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Fix a few bugs reported by devs #1893

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merged 4 commits into from
Sep 28, 2023
Merged

Fix a few bugs reported by devs #1893

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84a02a8
fix a date bugs in forecast_*det.sh, close namelist section and corre…
aerorahul Sep 27, 2023
568c587
add --utc to date command in j-jobs
aerorahul Sep 28, 2023
63bc50f
add --utc in forecast_predet.sh where middate was being calculated
aerorahul Sep 28, 2023
f0cf701
missed one instance of date in scripts
aerorahul Sep 28, 2023
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2 changes: 1 addition & 1 deletion jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT
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Expand Up @@ -10,7 +10,7 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalchkpt" -c "base ocnanal ocnana
##############################################
# Ignore possible spelling error (nothing is misspelled)
# shellcheck disable=SC2153
GDATE=$(date +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
export GDATE
export gPDY=${GDATE:0:8}
export gcyc=${GDATE:8:2}
Expand Down
2 changes: 1 addition & 1 deletion jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP
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Expand Up @@ -10,7 +10,7 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "ocnanalprep" -c "base ocnanal ocnanal
export CDUMP=${CDUMP:-${RUN:-"gfs"}}
# Ignore possible spelling error (nothing is misspelled)
# shellcheck disable=SC2153
GDATE=$(date +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
export GDATE
export gPDY=${GDATE:0:8}
export gcyc=${GDATE:8:2}
Expand Down
2 changes: 1 addition & 1 deletion jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY
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Expand Up @@ -10,7 +10,7 @@ export CDUMP=${CDUMP:-${RUN:-"gfs"}}
export GDUMP=${GDUMP:-"gdas"}
# Ignore possible spelling error (nothing is misspelled)
# shellcheck disable=SC2153
GDATE=$(date +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
export gPDY=${GDATE:0:8}
export gcyc=${GDATE:8:2}

Expand Down
2 changes: 1 addition & 1 deletion jobs/JGLOBAL_AERO_ANALYSIS_FINALIZE
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Expand Up @@ -9,7 +9,7 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "aeroanlfinal" -c "base aeroanl aeroan
# Set variables used in the script
##############################################
# shellcheck disable=SC2153
GDATE=$(date +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
gPDY=${GDATE:0:8}
gcyc=${GDATE:8:2}
GDUMP="gdas"
Expand Down
2 changes: 1 addition & 1 deletion jobs/JGLOBAL_AERO_ANALYSIS_INITIALIZE
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Expand Up @@ -8,7 +8,7 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "aeroanlinit" -c "base aeroanl aeroanl
# Set variables used in the script
##############################################
# shellcheck disable=SC2153
GDATE=$(date +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
gPDY=${GDATE:0:8}
gcyc=${GDATE:8:2}
GDUMP="gdas"
Expand Down
4 changes: 2 additions & 2 deletions jobs/JGLOBAL_ATMENS_ANALYSIS_INITIALIZE
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Expand Up @@ -8,7 +8,7 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "atmensanlinit" -c "base atmensanl atm
# Set variables used in the script
##############################################
# shellcheck disable=SC2153
GDATE=$(date +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
gPDY=${GDATE:0:8}
gcyc=${GDATE:8:2}
GDUMP="gdas"
Expand All @@ -20,7 +20,7 @@ GDUMP="gdas"
RUN=${GDUMP} YMD=${PDY} HH=${cyc} generate_com -rx COM_OBS

RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} generate_com -rx \
COM_ATMOS_ANALYSIS_PREV:COM_ATMOS_ANALYSIS_TMPL
COM_ATMOS_ANALYSIS_PREV:COM_ATMOS_ANALYSIS_TMPL

