Add fv3lam namelist for cold start with surface cycling and the scrip…

…ts to use it. (NOAA-EMC#221)

scripts/exregional_run_fcst.sh

@@ -190,8 +190,8 @@ if [ "${RUN_TASK_MAKE_GRID}" = "TRUE" ] && [ "${MACHINE}" != "WCOSS_CRAY" ]; the
 fi
 
 # Symlink to mosaic file with a completely different name.
-target="${FIXLAM}/${CRES}${DOT_OR_USCORE}mosaic.halo${NH4}.nc"   # Should this point to this halo4 file or a halo3 file???
-#target="${FIXLAM}/${CRES}${DOT_OR_USCORE}mosaic.halo${NH3}.nc"   # Should this point to this halo4 file or a halo3 file???
+#target="${FIXLAM}/${CRES}${DOT_OR_USCORE}mosaic.halo${NH4}.nc"   # Should this point to this halo4 file or a halo3 file???
+target="${FIXLAM}/${CRES}${DOT_OR_USCORE}mosaic.halo${NH3}.nc"   # Should this point to this halo4 file or a halo3 file???
 symlink="grid_spec.nc"
 if [ -f "${target}" ]; then
   ln_vrfy -sf ${relative_or_null} $target $symlink
@@ -469,12 +469,17 @@ ln_vrfy -sf ${relative_or_null} ${NEMS_YAML_FP} ${run_dir}
 if [ "${DO_ENSEMBLE}" = TRUE ]; then
   ln_vrfy -sf ${relative_or_null} "${FV3_NML_ENSMEM_FPS[$(( 10#${ensmem_indx}-1 ))]}" ${run_dir}/${FV3_NML_FN}
 else
-   if [ ${BKTYPE} -eq 0 ]; then
+  if [ ${BKTYPE} -eq 0 ]; then
     # cycling, using namelist for cycling forecast
     cp_vrfy ${FV3_NML_RESTART_FP} ${run_dir}/input.nml
   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
+    else
     # cold start, using namelist for cold start
-    cp_vrfy ${FV3_NML_FP} ${run_dir}/input.nml
+      cp_vrfy ${FV3_NML_FP} ${run_dir}/input.nml
+    fi
   fi
 fi
 #

scripts/exregional_run_prepstart.sh

@@ -180,6 +180,7 @@ if [ ${BKTYPE} -eq 1 ] ; then  # cold start, use prepare cold strat initial file
       done
 
 # rename the soil mositure and temperature fields in restart file
+      rm -f cycle_surface.done
       if [ "${bkpath_find}" == "missing" ]; then
         print_info_msg "Warning: cannot find surface from previous cycle"
       else
@@ -191,6 +192,7 @@ if [ ${BKTYPE} -eq 1 ] ; then  # cold start, use prepare cold strat initial file
           ln_vrfy -sf ${restart_prefix_find}sfc_data.nc sfc_data.tile7.halo0.nc
           ncks --append geolonlat.nc sfc_data.tile7.halo0.nc
           ncrename -v tslb,stc -v smois,smc -v sh2o,slc sfc_data.tile7.halo0.nc
+          echo "cycle surface with ${checkfile}" > cycle_surface.done
         else
           print_info_msg "Warning: cannot find surface from previous cycle"
         fi

ush/generate_FV3LAM_wflow.sh

@@ -684,10 +684,6 @@ if [ "${EXTRN_MDL_NAME_ICS}" = "HRRR" -o \
    [ "${SDF_USES_RUC_LSM}" = "TRUE" ]; then
   lsoil="9"
 fi
-if [ "${DO_SURFACE_CYCLE}" = "TRUE" ] && \
-   [ "${SDF_USES_RUC_LSM}" = "TRUE" ]; then
-  lsoil="9"
-fi
 #
 # Create a multiline variable that consists of a yaml-compliant string
 # specifying the values that the namelist variables that are physics-
@@ -873,7 +869,45 @@ for the various ensemble members failed."
 
 fi
 
+if [ "${DO_SURFACE_CYCLE}" = "TRUE" ]; then
+  nstf_name="2,0,0,0,0"
+  if [ "${SDF_USES_RUC_LSM}" = "TRUE" ]; then
+    lsoil="9"
+  fi
+# need to generate a namelist for surface cycle
+ settings="\
+ 'gfs_physics_nml': {
+     'lsoil': ${lsoil:-null},
+     'nst_anl' : false,
+     'nstf_name'  : [${nstf_name[@]}],
+   }"
+# commnet out for using current develop branch that has no radar tten code yet.
+# 'gfs_physics_nml': {
+#    'fh_dfi_radar': [${FH_DFI_RADAR[@]}],
+#  }"
+
+ $USHDIR/set_namelist.py -q \
+                         -n ${FV3_NML_FP} \
+                         -u "$settings" \
+                         -o ${FV3_NML_CYCSFC_FP} || \
+   print_err_msg_exit "\
+ Call to python script set_namelist.py to generate an restart FV3 namelist file
+ failed.  Parameters passed to this script are:
+   Full path to base namelist file:
+     FV3_NML_FP = \"${FV3_NML_FP}\"
+   Full path to output namelist file for DA:
+     FV3_NML_CYCSFC_FP = \"${FV3_NML_CYCSFC_FP}\"
+   Namelist settings specified on command line:
+     settings =
+ $settings"
+fi
+
 if [ "${DO_DACYCLE}" = "TRUE" ]; then
+  nstf_name="2,0,0,0,0"
+  if [ "${SDF_USES_RUC_LSM}" = "TRUE" ]; then
+    lsoil="9"
+  fi
+
 # need to generate a namelist for da cycle
  settings="\
  'fv_core_nml': {
@@ -883,6 +917,11 @@ if [ "${DO_DACYCLE}" = "TRUE" ]; then
      'nggps_ic'   : false,
      'mountain'  : true,
      'warm_start' : true,
+   }
+ 'gfs_physics_nml': {
+     'lsoil': ${lsoil:-null},
+     'nst_anl' : false,
+     'nstf_name'  : [${nstf_name[@]}],
    }"
 # commnet out for using current develop branch that has no radar tten code yet.
 # 'gfs_physics_nml': {

ush/setup.sh

@@ -1422,6 +1422,7 @@ DATA_TABLE_FP="${EXPTDIR}/${DATA_TABLE_FN}"
 FIELD_TABLE_FP="${EXPTDIR}/${FIELD_TABLE_FN}"
 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}/${FV3_NML_FN}_restart"
 NEMS_CONFIG_FP="${EXPTDIR}/${NEMS_CONFIG_FN}"
 #