Merge remote-tracking branch 'origin/EP5dtest' into SFS

NeilBarton-NOAA · Feb 29, 2024 · 37718c0 · 37718c0
2 parents d3a4927 + 4252ff1
commit 37718c0
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diff --git a/parm/config/gefs/config.efcs b/parm/config/gefs/config.efcs
@@ -43,23 +43,20 @@ export OUTPUT_FILETYPE_ATM="netcdf"
 export OUTPUT_FILETYPE_SFC="netcdf"
 
 # Stochastic physics parameters (only for ensemble forecasts)
+# ATM
 export DO_SKEB="YES"
-export SKEB=0.3
-export SKEB_TAU=21600.
-export SKEB_LSCALE=250000.
-export SKEBNORM=0
-export SKEB_NPASS=30
-export SKEB_VDOF=5
-export DO_SHUM="YES"
-export SHUM=0.005
-export SHUM_TAU=21600.
-export SHUM_LSCALE=500000.
 export DO_SPPT="YES"
-export SPPT=0.5
-export SPPT_TAU=21600.
-export SPPT_LSCALE=500000.
-export SPPT_LOGIT=".true."
-export SPPT_SFCLIMIT=".true."
+export DO_SHUM="NO"
+# OCN
+export DO_OCN_SPPT="YES"
+export DO_OCN_PERT_EPBL="YES"
+export ODA_INCUPD="True"
+export ODA_TEMPINC_VAR='t_pert'
+export ODA_SALTINC_VAR='s_pert'
+export ODA_THK_VAR='h_anl'
+export ODA_UINC_VAR='u_pert'
+export ODA_VINC_VAR='v_pert'
+export ODA_INCUPD_NHOURS=0.0
 
 export restart_interval="${restart_interval_gfs}"
 

diff --git a/parm/config/gefs/config.fcst b/parm/config/gefs/config.fcst
@@ -29,6 +29,9 @@ export FHMAX_HF=${FHMAX_HF_GFS}
 export FHOUT_HF=${FHOUT_HF_GFS}
 export FHOUT_OCNICE=${FHOUT_OCNICE_GFS}
 
+# Turn on the use of wildfire emissions bleneded to climatology
+export BLENDED_WILDFIRE_EMISSIONS=T
+
 # Get task specific resources
 source "${EXPDIR}/config.resources" fcst
 export domains_stack_size="16000000"
@@ -136,7 +139,11 @@ tbp=""
 if [[ "${progsigma}" == ".true." ]]; then tbp="_progsigma" ; fi
 
 # Radiation options
-export IAER=1011    ; #spectral band mapping method for aerosol optical properties
+if [[ "${DO_AERO}" == "YES" ]]; then
+    export IAER=2011    ; #spectral band mapping method for aerosol optical properties
+else
+    export IAER=1011    ; #spectral band mapping method for aerosol optical properties
+fi
 export iovr_lw=3    ; #de-correlation length cloud overlap method (Barker, 2008)
 export iovr_sw=3    ; #de-correlation length cloud overlap method (Barker, 2008)
 export iovr=3       ; #de-correlation length cloud overlap method (Barker, 2008)

diff --git a/parm/config/gefs/config.stage_ic b/parm/config/gefs/config.stage_ic
@@ -8,6 +8,12 @@ echo "BEGIN: config.stage_ic"
 source "${EXPDIR}/config.resources" stage_ic
 
 case "${CASE}" in
+  "C384")
+    export CPL_ATMIC=""
+    export CPL_ICEIC=""
+    export CPL_OCNIC=""
+    export CPL_WAVIC=""
+    ;;
   "C48")
     export CPL_ATMIC="gefs_test"
     export CPL_ICEIC="gefs_test"

