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=$2;                  shift 2;
  75                                 ((cnt=1))
  76                                 while [ $cnt -le $ab ]; do
  77                                         anr[$cnt]=$1;   shift 1;
  78                                         ((cnt+=1))
  79                                 done
  80                                 cutoff=$1;              shift 1;;
  81                 *)
  82                                 echo "options:"
  83                                 echo "########"
  84                                 echo "directory to progress:"
  85                                 echo "  -d <directory> (mandatory)"
  86                                 echo "png dim:"
  87                                 echo "  -w <width>"
  88                                 echo "  -h <height>"
  89                                 echo "atom size:"
  90                                 echo "  -r <radius>"
  91                                 echo "  -B <bond cylinder radius>"
  92                                 echo "unit cell:"
  93                                 echo "  -C <lattice constant>"
  94                                 echo "  -m <dimX> <dimY> <dimZ> (mirror atoms)"
  95                                 echo "visualization volume:"
  96                                 echo "  -nll <x> <y> <z> (near lower left)"
  97                                 echo "  -fur <x> <y> <z> (far upper right)"
  98                                 echo "  -o (ortographic)"
  99                                 echo "bounding box:"
 100                                 echo "  -b <x0> <y0> <z0> <x1> <y1> <z1>"
 101                                 echo "povray:"
 102                                 echo "  -c <x> <y> <z> (camera position)"
 103                                 echo "  -L <x> <y> <z> (camera look)"
 104                                 echo "  -l <x> <y> <z> (light source)"
 105                                 echo "bonds:"
 106                                 echo "  -ab <atom number> <cutoff> (auto bonds)"
 107                                 exit 1;;
 108         esac
 109 done
 110
 111 # calculation from lattic eunits to angstroms
 112
 113 [ "$lc" = "sic" ] && lc=4.359
 114 [ "$lc" = "si" ] && lc=5.480
 115 [ "$lc" = "c" ] && lc=3.566
 116
 117 #offset=`echo 0.125 \* $lc | bc`
 118 offset=0.0
 119
 120 x0=`echo $x0 \* $lc + $offset | bc`
 121 y0=`echo $y0 \* $lc + $offset | bc`
 122 z0=`echo $z0 \* $lc + $offset | bc`
 123 x1=`echo $x1 \* $lc + $offset | bc`
 124 y1=`echo $y1 \* $lc + $offset | bc`
 125 z1=`echo $z1 \* $lc + $offset | bc`
 126
 127 mx1=`echo $mx1 \* $lc + $offset | bc`
 128 my1=`echo $my1 \* $lc + $offset | bc`
 129 mz1=`echo $mz1 \* $lc + $offset | bc`
 130 mx2=`echo $mx2 \* $lc + $offset | bc`
 131 my2=`echo $my2 \* $lc + $offset | bc`
 132 mz2=`echo $mz2 \* $lc + $offset | bc`
 133 mx3=`echo $mx3 \* $lc + $offset | bc`
 134 my3=`echo $my3 \* $lc + $offset | bc`
 135 mz3=`echo $mz3 \* $lc + $offset | bc`
 136
 137 clx=`echo $clx \* $lc + $offset | bc`
 138 cly=`echo $cly \* $lc + $offset | bc`
 139 clz=`echo $clz \* $lc + $offset | bc`
 140
 141 if [ -n "$cx" -a -n "$cy" -a -n "$cz" ]; then
 142         cx=`echo $cx \* $lc + $offset | bc`
 143         cy=`echo $cy \* $lc + $offset | bc`
 144         cz=`echo $cz \* $lc + $offset | bc`
 145 fi
 146
 147 if [ -n "$bx0" ]; then
 148         bx0=`echo $bx0 \* $lc + $offset | bc`
 149         by0=`echo $by0 \* $lc + $offset | bc`
 150         bz0=`echo $bz0 \* $lc + $offset | bc`
 151         bx1=`echo $bx1 \* $lc + $offset | bc`
 152         by1=`echo $by1 \* $lc + $offset | bc`
 153         bz1=`echo $bz1 \* $lc + $offset | bc`
 154 fi
 155
 156 # povray command
 157
 158 POVRAY="povray -W${width} -H${height} -d"
 159
 160 # convert options
 161
 162 COPTS="-font /usr/share/fonts/truetype/ttf-dejavu/DejaVuSans.ttf"
 163 COPTS="$COPTS -depth 8 -fill white -stroke blue -pointsize 24"
 164
 165 # do it ...
