Add initial GSI-based soil analysis capability (#2263)

First set of changes for adding the new soil analysis, from the
assimilation of screen-level T and q. The changes here enable the
screen-level observations to be assimilated in the Hybrid (Var and EnKF)
update, and the soil temperature and soil moisture updates to be made in
the EnKF only. The functionality is turned on by setting GSI_SOILANAL to
YES in config.base.

Resolves #1479

parm/config/gfs/config.anal

@@ -50,6 +50,13 @@ export OZINFO=${FIXgfs}/gsi/global_ozinfo.txt
 export SATINFO=${FIXgfs}/gsi/global_satinfo.txt
 export OBERROR=${FIXgfs}/gsi/prepobs_errtable.global
 
+if [[ ${GSI_SOILANAL} = "YES" ]]; then
+    export hofx_2m_sfcfile=".true."
+    export reducedgrid=".false." # not possible for sfc analysis, Jeff Whitaker says it's not useful anyway
+    export paranc=".false." # temporary until sfc io coded for parance (PR being prepared by T. Gichamo)
+    export CONVINFO=${FIXgfs}/gsi/global_convinfo_2mObs.txt
+    export ANAVINFO=${FIXgfs}/gsi/global_anavinfo_soilanal.l127.txt
+fi
 
 # Use experimental dumps in EMC GFS v16 parallels
 if [[ ${RUN_ENVIR} == "emc" ]]; then

parm/config/gfs/config.base

@@ -331,6 +331,8 @@ fi
 
 if [[ "${DOIAU_ENKF}" = "NO" ]]; then export IAUFHRS_ENKF="6"; fi
 
+export GSI_SOILANAL=@GSI_SOILANAL@
+
 # 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

@@ -12,7 +12,7 @@ echo "BEGIN: config.esfc"
 # Set DOSFCANL_ENKF=NO to prevent creation of sfcanl at 
 # center of analysis window.  
 
-if [ $DOIAU_ENKF = "YES" ]; then
+if [[ ${DOIAU_ENKF} = "YES" ]]; then
    export DOSFCANL_ENKF="NO"
 fi
 
@@ -21,4 +21,10 @@ if [[ "${DO_JEDIATMENS}" == "YES" ]]; then
    export DONST="NO"
 fi
 
+# set up soil analysis
+if [[ ${GSI_SOILANAL} = "YES" ]]; then
+    export DO_LNDINC=".true."
+    export LND_SOI_FILE="lnd_incr"
+fi
+
 echo "END: config.esfc"

parm/config/gfs/yaml/defaults.yaml

@@ -8,6 +8,7 @@ base:
   DO_GOES: "NO"
   FHMAX_GFS: 120
   DO_VRFY_OCEANDA: "NO"
+  GSI_SOILANAL: "NO"
 
 atmanl:
   LAYOUT_X_ATMANL: 8

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=${ntiles:-6}
@@ -61,7 +62,6 @@ export DELTSFC=${DELTSFC:-6}
 APRUN_ESFC=${APRUN_ESFC:-${APRUN:-""}}
 NTHREADS_ESFC=${NTHREADS_ESFC:-${NTHREADS:-1}}
 
-
 ################################################################################
 # Preprocessing
 mkdata=NO
@@ -142,8 +142,10 @@ 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" \
@@ -153,7 +155,12 @@ if [ $DOIAU = "YES" ]; then
             ${NLN} "${FIXgfs}/orog/${CASE}/${CASE}_grid.tile${n}.nc"     "${DATA}/fngrid.${cmem}"
             ${NLN} "${FIXgfs}/orog/${CASE}/${CASE}.mx${OCNRES}_oro_data.tile${n}.nc" "${DATA}/fnorog.${cmem}"
 
-        done
+            if [[ ${GSI_SOILANAL} = "YES" ]]; then
+                FHR=6
+                ${NLN} "${COM_ATMOS_ANALYSIS_MEM}/${APREFIX_ENS}sfci00${FHR}.nc" \
+                   "${DATA}/lnd_incr.${cmem}"
+            fi
+        done # ensembles
 
         CDATE="${PDY}${cyc}" ${CYCLESH}
         export err=$?; err_chk

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_SOILANAL=${GSI_SOILANAL:-"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_SOILANAL = "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
 
@@ -238,10 +247,10 @@ for FHR in $nfhrs; do
    fi
 done
 
-if [ $USE_CFP = "YES" ]; then
+if [[ $USE_CFP = "YES" ]]; then
    chmod 755 $DATA/mp_untar.sh
    ncmd=$(cat $DATA/mp_untar.sh | wc -l)
-   if [ $ncmd -gt 0 ]; then
+   if [[ $ncmd -gt 0 ]]; then
       ncmd_max=$((ncmd < npe_node_max ? ncmd : npe_node_max))
       APRUNCFP=$(eval echo $APRUNCFP)
       $APRUNCFP $DATA/mp_untar.sh
@@ -398,8 +407,8 @@ cat stdout stderr > "${COM_ATMOS_ANALYSIS_STAT}/${ENKFSTAT}"
 
 ################################################################################
 #  Postprocessing
-cd $pwd
-[[ $mkdata = "YES" ]] && rm -rf $DATA
+cd "$pwd"
+[[ $mkdata = "YES" ]] && rm -rf "${DATA}"
 
 
-exit $err
+exit ${err}

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=${OPREFIX:-""}
@@ -748,6 +750,7 @@ cat > gsiparm.anl << EOF
 /
 &OBS_INPUT
   dmesh(1)=145.0,dmesh(2)=150.0,dmesh(3)=100.0,dmesh(4)=50.0,time_window_max=3.0,
+  hofx_2m_sfcfile=${hofx_2m_sfcfile},
   ${OBSINPUT}
 /
 OBS_INPUT::

versions/fix.ver

@@ -12,7 +12,7 @@ export gdas_fv3jedi_ver=20220805
 export gdas_gsibec_ver=20221031
 export gdas_obs_ver=20240213
 export glwu_ver=20220805
-export gsi_ver=20230911
+export gsi_ver=20240208
 export lut_ver=20220805
 export mom6_ver=20231219
 export orog_ver=20231027