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forecast_postdet.sh
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forecast_postdet.sh
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#! /usr/bin/env bash
# Disable variable not used warnings
# shellcheck disable=SC2034
FV3_postdet() {
echo "SUB ${FUNCNAME[0]}: Entering for RUN = ${RUN}"
echo "warm_start = ${warm_start}"
echo "RERUN = ${RERUN}"
#============================================================================
# First copy initial conditions
# cold start case
if [[ "${warm_start}" == ".false." ]]; then
# Get list of FV3 cold start files
local file_list
file_list=$(FV3_coldstarts)
echo "Copying FV3 cold start files for 'RUN=${RUN}' at '${current_cycle}' from '${COMIN_ATMOS_INPUT}'"
local fv3_file
for fv3_file in ${file_list}; do
${NCP} "${COMIN_ATMOS_INPUT}/${fv3_file}" "${DATA}/INPUT/${fv3_file}" \
|| ( echo "FATAL ERROR: Unable to copy FV3 IC, ABORT!"; exit 1 )
done
# warm start case
elif [[ "${warm_start}" == ".true." ]]; then
# Determine restart date and directory containing restarts
local restart_date restart_dir
if [[ "${RERUN}" == "YES" ]]; then
restart_date="${RERUN_DATE}"
restart_dir="${DATArestart}/FV3_RESTART"
else # "${RERUN}" == "NO"
restart_date="${model_start_date_current_cycle}"
restart_dir="${COMIN_ATMOS_RESTART_PREV}"
fi
# Get list of FV3 restart files
local file_list
file_list=$(FV3_restarts)
echo "Copying FV3 restarts for 'RUN=${RUN}' at '${restart_date}' from '${restart_dir}'"
local fv3_file restart_file
for fv3_file in ${file_list}; do
restart_file="${restart_date:0:8}.${restart_date:8:2}0000.${fv3_file}"
${NCP} "${restart_dir}/${restart_file}" "${DATA}/INPUT/${fv3_file}" \
|| ( echo "FATAL ERROR: Unable to copy FV3 IC, ABORT!"; exit 1 )
done
if [[ "${RERUN}" != "YES" ]]; then
# Replace sfc_data with sfcanl_data restart files from current cycle (if found)
local nn
for (( nn = 1; nn <= ntiles; nn++ )); do
if [[ -f "${COMOUT_ATMOS_RESTART}/${restart_date:0:8}.${restart_date:8:2}0000.sfcanl_data.tile${nn}.nc" ]]; then
rm -f "${DATA}/INPUT/sfc_data.tile${nn}.nc"
${NCP} "${COMOUT_ATMOS_RESTART}/${restart_date:0:8}.${restart_date:8:2}0000.sfcanl_data.tile${nn}.nc" \
"${DATA}/INPUT/sfc_data.tile${nn}.nc"
else
echo "'sfcanl_data.tile1.nc' not found in '${COMOUT_ATMOS_RESTART}', using 'sfc_data.tile1.nc'"
break
fi
done
# Replace fv_tracer with aeroanl_fv_tracer restart files from current cycle (if found)
local nn
local use_anl_aero="YES"
for (( nn = 1; nn <= ntiles; nn++ )); do
test_tracer_file="${COMOUT_ATMOS_RESTART}/${restart_date:0:8}.${restart_date:8:2}0000.aeroanl_fv_tracer.res.tile${nn}.nc"
if [[ ! -f "${test_tracer_file}" ]]; then
use_anl_aero="NO"
echo "WARNING: File ${test_tracer_file} does not exist, will not replace any files from the aerosol analysis"
break
fi
done
if [[ ${use_anl_aero} == "YES" ]]; then
for (( nn = 1; nn <= ntiles; nn++ )); do
rm -f "${DATA}/INPUT/fv_tracer.res.tile${nn}.nc"
${NCP} "${COMOUT_ATMOS_RESTART}/${restart_date:0:8}.${restart_date:8:2}0000.aeroanl_fv_tracer.res.tile${nn}.nc" \
"${DATA}/INPUT/fv_tracer.res.tile${nn}.nc"
done
fi # if [[ ${use_anl_aero} == "YES" ]]; then
fi # if [[ "${RERUN}" != "YES" ]]; then
fi # if [[ "${warm_start}" == ".true." ]]; then
#============================================================================
# Determine increment files when doing cold start
if [[ "${warm_start}" == ".false." ]]; then
if [[ "${REPLAY_ICS:-NO}" == "YES" ]]; then
IAU_FHROT=${half_window} # Replay ICs start at the end of the assimilation window
if (( MEMBER == 0 )); then
inc_files=()
else
inc_files=("atminc.nc")
read_increment=".true."
res_latlon_dynamics="atminc.nc"
fi
local increment_file
for inc_file in "${inc_files[@]}"; do
increment_file="${COMIN_ATMOS_INPUT}/${RUN}.t${cyc}z.${inc_file}"
if [[ -f "${increment_file}" ]]; then
${NCP} "${increment_file}" "${DATA}/INPUT/${inc_file}"
else
echo "FATAL ERROR: missing increment file '${increment_file}', ABORT!"
