GCAFS prep emissions update - fire emissions

.gitmodules

@@ -25,3 +25,7 @@
 [submodule "sorc/gsi_monitor.fd"]
   path = sorc/gsi_monitor.fd
   url = https://github.com/NOAA-EMC/GSI-Monitor.git
+[submodule "sorc/nexus.fd"]
+  path = sorc/nexus.fd
+  url = https://github.com/NOAA-OAR-ARL/NEXUS.git
+  branch = feature/gcafs

dev/jobs/prep_emissions.sh

@@ -11,6 +11,17 @@ status=$?
 export job="prep_emissions"
 export jobid="${job}.$$"
 
+###############################################################
+# Source relevant configs
+configs="base aero prep_emissions"
+for config in ${configs}; do
+    source "${EXPDIR}/config.${config}"
+    status=$?
+    if [[ ${status} -ne 0 ]]; then
+        exit "${status}"
+    fi
+done
+
 ###############################################################
 # Execute the JJOB
 "${HOMEgfs}/jobs/JGLOBAL_PREP_EMISSIONS"

dev/parm/config/gcafs/config.aero.j2

@@ -2,14 +2,18 @@
 
 # UFS-Aerosols settings
 
-# Path to the input data tree
+#================================================================================
+# 1. Aerosol settings
+#================================================================================
 export AERO_INPUTS_DIR="{{ AERO_INPUTS_DIR }}"
 
+#-----------------------------------------------
+# Diag Table and Field Table for GOCART aerosols
+#-----------------------------------------------
 export AERO_DIAG_TABLE="${PARMgfs}/ufs/fv3/diag_table.aero"
 export AERO_FIELD_TABLE="${PARMgfs}/ufs/fv3/field_table.aero"
-# Biomass burning emission dataset. Choose from: gbbepx, qfed, none
-export AERO_EMIS_FIRE="qfed"
-# Directory containing GOCART configuration files
+
+# Aerosol configuration
 export AERO_CONFIG_DIR="${PARMgfs}/ufs/gocart"
 
 # Aerosol convective scavenging factors (list of string array elements)
@@ -20,4 +24,74 @@ export fscav_aero="'*:0.3','so2:0.0','msa:0.0','dms:0.0','nh3:0.4','nh4:0.6','bc
 # Number of diagnostic aerosol tracers (default: 0)
 export dnats_aero=2
 
