Make aerosol output frequency variable

parm/archive/gdas.yaml.j2

@@ -67,7 +67,7 @@ gdas:
         - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}oznstat"
         - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}radstat"
             {% endif %}
-            {% if AERO_ANL_RUN == "gdas" or AERO_ANL_RUN == "both" %}
+            {% if DO_AERO and (AERO_ANL_RUN == "gdas" or AERO_ANL_RUN == "both") %}
         - "{{ COMIN_CHEM_ANALYSIS | relpath(ROTDIR) }}/{{ head }}aerostat"
             {% endif %}
             {% if DO_PREP_OBS_AERO %}

parm/archive/gfs_arcdir.yaml.j2

@@ -50,7 +50,7 @@
                                     ARCDIR ~ "/snowstat." ~ RUN ~ "." ~ cycle_YMDH ~ ".tgz"]) %}
     {% endif %}
 
-    {% if AERO_ANL_RUN == RUN or AERO_ANL_RUN == "both" %}
+    {% if DO_AERO and (AERO_ANL_RUN == RUN or AERO_ANL_RUN == "both") %}
         {% do det_anl_files.append([COMIN_CHEM_ANALYSIS ~ "/" ~ head ~ "aerostat",
                                     ARCDIR ~ "/aerostat." ~ RUN ~ "." ~ cycle_YMDH ]) %}
     {% endif %}

parm/archive/gfsa.yaml.j2

@@ -38,7 +38,7 @@ gfsa:
         {% else %}
         - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}gsistat"
         {% endif %}
-        {% if AERO_ANL_RUN == "gfs" or AERO_ANL_RUN == "both" %}
+        {% if DO_AERO and (AERO_ANL_RUN == "gfs" or AERO_ANL_RUN == "both") %}
         - "{{ COMIN_CHEM_ANALYSIS | relpath(ROTDIR) }}/{{ head }}aerostat"
         {% endif %}
         {% if DO_PREP_OBS_AERO %}

parm/archive/master_gfs.yaml.j2

@@ -33,7 +33,7 @@ datasets:
     {% endfilter %}
 {% endif %}
 
-{% if AERO_FCST_RUN == "gfs" or AERO_FCST_RUN == "both" %}
+{% if DO_AERO and (AERO_FCST_RUN == "gfs" or AERO_FCST_RUN == "both") %}
     # Aerosol forecasts
     {% filter indent(width=4) %}
 {% include "chem.yaml.j2" %}

parm/config/gefs/config.base

@@ -136,9 +136,8 @@ export DO_OCN="NO"
 export DO_ICE="NO"
 export DO_AERO="NO"
 export DO_EXTRACTVARS="@DO_EXTRACTVARS@" # Option to process and extract a subset of products to save on disk
-export AERO_FCST_RUN="" # When to run aerosol forecast: gdas, gfs, or both
-export AERO_ANL_RUN="" # When to run aerosol analysis: gdas, gfs, or both
-export WAVE_RUN="" # When to include wave suite: gdas, gfs, or both
+export AERO_FCST_RUN="gefs" # When to run aerosol forecast: gdas, gfs, or both
+export WAVE_RUN="gefs" # When to include wave suite: gdas, gfs, or both
 export DOBNDPNT_WAVE="NO" # The GEFS buoys file does not currently have any boundary points
 export DOIBP_WAV="NO" # Option to create point outputs from input boundary points
 export FRAC_GRID=".true."
@@ -184,13 +183,10 @@ case "${APP}" in
     ;;
   ATMA)
     export DO_AERO="YES"
-    export AERO_ANL_RUN="both"
-    export AERO_FCST_RUN="gdas"
     ;;
   ATMW)
     export DO_COUPLED="YES"
     export DO_WAVE="YES"
-    export WAVE_RUN="both"
     ;;
   NG-GODAS)
     export DO_ATM="NO"
@@ -204,13 +200,10 @@ case "${APP}" in
 
     if [[ "${APP}" =~ A$ ]]; then
         export DO_AERO="YES"
-        export AERO_ANL_RUN="both"
-        export AERO_FCST_RUN="gdas"
     fi
 
     if [[ "${APP}" =~ ^S2SW ]]; then
         export DO_WAVE="YES"
-        export WAVE_RUN="both"
     fi
     ;;
   *)
@@ -225,6 +218,7 @@ export FHMAX=9
 export FHOUT=3           # Will be changed to 1 in config.base if (DOHYBVAR set to NO and l4densvar set to false)
 export FHOUT_OCN=3
 export FHOUT_ICE=3
+export FHOUT_AERO=3
 