 166
 167 if [ -d $directory ]; then
 168         filesource=$directory/atomic_conf_*.xyz
 169 fi
 170
 171 if [ -f $directory ]; then
 172         filesource=$directory
 173 fi
 174
 175 for file in $filesource; do
 176
 177         cat > temp.pov <<-EOF
 178 #include "colors.inc"
 179 #include "textures.inc"
 180 #include "shapes.inc"
 181 #include "glass.inc"
 182 #include "metals.inc"
 183 #include "woods.inc"
 184 #include "stones.inc"
 185 EOF
 186
 187         # meta info
 188         count=`grep '# \[P\]' $file | awk '{ print $3 }'`
 189         time=`grep '# \[P\]' $file | awk '{ print $4 }'`
 190         camloc=`grep '# \[P\]' $file | awk '{ print $5 }'`
 191         [ -n "$cx" -a -n "$cy" -a -n "$cz" ] && camloc="<$cx,$cz,$cy>"
 192
 193         # atoms
 194 #echo "-----> $x0 $y0 $z0 $x1 $y1 $z1 <-----"
 195         if [ -n "$x0" ]; then
 196                 export x0 y0 z0 x1 y1 z1 radius extra
 197                 export mx1 mx2 mx3
 198                 export my1 my2 my3
 199                 export mz1 mz2 mz3
 200                 export mirror
 201                 cat $file | grep -v '#' | awk '\
 202                 BEGIN {
 203                         x0=ENVIRON["x0"]; y0=ENVIRON["y0"]; z0=ENVIRON["z0"];
 204                         x1=ENVIRON["x1"]; y1=ENVIRON["y1"]; z1=ENVIRON["z1"];
 205                         mx1=ENVIRON["mx1"]; my1=ENVIRON["my1"];
 206                         mz1=ENVIRON["mz1"]; mx2=ENVIRON["mx2"];
 207                         my2=ENVIRON["my2"]; mz2=ENVIRON["mz2"];
 208                         mx3=ENVIRON["mx3"]; my3=ENVIRON["my3"];
 209                         mz3=ENVIRON["mz3"]; mirror=ENVIRON["mirror"];
 210                         radius=ENVIRON["radius"]; extra=ENVIRON["extra"];
 211                         nx=0; ny=0; nz=0;
 212                 }
 213                 {
 214                         if(($2>=x0)&&($3>=y0)&&($4>=z0)&&\
 215                            ($2<=x1)&&($3<=y1)&&($4<=z1)) {
 216                                 print "sphere { <"$2","$4","$3">, "radius" ";
 217                                 if(extra)
 218                 print "texture { pigment { color rgb<"$6/4.4",0,"1-$6/4.4"> } ";
 219                                 else
 220                 print "texture { pigment { color "$5" } ";
 221                                 print "finish { phong 1 metallic } } }";
 222                         }
 223
 224                         if(mirror) {
 225
 226                         nx=$2-mx1; ny=$3-mx2; nz=$4-mx3;
 227                         if((nx>=x0)&&(ny>=y0)&&(nz>=z0)&&\
 228                            (nx<=x1)&&(ny<=y1)&&(nz<=z1)) {
 229 print "// translation: "$2/5.480" "$3/5.480" "$4/5.480" -> "nx/5.480" "ny/5.480" "nz/5.480" ...";
 230                                 print "sphere { <"nx","nz","ny">, "radius" ";
 231                                 if(extra)
 232                 print "texture { pigment { color rgb<"$6/4.4",0,"1-$6/4.4"> } ";
 233                                 else
 234                 print "texture { pigment { color "$5" } ";
 235                                 print "finish { phong 1 metallic } } }";
 236                         }
 237                         nx=$2-my1; ny=$3-my2; nz=$4-my3;
 238                         if((nx>=x0)&&(ny>=y0)&&(nz>=z0)&&\
 239                            (nx<=x1)&&(ny<=y1)&&(nz<=z1)) {
 240                                 print "sphere { <"nx","nz","ny">, "radius" ";
 241                                 if(extra)
 242                 print "texture { pigment { color rgb<"$6/4.4",0,"1-$6/4.4"> } ";
 243                                 else
 244                 print "texture { pigment { color "$5" } ";
 245                                 print "finish { phong 1 metallic } } }";
 246                         }
