Add in initial 3DVar aerosol DA cycling capability (#1106)

This PR adds an initial 3DVar aerosol DA cycling capability to support scientific development and testing towards an operationally viable candidate system for aerosol DA for GFSv17/GEFSv13.

This PR includes the following:
- Three new j-jobs and ex-scripts for aeroanlinit, aeroanlrun, and aeroanlfinal
- modifies the rocoto scripts that call the above j-jobs to actually call them
- makes modification to the config.resources and config.aeroanl files
- Introduces an object-oriented python structure to initialize/finalize the aerosol analysis with the intention of eventually using the top-level classes for other analysis jobs (soca, atm, land)

Closes #982

jobs/JGLOBAL_AERO_ANALYSIS_FINALIZE

@@ -0,0 +1,62 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+export WIPE_DATA="NO"
+export DATA=${DATA:-${DATAROOT}/${RUN}aeroanl_${cyc}}
+source "${HOMEgfs}/ush/jjob_header.sh" -e "aeroanlfinal" -c "base aeroanl aeroanlfinal"
+
+##############################################
+# Set variables used in the script
+##############################################
+export CDATE=${CDATE:-${PDY}${cyc}}
+export CDUMP=${CDUMP:-${RUN:-"gfs"}}
+
+
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
+
+GDATE=$(date +%Y%m%d%H -d "${CDATE:0:8} ${CDATE:8:2} - ${assim_freq} hours")
+export GDATE
+gPDY=${GDATE:0:8}
+export gcyc=${GDATE:8:2}
+export GDUMP=${GDUMP:-"gdas"}
+
+export OPREFIX="${CDUMP}.t${cyc}z."
+export GPREFIX="${GDUMP}.t${gcyc}z."
+export APREFIX="${CDUMP}.t${cyc}z."
+
+export COMOUT=${COMOUT:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/chem}
+
+mkdir -p "${COMOUT}"
+
+# COMIN_GES and COMIN_GES_ENS are used in script
+export COMIN_GES="${ROTDIR}/${GDUMP}.${gPDY}/${gcyc}/chem"
+export COMIN_GES_ENS="${ROTDIR}/enkf${GDUMP}.${gPDY}/${gcyc}/chem"
+
+###############################################################
+# Run relevant script
+
+EXSCRIPT=${GDASAEROFINALPY:-${HOMEgfs}/scripts/exglobal_aero_analysis_finalize.py}
+${EXSCRIPT}
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+##############################################
+# End JOB SPECIFIC work
+##############################################
+
+##############################################
+# Final processing
+##############################################
+if [[ -e "${pgmout}" ]] ; then
+  cat "${pgmout}"
+fi
+
+##########################################
+# Remove the Temporary working directory
+##########################################
+cd "${DATAROOT}" || exit 1
+[[ ${KEEPDATA} = "NO" ]] && rm -rf "${DATA}"
+
+exit 0

jobs/JGLOBAL_AERO_ANALYSIS_INITIALIZE

@@ -0,0 +1,55 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+export DATA=${DATA:-${DATAROOT}/${RUN}aeroanl_${cyc}}
+source "${HOMEgfs}/ush/jjob_header.sh" -e "aeroanlinit" -c "base aeroanl aeroanlinit"
+
+##############################################
+# Set variables used in the script
+##############################################
+export CDATE=${CDATE:-${PDY}${cyc}}
+export CDUMP=${CDUMP:-${RUN:-"gfs"}}
+
+
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
+
+GDATE=$(date +%Y%m%d%H -d "${CDATE:0:8} ${CDATE:8:2} - ${assim_freq} hours")
+export GDATE
+gPDY=${GDATE:0:8}
+export gcyc=${GDATE:8:2}
+export GDUMP=${GDUMP:-"gdas"}
+
+export OPREFIX="${CDUMP}.t${cyc}z."
+export GPREFIX="${GDUMP}.t${gcyc}z."
+export APREFIX="${CDUMP}.t${cyc}z."
+
+export COMOUT=${COMOUT:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/chem}
+
+mkdir -p "${COMOUT}"
+
+# COMIN_GES and COMIN_GES_ENS are used in script
+export COMIN_GES="${ROTDIR}/${GDUMP}.${gPDY}/${gcyc}/chem"
+export COMIN_GES_ENS="${ROTDIR}/enkf${GDUMP}.${gPDY}/${gcyc}/chem"
+
+###############################################################
+# Run relevant script
+
+EXSCRIPT=${GDASAEROINITPY:-${HOMEgfs}/scripts/exglobal_aero_analysis_initialize.py}
+${EXSCRIPT}
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+##############################################
+# End JOB SPECIFIC work
+##############################################
+
+##############################################
+# Final processing
+##############################################
+if [[ -e "${pgmout}" ]] ; then
+  cat "${pgmout}"
+fi
+
+exit 0