###############################################################
# Run relevant script
Expand Down
2 changes: 1 addition & 1 deletion jobs/JGLOBAL_ATM_ANALYSIS_FINALIZE
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Expand Up @@ -9,7 +9,7 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "atmanlfinal" -c "base atmanl atmanlfi
# Set variables used in the script
##############################################
# shellcheck disable=SC2153
GDATE=$(date +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
gPDY=${GDATE:0:8}
gcyc=${GDATE:8:2}
GDUMP="gdas"
Expand Down
2 changes: 1 addition & 1 deletion jobs/JGLOBAL_ATM_ANALYSIS_INITIALIZE
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Expand Up @@ -8,7 +8,7 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "atmanlinit" -c "base atmanl atmanlini
# Set variables used in the script
##############################################
# shellcheck disable=SC2153
GDATE=$(date +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
gPDY=${GDATE:0:8}
gcyc=${GDATE:8:2}
GDUMP="gdas"
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2 changes: 1 addition & 1 deletion jobs/JGLOBAL_FORECAST
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Expand Up @@ -38,7 +38,7 @@ esac

# Ignore possible spelling error (nothing is misspelled)
# shellcheck disable=SC2153
GDATE=$(date -d "${PDY} ${cyc} - ${assim_freq} hours" +%Y%m%d%H)
GDATE=$(date --utc -d "${PDY} ${cyc} - ${assim_freq} hours" +%Y%m%d%H)
declare -rx GDATE
# shellcheck disable=
declare -rx gPDY="${GDATE:0:8}"
Expand Down
2 changes: 1 addition & 1 deletion jobs/JGLOBAL_LAND_ANALYSIS
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Expand Up @@ -8,7 +8,7 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "landanl" -c "base landanl"
##############################################
# Ignore possible spelling error (nothing is misspelled)
# shellcheck disable=SC2153
GDATE=$(date +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
gPDY=${GDATE:0:8}
gcyc=${GDATE:8:2}
GDUMP="gdas"
Expand Down
2 changes: 1 addition & 1 deletion jobs/JGLOBAL_PREP_LAND_OBS
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Expand Up @@ -8,7 +8,7 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "preplandobs" -c "base preplandobs"
##############################################
# Ignore possible spelling error (nothing is misspelled)
# shellcheck disable=SC2153
GDATE=$(date +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
gPDY=${GDATE:0:8}
gcyc=${GDATE:8:2}
GDUMP="gdas"
Expand Down
2 changes: 1 addition & 1 deletion scripts/exglobal_stage_ic.sh
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Expand Up @@ -4,7 +4,7 @@ source "${HOMEgfs}/ush/preamble.sh"

# Locally scoped variables and functions
# shellcheck disable=SC2153
GDATE=$(date -d "${PDY} ${cyc} - ${assim_freq} hours" +%Y%m%d%H)
GDATE=$(date --utc -d "${PDY} ${cyc} - ${assim_freq} hours" +%Y%m%d%H)
gPDY="${GDATE:0:8}"
gcyc="${GDATE:8:2}"

Expand Down
36 changes: 18 additions & 18 deletions ush/forecast_postdet.sh
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Expand Up @@ -505,12 +505,12 @@ FV3_out() {
if [[ ${RUN} =~ "gdas" ]]; then
cd "${DATA}/RESTART"
mkdir -p "${COM_ATMOS_RESTART}"
local idate=$(date -d "${current_cycle:0:8} ${current_cycle:8:2} + ${restart_interval} hours" +%Y%m%d%H)
local idate=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} + ${restart_interval} hours" +%Y%m%d%H)
while [[ ${idate} -le ${forecast_end_cycle} ]]; do
for file in "${idate:0:8}.${idate:8:2}0000."*; do
${NCP} "${file}" "${COM_ATMOS_RESTART}/${file}"
done
local idate=$(date -d "${idate:0:8} ${idate:8:2} + ${restart_interval} hours" +%Y%m%d%H)
local idate=$(date --utc -d "${idate:0:8} ${idate:8:2} + ${restart_interval} hours" +%Y%m%d%H)
done
else
# No need to copy FV3 restart files when RUN=gfs or gefs
Expand Down Expand Up @@ -615,7 +615,7 @@ WW3_postdet() {
local fhr vdate FHINC wavGRD
fhr=${FHMIN_WAV}
while [[ ${fhr} -le ${FHMAX_WAV} ]]; do
vdate=$(date -d "${current_cycle:0:8} ${current_cycle:8:2} + ${fhr} hours" +%Y%m%d%H)
vdate=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} + ${fhr} hours" +%Y%m%d%H)
if [[ ${waveMULTIGRID} = ".true." ]]; then
for wavGRD in ${waveGRD} ; do
${NLN} "${COM_WAVE_HISTORY}/${wavprfx}.out_grd.${wavGRD}.${vdate:0:8}.${vdate:8:2}0000" "${DATA}/${vdate:0:8}.${vdate:8:2}0000.out_grd.${wavGRD}"
Expand All @@ -633,7 +633,7 @@ WW3_postdet() {
# Loop for point output (uses DTPNT)
fhr=${FHMIN_WAV}
while [[ ${fhr} -le ${FHMAX_WAV} ]]; do
vdate=$(date -d "${current_cycle:0:8} ${current_cycle:8:2} + ${fhr} hours" +%Y%m%d%H)
vdate=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} + ${fhr} hours" +%Y%m%d%H)
if [[ ${waveMULTIGRID} = ".true." ]]; then
${NLN} "${COM_WAVE_HISTORY}/${wavprfx}.out_pnt.${waveuoutpGRD}.${vdate:0:8}.${vdate:8:2}0000" "${DATA}/${vdate:0:8}.${vdate:8:2}0000.out_pnt.${waveuoutpGRD}"
else
Expand Down Expand Up @@ -763,8 +763,8 @@ MOM6_postdet() {
(( interval = fhr - last_fhr ))
(( midpoint = last_fhr + interval/2 ))