 # GFS cycle info
 export INTERVAL_GFS=@INTERVAL_GFS@ # Frequency of GFS forecast

parm/config/gefs/yaml/defaults.yaml

@@ -31,4 +31,6 @@ stage_ic:
   USE_ATM_ENS_PERTURB_FILES: "NO"
 ocn:
   MOM6_INTERP_ICS: "NO"
-
+# config.aero has just a system-specific path to add.
+# This is handled by the setup_expt.py, but it has to be told to write to it.
+aero: {}

parm/config/gfs/config.base

@@ -176,9 +176,9 @@ export DO_OCN="NO"
 export DO_ICE="NO"
 export DO_AERO="NO"
 export DO_PREP_OBS_AERO="NO"
-export AERO_FCST_RUN="" # When to run aerosol forecast: gdas, gfs, or both
-export AERO_ANL_RUN="" # When to run aerosol analysis: gdas, gfs, or both
-export WAVE_RUN="" # When to include wave suite: gdas, gfs, or both
+export AERO_FCST_RUN="gdas" # When to run aerosol forecast: gdas, gfs, or both
+export AERO_ANL_RUN="both" # When to run aerosol analysis: gdas, gfs, or both
+export WAVE_RUN="both" # When to include wave suite: gdas, gfs, or both
 export DOBNDPNT_WAVE="NO"
 export DOIBP_WAV="NO" # Option to create point outputs from input boundary points
 export FRAC_GRID=".true."
@@ -229,13 +229,10 @@ case "${APP}" in
     ;;
   ATMA)
     export DO_AERO="YES"
-    export AERO_ANL_RUN="both"
-    export AERO_FCST_RUN="gdas"
     ;;
   ATMW)
     export DO_COUPLED="YES"
     export DO_WAVE="YES"
-    export WAVE_RUN="both"
     ;;
   NG-GODAS)
     export DO_ATM="NO"
@@ -249,13 +246,10 @@ case "${APP}" in
 
     if [[ "${APP}" =~ A$ ]]; then
         export DO_AERO="YES"
-        export AERO_ANL_RUN="both"
-        export AERO_FCST_RUN="gdas"
     fi
 
     if [[ "${APP}" =~ ^S2SW ]]; then
         export DO_WAVE="YES"
-        export WAVE_RUN="both"
     fi
     ;;
   *)
@@ -278,6 +272,7 @@ export FHMAX=9
 export FHOUT=3           # Will be changed to 1 in config.base if (DOHYBVAR set to NO and l4densvar set to false)
 export FHOUT_OCN=3
 export FHOUT_ICE=3
+export FHOUT_AERO=3
 