exit 1
fi
done
fi
# Determine IAU and increment files when doing warm start
elif [[ "${warm_start}" == ".true." ]]; then
#--------------------------------------------------------------------------
if [[ "${RERUN}" == "YES" ]]; then
local restart_fhr
restart_fhr=$(nhour "${RERUN_DATE}" "${current_cycle}")
IAU_FHROT=$((IAU_OFFSET + restart_fhr))
if [[ "${DOIAU}" == "YES" ]]; then
IAUFHRS=-1
IAU_DELTHRS=0
IAU_INC_FILES="''"
fi
#--------------------------------------------------------------------------
else # "${RERUN}" == "NO"
# Need a coupler.res that is consistent with the model start time
if [[ "${DOIAU:-NO}" == "YES" ]]; then
local model_start_time="${previous_cycle}"
else
local model_start_time="${current_cycle}"
fi
local model_current_time="${model_start_date_current_cycle}"
rm -f "${DATA}/INPUT/coupler.res"
cat >> "${DATA}/INPUT/coupler.res" << EOF
3 (Calendar: no_calendar=0, thirty_day_months=1, julian=2, gregorian=3, noleap=4)
${model_start_time:0:4} ${model_start_time:4:2} ${model_start_time:6:2} ${model_start_time:8:2} 0 0 Model start time: year, month, day, hour, minute, second
${model_current_time:0:4} ${model_current_time:4:2} ${model_current_time:6:2} ${model_current_time:8:2} 0 0 Current model time: year, month, day, hour, minute, second
EOF
# Create a array of increment files
local inc_files inc_file iaufhrs iaufhr
if [[ "${DOIAU}" == "YES" ]]; then
# create an array of inc_files for each IAU hour
IFS=',' read -ra iaufhrs <<< "${IAUFHRS}"
inc_files=()
delimiter=""
IAU_INC_FILES=""
for iaufhr in "${iaufhrs[@]}"; do
if (( iaufhr == 6 )); then
inc_file="atminc.nc"
else
inc_file="atmi$(printf %03i "${iaufhr}").nc"
fi
inc_files+=("${inc_file}")
IAU_INC_FILES="${IAU_INC_FILES}${delimiter}'${inc_file}'"
delimiter=","
done
else # "${DOIAU}" == "NO"
inc_files=("atminc.nc")
read_increment=".true."
res_latlon_dynamics="atminc.nc"
if [[ "${REPLAY_ICS:-NO}" == "YES" ]]; then
IAU_FHROT=${half_window} # Replay ICs start at the end of the assimilation window
# Control member has no perturbation
if (( MEMBER == 0 )); then
inc_files=()
read_increment=".false."
res_latlon_dynamics='""'
fi
fi
fi
local increment_file
for inc_file in "${inc_files[@]}"; do
increment_file="${COMIN_ATMOS_ANALYSIS}/${RUN}.t${cyc}z.${PREFIX_ATMINC}${inc_file}"
if [[ -f "${increment_file}" ]]; then
${NCP} "${increment_file}" "${DATA}/INPUT/${inc_file}"
else
echo "FATAL ERROR: missing increment file '${increment_file}', ABORT!"
exit 1
fi
done
fi # if [[ "${RERUN}" == "YES" ]]; then
#--------------------------------------------------------------------------
fi # if [[ "${warm_start}" == ".true." ]]; then
#============================================================================
#============================================================================
# If doing IAU, change forecast hours
if [[ "${DOIAU:-NO}" == "YES" ]]; then
FHMAX=$((FHMAX + 6))
if (( FHMAX_HF > 0 )); then
FHMAX_HF=$((FHMAX_HF + 6))
fi
fi
#============================================================================
#============================================================================
# If warm starting from restart files, set the following flags
if [[ "${warm_start}" == ".true." ]]; then
# start from restart file
nggps_ic=".false."
ncep_ic=".false."
external_ic=".false."
mountain=".true."
# restarts contain non-hydrostatic state
[[ "${TYPE}" == "nh" ]] && make_nh=".false."
# do not pre-condition the solution
na_init=0
fi # warm_start == .true.
