From 2c8b1f9c5273d3913b0b2015a2ada9612ba4fa59 Mon Sep 17 00:00:00 2001
From: hackbard <hackbard@sage.physik.uni-augsburg.de>
Date: Thu, 20 May 2010 16:55:38 +0200
Subject: [PATCH] adjustments concerning crt

---
 runmd | 26 ++++++++++++++++++++++++--
 1 file changed, 24 insertions(+), 2 deletions(-)

diff --git a/runmd b/runmd
index 541734b..609bcf3 100755
--- 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
+
-- 
2.20.1