Merge branch 'develop' into feature/archive_expdir

.gitmodules

@@ -1,7 +1,6 @@
 [submodule "sorc/ufs_model.fd"]
   path = sorc/ufs_model.fd
   url = https://github.com/ufs-community/ufs-weather-model
-  ignore = dirty
 [submodule "sorc/wxflow"]
   path = sorc/wxflow
   url = https://github.com/NOAA-EMC/wxflow

parm/archive/enkf_restartb_grp.yaml.j2

@@ -27,8 +27,11 @@ enkf_restartb_grp:
         {% set r_dt = current_cycle | add_to_datetime(r_timedelta) %}
         {% set r_prefix = r_dt | to_YMD + "." + r_dt | strftime("%H") + "0000" %}
         {% for itile in range(1, 7) %}
-        {% for datatype in ["ca_data", "fv_core.res", "fv_srf_wnd.res", "fv_tracer.res", "phy_data", "sfc_data"] %}
+        {% for datatype in ["fv_core.res", "fv_srf_wnd.res", "fv_tracer.res", "phy_data", "sfc_data"] %}
         - "{{ COMIN_ATMOS_RESTART_MEM | relpath(ROTDIR) }}/{{ r_prefix }}.{{datatype}}.tile{{ itile }}.nc"
+        {% if DO_CA %}
+        - "{{ COMIN_ATMOS_RESTART_MEM | relpath(ROTDIR) }}/{{ r_prefix }}.ca_data.tile{{ itile }}.nc"
+        {% endif %}
         {% endfor %}
         {% endfor %}
         - "{{ COMIN_ATMOS_RESTART_MEM | relpath(ROTDIR) }}/{{ r_prefix }}.coupler.res"

parm/archive/gdas_restartb.yaml.j2

@@ -30,8 +30,11 @@ gdas_restartb:
         {% set r_HH = r_dt | strftime("%H") %}
         {% set r_prefix = r_YMD + "." + r_HH + "0000" %}
         {% for itile in range(1, 7) %}
-        {% for datatype in ["ca_data", "fv_core.res", "fv_srf_wnd.res", "fv_tracer.res", "phy_data", "sfc_data"] %}
+        {% for datatype in ["fv_core.res", "fv_srf_wnd.res", "fv_tracer.res", "phy_data", "sfc_data"] %}
         - "{{ COMIN_ATMOS_RESTART | relpath(ROTDIR) }}/{{ r_prefix }}.{{datatype}}.tile{{ itile }}.nc"
+        {% if DO_CA %}
+        - "{{ COMIN_ATMOS_RESTART | relpath(ROTDIR) }}/{{ r_prefix }}.ca_data.tile{{ itile }}.nc"
+        {% endif %}
         {% endfor %}
         {% endfor %}
         - "{{ COMIN_ATMOS_RESTART | relpath(ROTDIR) }}/{{ r_prefix }}.coupler.res"

parm/config/gefs/config.base

@@ -287,10 +287,17 @@ export DO_MERGENSST="NO"
 export NMEM_ENS=@NMEM_ENS@
 
 # set default member number memdir for control
-# this will be overwritten for the perturbed members
+# this will be overwridden for the perturbed members
 export ENSMEM=${ENSMEM:-"000"}
 export MEMDIR="mem${ENSMEM}"
 
+# cellular automata
+if (( ENSMEM == 0 )); then
+    export DO_CA="YES"
+else
+    export DO_CA="YES"
+fi
+
 export DOIAU="NO"  # While we are not doing IAU, we may want to warm start w/ IAU in the future
 
 # Check if cycle is warm starting with IAU

parm/config/gefs/config.efcs

@@ -44,16 +44,18 @@ export SPPT_TAU="2.16E4,2.592E5,2.592E6,7.776E6,3.1536E7"
 export SPPT_LSCALE="500.E3,1000.E3,2000.E3,2000.E3,2000.E3"
 export SPPT_LOGIT=".true."
 export SPPT_SFCLIMIT=".true."
-export DO_CA="YES"
 # OCN options
-export DO_OCN_SPPT="YES"
-export OCNSPPT="0.8,0.4,0.2,0.08,0.04"
-export OCNSPPT_TAU="2.16E4,2.592E5,2.592E6,7.776E6,3.1536E7"
-export OCNSPPT_LSCALE="500.E3,1000.E3,2000.E3,2000.E3,2000.E3"
-export DO_OCN_PERT_EPBL="YES"
-export EPBL="0.8,0.4,0.2,0.08,0.04"
-export EPBL_TAU="2.16E4,2.592E5,2.592E6,7.776E6,3.1536E7"
-export EPBL_LSCALE="500.E3,1000.E3,2000.E3,2000.E3,2000.E3"
+if (( OCNRES <= 100 )); then
+    # Ocean stochastic options not supported at 5p00
+    export DO_OCN_SPPT="YES"
+    export OCNSPPT="0.8,0.4,0.2,0.08,0.04"
+    export OCNSPPT_TAU="2.16E4,2.592E5,2.592E6,7.776E6,3.1536E7"
+    export OCNSPPT_LSCALE="500.E3,1000.E3,2000.E3,2000.E3,2000.E3"
+    export DO_OCN_PERT_EPBL="YES"
+    export EPBL="0.8,0.4,0.2,0.08,0.04"
+    export EPBL_TAU="2.16E4,2.592E5,2.592E6,7.776E6,3.1536E7"
+    export EPBL_LSCALE="500.E3,1000.E3,2000.E3,2000.E3,2000.E3"
+fi
 