 # Cycle to run EnKF  (set to BOTH for both gfs and gdas)
 export EUPD_CYC="@EUPD_CYC@"

parm/ufs/gocart/AERO_HISTORY.rc

@@ -58,7 +58,7 @@ PC720x361-DC.LM: 72
   inst_du_ss.mode:        'instantaneous',
   inst_du_ss.grid_label:  PC720x361-DC ,
   inst_du_ss.splitField:  1,
-  inst_du_ss.frequency:   120000 ,
+  inst_du_ss.frequency:   @[inst_du_ss_freq] ,
   inst_du_ss.duration:    010000 ,
   inst_du_ss.ref_time:    000000 ,
   inst_du_ss.nbits:       10,
@@ -72,7 +72,7 @@ PC720x361-DC.LM: 72
   tavg_du_ss.mode:        'time-averaged',
   tavg_du_ss.grid_label:  PC720x361-DC ,
   tavg_du_ss.splitField:  1,
-  tavg_du_ss.frequency:   120000 ,
+  tavg_du_ss.frequency:   @[tavg_du_ss_freq] ,
   tavg_du_ss.duration:    010000 ,
   tavg_du_ss.ref_time:    000000 ,
   tavg_du_ss.nbits:       10,
@@ -85,7 +85,7 @@ PC720x361-DC.LM: 72
   inst_ca.template:       '%y4%m2%d2_%h2%n2z.nc4',
   inst_ca.mode:           'instantaneous',
   inst_ca.grid_label:     PC720x361-DC ,
-  inst_ca.frequency:      120000 ,
+  inst_ca.frequency:      @[inst_ca_freq] ,
   inst_ca.duration:       010000 ,
   inst_ca.ref_time:       000000 ,
   inst_ca.nbits:          10,
@@ -100,7 +100,7 @@ PC720x361-DC.LM: 72
   inst_ni.template:       '%y4%m2%d2_%h2%n2z.nc4',
   inst_ni.mode:           'instantaneous',
   inst_ni.grid_label:     PC720x361-DC ,
-  inst_ni.frequency:      120000 ,
+  inst_ni.frequency:      @[inst_ni_freq] ,
   inst_ni.duration:       010000 ,
   inst_ni.ref_time:       000000 ,
   inst_ni.nbits:          10,
@@ -116,7 +116,7 @@ PC720x361-DC.LM: 72
   inst_su.template:       '%y4%m2%d2_%h2%n2z.nc4',
   inst_su.mode:           'instantaneous',
   inst_su.grid_label:     PC720x361-DC ,
-  inst_su.frequency:      120000 ,
+  inst_su.frequency:      @[inst_su_freq] ,
   inst_su.duration:       010000 ,
   inst_su.ref_time:       000000 ,
   inst_su.nbits:          10,
@@ -135,7 +135,7 @@ PC720x361-DC.LM: 72
   inst_du_bin.mode:       'instantaneous'
   inst_du_bin.grid_label: PC720x361-DC ,
   inst_du_bin.splitField: 1,
-  inst_du_bin.frequency:  010000 ,
+  inst_du_bin.frequency:  @[inst_du_bin_freq] ,
   inst_du_bin.duration:   010000 ,
   inst_du_bin.ref_time:   000000 ,
   inst_du_bin.nbits:      10,
@@ -152,7 +152,7 @@ PC720x361-DC.LM: 72
   tavg_du_bin.mode:       'time-averaged'
   tavg_du_bin.grid_label: PC720x361-DC ,
   tavg_du_bin.splitField: 1,
-  tavg_du_bin.frequency:  030000 ,
+  tavg_du_bin.frequency:  @[tavg_du_bin_freq] ,
   tavg_du_bin.duration:   010000 ,
   tavg_du_bin.ref_time:   000000 ,
   tavg_du_bin.nbits:      10,
@@ -169,7 +169,7 @@ PC720x361-DC.LM: 72
   inst_ss_bin.mode:       'instantaneous'
   inst_ss_bin.grid_label: PC720x361-DC ,
   inst_ss_bin.splitField: 1,
-  inst_ss_bin.frequency:  060000 ,
+  inst_ss_bin.frequency:  @[inst_ss_bin_freq] ,
   inst_ss_bin.duration:   010000 ,
   inst_ss_bin.ref_time:   000000 ,
   inst_ss_bin.nbits:      10,
@@ -186,7 +186,7 @@ PC720x361-DC.LM: 72
   inst_ca_bin.mode:       'instantaneous'
   inst_ca_bin.grid_label:  PC720x361-DC ,
   inst_ca_bin.splitField:  1,
-  inst_ca_bin.frequency:   120000 ,
+  inst_ca_bin.frequency:   @[inst_ca_bin_freq] ,
   inst_ca_bin.duration:    010000 ,
   inst_ca_bin.ref_time:    000000 ,
   inst_ca_bin.nbits:      10,
@@ -208,7 +208,7 @@ PC720x361-DC.LM: 72
   inst_ni_bin.mode:       'instantaneous',
   inst_ni_bin.grid_label:  PC720x361-DC ,
   inst_ni_bin.splitField:  1,
-  inst_ni_bin.frequency:   120000 ,
+  inst_ni_bin.frequency:   @[inst_ni_bin_freq] ,
   inst_ni_bin.duration:    010000 ,
   inst_ni_bin.ref_time:    000000 ,
   inst_ni_bin.nbits:      10,
@@ -225,7 +225,7 @@ PC720x361-DC.LM: 72
   inst_su_bin.mode:       'instantaneous',
   inst_su_bin.grid_label:  PC720x361-DC ,
   inst_su_bin.splitField:  1,
-  inst_su_bin.frequency:   120000 ,
+  inst_su_bin.frequency:   @[inst_su_bin_freq] ,
   inst_su_bin.duration:    010000 ,
   inst_su_bin.ref_time:    000000 ,
   inst_su_bin.nbits:      10,
@@ -244,7 +244,7 @@ PC720x361-DC.LM: 72
   inst_2d.template:   '%y4%m2%d2_%h2%n2z.nc4',
   inst_2d.archive:    '%c/Y%y4',
   inst_2d.mode:       'instantaneous'
-  inst_2d.frequency:  030000,
+  inst_2d.frequency:  @[inst_2d_freq],
   inst_2d.duration:   030000,
   inst_2d.ref_time:   000000,
   inst_2d.grid_label: PC720x361-DC
@@ -343,7 +343,7 @@ PC720x361-DC.LM: 72
   inst_3d.template:   '%y4%m2%d2_%h2%n2z.nc4' ,
   inst_3d.archive:    '%c/Y%y4' ,
   inst_3d.mode:       'instantaneous'
-  inst_3d.frequency:  060000,
+  inst_3d.frequency:  @[inst_3d_freq],
   inst_3d.duration:   010000,
   inst_3d.ref_time:   000000,
   inst_3d.grid_label: PC720x361-DC
@@ -381,7 +381,7 @@ PC720x361-DC.LM: 72
   inst_aod.template:   '%y4%m2%d2_%h2%n2z.nc4' ,
   inst_aod.archive:    '%c/Y%y4' ,
   inst_aod.mode:       'instantaneous'
-  inst_aod.frequency:  060000,
+  inst_aod.frequency:  @[inst_aod_freq],
   inst_aod.duration:   010000,
   inst_aod.ref_time:   000000,
   inst_aod.grid_label: PC720x361-DC
@@ -398,7 +398,7 @@ PC720x361-DC.LM: 72
   tavg_2d_rad.template:   '%y4%m2%d2_%h2%n2z.nc4',
   tavg_2d_rad.archive:    '%c/Y%y4',
   tavg_2d_rad.mode:       'time-averaged',
-  tavg_2d_rad.frequency:  120000,
+  tavg_2d_rad.frequency:  @[tavg_2d_rad_freq],
   tavg_2d_rad.duration:   120000,
   tavg_2d_rad.ref_time:   000000,
   tavg_2d_rad.grid_label: PC720x361-DC
@@ -432,7 +432,7 @@ PC720x361-DC.LM: 72
   tavg_3d_rad.template:   '%y4%m2%d2_%h2%n2z.nc4',
   tavg_3d_rad.archive:    '%c/Y%y4',
   tavg_3d_rad.mode:       'time-averaged',
-  tavg_3d_rad.frequency:  120000,
+  tavg_3d_rad.frequency:  @[tavg_3d_rad_freq],
   tavg_3d_rad.duration:   120000,
   tavg_3d_rad.ref_time:   000000,
   tavg_3d_rad.grid_label: PC720x361-DC

