more interstitial testing, added bond visualization

[physik/posic.git] / visualize

diff --git a/visualize b/visualize
index 6255e89..ab6e374 100755 (executable)
--- a/visualize
+++ b/visualize
@@ -14,17 +14,27 @@ pigment { color White }
 }
 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="";
 
 while [ "$1" ]; do
        case "$1" in
@@ -37,6 +47,9 @@ while [ "$1" ]; do
                -c)             cx=$2; cy=$3; cz=$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 "########"
@@ -47,10 +60,13 @@ while [ "$1" ]; do
                                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 "  -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> (light source)"
@@ -118,15 +134,14 @@ EOF
        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
-               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
@@ -145,6 +160,58 @@ EOF
                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      
+
        # add camera and light source
        cat >> temp.pov <<-EOF
 camera {