diff --git a/parm/config/gefs/config.ufs b/parm/config/gefs/config.ufs
@@ -124,7 +124,7 @@ case "${fv3_res}" in
         export layout_y=8
         export layout_x_gfs=8
         export layout_y_gfs=8
-        export nthreads_fv3=1
+        export nthreads_fv3=2
         export nthreads_fv3_gfs=2
         export cdmbgwd="1.1,0.72,1.0,1.0"  # mountain blocking, ogwd, cgwd, cgwd src scaling
         export cdmbgwd_gsl="5.0,5.0,1.0,1.0"   # settings for GSL drag suite
@@ -315,7 +315,7 @@ if [[ "${skip_mom6}" == "false" ]]; then
       FRUNOFF="runoff.daitren.clim.${NX_GLB}x${NY_GLB}.v20180328.nc"
       CHLCLIM="seawifs-clim-1997-2010.${NX_GLB}x${NY_GLB}.v20180328.nc"
       MOM6_RIVER_RUNOFF='True'
-      MOM6_RESTART_SETTING="r"
+      MOM6_RESTART_SETTING="n"
       eps_imesh="1.0e-1"
       if [[ "${DO_JEDIOCNVAR:-NO}" = "YES" ]]; then
         MOM6_DIAG_COORD_DEF_Z_FILE="oceanda_zgrid_75L.nc"
@@ -374,7 +374,7 @@ if [[ "${skip_cice6}" == "false" ]]; then
       cice6_processor_shape="slenderX2"
       ;;
     "025")
-      ntasks_cice6=120
+      ntasks_cice6=72
       cice6_processor_shape="slenderX2"
       ;;
     *)

diff --git a/parm/config/gefs/yaml/defaults.yaml b/parm/config/gefs/yaml/defaults.yaml
@@ -5,3 +5,5 @@ base:
   DO_JEDISNOWDA: "NO"
   DO_MERGENSST: "NO"
   FHMAX_GFS: 120
+  BASE_CPLIC: "/scratch2/NCEPDEV/stmp3/Neil.Barton/ICs"
+
diff --git a/parm/config/gfs/config.aero b/parm/config/gfs/config.aero
@@ -32,7 +32,7 @@ export AERO_INPUTS_DIR
 
 export AERO_DIAG_TABLE="${HOMEgfs}/parm/ufs/fv3/diag_table.aero"
 export AERO_FIELD_TABLE="${HOMEgfs}/parm/ufs/fv3/field_table.aero"
-# Biomass burning emission dataset. Choose from: gbbepx, qfed, none
+# Biomass burning emission dataset. Choose from: gbbepx, qfed, qfed_blended, none
 export AERO_EMIS_FIRE="qfed"
 # Directory containing GOCART configuration files
 export AERO_CONFIG_DIR="${HOMEgfs}/parm/ufs/gocart"

