Add initial GSI-based soil analysis capability

parm/config/gfs/config.anal

@@ -50,6 +50,14 @@ export OZINFO=${FIXgsi}/global_ozinfo.txt
 export SATINFO=${FIXgsi}/global_satinfo.txt
 export OBERROR=${FIXgsi}/prepobs_errtable.global
 
+if [[ $GSI_SOILANAL == ".true." ]]; then
+    export hofx_2m_sfcfile=".true."
+    export reducedgrid=".false." # not possible for sfc analysis, Jeff Whitaker says it's not useful anyway
+    export paranc=".false." # temporary until sfc io coded for parance (PR being prepared by T. Gichamo)
+    export DO_SFCCYCLE=".false."  # temporary, until sfccycle has handle fractional grids (PR very close)
+    export CONVINFO=/scratch2/BMC/gsienkf/Clara.Draper/2mDAfiles_gworkflow/global_convinfos.w2mobs.txt
+    export ANAVINFO=/scratch2/BMC/gsienkf/Clara.Draper/2mDAfiles_gworkflow/global_anavinfo.2mobs_soilupd.l127.txt
+fi
 
 # Use experimental dumps in EMC GFS v16 parallels
 if [[ ${RUN_ENVIR} == "emc" ]]; then

parm/config/gfs/config.base.emc.dyn

@@ -352,6 +352,8 @@ fi
 
 if [[ "${DOIAU_ENKF}" = "NO" ]]; then export IAUFHRS_ENKF="6"; fi
 
+export GSI_SOILANAL="YES"
+
 # turned on nsst in anal and/or fcst steps, and turn off rtgsst
 export DONST="YES"
 if [[ ${DONST} = "YES" ]]; then export FNTSFA="        "; fi

parm/config/gfs/config.esfc

@@ -16,4 +16,9 @@ if [ $DOIAU_ENKF = "YES" ]; then
    export DOSFCANL_ENKF="NO"
 fi
 
+if [ $GSI_SOILANAL = "YES" ]; then
+    export DO_LNDINC=".true."
+    export LND_SOI_FILE="lnd_incr"
+fi
+
 echo "END: config.esfc"

scripts/exgdas_enkf_sfc.sh

@@ -24,6 +24,7 @@ pwd=$(pwd)
 
 # Base variables
 DONST=${DONST:-"NO"}
+GSI_SOILANAL=${GSI_SOILANAL:-"NO"}
 DOSFCANL_ENKF=${DOSFCANL_ENKF:-"YES"}
 export CASE=${CASE:-384}
 ntiles=${ntiles:-6}
@@ -144,8 +145,10 @@ if [ $DOIAU = "YES" ]; then
             MEMDIR=${memchar} RUN="enkfgdas" YMD=${gPDY} HH=${gcyc} generate_com \
                 COM_ATMOS_RESTART_MEM_PREV:COM_ATMOS_RESTART_TMPL
 
-            [[ ${TILE_NUM} -eq 1 ]] && mkdir -p "${COM_ATMOS_RESTART_MEM}"
+            MEMDIR=${memchar} YMD=${PDY} HH=${cyc} generate_com \
+                COM_ATMOS_ANALYSIS_MEM:COM_ATMOS_ANALYSIS_TMPL
 
+            [[ ${TILE_NUM} -eq 1 ]] && mkdir -p "${COM_ATMOS_RESTART_MEM}"
             ${NCP} "${COM_ATMOS_RESTART_MEM_PREV}/${bPDY}.${bcyc}0000.sfc_data.tile${n}.nc" \
                 "${COM_ATMOS_RESTART_MEM}/${bPDY}.${bcyc}0000.sfcanl_data.tile${n}.nc"
             ${NLN} "${COM_ATMOS_RESTART_MEM_PREV}/${bPDY}.${bcyc}0000.sfc_data.tile${n}.nc" \
@@ -155,10 +158,18 @@ if [ $DOIAU = "YES" ]; then
             ${NLN} "${FIXorog}/${CASE}/${CASE}_grid.tile${n}.nc"     "${DATA}/fngrid.${cmem}"
             ${NLN} "${FIXorog}/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile${n}.nc" "${DATA}/fnorog.${cmem}"
 