#============================================================================
#============================================================================
if [[ "${QUILTING}" = ".true." ]] && [[ "${OUTPUT_GRID}" = "gaussian_grid" ]]; then
local FH2 FH3
for fhr in ${FV3_OUTPUT_FH}; do
FH3=$(printf %03i "${fhr}")
FH2=$(printf %02i "${fhr}")
# When replaying, the time format outputted by model in filename is HH-MM-SS
# because first fhr is a decimal number
if [[ ${REPLAY_ICS:-NO} == "YES" ]] && (( fhr >= OFFSET_START_HOUR )); then
local hhmmss_substring=${FV3_OUTPUT_FH_hhmmss/" ${FH3}-"*/} # Extract substring that contains all lead times up to the one space before target lead HHH-MM-SS
local hhmmss_substring_len=$(( ${#hhmmss_substring} + 1 )) # Get the size of the substring and add 1 to account for space
local f_hhmmss=${FV3_OUTPUT_FH_hhmmss:${hhmmss_substring_len}:9} # extract HHH-MM-SS for target lead time
${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.atmf${FH3}.nc" "atmf${f_hhmmss}.nc"
${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.sfcf${FH3}.nc" "sfcf${f_hhmmss}.nc"
${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.atm.logf${FH3}.txt" "log.atm.f${f_hhmmss}"
${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.cubed_sphere_grid_atmf${FH3}.nc" "cubed_sphere_grid_atmf${f_hhmmss}.nc"
${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.cubed_sphere_grid_sfcf${FH3}.nc" "cubed_sphere_grid_sfcf${f_hhmmss}.nc"
else
${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.atmf${FH3}.nc" "atmf${FH3}.nc"
${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.sfcf${FH3}.nc" "sfcf${FH3}.nc"
${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.atm.logf${FH3}.txt" "log.atm.f${FH3}"
${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.cubed_sphere_grid_atmf${FH3}.nc" "cubed_sphere_grid_atmf${FH3}.nc"
${NLN} "${COMOUT_ATMOS_HISTORY}/${RUN}.t${cyc}z.cubed_sphere_grid_sfcf${FH3}.nc" "cubed_sphere_grid_sfcf${FH3}.nc"
fi
if [[ "${WRITE_DOPOST}" == ".true." ]]; then
${NLN} "${COMOUT_ATMOS_MASTER}/${RUN}.t${cyc}z.master.grb2f${FH3}" "GFSPRS.GrbF${FH2}"
${NLN} "${COMOUT_ATMOS_MASTER}/${RUN}.t${cyc}z.sfluxgrbf${FH3}.grib2" "GFSFLX.GrbF${FH2}"
if [[ "${DO_NEST:-NO}" == "YES" ]] ; then
${NLN} "${COMOUT_ATMOS_MASTER}/${RUN}.t${cyc}z.nest.grb2f${FH3}" "GFSPRS.GrbF${FH2}.nest02"
${NLN} "${COMOUT_ATMOS_MASTER}/${RUN}.t${cyc}z.nest.sfluxgrbf${FH3}.grib2" "GFSFLX.GrbF${FH2}.nest02"
fi
fi
done
fi
#============================================================================
}
FV3_nml() {
# namelist output for a certain component
echo "SUB ${FUNCNAME[0]}: Creating name lists and model configure file for FV3"
source "${USHgfs}/parsing_namelists_FV3.sh"
source "${USHgfs}/parsing_model_configure_FV3.sh"
# Call the appropriate namelist functions
if [[ "${DO_NEST:-NO}" == "YES" ]] ; then
source "${USHgfs}/parsing_namelists_FV3_nest.sh"
FV3_namelists_nest global
FV3_namelists_nest nest
else
FV3_namelists
fi
FV3_model_configure
echo "SUB ${FUNCNAME[0]}: FV3 name lists and model configure file created"
}
FV3_out() {
echo "SUB ${FUNCNAME[0]}: copying output data for FV3"
# Copy configuration files
${NCP} "${DATA}/input.nml" "${COMOUT_CONF}/ufs.input.nml"
${NCP} "${DATA}/model_configure" "${COMOUT_CONF}/ufs.model_configure"
${NCP} "${DATA}/ufs.configure" "${COMOUT_CONF}/ufs.ufs.configure"
${NCP} "${DATA}/diag_table" "${COMOUT_CONF}/ufs.diag_table"
# Determine the dates for restart files to be copied to COM
local restart_date restart_dates
restart_dates=()
# Copy restarts in the assimilation window for RUN=gdas|enkfgdas|enkfgfs
if [[ "${RUN}" =~ "gdas" || "${RUN}" == "enkfgfs" ]]; then
restart_date="${model_start_date_next_cycle}"
while (( restart_date <= forecast_end_cycle )); do
restart_dates+=("${restart_date:0:8}.${restart_date:8:2}0000")
restart_date=$(date --utc -d "${restart_date:0:8} ${restart_date:8:2} + ${restart_interval} hours" +%Y%m%d%H)
done
elif [[ "${RUN}" == "gfs" || "${RUN}" == "gefs" ]]; then # Copy restarts at the end of the forecast segment for RUN=gfs|gefs
if [[ "${COPY_FINAL_RESTARTS}" == "YES" ]]; then
restart_dates+=("${forecast_end_cycle:0:8}.${forecast_end_cycle:8:2}0000")
fi
fi
### Check that there are restart files to copy
if [[ ${#restart_dates[@]} -gt 0 ]]; then
# Get list of FV3 restart files
local file_list fv3_file
file_list=$(FV3_restarts)
# Copy restarts for the dates collected above to COM
for restart_date in "${restart_dates[@]}"; do
echo "Copying FV3 restarts for 'RUN=${RUN}' at ${restart_date}"
for fv3_file in ${file_list}; do
${NCP} "${DATArestart}/FV3_RESTART/${restart_date}.${fv3_file}" \
"${COMOUT_ATMOS_RESTART}/${restart_date}.${fv3_file}"
done
done
echo "SUB ${FUNCNAME[0]}: Output data for FV3 copied"
fi
}
# Disable variable not used warnings
# shellcheck disable=SC2034
WW3_postdet() {
echo "SUB ${FUNCNAME[0]}: Linking input data for WW3"
local ww3_grid
# Copy initial condition files:
if [[ "${warm_start}" == ".true." ]]; then
local restart_date restart_dir
if [[ "${RERUN}" == "YES" ]]; then
restart_date="${RERUN_DATE}"
restart_dir="${DATArestart}/WW3_RESTART"
else
restart_date="${model_start_date_current_cycle}"
restart_dir="${COMIN_WAVE_RESTART_PREV}"
fi
echo "Copying WW3 restarts for 'RUN=${RUN}' at '${restart_date}' from '${restart_dir}'"
local ww3_restart_file
for ww3_grid in ${waveGRD} ; do
ww3_restart_file="${restart_dir}/${restart_date:0:8}.${restart_date:8:2}0000.restart.${ww3_grid}"
if [[ ! -f "${ww3_restart_file}" ]]; then
echo "WARNING: WW3 restart file '${ww3_restart_file}' not found for warm_start='${warm_start}', will start from rest!"