ush/forecast_postdet.sh

@@ -689,30 +689,15 @@ GOCART_rc() {
     [[ ${status} -ne 0 ]] && exit "${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 "${status}"; fi
-    fi
-  fi
+  source "${USHgfs}/parsing_namelists_GOCART.sh"
+  GOCART_namelists
 }
 
 GOCART_postdet() {
   echo "SUB ${FUNCNAME[0]}: Linking output data for GOCART"
 
   local vdate
-  for fhr in ${GOCART_OUTPUT_FH}; do
+  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
@@ -726,15 +711,27 @@ GOCART_postdet() {
   done
 }
 
+GOCART_output_fh() {
+  # This has to be called during postdet after FHROT has been set
+  local aero_min
+  local gocart_output_fh
+  # GOCART produces no AOD files at the initial forecast time, so start the time
+  #   after the forecast start (accounting for FHROT)
+  aero_min=$(( ${IAU_FHROT:-0} > FHMIN ? IAU_FHROT + FHOUT_AERO : FHMIN + FHOUT_AERO ))
+  gocart_output_fh=$(seq -s ' ' "$(( aero_min ))" "${FHOUT_AERO}" "${GOCART_MAX}")
+
+  echo "${gocart_output_fh}"
+}
+
 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
+
+  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)
     ${NCP} "${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"

ush/forecast_predet.sh

@@ -724,6 +724,8 @@ GOCART_predet(){
 
   if [[ ! -d "${COMOUT_CHEM_HISTORY}" ]]; then mkdir -p "${COMOUT_CHEM_HISTORY}"; fi
 
-  GOCART_OUTPUT_FH=$(seq -s ' ' "${FHMIN}" "6" "${FHMAX}")
-  # TODO: AERO_HISTORY.rc has hardwired output frequency to 6 hours
+  # FHMAX gets modified when IAU is on, so keep origianl value for GOCART output
+  GOCART_MAX=${FHMAX}
+
+  # GOCART output times can't be computed here because they may depend on FHROT
 }