 if [[ "${REPLAY_ICS:-NO}" == "YES" ]]; then
     export ODA_INCUPD="True"

parm/config/gefs/config.fcst

@@ -225,11 +225,12 @@ case ${imp_physics} in
 esac
 
 # Stochastic physics
-export DO_SPPT=${DO_SPPT:-"NO"}
-export DO_SKEB=${DO_SKEB:-"NO"}
-export DO_SHUM=${DO_SHUM:-"NO"}
-export DO_LAND_PERT=${DO_LAND_PERT:-"NO"}
-export DO_CA=${DO_CA:-"YES"}
+export DO_SPPT="NO"
+export DO_SKEB="NO"
+export DO_SHUM="NO"
+export DO_LAND_PERT="NO"
+export DO_OCN_SPPT="NO"
+export DO_OCN_PERT_EPBL="NO"
 
 #coupling settings
 export cplmode="ufs.frac"

parm/config/gfs/config.base

@@ -460,6 +460,9 @@ export INCVARS_EFOLD="5"
 export netcdf_diag=".true."
 export binary_diag=".false."
 
+# Cellular automata
+export DO_CA="YES"
+
 # Verification options
 export DO_METP="@DO_METP@"   # Run METPLUS jobs - set METPLUS settings in config.metp
 export DO_FIT2OBS="YES"      # Run fit to observations package

parm/config/gfs/config.fcst

@@ -245,14 +245,12 @@ case ${imp_physics} in
 esac
 
 # Stochastic physics
-export DO_SPPT=${DO_SPPT:-"NO"}
-export DO_SKEB=${DO_SKEB:-"NO"}
-export DO_SHUM=${DO_SHUM:-"NO"}
-export DO_LAND_PERT=${DO_LAND_PERT:-"NO"}
-export DO_CA=${DO_CA:-"YES"}
-if [[ "${DO_NEST:-NO}" == "YES" ]] ; then
-  export DO_CA="NO"  # CA does not work with nesting.
-fi
+export DO_SPPT="NO"
+export DO_SKEB="NO"
+export DO_SHUM="NO"
+export DO_LAND_PERT="NO"
+export DO_OCN_SPPT="NO"
+export DO_OCN_PERT_EPBL="NO"
 
 #coupling settings
 export cplmode="ufs.frac"

parm/stage/atmosphere_nest.yaml.j2

@@ -11,8 +11,11 @@ atmosphere_nest:
         {% for mem in range(first_mem, last_mem + 1) %}
         {% set imem = mem - first_mem %}
         {% set COMOUT_ATMOS_RESTART_PREV_MEM = COMOUT_ATMOS_RESTART_PREV_MEM_list[imem] %}
-        {% for ftype in ["ca_data", "fv_core.res", "fv_srf_wnd.res", "fv_tracer.res", "phy_data", "sfc_data"] %}
+        {% for ftype in ["fv_core.res", "fv_srf_wnd.res", "fv_tracer.res", "phy_data", "sfc_data"] %}
         - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_RESTART_PREV_MEM | relpath(ROTDIR) }}/{{ m_prefix }}.{{ ftype }}.tile{{ ntile }}.nc", "{{ COMOUT_ATMOS_RESTART_PREV_MEM }}/{{ m_prefix }}.{{ ftype }}.nest0{{ ntile-5 }}.tile{{ ntile }}.nc"]
+        {% if DO_CA %}
+        - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_RESTART_PREV_MEM | relpath(ROTDIR) }}/{{ m_prefix }}.ca_data.tile{{ ntile }}.nc", "{{ COMOUT_ATMOS_RESTART_PREV_MEM }}/{{ m_prefix }}.ca_data.nest0{{ ntile-5 }}.tile{{ ntile }}.nc"]
+        {% endif %}
         {% endfor %}
         {% endfor %} # mem loop
     {% else %} # cold start

