`
 116 y0=`echo $y0 \* $lc + $offset | bc`
 117 z0=`echo $z0 \* $lc + $offset | bc`
 118 x1=`echo $x1 \* $lc + $offset | bc`
 119 y1=`echo $y1 \* $lc + $offset | bc`
 120 z1=`echo $z1 \* $lc + $offset | bc`
 121
 122 mx1=`echo $mx1 \* $lc + $offset | bc`
 123 my1=`echo $my1 \* $lc + $offset | bc`
 124 mz1=`echo $mz1 \* $lc + $offset | bc`
 125 mx2=`echo $mx2 \* $lc + $offset | bc`
 126 my2=`echo $my2 \* $lc + $offset | bc`
 127 mz2=`echo $mz2 \* $lc + $offset | bc`
 128 mx3=`echo $mx3 \* $lc + $offset | bc`
 129 my3=`echo $my3 \* $lc + $offset | bc`
 130 mz3=`echo $mz3 \* $lc + $offset | bc`
 131
 132 clx=`echo $clx \* $lc + $offset | bc`
 133 cly=`echo $cly \* $lc + $offset | bc`
 134 clz=`echo $clz \* $lc + $offset | bc`
 135
 136 if [ -n "$cx" -a -n "$cy" -a -n "$cz" ]; then
 137         cx=`echo $cx \* $lc + $offset | bc`
 138         cy=`echo $cy \* $lc + $offset | bc`
 139         cz=`echo $cz \* $lc + $offset | bc`
 140 fi
 141
 142 if [ -n "$bx0" ]; then
 143         bx0=`echo $bx0 \* $lc + $offset | bc`
 144         by0=`echo $by0 \* $lc + $offset | bc`
 145         bz0=`echo $bz0 \* $lc + $offset | bc`
 146         bx1=`echo $bx1 \* $lc + $offset | bc`
 147         by1=`echo $by1 \* $lc + $offset | bc`
 148         bz1=`echo $bz1 \* $lc + $offset | bc`
 149 fi
 150
 151 # povray command
 152
 153 POVRAY="povray -W${width} -H${height} -d"
 154
 155 # convert options
 156
 157 COPTS="-font /usr/share/fonts/truetype/ttf-dejavu/DejaVuSans.ttf"
 158 COPTS="$COPTS -depth 8 -fill white -stroke blue -pointsize 24"
 159
 160 # do it ...
 161
 162 if [ -d $directory ]; then
 163         filesource=$directory/atomic_conf_*.xyz
 164 fi
 165
 166 if [ -f $directory ]; then
 167         filesource=$directory
 168 fi
 169
 170 for file in $filesource; do
 171
 172         cat > temp.pov <<-EOF
 173 #include "colors.inc"
 174 #include "textures.inc"
 175 #include "shapes.inc"
 176 #include "glass.inc"
 177 #include "metals.inc"
 178 #include "woods.inc"
 179 #include "stones.inc"
 180 EOF
 181
 182         # meta info
 183         count=`grep '# \[P\]' $file | awk '{ print $3 }'`
 184         time=`grep '# \[P\]' $file | awk '{ print $4 }'`
 185         camloc=`grep '# \[P\]' $file | awk '{ print $5 }'`
 186         [ -n "$cx" -a -n "$cy" -a -n "$cz" ] && camloc="<$cx,$cz,$cy>"
 187
 188         # atoms
 189 #echo "-----> $x0 $y0 $z0 $x1 $y1 $z1 <-----"
 190         if [ -n "$x0" ]; then
 191                 export x0 y0 z0 x1 y1 z1 radius extra
 192                 export mx1 mx2 mx3
 193                 export my1 my2 my3
 194                 export mz1 mz2 mz3
 195                 export mirror
 196                 cat $file | grep -v '#' | awk '\
 197                 BEGIN {
 198                         x0=ENVIRON["x0"]; y0=ENVIRON["y0"]; z0=ENVIRON["z0"];
 199                         x1=ENVIRON["x1"]; y1=ENVIRON["y1"]; z1=ENVIRON["z1"];
 200                         mx1=ENVIRON["mx1"]; my1=ENVIRON["my1"];
 201                         mz1=ENVIRON["mz1"]; mx2=ENVIRON["mx2"];
 202                         my2=ENVIRON["my2"]; mz2=ENVIRON["mz2"];
 203                         mx3=ENVIRON["mx3"]; my3=ENVIRON["my3"];
 204                         mz3=ENVIRON["mz3"]; mirror=ENVIRON["mirror"];
 205                         radius=ENVIRON["radius"]; extra=ENVIRON["extra"];
 206                         nx=0; ny=0; nz=0;
 207                 }
