X-Git-Url: https://hackdaworld.org/gitweb/?p=physik%2Fposic.git;a=blobdiff_plain;f=vasp_tools%2Fvisualize;fp=vasp_tools%2Fvisualize;h=1ed430ca0786a2c479baaa8f8c32e37c08a7acff;hp=0000000000000000000000000000000000000000;hb=6e6d7126ea9a845f11637d8e1b8eb2b570ac4dc9;hpb=97dc63eb6a519b8e1f4fbfaa9760dd94539436b0 diff --git a/vasp_tools/visualize b/vasp_tools/visualize new file mode 100755 index 0000000..1ed430c --- /dev/null +++ b/vasp_tools/visualize @@ -0,0 +1,453 @@ +#!/bin/sh + +# +# visualization script +# author: frank.zirkelbach@physik.uni-augsburg.de +# + +# help function +draw_cyl() { + cat >> temp.pov <<-EOF +cylinder { +<$1, $3, $2>, <$4, $6, $5>, 0.05 +pigment { color White } +} +EOF +} +draw_bond() { + cat >> temp.pov <<-EOF +cylinder { +<$1, $3, $2>, <$4, $6, $5>, $7 +pigment { color Blue } +} +EOF +} + +# defaults + +lc=5.429 +directory="doesnt_exist____for_sure" +width="640" +height="480" +radius="0.6" +x0="-0.6"; y0="-0.6"; z0="-0.6"; +x1="0.6"; y1="0.6"; z1="0.6"; +cx=""; cy=""; cz=""; +lx="0"; ly="-100"; lz="100"; +ortographic="" +bx0=""; by0=""; bz0=""; +bx1=""; by1=""; bz1=""; +bcr="0.1"; +clx="0"; cly="0"; clz="0"; +extra=0 +displace="" +mirror=0 +mx1=0; mx2=0; mx3=0; +my1=0; my2=0; my3=0; +mz1=0; mz2=0; mz3=0; +ab=0 + +# parse argv + +while [ "$1" ]; do + case "$1" in + -d) directory=$2; shift 2;; + -w) width=$2; shift 2;; + -h) height=$2; shift 2;; + -r) radius=$2; shift 2;; + -nll) x0=$2; y0=$3; z0=$4; shift 4;; + -fur) x1=$2; y1=$3; z1=$4; shift 4;; + -c) cx=$2; cy=$3; cz=$4; shift 4;; + -L) clx=$2; cly=$3; clz=$4; shift 4;; + -l) lx=$2; ly=$3; lz=$4; shift 4;; + -o) ortographic=1; shift 1;; + -b) bx0=$2; by0=$3; bz0=$4; + bx1=$5; by1=$6; bz1=$7; shift 7;; + -B) bcr=$2; shift 2;; + -C) lc=$2; shift 2;; + -e) extra=1; shift 1;; + -D) displace=$2; shift 2;; + -m) mx1=$2; mx2=$3; mx3=$4; + my1=$5; my2=$6; my3=$7; + mz1=$8; mz2=$9; mz3=${10}; + mirror=1; shift 10;; + -A) ab=$2; shift 2; + ((cnt=1)) + while [ $cnt -le $ab ]; do + anr[$cnt]=$1; shift 1; + ((cnt+=1)) + done + cutoff=$1; shift 1;; + *) + echo "options:" + echo "########" + echo "directory to progress:" + echo " -d (mandatory)" + echo "png dim:" + echo " -w " + echo " -h " + echo "atom size:" + echo " -r " + echo " -B " + echo "unit cell:" + echo " -C " + echo " -m (mirror atoms)" + echo "visualization volume:" + echo " -nll (near lower left)" + echo " -fur (far upper right)" + echo " -o (ortographic)" + echo "bounding box:" + echo " -b " + echo "povray:" + echo " -c (camera position)" + echo " -L (camera look)" + echo " -l (light source)" + echo "bonds:" + echo " -ab (auto bonds)" + exit 1;; + esac +done + +# calculation from lattic eunits to angstroms + +[ "$lc" = "sic" ] && lc=4.359 +[ "$lc" = "si" ] && lc=5.480 +[ "$lc" = "c" ] && lc=3.566 + +#offset=`echo 0.125 \* $lc | bc` +offset=0.0 + +x0=`echo $x0 \* $lc + $offset | bc` +y0=`echo $y0 \* $lc + $offset | bc` +z0=`echo $z0 \* $lc + $offset | bc` +x1=`echo $x1 \* $lc + $offset | bc` +y1=`echo $y1 \* $lc + $offset | bc` +z1=`echo $z1 \* $lc + $offset | bc` + +mx1=`echo $mx1 \* $lc + $offset | bc` +my1=`echo $my1 \* $lc + $offset | bc` +mz1=`echo $mz1 \* $lc + $offset | bc` +mx2=`echo $mx2 \* $lc + $offset | bc` +my2=`echo $my2 \* $lc + $offset | bc` +mz2=`echo $mz2 \* $lc + $offset | bc` +mx3=`echo $mx3 \* $lc + $offset | bc` +my3=`echo $my3 \* $lc + $offset | bc` +mz3=`echo $mz3 \* $lc + $offset | bc` + +clx=`echo $clx \* $lc + $offset | bc` +cly=`echo $cly \* $lc + $offset | bc` +clz=`echo $clz \* $lc + $offset | bc` + +if [ -n "$cx" -a -n "$cy" -a -n "$cz" ]; then + cx=`echo $cx \* $lc + $offset | bc` + cy=`echo $cy \* $lc + $offset | bc` + cz=`echo $cz \* $lc + $offset | bc` +fi + +if [ -n "$bx0" ]; then + bx0=`echo $bx0 \* $lc + $offset | bc` + by0=`echo $by0 \* $lc + $offset | bc` + bz0=`echo $bz0 \* $lc + $offset | bc` + bx1=`echo $bx1 \* $lc + $offset | bc` + by1=`echo $by1 \* $lc + $offset | bc` + bz1=`echo $bz1 \* $lc + $offset | bc` +fi + +# povray command + +POVRAY="povray -W${width} -H${height} -d" + +# convert options + +COPTS="-font /usr/share/fonts/truetype/ttf-dejavu/DejaVuSans.ttf" +COPTS="$COPTS -depth 8 -fill white -stroke blue -pointsize 24" + +# do it ... + +if [ -d $directory ]; then + filesource=$directory/atomic_conf_*.xyz +fi + +if [ -f $directory ]; then + filesource=$directory +fi + +for file in $filesource; do + + cat > temp.pov <<-EOF +#include "colors.inc" +#include "textures.inc" +#include "shapes.inc" +#include "glass.inc" +#include "metals.inc" +#include "woods.inc" +#include "stones.inc" +EOF + + # meta info + count=`grep '# \[P\]' $file | awk '{ print $3 }'` + time=`grep '# \[P\]' $file | awk '{ print $4 }'` + camloc=`grep '# \[P\]' $file | awk '{ print $5 }'` + [ -n "$cx" -a -n "$cy" -a -n "$cz" ] && camloc="<$cx,$cz,$cy>" + + # atoms +#echo "-----> $x0 $y0 $z0 $x1 $y1 $z1 <-----" + if [ -n "$x0" ]; then + export x0 y0 z0 x1 y1 z1 radius extra + export mx1 mx2 mx3 + export my1 my2 my3 + export mz1 mz2 mz3 + export mirror + cat $file | grep -v '#' | awk '\ + BEGIN { + x0=ENVIRON["x0"]; y0=ENVIRON["y0"]; z0=ENVIRON["z0"]; + x1=ENVIRON["x1"]; y1=ENVIRON["y1"]; z1=ENVIRON["z1"]; + mx1=ENVIRON["mx1"]; my1=ENVIRON["my1"]; + mz1=ENVIRON["mz1"]; mx2=ENVIRON["mx2"]; + my2=ENVIRON["my2"]; mz2=ENVIRON["mz2"]; + mx3=ENVIRON["mx3"]; my3=ENVIRON["my3"]; + mz3=ENVIRON["mz3"]; mirror=ENVIRON["mirror"]; + radius=ENVIRON["radius"]; extra=ENVIRON["extra"]; + nx=0; ny=0; nz=0; + } + { + if(($2>=x0)&&($3>=y0)&&($4>=z0)&&\ + ($2<=x1)&&($3<=y1)&&($4<=z1)) { + print "sphere { <"$2","$4","$3">, "radius" "; + if(extra) + print "texture { pigment { color rgb<"$6/4.4",0,"1-$6/4.4"> } "; + else + print "texture { pigment { color "$5" } "; + print "finish { phong 1 metallic } } }"; + } + + if(mirror) { + + nx=$2-mx1; ny=$3-mx2; nz=$4-mx3; + if((nx>=x0)&&(ny>=y0)&&(nz>=z0)&&\ + (nx<=x1)&&(ny<=y1)&&(nz<=z1)) { +print "// translation: "$2/5.480" "$3/5.480" "$4/5.480" -> "nx/5.480" "ny/5.480" "nz/5.480" ..."; + print "sphere { <"nx","nz","ny">, "radius" "; + if(extra) + print "texture { pigment { color rgb<"$6/4.4",0,"1-$6/4.4"> } "; + else + print "texture { pigment { color "$5" } "; + print "finish { phong 1 metallic } } }"; + } + nx=$2-my1; ny=$3-my2; nz=$4-my3; + if((nx>=x0)&&(ny>=y0)&&(nz>=z0)&&\ + (nx<=x1)&&(ny<=y1)&&(nz<=z1)) { + print "sphere { <"nx","nz","ny">, "radius" "; + if(extra) + print "texture { pigment { color rgb<"$6/4.4",0,"1-$6/4.4"> } "; + else + print "texture { pigment { color "$5" } "; + print "finish { phong 1 metallic } } }"; + } + nx=$2-mz1; ny=$3-mz2; nz=$4-mz3; + if((nx>=x0)&&(ny>=y0)&&(nz>=z0)&&\ + (nx<=x1)&&(ny<=y1)&&(nz<=z1)) { + print "sphere { <"nx","nz","ny">, "radius" "; + if(extra) + print "texture { pigment { color rgb<"$6/4.4",0,"1-$6/4.4"> } "; + else + print "texture { pigment { color "$5" } "; + print "finish { phong 1 metallic } } }"; + } + + } + + }' >> temp.pov + else + cat $file | grep -v '#' | while read name x y z color temp; do + cat >> temp.pov <<-EOF +sphere { +<$x, $z, $y>, $radius +texture { +pigment { color $color } +finish { +phong 1 +metallic +} +} +} +EOF + done + fi + + # boundaries + if [ -z "$bx0" ]; then + + #if [ -z "$x0" ]; then + + cat $file | grep '# \[D\]' | while read foo bar x1 y1 z1 x2 y2 z2 ; do + draw_cyl $x1 $y1 $z1 $x2 $y2 $z2 0.05 + done + + #else + + # manually drawing the 3x4 boundaries ... +# draw_cyl $x0 $y0 $z0 $x1 $y0 $z0 +# draw_cyl $x0 $y0 $z0 $x0 $y1 $z0 +# draw_cyl $x1 $y1 $z0 $x1 $y0 $z0 +# draw_cyl $x0 $y1 $z0 $x1 $y1 $z0 + +# draw_cyl $x0 $y0 $z1 $x1 $y0 $z1 +# draw_cyl $x0 $y0 $z1 $x0 $y1 $z1 +# draw_cyl $x1 $y1 $z1 $x1 $y0 $z1 +# draw_cyl $x0 $y1 $z1 $x1 $y1 $z1 + +# draw_cyl $x0 $y0 $z1 $x0 $y0 $z0 +# draw_cyl $x0 $y1 $z1 $x0 $y1 $z0 +# draw_cyl $x1 $y0 $z1 $x1 $y0 $z0 +# draw_cyl $x1 $y1 $z1 $x1 $y1 $z0 +# fi + + else + + # manually drawing the 3x4 boundaries specified by argv ... + draw_cyl $bx0 $by0 $bz0 $bx1 $by0 $bz0 + draw_cyl $bx0 $by0 $bz0 $bx0 $by1 $bz0 + draw_cyl $bx1 $by1 $bz0 $bx1 $by0 $bz0 + draw_cyl $bx0 $by1 $bz0 $bx1 $by1 $bz0 + + draw_cyl $bx0 $by0 $bz1 $bx1 $by0 $bz1 + draw_cyl $bx0 $by0 $bz1 $bx0 $by1 $bz1 + draw_cyl $bx1 $by1 $bz1 $bx1 $by0 $bz1 + draw_cyl $bx0 $by1 $bz1 $bx1 $by1 $bz1 + + draw_cyl $bx0 $by0 $bz1 $bx0 $by0 $bz0 + draw_cyl $bx0 $by1 $bz1 $bx0 $by1 $bz0 + draw_cyl $bx1 $by0 $bz1 $bx1 $by0 $bz0 + draw_cyl $bx1 $by1 $bz1 $bx1 $by1 $bz0 + + fi + + # bonds + if [ -n "$bcr" ]; then + + if [ -z "$x0" ]; then + + cat $file | grep '# \[B\]' | while read foo bar x1 y1 z1 x2 y2 z2 ; do + draw_bond $x1 $z1 $y1 $x2 $z2 $y2 $bcr + done + + else + + export x0 y0 z0 x1 y1 z1 bcr + cat $file | grep '# \[B\]' | awk '\ + BEGIN { + x0=ENVIRON["x0"]; y0=ENVIRON["y0"]; z0=ENVIRON["z0"]; + x1=ENVIRON["x1"]; y1=ENVIRON["y1"]; z1=ENVIRON["z1"]; + bcr=ENVIRON["bcr"]; + } + { + if(($3>=x0)&&($4>=y0)&&($5>=z0)&&\ + ($3<=x1)&&($4<=y1)&&($5<=z1)) { + print "cylinder {"; + print "<"$3","$5","$4">,"; + print "<"$6","$8","$7">, "bcr; + print "pigment { color Blue }"; + print "}"; + } + }' >> temp.pov + + fi + fi + + # auto bonds + if [ "$ab" != "0" ]; then + ((cnt=1)) + while [ $cnt -le $ab ]; do + anr=${anr[$cnt]} + + ((tmp=anr+1)) + line="`sed -n ${tmp}p $file`" + aX=`echo $line | awk '{ print $2 }'` + aY=`echo $line | awk '{ print $3 }'` + aZ=`echo $line | awk '{ print $4 }'` + export aX aY aZ cutoff mirror + cat $file | grep -v '#' | awk '\ + BEGIN { + x=ENVIRON["aX"]; y=ENVIRON["aY"]; z=ENVIRON["aZ"]; + co=ENVIRON["cutoff"]; dist=0; bcr=ENVIRON["bcr"]; + mx1=ENVIRON["mx1"]; my1=ENVIRON["my1"]; + mz1=ENVIRON["mz1"]; mx2=ENVIRON["mx2"]; + my2=ENVIRON["my2"]; mz2=ENVIRON["mz2"]; + mx3=ENVIRON["mx3"]; my3=ENVIRON["my3"]; + mz3=ENVIRON["mz3"]; mirror=ENVIRON["mirror"]; + } + { + dist=sqrt((x-$2)^2+(y-$3)^2+(z-$4)^2); + if((dist<=co)&&(dist>0.01)) { + print "cylinder {"; + print "<"x","z","y">,"; + print "<"$2","$4","$3">, "bcr; + print "pigment { color Blue }"; + print "}"; + } + + if(mirror) { + nx=$2-mx1; ny=$3-mx2; nz=$4-mx3; + dist=sqrt((x-nx)^2+(y-ny)^2+(z-nz)^2) + if((dist<=co)&&(dist>0.01)) { + print "cylinder {"; + print "<"x","z","y">,"; + print "<"nx","nz","ny">, "bcr; + print "pigment { color Blue }"; + print "}"; + } + nx=$2-my1; ny=$3-my2; nz=$4-my3; + dist=sqrt((x-nx)^2+(y-ny)^2+(z-nz)^2) + if((dist<=co)&&(dist>0.01)) { + print "cylinder {"; + print "<"x","z","y">,"; + print "<"nx","nz","ny">, "bcr; + print "pigment { color Blue }"; + print "}"; + } + nx=$2-mz1; ny=$3-mz2; nz=$4-mz3; + dist=sqrt((x-nx)^2+(y-ny)^2+(z-nz)^2) + if((dist<=co)&&(dist>0.01)) { + print "cylinder {"; + print "<"x","z","y">,"; + print "<"nx","nz","ny">, "bcr; + print "pigment { color Blue }"; + print "}"; + } + } + + }' >> temp.pov + + ((cnt+=1)) + done + fi + + # add camera and light source + cat >> temp.pov <<-EOF +camera { +EOF + if [ -n "$ortographic" ]; then cat >> temp.pov <<-EOF +orthographic +EOF + fi + cat >> temp.pov <<-EOF +location $camloc +look_at <$clx,$clz,$clz> +} +light_source { <0,100,-100> color White shadowless } +EOF + + # mv png + $POVRAY temp.pov > /dev/null 2>&1 + time=`basename $file | awk -F. '{ print $1 }' | awk -F_ '{ print $3 }'` + if [ ! -z $displace ]; then + convert $COPTS -draw "text 5,20 'd = $displace %'" temp.png temp.png + else + convert $COPTS -draw "text 5,20 't = $time fs'" temp.png temp.png + fi + mv temp.png `echo $file | sed 's/\.xyz/\.png/'` + +done + +echo "done"