amu_setup

#!/bin/bash
[ $AMU_HOME ] || { echo "AMU_HOME not set. Exiting" ; exit;  }
source $AMU_HOME/ambermd_util.bash

if [ ! -f settings ] ; then
    #you nub, no settings, lets load defaults
    #echo "No settings file in this directory. Using defaults"
    cat << EOF > settings
[ "\$AMU_SIM_BIN" ] || AMU_SIM_BIN="pmemd.cuda"
[ "\$AMU_SIM_EXTRA_ARGS" ] || AMU_SIM_EXTRA_ARGS=""
EOF
fi
source settings
PROJ=`amu_get_project_name`
NAME=`amu_get_step`

[ ! -f $PROJ-$NAME.mdout ] && touch $PROJ-$NAME.mdout
[ ! -f $PROJ-$NAME.rst7 ] && touch $PROJ-$NAME.rst7 
[ ! -f $PROJ-$NAME.nc ] && touch $PROJ-$NAME.nc   
[ ! -f $PROJ-$NAME.inf ] && touch $PROJ-$NAME.inf  
ln -sf $PROJ-$NAME.mdout mdout
ln -sf $PROJ-$NAME.rst7  inpcrd.rst7
ln -sf $PROJ-$NAME.nc    mdcrd
ln -sf $PROJ-$NAME.nc    mdcrd.nc
ln -sf $PROJ-$NAME.inf   mdinfo
prev=`printf "%d" $(( NAME - 1 ))`
cat << EOF > run.com 
#!/bin/bash
source ./settings
err=\$(mktemp)
\$AMU_SIM_BIN -O \\
      -p ../inpcrd.parm7 \\
      -c ../$prev/inpcrd.rst7 \\
      -r inpcrd.rst7 \\
      -ref ../$prev/inpcrd.rst7  \$AMU_SIM_EXTRA_ARGS 2>\$err >/dev/null
code=\$?
ret=\$(<\$err)
compl=\$( egrep 'TIMING|FINAL\s*RESULTS' mdout ) 
if [ "\$ret" ] ; then 
	# logged an error, so report it and maybe exit
	d=\`date +"%Y/%m/%d-%R:%S"\`
	while read line ; do
		echo "[\${d}] \$line" >>  error.log
	done < \$err
	echo "[\${d}] (Return status \${code})" >>  error.log
else
	echo "[\${d}] Process died before completing! (Return status \${code})" >>  error.log
fi
if [ -z "\$compl" ] ; then
    echo "[\${d}] Failure. Simulation did not finish." >>  error.log
	rm \$err
	exit 1
fi
rm \$err
exit 0
EOF
chmod u+x run.com
cat << EOF > Makefile
SHELL := /bin/bash -O extglob

default:
	./run.com

clean:
	rm -f !(Makefile|mdin|settings|run.com)
	> mdcrd.nc
	> mdout
	> inpcrd.rst7
	> mdinfo
	amu_setup
EOF