diff --git a/parm/ufs/gocart/ExtData.qfed_blended b/parm/ufs/gocart/ExtData.qfed_blended
@@ -0,0 +1,8 @@
+#====== BIOMASS BURNING EMISSIONS =======================================
+
+# QFED
+#--------------------------------------------------------------------------------------------------------------------------------
+SU_BIOMASS NA  N Y %y4-%m2-%d2t12:00:00 none 0.7778 SO2 qfed_blended_so2.nc
+OC_BIOMASS NA  N Y %y4-%m2-%d2t12:00:00 none 0.7778 OC  qfed_blended_oc.nc
+BC_BIOMASS NA  N Y %y4-%m2-%d2t12:00:00 none 0.7778 BC qfed_blended_bc.nc
+# EMI_NH3_BB NA  N Y %y4-%m2-%d2t12:00:00 none 0.7778 NH3 qfed_bledned_nh3.nc
diff --git a/scripts/exglobal_stage_ic.sh b/scripts/exglobal_stage_ic.sh
@@ -77,8 +77,10 @@ for MEMDIR in "${MEMDIR_ARRAY[@]}"; do
   if [[ "${DO_OCN:-}" = "YES" ]]; then
     RUN=${rCDUMP} YMD=${gPDY} HH=${gcyc} generate_com COM_OCEAN_RESTART_PREV:COM_OCEAN_RESTART_TMPL
     [[ ! -d "${COM_OCEAN_RESTART_PREV}" ]] && mkdir -p "${COM_OCEAN_RESTART_PREV}"
-    src="${BASE_CPLIC}/${CPL_OCNIC:-}/${PDY}${cyc}/${MEMDIR}/ocean/${PDY}.${cyc}0000.MOM.res.nc"
-    tgt="${COM_OCEAN_RESTART_PREV}/${PDY}.${cyc}0000.MOM.res.nc"
+    #src="${BASE_CPLIC}/${CPL_OCNIC:-}/${PDY}${cyc}/${MEMDIR}/ocean/${PDY}.${cyc}0000.MOM.res.nc"
+    #tgt="${COM_OCEAN_RESTART_PREV}/${PDY}.${cyc}0000.MOM.res.nc"
+    src="${BASE_CPLIC}/${CPL_OCNIC:-}/${PDY}${cyc}/${MEMDIR}/ocean/ORAS5.mx${OCNRES}.ic.nc"
+    tgt="${COM_OCEAN_RESTART_PREV}/ORAS5.mx${OCNRES}.ic.nc"
     ${NCP} "${src}" "${tgt}"
     rc=$?
     ((rc != 0)) && error_message "${src}" "${tgt}" "${rc}"
@@ -88,21 +90,31 @@ for MEMDIR in "${MEMDIR_ARRAY[@]}"; do
         # Nothing more to do for these resolutions
         ;;
       "025" )
-        for nn in $(seq 1 3); do
-          src="${BASE_CPLIC}/${CPL_OCNIC:-}/${PDY}${cyc}/${MEMDIR}/ocean/${PDY}.${cyc}0000.MOM.res_${nn}.nc"
-          tgt="${COM_OCEAN_RESTART_PREV}/${PDY}.${cyc}0000.MOM.res_${nn}.nc"
-          ${NCP} "${src}" "${tgt}"
-          rc=$?
-          ((rc != 0)) && error_message "${src}" "${tgt}" "${rc}"
-          err=$((err + rc))
-        done
+        # Nothing to do for ORAS5 initialization
+        #for nn in $(seq 1 3); do
+        #  src="${BASE_CPLIC}/${CPL_OCNIC:-}/${PDY}${cyc}/${MEMDIR}/ocean/${PDY}.${cyc}0000.MOM.res_${nn}.nc"
+        #  tgt="${COM_OCEAN_RESTART_PREV}/${PDY}.${cyc}0000.MOM.res_${nn}.nc"
+        #  ${NCP} "${src}" "${tgt}"
+        #  rc=$?
+        #  ((rc != 0)) && error_message "${src}" "${tgt}" "${rc}"
+        #  err=$((err + rc))
+        #done
         ;;
       *)
         echo "FATAL ERROR: Unsupported ocean resolution ${OCNRES}"
         rc=1
         err=$((err + rc))
         ;;
     esac
+
+    # Ocean Perturbation Files
+    if [[ "${MEMDIR}" != "mem000" ]]; then
+        src="${BASE_CPLIC}/${CPL_OCNIC:-}/${PDY}${cyc}/${MEMDIR}/ocean/${PDY}.${cyc}0000.mom6_increment.nc"
+        tgt="${COM_OCEAN_RESTART_PREV}/${PDY}.${cyc}0000.mom6_increment.nc"
+        ${NCP} "${src}" "${tgt}"
+        rc=$?
+        ((rc != 0)) && error_message "${src}" "${tgt}" "${rc}"
+    fi
 
