Bring in recent changes from NorESM

cime_config/stream_cdeps.py

@@ -76,7 +76,8 @@ def create_stream_xml(
         data_list_file,
         user_mods_file,
         available_neon_data=None,
-        available_plumber_data=None
+        available_plumber_data=None,
+        lnd2rof_nonh2o_number=0,
     ):
         """
         Create the stream xml file and append the required stream input data to the input data list file
@@ -230,6 +231,7 @@ def create_stream_xml(
                         datavars = child.xml_element.text.strip()
                         datavars = self._resolve_values(case, datavars)
                         datavars = self._sub_glc_fields(datavars, case)
+                        datavars = self._sub_rof_fields(datavars, case, lnd2rof_nonh2o_number=lnd2rof_nonh2o_number)
                         datavars = self._add_xml_delimiter(datavars.split("\n"), "var")
                         if stream_vars[node_name]:
                             stream_vars[node_name] = (
@@ -520,11 +522,11 @@ def _sub_glc_fields(self, datavars, case):
 
         Returns a string.
 
-        Example: If `_sub_fields` is called with an array containing two
+        Example: If `_sub_glc_fields` is called with an array containing two
         elements, each of which contains two strings, and glc_nec=3:
              foo               bar
              s2x_Ss_tsrf%glc   tsrf%glc
-         then the returned array will be:
+        then the returned array will be:
              foo               bar
              s2x_Ss_tsrf00     tsrf00
              s2x_Ss_tsrf01     tsrf01
@@ -547,6 +549,56 @@ def _sub_glc_fields(self, datavars, case):
                 new_lines.append(line)
         return "\n".join(new_lines)
 
+    def _sub_rof_fields(self, datavars, case, lnd2rof_nonh2o_number=0):
+        """Substitute indicators with given values in a list of fields.
+        Replace any instance of the following substring indicators with the
+        appropriate values:
+            %lnd2rof_nonh2o_number = two-digit number from 0 through the number
+             of non-h2o tracers sent from the dlnd to mosart.
+
+        The difference between this function and `_sub_paths` is that this
+        function is intended to be used for variable names (especially from the
+        `strm_datvar` defaults), whereas `_sub_paths` is intended for use on
+        input data file paths.
+
+        Returns a string.
+
+        Example: If `_sub_rof_fields` is called with an array containing only one
+        element, and lnd2rof_nonh2o_number = 2
+             foo               bar
+	     lndImp_Flrl_rofsur_nonh2o%rof Flrl_rofsur_nonh2o%rof
+        then the returned array will be:
+             foo               bar
+	     lndImp_Flrl_rofsur_nonh2o Flrl_rofsur_nonh2o
+
+        Example: If `_sub_rof_fields` is called with an array containing two
+        elements, each of which contains two strings, and lnd2rof_nonh2o_number = 2
+             foo               bar
+	     lndImp_Flrl_rofsur_nonh2o%rof Flrl_rofsur_nonh2o%rof
+        then the returned array will be:
+             foo               bar
+	     lndImp_Flrl_rofsur_nonh2o%01 Flrl_rofsur_nonh2o%01
+	     lndImp_Flrl_rofsur_nonh2o%02 Flrl_rofsur_nonh2o%02
+        """
+        lines = datavars.split("\n")
+        new_lines = []
+        for line in lines:
+            if not line:
+                continue
+            if "%rof" in line:
+                if lnd2rof_nonh2o_number == 0:
+                    lnd2rof_indices = []
+                else:
+                    lnd2rof_indices = range(1,lnd2rof_nonh2o_number + 1)
+                for i in lnd2rof_indices:
+                    if len(lnd2rof_indices) == 1:
+                        new_lines.append(line.replace("%rof", "".format(i)))
+                    else:
+                        new_lines.append(line.replace("%rof", "{:02d}".format(i)))
+            else:
+                new_lines.append(line)
+        return "\n".join(new_lines)
+
     @staticmethod
     def _days_in_month(month, year=1):
         """Number of days in the given month (specified as an int, 1-12).
@@ -665,7 +717,10 @@ def _sub_paths(
                                 adjusted_year, adjusted_month, adjusted_day
                             )
                             new_line = line.replace(match.group(0), date_string)
-                            new_lines.append(new_line)
+                            if os.path.exists(new_line):
+                                new_lines.append(new_line)
+                            else:
+                                print(f"   WARNING:not adding missing file {new_line}")
                 elif match.group("month"):
                     for month in range(1, 13):
                         date_string = (year_format + "-{:02d}").format(year, month)