local vdate=$(date -d "${current_cycle:0:8} ${current_cycle:8:2} + ${fhr} hours" +%Y%m%d%H)
local vdate_mid=$(date -d "${current_cycle:0:8} ${current_cycle:8:2} + ${midpoint} hours" +%Y%m%d%H)
local vdate=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} + ${fhr} hours" +%Y%m%d%H)
local vdate_mid=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} + ${midpoint} hours" +%Y%m%d%H)


# Native model output uses window midpoint in the filename, but we are mapping that to the end of the period for COM
Expand All @@ -786,7 +786,7 @@ MOM6_postdet() {

# Save MOM6 backgrounds
for fhr in ${FV3_OUTPUT_FH}; do
local idatestr=$(date -d "${current_cycle:0:8} ${current_cycle:8:2} + ${fhr} hours" +%Y_%m_%d_%H)
local idatestr=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} + ${fhr} hours" +%Y_%m_%d_%H)
local fhr3=$(printf %03i "${fhr}")
${NLN} "${COM_OCEAN_HISTORY}/${RUN}.t${cyc}z.ocnf${fhr3}.nc" "${DATA}/ocn_da_${idatestr}.nc"
done
Expand All @@ -809,7 +809,7 @@ MOM6_postdet() {
esac

# Loop over restart_interval frequency and link restarts from DATA to COM
local idate=$(date -d "${current_cycle:0:8} ${current_cycle:8:2} + ${restart_interval} hours" +%Y%m%d%H)
local idate=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} + ${restart_interval} hours" +%Y%m%d%H)
while [[ ${idate} -lt ${forecast_end_cycle} ]]; do
local idatestr=$(date +%Y-%m-%d-%H -d "${idate:0:8} ${idate:8:2}")
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${NLN} "${COM_OCEAN_RESTART}/${idate:0:8}.${idate:8:2}0000.MOM.res.nc" "${DATA}/MOM6_RESTART/"
Expand All @@ -820,7 +820,7 @@ MOM6_postdet() {
done
;;
esac
local idate=$(date -d "${idate:0:8} ${idate:8:2} + ${restart_interval} hours" +%Y%m%d%H)
local idate=$(date --utc -d "${idate:0:8} ${idate:8:2} + ${restart_interval} hours" +%Y%m%d%H)
done

