Process aerosol analysis in grib2 format via UPP in GCAFS

dev/parm/config/gcafs/config.anal

@@ -0,0 +1 @@
+../gfs/config.anal

dev/parm/config/gcafs/config.analcalc

@@ -0,0 +1 @@
+../gfs/config.analcalc

dev/parm/config/gcafs/config.base.j2

@@ -381,6 +381,8 @@ export SMOOTH_ENKF="NO"
 export l4densvar=".true."
 export lwrite4danl=".true."
 export DO_CALC_INCREMENT="NO"
+export USE_BUILD_GSINFO="NO"
+export BUILD_GSINFO_DIR="${PARMgfs}/gsinfo"
 
 # Early-cycle EnKF parameters
 export NMEM_ENS_GFS="{{ NMEM_ENS_GFS }}"

dev/parm/config/gcafs/config.resources

@@ -703,7 +703,7 @@ case ${step} in
 
 
   "anal")
-    if [[ "${RUN}" = *gdas ]]; then
+    if [[ "${RUN}" = *gdas || "${RUN}" = gcdas ]]; then
       walltime="01:20:00"
       case ${CASE} in
         "C1152" | "C768")

dev/parm/config/gcafs/config.upp

@@ -0,0 +1,16 @@
+#! /usr/bin/env bash
+
+########## config.upp ##########
+# UPP specific
+
+echo "BEGIN: config.upp"
+
+# Get task specific resources
+. "${EXPDIR}/config.resources" upp
+
+export UPP_CONFIG="${PARMgfs}/post/upp_gcafs.yaml"
+
+# No. of forecast hours to process in a single job
+export NFHRS_PER_GROUP=3
+
+echo "END: config.upp"

dev/workflow/applications/gcafs_cycled.py

@@ -136,6 +136,7 @@ def _get_app_configs(self, run):
         if options['do_aero_anl']:
             configs += ['aeroanlgenb', 'aeroanlinit', 'aeroanlvar', 'aeroanlfinal']
             configs += ['prepobsaero']
+            configs += ['analcalc']
 
         if options['do_anlstat']:
             configs += ['anlstat']
@@ -204,6 +205,8 @@ def get_task_names(self):
                     task_names[run] += ['aeroanlgenb']
                     task_names[run] += ['aeroanlinit', 'aeroanlvar', 'aeroanlfinal']
                     task_names[run] += ['prepobsaero']
+                    task_names[run] += ['analcalc']
+                    task_names[run] += ['atmanlupp']
 
                 if options['do_anlstat']:
                     task_names[run] += ['anlstat']

dev/workflow/rocoto/gcafs_tasks.py

@@ -462,6 +462,34 @@ def aeroanlfinal(self):
 
         return task
 
+    def analcalc(self):
+
+        deps = []
+        dep_dict = {'type': 'task', 'name': f'{self.run}_offlineanl'}
+        deps.append(rocoto.add_dependency(dep_dict))
+        dep_dict = {'type': 'task', 'name': f'{self.run}_sfcanl'}
+        deps.append(rocoto.add_dependency(dep_dict))
+        dep_dict = {'type': 'task', 'name': f'{self.run}_aeroanlfinal'}
+        deps.append(rocoto.add_dependency(dep_dict))
+        dependencies = rocoto.create_dependency(dep_condition='and', dep=deps)
+
+        resources = self.get_resource('analcalc')
+        task_name = f'{self.run}_analcalc'
+        task_dict = {'task_name': task_name,
+                     'resources': resources,
+                     'dependency': dependencies,
+                     'envars': self.envars,
+                     'cycledef': self.run.replace('enkf', ''),
+                     'command': f'{self.HOMEgfs}/dev/jobs/analcalc.sh',
+                     'job_name': f'{self.pslot}_{task_name}_@H',
+                     'log': f'{self.rotdir}/logs/@Y@m@d@H/{task_name}.log',
+                     'maxtries': '&MAXTRIES;'
+                     }
+
+        task = rocoto.create_task(task_dict)
+
+        return task
+
     def aerosol_init(self):
         """
         Create a task for aerosol initialization.
@@ -755,18 +783,12 @@ def atmanlupp(self):
         for key, value in postenvar_dict.items():
             postenvars.append(rocoto.create_envar(name=key, value=str(value)))
 
