%include <head.h>

if [[ "%NWM_ENSEMBLE_MEM%" == "" ]]; then
    echo "=== STARTING NWM MODEL %NWM_CYCLE% ==="
    export WRF_HYDRO_ROOT=%NWM_JOBDIR%/%NWM_DOMAIN%/%NWM_CYCLE%/nwm
else
    echo "=== STARTING NWM MODEL %NWM_CYCLE%, MEMBER %NWM_ENSEMBLE_MEM% ==="
    export WRF_HYDRO_ROOT=%NWM_JOBDIR%/%NWM_DOMAIN%/%NWM_CYCLE%_mem%NWM_ENSEMBLE_MEM%/nwm
fi

mkdir -p $WRF_HYDRO_ROOT

length_hrs=%LENGTH_HRS%

if [[ %LENGTH_HRS% < 0 ]]; then
    cycle_date=$(date -ud "%CYCLE_DATE% %CYCLE_TIME% +%LENGTH_HRS% hours" +%%Y%%m%%d)
    cycle_time=$(date -ud "%CYCLE_DATE% %CYCLE_TIME% +%LENGTH_HRS% hours" +%%H%%M)
    length_hrs=$(($length_hrs*-1))
    ana_flag=1
else
    cycle_date=$(date -ud "%CYCLE_DATE% %CYCLE_TIME%" +%%Y%%m%%d)
    cycle_time=$(date -ud "%CYCLE_DATE% %CYCLE_TIME%" +%%H%%M)
    ana_flag=''
fi

# cp %ECF_HOME%/nwm/%NWM_DOMAIN%/params/* $WRF_HYDRO_ROOT
cp --no-preserve=mode %MODEL_TABLES_DIR%/*.TBL $WRF_HYDRO_ROOT                  # get the latest TBL files
cp --no-preserve=mode %ECF_HOME%/nwm/%NWM_DOMAIN%/namelists/%NWM_CYCLE%/* $WRF_HYDRO_ROOT

rm -rf $WRF_HYDRO_ROOT/DOMAIN
ln -sf %DOMAIN_DIR% $WRF_HYDRO_ROOT/DOMAIN
ln -sfn ../../%NWM_BASE_CYCLE%/forcings-output/$(date -ud "%CYCLE_DATE% %CYCLE_TIME%" +%%Y%%m%%d%%H) $WRF_HYDRO_ROOT/forcing
ln -sf %MODEL_EXECUTABLE% $WRF_HYDRO_ROOT/wrf_hydro.exe

# TODO link realtime timeslice directories for operational mode
mkdir -p $WRF_HYDRO_ROOT/nudgingTimeSliceObs

# clean out old nudging symlinks if there are any

if [[ `ls -1 $WRF_HYDRO_ROOT/nudgingTimeSliceObs 2>/dev/null` ]]; then
  rm -f $WRF_HYDRO_ROOT/nudgingTimeSliceObs/*
fi

rm -f $WRF_HYDRO_ROOT/rfc_timeseries
rm -f $WRF_HYDRO_ROOT/usgs_timeslices
rm -f $WRF_HYDRO_ROOT/usace_timeslices

if [[ "%USE_DA%" == "true" && "%TIMESLICE_ARCHIVE_DIR%" != "" ]]; then
    # temporary for gauge ingest
    archive_dir=%TIMESLICE_ARCHIVE_DIR%

    if [[ -d $archive_dir/merged_usgs_and_ca_timeslices ]]; then
      ln -sf $archive_dir/merged_usgs_and_ca_timeslices $WRF_HYDRO_ROOT/usgs_timeslices
      ln -sf $WRF_HYDRO_ROOT/usgs_timeslices/* $WRF_HYDRO_ROOT/nudgingTimeSliceObs/.
    elif [[ -d $archive_dir/usgs_timeslices ]]; then
      ln -sf $archive_dir/usgs_timeslices $WRF_HYDRO_ROOT/.
      ln -sf $WRF_HYDRO_ROOT/usgs_timeslices/* $WRF_HYDRO_ROOT/nudgingTimeSliceObs/.
    fi
    if [[ -d $archive_dir/usace_timeslices ]]; then
      ln -sf $archive_dir/usace_timeslices $WRF_HYDRO_ROOT/.
      ln -sf $WRF_HYDRO_ROOT/usace_timeslices/* $WRF_HYDRO_ROOT/nudgingTimeSliceObs/.
    fi
fi

hydro_namelist=$WRF_HYDRO_ROOT/hydro.namelist
hrldas_namelist=$WRF_HYDRO_ROOT/namelist.hrldas

start_date=$cycle_date
start_year=${start_date:0:4}
start_month=${start_date:4:2}
start_day=${start_date:6:2}

start_time=$cycle_time
start_hour=${start_time:0:2}
start_minute=${start_time:2:2}

sed -i "s|^START_YEAR .*|START_YEAR = ${start_year}|;" ${hrldas_namelist}
sed -i "s|^START_MONTH .*|START_MONTH = ${start_month}|;" ${hrldas_namelist}
sed -i "s|^START_DAY .*|START_DAY = ${start_day}|;" ${hrldas_namelist}
sed -i "s|^START_HOUR .*|START_HOUR = ${start_hour}|;" ${hrldas_namelist}
sed -i "s|^START_MIN .*|START_MIN = ${start_minute}|;" ${hrldas_namelist}
sed -i "s|^KHOUR .*|KHOUR = ${length_hrs}|;" ${hrldas_namelist}