if [[ "${RERUN}" == "YES" ]]; then
# In the case of a RERUN, the WW3 restart file is required
echo "FATAL ERROR: WW3 restart file '${ww3_restart_file}' not found for RERUN='${RERUN}', ABORT!"
exit 1
fi
fi
if [[ "${waveMULTIGRID}" == ".true." ]]; then
${NCP} "${ww3_restart_file}" "${DATA}/restart.${ww3_grid}" \
|| ( echo "FATAL ERROR: Unable to copy WW3 IC, ABORT!"; exit 1 )
else
${NCP} "${ww3_restart_file}" "${DATA}/restart.ww3" \
|| ( echo "FATAL ERROR: Unable to copy WW3 IC, ABORT!"; exit 1 )
fi
done
else # cold start
echo "WW3 will start from rest!"
fi # [[ "${warm_start}" == ".true." ]]
# Link output files
local wavprfx="${RUN}wave${WAV_MEMBER:-}"
if [[ "${waveMULTIGRID}" == ".true." ]]; then
${NLN} "${COMOUT_WAVE_HISTORY}/${wavprfx}.log.mww3.${PDY}${cyc}" "log.mww3"
for ww3_grid in ${waveGRD}; do
${NLN} "${COMOUT_WAVE_HISTORY}/${wavprfx}.log.${ww3_grid}.${PDY}${cyc}" "log.${ww3_grid}"
done
else
${NLN} "${COMOUT_WAVE_HISTORY}/${wavprfx}.log.${waveGRD}.${PDY}${cyc}" "log.ww3"
fi
# Loop for gridded output (uses FHINC)
local fhr vdate FHINC ww3_grid
fhr=${FHMIN_WAV}
fhinc=${FHOUT_WAV}
while (( fhr <= FHMAX_WAV )); do
vdate=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} + ${fhr} hours" +%Y%m%d.%H0000)
if [[ "${waveMULTIGRID}" == ".true." ]]; then
for ww3_grid in ${waveGRD} ; do
${NLN} "${COMOUT_WAVE_HISTORY}/${wavprfx}.out_grd.${ww3_grid}.${vdate}" "${DATA}/${vdate}.out_grd.${ww3_grid}"
done
else
${NLN} "${COMOUT_WAVE_HISTORY}/${wavprfx}.out_grd.${waveGRD}.${vdate}" "${DATA}/${vdate}.out_grd.ww3"
fi
if (( FHMAX_HF_WAV > 0 && FHOUT_HF_WAV > 0 && fhr < FHMAX_HF_WAV )); then
fhinc=${FHOUT_HF_WAV}
fi
fhr=$((fhr + fhinc))
done
# Loop for point output (uses DTPNT)
fhr=${FHMIN_WAV}
fhinc=${FHINCP_WAV}
while (( fhr <= FHMAX_WAV )); do
vdate=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} + ${fhr} hours" +%Y%m%d.%H0000)
if [[ "${waveMULTIGRID}" == ".true." ]]; then
${NLN} "${COMOUT_WAVE_HISTORY}/${wavprfx}.out_pnt.${waveuoutpGRD}.${vdate}" "${DATA}/${vdate}.out_pnt.${waveuoutpGRD}"
else
${NLN} "${COMOUT_WAVE_HISTORY}/${wavprfx}.out_pnt.${waveuoutpGRD}.${vdate}" "${DATA}/${vdate}.out_pnt.ww3"
fi
fhr=$((fhr + fhinc))
done
}
WW3_nml() {
echo "SUB ${FUNCNAME[0]}: Copying input files for WW3"
source "${USHgfs}/parsing_namelists_WW3.sh"
WW3_namelists
}
WW3_out() {
echo "SUB ${FUNCNAME[0]}: Copying output data for WW3"
# TODO: Need to add logic to copy restarts from DATArestart/WW3_RESTART to COMOUT_WAVE_RESTART
}
CPL_out() {
echo "SUB ${FUNCNAME[0]}: Copying output data for general cpl fields"
if [[ "${esmf_profile:-.false.}" == ".true." ]]; then
${NCP} "${DATA}/ESMF_Profile.summary" "${COMOUT_ATMOS_HISTORY}/ESMF_Profile.summary"
fi
}
MOM6_postdet() {
echo "SUB ${FUNCNAME[0]}: MOM6 after run type determination"
local restart_dir restart_date
if [[ "${RERUN}" == "YES" ]]; then
restart_dir="${DATArestart}/MOM6_RESTART"
restart_date="${RERUN_DATE}"
else # "${RERUN}" == "NO"
restart_dir="${COMIN_OCEAN_RESTART_PREV}"