 247                         nx=$2-mz1; ny=$3-mz2; nz=$4-mz3;
 248                         if((nx>=x0)&&(ny>=y0)&&(nz>=z0)&&\
 249                            (nx<=x1)&&(ny<=y1)&&(nz<=z1)) {
 250                                 print "sphere { <"nx","nz","ny">, "radius" ";
 251                                 if(extra)
 252                 print "texture { pigment { color rgb<"$6/4.4",0,"1-$6/4.4"> } ";
 253                                 else
 254                 print "texture { pigment { color "$5" } ";
 255                                 print "finish { phong 1 metallic } } }";
 256                         }
 257
 258                         }
 259
 260                 }' >> temp.pov
 261         else
 262                 cat $file | grep -v '#' | while read name x y z color temp; do
 263                         cat >> temp.pov <<-EOF
 264 sphere {
 265 <$x, $z, $y>, $radius
 266 texture {
 267 pigment { color $color }
 268 finish {
 269 phong 1
 270 metallic
 271 }
 272 }
 273 }
 274 EOF
 275                 done
 276         fi
 277
 278         # boundaries
 279         if [ -z "$bx0" ]; then
 280
 281         #if [ -z "$x0" ]; then
 282
 283         cat $file | grep '# \[D\]' | while read foo bar x1 y1 z1 x2 y2 z2 ; do
 284                 draw_cyl $x1 $y1 $z1 $x2 $y2 $z2 0.05
 285         done
 286
 287         #else
 288
 289                 # manually drawing the 3x4 boundaries ...
 290 #               draw_cyl $x0 $y0 $z0 $x1 $y0 $z0
 291 #               draw_cyl $x0 $y0 $z0 $x0 $y1 $z0
 292 #               draw_cyl $x1 $y1 $z0 $x1 $y0 $z0
 293 #               draw_cyl $x0 $y1 $z0 $x1 $y1 $z0
 294
 295 #               draw_cyl $x0 $y0 $z1 $x1 $y0 $z1
 296 #               draw_cyl $x0 $y0 $z1 $x0 $y1 $z1
 297 #               draw_cyl $x1 $y1 $z1 $x1 $y0 $z1
 298 #               draw_cyl $x0 $y1 $z1 $x1 $y1 $z1
 299
 300 #               draw_cyl $x0 $y0 $z1 $x0 $y0 $z0
 301 #               draw_cyl $x0 $y1 $z1 $x0 $y1 $z0
 302 #               draw_cyl $x1 $y0 $z1 $x1 $y0 $z0
 303 #               draw_cyl $x1 $y1 $z1 $x1 $y1 $z0
 304 #       fi
 305
 306         else
 307
 308                 # manually drawing the 3x4 boundaries specified by argv ...
 309                 draw_cyl $bx0 $by0 $bz0 $bx1 $by0 $bz0
 310                 draw_cyl $bx0 $by0 $bz0 $bx0 $by1 $bz0
 311                 draw_cyl $bx1 $by1 $bz0 $bx1 $by0 $bz0
 312                 draw_cyl $bx0 $by1 $bz0 $bx1 $by1 $bz0
 313
 314                 draw_cyl $bx0 $by0 $bz1 $bx1 $by0 $bz1
 315                 draw_cyl $bx0 $by0 $bz1 $bx0 $by1 $bz1
 316                 draw_cyl $bx1 $by1 $bz1 $bx1 $by0 $bz1
 317                 draw_cyl $bx0 $by1 $bz1 $bx1 $by1 $bz1
 318
 319                 draw_cyl $bx0 $by0 $bz1 $bx0 $by0 $bz0
 320                 draw_cyl $bx0 $by1 $bz1 $bx0 $by1 $bz0
 321                 draw_cyl $bx1 $by0 $bz1 $bx1 $by0 $bz0
 322                 draw_cyl $bx1 $by1 $bz1 $bx1 $by1 $bz0
 323
 324         fi
 325
 326         # bonds
 327         if [ -n "$bcr" ]; then
 328
 329                 if [ -z "$x0" ]; then
 330
 331         cat $file | grep '# \[B\]' | while read foo bar x1 y1 z1 x2 y2 z2 ; do
 332                 draw_bond $x1 $z1 $y1 $x2 $z2 $y2 $bcr
 333         done
 334
 335                 else
 336
 337                 export x0 y0 z0 x1 y1 z1 bcr
 338                 cat $file | grep '# \[B\]' | awk '\
 339                 BEGIN {
 340                         x0=ENVIRON["x0"]; y0=ENVIRON["y0"]; z0=ENVIRON["z0"];
 341                         x1=ENVIRON["x1"]; y1=ENVIRON["y1"]; z1=ENVIRON["z1"];
 342                         bcr=ENVIRON["bcr"];
 343                 }
 344                 {
 345                         if(($3>=x0)&&($4>=y0)&&($5>=z0)&&\
 346                            ($3<=x1)&&($4<=y1)&&($5<=z1)) {
 347                                 print "cylinder {";
