Add missing user-defined stochastic physics options; fix stochastic p…

…hysics seed generation script (#704)

## DESCRIPTION OF CHANGES: 
Add missing user-defined options for tendency-based stochastic physics and fix the ensemble-based seed generation script to work regardless of whether stochastic physics is turned on or not.

## TESTS CONDUCTED: 
Tested on Hera using the following WE2E configurations with and without stochastic physics:

config.grid_RRFS_CONUS_3km_ics_HRRR_lbcs_RAP_suite_HRRR.sh
config.community_ensemble_2mems.sh

## ISSUE (optional): 
[Issue #702](#702)

## CONTRIBUTORS (optional): 
Thanks to @mkavulich and @chan-hoo for finding this problem.

scripts/exregional_run_fcst.sh

@@ -9,7 +9,7 @@
 #
 . ${GLOBAL_VAR_DEFNS_FP}
 . $USHDIR/source_util_funcs.sh
-. $USHDIR/set_FV3nml_stoch_params.sh
+. $USHDIR/set_FV3nml_ens_stoch_seeds.sh
 #
 #-----------------------------------------------------------------------
 #
@@ -444,8 +444,9 @@ if [ ${WRITE_DOPOST} = "TRUE" ]; then
   cp_vrfy ${UPP_DIR}/parm/params_grib2_tbl_new .
 fi
 
-if [ "${DO_ENSEMBLE}" = TRUE ]; then
-  set_FV3nml_stoch_params cdate="$cdate" || print_err_msg_exit "\
+if [ "${DO_ENSEMBLE}" = TRUE ] && ([ "${DO_SPP}" = TRUE ] || [ "${DO_SPPT}" = TRUE ] || [ "${DO_SHUM}" = TRUE ] \
+   [ "${DO_SKEB}" = TRUE ] || [ "${DO_LSM_SPP}" =  TRUE ]); then
+  set_FV3nml_ens_stoch_seeds cdate="$cdate" || print_err_msg_exit "\
 Call to function to create the ensemble-based namelist for the current
 cycle's (cdate) run directory (run_dir) failed:
   cdate = \"${cdate}\"

ush/config_defaults.sh

@@ -1504,6 +1504,7 @@ FIXgsm_FILES_TO_COPY_TO_FIXam=( \
 "global_hyblev.l65.txt" \
 "global_zorclim.1x1.grb" \
 "global_sfc_emissivity_idx.txt" \
+"global_tg3clim.2.6x1.5.grb" \
 "global_solarconstant_noaa_an.txt" \
 "global_albedo4.1x1.grb" \
 "geo_em.d01.lat-lon.2.5m.HGT_M.nc" \
@@ -1558,6 +1559,7 @@ CYCLEDIR_LINKS_TO_FIXam_FILES_MAPPING=( \
 "global_h2oprdlos.f77       | global_h2o_pltc.f77" \
 "global_albedo4.1x1.grb     | global_albedo4.1x1.grb" \
 "global_zorclim.1x1.grb     | global_zorclim.1x1.grb" \
+"global_tg3clim.2.6x1.5.grb | global_tg3clim.2.6x1.5.grb" \
 "sfc_emissivity_idx.txt     | global_sfc_emissivity_idx.txt" \
 "solarconstant_noaa_an.txt  | global_solarconstant_noaa_an.txt" \
 "global_o3prdlos.f77        | " \
@@ -1793,18 +1795,25 @@ NUM_ENS_MEMBERS="1"
 DO_SHUM="FALSE"
 DO_SPPT="FALSE"
 DO_SKEB="FALSE"
+ISEED_SPPT="1"
+ISEED_SHUM="2"
+ISEED_SKEB="3"
+NEW_LSCALE="TRUE"
 SHUM_MAG="0.006" #Variable "shum" in input.nml
 SHUM_LSCALE="150000"
 SHUM_TSCALE="21600" #Variable "shum_tau" in input.nml
 SHUM_INT="3600" #Variable "shumint" in input.nml
 SPPT_MAG="0.7" #Variable "sppt" in input.nml
+SPPT_LOGIT="TRUE"
 SPPT_LSCALE="150000"
 SPPT_TSCALE="21600" #Variable "sppt_tau" in input.nml
 SPPT_INT="3600" #Variable "spptint" in input.nml
+SPPT_SFCLIMIT="TRUE"
 SKEB_MAG="0.5" #Variable "skeb" in input.nml
 SKEB_LSCALE="150000"
 SKEB_TSCALE="21600" #Variable "skeb_tau" in input.nml
 SKEB_INT="3600" #Variable "skebint" in input.nml
+SKEBNORM="1"
 SKEB_VDOF="10"
 USE_ZMTNBLCK="FALSE"
 #