jobs/JGLOBAL_AERO_ANALYSIS_RUN

@@ -0,0 +1,56 @@
+#! /usr/bin/env bash
+
+source "${HOMEgfs}/ush/preamble.sh"
+export WIPE_DATA="NO"
+export DATA=${DATA:-${DATAROOT}/${RUN}aeroanl_${cyc}}
+source "${HOMEgfs}/ush/jjob_header.sh" -e "aeroanlrun" -c "base aeroanl aeroanlrun"
+
+##############################################
+# Set variables used in the script
+##############################################
+export CDATE=${CDATE:-${PDY}${cyc}}
+export CDUMP=${CDUMP:-${RUN:-"gfs"}}
+
+
+##############################################
+# Begin JOB SPECIFIC work
+##############################################
+
+GDATE=$(date +%Y%m%d%H -d "${CDATE:0:8} ${CDATE:8:2} - ${assim_freq} hours")
+export GDATE
+gPDY=${GDATE:0:8}
+export gcyc=${GDATE:8:2}
+export GDUMP=${GDUMP:-"gdas"}
+
+export OPREFIX="${CDUMP}.t${cyc}z."
+export GPREFIX="${GDUMP}.t${gcyc}z."
+export APREFIX="${CDUMP}.t${cyc}z."
+
+export COMOUT=${COMOUT:-${ROTDIR}/${CDUMP}.${PDY}/${cyc}/chem}
+
+mkdir -p "${COMOUT}"
+
+# COMIN_GES and COMIN_GES_ENS are used in script
+export COMIN_GES="${ROTDIR}/${GDUMP}.${gPDY}/${gcyc}/chem"
+export COMIN_GES_ENS="${ROTDIR}/enkf${GDUMP}.${gPDY}/${gcyc}/chem"
+
+###############################################################
+# Run relevant script
+
+EXSCRIPT=${GDASAERORUNSH:-${HOMEgfs}/scripts/exglobal_aero_analysis_run.sh}
+${EXSCRIPT}
+status=$?
+[[ ${status} -ne 0 ]] && exit "${status}"
+
+##############################################
+# End JOB SPECIFIC work
+##############################################
+
+##############################################
+# Final processing
+##############################################
+if [[ -e "${pgmout}" ]] ; then
+  cat "${pgmout}"
+fi
+
+exit 0

jobs/rocoto/aeroanlfinal.sh

@@ -1,15 +1,23 @@
 #! /usr/bin/env bash
 
-source "$HOMEgfs/ush/preamble.sh"
+source "${HOMEgfs}/ush/preamble.sh"
 
 ###############################################################
-# Source FV3GFS workflow modules
-. $HOMEgfs/ush/load_fv3gfs_modules.sh
+# Source UFSDA workflow modules
+. "${HOMEgfs}/ush/load_ufsda_modules.sh"
 status=$?
-[[ $status -ne 0 ]] && exit $status
+[[ ${status} -ne 0 ]] && exit "${status}"
 
 export job="aeroanlfinal"
 export jobid="${job}.$$"
 
 ###############################################################
-echo "Do nothing for now"
+# setup python path for workflow utilities and tasks
+pygwPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/pygw/src"
+PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${pygwPATH}"
+export PYTHONPATH
+###############################################################
+# Execute the JJOB
+"${HOMEgfs}/jobs/JGLOBAL_AERO_ANALYSIS_FINALIZE"
+status=$?
+exit "${status}"

jobs/rocoto/aeroanlinit.sh

@@ -1,15 +1,24 @@
 #! /usr/bin/env bash
 
-source "$HOMEgfs/ush/preamble.sh"
+source "${HOMEgfs}/ush/preamble.sh"
 
 ###############################################################
-# Source FV3GFS workflow modules
-. $HOMEgfs/ush/load_fv3gfs_modules.sh
+# Source UFSDA workflow modules
+. "${HOMEgfs}/ush/load_ufsda_modules.sh"
 status=$?
-[[ $status -ne 0 ]] && exit $status
+[[ ${status} -ne 0 ]] && exit "${status}"
 
 export job="aeroanlinit"
 export jobid="${job}.$$"
 