restart_date="${model_start_date_current_cycle}"
fi
# Copy MOM6 ICs
${NCP} "${restart_dir}/${restart_date:0:8}.${restart_date:8:2}0000.MOM.res.nc" "${DATA}/INPUT/MOM.res.nc" \
|| ( echo "FATAL ERROR: Unable to copy MOM6 IC, ABORT!"; exit 1 )
case ${OCNRES} in
"025")
local nn
for (( nn = 1; nn <= 4; nn++ )); do
if [[ -f "${restart_dir}/${restart_date:0:8}.${restart_date:8:2}0000.MOM.res_${nn}.nc" ]]; then
${NCP} "${restart_dir}/${restart_date:0:8}.${restart_date:8:2}0000.MOM.res_${nn}.nc" "${DATA}/INPUT/MOM.res_${nn}.nc" \
|| ( echo "FATAL ERROR: Unable to copy MOM6 IC, ABORT!"; exit 1 )
fi
done
;;
*) ;;
esac
# Copy increment (only when RERUN=NO)
if [[ "${RERUN}" == "NO" ]]; then
if [[ "${DO_JEDIOCNVAR:-NO}" == "YES" ]]; then
${NCP} "${COMIN_OCEAN_ANALYSIS}/${RUN}.t${cyc}z.ocninc.nc" "${DATA}/INPUT/mom6_increment.nc" \
|| ( echo "FATAL ERROR: Unable to copy MOM6 increment, ABORT!"; exit 1 )
fi
# GEFS perturbations
# TODO if [[ $RUN} == "gefs" ]] block maybe be needed
# to ensure it does not interfere with the GFS when ensemble is updated in the GFS
if (( MEMBER > 0 )) && [[ "${ODA_INCUPD:-False}" == "True" ]]; then
${NCP} "${COMIN_OCEAN_ANALYSIS}/mom6_increment.nc" "${DATA}/INPUT/mom6_increment.nc" \
|| ( echo "FATAL ERROR: Unable to copy ensemble MOM6 increment, ABORT!"; exit 1 )
fi
fi # if [[ "${RERUN}" == "NO" ]]; then
# Link output files
if [[ "${RUN}" =~ "gfs" || "${RUN}" == "gefs" ]]; then # Link output files for RUN=gfs|enkfgfs|gefs
# Looping over MOM6 output hours
local fhr fhr3 last_fhr interval midpoint vdate vdate_mid source_file dest_file
for fhr in ${MOM6_OUTPUT_FH}; do
fhr3=$(printf %03i "${fhr}")
if [[ -z ${last_fhr:-} ]]; then
last_fhr=${fhr}
continue
fi
(( interval = fhr - last_fhr ))
(( midpoint = last_fhr + interval/2 ))
vdate=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} + ${fhr} hours" +%Y%m%d%H)
#If OFFSET_START_HOUR is greater than 0, OFFSET_START_HOUR should be added to the midpoint for first lead time
if (( OFFSET_START_HOUR > 0 )) && (( fhr == FHOUT_OCN ));then
vdate_mid=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} + $(( midpoint + OFFSET_START_HOUR )) hours" +%Y%m%d%H)
else
vdate_mid=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} + ${midpoint} hours" +%Y%m%d%H)
fi
# Native model output uses window midpoint in the filename, but we are mapping that to the end of the period for COM
if (( OFFSET_START_HOUR > 0 )) && (( fhr == FHOUT_OCN ));then
source_file="ocn_lead1_${vdate_mid:0:4}_${vdate_mid:4:2}_${vdate_mid:6:2}_${vdate_mid:8:2}.nc"
else
source_file="ocn_${vdate_mid:0:4}_${vdate_mid:4:2}_${vdate_mid:6:2}_${vdate_mid:8:2}.nc"
fi
dest_file="${RUN}.ocean.t${cyc}z.${interval}hr_avg.f${fhr3}.nc"
${NLN} "${COMOUT_OCEAN_HISTORY}/${dest_file}" "${DATA}/MOM6_OUTPUT/${source_file}"
last_fhr=${fhr}
done
elif [[ "${RUN}" =~ "gdas" ]]; then # Link output files for RUN=gdas|enkfgdas
# Save (instantaneous) MOM6 backgrounds
local fhr3 vdatestr