datm/atm_comp_nuopc.F90

@@ -356,6 +356,10 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
     if ( trim(datamode) == 'CORE2_NYF'    .or. &
          trim(datamode) == 'CORE2_IAF'    .or. &
          trim(datamode) == 'CORE_IAF_JRA' .or. &
+         trim(datamode) == 'CORE_RYF6162_JRA' .or. &
+         trim(datamode) == 'CORE_RYF8485_JRA' .or. &
+         trim(datamode) == 'CORE_RYF9091_JRA' .or. &
+         trim(datamode) == 'CORE_RYF0304_JRA' .or. &
          trim(datamode) == 'CLMNCEP'      .or. &
          trim(datamode) == 'CPLHIST'      .or. &
          trim(datamode) == 'GEFS'         .or. &
@@ -372,7 +376,7 @@ subroutine InitializeAdvertise(gcomp, importState, exportState, clock, rc)
        call datm_datamode_core2_advertise(exportState, fldsExport, flds_scalar_name, &
             flds_co2, flds_wiso, flds_presaero, flds_presndep, rc)
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
-    case ('CORE_IAF_JRA')
+    case ('CORE_IAF_JRA', 'CORE_RYF6162_JRA', 'CORE_RYF8485_JRA', 'CORE_RYF9091_JRA', 'CORE_RYF0304_JRA')
        call datm_datamode_jra_advertise(exportState, fldsExport, flds_scalar_name, &
             flds_co2, flds_wiso, flds_presaero, flds_presndep, rc)
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
@@ -621,7 +625,7 @@ subroutine datm_comp_run(gcomp, importState, exportState, target_ymd, target_tod
        case('CORE2_NYF','CORE2_IAF')
           call datm_datamode_core2_init_pointers(exportState, sdat, datamode, factorfn_mesh, factorfn_data, rc)
           if (ChkErr(rc,__LINE__,u_FILE_u)) return
-       case('CORE_IAF_JRA')
+       case ('CORE_IAF_JRA', 'CORE_RYF6162_JRA', 'CORE_RYF8485_JRA', 'CORE_RYF9091_JRA', 'CORE_RYF0304_JRA')
           call datm_datamode_jra_init_pointers(exportState, sdat, rc)
           if (ChkErr(rc,__LINE__,u_FILE_u)) return
        case('CLMNCEP')
@@ -646,7 +650,7 @@ subroutine datm_comp_run(gcomp, importState, exportState, target_ymd, target_tod
           call shr_get_rpointer_name(gcomp, 'atm', target_ymd, target_tod, rpfile, 'read', rc)
           if (ChkErr(rc,__LINE__,u_FILE_u)) return
           select case (trim(datamode))
-          case('CORE2_NYF','CORE2_IAF','CORE_IAF_JRA','CLMNCEP','CPLHIST','ERA5','GEFS','SIMPLE')
+          case('CORE2_NYF','CORE2_IAF','CORE_IAF_JRA','CORE_RYF6162_JRA','CORE_RYF8485_JRA','CORE_RYF9091_JRA','CORE_RYF0304_JRA','CLMNCEP','CPLHIST','ERA5','GEFS','SIMPLE')
              call dshr_restart_read(restfilm, rpfile, logunit, my_task, mpicom, sdat, rc)
              if (ChkErr(rc,__LINE__,u_FILE_u)) return
           case default
@@ -686,7 +690,7 @@ subroutine datm_comp_run(gcomp, importState, exportState, target_ymd, target_tod
        call datm_datamode_core2_advance(datamode, target_ymd, target_tod, target_mon, &
             sdat%model_calendar, factorfn_mesh, rc)
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
-    case('CORE_IAF_JRA')
+    case('CORE_IAF_JRA','CORE_RYF6162_JRA','CORE_RYF8485_JRA','CORE_RYF9091_JRA','CORE_RYF0304_JRA')
        call datm_datamode_jra_advance(exportstate, target_ymd, target_tod, sdat%model_calendar, rc)
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
     case('CLMNCEP')
@@ -714,7 +718,7 @@ subroutine datm_comp_run(gcomp, importState, exportState, target_ymd, target_tod
        call shr_get_rpointer_name(gcomp, 'atm', target_ymd, target_tod, rpfile, 'write', rc)
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
        select case (trim(datamode))
-       case('CORE2_NYF','CORE2_IAF','CORE_IAF_JRA','CLMNCEP','CPLHIST','ERA5','GEFS','SIMPLE')
+       case('CORE2_NYF','CORE2_IAF','CORE_IAF_JRA','CORE_RYF6162_JRA','CORE_RYF8485_JRA','CORE_RYF9091_JRA','CORE_RYF0304_JRA','CLMNCEP','CPLHIST','ERA5','GEFS','SIMPLE')
           call dshr_restart_write(rpfile, case_name, 'datm', inst_suffix, target_ymd, target_tod, logunit, &
                my_task, sdat, rc)
           if (ChkErr(rc,__LINE__,u_FILE_u)) return

