From 11f9a1d3e8ba1f80cd0e7e2a631814fcac1c6421 Mon Sep 17 00:00:00 2001
From: "Walter.Kolczynski" <Walter.Kolczynski@noaa.gov>
Date: Thu, 3 Oct 2024 23:43:13 -0500
Subject: [PATCH 01/13] Make aerosol output frequency variable

The `AERO_HISTORY.rc` file that controls the GOCART output is turned
into a template usint `@[ ]` syntax to allow for variable output
times. A new "parsing" script is created for GOCART that handles
parsing the `AERO_HISTORY.rc` file through `atparse`. Other manip-
ulation of these files is also moved to the new parsing script to be
consistent with other components.

A new variable, `FHOUT_AERO` is introduced to control the output
frequency of the GOCART output. This is initially set to 3 to match
other components (this is a change from the current value of 6).
Since some aerosol fields are also included as part of the atmos
output, it may be desirable to meld this back into `FHOUT` later.
However, the atmos output has two frequencies (`FHOUT_HF` and
`FHOUT`), a feature not supported by other components.

The RUN lists for aero fcst, aero analysis, and waves is simplified
to avoid confusion, since there is no need for them to only be set
if the components are on.

Resolves #2072
---
 parm/config/gefs/config.base    |  9 ++----
 parm/config/gfs/config.base     | 13 +++------
 parm/ufs/gocart/AERO_HISTORY.rc | 32 ++++++++++-----------
 ush/forecast_postdet.sh         | 19 ++----------
 ush/forecast_predet.sh          |  3 +-
 ush/parsing_namelists_GOCART.sh | 51 +++++++++++++++++++++++++++++++++
 6 files changed, 77 insertions(+), 50 deletions(-)
 create mode 100644 ush/parsing_namelists_GOCART.sh

diff --git a/parm/config/gefs/config.base b/parm/config/gefs/config.base
index 6cf8488f916..deff1b79e8f 100644
--- a/parm/config/gefs/config.base
+++ b/parm/config/gefs/config.base
@@ -135,9 +135,8 @@ 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."
@@ -203,13 +202,10 @@ 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"
         export cplwav2atm=".true."
     fi
     ;;
@@ -225,6 +221,7 @@ 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 gfs_cyc=@gfs_cyc@ # 0: no GFS cycle, 1: 00Z only, 2: 00Z and 12Z only, 4: all 4 cycles.
diff --git a/parm/config/gfs/config.base b/parm/config/gfs/config.base
index 7fa8245057d..f24b264207f 100644
--- a/parm/config/gfs/config.base
+++ b/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@"
diff --git a/parm/ufs/gocart/AERO_HISTORY.rc b/parm/ufs/gocart/AERO_HISTORY.rc
index 4c7df15b2a7..db1b934f5f3 100644
--- a/parm/ufs/gocart/AERO_HISTORY.rc
+++ b/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
diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
index 58755d41d91..75a318fe516 100755
--- a/ush/forecast_postdet.sh
+++ b/ush/forecast_postdet.sh
@@ -682,23 +682,8 @@ 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() {
diff --git a/ush/forecast_predet.sh b/ush/forecast_predet.sh
index 5aa9dc9ac7a..4e30608c941 100755
--- a/ush/forecast_predet.sh
+++ b/ush/forecast_predet.sh
@@ -713,6 +713,5 @@ GOCART_predet(){
 
   if [[ ! -d "${COMOUT_CHEM_HISTORY}" ]]; then mkdir -p "${COMOUT_CHEM_HISTORY}"; fi
 