ush/generate_FV3LAM_wflow.sh

@@ -790,22 +790,6 @@ settings="\
     'lndp_type': ${LNDP_TYPE},
     'lndp_each_step': ${LSM_SPP_EACH_STEP},
     'fhcyc': ${FHCYC_LSM_SPP_OR_NOT}, 
-  }
-'nam_stochy': {
-    'shum': ${SHUM_MAG},
-    'shum_lscale': ${SHUM_LSCALE},
-    'shum_tau': ${SHUM_TSCALE},
-    'shumint': ${SHUM_INT},
-    'sppt': ${SPPT_MAG},
-    'sppt_lscale': ${SPPT_LSCALE},
-    'sppt_tau': ${SPPT_TSCALE},
-    'spptint': ${SPPT_INT},
-    'skeb': ${SKEB_MAG},
-    'skeb_lscale': ${SKEB_LSCALE},
-    'skeb_tau': ${SKEB_TSCALE},
-    'skebint': ${SKEB_INT},
-    'skeb_vdof': ${SKEB_VDOF},
-    'use_zmtnblck': ${USE_ZMTNBLCK},
   }"
 #
 # Add to "settings" the values of those namelist variables that specify
@@ -862,6 +846,51 @@ done
 settings="$settings
   }"
 #
+# Add the relevant tendency-based stochastic physics namelist variables to
+# "settings" when running with SPPT, SHUM, or SKEB turned on. 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},
+    'use_zmtnblck': ${USE_ZMTNBLCK},"
+fi
+
+if [ "${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},
+    'use_zmtnblck': ${USE_ZMTNBLCK},"
+fi
+settings="$settings
+  }"
+#
 # Add the relevant SPP namelist variables to "settings" when running with 
 # SPP turned on.  Otherwise only include an empty "nam_sppperts" stanza.
 #
@@ -1067,9 +1096,6 @@ fi
 
 }
 
-
-
-
 #
 #-----------------------------------------------------------------------
 #

ush/set_FV3nml_stoch_params.sh → ush/set_FV3nml_ens_stoch_seeds.sh

@@ -13,7 +13,7 @@
 #
 #-----------------------------------------------------------------------
 #
-function set_FV3nml_stoch_params() {
+function set_FV3nml_ens_stoch_seeds() {
 #
 #-----------------------------------------------------------------------
 #
@@ -98,48 +98,67 @@ function set_FV3nml_stoch_params() {
 
   ensmem_num=$((10#${ENSMEM_INDX}))
 
+  settings="\
+'nam_stochy': {"
+
+  if [ ${DO_SPPT} = TRUE ]; then
+
+  iseed_sppt=$(( cdate*1000 + ensmem_num*10 + 1 ))
+    settings="$settings
+  'iseed_sppt': ${iseed_sppt},"
+
+  fi
+
+  if [ ${DO_SHUM} = TRUE ]; then
+
   iseed_shum=$(( cdate*1000 + ensmem_num*10 + 2 ))
+    settings="$settings
+  'iseed_shum': ${iseed_shum},"
+
+  fi
+
+  if [ ${DO_SKEB} = TRUE ]; then
+
   iseed_skeb=$(( cdate*1000 + ensmem_num*10 + 3 ))
-  iseed_sppt=$(( cdate*1000 + ensmem_num*10 + 1 ))
-  iseed_lsm_spp=$(( cdate*1000 + ensmem_num*10 + 9))
+    settings="$settings
+  'iseed_skeb': ${iseed_skeb},"
+
+  fi
+  settings="$settings
+    }"
+
+  settings="$settings
+'nam_sppperts': {"
+
+  if [ ${DO_SPP} = TRUE ]; then
 
   num_iseed_spp=${#ISEED_SPP[@]}
   for (( i=0; i<${num_iseed_spp}; i++ )); do
     iseed_spp[$i]=$(( cdate*1000 + ensmem_num*10 + ${ISEED_SPP[$i]} ))
   done
 
-  settings=""
-
-  if [ ${DO_SPPT} = TRUE ] || [ ${DO_SHUM} = TRUE ] || [ ${DO_SKEB} = TRUE ]; then
-
-    settings=$settings"\
-'nam_stochy': {
-  'iseed_shum': ${iseed_shum},
-  'iseed_skeb': ${iseed_skeb},
-  'iseed_sppt': ${iseed_sppt},
-  }
-"
+    settings="$settings
+  'iseed_spp': [ $( printf "%s, " "${iseed_spp[@]}" ) ],"
+
   fi
 
-  if [ ${DO_SPP} = TRUE ]; then
+  settings="$settings
+    }"
 
-    settings=$settings"\
-'nam_sppperts': {
-  'iseed_spp': [ $( printf "%s, " "${iseed_spp[@]}" ) ]
-  }
-"
-  fi
+  settings="$settings
+'nam_sfcperts': {"
 
   if [ ${DO_LSM_SPP} = TRUE ]; then
+
+  iseed_lsm_spp=$(( cdate*1000 + ensmem_num*10 + 9))
+
+    settings="$settings
+  'iseed_lndp': [ $( printf "%s, " "${iseed_lsm_spp[@]}" ) ],"
 
-    settings=$settings"\
-'nam_sfcperts': {
-  'iseed_lndp': [ $( printf "%s, " "${iseed_lsm_spp[@]}" ) ]
-  }
-"
   fi
 
-  if [ -n "$settings" ]; then
+  settings="$settings
+    }"
 
   $USHDIR/set_namelist.py -q \
                           -n ${FV3_NML_FP} \
@@ -156,14 +175,6 @@ failed.  Parameters passed to this script are:
   Namelist settings specified on command line (these have highest precedence):
     settings =
 $settings"
-
-  else
-
-  print_info_msg "\
-The variable \"settings\" is empty, so not setting any namelist values."
-
-  fi
-
 #
 #-----------------------------------------------------------------------
 #