if [ -z "$1" ]; then
	echo "specify a directory for logging and save files"
	exit
fi

if [ ! -f ./config ]; then
	echo "no config file found"
	exit
fi

[ ! -d $1 ] && mkdir -p $1

./clean $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
	if [ "$1" ] ; then
		# whole simulation cell
		#./visualize -w 640 -h 480 -d $1

		# 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 \
			    -c -0.2 -2.0 0.6 -L 0 0 -0.1 \
			    -r 0.6 -B 0.1

		# old rasmol
		#rasmol -32 -nodisplay < $1/visualize.scr > /dev/null 2>&1
		./ppm2avi $1

	fi
fi