 208                 {
 209                         if(($2>=x0)&&($3>=y0)&&($4>=z0)&&\
 210                            ($2<=x1)&&($3<=y1)&&($4<=z1)) {
 211                                 print "sphere { <"$2","$4","$3">, "radius" ";
 212                                 if(extra)
 213                 print "texture { pigment { color rgb<"$6/4.4",0,"1-$6/4.4"> } ";
 214                                 else
 215                 print "texture { pigment { color "$5" } ";
 216                                 print "finish { phong 1 metallic } } }";
 217                         }
 218
 219                         if(mirror) {
 220
 221                         nx=$2-mx1; ny=$3-mx2; nz=$4-mx3;
 222                         if((nx>=x0)&&(ny>=y0)&&(nz>=z0)&&\
 223                            (nx<=x1)&&(ny<=y1)&&(nz<=z1)) {
 224 print "// translation: "$2/5.480" "$3/5.480" "$4/5.480" -> "nx/5.480" "ny/5.480" "nz/5.480" ...";
 225                                 print "sphere { <"nx","nz","ny">, "radius" ";
 226                                 if(extra)
 227                 print "texture { pigment { color rgb<"$6/4.4",0,"1-$6/4.4"> } ";
 228                                 else
 229                 print "texture { pigment { color "$5" } ";
 230                                 print "finish { phong 1 metallic } } }";
 231                         }
 232                         nx=$2-my1; ny=$3-my2; nz=$4-my3;
 233                         if((nx>=x0)&&(ny>=y0)&&(nz>=z0)&&\
 234                            (nx<=x1)&&(ny<=y1)&&(nz<=z1)) {
 235                                 print "sphere { <"nx","nz","ny">, "radius" ";
 236                                 if(extra)
 237                 print "texture { pigment { color rgb<"$6/4.4",0,"1-$6/4.4"> } ";
 238                                 else
 239                 print "texture { pigment { color "$5" } ";
 240                                 print "finish { phong 1 metallic } } }";
 241                         }
 242                         nx=$2-mz1; ny=$3-mz2; nz=$4-mz3;
 243                         if((nx>=x0)&&(ny>=y0)&&(nz>=z0)&&\
 244                            (nx<=x1)&&(ny<=y1)&&(nz<=z1)) {
 245                                 print "sphere { <"nx","nz","ny">, "radius" ";
 246                                 if(extra)
 247                 print "texture { pigment { color rgb<"$6/4.4",0,"1-$6/4.4"> } ";
 248                                 else
 249                 print "texture { pigment { color "$5" } ";
 250                                 print "finish { phong 1 metallic } } }";
 251                         }
 252
 253                         }
 254
 255                 }' >> temp.pov
 256         else
 257                 cat $file | grep -v '#' | while read name x y z color temp; do
 258                         cat >> temp.pov <<-EOF
 259 sphere {
 260 <$x, $z, $y>, $radius
 261 texture {
 262 pigment { color $color }
 263 finish {
 264 phong 1
 265 metallic
 266 }
 267 }
 268 }
 269 EOF
 270                 done
 271         fi
 272
 273         # boundaries
 274         if [ -z "$bx0" ]; then
 275
 276         #if [ -z "$x0" ]; then
 277
 278         cat $file | grep '# \[D\]' | while read foo bar x1 y1 z1 x2 y2 z2 ; do
 279                 draw_cyl $x1 $y1 $z1 $x2 $y2 $z2 0.05
 280         done
 281
 282         #else
 283
 284                 # manually drawing the 3x4 boundaries ...