-        done
-
-        CDATE="${PDY}${cyc}" ${CYCLESH}
-        export err=$?; err_chk
+            if [ ${GSI_SOILANAL} = "YES" ]; then
+                FHR=6
+                ${NLN} "${COM_ATMOS_ANALYSIS_MEM}/${APREFIX_ENS}sfci00${FHR}.nc" \
+                   "${DATA}/lnd_incr.${cmem}"
+            fi
+        done # ensembles
+
+        if [ ${GSI_SOILANAL} = "YES" ]; then
+            export DONST="NO" #  temporary, until fractional grids solved
+            CDATE="${PDY}${cyc}" ${CYCLESH}
+            export err=$?; err_chk
+        fi
 
     done
 

scripts/exgdas_enkf_update.sh

@@ -87,6 +87,7 @@ else
    DO_CALC_INCREMENT=${DO_CALC_INCREMENT:-"NO"}
 fi
 INCREMENTS_TO_ZERO=${INCREMENTS_TO_ZERO:-"'NONE'"}
+GSI_SOILINC=${GSI_SOILINC:-"NO"}
 
 ################################################################################
 
@@ -203,6 +204,10 @@ for imem in $(seq 1 $NMEM_ENS); do
    for FHR in $nfhrs; do
       ${NLN} "${COM_ATMOS_HISTORY_MEM_PREV}/${GPREFIX}atmf00${FHR}${ENKF_SUFFIX}.nc" \
          "sfg_${PDY}${cyc}_fhr0${FHR}_${memchar}"
+      if [ $GSI_SOILINC = "YES" ]; then
+         ${NLN} "${COM_ATMOS_HISTORY_MEM_PREV}/${GPREFIX}sfcf00${FHR}${ENKF_SUFFIX}.nc" \
+             "bfg_${PDY}${cyc}_fhr0${FHR}_${memchar}"
+      fi
       if [ $cnvw_option = ".true." ]; then
          ${NLN} "${COM_ATMOS_HISTORY_MEM_PREV}/${GPREFIX}sfcf00${FHR}.nc" \
             "sfgsfc_${PDY}${cyc}_fhr0${FHR}_${memchar}"
@@ -224,6 +229,10 @@ for imem in $(seq 1 $NMEM_ENS); do
                "incr_${PDY}${cyc}_fhr0${FHR}_${memchar}"
          fi
       fi
+      if [ $GSI_SOILANAL = "YES" ]; then
+          ${NLN} "${COM_ATMOS_ANALYSIS_MEM}/${APREFIX}sfci00${FHR}.nc" \
+           "sfcincr_${PDY}${cyc}_fhr0${FHR}_${memchar}"
+      fi
    done
 done
 

scripts/exglobal_atmos_analysis.sh

@@ -89,6 +89,8 @@ SENDDBN=${SENDDBN:-"NO"}
 RUN_GETGES=${RUN_GETGES:-"NO"}
 GETGESSH=${GETGESSH:-"getges.sh"}
 export gesenvir=${gesenvir:-${envir}}
+
+export hofx_2m_sfcfile=${hofx_2m_sfcfile:-".false."}
 
 # Observations
 OPREFIX=${OPREFIX:-""}
@@ -296,6 +298,7 @@ RADCLOUDINFO=${RADCLOUDINFO:-${FIXgsi}/cloudy_radiance_info.txt}
 ATMSFILTER=${ATMSFILTER:-${FIXgsi}/atms_beamwidth.txt}
 ANAVINFO=${ANAVINFO:-${FIXgsi}/global_anavinfo.l${LEVS}.txt}
 CONVINFO=${CONVINFO:-${FIXgsi}/global_convinfo.txt}
+
 vqcdat=${vqcdat:-${FIXgsi}/vqctp001.dat}
 INSITUINFO=${INSITUINFO:-${FIXgsi}/global_insituinfo.txt}
 OZINFO=${OZINFO:-${FIXgsi}/global_ozinfo.txt}
@@ -748,6 +751,7 @@ cat > gsiparm.anl << EOF
 /
 &OBS_INPUT
   dmesh(1)=145.0,dmesh(2)=150.0,dmesh(3)=100.0,dmesh(4)=50.0,time_window_max=3.0,
+  hofx_2m_sfcfile=${hofx_2m_sfcfile},
   ${OBSINPUT}
 /
 OBS_INPUT::
@@ -909,7 +913,6 @@ ${NCP} ${GSIEXEC} ${DATA}
 ${APRUN_GSI} ${DATA}/$(basename ${GSIEXEC}) 1>&1 2>&2
 export err=$?; err_chk
 