for fhr in ${MOM6_OUTPUT_FH}; do
fhr3=$(printf %03i "${fhr}")
vdatestr=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} + ${fhr} hours" +%Y_%m_%d_%H)
${NLN} "${COMOUT_OCEAN_HISTORY}/${RUN}.ocean.t${cyc}z.inst.f${fhr3}.nc" "${DATA}/MOM6_OUTPUT/ocn_da_${vdatestr}.nc"
done
fi
echo "SUB ${FUNCNAME[0]}: MOM6 input data linked/copied"
}
MOM6_nml() {
echo "SUB ${FUNCNAME[0]}: Creating name list for MOM6"
source "${USHgfs}/parsing_namelists_MOM6.sh"
MOM6_namelists
}
MOM6_out() {
echo "SUB ${FUNCNAME[0]}: Copying output data for MOM6"
# Copy MOM_input from DATA to COMOUT_CONF after the forecast is run (and successfull)
${NCP} "${DATA}/INPUT/MOM_input" "${COMOUT_CONF}/ufs.MOM_input"
# Create a list of MOM6 restart files
# Coarser than 1/2 degree has a single MOM restart
local mom6_restart_files mom6_restart_file restart_file
mom6_restart_files=(MOM.res.nc)
# 1/4 degree resolution has 3 additional restarts
case "${OCNRES}" in
"025")
local nn
for (( nn = 1; nn <= 3; nn++ )); do
mom6_restart_files+=("MOM.res_${nn}.nc")
done
;;
*) ;;
esac
# Copy MOM6 restarts at the end of the forecast segment to COM for RUN=gfs|gefs
if [[ "${COPY_FINAL_RESTARTS}" == "YES" ]]; then
local restart_file
if [[ "${RUN}" == "gfs" || "${RUN}" == "gefs" ]]; then
echo "Copying MOM6 restarts for 'RUN=${RUN}' at ${forecast_end_cycle}"
for mom6_restart_file in "${mom6_restart_files[@]}"; do
restart_file="${forecast_end_cycle:0:8}.${forecast_end_cycle:8:2}0000.${mom6_restart_file}"
${NCP} "${DATArestart}/MOM6_RESTART/${restart_file}" \
"${COMOUT_OCEAN_RESTART}/${restart_file}"
done
fi
fi
# Copy restarts for the next cycle for RUN=gdas|enkfgdas|enkfgfs
if [[ "${RUN}" =~ "gdas" || "${RUN}" == "enkfgfs" ]]; then
local restart_date
restart_date="${model_start_date_next_cycle}"
echo "Copying MOM6 restarts for 'RUN=${RUN}' at ${restart_date}"
for mom6_restart_file in "${mom6_restart_files[@]}"; do
restart_file="${restart_date:0:8}.${restart_date:8:2}0000.${mom6_restart_file}"
${NCP} "${DATArestart}/MOM6_RESTART/${restart_file}" \
"${COMOUT_OCEAN_RESTART}/${restart_file}"
done
fi
}
CICE_postdet() {
echo "SUB ${FUNCNAME[0]}: CICE after run type determination"
local restart_date cice_restart_file
if [[ "${RERUN}" == "YES" ]]; then
restart_date="${RERUN_DATE}"
local seconds
seconds=$(to_seconds "${restart_date:8:2}0000") # convert HHMMSS to seconds
cice_restart_file="${DATArestart}/CICE_RESTART/cice_model.res.${restart_date:0:4}-${restart_date:4:2}-${restart_date:6:2}-${seconds}.nc"
else # "${RERUN}" == "NO"
restart_date="${model_start_date_current_cycle}"
cice_restart_file="${COMIN_ICE_RESTART_PREV}/${restart_date:0:8}.${restart_date:8:2}0000.cice_model.res.nc"
if [[ "${DO_JEDIOCNVAR:-NO}" == "YES" ]]; then
cice_restart_file="${COMIN_ICE_ANALYSIS}/${restart_date:0:8}.${restart_date:8:2}0000.cice_model_anl.res.nc"
fi
fi
# Copy CICE ICs
${NCP} "${cice_restart_file}" "${DATA}/cice_model.res.nc" \
|| ( echo "FATAL ERROR: Unable to copy CICE IC, ABORT!"; exit 1 )
