Add fire blending to GOCART

ci/scripts/utils/publish_logs.py

@@ -91,7 +91,7 @@ def upload_logs_to_repo(args, emcbot_gh, emcbot_ci_url):
         file_path_in_repo = f"{repo_path}/{path_header}/" + str(os.path.basename(file.name))
         emcbot_gh.repo.create_file(file_path_in_repo, "Adding error log file", file_content, branch="error_logs")
 
-    file_url = f"{emcbot_ci_url.rsplit('.',1)[0]}/tree/{repo_branch}/{repo_path}/{path_header}"
+    file_url = f"{emcbot_ci_url.rsplit('.', 1)[0]}/tree/{repo_branch}/{repo_path}/{path_header}"
     print(file_url)
 
 

jobs/JGLOBAL_PREP_EMISSIONS

@@ -13,6 +13,8 @@ source "${HOMEgfs}/ush/jjob_header.sh" -e "prep_emissions" -c "base prep_emissio
 ##############################################
 # Generate COM variables from templates
 # TODO: Add necessary COMIN, COMOUT variables for this job
+YMD="${PDY}" HH="${cyc}" declare_from_tmpl -rx \
+    COMOUT_CHEM_HISTORY:COM_CHEM_HISTORY_TMPL
 
 ###############################################################
 # Run relevant script
@@ -32,4 +34,10 @@ if [[ -e "${pgmout}" ]] ; then
   cat "${pgmout}"
 fi
 
+##########################################
+# Remove the Temporary working directory
+##########################################
+cd "${DATAROOT}" || exit 1
+[[ ${KEEPDATA} = "NO" ]] && rm -rf "${DATA}"
+
 exit 0

parm/config/gefs/config.prep_emissions

@@ -2,10 +2,37 @@
 
 ########## config.prep_emissions ##########
 # aerosol emissions preprocessing specific
+# TODO: this is duplicated in the config.aero file.  Should use a common function
+case ${machine} in
+  "HERA")
+    AERO_INPUTS_DIR="/scratch1/NCEPDEV/global/glopara/data/gocart_emissions"
+    ;;
+  "ORION" | "HERCULES")
+    AERO_INPUTS_DIR="/work2/noaa/global/wkolczyn/noscrub/global-workflow/gocart_emissions"
+    ;;
+  "S4")
+    AERO_INPUTS_DIR="/data/prod/glopara/gocart_emissions"
+    ;;
+  "WCOSS2")
+    AERO_INPUTS_DIR="/lfs/h2/emc/global/noscrub/emc.global/data/gocart_emissions"
+    ;;
+  "GAEA")
+    AERO_INPUTS_DIR="/gpfs/f5/epic/proj-shared/global/glopara/data/gocart_emissions"
+    ;;
+  "JET")
+    AERO_INPUTS_DIR="/lfs4/HFIP/hfv3gfs/glopara/data/gocart_emissions"
+    ;;
+  *)
+    echo "FATAL ERROR: Machine ${machine} unsupported for aerosols"
+    exit 2
+    ;;
+esac
+export AERO_INPUTS_DIR
 
 echo "BEGIN: config.prep_emissions"
 
 # Get task specific resources
+export PREP_EMISSION_CONFIG="${PARMgfs}/prep/aero_emissions.yaml"
 source "${EXPDIR}/config.resources" prep_emissions
 
 echo "END: config.prep_emissions"

parm/config/gefs/config.resources

@@ -82,7 +82,7 @@ case ${step} in
     export ntasks=1
     export threads_per_task=1
     export tasks_per_node=$(( max_tasks_per_node / threads_per_task ))
-    export memory="1GB"
+    export memory="20GB"
     ;;
 
   "fcst" | "efcs")

parm/config/gfs/config.aero

@@ -35,7 +35,7 @@ export AERO_INPUTS_DIR
 
 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
+# Biomass burning emission dataset. Choose from: gbbepx, qfed, hfed, blended, none
 export AERO_EMIS_FIRE="qfed"
 # Directory containing GOCART configuration files
 export AERO_CONFIG_DIR="${PARMgfs}/ufs/gocart"

parm/config/gfs/config.resources

@@ -11,7 +11,7 @@ if (( $# != 1 )); then
 
     echo "Must specify an input task argument to set resource variables!"
     echo "argument can be any one of the following:"
-    echo "stage_ic aerosol_init"
+    echo "stage_ic aerosol_init prep_emissions"
     echo "prep prepsnowobs prepatmiodaobs"
     echo "atmanlinit atmanlvar atmanlfv3inc atmanlfinal"
     echo "atmensanlinit atmensanlobs atmensanlsol atmensanlletkf atmensanlfv3inc atmensanlfinal"