     # TODO: Do mediator restarts exists in a ATMW configuration?
     # TODO: No mediator is presumably involved in an ATMA configuration

diff --git a/ush/forecast_postdet.sh b/ush/forecast_postdet.sh
@@ -240,12 +240,12 @@ EOF
       MM=$(printf %02d "${month}")
       ${NLN} "${FIXgfs}/aer/merra2.aerclim.2003-2014.m${MM}.nc" "aeroclim.m${MM}.nc"
     done
-    ${NLN} "${FIXgfs}/lut/optics_BC.v1_3.dat"  "${DATA}/optics_BC.dat"
-    ${NLN} "${FIXgfs}/lut/optics_OC.v1_3.dat"  "${DATA}/optics_OC.dat"
-    ${NLN} "${FIXgfs}/lut/optics_DU.v15_3.dat" "${DATA}/optics_DU.dat"
-    ${NLN} "${FIXgfs}/lut/optics_SS.v3_3.dat"  "${DATA}/optics_SS.dat"
-    ${NLN} "${FIXgfs}/lut/optics_SU.v1_3.dat"  "${DATA}/optics_SU.dat"
   fi
+  ${NLN} "${FIXlut}/optics_BC.v1_3.dat"  "${DATA}/optics_BC.dat"
+  ${NLN} "${FIXlut}/optics_OC.v1_3.dat"  "${DATA}/optics_OC.dat"
+  ${NLN} "${FIXlut}/optics_DU.v15_3.dat" "${DATA}/optics_DU.dat"
+  ${NLN} "${FIXlut}/optics_SS.v3_3.dat"  "${DATA}/optics_SS.dat"
+  ${NLN} "${FIXlut}/optics_SU.v1_3.dat"  "${DATA}/optics_SU.dat"
 
   ${NLN} "${FIXgfs}/am/global_co2historicaldata_glob.txt" "${DATA}/co2historicaldata_glob.txt"
   ${NLN} "${FIXgfs}/am/co2monthlycyc.txt"                 "${DATA}/co2monthlycyc.txt"
@@ -431,23 +431,45 @@ EOF
 
   # Stochastic Physics Options
   if [[ ${SET_STP_SEED:-"YES"} = "YES" ]]; then
-    ISEED_SKEB=$((current_cycle*1000 + MEMBER*10 + 1))
+    ISEED_SPPT=$((CDATE*10000 + ${MEMBER#0}*100 + 3)),$((CDATE*10000 + ${MEMBER#0}*100 + 4)),$((CDATE*10000 + ${MEMBER#0}*100 + 5)),$((CDATE*10000 + ${MEMBER#0}*100 + 6)),$((CDATE*10000 + ${MEMBER#0}*100 + 7))
+    ISEED_CA=$(( (CDATE*10000 + ${MEMBER#0}*100 + 18) % 2147483647 )) 
+    ISEED_SKEB=$((current_cycle*1000 + MEMBER*10 +1))
     ISEED_SHUM=$((current_cycle*1000 + MEMBER*10 + 2))
-    ISEED_SPPT=$((current_cycle*1000 + MEMBER*10 + 3))
-    ISEED_CA=$(( (current_cycle*1000 + MEMBER*10 + 4) % 2147483647 ))
     ISEED_LNDP=$(( (current_cycle*1000 + MEMBER*10 + 5) % 2147483647 ))
   else
     ISEED=${ISEED:-0}
   fi
   if [[ ${DO_SKEB} = "YES" ]]; then
     do_skeb=".true."
+    SKEB=${SKEB:-0.8,-999,-999,-999,-999}
+    iseed_skeb=${ISEED_SKEB}
+    SKEB_TAU=${SKEB_TAU:-2.16E4,1.728E5,2.592E6,7.776E6,3.1536E7}
+    SKEB_LSCALE=${SKEB_LSCALE:-500.E3,1000.E3,2000.E3,2000.E3,2000.E3}
+    SKEBNORM=${SKEBNORM:-1}
   fi
   if [[ ${DO_SPPT} = "YES" ]]; then
     do_sppt=".true."
+    SPPT=${SPPT:-0.56,0.28,0.14,0.056,0.028}
+    iseed_sppt=${ISEED_SPPT}
+    SPPT_TAU=${SPPT_TAU:-2.16E4,2.592E5,2.592E6,7.776E6,3.1536E7}
+    SPPT_LSCALE=${SPPT_LSCALE:-500.E3,1000.E3,2000.E3,2000.E3,2000.E3}
+    sppt_logit=.TRUE.
+    sppt_sfclimit=.true.
+    use_zmtnlck=.true.
   fi
   if [[ ${DO_SHUM} = "YES" ]]; then
     do_shum=".true."
   fi
+  if [[ ${DO_OCN_SPPT} = "YES" ]]; then
+    OCNSPPT=${OCNSPPT:-0.8,0.4,0.2,0.08,0.04}
+    OCNSPPT_TAU=${OCNSPPT_TAU:-2.16E4,2.592E5,2.592E6,7.776E6,3.1536E7}
+    OCNSPPT_LSCALE=${OCNSPPT_LSCALE:-500.E3,1000.E3,2000.E3,2000.E3,2000.E3}
+  fi
+  if [[ ${DO_OCN_PERT_EPBL} = "YES" ]]; then
+    EPBL=${EPBL:-0.8,0.4,0.2,0.08,0.04}
+    EPBL_TAU=${EPBL_TAU:-2.16E4,2.592E5,2.592E6,7.776E6,3.1536E7}
+    EPBL_LSCALE=${EPBL_LSCALE:-500.E3,1000.E3,2000.E3,2000.E3,2000.E3}
+  fi
   if [[ ${DO_LAND_PERT} = "YES" ]]; then
     lndp_type=${lndp_type:-2}
     LNDP_TAU=${LNDP_TAU:-21600}
@@ -672,17 +694,17 @@ MOM6_postdet() {
   echo "SUB ${FUNCNAME[0]}: MOM6 after run type determination"
 
