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1 #!/bin/sh
2
3 #
4 # visualization script
5 # author: frank.zirkelbach@physik.uni-augsburg.de
6 #
7
8 # help function
9 draw_cyl() {
10         cat >> temp.pov <<-EOF
11 cylinder {
12 <$1, $3, $2>, <$4, $6, $5>, 0.05
13 pigment { color White }
14 }
15 EOF
16 }
17 draw_bond() {
18         cat >> temp.pov <<-EOF
19 cylinder {
20 <$1, $3, $2>, <$4, $6, $5>, $7
21 pigment { color Blue }
22 }
23 EOF
24 }
25
26 # defaults
27
28 lc=5.429
29 directory="doesnt_exist____for_sure"
30 width="640"
31 height="480"
32 radius="0.6"
33 x0="-0.6"; y0="-0.6"; z0="-0.6";
34 x1="0.6"; y1="0.6"; z1="0.6";
35 cx=""; cy=""; cz="";
36 lx="0"; ly="-100"; lz="100";
37 ortographic=""
38 bx0=""; by0=""; bz0="";
39 bx1=""; by1=""; bz1="";
40 bcr="";
41 clx="0"; cly="0"; clz="0";
42
43 # parse argv
44
45 while [ "$1" ]; do
46         case "$1" in
47                 -d)             directory=$2;           shift 2;;
48                 -w)             width=$2;               shift 2;;
49                 -h)             height=$2;              shift 2;;
50                 -r)             radius=$2;              shift 2;;
51                 -nll)           x0=$2; y0=$3; z0=$4;    shift 4;;
52                 -fur)           x1=$2; y1=$3; z1=$4;    shift 4;;
53                 -c)             cx=$2; cy=$3; cz=$4;    shift 4;;
54                 -L)             clx=$2; cly=$3; clz=$4; shift 4;;
55                 -l)             lx=$2; ly=$3; lz=$4;    shift 4;;
56                 -o)             ortographic=1;          shift 1;;
57                 -b)             bx0=$2; by0=$3; bz0=$4;
58                                 bx1=$5; by1=$6; bz1=$7; shift 7;;
59                 -B)             bcr=$2;                 shift 2;;
60                 -C)             lc=$2;                  shift 2;;
61                 *)
62                                 echo "options:"
63                                 echo "########"
64                                 echo "directory to progress:"
65                                 echo "  -d <directory> (mandatory)"
66                                 echo "png dim:"
67                                 echo "  -w <width>"
68                                 echo "  -h <height>"
69                                 echo "atom size:"
70                                 echo "  -r <radius>"
71                                 echo "  -B <bond cylinder radius>"
72                                 echo "unit cell:"
73                                 echo "  -C <lattice constant>"
74                                 echo "visualization volume:"
75                                 echo "  -nll <x> <y> <z> (near lower left)"
76                                 echo "  -fur <x> <y> <z> (far upper right)"
77                                 echo "  -o (ortographic)"
78                                 echo "bounding box:"
79                                 echo "  -b <x0> <y0> <z0> <x1> <y1> <z1>"
80                                 echo "povray:"
81                                 echo "  -c <x> <y> <z> (camera position)"
82                                 echo "  -L <x> <y> <z> (camera look)"
83                                 echo "  -l <x> <y> <z> (light source)"
84                                 exit 1;;
85         esac
86 done
87
88 # calculation from lattic eunits to angstroms
89
90 [ "$lc" = "sic" ] && lc=4.359
91 [ "$lc" = "si" ] && lc=5.429
92 [ "$lc" = "c" ] && lc=3.566
93
94 offset=`echo 0.125 \* $lc | bc`
95 #offset=0.0
96
97 x0=`echo $x0 \* $lc + $offset | bc`
98 y0=`echo $y0 \* $lc + $offset | bc`
99 z0=`echo $z0 \* $lc + $offset | bc`
100 x1=`echo $x1 \* $lc + $offset | bc`
101 y1=`echo $y1 \* $lc + $offset | bc`
102 z1=`echo $z1 \* $lc + $offset | bc`
103
104 clx=`echo $clx \* $lc + $offset | bc`
105 cly=`echo $cly \* $lc + $offset | bc`
106 clz=`echo $clz \* $lc + $offset | bc`
107
108 if [ -n "$cx" -a -n "$cy" -a -n "$cz" ]; then
109         cx=`echo $cx \* $lc + $offset | bc`
110         cy=`echo $cy \* $lc + $offset | bc`
111         cz=`echo $cz \* $lc + $offset | bc`
112 fi
113
114 if [ -n "$bx0" ]; then
115         bx0=`echo $bx0 \* $lc + $offset | bc`
116         by0=`echo $by0 \* $lc + $offset | bc`
117         bz0=`echo $bz0 \* $lc + $offset | bc`
118         bx1=`echo $bx1 \* $lc + $offset | bc`
119         by1=`echo $by1 \* $lc + $offset | bc`
120         bz1=`echo $bz1 \* $lc + $offset | bc`
121 fi
122
123 # povray command
124
125 POVRAY="povray -W${width} -H${height} -d" 
126
127 # do it ...