parm/prep/aero_emissions.yaml

@@ -0,0 +1,39 @@
+aero_emissions:
+  config:
+    debug: False
+    ratio: 0.95                                    # weighting ratio
+    emistype: 'QFED'                               # EMission Type, Valid answers: 'QFED, GBBEPx, HFED'
+    climfile_str: 'GBBEPx-all01GRID_v4r0_climMean' # climate file base string used for glob later
+    GBBEPx_version: 'v4r0'                         # gbbepx version
+    qfed_version: '006'                            # qfed version
+    species: [ 'so2','oc','bc' ]                   # species to be used
+    historical: False                              # set to true to just use true data for the given day
+    coarsen_scale: 150                             # scale for coarsen function to generate weights
+    output_vars: ["BC", "CH4", "CO", "CO2", "NH3", "NOx", "OC", "PM2.5", "SO2"]
+    input_vars: ["bc", "ch4", "co", "co2", "nh3", "no", "oc", "pm25", "so2"]
+    data_in:
+      mkdir:
+        - "{{ DATA }}"
+        - "{{ COMOUT_CHEM_HISTORY}}"
+      qfed: # copy qfed
+        copy:
+          - ["{{ AERO_INPUTS_DIR }}/nexus/QFED/{{ current_cycle | strftime('%Y/%m') }}/qfed2.emis_oc.006.{{ current_cycle | to_YMD }}.nc4", "{{ DATA }}/"]
+          - ["{{ AERO_INPUTS_DIR }}/nexus/QFED/{{ current_cycle | strftime('%Y/%m') }}/qfed2.emis_so2.006.{{ current_cycle | to_YMD }}.nc4", "{{ DATA }}/"]
+          - ["{{ AERO_INPUTS_DIR }}/nexus/QFED/{{ current_cycle | strftime('%Y/%m') }}/qfed2.emis_bc.006.{{ current_cycle | to_YMD }}.nc4", "{{ DATA }}/"]
+      hfed: # copy hfed
+        copy:
+          - ["{{ AERO_INPUTS_DIR }}/nexus/HFED/{{ current_cycle | strftime('%Y/M%m') }}/hfed.emis_oc.x576_y361.{{ current_cycle | strftime('%Y%j') }}.nc4", "{{ DATA }}/"]
+          - ["{{ AERO_INPUTS_DIR }}/nexus/HFED/{{ current_cycle | strftime('%Y/M%m') }}/hfed.emis_bc.x576_y361.{{ current_cycle | strftime('%Y%j') }}.nc4", "{{ DATA }}/"]
+          - ["{{ AERO_INPUTS_DIR }}/nexus/HFED/{{ current_cycle | strftime('%Y/M%m') }}/hfed.emis_so2.x576_y361.{{ current_cycle | strftime('%Y%j') }}.nc4", "{{ DATA }}/"]
+      gbbepx:
+        copy:
+          - ["{{ AERO_INPUTS_DIR }}/nexus/GBBEPx/v4/GBBEPx_all01GRID_v4r0_climMean_{{ current_cycle | strftime('%m%d') }}.nc", "{{ DATA }}/"] # copy climo files
+      climo: # copy climatology
+        copy:
+          - ["{{ AERO_INPUTS_DIR }}/nexus/GBBEPx/v4/climMean/GBBEPx-all01GRID_v4r0_climMean_{{ current_cycle | strftime('%m%d') }}.nc", "{{ DATA }}/"] # copy climo files
+          {% for fdate in forecast_dates %}
+          - ["{{ AERO_INPUTS_DIR }}/nexus/GBBEPx/v4/climMean/GBBEPx-all01GRID_v4r0_climMean_{{ fdate | strftime('%m%d') }}.nc", "{{ DATA }}/"] # copy climo files
+          {% endfor %}
+    data_out:
+      copy:
+        - ["{{ DATA }}/{{ RUN }}_blended_emissions.{{ current_cycle | to_YMD }}.nc", "{{ COMOUT_CHEM_HISTORY }}/{{ RUN }}.{{ current_cycle | to_YMD }}.{{ RUN }}_blended_emissions.nc"]

parm/ufs/gocart/ExtData.blended

@@ -0,0 +1,8 @@
+#====== BIOMASS BURNING EMISSIONS =======================================
+
+# Blended Emissions
+#--------------------------------------------------------------------------------------------------------------------------------
+SU_BIOMASS NA  N Y %y4-%m2-%d2t12:00:00 none 0.7778 SO2 gefs.%y4%m2%d2.gefs_blended_emissions.nc
+OC_BIOMASS NA  N Y %y4-%m2-%d2t12:00:00 none 0.7778 OC gefs.%y4%m2%d2.gefs_blended_emissions.nc
+BC_BIOMASS NA  N Y %y4-%m2-%d2t12:00:00 none 0.7778 BC gefs.%y4%m2%d2.gefs_blended_emissions.nc
+# EMI_NH3_BB NA  N Y %y4-%m2-%d2t12:00:00 none 0.7778 NH3 gefs.%y4%m2%d2.gefs_blended_emissions.nc

