#!/bin/bash
########################################################
#  Define files and run parameters
########################################################
#
# Name used for the input files. For example croco_grd.nc
MODEL=croco

# Scratch directory where the model is run
SCRATCHDIR=`pwd`/SCRATCH

# Input directory where the croco_inter.in input file is located
INPUTDIR=`pwd`/CROCO_IN  # prod architecture
#INPUTDIR=`pwd`          # dev architecture

# AGRIF input file which defines the position of child grids
AGRIF_FILE=AGRIF_FixedGrids.in

# Directory where the croco input NetCDF files (croco_grd.nc, ...) are stored
MSSDIR=`pwd`/CROCO_FILES

# Directory where the croco output and restart NetCDF files (croco_his.nc, ...) are stored
MSSOUT=$SCRATCHDIR

# CROCO executable
CODFILE=croco

# number of processors for MPI run
NBPROCS=8

# command for running the mode : ./ for sequential job, mpirun -np NBPROCS for mpi run
# WARNING: for mpi run command, it is needed to add a space at the end!
RUNCMD='./'
#RUNCMD="mpirun -np $NBPROCS "
#RUNCMD="$MPI_LAUNCH "
#RUNCMD="srun "

#  Define environment variables for OPENMP
OMP_SCHEDULE=static
OMP_NUM_THREADS=2
OMP_DYNAMIC=false
OMP_NESTED=false
KMP_LIBRARY=throughput
KMP_STACKSIZE=2m
KMP_DUPLICATE_LIB_OK=TRUE

# Model time step [seconds]
DT=3600
# Number of barotropic time steps within one baroclinic time step [number], NDTFAST in croco.in
NFAST=60

# number total of grid levels
NLEVEL=1
# AGRIF nesting refinement coefficient
AGRIF_REF=3

# Start and End year 
NY_START=1
NY_END=10
# Start and End month
NM_START=1
NM_END=12
# Set month format at 1 or 2 digits (for output files): "%01d" = 1 digit/ "%02d" = 2 digit  
MTH_FORMAT="%01d"
# Number of days per month
NDAYS=30
#  Time Schedule  -  TIME_SCHED=0 --> yearly files
#                    TIME_SCHED=1 --> monthly files
TIME_SCHED=1

# Output frequency [days]
#   average
ND_AVG=3
#   history (if = 1, set equal to NUMTIMES)
ND_HIS=-1
#   restart (if = -1 set equal to NUMTIMES)
ND_RST=-1

# Flag for using exact restart - EXACT_RST=1 --> Exact restart ON
EXACT_RST=0

#unalias cp
#unalias mv
#limit coredumpsize unlimited
CP=/bin/cp
MV=/bin/mv
LN=/bin/ln
#
########################################################
#  END USER CHANGE
########################################################
#
if [[ $TIME_SCHED == 0 ]]; then
    NM_START=1
    NM_END=1
fi
#
# coarse netcdf file names
#
GRDFILE=${MODEL}_grd.nc
FORFILE=${MODEL}_frc.nc
BLKFILE=${MODEL}_blk.nc
BRYFILE=${MODEL}_bry.nc
CLMFILE=${MODEL}_clm.nc
INIFILE=${MODEL}_ini.nc
RNFFILE=${MODEL}_runoff.nc
#
#  Restart file - RSTFLAG=0 --> No Restart
#		  RSTFLAG=1 --> Restart
#
if [[ $NY_START == 1 && $NM_START == 1 ]]; then
    RSTFLAG=0
else
    RSTFLAG=1
fi
#  Exact restart 
if [[ $EXACT_RST == 1 ]]; then
    echo "Exact restart defined"
    if [[ $NY == $NY_START && $NM == $NM_START ]]; then
	NUMRECINI=1
	echo "set NUMRECINI = $NUMRECINI"
    else  # no exact restart
	NUMRECINI=2
	echo "set NUMRECINI = $NUMRECINI"
    fi
else
    echo "No exact restart"
    NUMRECINI=1
    echo "set NUMRECINI = $NUMRECINI"
fi