128
129 if [ -d $directory ]; then
130         filesource=$directory/atomic_conf_*.xyz
131 fi
132
133 if [ -f $directory ]; then
134         filesource=$directory
135 fi
136
137 for file in $filesource; do
138
139         cat > temp.pov <<-EOF
140 #include "colors.inc"
141 #include "textures.inc"
142 #include "shapes.inc"
143 #include "glass.inc"
144 #include "metals.inc"
145 #include "woods.inc"
146 #include "stones.inc"
147 EOF
148
149         # meta info
150         count=`grep '# \[P\]' $file | awk '{ print $3 }'`
151         time=`grep '# \[P\]' $file | awk '{ print $4 }'`
152         camloc=`grep '# \[P\]' $file | awk '{ print $5 }'`
153         [ -n "$cx" -a -n "$cy" -a -n "$cz" ] && camloc="<$cx,$cz,$cy>"
154
155         # atoms
156         if [ -n "$x0" ]; then
157                 export x0 y0 z0 x1 y1 z1 radius
158                 cat $file | grep -v '#' | awk '\
159                 BEGIN {
160                         x0=ENVIRON["x0"]; y0=ENVIRON["y0"]; z0=ENVIRON["z0"];
161                         x1=ENVIRON["x1"]; y1=ENVIRON["y1"]; z1=ENVIRON["z1"];
162                         radius=ENVIRON["radius"];
163                 }
164                 {
165                         if(($2>=x0)&&($3>=y0)&&($4>=z0)&&\
166                            ($2<=x1)&&($3<=y1)&&($4<=z1)) {
167                                 print "sphere { <"$2","$4","$3">, "radius" ";
168                                 print "texture { pigment { color "$5" } ";
169                                 print "finish { phong 1 metallic } } }";
170                         }
171                 }' >> temp.pov
172         else
173                 cat $file | grep -v '#' | while read name x y z color temp; do
174                         cat >> temp.pov <<-EOF
175 sphere {
176 <$x, $z, $y>, $radius
177 texture {
178 pigment { color $color }
179 finish {
180 phong 1
181 metallic
182 }
183 }
184 }
185 EOF
186                 done
187         fi
188
189         # boundaries
190         if [ -z "$bx0" ]; then
191
192         if [ -z "$x0" ]; then
193
194         cat $file | grep '# \[D\]' | while read foo bar x1 y1 z1 x2 y2 z2 ; do
195                 draw_cyl $x1 $z1 $y1 $x2 $z2 $y2 0.05
196         done
197
198         else
199                 # manually drawing the 3x4 boundaries ...