# TODO: mediator should have its own CMEPS_postdet() function
Expand All @@ -830,12 +830,12 @@ MOM6_postdet() {
# Instead of linking, copy the mediator files after the model finishes
#local COMOUTmed="${ROTDIR}/${RUN}.${PDY}/${cyc}/med"
#mkdir -p "${COMOUTmed}/RESTART"
#local idate=$(date -d "${current_cycle:0:8} ${current_cycle:8:2} + ${restart_interval} hours" +%Y%m%d%H)
#local idate=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} + ${restart_interval} hours" +%Y%m%d%H)
#while [[ ${idate} -le ${forecast_end_cycle} ]]; do
# local seconds=$(to_seconds ${idate:8:2}0000) # use function to_seconds from forecast_predet.sh to convert HHMMSS to seconds
# local idatestr="${idate:0:4}-${idate:4:2}-${idate:6:2}-${seconds}"
# ${NLN} "${COMOUTmed}/RESTART/${idate:0:8}.${idate:8:2}0000.ufs.cpld.cpl.r.nc" "${DATA}/RESTART/ufs.cpld.cpl.r.${idatestr}.nc"
# local idate=$(date -d "${idate:0:8} ${idate:8:2} + ${restart_interval} hours" +%Y%m%d%H)
# local idate=$(date --utc -d "${idate:0:8} ${idate:8:2} + ${restart_interval} hours" +%Y%m%d%H)
#done

echo "SUB ${FUNCNAME[0]}: MOM6 input data linked/copied"
Expand All @@ -860,7 +860,7 @@ MOM6_out() {
# Linking mediator restarts to COM causes the model to fail with a message.
# See MOM6_postdet() function for error message
mkdir -p "${COM_MED_RESTART}"
local idate=$(date -d "${current_cycle:0:8} ${current_cycle:8:2} + ${restart_interval} hours" +%Y%m%d%H)
local idate=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} + ${restart_interval} hours" +%Y%m%d%H)
while [[ ${idate} -le ${forecast_end_cycle} ]]; do
local seconds=$(to_seconds "${idate:8:2}"0000) # use function to_seconds from forecast_predet.sh to convert HHMMSS to seconds
local idatestr="${idate:0:4}-${idate:4:2}-${idate:6:2}-${seconds}"
Expand All @@ -870,7 +870,7 @@ MOM6_out() {
else
echo "Mediator restart ${mediator_file} not found."
fi
local idate=$(date -d "${idate:0:8} ${idate:8:2} + ${restart_interval} hours" +%Y%m%d%H)
local idate=$(date --utc -d "${idate:0:8} ${idate:8:2} + ${restart_interval} hours" +%Y%m%d%H)
done
}

Expand Down Expand Up @@ -932,7 +932,7 @@ CICE_postdet() {
# TODO: consult w/ NB on how to improve on this. Gather requirements and more information on what these files are and how they are used to properly catalog them
local vdate seconds vdatestr fhr last_fhr
for fhr in ${FV3_OUTPUT_FH}; do
vdate=$(date -d "${current_cycle:0:8} ${current_cycle:8:2} + ${fhr} hours" +%Y%m%d%H)
vdate=$(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}"

Expand All @@ -958,7 +958,7 @@ CICE_postdet() {
local vdate vdatestr seconds fhr fhr3
fhr="${FHOUT}"
while [[ "${fhr}" -le "${FHMAX}" ]]; do
vdate=$(date -d "${current_cycle:0:8} ${current_cycle:8:2} + ${fhr} hours" +%Y%m%d%H)
vdate=$(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}-${seconds}"
fhr3=$(printf %03i "${fhr}")
Expand All @@ -971,12 +971,12 @@ CICE_postdet() {
# Link CICE restarts from CICE_RESTART to COMOUTice/RESTART
# Loop over restart_interval and link restarts from DATA to COM
local vdate vdatestr seconds
vdate=$(date -d "${current_cycle:0:8} ${current_cycle:8:2} + ${restart_interval} hours" +%Y%m%d%H)
vdate=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} + ${restart_interval} hours" +%Y%m%d%H)
while [[ ${vdate} -le ${forecast_end_cycle} ]]; do
seconds=$(to_seconds "${vdate:8:2}0000") # convert HHMMSS to seconds
vdatestr="${vdate:0:4}-${vdate:4:2}-${vdate:6:2}-${seconds}"
${NLN} "${COM_ICE_RESTART}/${vdate:0:8}.${vdate:8:2}0000.cice_model.res.nc" "${DATA}/CICE_RESTART/cice_model.res.${vdatestr}.nc"
vdate=$(date -d "${vdate:0:8} ${vdate:8:2} + ${restart_interval} hours" +%Y%m%d%H)
vdate=$(date --utc -d "${vdate:0:8} ${vdate:8:2} + ${restart_interval} hours" +%Y%m%d%H)
done
}

