Add cycle-specific stochastics namelists (NOAA-EMC#430)

* Add cycle-specific stochastics namelists * Update exregional_run_fcst.sh
EricJames-NOAA · Oct 8, 2022 · 2aa29cd · 2aa29cd
1 parent 9c04aca
commit 2aa29cd
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Showing 7 changed files with 194 additions and 108 deletions.
diff --git a/scripts/exregional_run_fcst.sh b/scripts/exregional_run_fcst.sh
@@ -493,22 +493,50 @@ ln_vrfy -sf ${relative_or_null} ${FIELD_TABLE_FP} ${run_dir}
 ln_vrfy -sf ${relative_or_null} ${NEMS_CONFIG_FP} ${run_dir}
 ln_vrfy -sf ${relative_or_null} ${NEMS_YAML_FP} ${run_dir}
 
+#
+# Determine if running stochastic physics for the specified cycles in CYCL_HRS_STOCH
+#
+STOCH="FALSE"
+if [ "${DO_ENSEMBLE}" = TRUE ] && ([ "${DO_SPP}" = TRUE ] || [ "${DO_SPPT}" = TRUE ] || [ "${DO_SHUM}" = TRUE ] \
+  || [ "${DO_SKEB}" = TRUE ] || [ "${DO_LSM_SPP}" =  TRUE ]); then
+   for cyc_start in "${CYCL_HRS_STOCH[@]}"; do
+     if [ ${HH} -eq ${cyc_start} ]; then 
+       if [ "${DO_ENSFCST}" = TRUE ]; then
+         if [ ${cycle_type} == "ensfcst" ]; then 
+           STOCH="TRUE"
+         else
+           STOCH="FALSE"
+         fi
+       else
+         STOCH="TRUE"
+       fi
+     fi
+   done
+fi
+
 if [ ${BKTYPE} -eq 0 ]; then
   # cycling, using namelist for cycling forecast
-  cp_vrfy ${FV3_NML_RESTART_FP} ${run_dir}/input.nml
+  if [ "${STOCH}" == "TRUE" ]; then
+    cp_vrfy ${FV3_NML_RESTART_STOCH_FP} ${run_dir}/${FV3_NML_FN}
+   else
+    cp_vrfy ${FV3_NML_RESTART_FP} ${run_dir}/${FV3_NML_FN}
+  fi
 else
   if [ -f "INPUT/cycle_surface.done" ]; then
   # namelist for cold start with surface cycle
-    cp_vrfy ${FV3_NML_CYCSFC_FP} ${run_dir}/input.nml
+    cp_vrfy ${FV3_NML_CYCSFC_FP} ${run_dir}/${FV3_NML_FN}
   else
   # cold start, using namelist for cold start
-    cp_vrfy ${FV3_NML_FP} ${run_dir}/input.nml
+    if [ "${STOCH}" == "TRUE" ]; then
+      cp_vrfy ${FV3_NML_STOCH_FP} ${run_dir}/${FV3_NML_FN}
+     else
+      cp_vrfy ${FV3_NML_FP} ${run_dir}/${FV3_NML_FN}
+    fi
   fi
 fi
 
-if [ "${DO_ENSEMBLE}" = TRUE ] && ([ "${DO_SPP}" = TRUE ] || [ "${DO_SPPT}" = TRUE ] || [ "${DO_SHUM}" = TRUE ] \
-   [ "${DO_SKEB}" = TRUE ] || [ "${DO_LSM_SPP}" =  TRUE ]); then
-  cp ${run_dir}/input.nml ${run_dir}/input.nml_base
+if [ "${STOCH}" == "TRUE" ]; then
+  cp ${run_dir}/${FV3_NML_FN} ${run_dir}/${FV3_NML_FN}_base
   set_FV3nml_ens_stoch_seeds cdate="$cdate" || print_err_msg_exit "\
  Call to function to create the ensemble-based namelist for the current 
  cycle's (cdate) run directory (run_dir) failed: 

diff --git a/ush/config.sh.RRFS_CONUS_3km_ens b/ush/config.sh.RRFS_CONUS_3km_ens
@@ -89,6 +89,7 @@ CYCL_HRS_PRODSTART=("09" "21")
 CYCL_HRS_PRODSTART=("18")
 CYCL_HRS_ENSINIT=("18")
 CYCL_HRS_ENSFCST=("00")
+CYCL_HRS_STOCH=("00")
 #CYCL_HRS_RECENTER=("19")
 #CYCLEMONTH="5"
 #CYCLEDAY="11-12"
@@ -211,7 +212,7 @@ fi
 if [[ ${DO_ENSEMBLE}  == "TRUE" ]]; then
    NUM_ENS_MEMBERS=30
 #   DO_SPPT=TRUE
-#   DO_SPP=TRUE
+   DO_SPP=TRUE
 #   SPPT_MAG=0.5
 #   DO_ENSCONTROL="TRUE"
    DO_GSIOBSERVER="TRUE"