# Link iceh_ic file to COM. This is the initial condition file from CICE (f000)
# TODO: Is this file needed in COM? Is this going to be used for generating any products?
local vdate seconds vdatestr fhr fhr3 interval last_fhr
seconds=$(to_seconds "${model_start_date_current_cycle:8:2}0000") # convert HHMMSS to seconds
vdatestr="${model_start_date_current_cycle:0:4}-${model_start_date_current_cycle:4:2}-${model_start_date_current_cycle:6:2}-${seconds}"
${NLN} "${COMOUT_ICE_HISTORY}/${RUN}.ice.t${cyc}z.ic.nc" "${DATA}/CICE_OUTPUT/iceh_ic.${vdatestr}.nc"
# Link CICE forecast output files from DATA/CICE_OUTPUT to COM
local source_file dest_file
for fhr in "${CICE_OUTPUT_FH[@]}"; do
if [[ -z ${last_fhr:-} ]]; then
last_fhr=${fhr}
continue
fi
fhr3=$(printf %03i "${fhr}")
(( interval = fhr - last_fhr ))
vdate=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} + ${fhr} hours" +%Y%m%d%H)
seconds=$(to_seconds "${vdate:8:2}0000") # convert HHMMSS to seconds
vdatestr="${vdate:0:4}-${vdate:4:2}-${vdate:6:2}-${seconds}"
if [[ "${RUN}" =~ "gfs" || "${RUN}" =~ "gefs" ]]; then
source_file="iceh_$(printf "%0.2d" "${FHOUT_ICE}")h.${vdatestr}.nc"
dest_file="${RUN}.ice.t${cyc}z.${interval}hr_avg.f${fhr3}.nc"
elif [[ "${RUN}" =~ "gdas" ]]; then
source_file="iceh_inst.${vdatestr}.nc"
dest_file="${RUN}.ice.t${cyc}z.inst.f${fhr3}.nc"
fi
${NLN} "${COMOUT_ICE_HISTORY}/${dest_file}" "${DATA}/CICE_OUTPUT/${source_file}"
last_fhr=${fhr}
done
}
CICE_nml() {
echo "SUB ${FUNCNAME[0]}: Creating name list for CICE"
source "${USHgfs}/parsing_namelists_CICE.sh"
CICE_namelists
}
CICE_out() {
echo "SUB ${FUNCNAME[0]}: Copying output data for CICE"
# Copy ice_in namelist from DATA to COMOUT_CONF after the forecast is run (and successfull)
${NCP} "${DATA}/ice_in" "${COMOUT_CONF}/ufs.ice_in"
# Copy CICE restarts at the end of the forecast segment to COM for RUN=gfs|gefs
if [[ "${COPY_FINAL_RESTARTS}" == "YES" ]]; then
local seconds source_file target_file
if [[ "${RUN}" == "gfs" || "${RUN}" == "gefs" ]]; then
echo "Copying CICE restarts for 'RUN=${RUN}' at ${forecast_end_cycle}"
seconds=$(to_seconds "${forecast_end_cycle:8:2}0000") # convert HHMMSS to seconds
source_file="cice_model.res.${forecast_end_cycle:0:4}-${forecast_end_cycle:4:2}-${forecast_end_cycle:6:2}-${seconds}.nc"
target_file="${forecast_end_cycle:0:8}.${forecast_end_cycle:8:2}0000.cice_model.res.nc"
${NCP} "${DATArestart}/CICE_RESTART/${source_file}" \
"${COMOUT_ICE_RESTART}/${target_file}"
fi
fi
# Copy restarts for next cycle for RUN=gdas|enkfgdas|enkfgfs
if [[ "${RUN}" =~ "gdas" || "${RUN}" == "enkfgfs" ]]; then
local restart_date
restart_date="${model_start_date_next_cycle}"
echo "Copying CICE restarts for 'RUN=${RUN}' at ${restart_date}"
seconds=$(to_seconds "${restart_date:8:2}0000") # convert HHMMSS to seconds
source_file="cice_model.res.${restart_date:0:4}-${restart_date:4:2}-${restart_date:6:2}-${seconds}.nc"
target_file="${restart_date:0:8}.${restart_date:8:2}0000.cice_model.res.nc"
${NCP} "${DATArestart}/CICE_RESTART/${source_file}" \
"${COMOUT_ICE_RESTART}/${target_file}"
fi
}
GOCART_rc() {
echo "SUB ${FUNCNAME[0]}: Linking input data and copying config files for GOCART"
# set input directory containing GOCART input data and configuration files
# this variable is platform-dependent and should be set via a YAML file
# link directory containing GOCART input dataset, if provided
if [[ -n "${AERO_INPUTS_DIR}" ]]; then
${NLN} "${AERO_INPUTS_DIR}" "${DATA}/ExtData"
status=$?
[[ ${status} -ne 0 ]] && exit "${status}"
fi
# copying GOCART configuration files
if [[ -n "${AERO_CONFIG_DIR}" ]]; then
${NCP} "${AERO_CONFIG_DIR}"/*.rc "${DATA}"
status=$?
[[ ${status} -ne 0 ]] && exit "${status}"
# attempt to generate ExtData configuration file if not provided
if [[ ! -f "${DATA}/AERO_ExtData.rc" ]]; then
{ \
echo "PrimaryExports%%" ; \
cat "${AERO_CONFIG_DIR}/ExtData.other" ; \
cat "${AERO_CONFIG_DIR}/ExtData.${AERO_EMIS_FIRE:-none}" ; \
echo "%%" ; \
} > "${DATA}/AERO_ExtData.rc"
status=$?