-  GOCART_OUTPUT_FH=$(seq -s ' ' "${FHMIN}" "6" "${FHMAX}")
-  # TODO: AERO_HISTORY.rc has hardwired output frequency to 6 hours
+  GOCART_OUTPUT_FH=$(seq -s ' ' "${FHMIN}" "${FHOUT_AERO}" "${FHMAX}")
 }
diff --git a/ush/parsing_namelists_GOCART.sh b/ush/parsing_namelists_GOCART.sh
new file mode 100644
index 00000000000..ea3a7c6c60b
--- /dev/null
+++ b/ush/parsing_namelists_GOCART.sh
@@ -0,0 +1,51 @@
+#! /usr/bin/env bash
+
+# Disable variable not used warnings
+# shellcheck disable=SC2034
+GOCART_namelists() {
+  # copying GOCART configuration files
+  if [[  -n "${AERO_CONFIG_DIR}" ]]; then
+
+    local base_in
+    local fhout_aero_padded
+    fhout_aero_padded=$(printf "%02d" "${FHOUT_AERO}")
+    # Only instantaneous AOD is output right now
+    local inst_aod_freq="${fhout_aero_padded}0000"
+
+    # Other gocart fields not currently used
+    local inst_du_ss_freq="120000"
+    local tavg_du_ss_freq="120000"
+    local inst_ca_freq="120000"
+    local inst_ni_freq="120000"
+    local inst_su_freq="120000"
+    local inst_du_bin_freq="010000"
+    local tavg_du_bin_freq="030000"
+    local inst_ss_bin_freq="060000"
+    local inst_ca_bin_freq="120000"
+    local inst_ni_bin_freq="120000"
+    local inst_su_bin_freq="120000"
+    local inst_2d_freq="030000"
+    local inst_3d_freq="060000"
+    local tavg_2d_rad_freq="120000"
+    local tavg_3d_rad_freq="120000"
+
+    for template_in in "${AERO_CONFIG_DIR}/"*.rc; do
+      base_in="$(basename "${template_in}")"
+      atparse < "${template_in}" >> "${DATA}/${base_in}"
+      status=$?
+      [[ ${status} -ne 0 ]] && exit "${status}"
+    done
+
+    # 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
+}

From 9dcae263790ebcb6de2660bfb127d7cf7dc5a66c Mon Sep 17 00:00:00 2001
From: "Walter.Kolczynski" <Walter.Kolczynski@noaa.gov>
Date: Fri, 4 Oct 2024 00:02:55 -0500
Subject: [PATCH 02/13] Correct shellcheck error

---
 ush/parsing_namelists_GOCART.sh | 1 +
 1 file changed, 1 insertion(+)

diff --git a/ush/parsing_namelists_GOCART.sh b/ush/parsing_namelists_GOCART.sh
index ea3a7c6c60b..e39f0808ab5 100644
--- a/ush/parsing_namelists_GOCART.sh
+++ b/ush/parsing_namelists_GOCART.sh
@@ -44,6 +44,7 @@ GOCART_namelists() {
         cat "${AERO_CONFIG_DIR}/ExtData.${AERO_EMIS_FIRE:-none}" ; \
         echo "%%" ; \
       } > "${DATA}/AERO_ExtData.rc"
+      # shellcheck disable=SC2320
       status=$?
       if (( status != 0 )); then exit "${status}"; fi
     fi

From ee8b3dcafea9dbd4bcfa988bab29e86d152ddb9e Mon Sep 17 00:00:00 2001
From: "Walter.Kolczynski" <Walter.Kolczynski@noaa.gov>
Date: Wed, 9 Oct 2024 14:38:10 -0500
Subject: [PATCH 03/13] Fix issue with determination of gocart archival

The archive job was using `AERO_ANL_RUN` to determine whether to
archive certain files. With the move to a static declaration of that
instead of only turning it on when aerosols are on, an additional
check is needed.
---
 parm/archive/gdas.yaml.j2       | 2 +-
 parm/archive/master_gfs.yaml.j2 | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/parm/archive/gdas.yaml.j2 b/parm/archive/gdas.yaml.j2
index 030678f31f4..749d609fe35 100644
--- a/parm/archive/gdas.yaml.j2
+++ b/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 %}
diff --git a/parm/archive/master_gfs.yaml.j2 b/parm/archive/master_gfs.yaml.j2
index ab9a00c95e3..e9fa3b8049a 100644
--- a/parm/archive/master_gfs.yaml.j2
+++ b/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_ANL_RUN == "gfs" or AERO_ANL_RUN == "both") %}
     # Aerosol forecasts
     {% filter indent(width=4) %}
 {% include "chem.yaml.j2" %}

From 059ed644c1fb1f1666624ff96a82c8060b8e253d Mon Sep 17 00:00:00 2001
From: "Walter.Kolczynski" <Walter.Kolczynski@noaa.gov>
Date: Wed, 9 Oct 2024 23:46:00 -0500
Subject: [PATCH 04/13] More archive modifications