#
if [[ $RSTFLAG != 0 ]]; then
    NY=$NY_START
    NM=$NM_START
    if [[ $TIME_SCHED == 0 ]]; then
	NY=$((NY - 1))
	TIME=Y${NY}
    else
	NM=$((NM - 1))
	if [[ $NM == 0 ]]; then
	    NM=12 
	    NY=$((NY - 1))
	fi
	TIME=Y${NY}M$( printf ${MTH_FORMAT} ${NM})
    fi
    RSTFILE=${MODEL}_rst_${TIME}.nc
fi
#
# Get the code
#
if [ ! -e $SCRATCHDIR ] ; then
    mkdir $SCRATCHDIR
fi
cd $SCRATCHDIR
echo "Getting $CODFILE from $INPUTDIR"
$CP -f $INPUTDIR/$CODFILE $SCRATCHDIR
chmod u+x $CODFILE
if [[ $NLEVEL -gt 1 ]]; then
    echo "Getting $AGRIF_FILE from $INPUTDIR"
    $CP -f $INPUTDIR/$AGRIF_FILE $SCRATCHDIR
fi
#
# Get the netcdf files
#
LEVEL=0
echo "Getting ${BRYFILE} from $MSSDIR"
$LN -sf $MSSDIR/${BRYFILE} $SCRATCHDIR
while [[ $LEVEL != $NLEVEL ]]; do
    if [[ ${LEVEL} == 0 ]]; then
	ENDF=
    else
	ENDF=.${LEVEL}
    fi
    echo "Getting ${GRDFILE}${ENDF} from $MSSDIR"
    $LN -sf $MSSDIR/${GRDFILE}${ENDF} $SCRATCHDIR
    echo "Getting ${FORFILE}${ENDF} from $MSSDIR"
    $LN -sf $MSSDIR/${FORFILE}${ENDF} $SCRATCHDIR
    echo "Getting ${BLKFILE}${ENDF} from $MSSDIR"
    $LN -sf $MSSDIR/${BLKFILE}${ENDF} $SCRATCHDIR
    echo "Getting ${CLMFILE}${ENDF} from $MSSDIR"
    $LN -sf $MSSDIR/${CLMFILE}${ENDF} $SCRATCHDIR
    echo "Getting ${RNFFILE}${ENDF} from $MSSDIR"
    $LN -sf $MSSDIR/${RNFFILE}${ENDF} $SCRATCHDIR
    if [[ $RSTFLAG == 0 ]]; then
	echo "Getting ${INIFILE}${ENDF} from $MSSDIR"
	$CP -f $MSSDIR/${INIFILE}${ENDF} $SCRATCHDIR
    else
	echo "Getting ${RSTFILE}${ENDF} from $MSSOUT"
	$CP -f $MSSOUT/${RSTFILE}${ENDF} $SCRATCHDIR
	$CP -f ${RSTFILE}${ENDF} ${MODEL}_ini.nc${ENDF}
    fi
    echo "Getting ${MODEL}_inter.in${ENDF} from $INPUTDIR"
    $CP -f $INPUTDIR/${MODEL}_inter.in${ENDF} ${MODEL}_inter.in${ENDF}

    LEVEL=$((LEVEL + 1))
done
#
# Put the number of time steps in the .in files
#
NUMTIMES=0
NUMTIMES=$((NDAYS * 24 * 3600))
NUMTIMES=$((NUMTIMES / DT))
if [[ $TIME_SCHED == 0 ]]; then
	NUMTIMES=$((NUMTIMES * 12))
fi

DT0=$DT
LEVEL=0
while [[ $LEVEL != $NLEVEL ]]; do
    if [[ ${LEVEL} == 0 ]]; then
	ENDF=''
    else
	ENDF=.${LEVEL}
	NUMTIMES=$((AGRIF_REF * NUMTIMES))
	DT=$((DT / AGRIF_REF))
    fi
    NUMAVG=$((ND_AVG * 86400 / DT ))
    if [[ $ND_HIS -ne -1 ]]; then
	NUMHIS=$((ND_HIS * 86400 / DT ))
    else
	NUMHIS=$NUMTIMES
    fi
    if [[ $ND_RST -ne -1 ]]; then
	NUMRST=$((ND_RST * 86400 / DT ))
    else
	NUMRST=$NUMTIMES
    fi
    echo " "
    echo "Writing in ${MODEL}_inter.in${ENDF}"
    echo "USING DT       = $DT"
    echo "USING NFAST    = $NFAST"
    echo "USING NUMTIMES = $NUMTIMES"
    echo "USING NUMAVG   = $NUMAVG"
    echo "USING NUMHIS   = $NUMHIS"
    echo "USING NUMRST   = $NUMRST"
    
