--- /dev/null
+#!/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=$1; shift 1;;
+ *)
+ echo "options:"
+ echo "########"
+ echo "directory to progress:"
+ echo " -d <directory> (mandatory)"
+ echo "png dim:"
+ echo " -w <width>"
+ echo " -h <height>"
+ echo "atom size:"
+ echo " -r <radius>"
+ echo " -B <bond cylinder radius>"
+ echo "unit cell:"
+ echo " -C <lattice constant>"
+ echo " -m <dimX> <dimY> <dimZ> (mirror atoms)"
+ echo "visualization volume:"
+ echo " -nll <x> <y> <z> (near lower left)"
+ echo " -fur <x> <y> <z> (far upper right)"
+ echo " -o (ortographic)"
+ echo "bounding box:"
+ echo " -b <x0> <y0> <z0> <x1> <y1> <z1>"
+ echo "povray:"
+ echo " -c <x> <y> <z> (camera position)"
+ echo " -L <x> <y> <z> (camera look)"
+ echo " -l <x> <y> <z> (light source)"
+ echo "bonds:"
+ echo " -ab <atom number> <cutoff> (auto bonds)"
+ exit 1;;
+ esac
+done
+
+# calculation from lattic eunits to angstroms
+
+[ "$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"
projects / physik / posic.git / blobdiff