-        atm_anl_path = self._template_to_rocoto_cycstring(self._base["COM_ATMOS_ANALYSIS_TMPL"])
         deps = []
-        data = f'{atm_anl_path}/{self.run}.t@Hz.analysis.atm.a006.nc'
-        dep_dict = {'type': 'data', 'data': data, 'age': 120}
-        deps.append(rocoto.add_dependency(dep_dict))
-        data = f'{atm_anl_path}/{self.run}.t@Hz.analysis.sfc.a006.nc'
-        dep_dict = {'type': 'data', 'data': data, 'age': 120}
-        deps.append(rocoto.add_dependency(dep_dict))
-        data = f'{atm_anl_path}/{self.run}.t@Hz.done.txt'
-        dep_dict = {'type': 'data', 'data': data, 'age': 60}
+        dep_dict = {'type': 'task', 'name': f'{self.run}_analcalc'}
         deps.append(rocoto.add_dependency(dep_dict))
+
         dependencies = rocoto.create_dependency(dep=deps, dep_condition='and')
+
         resources = self.get_resource('upp')
         task_name = f'{self.run}_atmanlupp'
         task_dict = {'task_name': task_name,
@@ -792,7 +814,7 @@ def atmanlprod(self):
 
         atm_master_path = self._template_to_rocoto_cycstring(self._base["COM_ATMOS_MASTER_TMPL"])
         deps = []
-        data = f'{atm_master_path}/{self.run}.t@Hz.master.grb2anl'
+        data = f'{atm_master_path}/{self.run}.t@Hz.master.analysis.grib2'
         dep_dict = {'type': 'data', 'data': data, 'age': 120}
         deps.append(rocoto.add_dependency(dep_dict))
         dependencies = rocoto.create_dependency(dep=deps)

jobs/JGLOBAL_ATMOS_ANALYSIS_CALC

@@ -15,7 +15,8 @@ export DO_CALC_ANALYSIS=${DO_CALC_ANALYSIS:-"YES"}
 GDATE=$(date --utc +%Y%m%d%H -d "${PDY} ${cyc} - ${assim_freq} hours")
 export gPDY=${GDATE:0:8}
 export gcyc=${GDATE:8:2}
-export GDUMP="gdas"
+#export GDUMP="gdas"
+export GDUMP="${RUN}"
 export GDUMP_ENS="enkf${GDUMP}"
 
 export OPREFIX="${rCDUMP}.t${cyc}z."
@@ -28,7 +29,8 @@ RUN=${rCDUMP} YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
 
 YMD=${PDY} HH=${cyc} declare_from_tmpl -rx \
     COMOUT_ATMOS_ANALYSIS:COM_ATMOS_ANALYSIS_TMPL \
-    COMIN_ATMOS_RESTART:COM_ATMOS_RESTART_TMPL
+    COMIN_ATMOS_RESTART:COM_ATMOS_RESTART_TMPL \
+    COMIN_CHEM_ANALYSIS:COM_CHEM_ANALYSIS_TMPL
 
 RUN=${GDUMP} YMD=${gPDY} HH=${gcyc} declare_from_tmpl -rx \
     COMIN_OBS_PREV:COM_OBS_TMPL \