Expand Down Expand Up @@ -1031,7 +1031,7 @@ GOCART_postdet() {
if [[ ! -d "${COM_CHEM_HISTORY}" ]]; then mkdir -p "${COM_CHEM_HISTORY}"; fi

for fhr in ${FV3_OUTPUT_FH}; do
local vdate=$(date -d "${current_cycle:0:8} ${current_cycle:8:2} + ${fhr} hours" +%Y%m%d%H)
local vdate=$(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 "${COM_CHEM_HISTORY}/gocart.inst_aod.${vdate:0:8}_${vdate:8:2}00z.nc4" ]]; then
Expand Down
10 changes: 5 additions & 5 deletions ush/forecast_predet.sh
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Expand Up @@ -29,7 +29,7 @@ middle_date(){
local date1s=$(date --utc -d "${date1:0:8} ${date1:8:2}:00:00" +%s)
local date2s=$(date --utc -d "${date2:0:8} ${date2:8:2}:00:00" +%s)
local dtsecsby2=$(( $((date2s - date1s)) / 2 ))
local mid_date=$(date -d "${date1:0:8} ${date1:8:2} + ${dtsecsby2} seconds" +%Y%m%d%H%M%S)
local mid_date=$(date --utc -d "${date1:0:8} ${date1:8:2} + ${dtsecsby2} seconds" +%Y%m%d%H%M%S)
echo "${mid_date:0:10}"
}

Expand Down Expand Up @@ -65,11 +65,11 @@ common_predet(){

# Define significant cycles
current_cycle=${CDATE}
previous_cycle=$(date -d "${current_cycle:0:8} ${current_cycle:8:2} - ${assim_freq} hours" +%Y%m%d%H)
previous_cycle=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} - ${assim_freq} hours" +%Y%m%d%H)
# ignore errors that variable isn't used
# shellcheck disable=SC2034
next_cycle=$(date -d "${current_cycle:0:8} ${current_cycle:8:2} + ${assim_freq} hours" +%Y%m%d%H)
forecast_end_cycle=$(date -d "${current_cycle:0:8} ${current_cycle:8:2} + ${FHMAX} hours" +%Y%m%d%H)
next_cycle=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} + ${assim_freq} hours" +%Y%m%d%H)
forecast_end_cycle=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} + ${FHMAX} hours" +%Y%m%d%H)

cd "${DATA}" || ( echo "FATAL ERROR: Unable to 'cd ${DATA}', ABORT!"; exit 8 )
}
Expand Down Expand Up @@ -217,7 +217,7 @@ FV3_predet(){
fi

if [[ "${DOIAU}" = "YES" ]]; then
sCDATE=$(date -d "${current_cycle:0:8} ${current_cycle:8:2} - 3 hours" +%Y%m%d%H)
sCDATE=$(date --utc -d "${current_cycle:0:8} ${current_cycle:8:2} - 3 hours" +%Y%m%d%H)
sPDY="${sCDATE:0:8}"
scyc="${sCDATE:8:2}"
tPDY=${previous_cycle:0:8}
Expand Down
2 changes: 1 addition & 1 deletion ush/nems_configure.sh
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Expand Up @@ -56,7 +56,7 @@ if [[ "${cplflx}" = ".true." ]]; then
local CPLMODE="${cplmode}"
local coupling_interval_fast_sec="${CPL_FAST}"
local RESTART_N="${restart_interval}"
local ATMTILESIZE="${CASE:2:}"
local ATMTILESIZE="${CASE:1}"
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fi

if [[ "${cplice}" = ".true." ]]; then
Expand Down
5 changes: 5 additions & 0 deletions ush/parsing_namelists_FV3.sh
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Expand Up @@ -422,6 +422,11 @@ if [[ ${DO_LAND_PERT:-"NO"} = "YES" ]]; then
EOF
fi

# Close &gfs_physics_nml section
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cat >> input.nml << EOF
/
EOF

if [[ ${knob_ugwp_version} -eq 0 ]]; then
cat >> input.nml << EOF
&cires_ugwp_nml
Expand Down