 285 #               draw_cyl $x0 $y0 $z0 $x1 $y0 $z0
 286 #               draw_cyl $x0 $y0 $z0 $x0 $y1 $z0
 287 #               draw_cyl $x1 $y1 $z0 $x1 $y0 $z0
 288 #               draw_cyl $x0 $y1 $z0 $x1 $y1 $z0
 289
 290 #               draw_cyl $x0 $y0 $z1 $x1 $y0 $z1
 291 #               draw_cyl $x0 $y0 $z1 $x0 $y1 $z1
 292 #               draw_cyl $x1 $y1 $z1 $x1 $y0 $z1
 293 #               draw_cyl $x0 $y1 $z1 $x1 $y1 $z1
 294
 295 #               draw_cyl $x0 $y0 $z1 $x0 $y0 $z0
 296 #               draw_cyl $x0 $y1 $z1 $x0 $y1 $z0
 297 #               draw_cyl $x1 $y0 $z1 $x1 $y0 $z0
 298 #               draw_cyl $x1 $y1 $z1 $x1 $y1 $z0
 299 #       fi
 300
 301         else
 302
 303                 # manually drawing the 3x4 boundaries specified by argv ...
 304                 draw_cyl $bx0 $by0 $bz0 $bx1 $by0 $bz0
 305                 draw_cyl $bx0 $by0 $bz0 $bx0 $by1 $bz0
 306                 draw_cyl $bx1 $by1 $bz0 $bx1 $by0 $bz0
 307                 draw_cyl $bx0 $by1 $bz0 $bx1 $by1 $bz0
 308
 309                 draw_cyl $bx0 $by0 $bz1 $bx1 $by0 $bz1
 310                 draw_cyl $bx0 $by0 $bz1 $bx0 $by1 $bz1
 311                 draw_cyl $bx1 $by1 $bz1 $bx1 $by0 $bz1
 312                 draw_cyl $bx0 $by1 $bz1 $bx1 $by1 $bz1
 313
 314                 draw_cyl $bx0 $by0 $bz1 $bx0 $by0 $bz0
 315                 draw_cyl $bx0 $by1 $bz1 $bx0 $by1 $bz0
 316                 draw_cyl $bx1 $by0 $bz1 $bx1 $by0 $bz0
 317                 draw_cyl $bx1 $by1 $bz1 $bx1 $by1 $bz0
 318
 319         fi
 320
 321         # bonds
 322         if [ -n "$bcr" ]; then
 323
 324                 if [ -z "$x0" ]; then
 325
 326         cat $file | grep '# \[B\]' | while read foo bar x1 y1 z1 x2 y2 z2 ; do
 327                 draw_bond $x1 $z1 $y1 $x2 $z2 $y2 $bcr
 328         done
 329
 330                 else
 331
 332                 export x0 y0 z0 x1 y1 z1 bcr
 333                 cat $file | grep '# \[B\]' | awk '\
 334                 BEGIN {
 335                         x0=ENVIRON["x0"]; y0=ENVIRON["y0"]; z0=ENVIRON["z0"];
 336                         x1=ENVIRON["x1"]; y1=ENVIRON["y1"]; z1=ENVIRON["z1"];
 337                         bcr=ENVIRON["bcr"];
 338                 }
 339                 {
 340                         if(($3>=x0)&&($4>=y0)&&($5>=z0)&&\
 341                            ($3<=x1)&&($4<=y1)&&($5<=z1)) {
 342                                 print "cylinder {";
 343                                 print "<"$3","$5","$4">,";
 344                                 print "<"$6","$8","$7">, "bcr;
 345                                 print "pigment { color Blue }";
 346                                 print "}";
 347                         }
 348                 }' >> temp.pov
 349
 350                 fi
 351         fi
 352
 353         # auto bonds
 354         if [ "$ab" = "1" ]; then
 355                 ((tmp=anr+1))
 356                 line="`sed -n ${tmp}p $file`"
 357                 aX=`echo $line | awk '{ print $2 }'`
 358                 aY=`echo $line | awk '{ print $3 }'`
 359                 aZ=`echo $line | awk '{ print $4 }'`
 360                 export aX aY aZ cutoff mirror
 361                 cat $file | grep -v '#' | awk '\
 362                 BEGIN {
 363                         x=ENVIRON["aX"]; y=ENVIRON["aY"]; z=ENVIRON["aZ"];
 364                         co=ENVIRON["cutoff"]; dist=0; bcr=ENVIRON["bcr"];
 365                         mx1=ENVIRON["mx1"]; my1=ENVIRON["my1"];
 366                         mz1=ENVIRON["mz1"]; mx2=ENVIRON["mx2"];