 ###############################################################
-echo "Do nothing for now"
+# setup python path for workflow utilities and tasks
+pygwPATH="${HOMEgfs}/ush/python:${HOMEgfs}/ush/python/pygw/src"
+PYTHONPATH="${PYTHONPATH:+${PYTHONPATH}:}${pygwPATH}"
+export PYTHONPATH
+
+###############################################################
+# Execute the JJOB
+"${HOMEgfs}/jobs/JGLOBAL_AERO_ANALYSIS_INITIALIZE"
+status=$?
+exit "${status}"

jobs/rocoto/aeroanlrun.sh

@@ -1,15 +1,18 @@
 #! /usr/bin/env bash
 
-source "$HOMEgfs/ush/preamble.sh"
+source "${HOMEgfs}/ush/preamble.sh"
 
 ###############################################################
-# Source FV3GFS workflow modules
-. $HOMEgfs/ush/load_fv3gfs_modules.sh
+# Source UFSDA workflow modules
+. "${HOMEgfs}/ush/load_ufsda_modules.sh"
 status=$?
-[[ $status -ne 0 ]] && exit $status
+[[ ${status} -ne 0 ]] && exit "${status}"
 
 export job="aeroanlrun"
 export jobid="${job}.$$"
 
 ###############################################################
-echo "Do nothing for now"
+# Execute the JJOB
+"${HOMEgfs}/jobs/JGLOBAL_AERO_ANALYSIS_RUN"
+status=$?
+exit "${status}"

parm/config/config.aeroanl

@@ -5,13 +5,20 @@
 
 echo "BEGIN: config.aeroanl"
 
-export OBS_YAML_DIR=$HOMEgfs/sorc/gdas.cd/parm/aero/obs/config/
-export OBS_LIST=$HOMEgfs/sorc/gdas.cd/parm/aero/obs/lists/aero_prototype.yaml
-export AEROVARYAML=$HOMEgfs/sorc/gdas.cd/parm/aero/variational/3dvar_dripcg.yaml
-export BERROR_YAML=$HOMEgfs/sorc/gdas.cd/parm/aero/berror/static_bump.yaml
-export FV3JEDI_FIX=$HOMEgfs/fix/gdas
+export CASE_ANL=${CASE}
+export OBS_YAML_DIR=${HOMEgfs}/sorc/gdas.cd/parm/aero/obs/config/
+export OBS_LIST=${HOMEgfs}/sorc/gdas.cd/parm/aero/obs/lists/gdas_aero_prototype.yaml
+export AEROVARYAML=${HOMEgfs}/sorc/gdas.cd/parm/aero/variational/3dvar_gfs_aero.yaml
+export STATICB_TYPE='identity'
+export BERROR_YAML=${HOMEgfs}/sorc/gdas.cd/parm/aero/berror/staticb_${STATICB_TYPE}.yaml
+export FV3JEDI_FIX=${HOMEgfs}/fix/gdas
+export BERROR_DATA_DIR=${FV3JEDI_FIX}/bump/aero/${CASE_ANL}/
+export BERROR_DATE="20160630.000000"
 
 export io_layout_x=@IO_LAYOUT_X@
 export io_layout_y=@IO_LAYOUT_Y@
 
+export JEDIVAREXE=${HOMEgfs}/exec/fv3jedi_var.x
+export CRTM_VER="2.3.0"
+
 echo "END: config.aeroanl"

parm/config/config.aeroanlrun

@@ -8,7 +8,4 @@ echo "BEGIN: config.aeroanlrun"
 # Get task specific resources
 . $EXPDIR/config.resources aeroanlrun
 
-# Task specific variables
-export JEDIVAREXE=$HOMEgfs/exec/fv3jedi_var.x
-
 echo "END: config.aeroanlrun"

parm/config/config.resources

@@ -193,6 +193,28 @@ elif [[ "${step}" = "atmanalpost" ]]; then
 
 elif [[ "${step}" = "aeroanlinit" ]]; then
 
+   # below lines are for creating JEDI YAML
+   case ${CASE} in
+     C768)
+        layout_x=6
+        layout_y=6
+        ;;
+      C384)
+        layout_x=5
+        layout_y=5
+        ;;
+     C192 | C96 | C48)
+        layout_x=8
+        layout_y=8
+        ;;
+      *)
+          echo "FATAL ERROR: Resolution not supported for aerosol analysis'"
+          exit 1
+    esac
+
+    export layout_x
+    export layout_y
+
     export wtime_aeroanlinit="00:10:00"
     export npe_aeroanlinit=1
     export nth_aeroanlinit=1
@@ -212,14 +234,17 @@ elif [[ "${step}" = "aeroanlrun" ]]; then
         layout_y=5
         ;;
      C192 | C96 | C48)
-        layout_x=3
-        layout_y=3
+        layout_x=8
+        layout_y=8
         ;;
       *)
           echo "FATAL: Resolution not supported'"
           exit 1
     esac
 