diff --git a/ush/config_defaults.sh b/ush/config_defaults.sh
@@ -488,6 +488,10 @@ WFLOW_LAUNCH_LOG_FN="log.launch_FV3LAM_wflow"
 # CYCL_HRS_ENSFCST
 # An array containing the hours of the day at which the ensemble free forecast is on
 #
+# CYCL_HRS_STOCH
+# An array containing the hours of the day at which the stochastics physcis is on
+# this might include: SPPT, SHUM, SKEB, SPP, LSM_SPP
+#
 # BOUNDARY_LEN_HRS
 # The length of boundary condition for normal forecast, in integer hours.
 #
@@ -533,6 +537,7 @@ CYCL_HRS_PRODSTART=( "HH1" "HH2" )
 CYCL_HRS_RECENTER=( "HH1" "HH2" )
 CYCL_HRS_ENSINIT=( "HH1" "HH2" )
 CYCL_HRS_ENSFCST=( "HH1" "HH2" )
+CYCL_HRS_STOCH=( "HH1" "HH2" )
 BOUNDARY_LEN_HRS="0"
 BOUNDARY_LONG_LEN_HRS="0"
 POSTPROC_LEN_HRS="1"

diff --git a/ush/generate_FV3LAM_wflow.sh b/ush/generate_FV3LAM_wflow.sh
@@ -413,6 +413,7 @@ settings="\
   'cycl_hrs_recenter': [ $( printf "\'%s\', " "${CYCL_HRS_RECENTER[@]}" ) ]
   'cycl_hrs_ensinit': [ $( printf "\'%s\', " "${CYCL_HRS_ENSINIT[@]}" ) ]
   'cycl_hrs_ensfcst': [ $( printf "\'%s\', " "${CYCL_HRS_ENSFCST[@]}" ) ]
+  'cycl_hrs_stoch': [ $( printf "\'%s\', " "${CYCL_HRS_STOCH[@]}" ) ]
   'cycl_hrs_hyb_fv3lam_ens': [ $( printf "\'%s\', " "${CYCL_HRS_HYB_FV3LAM_ENS[@]}" ) ]
   'restart_hrs_prod': ${RESTART_INTERVAL}
   'cycl_freq': !!str 12:00:00
@@ -835,15 +836,6 @@ settings="\
 'gfs_physics_nml': {
     'kice': ${kice:-null},
     'lsoil': ${lsoil:-null},
-    'do_shum': ${DO_SHUM},
-    'do_sppt': ${DO_SPPT},
-    'do_skeb': ${DO_SKEB},
-    'do_spp': ${DO_SPP},
-    'n_var_spp': ${N_VAR_SPP},
-    'n_var_lndp': ${N_VAR_LNDP},
-    'lndp_type': ${LNDP_TYPE},
-    'lndp_each_step': ${LSM_SPP_EACH_STEP},
-    'fhcyc': ${FHCYC_LSM_SPP_OR_NOT},
     'print_diff_pgr': ${PRINT_DIFF_PGR},
   }"
 #
@@ -901,96 +893,6 @@ done
 settings="$settings
   }"
 #
-# Add the relevant tendency-based stochastic physics namelist variables to
-# "settings" when running with SPPT, SHUM, or SKEB turned on. If running 
-# with SPP or LSM SPP, set the "new_lscale" variable.  Otherwise only 
-# include an empty "nam_stochy" stanza. 
-#
-settings="$settings
-'nam_stochy': {"
-if [ "${DO_SPPT}" = "TRUE" ]; then 
-    settings="$settings
-    'iseed_sppt': ${ISEED_SPPT},
-    'new_lscale': ${NEW_LSCALE},
-    'sppt': ${SPPT_MAG},
-    'sppt_logit': ${SPPT_LOGIT},
-    'sppt_lscale': ${SPPT_LSCALE},
-    'sppt_sfclimit': ${SPPT_SFCLIMIT},
-    'sppt_tau': ${SPPT_TSCALE},
-    'spptint': ${SPPT_INT},
-    'use_zmtnblck': ${USE_ZMTNBLCK},"
-fi
-
-if [ "${DO_SHUM}" = "TRUE" ]; then 
-    settings="$settings
-    'iseed_shum': ${ISEED_SHUM},
-    'new_lscale': ${NEW_LSCALE},
-    'shum': ${SHUM_MAG},
-    'shum_lscale': ${SHUM_LSCALE},
-    'shum_tau': ${SHUM_TSCALE},
-    'shumint': ${SHUM_INT},"
-fi
-
-if [ "${DO_SKEB}" = "TRUE" ]; then
-    settings="$settings
-    'iseed_skeb': ${ISEED_SKEB},
-    'new_lscale': ${NEW_LSCALE},
-    'skeb': ${SKEB_MAG},
-    'skeb_lscale': ${SKEB_LSCALE},
-    'skebnorm': ${SKEBNORM},
-    'skeb_tau': ${SKEB_TSCALE},
-    'skebint': ${SKEB_INT},
-    'skeb_vdof': ${SKEB_VDOF},"
-fi
-
-if [ "${DO_SPP}" = "TRUE" ] || [ "${DO_LSM_SPP}" = "TRUE" ]; then
-    settings="$settings
-    'new_lscale': ${NEW_LSCALE},"
-fi
-settings="$settings
-  }"
-#
-# Add the relevant SPP namelist variables to "settings" when running with
-# SPP turned on.  Otherwise only include an empty "nam_sppperts" stanza.