200                 draw_cyl $x0 $y0 $z0 $x1 $y0 $z0
201                 draw_cyl $x0 $y0 $z0 $x0 $y1 $z0
202                 draw_cyl $x1 $y1 $z0 $x1 $y0 $z0
203                 draw_cyl $x0 $y1 $z0 $x1 $y1 $z0
204
205                 draw_cyl $x0 $y0 $z1 $x1 $y0 $z1
206                 draw_cyl $x0 $y0 $z1 $x0 $y1 $z1
207                 draw_cyl $x1 $y1 $z1 $x1 $y0 $z1
208                 draw_cyl $x0 $y1 $z1 $x1 $y1 $z1
209
210                 draw_cyl $x0 $y0 $z1 $x0 $y0 $z0
211                 draw_cyl $x0 $y1 $z1 $x0 $y1 $z0
212                 draw_cyl $x1 $y0 $z1 $x1 $y0 $z0
213                 draw_cyl $x1 $y1 $z1 $x1 $y1 $z0
214         fi
215
216         else
217
218                 # manually drawing the 3x4 boundaries specified by argv ...
219                 draw_cyl $bx0 $by0 $bz0 $bx1 $by0 $bz0
220                 draw_cyl $bx0 $by0 $bz0 $bx0 $by1 $bz0
221                 draw_cyl $bx1 $by1 $bz0 $bx1 $by0 $bz0
222                 draw_cyl $bx0 $by1 $bz0 $bx1 $by1 $bz0
223
224                 draw_cyl $bx0 $by0 $bz1 $bx1 $by0 $bz1
225                 draw_cyl $bx0 $by0 $bz1 $bx0 $by1 $bz1
226                 draw_cyl $bx1 $by1 $bz1 $bx1 $by0 $bz1
227                 draw_cyl $bx0 $by1 $bz1 $bx1 $by1 $bz1
228
229                 draw_cyl $bx0 $by0 $bz1 $bx0 $by0 $bz0
230                 draw_cyl $bx0 $by1 $bz1 $bx0 $by1 $bz0
231                 draw_cyl $bx1 $by0 $bz1 $bx1 $by0 $bz0
232                 draw_cyl $bx1 $by1 $bz1 $bx1 $by1 $bz0
233
234         fi      
235
236         # bonds
237         if [ -n "$bcr" ]; then
238
239                 if [ -z "$x0" ]; then
240
241         cat $file | grep '# \[B\]' | while read foo bar x1 y1 z1 x2 y2 z2 ; do
242                 draw_bond $x1 $z1 $y1 $x2 $z2 $y2 $bcr
243         done
244
245                 else
246
247                 export x0 y0 z0 x1 y1 z1 bcr
248                 cat $file | grep '# \[B\]' | awk '\
249                 BEGIN {
250                         x0=ENVIRON["x0"]; y0=ENVIRON["y0"]; z0=ENVIRON["z0"];
251                         x1=ENVIRON["x1"]; y1=ENVIRON["y1"]; z1=ENVIRON["z1"];
252                         bcr=ENVIRON["bcr"];
253                 }
254                 {
255                         if(($3>=x0)&&($4>=y0)&&($5>=z0)&&\
256                            ($3<=x1)&&($4<=y1)&&($5<=z1)) {
257                                 print "cylinder {";
258                                 print "<"$3","$5","$4">,";
259                                 print "<"$6","$8","$7">, "bcr;
260                                 print "pigment { color Blue }";
261                                 print "}";
262                         }
263                 }' >> temp.pov
264
265                 fi
266         fi      
267
268         # add camera and light source
269         cat >> temp.pov <<-EOF
270 camera {
271 EOF
272         if [ -n "$ortographic" ]; then  cat >> temp.pov <<-EOF
273 orthographic
274 EOF
275         fi
276         cat >> temp.pov <<-EOF
277 location $camloc
278 look_at <$clx,$clz,$clz>
279 }
280 light_source { <0,100,-100> color White shadowless }
281 EOF
282
283         # mv png
284         $POVRAY temp.pov > /dev/null 2>&1
285         mv temp.png `echo $file | sed 's/\.xyz/\.png/'`
286
287 done
288
289 echo "done"