parm/archive/master_gcdas.yaml.j2

@@ -19,6 +19,12 @@ datasets:
                 {% for itile in range(1,7) %}
             - "{{ COMIN_CHEM_ANALYSIS | relpath(ROTDIR) }}/aeroinc.{{ cycle_YMD }}.{{ cycle_HH }}0000.fv_tracer.res.tile{{ itile }}.nc"
                 {% endfor %}
+            # Analysis Master GRIB2 data
+            - "{{ COMIN_ATMOS_MASTER | relpath(ROTDIR) }}/{{ head }}master.analysis.grib2"
+            - "{{ COMIN_ATMOS_MASTER | relpath(ROTDIR) }}/{{ head }}master.analysis.grib2.idx"
+            # Analysis netCDF (raw) data
+            - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}analysis.atm.a006.nc"
+            - "{{ COMIN_ATMOS_ANALYSIS | relpath(ROTDIR) }}/{{ head }}analysis.sfc.a006.nc"
             {% endif %}
             {% if DO_PREP_OBS_AERO %}
             - "{{ COMIN_OBS | relpath(ROTDIR) }}/{{ head }}aeroobs"
@@ -65,6 +71,8 @@ datasets:
             - "{{ COMIN_ATMOS_RESTART | relpath(ROTDIR) }}/{{ r_prefix }}.coupler.res"
             - "{{ COMIN_ATMOS_RESTART | relpath(ROTDIR) }}/{{ r_prefix }}.fv_core.res.nc"
             {% endfor %}
+
+
 # Archive the EXPDIR if requested
 {% if archive_expdir %}
 {% filter indent(width=4) %}

parm/post/itag.jinja

@@ -12,5 +12,6 @@
   kpo = {{ po | length }},
   po = {{ po | join(', ') }},
   rdaod = {{ rdaod | to_f90bool }}
+  nasa_on = {{ nasa_on | to_f90bool }}
 /
 

parm/post/upp_gcafs.yaml

@@ -0,0 +1,37 @@
+upp:
+  config:
+    grib_version: "grib2"
+    ioform: "netcdfpara"
+    po: [1000.,975.,950.,925.,900.,875.,850.,825.,800.,775.,750.,725.,700.,675.,650.,625.,600.,575.,550.,525.,500.,475.,450.,425.,400.,375.,350.,325.,300.,275.,250.,225.,200.,175.,150.,125.,100.,70.,50.,40.,30.,20.,15.,10.,7.,5.,3.,2.,1.,0.7,0.4,0.2,0.1,0.07,0.04,0.02,0.01]
+    rdaod: False
+    nasa_on: False
+  fix_data:
+    mkdir:
+      - "{{ DATA }}"
+    copy:
+      - ["{{ 'g2tmpl_ROOT' | getenv }}/share/params_grib2_tbl_new", "{{ DATA }}/params_grib2_tbl_new"]
+      - ["{{ PARMgfs }}/post/nam_micro_lookup.dat", "{{ DATA }}/eta_micro_lookup.dat"]
+      - ["{{ EXECgfs }}/upp.x", "{{ DATA }}/"]
+      - ["{{ PARMgfs }}/post/itag.jinja", "{{ DATA }}/"]
+      - ["{{ PARMgfs }}/post/optics_luts_DUST_nasa.dat", "{{ DATA }}/optics_luts_DUST_nasa.dat"]
+      - ["{{ PARMgfs }}/post/optics_luts_NITR_nasa.dat", "{{ DATA }}/optics_luts_NITR_nasa.dat"]
+      - ["{{ PARMgfs }}/post/optics_luts_SALT_nasa.dat", "{{ DATA }}/optics_luts_SALT_nasa.dat"]
+      - ["{{ PARMgfs }}/post/optics_luts_SOOT_nasa.dat", "{{ DATA }}/optics_luts_SOOT_nasa.dat"]
+      - ["{{ PARMgfs }}/post/optics_luts_SUSO_nasa.dat", "{{ DATA }}/optics_luts_SUSO_nasa.dat"]
+      - ["{{ PARMgfs }}/post/optics_luts_WASO_nasa.dat", "{{ DATA }}/optics_luts_WASO_nasa.dat"]
+
+analysis:
+  config:
+    rdaod: True
+    nasa_on: True
+    NET: GFS   # upp doesn't work with GCAFS,set to GFS instead
+  data_in:
+    copy:
+      - ["{{ PARMgfs }}/post/gcafs/postxconfig-NT-gcafs.txt", "{{ DATA }}/postxconfig-NT.txt"]
+      - ["{{ COMIN_ATMOS_ANALYSIS }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.analysis.atm.a006.nc", "{{ DATA }}/{{ atmos_filename }}"]
+      - ["{{ COMIN_ATMOS_ANALYSIS }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.analysis.sfc.a006.nc", "{{ DATA }}/{{ flux_filename }}"]
+  data_out:
+    copy:
+      - ["{{ DATA }}/GFSPRS.GrbF00", "{{ COMOUT_ATMOS_MASTER }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.master.analysis.grib2"]
+      - ["{{ DATA }}/GFSPRS.GrbF00.idx", "{{ COMOUT_ATMOS_MASTER }}/{{ RUN }}.t{{ current_cycle | strftime('%H') }}z.master.analysis.grib2.idx"]
+