   # Copy MOM6 ICs
-  ${NLN} "${COM_OCEAN_RESTART_PREV}/${sPDY}.${scyc}0000.MOM.res.nc" "${DATA}/INPUT/MOM.res.nc"
-  case ${OCNRES} in
-    "025")
-      local nn
-      for nn in $(seq 1 4); do
-        if [[ -f "${COM_OCEAN_RESTART_PREV}/${sPDY}.${scyc}0000.MOM.res_${nn}.nc" ]]; then
-          ${NLN} "${COM_OCEAN_RESTART_PREV}/${sPDY}.${scyc}0000.MOM.res_${nn}.nc" "${DATA}/INPUT/MOM.res_${nn}.nc"
-        fi
-      done
-    ;;
-  esac
+  ${NLN} "${COM_OCEAN_RESTART_PREV}/ORAS5.mx${OCNRES}.ic.nc" "${DATA}/INPUT/ORAS5.mx${OCNRES}.ic.nc"
+  #${NLN} "${COM_OCEAN_RESTART_PREV}/${sPDY}.${scyc}0000.MOM.res.nc" "${DATA}/INPUT/MOM.res.nc"
+  #case ${OCNRES} in
+  #  "025")
+  #    for nn in $(seq 1 4); do
+  #      if [[ -f "${COM_OCEAN_RESTART_PREV}/${sPDY}.${scyc}0000.MOM.res_${nn}.nc" ]]; then
+  #        ${NLN} "${COM_OCEAN_RESTART_PREV}/${sPDY}.${scyc}0000.MOM.res_${nn}.nc" "${DATA}/INPUT/MOM.res_${nn}.nc"
+  #      fi
+  #    done
+  #  ;;
+  #esac
 
   # Link increment
   if [[ "${DO_JEDIOCNVAR:-NO}" = "YES" ]]; then
@@ -693,6 +715,10 @@ MOM6_postdet() {
       ${NLN} "${COM_OCEAN_ANALYSIS}/${RUN}.t${cyc}z.ocninc.nc" "${DATA}/INPUT/mom6_increment.nc"
   fi
 
+  if [[ "${DO_OCN_SPPT}" == "YES" ]]; then
+    ${NLN} "${COM_OCEAN_RESTART_PREV}/${sPDY}.${scyc}0000.mom6_increment.nc" "${DATA}/INPUT/mom6_increment.nc"
+  fi
+
   # Copy MOM6 fixed files
   ${NCP} "${FIXgfs}/mom6/${OCNRES}/"* "${DATA}/INPUT/"  # TODO: These need to be explicit
 