datm/cime_config/config_component.xml

@@ -10,7 +10,7 @@
        This file may have atm desc entries.
   -->
   <description modifier_mode="1">
-    <desc atm="DATM[%QIA][%WISOQIA][%CRUJRA2024][%CRUv7][%GSWP3v1][%MOSARTTEST][%NLDAS2][%CPLHIST][%1PT][%NYF][%IAF][%JRA][%JRA-1p4-2018][%JRA-1p5-2023][%JRA-RYF8485][%JRA-RYF9091][%JRA-RYF0304][%SIMPLE]"> Data driven ATM </desc>
+    <desc atm="DATM[%QIA][%WISOQIA][%CRUJRA2024][%CRUv7][%GSWP3v1][%MOSARTTEST][%NLDAS2][%CPLHIST][%1PT][%NYF][%IAF][%JRA][%JRA-1p4-2018][%JRA-1p5-2023][%JRA-RYF6162][%JRA-RYF8485][%JRA-RYF9091][%JRA-RYF0304][%SIMPLE]"> Data driven ATM </desc>
     <desc option="QIA"> QIAN data set </desc>
     <desc option="WISOQIA">QIAN with water isotopes</desc>
     <desc option="CRUJRA2024"> CRUJRA 2024 data set </desc>
@@ -24,6 +24,7 @@
     <desc option="JRA">interannual JRA55 forcing</desc>
     <desc option="JRA-1p4-2018">interannual JRA55 forcing, v1.4, through 2018</desc>
     <desc option="JRA-1p5-2023">interannual JRA55 forcing, v1.5, through 2023</desc>
+    <desc option="JRA-RYF6162"> JRA55 Repeat Year Forcing v1.3 1961-1962</desc>
     <desc option="JRA-RYF8485"> JRA55 Repeat Year Forcing v1.3 1984-1985</desc>
     <desc option="JRA-RYF9091"> JRA55 Repeat Year Forcing v1.3 1990-1991</desc>
     <desc option="JRA-RYF0304"> JRA55 Repeat Year Forcing v1.3 2003-2004</desc>
@@ -42,7 +43,7 @@
 