-#
-settings="$settings
-'nam_sppperts': {"
-if [ "${DO_SPP}" = "TRUE" ]; then
-    settings="$settings
-    'iseed_spp': [ $( printf "%s, " "${ISEED_SPP[@]}" ) ],
-    'spp_lscale': [ $( printf "%s, " "${SPP_LSCALE[@]}" ) ],
-    'spp_prt_list': [ $( printf "%s, " "${SPP_MAG_LIST[@]}" ) ],
-    'spp_sigtop1': [ $( printf "%s, " "${SPP_SIGTOP1[@]}" ) ],
-    'spp_sigtop2': [ $( printf "%s, " "${SPP_SIGTOP2[@]}" ) ],
-    'spp_stddev_cutoff': [ $( printf "%s, " "${SPP_STDDEV_CUTOFF[@]}" ) ],
-    'spp_tau': [ $( printf "%s, " "${SPP_TSCALE[@]}" ) ],
-    'spp_var_list': [ $( printf "%s, " "${SPP_VAR_LIST[@]}" ) ],"
-fi
-settings="$settings
-  }"
-#
-# Add the relevant LSM SPP namelist variables to "settings" when running with
-# LSM SPP turned on.
-#
-settings="$settings
-'nam_sfcperts': {"
-if [ "${DO_LSM_SPP}" = "TRUE" ]; then
-    settings="$settings
-    'lndp_type': ${LNDP_TYPE},
-    'lndp_tau': [ $( printf "%s, " "${LSM_SPP_TSCALE[@]}" ) ],
-    'lndp_lscale': [ $( printf "%s, " "${LSM_SPP_LSCALE[@]}" ) ],
-    'iseed_lndp': [ $( printf "%s, " "${ISEED_LSM_SPP[@]}" ) ],
-    'lndp_var_list': [ $( printf "%s, " "${LSM_SPP_VAR_LIST[@]}" ) ],
-    'lndp_prt_list': [ $( printf "%s, " "${LSM_SPP_MAG_LIST[@]}" ) ],"
-fi
-settings="$settings
-  }"
-print_info_msg $VERBOSE "
-The variable \"settings\" specifying values of the namelist variables
-has been set as follows:
-
-settings =
-$settings"
 #
 #-----------------------------------------------------------------------
 #
@@ -1115,6 +1017,149 @@ if [[ "${DO_DACYCLE}" = "TRUE" || "${DO_ENKFUPDATE}" = "TRUE" ]]; then
    Namelist settings specified on command line:
      settings =
  $settings"
+fi
+#
+# Add the relevant tendency-based stochastic physics namelist variables to
+# "settings" when running with SPPT, SHUM, or SKEB turned on. If running 
+# with SPP or LSM SPP, set the "new_lscale" variable.  Otherwise only 
+# include an empty "nam_stochy" stanza. 
+#
+settings="\
+'gfs_physics_nml': {
+    'do_shum': ${DO_SHUM},
+    'do_sppt': ${DO_SPPT},
+    'do_skeb': ${DO_SKEB},
+    'do_spp': ${DO_SPP},
+    'n_var_spp': ${N_VAR_SPP},
+    'n_var_lndp': ${N_VAR_LNDP},
+    'lndp_type': ${LNDP_TYPE},
+    'lndp_each_step': ${LSM_SPP_EACH_STEP},
+    'fhcyc': ${FHCYC_LSM_SPP_OR_NOT},
+  }"
+settings="$settings
+'nam_stochy': {"
+if [ "${DO_SPPT}" = "TRUE" ]; then 
+    settings="$settings
+    'iseed_sppt': ${ISEED_SPPT},
+    'sppt': ${SPPT_MAG},
+    'sppt_logit': ${SPPT_LOGIT},
+    'sppt_lscale': ${SPPT_LSCALE},
+    'sppt_sfclimit': ${SPPT_SFCLIMIT},
+    'sppt_tau': ${SPPT_TSCALE},
+    'spptint': ${SPPT_INT},
+    'use_zmtnblck': ${USE_ZMTNBLCK},"
+fi
+
+if [ "${DO_SHUM}" = "TRUE" ]; then 
+    settings="$settings
+    'iseed_shum': ${ISEED_SHUM},
+    'shum': ${SHUM_MAG},
+    'shum_lscale': ${SHUM_LSCALE},
+    'shum_tau': ${SHUM_TSCALE},
+    'shumint': ${SHUM_INT},"
+fi
+
+if [ "${DO_SKEB}" = "TRUE" ]; then
+    settings="$settings
+    'iseed_skeb': ${ISEED_SKEB},
+    'skeb': ${SKEB_MAG},
+    'skeb_lscale': ${SKEB_LSCALE},
+    'skebnorm': ${SKEBNORM},
+    'skeb_tau': ${SKEB_TSCALE},
+    'skebint': ${SKEB_INT},
+    'skeb_vdof': ${SKEB_VDOF},"
+fi
+
+if [ "${DO_SPP}" = "TRUE" ] || [ "${DO_LSM_SPP}" = "TRUE" ] || [ "${DO_SPPT}" = "TRUE" ] || [ "${DO_SHUM}" = "TRUE" ] || [ "${DO_SKEB}" = "TRUE" ]; then
+    settings="$settings
+    'new_lscale': ${NEW_LSCALE},"
+fi
+settings="$settings
