}
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="1024"
-height="768"
-radius="1.0"
-x0=""; y0=""; z0="";
-x1=""; y1=""; z1="";
+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="";
+clx="0"; cly="0"; clz="0";
+extra=0
+
+# parse argv
while [ "$1" ]; do
case "$1" in
-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;;
*)
echo "options:"
echo "########"
echo " -h <height>"
echo "atom size:"
echo " -r <radius>"
+ echo " -B <bond cylinder radius>"
+ echo "unit cell:"
+ echo " -C <lattice constant>"
echo "visualization volume:"
echo " -nll <x> <y> <z> (near lower left)"
echo " -fur <x> <y> <z> (far upper right)"
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)"
exit 1;;
esac
done
-if [ ! -d $directory ] ; then
- echo "no valid directory"
- exit 1
+# calculation from lattic eunits to angstroms
+
+[ "$lc" = "sic" ] && lc=4.359
+[ "$lc" = "si" ] && lc=5.429
+[ "$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`
+
+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"
-for file in $directory/atomic_conf_*.xyz; do
+# convert options
+
+COPTS="-font /usr/share/fonts/truetype/ttf-dejavu/DejaVuSans.ttf"
+COPTS="$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 $filesource; do
cat > temp.pov <<-EOF
#include "colors.inc"
# atoms
if [ -n "$x0" ]; then
- export x0 y0 z0 x1 y1 z1 radius
+ export x0 y0 z0 x1 y1 z1 radius extra
cat $file | grep -v '#' | awk '\
BEGIN {
x0=ENVIRON["x0"]; y0=ENVIRON["y0"]; z0=ENVIRON["z0"];
x1=ENVIRON["x1"]; y1=ENVIRON["y1"]; z1=ENVIRON["z1"];
- radius=ENVIRON["radius"];
+ radius=ENVIRON["radius"]; extra=ENVIRON["extra"];
}
{
if(($2>=x0)&&($3>=y0)&&($4>=z0)&&\
($2<=x1)&&($3<=y1)&&($4<=z1)) {
print "sphere { <"$2","$4","$3">, "radius" ";
- print "texture { pigment { color "$5" } ";
+ if(extra)
+ print "texture { pigment { color rgb<"$6/4.4",0,"1-$6/4.4"> } ";
+ else
+ print "texture { pigment { color "$5" } ";
print "finish { phong 1 metallic } } }";
}
}' >> temp.pov
# boundaries
if [ -z "$bx0" ]; then
- if [ -z "$x0" ]; then
+ #if [ -z "$x0" ]; then
+
cat $file | grep '# \[D\]' | while read foo bar x1 y1 z1 x2 y2 z2 ; do
- cat >> temp.pov <<-EOF
-cylinder {
-<$x1, $z1, $y1>, <$x2, $z2, $y2>, 0.05
-pigment { color White }
-}
-EOF
+ draw_cyl $x1 $y1 $z1 $x2 $y2 $z2 0.05
done
- else
+
+ #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
+# 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 $z0
+# fi
else
fi
+ # bonds
+ if [ -n "$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
+
# add camera and light source
cat >> temp.pov <<-EOF
camera {
fi
cat >> temp.pov <<-EOF
location $camloc
-look_at <0,0,0>
+look_at <$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 }'`
+ convert $COPTS -draw "text 5,20 't = $time fs'" temp.png temp.png
mv temp.png `echo $file | sed 's/\.xyz/\.png/'`
done
projects / physik / posic.git / blobdiff