scripts/exglobal_atmos_analysis_calc.sh

@@ -78,6 +78,7 @@ ATMANL=${ATMANL:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}analysis.atm.a006.nc}
 
 # Increment files
 ATMINC=${ATMINC:-${COMOUT_ATMOS_ANALYSIS}/${APREFIX}increment.atm.i006.nc}
+AEROINC=${AEROINC:-${COMIN_CHEM_ANALYSIS}/${APREFIX}aeroinc.nc}
 
 # Set script / GSI control parameters
 DOHYBVAR=${DOHYBVAR:-"NO"}
@@ -115,53 +116,69 @@ rm -rf dir.*
 ##############################################################
 # If analysis increment is written by GSI, produce an analysis file here
 if [[ "${DO_CALC_ANALYSIS}" == "YES" ]]; then
-   # link analysis and increment files
-   ${NLN} "${ATMANL}" siganl
-   ${NLN} "${ATMINC}" siginc.nc
-   if [[ "${DOHYBVAR}" == "YES" && "${l4densvar}" == ".true." && "${lwrite4danl}" == ".true." ]]; then
-      ${NLN} "${ATMA03}"   siga03
-      ${NLN} "${ATMI03}"   sigi03.nc
-      ${NLN} "${ATMA04}"   siga04
-      ${NLN} "${ATMI04}"   sigi04.nc
-      ${NLN} "${ATMA05}"   siga05
-      ${NLN} "${ATMI05}"   sigi05.nc
-      ${NLN} "${ATMA07}"   siga07
-      ${NLN} "${ATMI07}"   sigi07.nc
-      ${NLN} "${ATMA08}"   siga08
-      ${NLN} "${ATMI08}"   sigi08.nc
-      ${NLN} "${ATMA09}"   siga09
-      ${NLN} "${ATMI09}"   sigi09.nc
-   fi
-   # link guess files
-   ${NLN} "${ATMG03}" sigf03
-   ${NLN} "${ATMGES}" sigf06
-   ${NLN} "${ATMG09}" sigf09
-
-   if [[ -f "${ATMG04}" ]]; then
-       ${NLN} "${ATMG04}" sigf04
-   fi
-   if [[ -f "${ATMG05}" ]]; then
-       ${NLN} "${ATMG05}" sigf05
-   fi
-   if [[ -f "${ATMG07}" ]]; then
-       ${NLN} "${ATMG07}" sigf07
-   fi
-   if [[ -f "${ATMG08}" ]]; then
-       ${NLN} "${ATMG08}" sigf08
-   fi
-
-   # Link hourly backgrounds (if present)
-   if [[ -f "${ATMG04}" && -f "${ATMG05}" && -f "${ATMG07}" && -f "${ATMG08}" ]]; then
-      nhr_obsbin=1
-   fi
-
-   ${CALCANLPY}
-   export err=$?
-   if [[ ${err} -ne 0 ]]; then
-      err_exit "Failed to run ${CALCANLPY}"
-   fi
+  ##############################################################
+  # If aerosol increment is written by GCDAS, produce aerosol analysis in atmos analysis file
+    if [[ "${RUN}" == "gcdas" ]]; then
+        # link analysis and increment files
+        ${NLN} "${ATMANL}" siganl
+        ${NLN} "${AEROINC}" siginc.nc
+        # link guess files
+        ${NLN} "${ATMGES}" sigf06
+
+        ${CALCANLPY}
+        export err=$?
+        if [[ ${err} -ne 0 ]]; then
+            err_exit "Failed to run ${CALCANLPY}"
+        fi
+    else   
+        # link analysis and increment files
+        ${NLN} "${ATMANL}" siganl
+        ${NLN} "${ATMINC}" siginc.nc
+        if [[ "${DOHYBVAR}" == "YES" && "${l4densvar}" == ".true." && "${lwrite4danl}" == ".true." ]]; then
+            ${NLN} "${ATMA03}"   siga03
+            ${NLN} "${ATMI03}"   sigi03.nc
+            ${NLN} "${ATMA04}"   siga04
+            ${NLN} "${ATMI04}"   sigi04.nc
+            ${NLN} "${ATMA05}"   siga05
+            ${NLN} "${ATMI05}"   sigi05.nc
+            ${NLN} "${ATMA07}"   siga07
+            ${NLN} "${ATMI07}"   sigi07.nc
+            ${NLN} "${ATMA08}"   siga08
+            ${NLN} "${ATMI08}"   sigi08.nc
+            ${NLN} "${ATMA09}"   siga09
+            ${NLN} "${ATMI09}"   sigi09.nc
+        fi
+        # link guess files
+        ${NLN} "${ATMG03}" sigf03
+        ${NLN} "${ATMGES}" sigf06
+        ${NLN} "${ATMG09}" sigf09
+
+        if [[ -f "${ATMG04}" ]]; then
+            ${NLN} "${ATMG04}" sigf04
+        fi
+        if [[ -f "${ATMG05}" ]]; then
+            ${NLN} "${ATMG05}" sigf05
+        fi
+        if [[ -f "${ATMG07}" ]]; then
+           ${NLN} "${ATMG07}" sigf07
+        fi
+        if [[ -f "${ATMG08}" ]]; then
+           ${NLN} "${ATMG08}" sigf08
+        fi
+
+        # Link hourly backgrounds (if present)
+        if [[ -f "${ATMG04}" && -f "${ATMG05}" && -f "${ATMG07}" && -f "${ATMG08}" ]]; then
+            nhr_obsbin=1
+        fi
+
+        ${CALCANLPY}
+        export err=$?
+        if [[ ${err} -ne 0 ]]; then
+            err_exit "Failed to run ${CALCANLPY}"
+        fi
+    fi
 else
-   echo "WARNING Neither increment nor analysis are generated by external utils"
+    echo "WARNING Neither increment nor analysis are generated by external utils"
 fi
 