 367                         my2=ENVIRON["my2"]; mz2=ENVIRON["mz2"];
 368                         mx3=ENVIRON["mx3"]; my3=ENVIRON["my3"];
 369                         mz3=ENVIRON["mz3"]; mirror=ENVIRON["mirror"];
 370                 }
 371                 {
 372                         dist=sqrt((x-$2)^2+(y-$3)^2+(z-$4)^2);
 373                         if((dist<=co)&&(dist>0.01)) {
 374                                 print "cylinder {";
 375                                 print "<"x","z","y">,";
 376                                 print "<"$2","$4","$3">, "bcr;
 377                                 print "pigment { color Blue }";
 378                                 print "}";
 379                         }
 380
 381                         if(mirror) {
 382                                 nx=$2-mx1; ny=$3-mx2; nz=$4-mx3;
 383                                 dist=sqrt((x-nx)^2+(y-ny)^2+(z-nz)^2)
 384                                 if((dist<=co)&&(dist>0.01)) {
 385                                         print "cylinder {";
 386                                         print "<"x","z","y">,";
 387                                         print "<"nx","nz","ny">, "bcr;
 388                                         print "pigment { color Blue }";
 389                                         print "}";
 390                                 }
 391                                 nx=$2-my1; ny=$3-my2; nz=$4-my3;
 392                                 dist=sqrt((x-nx)^2+(y-ny)^2+(z-nz)^2)
 393                                 if((dist<=co)&&(dist>0.01)) {
 394                                         print "cylinder {";
 395                                         print "<"x","z","y">,";
 396                                         print "<"nx","nz","ny">, "bcr;
 397                                         print "pigment { color Blue }";
 398                                         print "}";
 399                                 }
 400                                 nx=$2-mz1; ny=$3-mz2; nz=$4-mz3;
 401                                 dist=sqrt((x-nx)^2+(y-ny)^2+(z-nz)^2)
 402                                 if((dist<=co)&&(dist>0.01)) {
 403                                         print "cylinder {";
 404                                         print "<"x","z","y">,";
 405                                         print "<"nx","nz","ny">, "bcr;
 406                                         print "pigment { color Blue }";
 407                                         print "}";
 408                                 }
 409                         }
 410
 411                 }' >> temp.pov
 412         fi
 413
 414         # add camera and light source
 415         cat >> temp.pov <<-EOF
 416 camera {
 417 EOF
 418         if [ -n "$ortographic" ]; then  cat >> temp.pov <<-EOF
 419 orthographic
 420 EOF
 421         fi
 422         cat >> temp.pov <<-EOF
 423 location $camloc
 424 look_at <$clx,$clz,$clz>
 425 }
 426 light_source { <0,100,-100> color White shadowless }
 427 EOF
 428
 429         # mv png
 430         $POVRAY temp.pov > /dev/null 2>&1
 431         time=`basename $file | awk -F. '{ print $1 }' | awk -F_ '{ print $3 }'`
 432         if [ ! -z $displace ]; then
 433         convert $COPTS -draw "text 5,20 'd = $displace %'" temp.png temp.png
 434         else
 435         convert $COPTS -draw "text 5,20 't = $time fs'" temp.png temp.png
 436         fi
 437         mv temp.png `echo $file | sed 's/\.xyz/\.png/'`
 438
 439 done
 440
 441 echo "done"