+  }"
+#
+# Add the relevant SPP namelist variables to "settings" when running with
+# SPP turned on.  Otherwise only include an empty "nam_sppperts" stanza.
+#
+settings="$settings
+'nam_sppperts': {"
+if [ "${DO_SPP}" = "TRUE" ]; then
+    settings="$settings
+    'iseed_spp': [ $( printf "%s, " "${ISEED_SPP[@]}" ) ],
+    'spp_lscale': [ $( printf "%s, " "${SPP_LSCALE[@]}" ) ],
+    'spp_prt_list': [ $( printf "%s, " "${SPP_MAG_LIST[@]}" ) ],
+    'spp_sigtop1': [ $( printf "%s, " "${SPP_SIGTOP1[@]}" ) ],
+    'spp_sigtop2': [ $( printf "%s, " "${SPP_SIGTOP2[@]}" ) ],
+    'spp_stddev_cutoff': [ $( printf "%s, " "${SPP_STDDEV_CUTOFF[@]}" ) ],
+    'spp_tau': [ $( printf "%s, " "${SPP_TSCALE[@]}" ) ],
+    'spp_var_list': [ $( printf "%s, " "${SPP_VAR_LIST[@]}" ) ],"
+fi
+settings="$settings
+  }"
+#
+# Add the relevant LSM SPP namelist variables to "settings" when running with
+# LSM SPP turned on.
+#
+settings="$settings
+'nam_sfcperts': {"
+if [ "${DO_LSM_SPP}" = "TRUE" ]; then
+    settings="$settings
+    'lndp_type': ${LNDP_TYPE},
+    'lndp_tau': [ $( printf "%s, " "${LSM_SPP_TSCALE[@]}" ) ],
+    'lndp_lscale': [ $( printf "%s, " "${LSM_SPP_LSCALE[@]}" ) ],
+    'iseed_lndp': [ $( printf "%s, " "${ISEED_LSM_SPP[@]}" ) ],
+    'lndp_var_list': [ $( printf "%s, " "${LSM_SPP_VAR_LIST[@]}" ) ],
+    'lndp_prt_list': [ $( printf "%s, " "${LSM_SPP_MAG_LIST[@]}" ) ],"
+fi
+settings="$settings
+  }"
+print_info_msg $VERBOSE "
+The variable \"settings\" specifying values of the namelist variables
+has been set as follows:
+
+settings =
+$settings"
+#
+#-----------------------------------------------------------------------
+#
+# Generate namelist files with stochastic physics if needed
+#
+if [ "${DO_ENSEMBLE}" = TRUE ] && ([ "${DO_SPP}" = TRUE ] || [ "${DO_SPPT}" = TRUE ] || [ "${DO_SHUM}" = TRUE ] \
+  || [ "${DO_SKEB}" = TRUE ] || [ "${DO_LSM_SPP}" =  TRUE ]); then
+
+$USHDIR/set_namelist.py -q \
+                         -n  ${FV3_NML_FP}  \
+                         -u "$settings" \
+                         -o ${FV3_NML_STOCH_FP} || \
+   print_err_msg_exit "\
+ Call to python script set_namelist.py to generate an FV3 namelist file with stochastics
+ failed.  Parameters passed to this script are:
+   Full path to base namelist file:
+     FV3_NML_FP = \"${FV3_NML_FP}\"
+   Full path to output namelist file for stochastics:
+     FV3_NML_STOCH_FP = \"${FV3_NML_STOCH_FP}\"
+   Namelist settings specified on command line:
+     settings =
+ $settings"
+#
+#-----------------------------------------------------------------------
+#
+if [[ "${DO_DACYCLE}" = "TRUE" || "${DO_ENKFUPDATE}" = "TRUE" ]]; then
+$USHDIR/set_namelist.py -q \
+                         -n  ${FV3_NML_RESTART_FP}  \
+                         -u "$settings" \
+                         -o ${FV3_NML_RESTART_STOCH_FP} || \
+   print_err_msg_exit "\
+ Call to python script set_namelist.py to generate an restart FV3 namelist file with stochastics
+ failed.  Parameters passed to this script are:
+   Full path to base namelist file:
+     FV3_NML_RESTART_FP = \"${FV3_NML_RESTART_FP}\"
+   Full path to output namelist file for DA with stochastics:
+     FV3_NML_RESTART_STOCH_FP = \"${FV3_NML_RESTART_STOCH_FP}\"
+   Namelist settings specified on command line:
+     settings =
+ $settings"
+fi
+
 fi
 #
 #-----------------------------------------------------------------------

