adjustments concerning crt

diff --git a/runmd b/runmd
index 541734bc431d80fc4505df537fe3695a569125a3..609bcf316e8abdd5f3df8638582027df4f3014c8 100755 (executable)
--- a/runmd
+++ b/runmd
@@ -15,7 +15,8 @@ fi
 cp -v config $1/config
 
 mkdir -p logs
-time ./mdrun -c ./config -s $1 | tee logs/run_`basename $1`.log
+logfile=logs/run_`basename $1`.log
+time ./mdrun -c ./config -s $1 | tee $logfile
 
 if [ "$?" == "0" ]; then
        #./perms
@@ -23,7 +24,26 @@ if [ "$?" == "0" ]; then
                # whole simulation cell
                #./visualize -w 640 -h 480 -d $1
 
-               # center unit cell
+               # crt
+               mkdir -p $1/crt
+               check=`grep crt\ init $logfile`
+               if [ "$check" = "  crt init" ]; then
+                       grep crt\ energy $logfile | \
+                               awk -F: '{ print $2 }' | \
+                               awk -F\ -\  '{ print $1 " " $2 }' > \
+                               $1/crt/energy
+                       for i in $1/s-crt_*.save; do
+                               nr=`basename $i | awk -F_ '{ print $2 }' | \
+                                       awk -F. '{ print $1 }'`
+                               ./s2xyz $i > $1/crt/atomic_conf_${nr}.xyz
+                       done
+                       ./visualize -w 640 -h 480 -d $1/crt \
+                                   -nll -0.56 -0.56 -0.76 -fur 0.56 0.56 0.56 \
+                                   -b -0.5 -0.5 -0.5 0.5 0.5 0.5 \
+                                   -c -0.2 -2.0 0.6 -L 0 0 -0.1 \
+                                   -r 0.6 -B 0.1
+               fi
+
                ./visualize -w 640 -h 480 -d $1 \
                            -nll -0.56 -0.56 -0.76 -fur 0.56 0.56 0.56 \
                            -b -0.5 -0.5 -0.5 0.5 0.5 0.5 \
@@ -33,5 +53,7 @@ if [ "$?" == "0" ]; then
                # old rasmol
                #rasmol -32 -nodisplay < $1/visualize.scr > /dev/null 2>&1
                ./ppm2avi $1
+
        fi
 fi
+