   <entry id="DATM_MODE">
     <type>char</type>
-    <valid_values>CORE2_NYF,CORE2_IAF,CLM_QIAN,CLM_QIAN_WISO,1PT,CLMCRUJRA2024,CLMCRUNCEPv7,CLMGSWP3v1,CLMNLDAS2,CPLHIST,CORE_IAF_JRA,CORE_IAF_JRA_1p4_2018,CORE_IAF_JRA_1p5_2023,ERA5,SIMPLE</valid_values>
+    <valid_values>CORE2_NYF,CORE2_IAF,CLM_QIAN,CLM_QIAN_WISO,1PT,CLMCRUJRA2024,CLMCRUNCEPv7,CLMGSWP3v1,CLMNLDAS2,CPLHIST,CORE_IAF_JRA,CORE_IAF_JRA_1p4_2018,CORE_IAF_JRA_1p5_2023,CORE_RYF6162_JRA,CORE_RYF8485_JRA,CORE_RYF9091_JRA,CORE_RYF0304_JRA,ERA5,SIMPLE</valid_values>
     <default_value>CORE2_NYF</default_value>
     <group>run_component_datm</group>
     <file>env_run.xml</file>
@@ -56,6 +57,10 @@
       <value compset="DATM%JRA">CORE_IAF_JRA</value>
       <value compset="DATM%JRA-1p4-2018">CORE_IAF_JRA_1p4_2018</value>
       <value compset="DATM%JRA-1p5-2023">CORE_IAF_JRA_1p5_2023</value>
+      <value compset="DATM%JRA-RYF6162">CORE_RYF6162_JRA</value>
+      <value compset="DATM%JRA-RYF8485">CORE_RYF8485_JRA</value>
+      <value compset="DATM%JRA-RYF9091">CORE_RYF9091_JRA</value>
+      <value compset="DATM%JRA-RYF0304">CORE_RYF0304_JRA</value>
       <value compset="DATM%QIA">CLM_QIAN</value>
       <value compset="DATM%WISOQIA">CLM_QIAN_WISO</value>
       <value compset="DATM%CRUJRA2024">CLMCRUJRA2024</value>

datm/cime_config/namelist_definition_datm.xml

@@ -61,6 +61,9 @@
       <value datm_mode="CORE_IAF_JRA_1p5_2023" >
         CORE_IAF_JRA_1p5_2023.GCGCS.PREC,CORE_IAF_JRA_1p5_2023.GISS.LWDN,CORE_IAF_JRA_1p5_2023.GISS.SWDN,CORE_IAF_JRA_1p5_2023.NCEP.Q_10,CORE_IAF_JRA_1p5_2023.NCEP.SLP_,CORE_IAF_JRA_1p5_2023.NCEP.T_10,CORE_IAF_JRA_1p5_2023.NCEP.U_10,CORE_IAF_JRA_1p5_2023.NCEP.V_10
       </value>
+      <value datm_mode="CORE_RYF6162_JRA">
+        CORE_RYF6162_JRA.GISS.LWDN,CORE_RYF6162_JRA.GISS.SWDN,CORE_RYF6162_JRA.GCGCS,CORE_RYF6162_JRA.NCEP
+      </value>
       <value datm_mode="CORE_RYF8485_JRA">
         CORE_RYF8485_JRA.GISS.LWDN,CORE_RYF8485_JRA.GISS.SWDN,CORE_RYF8485_JRA.GCGCS,CORE_RYF8485_JRA.NCEP
       </value>
@@ -90,7 +93,7 @@
     <type>char</type>
     <category>datm</category>
     <group>datm_nml</group>
-    <valid_values>CLMNCEP,CORE2_NYF,CORE2_IAF,CORE_IAF_JRA,ERA5,SIMPLE,CPLHIST,1PT</valid_values>
+    <valid_values>CLMNCEP,CORE2_NYF,CORE2_IAF,CORE_IAF_JRA,CORE_RYF6162_JRA,CORE_RYF8485_JRA,CORE_RYF9091_JRA,CORE_RYF0304_JRA,ERA5,SIMPLE,CPLHIST,1PT</valid_values>
     <desc>
       general method that operates on the data.
       ----datamode = "CPLHIST"----
@@ -115,6 +118,14 @@
       Clm Dyn doi 10.1007/s00382-008-0441-3.
       ----datamode = "CORE_IAF_JRA"----
       JRA55 intra-annual year forcing
+      ----datamode = "CORE_RYF6162_JRA"----
+      JRA55 Repeat Year Forcing 1961-1962
+      ----datamode = "CORE_RYF8485_JRA"----
+      JRA55 Repeat Year Forcing 1984-1985
+      ----datamode = "CORE_RYF9091_JRA"----
+      JRA55 Repeat Year Forcing 1990-1991
+      ----datamode = "CORE_RYF0304_JRA"----
+      JRA55 Repeat Year Forcing 2003-2004
       ----datamode = "CLMNCEP"----
       In conjunction with NCEP climatological atmosphere data, provides the
       atmosphere forcing favored by the Land Model Working Group when