 348                                 print "<"$3","$5","$4">,";
 349                                 print "<"$6","$8","$7">, "bcr;
 350                                 print "pigment { color Blue }";
 351                                 print "}";
 352                         }
 353                 }' >> temp.pov
 354
 355                 fi
 356         fi
 357
 358         # auto bonds
 359         if [ "$ab" != "0" ]; then
 360                 ((cnt=1))
 361                 while [ $cnt -le $ab ]; do
 362                         anr=${anr[$cnt]}
 363
 364                 ((tmp=anr+1))
 365                 line="`sed -n ${tmp}p $file`"
 366                 aX=`echo $line | awk '{ print $2 }'`
 367                 aY=`echo $line | awk '{ print $3 }'`
 368                 aZ=`echo $line | awk '{ print $4 }'`
 369                 export aX aY aZ cutoff mirror
 370                 cat $file | grep -v '#' | awk '\
 371                 BEGIN {
 372                         x=ENVIRON["aX"]; y=ENVIRON["aY"]; z=ENVIRON["aZ"];
 373                         co=ENVIRON["cutoff"]; dist=0; bcr=ENVIRON["bcr"];
 374                         mx1=ENVIRON["mx1"]; my1=ENVIRON["my1"];
 375                         mz1=ENVIRON["mz1"]; mx2=ENVIRON["mx2"];
 376                         my2=ENVIRON["my2"]; mz2=ENVIRON["mz2"];
 377                         mx3=ENVIRON["mx3"]; my3=ENVIRON["my3"];
 378                         mz3=ENVIRON["mz3"]; mirror=ENVIRON["mirror"];
 379                 }
 380                 {
 381                         dist=sqrt((x-$2)^2+(y-$3)^2+(z-$4)^2);
 382                         if((dist<=co)&&(dist>0.01)) {
 383                                 print "cylinder {";
 384                                 print "<"x","z","y">,";
 385                                 print "<"$2","$4","$3">, "bcr;
 386                                 print "pigment { color Blue }";
 387                                 print "}";
 388                         }
 389
 390                         if(mirror) {
 391                                 nx=$2-mx1; ny=$3-mx2; nz=$4-mx3;
 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-my1; ny=$3-my2; nz=$4-my3;
 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                                 nx=$2-mz1; ny=$3-mz2; nz=$4-mz3;
 410                                 dist=sqrt((x-nx)^2+(y-ny)^2+(z-nz)^2)
 411                                 if((dist<=co)&&(dist>0.01)) {
 412                                         print "cylinder {";
 413                                         print "<"x","z","y">,";
 414                                         print "<"nx","nz","ny">, "bcr;
 415                                         print "pigment { color Blue }";
 416                                         print "}";
 417                                 }
 418                         }
 419
 420                 }' >> temp.pov
 421
 422                         ((cnt+=1))
 423                 done
 424         fi
 425
 426         # add camera and light source
 427         cat >> temp.pov <<-EOF
 428 camera {
 429 EOF
 430         if [ -n "$ortographic" ]; then  cat >> temp.pov <<-EOF
 431 orthographic
 432 EOF
 433         fi
 434         cat >> temp.pov <<-EOF
 435 location $camloc
 436 look_at <$clx,$clz,$clz>
 437 }
 438 light_source { <0,100,-100> color White shadowless }
 439 EOF
 440
 441         # mv png
 442         $POVRAY temp.pov > /dev/null 2>&1
 443         time=`basename $file | awk -F. '{ print $1 }' | awk -F_ '{ print $3 }'`
 444         if [ ! -z $displace ]; then
 445         convert $COPTS -draw "text 5,20 'd = $displace %'" temp.png temp.png
 446         else
 447         convert $COPTS -draw "text 5,20 't = $time fs'" temp.png temp.png
 448         fi
 449         mv temp.png `echo $file | sed 's/\.xyz/\.png/'`
 450
 451 done
 452
 453 echo "done"