+    export layout_x
+    export layout_y
+
     export wtime_aeroanlrun="00:30:00"
     npe_aeroanlrun=$(echo "${layout_x} * ${layout_y} * 6" | bc)
     export npe_aeroanlrun

parm/parm_gdas/aero_crtm_coeff.yaml

@@ -0,0 +1,23 @@
+mkdir:
+- !ENV ${DATA}/crtm/
+copy:
+- - !ENV ${FV3JEDI_FIX}/crtm/${CRTM_VER}/AerosolCoeff.bin
+  - !ENV ${DATA}/crtm/AerosolCoeff.bin
+- - !ENV ${FV3JEDI_FIX}/crtm/${CRTM_VER}/CloudCoeff.bin
+  - !ENV ${DATA}/crtm/CloudCoeff.bin
+- - !ENV ${FV3JEDI_FIX}/crtm/${CRTM_VER}/v.viirs-m_npp.SpcCoeff.bin
+  - !ENV ${DATA}/crtm/v.viirs-m_npp.SpcCoeff.bin
+- - !ENV ${FV3JEDI_FIX}/crtm/${CRTM_VER}/v.viirs-m_npp.TauCoeff.bin
+  - !ENV ${DATA}/crtm/v.viirs-m_npp.TauCoeff.bin
+- - !ENV ${FV3JEDI_FIX}/crtm/${CRTM_VER}/v.viirs-m_j1.SpcCoeff.bin
+  - !ENV ${DATA}/crtm/v.viirs-m_j1.SpcCoeff.bin
+- - !ENV ${FV3JEDI_FIX}/crtm/${CRTM_VER}/v.viirs-m_j1.TauCoeff.bin
+  - !ENV ${DATA}/crtm/v.viirs-m_j1.TauCoeff.bin
+- - !ENV ${FV3JEDI_FIX}/crtm/${CRTM_VER}/NPOESS.VISice.EmisCoeff.bin
+  - !ENV ${DATA}/crtm/NPOESS.VISice.EmisCoeff.bin
+- - !ENV ${FV3JEDI_FIX}/crtm/${CRTM_VER}/NPOESS.VISland.EmisCoeff.bin
+  - !ENV ${DATA}/crtm/NPOESS.VISland.EmisCoeff.bin
+- - !ENV ${FV3JEDI_FIX}/crtm/${CRTM_VER}/NPOESS.VISsnow.EmisCoeff.bin
+  - !ENV ${DATA}/crtm/NPOESS.VISsnow.EmisCoeff.bin
+- - !ENV ${FV3JEDI_FIX}/crtm/${CRTM_VER}/NPOESS.VISwater.EmisCoeff.bin
+  - !ENV ${DATA}/crtm/NPOESS.VISwater.EmisCoeff.bin

parm/parm_gdas/aero_jedi_fix.yaml

@@ -0,0 +1,11 @@
+mkdir:
+- !ENV ${DATA}/fv3jedi
+copy:
+- - !ENV ${FV3JEDI_FIX}/fv3jedi/fv3files/akbk$(npz).nc4
+  - !ENV ${DATA}/fv3jedi/akbk.nc4
+- - !ENV ${FV3JEDI_FIX}/fv3jedi/fv3files/fmsmpp.nml
+  - !ENV ${DATA}/fv3jedi/fmsmpp.nml
+- - !ENV ${FV3JEDI_FIX}/fv3jedi/fv3files/field_table_gfdl
+  - !ENV ${DATA}/fv3jedi/field_table
+- - !ENV ${FV3JEDI_FIX}/fv3jedi/fieldmetadata/gfs-aerosol.yaml
+  - !ENV ${DATA}/fv3jedi/gfs-restart.yaml

parm/parm_gdas/aeroanl_inc_vars.yaml

@@ -0,0 +1 @@
+['dust1', 'dust2', 'dust3', 'dust4', 'dust5', 'seas1', 'seas2', 'seas3', 'seas4', 'so4', 'oc1', 'oc2', 'bc1', 'bc2']