datm/cime_config/stream_definition_datm.xml

@@ -39,6 +39,7 @@
   CORE_IAF_JRA          = JRA55 intra-annual year forcing (for forcing MOM6 and CICE)
   CORE_IAF_JRA_1p4_2018 = JRA55 intra-annual year forcing, v1.4, through 2018 (for forcing MOM6 and CICE)
   CORE_IAF_JRA_1p5_2023 = JRA55 intra-annual year forcing, v1.5, through 2023 (for forcing MOM6 and CICE)
+  CORE_RYF6162_JRA      = JRA55 repeat year forcing, v1.3, 1961-1962 (for forcing MOM6 and CICE)
   CORE_RYF8485_JRA      = JRA55 repeat year forcing, v1.3, 1984-1985 (for forcing MOM6 and CICE)
   CORE_RYF9091_JRA      = JRA55 repeat year forcing, v1.3, 1990-1991 (for forcing MOM6 and CICE)
   CORE_RYF0304_JRA      = JRA55 repeat year forcing, v1.3, 2003-2004 (for forcing MOM6 and CICE)
@@ -2788,6 +2789,138 @@
     <stream_readmode>single</stream_readmode>
   </stream_entry>
 
+  <!-- ================================ -->
+  <!-- datm_mode CORE_RYF6162_JRA -->
+  <!-- ================================ -->
+
+  <stream_entry name="CORE_RYF6162_JRA.GISS.LWDN">
+    <stream_meshfile>
+      <meshfile>$DIN_LOC_ROOT/share/meshes/TL319_151007_ESMFmesh.nc</meshfile>
+    </stream_meshfile>
+    <stream_datafiles>
+      <file>$DIN_LOC_ROOT/ocn/jra55/v1.3_ryf/RAF_6162.JRA.v1.3.radiation.lwdn.TL319.250427.nc</file>
+    </stream_datafiles>
+    <stream_datavars>
+      <var>lwdn  Faxa_lwdn</var>
+    </stream_datavars>
+    <stream_lev_dimname>null</stream_lev_dimname>
+    <stream_mapalgo>
+      <mapalgo>bilinear</mapalgo>
+    </stream_mapalgo>
+    <stream_vectors>null</stream_vectors>
+    <stream_year_align>1</stream_year_align>
+    <stream_year_first>1961</stream_year_first>
+    <stream_year_last>1961</stream_year_last>
+    <stream_offset>0</stream_offset>
+    <stream_tintalgo>
+      <tintalgo>linear</tintalgo>
+    </stream_tintalgo>
+    <stream_taxmode>
+      <taxmode>cycle</taxmode>
+    </stream_taxmode>
+    <stream_dtlimit>
+      <dtlimit>1.5</dtlimit>
+    </stream_dtlimit>
+    <stream_readmode>single</stream_readmode>
+  </stream_entry>
+
+  <stream_entry name="CORE_RYF6162_JRA.GISS.SWDN">
+    <stream_meshfile>
+      <meshfile>$DIN_LOC_ROOT/share/meshes/TL319_151007_ESMFmesh.nc</meshfile>
+    </stream_meshfile>
+    <stream_datafiles>
+      <file>$DIN_LOC_ROOT/ocn/jra55/v1.3_ryf/RAF_6162.JRA.v1.3.radiation.swdn.TL319.250427.nc</file>
+    </stream_datafiles>
+    <stream_datavars>
+      <var>swdn  Faxa_swdn</var>
+    </stream_datavars>
+    <stream_lev_dimname>null</stream_lev_dimname>
+    <stream_mapalgo>
+      <mapalgo>bilinear</mapalgo>
+    </stream_mapalgo>
+    <stream_vectors>null</stream_vectors>
+    <stream_year_align>1</stream_year_align>
+    <stream_year_first>1961</stream_year_first>