diff --git a/ush/set_FV3nml_ens_stoch_seeds.sh b/ush/set_FV3nml_ens_stoch_seeds.sh
@@ -94,8 +94,8 @@ function set_FV3nml_ens_stoch_seeds() {
 #
   ensmem_name="mem${ENSMEM_INDX}"
 
-  fv3_nml_ensmem_fp_base="${CYCLE_BASEDIR}/${cdate}/${ensmem_name}/fcst_fv3lam/input.nml_base"
-  fv3_nml_ensmem_fp="${CYCLE_BASEDIR}/${cdate}/${ensmem_name}/fcst_fv3lam/input.nml"
+  fv3_nml_ensmem_fp_base="${run_dir}/input.nml_base"
+  fv3_nml_ensmem_fp="${run_dir}/input.nml"
 
   ensmem_num=$((10#${ENSMEM_INDX}))
 

diff --git a/ush/setup.sh b/ush/setup.sh
@@ -1559,6 +1559,8 @@ FV3_NML_FN="${FV3_NML_BASE_SUITE_FN%.*}"
 FV3_NML_FP="${EXPTDIR}/${FV3_NML_FN}"
 FV3_NML_CYCSFC_FP="${EXPTDIR}/${FV3_NML_FN}_cycsfc"
 FV3_NML_RESTART_FP="${EXPTDIR}/${FV3_NML_FN}_restart"
+FV3_NML_STOCH_FP="${EXPTDIR}/${FV3_NML_FN}_stoch"
+FV3_NML_RESTART_STOCH_FP="${EXPTDIR}/${FV3_NML_FN}_restart_stoch"
 NEMS_CONFIG_FP="${EXPTDIR}/${NEMS_CONFIG_FN}"
 #
 #-----------------------------------------------------------------------
@@ -2787,6 +2789,8 @@ FV3_NML_FN="${FV3_NML_FN}"   # This may not be necessary...
 FV3_NML_FP="${FV3_NML_FP}"
 FV3_NML_CYCSFC_FP="${FV3_NML_CYCSFC_FP}"
 FV3_NML_RESTART_FP="${FV3_NML_RESTART_FP}"
+FV3_NML_STOCH_FP="${FV3_NML_STOCH_FP}"
+FV3_NML_RESTART_STOCH_FP="${FV3_NML_RESTART_STOCH_FP}"
 NEMS_CONFIG_FP="${NEMS_CONFIG_FP}"
 NEMS_YAML_FP="${NEMS_YAML_FP}"