---
 parm/archive/gfs_arcdir.yaml.j2 | 2 +-
 parm/archive/gfsa.yaml.j2       | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/parm/archive/gfs_arcdir.yaml.j2 b/parm/archive/gfs_arcdir.yaml.j2
index 57dbc78885e..58e2cdc6990 100644
--- a/parm/archive/gfs_arcdir.yaml.j2
+++ b/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 %}
diff --git a/parm/archive/gfsa.yaml.j2 b/parm/archive/gfsa.yaml.j2
index 226a7178fa3..608447b0b33 100644
--- a/parm/archive/gfsa.yaml.j2
+++ b/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 %}

From 376faebea6c1fad6a12ff5c1b49945bffe043d46 Mon Sep 17 00:00:00 2001
From: "Walter.Kolczynski" <Walter.Kolczynski@noaa.gov>
Date: Fri, 8 Nov 2024 03:57:27 -0600
Subject: [PATCH 05/13] Fix GOCART output times

GOCART output does not start until the first output time after FHMIN,
so the list of output times should reflect that to avoid trying to
copy files that don't exist.
---
 ush/forecast_postdet.sh | 1 -
 ush/forecast_predet.sh  | 2 +-
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
index 6effe187b18..50fd40d9fd2 100755
--- a/ush/forecast_postdet.sh
+++ b/ush/forecast_postdet.sh
@@ -719,7 +719,6 @@ GOCART_out() {
   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"
diff --git a/ush/forecast_predet.sh b/ush/forecast_predet.sh
index 8ad91c859cb..2e0af396664 100755
--- a/ush/forecast_predet.sh
+++ b/ush/forecast_predet.sh
@@ -713,5 +713,5 @@ GOCART_predet(){
 
   if [[ ! -d "${COMOUT_CHEM_HISTORY}" ]]; then mkdir -p "${COMOUT_CHEM_HISTORY}"; fi
 
-  GOCART_OUTPUT_FH=$(seq -s ' ' "${FHMIN}" "${FHOUT_AERO}" "${FHMAX}")
+  GOCART_OUTPUT_FH=$(seq -s ' ' "$(( FHMIN + FHOUT_AERO ))" "${FHOUT_AERO}" "${FHMAX}")
 }

From 376af38719977149509ab825dd6b319e3f1fa116 Mon Sep 17 00:00:00 2001
From: "Walter.Kolczynski" <Walter.Kolczynski@noaa.gov>
Date: Tue, 12 Nov 2024 10:07:35 -0600
Subject: [PATCH 06/13] Correct first output time of GOCART

GOCART needs to use the bigger of FHMIN and FHROT when determining
the first output time.
---
 ush/forecast_predet.sh | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/ush/forecast_predet.sh b/ush/forecast_predet.sh
index 2e0af396664..e0c5b36ecc7 100755
--- a/ush/forecast_predet.sh
+++ b/ush/forecast_predet.sh
@@ -713,5 +713,7 @@ GOCART_predet(){
 
   if [[ ! -d "${COMOUT_CHEM_HISTORY}" ]]; then mkdir -p "${COMOUT_CHEM_HISTORY}"; fi
 
-  GOCART_OUTPUT_FH=$(seq -s ' ' "$(( FHMIN + FHOUT_AERO ))" "${FHOUT_AERO}" "${FHMAX}")
+  local aero_min=$(( FHROT > FHMIN ? FHROT + FHOUT_AERO : FHMIN + FHOUT_AERO ))
+
+  GOCART_OUTPUT_FH=$(seq -s ' ' "$(( aero_min ))" "${FHOUT_AERO}" "${FHMAX}")
 }

From 2aca0553bdd34386aa928b4edffe65a8502b0f9f Mon Sep 17 00:00:00 2001
From: "Walter.Kolczynski" <Walter.Kolczynski@noaa.gov>
Date: Wed, 13 Nov 2024 02:14:40 -0600
Subject: [PATCH 07/13] Make further corrections to gocart forecast hours

---
 ush/forecast_predet.sh | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/ush/forecast_predet.sh b/ush/forecast_predet.sh
index e0c5b36ecc7..bb1df19c2e2 100755
--- a/ush/forecast_predet.sh
+++ b/ush/forecast_predet.sh
@@ -713,7 +713,6 @@ GOCART_predet(){
 
   if [[ ! -d "${COMOUT_CHEM_HISTORY}" ]]; then mkdir -p "${COMOUT_CHEM_HISTORY}"; fi
 
