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Merged
drroe merged 1 commit into from
Feb 6, 2026
Merged

Ensure status is properly reported when no status file is specified #13

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24 changes: 15 additions & 9 deletions AmberMdPrep.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@
# NIH/NHLBI
# 2020-08-07

VERSION='0.7 (beta)'
VERSION='0.8 (beta)'
MPIRUN=`which mpirun`
CPPTRAJ=`which cpptraj`

Expand Down Expand Up @@ -51,6 +51,15 @@ PRODUCTION_DT='0.002' # Default time step for 'production' steps (9 and final)
STATUSFILE=''

# ------------------------------------------------------------------------------
# ReportStatus <message>
# Report job status to stdout and STATUSFILE if not blank.
ReportStatus() {
echo $1
if [ ! -z "$STATUSFILE" ] ; then
echo $1 > $STATUSFILE
fi
}

# DetectSystemType <topology file>
# Use cpptraj to print out residues from a topology file. Determine the
# type of each residue and keep track.
Expand Down Expand Up @@ -497,9 +506,7 @@ if [ ! -z "$PRODUCTIONMASK" -a -z "$PRODUCTIONWT" ] ; then
exit 1
fi

if [ -z "$STATUSFILE" ] ; then
STATUSFILE=/dev/stdout
else
if [ ! -z "$STATUSFILE" ] ; then
echo "Status file is $STATUSFILE"
fi

Expand Down Expand Up @@ -855,7 +862,7 @@ EOF
fi
if [ $? -ne 0 ] ; then
echo "Error: MD failed: $MDIN" >> /dev/stderr
echo "Equilibration failed" > $STATUSFILE
ReportStatus "Equilibration failed"
exit 1
fi
else
Expand Down Expand Up @@ -979,19 +986,18 @@ EOF
echo "Complete."
DONE=1
if [ $TEST -eq 0 ] ; then
echo "Equilibration success" > $STATUSFILE
ReportStatus "Equilibration success"
fi
elif [ $ERR -eq 2 ] ; then
echo "Equlibration eval failed"
echo "Equlibration eval failed" > $STATUSFILE
ReportStatus "Equlibration eval failed"
break
else
INPCRD="final.$num.ncrst"
((num++))
# Safety valve
if [ $num -gt 20 ] ; then
echo "More than 20 iterations of final density equil required. Bailing out."
echo "Too many final iterations" > $STATUSFILE
ReportStatus "Too many final iterations"
DONE=1
continue
fi
Expand Down