+#================================================================================
+# 2. Aerosol emissions settings
+#================================================================================
+# Biomass burning emission dataset. Choose from: gbbepx, qfed, none
+export AERO_EMIS_FIRE="qfed"
+export AERO_EMIS_FIRE_VERSION="061"
+export AERO_EMIS_FIRE_HIST=1 # Use historical fire emissions | 1 = true 0 = false
+export FIRE_EMIS_NRT_DIR="" #TODO: set to DCOM for WCOSS2 "${DCOMROOT}/YYYYMMDD/firewx" # Directory containing NRT fire emissions
+
+#===============================================================================
+# 3. NEXUS settings
+#===============================================================================
+# NEXUS aerosol emissions dataset. Choose from: gocart, none
+
+# NEXUS configuration set
+export NEXUS_CONFIG="{{ NEXUS_CONFIG | default('gocart') }}" # Options: gocart, none
+export NEXUS_CONFIG_DIR="${PARMgfs}/chem/nexus/${NEXUS_CONFIG}" # Directory containing NEXUS configuration files
+
+# NEXUS Inputs
+# TODO: when this is merged this will point to AERO_INPUTS_DIR for operations
+# export NEXUS_INPUT_DIR="${AERO_INPUTS_DIR}/nexus"
+export NEXUS_INPUT_DIR="/gpfs/f6/bil-fire3/world-shared/Emissions/GEFS_ExtData/nexus"
+
+#--------------------------
+# NEXUS Time Step (seconds)
+#--------------------------
+export NEXUS_TSTEP="{{ NEXUS_TSTEP | default(3600) }}" # Default NEXUS time step in seconds
+
+#------------------
+# NEXUS Grid
+#------------------
+export NEXUS_NX="{{ NEXUS_NX | default(1440) }}"
+export NEXUS_NY="{{ NEXUS_NY | default(720) }}"
+export NEXUS_XMIN="{{ NEXUS_XMIN | default(-180.0) }}"
+export NEXUS_XMAX="{{ NEXUS_XMAX | default(180.0) }}"
+export NEXUS_YMIN="{{ NEXUS_YMIN | default(-90.0) }}"
+export NEXUS_YMAX="{{ NEXUS_YMAX | default(90.0) }}"
+export NEXUS_NZ="{{ NEXUS_NZ | default(1) }}"
+
+#-------------------
+# NEXUS Config Files
+#-------------------
+export NEXUS_GRID_NAME="{{ NEXUS_GRID_NAME | default('HEMCO_sa_Grid.rc') }}"
+export NEXUS_TIME_NAME="{{ NEXUS_TIME_NAME | default('HEMCO_sa_Time.rc') }}"
+export NEXUS_DIAG_NAME="{{ NEXUS_DIAG_NAME | default('HEMCO_sa_Diag.rc') }}"
+export NEXUS_SPEC_NAME="{{ NEXUS_SPEC_NAME | default('HEMCO_sa_Spec.rc') }}"
+export NEXUS_CONFIG_NAME="{{ NEXUS_CONFIG_NAME | default('NEXUS_Config.rc') }}"
+
+#------------------
+# NEXUS Diagnostics
+#------------------
+export NEXUS_DIAG_PREFIX="{{ NEXUS_DIAG_PREFIX | default('NEXUS_DIAG') }}"
+export NEXUS_DIAG_FREQ="{{ NEXUS_DIAG_FREQ | default('Hourly') }}" # Options: Hourly, Daily, Monthly
+
+#------------------
+# NEXUS Logging
+#------------------
+export NEXUS_LOGFILE="{{ NEXUS_LOGFILE | default('NEXUS.log') }}"
+
+#------------------
+# NEXUS Emissions
+#------------------
+export NEXUS_DO_MEGAN=.false # TODO: Add MEGAN biogenic emissions in the furture
+export NEXUS_DO_CEDS2019=.true. # Use CEDS2019 emissions
+export NEXUS_DO_CEDS2024=.false. # Use CEDS2024 emissions
+export NEXUS_DO_HTAPv2=.true. # Use HTAPv2 emissions
+export NEXUS_DO_HTAPv3=.false. # TODO: Currently only uses HTAPv2 for this.
+export NEXUS_DO_CAMS=.false. # Use CAMS global emissions
+export NEXUS_DO_CAMSTEMPO=.false. # Use CAMS temporal emissions
+
 echo "END: config.aero"

dev/parm/config/gcafs/config.prep_emissions

@@ -8,4 +8,6 @@ echo "BEGIN: config.prep_emissions"
 # Get task specific resources
 source "${EXPDIR}/config.resources" prep_emissions
 
+source "${EXPDIR}/config.aero"
+
 echo "END: config.prep_emissions"

dev/parm/config/gcafs/config.resources

@@ -816,10 +816,11 @@ case ${step} in
     ;;
 
   "prep_emissions")
-    export walltime="00:10:00"
+    export walltime="00:20:00"
     export ntasks=1
-    export threads_per_task=1
-    export tasks_per_node=$(( max_tasks_per_node / threads_per_task ))
+    export threads_per_task=$(( max_tasks_per_node / 2 ))
+    export tasks_per_node=1
+    export OMP_NUM_THREADS="${threads_per_task}"
     ;;
 
   "fcst" | "efcs")

dev/parm/config/gfs/config.com

@@ -110,5 +110,7 @@ declare -rx COM_CHEM_HISTORY_TMPL=${COM_BASE}'/model/chem/history'
 declare -rx COM_CHEM_ANALYSIS_TMPL=${COM_BASE}'/analysis/chem'
 declare -rx COM_CHEM_BMAT_TMPL=${COM_CHEM_ANALYSIS_TMPL}'/bmatrix'
 declare -rx COM_CHEM_ANLMON_TMPL=${COM_BASE}'/products/chem/anlmon'
+declare -rx COM_CHEM_INPUT_TMPL=${COM_BASE}'/model/chem/input'
+declare -rx COM_CHEM_RESTART_TMPL=${COM_BASE}'/model/chem/restart'
 
 declare -rx COM_MED_RESTART_TMPL=${COM_BASE}'/model/med/restart'