-  local aero_min=$(( FHROT > FHMIN ? FHROT + FHOUT_AERO : FHMIN + FHOUT_AERO ))
-
+  local aero_min=$(( ${FHROT:-0} > FHMIN ? FHROT + FHOUT_AERO : FHMIN + FHOUT_AERO ))
   GOCART_OUTPUT_FH=$(seq -s ' ' "$(( aero_min ))" "${FHOUT_AERO}" "${FHMAX}")
 }

From 50a15d300c0a607e92718cdc927bee4f3c82ac4a Mon Sep 17 00:00:00 2001
From: "Walter.Kolczynski" <Walter.Kolczynski@noaa.gov>
Date: Thu, 14 Nov 2024 02:07:35 -0600
Subject: [PATCH 08/13] Fix GOCART output times

Moves computation of GOCART output times to postdet, since FHROT is
not computed until then.
---
 ush/forecast_postdet.sh | 7 ++++++-
 ush/forecast_predet.sh  | 3 +--
 2 files changed, 7 insertions(+), 3 deletions(-)

diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
index 50fd40d9fd2..3fed72f1e8b 100755
--- a/ush/forecast_postdet.sh
+++ b/ush/forecast_postdet.sh
@@ -718,7 +718,12 @@ GOCART_out() {
   # TODO: this should be linked but there are issues where gocart crashing if it is linked
   local fhr
   local vdate
-  for fhr in ${GOCART_OUTPUT_FH}; do
+  local aero_min
+  local gocart_output_fh
+  aero_min=$(( ${IAU_FHROT:-0} > FHMIN ? IAU_FHROT + FHOUT_AERO : FHMIN + FHOUT_AERO ))
+  gocart_output_fh=$(seq -s ' ' "$(( aero_min ))" "${FHOUT_AERO}" "${FHMAX}")
+
+  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"
diff --git a/ush/forecast_predet.sh b/ush/forecast_predet.sh
index bb1df19c2e2..7ffbd699a90 100755
--- a/ush/forecast_predet.sh
+++ b/ush/forecast_predet.sh
@@ -713,6 +713,5 @@ GOCART_predet(){
 
   if [[ ! -d "${COMOUT_CHEM_HISTORY}" ]]; then mkdir -p "${COMOUT_CHEM_HISTORY}"; fi
 
-  local aero_min=$(( ${FHROT:-0} > FHMIN ? FHROT + FHOUT_AERO : FHMIN + FHOUT_AERO ))
-  GOCART_OUTPUT_FH=$(seq -s ' ' "$(( aero_min ))" "${FHOUT_AERO}" "${FHMAX}")
+  # GOCART output times can't be computed here because they may depend on FHROT
 }

From 13ec408b4db1bed3ac49697b002a708dee35fe15 Mon Sep 17 00:00:00 2001
From: "Walter.Kolczynski" <Walter.Kolczynski@noaa.gov>
Date: Thu, 14 Nov 2024 02:45:02 -0600
Subject: [PATCH 09/13] Make GOCART output times a function

Makes GOCART output times a function since it is needed in two places.
---
 ush/forecast_postdet.sh | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
index 3fed72f1e8b..aa278dadf7e 100755
--- a/ush/forecast_postdet.sh
+++ b/ush/forecast_postdet.sh
@@ -697,7 +697,7 @@ 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
@@ -711,6 +711,16 @@ 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
+  aero_min=$(( ${IAU_FHROT:-0} > FHMIN ? IAU_FHROT + FHOUT_AERO : FHMIN + FHOUT_AERO ))
+  gocart_output_fh=$(seq -s ' ' "$(( aero_min ))" "${FHOUT_AERO}" "${FHMAX}")
+
+  echo "${gocart_output_fh}"
+}
+
 GOCART_out() {
   echo "SUB ${FUNCNAME[0]}: Copying output data for GOCART"
 
@@ -718,12 +728,8 @@ GOCART_out() {
   # TODO: this should be linked but there are issues where gocart crashing if it is linked
   local fhr
   local vdate
-  local aero_min
-  local gocart_output_fh
-  aero_min=$(( ${IAU_FHROT:-0} > FHMIN ? IAU_FHROT + FHOUT_AERO : FHMIN + FHOUT_AERO ))
-  gocart_output_fh=$(seq -s ' ' "$(( aero_min ))" "${FHOUT_AERO}" "${FHMAX}")
 