parm/stage/atmosphere_warm.yaml.j2

@@ -15,9 +15,12 @@ atmosphere_warm:
         {% for ftype in ["coupler.res", "fv_core.res.nc"] %}
         - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_RESTART_PREV_MEM | relpath(ROTDIR) }}/{{ m_prefix }}.{{ ftype }}", "{{ COMOUT_ATMOS_RESTART_PREV_MEM }}"]
         {% endfor %}
-        {% for ftype in ["ca_data", "fv_core.res", "fv_srf_wnd.res", "fv_tracer.res", "phy_data", "sfc_data"] %}
+        {% for ftype in ["fv_core.res", "fv_srf_wnd.res", "fv_tracer.res", "phy_data", "sfc_data"] %}
         {% for ntile in range(1, ntiles + 1) %}
         - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_RESTART_PREV_MEM | relpath(ROTDIR) }}/{{ m_prefix }}.{{ ftype }}.tile{{ ntile }}.nc", "{{ COMOUT_ATMOS_RESTART_PREV_MEM }}"]
+        {% if DO_CA %}
+        - ["{{ ICSDIR }}/{{ COMOUT_ATMOS_RESTART_PREV_MEM | relpath(ROTDIR) }}/{{ m_prefix }}.ca_data.tile{{ ntile }}.nc", "{{ COMOUT_ATMOS_RESTART_PREV_MEM }}"]
+        {% endif %}
         {% endfor %} # ntile
         {% endfor %} # ftype
         {% for ntile in range(1, ntiles + 1) %}

scripts/exgdas_enkf_earc.py

@@ -25,7 +25,7 @@ def main():
             'lobsdiag_forenkf', 'FHMIN_ENKF', 'FHMAX_ENKF_GFS',
             'FHOUT_ENKF_GFS', 'FHMAX_ENKF', 'FHOUT_ENKF', 'ENKF_SPREAD',
             'restart_interval_enkfgdas', 'restart_interval_enkfgfs',
-            'DOHYBVAR', 'DOIAU_ENKF', 'IAU_OFFSET', 'DOIAU',
+            'DOHYBVAR', 'DOIAU_ENKF', 'IAU_OFFSET', 'DOIAU', 'DO_CA',
             'DO_CALC_INCREMENT', 'assim_freq', 'ARCH_CYC',
             'ARCH_WARMICFREQ', 'ARCH_FCSTICFREQ',
             'IAUFHRS_ENKF', 'NET']

scripts/exglobal_archive.py

@@ -29,7 +29,7 @@ def main():
             'DOIAU', 'OCNRES', 'ICERES', 'NUM_SND_COLLECTIVES', 'FHOUT_WAV',
             'FHOUT_HF_WAV', 'FHMAX_WAV', 'FHMAX_HF_WAV', 'FHMAX_WAV_GFS',
             'restart_interval_gdas', 'restart_interval_gfs',
-            'DO_AERO_ANL', 'DO_AERO_FCST', 'DOIBP_WAV', 'DO_JEDIOCNVAR',
+            'DO_AERO_ANL', 'DO_AERO_FCST', 'DO_CA', 'DOIBP_WAV', 'DO_JEDIOCNVAR',
             'NMEM_ENS', 'DO_JEDIATMVAR', 'DO_VRFY_OCEANDA', 'FHMAX_FITS', 'waveGRD',
             'IAUFHRS', 'DO_FIT2OBS', 'NET', 'FHOUT_HF_GFS', 'FHMAX_HF_GFS', 'REPLAY_ICS',
             'OFFSET_START_HOUR', 'ARCH_EXPDIR', 'EXPDIR', 'ARCH_EXPDIR_FREQ', 'ARCH_HASHES',

scripts/exglobal_stage_ic.py

@@ -22,7 +22,7 @@ def main():
             'assim_freq', 'current_cycle', 'previous_cycle',
             'ROTDIR', 'ICSDIR', 'STAGE_IC_YAML_TMPL', 'DO_JEDIATMVAR',
             'OCNRES', 'waveGRD', 'ntiles', 'DOIAU', 'DO_JEDIOCNVAR',
-            'REPLAY_ICS', 'DO_WAVE', 'DO_OCN', 'DO_ICE', 'DO_NEST',
+            'REPLAY_ICS', 'DO_WAVE', 'DO_OCN', 'DO_ICE', 'DO_NEST', 'DO_CA',
             'USE_ATM_ENS_PERTURB_FILES', 'USE_OCN_ENS_PERTURB_FILES']
 
     stage_dict = AttrDict()

ush/forecast_postdet.sh

@@ -47,7 +47,19 @@ FV3_postdet() {
       || ( echo "FATAL ERROR: Unable to copy FV3 IC, ABORT!"; exit 1 )
     done
 
