}
EOF
}
+draw_bond() {
+ cat >> temp.pov <<-EOF
+cylinder {
+<$1, $3, $2>, <$4, $6, $5>, $7
+pigment { color Blue }
+}
+EOF
+}
directory="doesnt_exist____for_sure"
-width="1024"
-height="768"
+width="640"
+height="480"
radius="1.0"
x0=""; y0=""; z0="";
x1=""; y1=""; z1="";
cx=""; cy=""; cz="";
lx="0"; ly="-100"; lz="100";
+ortographic=""
bx0=""; by0=""; bz0="";
bx1=""; by1=""; bz1="";
+bcr="";
+clx="0"; cly="0"; clz="0";
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;;
*)
echo "options:"
echo "########"
echo " -h <height>"
echo "atom size:"
echo " -r <radius>"
+ echo " -B <bond cylinder radius>"
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 $directory ] ; then
- echo "no valid directory"
- exit 1
+POVRAY="povray -W${width} -H${height} -d"
+
+if [ -d $directory ]; then
+ filesource=$directory/atomic_conf_*.xyz
fi
-POVRAY="povray -W${width} -H${height} -d"
+if [ -f $directory ]; then
+ filesource=$directory
+fi
-for file in $directory/atomic_conf_*.xyz; do
+for file in $filesource; do
cat > temp.pov <<-EOF
#include "colors.inc"
if [ -z "$bx0" ]; 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 $z1 $y1 $x2 $z2 $y2 0.05
done
+
else
# manually drawing the 3x4 boundaries ...
draw_cyl $x0 $y0 $z0 $x1 $y0 $z0
fi
+ # bonds
+ if [ -n "$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