+    <stream_year_last>1961</stream_year_last>
+    <stream_offset>0</stream_offset>
+    <stream_tintalgo>
+      <tintalgo>linear</tintalgo>
+    </stream_tintalgo>
+    <stream_taxmode>
+      <taxmode>cycle</taxmode>
+    </stream_taxmode>
+    <stream_dtlimit>
+      <dtlimit>1.5</dtlimit>
+    </stream_dtlimit>
+    <stream_readmode>single</stream_readmode>
+  </stream_entry>
+
+  <stream_entry name="CORE_RYF6162_JRA.GCGCS">
+    <stream_meshfile>
+      <meshfile>$DIN_LOC_ROOT/share/meshes/TL319_151007_ESMFmesh.nc</meshfile>
+    </stream_meshfile>
+    <stream_datafiles>
+      <file>$DIN_LOC_ROOT/ocn/jra55/v1.3_ryf/RAF_6162.JRA.v1.3.prec.TL319.250427.nc</file>
+    </stream_datafiles>
+    <stream_datavars>
+      <var>prec  Faxa_prec</var>
+    </stream_datavars>
+    <stream_lev_dimname>null</stream_lev_dimname>
+    <stream_mapalgo>
+      <mapalgo>bilinear</mapalgo>
+    </stream_mapalgo>
+    <stream_vectors>null</stream_vectors>
+    <stream_year_align>1</stream_year_align>
+    <stream_year_first>1961</stream_year_first>
+    <stream_year_last>1961</stream_year_last>
+    <stream_offset>0</stream_offset>
+    <stream_tintalgo>
+      <tintalgo>linear</tintalgo>
+    </stream_tintalgo>
+    <stream_taxmode>
+      <taxmode>cycle</taxmode>
+    </stream_taxmode>
+    <stream_dtlimit>
+      <dtlimit>1.5</dtlimit>
+    </stream_dtlimit>
+    <stream_readmode>single</stream_readmode>
+  </stream_entry>
+
+  <stream_entry name="CORE_RYF6162_JRA.NCEP">
+    <stream_meshfile>
+      <meshfile>$DIN_LOC_ROOT/share/meshes/TL319_151007_ESMFmesh.nc</meshfile>
+    </stream_meshfile>
+    <stream_datafiles>
+      <file>$DIN_LOC_ROOT/ocn/jra55/v1.3_ryf/RAF_6162.JRA.v1.3.states.TL319.250427.nc</file>
+    </stream_datafiles>
+    <stream_datavars>
+      <var>u_10  Sa_u</var>
+      <var>v_10  Sa_v</var>
+      <var>t_10  Sa_tbot</var>
+      <var>q_10  Sa_shum</var>
+      <var>slp   Sa_pslv</var>
+    </stream_datavars>
+    <stream_lev_dimname>null</stream_lev_dimname>
+    <stream_mapalgo>
+      <mapalgo>bilinear</mapalgo>
+    </stream_mapalgo>
+    <stream_vectors>Sa_u:Sa_v</stream_vectors>
+    <stream_year_align>1</stream_year_align>
+    <stream_year_first>1961</stream_year_first>
+    <stream_year_last>1961</stream_year_last>
+    <stream_offset>0</stream_offset>
+    <stream_tintalgo>
+      <tintalgo>linear</tintalgo>
+    </stream_tintalgo>
+    <stream_taxmode>
+      <taxmode>cycle</taxmode>
+    </stream_taxmode>
+    <stream_dtlimit>
+      <dtlimit>1.5</dtlimit>
+    </stream_dtlimit>
+    <stream_readmode>single</stream_readmode>
+  </stream_entry>
+
   <!-- ================================ -->
   <!-- datm_mode CORE_RYF8485_JRA -->
   <!-- ================================ -->