 ##############################################################

sorc/link_workflow.sh

@@ -150,14 +150,21 @@ ${LINK_OR_COPY} "${HOMEgfs}/sorc/ufs_model.fd/tests/parm/noahmptable.tbl" .
 cd "${HOMEgfs}/parm/post" || exit 1
 ${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/parm/params_grib2_tbl_new" .
 ${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/fix/nam_micro_lookup.dat" .
-for dir in gfs gefs sfs
+for dir in gfs gcafs gefs sfs
 do
   ${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/parm/${dir}" .
 done
 for file in ice_gfs.csv ice_gefs.csv ocean_gfs.csv ocean_gefs.csv ocnicepost.nml.jinja2; do
   ${LINK_OR_COPY} "${HOMEgfs}/sorc/gfs_utils.fd/parm/ocnicepost/${file}" .
 done
 
+for file in optics_luts_DUST.dat optics_luts_DUST_nasa.dat optics_luts_NITR_nasa.dat \
+    optics_luts_SALT.dat optics_luts_SALT_nasa.dat optics_luts_SOOT.dat optics_luts_SOOT_nasa.dat \
+    optics_luts_SUSO.dat optics_luts_SUSO_nasa.dat optics_luts_WASO.dat optics_luts_WASO_nasa.dat
+do
+  ${LINK_OR_COPY} "${HOMEgfs}/sorc/upp.fd/fix/chem/${file}" .
+done
+
 cd "${HOMEgfs}/scripts" || exit 8
 if [[ -d "${HOMEgfs}/sorc/gdas.cd" ]]; then
   declare -a gdas_scripts=(exglobal_prep_ocean_obs.py)