parm/ufs/gocart/ExtData.hfed

@@ -0,0 +1,8 @@
+#====== BIOMASS BURNING EMISSIONS =======================================
+
+# HFED
+#--------------------------------------------------------------------------------------------------------------------------------
+SU_BIOMASS NA  N Y %y4-%m2-%d2t12:00:00 none 0.7778 biomass ExtData/nexus/HFED/Y1994/M%m2/hfed.emis_so2.x576_y361.%y4%m2.nc4
+OC_BIOMASS NA  N Y %y4-%m2-%d2t12:00:00 none 0.7778 biomass ExtData/nexus/HFED/Y1994/M%m2/hfed.emis_oc.x576_y361.%y4%m2.nc4
+BC_BIOMASS NA  N Y %y4-%m2-%d2t12:00:00 none 0.7778 biomass ExtData/nexus/HFED/Y1994/M%m2/hfed.emis_bc.x576_y361.%y4%m2.nc4
+# EMI_NH3_BB NA  N Y %y4-%m2-%d2t12:00:00 none 0.7778 biomass ExtData/nexus/HFED/Y1994/M%m2/hfed.emis_nh3.x576_y361.%y4%m2.nc4

scripts/exglobal_prep_emissions.py

@@ -1,10 +1,20 @@
 #!/usr/bin/env python3
-# exglobal_prep_emissions.py
-# This script creates a emissions object
-# which perform the pre-processing for aerosol emissions
+"""
+This script initializes a logger, reads configuration from the environment, and performs emissions pre-processing tasks using the AerosolEmissions class.
+
+The script does the following:
+1. Initializes a root logger with the specified logging level and colored log output.
+2. Reads configuration from the environment and converts it into a Python dictionary.
+3. Instantiates an AerosolEmissions object with the configuration.
+4. Retrieves specific keys from the emissions task configuration and stores them in a dictionary.
+5. Sets the 'emistype' attribute in the configuration dictionary based on the 'emistype' value in the emissions configuration.
+6. Initializes, configures, runs, and finalizes the emissions task using the provided parameters.
+
+Note: Make sure to have the necessary dependencies (wxflow, pygfs) installed to run this script successfully.
+"""
 import os
 
-from wxflow import Logger, cast_strdict_as_dtypedict
+from wxflow import Logger, AttrDict, cast_strdict_as_dtypedict
 from pygfs import AerosolEmissions
 
 
@@ -19,7 +29,18 @@
 
     # Instantiate the emissions pre-processing task
     emissions = AerosolEmissions(config)
-    emissions.initialize()
-    emissions.configure()
-    emissions.execute(emissions.task_config.DATA, emissions.task_config.APRUN)
-    emissions.finalize()
+
+    # get local keys for configuration
+    keys = ['DATA', 'forecast_dates', 'PDY', 'cyc', 'aero_emission_yaml']
+    edict = AttrDict()
+    for key in keys:
+        edict[key] = emissions.task_config[key]
+    edict['CONFIG'] = edict.aero_emission_yaml.aero_emissions['config']
+    edict.aero_emission_yaml['emistype'] = edict['CONFIG'].emistype
+    print(edict)
+
+    # print(aero_emission_yaml.aero_emissions['fix_data'])
+    emissions.initialize(edict.CONFIG)
+    emissions.configure(edict.aero_emission_yaml)
+    emissions.run(workdir=edict.DATA, current_date=edict.PDY, forecast_dates=edict.forecast_dates, Config_dict=edict.CONFIG)
+    emissions.finalize(edict['CONFIG'])

scripts/exglobal_stage_ic.py

@@ -28,7 +28,7 @@ def main():
     for key in keys:
         # Make sure OCNRES is three digits
         if key == "OCNRES":
-            stage.task_config.OCNRES = f"{stage.task_config.OCNRES :03d}"
+            stage.task_config.OCNRES = f"{stage.task_config.OCNRES:03d}"
         stage_dict[key] = stage.task_config[key]
 
     # Also import all COM* directory and template variables

ush/compare_f90nml.py

@@ -78,7 +78,7 @@ def _print_diffs(diff_dict: Dict) -> None:
             for kk in diff_dict[path].keys():
                 items = diff_dict[path][kk]
                 print(
-                    f"{kk:>{max_len+2}} : {' | '.join(map(str, diff_dict[path][kk]))}")
+                    f"{kk:>{max_len + 2}} : {' | '.join(map(str, diff_dict[path][kk]))}")
 
     _print_diffs(result)
 

ush/forecast_postdet.sh

@@ -675,13 +675,19 @@ GOCART_rc() {
   # set input directory containing GOCART input data and configuration files
   # this variable is platform-dependent and should be set via a YAML file
 
+  local vdate
   # link directory containing GOCART input dataset, if provided
   if [[ -n "${AERO_INPUTS_DIR}" ]]; then
     ${NLN} "${AERO_INPUTS_DIR}" "${DATA}/ExtData"
     status=$?
     [[ ${status} -ne 0 ]] && exit "${status}"
   fi
 
+  # Link blending emissions if AERO_EMIS_FIRE == blending
+  if [[ "${AERO_EMIS_FIRE}" == "blending" && "${RUN}" == "gefs" ]]; then 
+    ${NCP} "${COMOUT_CHEM_HISTORY}/${RUN}.${vdate:0:8}.${RUN}.blended_emissions.nc" "${DATA}"
+  fi 
+
   # copying GOCART configuration files
   if [[  -n "${AERO_CONFIG_DIR}" ]]; then
     ${NCP} "${AERO_CONFIG_DIR}"/*.rc "${DATA}"