-
 ##############################################################
 # If full analysis field written, calculate analysis increment
 # here before releasing FV3 forecast

scripts/exglobal_atmos_sfcanl.sh

@@ -58,6 +58,9 @@ export DELTSFC=${DELTSFC:-6}
 export FIXam=${FIXam:-${HOMEgfs}/fix/am}
 export FIXorog=${FIXorog:-${HOMEgfs}/fix/orog}
 
+# temporary - skip global_cycle, until can deal with fractional grids
+SKIP_GCYCLE="YES" 
+
 # FV3 specific info (required for global_cycle)
 export CASE=${CASE:-"C384"}
 ntiles=${ntiles:-6}
@@ -180,13 +183,16 @@ if [[ ${DOIAU} = "YES" ]]; then
         ${NLN} "${FIXorog}/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile${n}.nc"                     "${DATA}/fnorog.00${n}"
     done
 
-    export APRUNCY=${APRUN_CYCLE}
-    export OMP_NUM_THREADS_CY=${NTHREADS_CYCLE}
-    export MAX_TASKS_CY=${ntiles}
-
-    CDATE="${PDY}${cyc}" ${CYCLESH}
-    export err=$?; err_chk
+    # skip calling global_cycle, until fractional grids issues is resolved
+    if [ $SKIP_GCYCLE = "NO" ]; then
+        export APRUNCY=${APRUN_CYCLE}
+        export OMP_NUM_THREADS_CY=${NTHREADS_CYCLE}
+        export MAX_TASKS_CY=${ntiles}
+        CDATE="${PDY}${cyc}" ${CYCLESH}
+        export err=$?; err_chk
+    fi
 fi
+# CSD should above be an else statement? i.e, for IAU do we use the restarts in the middle of the window?
 
 # Update surface restarts at middle of window
 for n in $(seq 1 ${ntiles}); do
@@ -203,12 +209,15 @@ for n in $(seq 1 ${ntiles}); do
     ${NLN} "${FIXorog}/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile${n}.nc"                   "${DATA}/fnorog.00${n}"
 done
 
-export APRUNCY=${APRUN_CYCLE}
-export OMP_NUM_THREADS_CY=${NTHREADS_CYCLE}
-export MAX_TASKS_CY=${ntiles}
+# skip calling global_cycle, until fractional grids issues is resolved
+if [ $SKIP_GCYCLE = "NO" ]; then
+    export APRUNCY=${APRUN_CYCLE}
+    export OMP_NUM_THREADS_CY=${NTHREADS_CYCLE}
+    export MAX_TASKS_CY=${ntiles}
 
-CDATE="${PDY}${cyc}" ${CYCLESH}
-export err=$?; err_chk
+    CDATE="${PDY}${cyc}" ${CYCLESH}
+    export err=$?; err_chk
+fi
 
 
 ################################################################################

ush/forecast_postdet.sh

@@ -33,7 +33,7 @@ FV3_postdet(){
       done
 
       # Replace sfc_data with sfcanl_data restart files from current cycle (if found)
-      if [[ "${MODE}" = "cycled" ]] && [[ "${CCPP_SUITE}" = "FV3_GFS_v16" ]]; then  # TODO: remove if statement when global_cycle can handle NOAHMP
+      if [[ "${MODE}" = "cycled" ]]; then
         for file in "${COM_ATMOS_RESTART}/${sPDY}.${scyc}0000."*.nc; do
           file2=$(basename "${file}")
           file2=$(echo "${file2}" | cut -d. -f3-) # remove the date from file