    if [ ! -f ${MODEL}_inter.in${ENDF} ]; then
	echo "=="
	echo "=> ERROR : miss the ${MODEL}_inter.in${ENDF} file"
	echo "=="
	exit 1
    fi
    sed -e 's/NUMTIMES/'$NUMTIMES'/' -e 's/TIMESTEP/'$DT'/' -e 's/NFAST/'$NFAST'/' \
	-e 's/\bNUMAVG\b/'$NUMAVG'/' \
	-e 's/\bNUMHIS\b/'$NUMHIS'/' \
	-e 's/\bNUMRST\b/'$NUMRST'/' < ${MODEL}_inter.in${ENDF} > ${MODEL}_inter.in${ENDF}.tmp1
    
    LEVEL=$((LEVEL + 1))
done
DT=$DT0
#
###########################################################
#  Compute
###########################################################
#
NY_END=$((NY_END + 1))
NM_END=$((NM_END + 1))
NY=$NY_START
while [[ $NY != $NY_END ]]; do
    if [[ $NY == $NY_START ]]; then
	NM=$NM_START
    else 
	NM=1
    fi
    MY_YEAR=$NY
    MY_YEAR=$((MY_YEAR + 1))
    if [[ $MY_YEAR == $NY_END ]]; then
	MONTH_END=$NM_END
    else 
	MONTH_END=13
    fi
    if [[ $TIME_SCHED == 0 ]]; then
	MONTH_END=2
    fi
    while [[ $NM != $MONTH_END ]]; do
	if [[ $TIME_SCHED == 0 ]]; then
	    TIME=Y${NY}
	else
	    TIME=Y${NY}M$( printf ${MTH_FORMAT} ${NM})
	fi
	
	#
	LEVEL=0
	while [[ $LEVEL != $NLEVEL ]]; do
	    if [[ ${LEVEL} == 0 ]]; then
		ENDF=''
	    else
		ENDF=.${LEVEL}
	    fi
	if [[ $EXACT_RST == 1 ]]; then
	    echo "Exact restart defined"
	    if [[ $NY == $NY_START && $NM == $NM_START ]]; then
		NUMRECINI=1
		echo "set NUMRECINI = $NUMRECINI"
	    else  # no exact restart
		NUMRECINI=2
		echo "set NUMRECINI = $NUMRECINI"
	    fi
	else
	    echo "No exact restart"
	    NUMRECINI=1
	    echo "set NUMRECINI = $NUMRECINI"
	fi
	#
	sed -e 's/NUMRECINI/'$NUMRECINI'/' < ${MODEL}_inter.in${ENDF}.tmp1 > ${MODEL}.in${ENDF}
	#
	    LEVEL=$((LEVEL + 1))
	done
	#
	#  COMPUTE
	#
	echo " "
	echo "Computing for $TIME"
	date
	${RUNCMD}$CODFILE  ${MODEL}.in > ${MODEL}_${TIME}.out
	date
	#
	# Test if the month has finised properly
	echo "Test ${MODEL}_${TIME}.out"
	status=`tail -2 ${MODEL}_${TIME}.out | grep DONE | wc -l`
	if [[ $status -eq 1 ]]; then
	    echo "All good"
	    echo "XXXX${MYTEST}XXXX"
	else
	    echo
	    echo "Warning: month not finished properly"
	    echo
	    tail -20 ${MODEL}_${TIME}.out
	    echo
	    echo "Month ${TIME} did not work"
	    echo
	    exit 1
	fi
	#
	#  Archive
	#
	LEVEL=0
	while [[ $LEVEL != $NLEVEL ]]; do
	    if [[ ${LEVEL} == 0 ]]; then
		ENDF=
	    else
		ENDF=.${LEVEL}
	    fi
	    $CP -f ${MODEL}_rst.nc${ENDF} ${INIFILE}${ENDF}
	    $MV -f ${MODEL}_his.nc${ENDF} ${MSSOUT}/${MODEL}_his_${TIME}.nc${ENDF}
	    $MV -f ${MODEL}_rst.nc${ENDF} ${MSSOUT}/${MODEL}_rst_${TIME}.nc${ENDF}
	    $MV -f ${MODEL}_avg.nc${ENDF} ${MSSOUT}/${MODEL}_avg_${TIME}.nc${ENDF}

	    LEVEL=$((LEVEL + 1))
	done
	NM=$((NM + 1))
    done
    NY=$((NY + 1))
done
#
#############################################################