Fix a few bugs reported by devs (#1893)

This PR fixes a few bugs that were reported by developers:
- a namelist section is unclosed in `parsing_namelists_FV3.sh`
- resolution is not being properly cut from `CASE`
- date should be in UTC to properly go back and forth around DST dates. 
 
Resolves #1796

jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_CHKPT

@@ -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}

jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_PREP

@@ -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}

jobs/JGDAS_GLOBAL_OCEAN_ANALYSIS_VRFY

@@ -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}
 

jobs/JGLOBAL_AERO_ANALYSIS_FINALIZE

@@ -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"

jobs/JGLOBAL_AERO_ANALYSIS_INITIALIZE

@@ -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"

jobs/JGLOBAL_ATMENS_ANALYSIS_INITIALIZE

@@ -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=${GDATE:8:2}
 GDUMP="gdas"
@@ -20,7 +20,7 @@ GDUMP="gdas"
 RUN=${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

jobs/JGLOBAL_ATM_ANALYSIS_FINALIZE

@@ -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"

jobs/JGLOBAL_ATM_ANALYSIS_INITIALIZE

@@ -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"

jobs/JGLOBAL_FORECAST

@@ -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}"

jobs/JGLOBAL_LAND_ANALYSIS

@@ -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"

jobs/JGLOBAL_PREP_LAND_OBS

@@ -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"

scripts/exglobal_stage_ic.sh

@@ -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}"
 

ush/forecast_postdet.sh

@@ -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} + ${restart_interval} hours" +%Y%m%d%H)
     done
   else
     # No need to copy FV3 restart files when RUN=gfs or gefs
@@ -615,7 +615,7 @@ WW3_postdet() {
   local fhr vdate FHINC wavGRD
   fhr=${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}"
@@ -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
@@ -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
@@ -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
@@ -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}")
     ${NLN} "${COM_OCEAN_RESTART}/${idate:0:8}.${idate:8:2}0000.MOM.res.nc" "${DATA}/MOM6_RESTART/"
@@ -820,7 +820,7 @@ MOM6_postdet() {
         done
         ;;
     esac
-    local idate=$(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
@@ -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 ${FUNCNAME[0]}: MOM6 input data linked/copied"
@@ -860,7 +860,7 @@ MOM6_out() {
   # Linking mediator restarts to COM causes the model to fail with a message.
   # See MOM6_postdet() function for error message
   mkdir -p "${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}"
@@ -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
 }
 
@@ -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}"
 
@@ -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 "${fhr}")
@@ -971,12 +971,12 @@ CICE_postdet() {
   # Link CICE restarts from CICE_RESTART to COMOUTice/RESTART
   # Loop over restart_interval and link restarts from DATA to COM
   local vdate vdatestr seconds
-  vdate=$(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
 }
 
@@ -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

ush/forecast_predet.sh

@@ -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}"
 }
 
@@ -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 )
 }
@@ -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}

ush/nems_configure.sh

@@ -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}"
 fi
 
 if [[ "${cplice}" = ".true." ]]; then

ush/parsing_namelists_FV3.sh

@@ -422,6 +422,11 @@ if [[ ${DO_LAND_PERT:-"NO"} = "YES" ]]; then
 EOF
 fi
 
+# Close &gfs_physics_nml section
+cat >> input.nml << EOF
+/
+EOF
+
 if [[ ${knob_ugwp_version} -eq 0 ]]; then
   cat >> input.nml << EOF
 &cires_ugwp_nml