X-Git-Url: https://hackdaworld.org/gitweb/?p=physik%2Fposic.git;a=blobdiff_plain;f=runmd;h=609bcf316e8abdd5f3df8638582027df4f3014c8;hp=c09780c68380f97389194234010e8c19e5145aa7;hb=HEAD;hpb=0d1dfb1e5027d215fced8ca306dd658f692a2a44

diff --git a/runmd b/runmd
index c09780c..609bcf3 100755
--- a/runmd
+++ b/runmd
@@ -8,11 +8,15 @@ if [ ! -f ./config ]; then
 	exit
 fi
 
-[ ! -d $1 ] && mkdir $1
+[ ! -d $1 ] && mkdir -p $1
 
 ./clean $1
 
-./mdrun -c ./config -s $1
+cp -v config $1/config
+
+mkdir -p logs
+logfile=logs/run_`basename $1`.log
+time ./mdrun -c ./config -s $1 | tee $logfile
 
 if [ "$?" == "0" ]; then
 	#./perms
@@ -20,9 +24,28 @@ if [ "$?" == "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 $1 \
-		            -nll -0.56 -0.56 -0.56 -fur 0.56 0.56 0.56 \
+		            -nll -0.56 -0.56 -0.76 -fur 0.56 0.56 0.56 \
 			    -b -0.5 -0.5 -0.5 0.5 0.5 0.5 \
 			    -c -0.2 -2.0 0.6 -L 0 0 -0.1 \
 			    -r 0.6 -B 0.1
@@ -31,7 +54,6 @@ if [ "$?" == "0" ]; then
 		#rasmol -32 -nodisplay < $1/visualize.scr > /dev/null 2>&1
 		./ppm2avi $1
 
-		# copy config
-		cp -v config $1/config
 	fi
 fi
+