-    if [[ "${RERUN}" != "YES" ]]; then
+    if [[ "${RERUN}" == "YES" ]]; then
+      if [[ "${DO_SPPT:-}" == "YES" || "${DO_SKEB:-}" == "YES" || \
+            "${DO_SHUM:-}" == "YES" || "${DO_LAND_PERT:-}" == "YES" ]]; then
+        stochini=".true."
+        file_list=$(stoch_restarts)
+        echo "Copying stochastic restarts for 'RUN=${RUN}' at '${restart_date}' from '${restart_dir}'"
+        for stoch_file in $(stoch_restarts); do
+          restart_file="${restart_date:0:8}.${restart_date:8:2}0000.${stoch_file}"
+          ${NCP} "${restart_dir}/${restart_file}" "${DATA}/INPUT/${stoch_file}" \
+          || ( echo "FATAL ERROR: Unable to copy stochastic restart, ABORT!"; exit 1 )
+        done
+      fi
+    else
       # Replace sfc_data with sfcanl_data restart files from current cycle (if found)
       local nn
       for (( nn = 1; nn <= ntiles; nn++ )); do
@@ -78,7 +90,7 @@ FV3_postdet() {
                  "${DATA}/INPUT/fv_tracer.res.tile${nn}.nc"
         done
       fi # if [[ ${use_anl_aero} == "YES" ]]; then
-    fi  # if [[ "${RERUN}" != "YES" ]]; then
+    fi  # if [[ "${RERUN}" == "YES" ]]; then
 
   fi  # if [[ "${warm_start}" == ".true." ]]; then
 

ush/forecast_predet.sh

@@ -57,7 +57,10 @@ FV3_restarts(){
   # Create an array of FV3 restart files
   local fv3_restart_files tile_files
   fv3_restart_files=(coupler.res fv_core.res.nc)
-  tile_files=(fv_core.res fv_srf_wnd.res fv_tracer.res phy_data sfc_data ca_data)
+  tile_files=(fv_core.res fv_srf_wnd.res fv_tracer.res phy_data sfc_data)
+  if [[ ${DO_CA:-"NO"} == "YES" ]]; then
+    tile_files+=(ca_data)
+  fi
   local nn tt
   for (( nn = 1; nn <= ntiles; nn++ )); do
     for tt in "${tile_files[@]}"; do
@@ -68,6 +71,22 @@ FV3_restarts(){
   IFS=, echo "${fv3_restart_files[*]}"
 }
 
+stoch_restarts(){
+  # These only get copied for reruns
+  local stoch_restart_files
+  stoch_restart_files=(  )
+
+  if [[ "${DO_SPPT:-}" == "YES" || "${DO_SKEB:-}" == "YES" || \
+        "${DO_SHUM:-}" == "YES" || "${DO_LAND_PERT:-}" == "YES" ]]; then
+    stoch_restart_files+=(atm_stoch.res.nc)
+  fi
+  if [[ "${DO_OCN:-}" == "YES" && ( "${DO_OCN_SPPT:-}" == "YES" || "${DO_OCN_PERT_EPBL}" == "YES" ) ]]; then
+    stoch_restart_files+=(ocn_stoch.res.nc)
+  fi
+  # Create a comma separated string from array using IFS
+  IFS=, echo "${stoch_restart_files[*]}"
+}
+
 # shellcheck disable=SC2034
 common_predet(){
   echo "SUB ${FUNCNAME[0]}: Defining variables for shared through model components"
@@ -377,41 +396,38 @@ FV3_predet(){
   do_sppt=".false."
   do_ca=".false."
   ISEED=0
-  if (( MEMBER > 0 )); then  # these are only applicable for ensemble members
-    local imem=${MEMBER#0}
-    local base_seed=$((current_cycle*10000 + imem*100))
-
-    if [[ "${DO_SKEB:-}" == "YES" ]]; then
-      do_skeb=".true."
-      ISEED_SKEB=$((base_seed + 1))
-    fi
+  local imem=${MEMBER#0}
+  local base_seed=$((current_cycle*10000 + imem*100))
 
-    if [[ "${DO_SHUM:-}" == "YES" ]]; then
-      do_shum=".true."
-      ISEED_SHUM=$((base_seed + 2))
-    fi
+  if [[ "${DO_SKEB:-}" == "YES" ]]; then
+    do_skeb=".true."
+    ISEED_SKEB=$((base_seed + 1))
+  fi
 