-  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)
     ${NCP} "${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"

From d953c49c5ff0245b804906358872aca9316a18b7 Mon Sep 17 00:00:00 2001
From: "Walter.Kolczynski" <Walter.Kolczynski@noaa.gov>
Date: Thu, 14 Nov 2024 04:12:21 -0600
Subject: [PATCH 10/13] Add mixing defaults entry for aero in GEFS

The defulats file for GEFS was missing an entry for aero to ensure
@field@ get parsed at expt setup time. This was added to gfs as
part of #3053, but gefs was missed.
---
 parm/config/gefs/yaml/defaults.yaml | 4 +++-
 1 file changed, 3 insertions(+), 1 deletion(-)

diff --git a/parm/config/gefs/yaml/defaults.yaml b/parm/config/gefs/yaml/defaults.yaml
index f0e8772b671..cda90c54851 100644
--- a/parm/config/gefs/yaml/defaults.yaml
+++ b/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: {}

From 90b49ff262d466e0ab263d0c50db4d0271747c90 Mon Sep 17 00:00:00 2001
From: "Walter.Kolczynski" <Walter.Kolczynski@noaa.gov>
Date: Tue, 19 Nov 2024 07:19:24 -0600
Subject: [PATCH 11/13] Assign gocart fhmax before it is adjusted by IAU

---
 ush/forecast_postdet.sh | 2 +-
 ush/forecast_predet.sh  | 3 +++
 2 files changed, 4 insertions(+), 1 deletion(-)

diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
index aa278dadf7e..78714fd5aa5 100755
--- a/ush/forecast_postdet.sh
+++ b/ush/forecast_postdet.sh
@@ -716,7 +716,7 @@ GOCART_output_fh() {
   local aero_min
   local gocart_output_fh
   aero_min=$(( ${IAU_FHROT:-0} > FHMIN ? IAU_FHROT + FHOUT_AERO : FHMIN + FHOUT_AERO ))
-  gocart_output_fh=$(seq -s ' ' "$(( aero_min ))" "${FHOUT_AERO}" "${FHMAX}")
+  gocart_output_fh=$(seq -s ' ' "$(( aero_min ))" "${FHOUT_AERO}" "${GOCART_MAX}")
 
   echo "${gocart_output_fh}"
 }
diff --git a/ush/forecast_predet.sh b/ush/forecast_predet.sh
index 94965f4e978..3c3dd719ef1 100755
--- a/ush/forecast_predet.sh
+++ b/ush/forecast_predet.sh
@@ -724,5 +724,8 @@ GOCART_predet(){
 
   if [[ ! -d "${COMOUT_CHEM_HISTORY}" ]]; then mkdir -p "${COMOUT_CHEM_HISTORY}"; fi
 
+  # 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
 }

From 3070f0fd422183c64d6cc5311af2e3bbfeab0e76 Mon Sep 17 00:00:00 2001
From: "Walter.Kolczynski" <Walter.Kolczynski@noaa.gov>
Date: Tue, 19 Nov 2024 12:36:32 -0600
Subject: [PATCH 12/13] Fix control of gfs aod files

---
 parm/archive/master_gfs.yaml.j2 | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/parm/archive/master_gfs.yaml.j2 b/parm/archive/master_gfs.yaml.j2
index e9fa3b8049a..3f7c2e9d14e 100644
--- a/parm/archive/master_gfs.yaml.j2
+++ b/parm/archive/master_gfs.yaml.j2
@@ -33,7 +33,7 @@ datasets:
     {% endfilter %}
 {% endif %}
 
-{% if DO_AERO and (AERO_ANL_RUN == "gfs" or AERO_ANL_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" %}

From 6616191b8b2b756c49cdb7cad9a23b251e566fb0 Mon Sep 17 00:00:00 2001
From: "Walter.Kolczynski" <Walter.Kolczynski@noaa.gov>
Date: Fri, 22 Nov 2024 08:03:19 -0600
Subject: [PATCH 13/13] Add comment on gocart min fh

---
 ush/forecast_postdet.sh | 2 ++
 1 file changed, 2 insertions(+)

diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
index 78714fd5aa5..310fcf0afa8 100755
--- a/ush/forecast_postdet.sh
+++ b/ush/forecast_postdet.sh
@@ -715,6 +715,8 @@ 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}")