@@ -709,8 +735,8 @@ MOM6_postdet() {
   # largest signed integer
   if [[ "${DO_OCN_SPPT}" = "YES" ]] || [[ "${DO_OCN_PERT_EPBL}" = "YES" ]]; then
     if [[ ${SET_STP_SEED:-"YES"} = "YES" ]]; then
-      ISEED_OCNSPPT=$(( (current_cycle*1000 + MEMBER*10 + 6) % 2147483647 ))
-      ISEED_EPBL=$(( (current_cycle*1000 + MEMBER*10 + 7) % 2147483647 ))
+      ISEED_OCNSPPT=$((CDATE*10000 + ${MEMBER#0}*100 + 8)),$((CDATE*10000 + ${MEMBER#0}*100 + 9)),$((CDATE*10000 + ${MEMBER#0}*100 + 10)),$((CDATE*10000 + ${MEMBER#0}*100 + 11)),$((CDATE*10000 + ${MEMBER#0}*100 + 12))
+      ISEED_EPBL=$((CDATE*10000 + ${MEMBER#0}*100 + 13)),$((CDATE*10000 + ${MEMBER#0}*100 + 14)),$((CDATE*10000 + ${MEMBER#0}*100 + 15)),$((CDATE*10000 + ${MEMBER#0}*100 + 16)),$((CDATE*10000 + ${MEMBER#0}*100 + 17))
     else
       ISEED=${ISEED:-0}
     fi
@@ -924,6 +950,15 @@ GOCART_rc() {
       if (( status != 0 )); then exit "${status}"; fi
     fi
   fi
+
+  if [[ ${BLENDED_WILDFIRE_EMISSIONS} == T ]]; then
+    fire_org='qfed_blended_so2.nc'
+    sed -i "s:${fire_org}:${fire_out}:g" ${DATA}/AERO_ExtData.rc
+    fire_org='qfed_blended_oc.nc'
+    sed -i "s:${fire_org}:${fire_out}:g" ${DATA}/AERO_ExtData.rc
+    fire_org='qfed_blended_bc.nc'
+    sed -i "s:${fire_org}:${fire_out}:g" ${DATA}/AERO_ExtData.rc
+  fi
 }
 
 GOCART_postdet() {
@@ -937,6 +972,19 @@ GOCART_postdet() {
       rm -f "${COM_CHEM_HISTORY}/gocart.inst_aod.${vdate:0:8}_${vdate:8:2}00z.nc4"
     fi
 
+    # Blended Wildire Emissions
+    BLENDED_WILDFIRE_EMISSIONS=${BLENDED_WILDFIRE_EMISSIONS:-F}
+    if [[ ${BLENDED_WILDFIRE_EMISSIONS} == T ]]; then
+        local EMISSION_DIR=${AERO_INPUTS_DIR}/nexus/GBBEPx/v4/climMean
+        local fhmax_day=$(( ${FHMAX_GFS} / 24 ))
+        local fire_in="${AERO_INPUTS_DIR}/nexus/QFED/${vdate:0:4}/${vdate:4:2}/qfed2.emis_*.${PDY}.nc4"
+        fire_out="${COM_TOP}/${MEMDIR}/model_data/chem/input/QFED_Blended_${PDY}_${fhmax_day}.nc"
+        if [[ ! -f ${fire_out} ]]; then
+            mkdir -p $(dirname ${fire_out})
+            ${HOMEgfs}/ush/gefs_fireclimo_blend.py -s ${PDY} -n ${fhmax_day} -c ${EMISSION_DIR} -f ${fire_in} -o ${fire_out} -r 0.95    
+        fi
+    fi
+
     #To Do: Temporarily removing this as this will crash gocart, adding copy statement at the end
     #${NLN} "${COM_CHEM_HISTORY}/gocart.inst_aod.${vdate:0:8}_${vdate:8:2}00z.nc4" \
     #       "${DATA}/gocart.inst_aod.${vdate:0:8}_${vdate:8:2}00z.nc4"