hrldas_restart=RESTART.${start_year}${start_month}${start_day}${start_hour}_DOMAIN1
hydro_restart=HYDRO_RST.${start_year}-${start_month}-${start_day}_${start_hour}\:00_DOMAIN1

if [[ "%HRLDAS_RESTART%" != "" && "%HYDRO_RESTART%" != "" ]]; then
    if [[ "$WRF_HYDRO_ROOT/$hrldas_restart" != "%HRLDAS_RESTART%" ]]; then
      cp --no-preserve=mode %HRLDAS_RESTART% $WRF_HYDRO_ROOT/$hrldas_restart
    fi
    if [[ "$WRF_HYDRO_ROOT/$hydro_restart" != "%HYDRO_RESTART%" ]]; then
      cp --no-preserve=mode %HYDRO_RESTART% $WRF_HYDRO_ROOT/$hydro_restart
    fi
    sed -i "s|^RESTART_FILE .*|RESTART_FILE = '${hydro_restart}'|;" ${hydro_namelist}
    sed -i "s|^RESTART_FILENAME_REQUESTED .*|RESTART_FILENAME_REQUESTED = '${hrldas_restart}'|;" ${hrldas_namelist}
    echo sed -i "s|^RESTART_FILENAME_REQUESTED .*|RESTART_FILENAME_REQUESTED = '${hrldas_restart}'|;" ${hrldas_namelist}
elif [[ "%NWM_RESTART_CYCLE%" != "" ]]; then
    cp --no-preserve=mode %ECF_HOME%/jobdir/%NWM_DOMAIN%/%NWM_RESTART_CYCLE%/nwm/$hrldas_restart $WRF_HYDRO_ROOT
    cp --no-preserve=mode %ECF_HOME%/jobdir/%NWM_DOMAIN%/%NWM_RESTART_CYCLE%/nwm/$hydro_restart $WRF_HYDRO_ROOT
    sed -i "s|^RESTART_FILE .*|RESTART_FILE = '${hydro_restart}'|;" ${hydro_namelist}
    sed -i "s|^RESTART_FILENAME_REQUESTED .*|RESTART_FILENAME_REQUESTED = '${hrldas_restart}'|;" ${hrldas_namelist}
else
    sed -i "s|^RESTART_FILE .*|!RESTART_FILE = '${hydro_restart}'|;" ${hydro_namelist}
    sed -i "s|^RESTART_FILENAME_REQUESTED .*|!RESTART_FILENAME_REQUESTED = '${hrldas_restart}'|;" ${hrldas_namelist}
fi

#sed -i "s|^RESTART_FILE .*|\!RESTART_FILE = ${hydro_restart}|;" ${hydro_namelist}
#sed -i "s|^RESTART_FILENAME_REQUESTED .*|\!RESTART_FILENAME_REQUESTED = ${hrldas_restart}|;" ${hrldas_namelist}

## change output type to 6 until short-range is updated to include q_lateral
sed -i "s|^io_config_outputs = .*|io_config_outputs = 5|;" ${hydro_namelist}

## if we're running as AnA, don't output at t=0
if [[ -n $ana_flag ]]; then
    echo "Suppressing t0 output for AnA"
    sed -i "s|^t0OutputFlag = .*|t0OutputFlag = 0|;" ${hydro_namelist}
fi

# call the model!

cd $WRF_HYDRO_ROOT
qsub -V -A %PROJ% -q %QUEUE% -o %ECF_JOBOUT% -W block=true -l select=%NUM_COMPUTE_NODES%:ncpus=%NUM_CPUS%:mem=%MEMORY_GB%g:mpiprocs=%NUM_CPUS% -l walltime=%WALLTIME% %ECF_HOME%/nwm/run_wrf_hydro.sh &

%include <wait_for_process.h>

%include <tail.h>

%manual
This task sets up the 'Run' directory for the WRF-Hydro model run, and submits the model job to PBS

Forcings
--------
Forcings are linked from NWM_BASE_CYCLE/forcings-output/YYYYMMDDHH

Restarts
--------
If $HRLDAS_RESTART and $HYDRO_RESTART are populated, they are used as restart files.

If $NWM_RESTART_CYCLE is populated, restarts for the current cycle time are copied from the
restart cycle's run directory.

Otherwise, the model is run in 'cold start' mode.

Data Assimilation
-----------------
If $USE_DA is true and $TIMESLICE_ARCHIVE_DIR is populated, gage observations are copied from:

  $TIMESLICE_ARCHIVE_DIR/rfc_timeseries
  $TIMESLICE_ARCHIVE_DIR/usgs_timeslices
  $TIMESLICE_ARCHIVE_DIR/usace_timeslices

Namelists and .TBL files
------------------------
Namelists are copied from:

  $ECF_HOME/nwm/$NWM_DOMAIN/namelists/$NWM_CYCLE

.TBL files are copied from:

  $MODEL_TABLES_DIR

%end