-    if [[ "${DO_SPPT:-}" == "YES" ]]; then
-      do_sppt=".true."
-      ISEED_SPPT=$((base_seed + 3)),$((base_seed + 4)),$((base_seed + 5)),$((base_seed + 6)),$((base_seed + 7))
-    fi
+  if [[ "${DO_SHUM:-}" == "YES" ]]; then
+    do_shum=".true."
+    ISEED_SHUM=$((base_seed + 2))
+  fi
 
-    if [[ "${DO_CA:-}" == "YES" ]]; then
-      do_ca=".true."
-      ISEED_CA=$(( (base_seed + 18) % 2147483647 ))
-    fi
+  if [[ "${DO_SPPT:-}" == "YES" ]]; then
+    do_sppt=".true."
+    ISEED_SPPT=$((base_seed + 3)),$((base_seed + 4)),$((base_seed + 5)),$((base_seed + 6)),$((base_seed + 7))
+  fi
 
-    if [[ "${DO_LAND_PERT:-}" == "YES" ]]; then
-      lndp_type=${lndp_type:-2}
-      ISEED_LNDP=$(( (base_seed + 5) % 2147483647 ))
-      LNDP_TAU=${LNDP_TAU:-21600}
-      LNDP_SCALE=${LNDP_SCALE:-500000}
-      lndp_var_list=${lndp_var_list:-"'smc', 'vgf',"}
-      lndp_prt_list=${lndp_prt_list:-"0.2,0.1"}
-      n_var_lndp=$(echo "${lndp_var_list}" | wc -w)
-    fi
+  if [[ "${DO_CA:-}" == "YES" ]]; then
+    do_ca=".true."
+    ISEED_CA=$(( (base_seed + 18) % 2147483647 ))
+  fi
 
-  fi  # end of ensemble member specific options
+  if [[ "${DO_LAND_PERT:-}" == "YES" ]]; then
+    lndp_type=${lndp_type:-2}
+    ISEED_LNDP=$(( (base_seed + 5) % 2147483647 ))
+    LNDP_TAU=${LNDP_TAU:-21600}
+    LNDP_SCALE=${LNDP_SCALE:-500000}
+    lndp_var_list=${lndp_var_list:-"'smc', 'vgf',"}
+    lndp_prt_list=${lndp_prt_list:-"0.2,0.1"}
+    n_var_lndp=$(echo "${lndp_var_list}" | wc -w)
+  fi
 
   #--------------------------------------------------------------------------
 
@@ -680,17 +696,15 @@ MOM6_predet(){
 
   # If using stochastic parameterizations, create a seed that does not exceed the
   # largest signed integer
-  if (( MEMBER > 0 )); then  # these are only applicable for ensemble members
-    local imem=${MEMBER#0}
-    local base_seed=$((current_cycle*10000 + imem*100))
+  local imem=${MEMBER#0}
+  local base_seed=$((current_cycle*10000 + imem*100))
 
-    if [[ "${DO_OCN_SPPT:-}" == "YES" ]]; then
-      ISEED_OCNSPPT=$((base_seed + 8)),$((base_seed + 9)),$((base_seed + 10)),$((base_seed + 11)),$((base_seed + 12))
-    fi
+  if [[ "${DO_OCN_SPPT:-}" == "YES" ]]; then
+    ISEED_OCNSPPT=$((base_seed + 8)),$((base_seed + 9)),$((base_seed + 10)),$((base_seed + 11)),$((base_seed + 12))
+  fi
 
-    if [[ "${DO_OCN_PERT_EPBL:-}" == "YES" ]]; then
-      ISEED_EPBL=$((base_seed + 13)),$((base_seed + 14)),$((base_seed + 15)),$((base_seed + 16)),$((base_seed + 17))
-    fi
+  if [[ "${DO_OCN_PERT_EPBL:-}" == "YES" ]]; then
+    ISEED_EPBL=$((base_seed + 13)),$((base_seed + 14)),$((base_seed + 15)),$((base_seed + 16)),$((base_seed + 17))
   fi
 
   # Fix files

ush/parsing_namelists_FV3.sh

@@ -656,6 +656,7 @@ if [[ "${DO_SPPT}" = "YES" || "${DO_SHUM}" = "YES" || "${DO_SKEB}" = "YES" || "$
 
     cat >> input.nml << EOF
 &nam_stochy
+  stochini=${stochini:-".false."}
 EOF
 
   if [[ ${DO_SKEB} = "YES" ]]; then