if (( status != 0 )); then exit "${status}"; fi
fi
fi
}
GOCART_postdet() {
echo "SUB ${FUNCNAME[0]}: Linking output data for GOCART"
local vdate
for fhr in ${GOCART_OUTPUT_FH}; do
vdate=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} + ${fhr} hours" +%Y%m%d%H)
# Temporarily delete existing files due to noclobber in GOCART
if [[ -e "${COMOUT_CHEM_HISTORY}/gocart.inst_aod.${vdate:0:8}_${vdate:8:2}00z.nc4" ]]; then
rm -f "${COMOUT_CHEM_HISTORY}/gocart.inst_aod.${vdate:0:8}_${vdate:8:2}00z.nc4"
fi
#TODO: Temporarily removing this as this will crash gocart, adding copy statement at the end
#${NLN} "${COMOUT_CHEM_HISTORY}/gocart.inst_aod.${vdate:0:8}_${vdate:8:2}00z.nc4" \
# "${DATA}/gocart.inst_aod.${vdate:0:8}_${vdate:8:2}00z.nc4"
done
}
GOCART_out() {
echo "SUB ${FUNCNAME[0]}: Copying output data for GOCART"
# Copy gocart.inst_aod after the forecast is run (and successfull)
# TODO: this should be linked but there are issues where gocart crashing if it is linked
local fhr
local vdate
for fhr in ${GOCART_OUTPUT_FH}; do
if (( fhr == 0 )); then continue; fi
vdate=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} + ${fhr} hours" +%Y%m%d%H)
${NCP} "${DATA}/gocart.inst_aod.${vdate:0:8}_${vdate:8:2}00z.nc4" \
"${COMOUT_CHEM_HISTORY}/gocart.inst_aod.${vdate:0:8}_${vdate:8:2}00z.nc4"
done
}
CMEPS_postdet() {
echo "SUB ${FUNCNAME[0]}: Linking output data for CMEPS mediator"
if [[ "${warm_start}" == ".true." ]]; then
# Determine the appropriate restart file
local restart_date cmeps_restart_file
if [[ "${RERUN}" == "YES" ]]; then
restart_date="${RERUN_DATE}"
local seconds
seconds=$(to_seconds "${restart_date:8:2}0000") # convert HHMMSS to seconds
cmeps_restart_file="${DATArestart}/CMEPS_RESTART/ufs.cpld.cpl.r.${restart_date:0:4}-${restart_date:4:2}-${restart_date:6:2}-${seconds}.nc"
else # "${RERUN}" == "NO"
restart_date="${model_start_date_current_cycle}"
cmeps_restart_file="${COMIN_MED_RESTART_PREV}/${restart_date:0:8}.${restart_date:8:2}0000.ufs.cpld.cpl.r.nc"
fi
# Copy CMEPS restarts
if [[ -f "${cmeps_restart_file}" ]]; then
${NCP} "${cmeps_restart_file}" "${DATA}/ufs.cpld.cpl.r.nc" \
|| ( echo "FATAL ERROR: Unable to copy CMEPS restarts, ABORT!"; exit 1 )
rm -f "${DATA}/rpointer.cpl"
touch "${DATA}/rpointer.cpl"
echo "ufs.cpld.cpl.r.nc" >> "${DATA}/rpointer.cpl"
else
# We have a choice to make here.
# Either we can FATAL ERROR out, or we can let the coupling fields initialize from zero
# cmeps_run_type is determined based on the availability of the CMEPS restart file
echo "WARNING: CMEPS restart file '${cmeps_restart_file}' not found for warm_start='${warm_start}', will initialize!"
if [[ "${RERUN}" == "YES" ]]; then
# In the case of a RERUN, the CMEPS restart file is required
echo "FATAL ERROR: CMEPS restart file '${cmeps_restart_file}' not found for RERUN='${RERUN}', ABORT!"
exit 1
fi
fi
fi # [[ "${warm_start}" == ".true." ]];
}
CMEPS_out() {
echo "SUB ${FUNCNAME[0]}: Copying output data for CMEPS mediator"
# Copy mediator restarts at the end of the forecast segment to COM for RUN=gfs|gefs
if [[ "${COPY_FINAL_RESTARTS}" == "YES" ]]; then
echo "Copying mediator restarts for 'RUN=${RUN}' at ${forecast_end_cycle}"
local seconds source_file target_file
seconds=$(to_seconds "${forecast_end_cycle:8:2}"0000)
source_file="ufs.cpld.cpl.r.${forecast_end_cycle:0:4}-${forecast_end_cycle:4:2}-${forecast_end_cycle:6:2}-${seconds}.nc"
target_file="${forecast_end_cycle:0:8}.${forecast_end_cycle:8:2}0000.ufs.cpld.cpl.r.nc"
if [[ -f "${DATArestart}/CMEPS_RESTART/${source_file}" ]]; then
${NCP} "${DATArestart}/CMEPS_RESTART/${source_file}" \
"${COMOUT_MED_RESTART}/${target_file}"
else
echo "Mediator restart '${DATArestart}/CMEPS_RESTART/${source_file}' not found."
fi
fi
# Copy restarts for the next cycle to COM for RUN=gdas|enkfgdas|enkfgfs
if [[ "${RUN}" =~ "gdas" || "${RUN}" == "enkfgfs" ]]; then
local restart_date
restart_date="${model_start_date_next_cycle}"
echo "Copying mediator restarts for 'RUN=${RUN}' at ${restart_date}"
seconds=$(to_seconds "${restart_date:8:2}"0000)
source_file="ufs.cpld.cpl.r.${restart_date:0:4}-${restart_date:4:2}-${restart_date:6:2}-${seconds}.nc"
target_file="${restart_date:0:8}.${restart_date:8:2}0000.ufs.cpld.cpl.r.nc"
if [[ -f "${DATArestart}/CMEPS_RESTART/${source_file}" ]]; then
${NCP} "${DATArestart}/CMEPS_RESTART/${source_file}" \
"${COMOUT_MED_RESTART}/${target_file}"
else
echo "Mediator restart '${DATArestart}/CMEPS_RESTART/${source_file}' not found."
fi
fi
}