more structured run script (concerning visualization)

diff --git a/run b/run
index 67d6d73d4c04e64dac21c781b146df29a40150dd..b46f2ca4e4c60d9040e43aa91be510e4fee68b58 100755 (executable)
--- a/run
+++ b/run
@@ -8,10 +8,20 @@ fi
 if [ "$?" == "0" ]; then
        #./perms
        if [ "$1" ] ; then
+               # whole simulation cell
                #./visualize -w 640 -h 480 -d $1
-               #./visualize -w 640 -h 480 -d $1 -nll -2.4 -2.4 -2.4 -fur 3.8 3.8 3.8 -b -2.03 -2.03 -2.03 3.39 3.39 3.39 -r 0.6 -c 1.5 -15.0 1.5 -B 0.1
+
+               # center unit cell
+               ./visualize -w 640 -h 480 -d $1 \
+                           -nll -2.4 -2.4 -2.4 -fur 3.8 3.8 3.8 \
+                           -b -2.03 -2.03 -2.03 3.39 3.39 3.39 \
+                           -r 0.6 -c 1.5 -15.0 1.5 -B 0.1
+
+               # old rasmol
                #rasmol -32 -nodisplay < $1/visualize.scr > /dev/null 2>&1
-               #./ppm2avi $1
+               ./ppm2avi $1
+
+               # copy config and main prog
                cp -v sic.c $1/sic.c
                cp -v config.h $1/config.h
        fi