Merge branch 'main' into add_jra1_5

ESCOMP · Oct 25, 2024 · 573df5d · 573df5d
2 parents 37b1a13 + 1eacdcc
commit 573df5d
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diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -71,18 +71,6 @@ add_subdirectory(streams)
 add_subdirectory(dshr)
 
 if(NOT DISABLE_FoX)
-   FetchContent_Declare(fox
-     GIT_REPOSITORY https://github.com/ESMCI/fox.git
-     GIT_TAG 4.1.2.1
-     SOURCE_DIR ${FOX_ROOT}
-     BINARY_DIR ${FOX_ROOT}/..
-   )
-   FetchContent_GetProperties(fox)
-   if(NOT fox_POPULATED)
-     FetchContent_Populate(fox)
-     message(STATUS "FoX source dir: ${fox_SOURCE_DIR}")
-     message(STATUS "FoX binary dir: ${fox_BINARY_DIR}")
-   endif()
   add_subdirectory(fox)
 
   target_include_directories(streams PUBLIC $<BUILD_INTERFACE:${CMAKE_CURRENT_BINARY_DIR}/fox/include>

diff --git a/cime_config/stream_cdeps.py b/cime_config/stream_cdeps.py
@@ -76,6 +76,7 @@ def create_stream_xml(
         data_list_file,
         user_mods_file,
         available_neon_data=None,
+        available_plumber_data=None
     ):
         """
         Create the stream xml file and append the required stream input data to the input data list file
@@ -187,7 +188,17 @@ def create_stream_xml(
                     {"name": "NEON.NEON_PRECIP.$NEONSITE"},
                     err_msg="No stream_entry {} found".format(stream_name),
                 )
+            elif stream_name.startswith("PLUMBER2"):
+                self.stream_nodes = super(StreamCDEPS, self).get_child(
+                    "stream_entry",
+                    {"name": "PLUMBER2.$PLUMBER2SITE"},
+                    err_msg="No stream_entry {} found".format(stream_name),
+                )
             elif stream_name.startswith("CLM_USRDAT."):
+                if 'PLUMBER2' in stream_name:
+                    # if PLUMBER2 is in the stream name
+                    # we want to use PLUMBER2.PLUMBER2SITE instead of CLM_USRDAT.PLUMBER2
+                    continue
                 self.stream_nodes = super(StreamCDEPS, self).get_child(
                     "stream_entry",
                     {"name": "CLM_USRDAT.$CLM_USRDAT_NAME"},
@@ -244,6 +255,13 @@ def create_stream_xml(
                                     os.path.join(rundir, "inputdata", "atm", neon)
                                     + "\n"
                                 )
+                        elif available_plumber_data and stream_name.startswith("PLUMBER2"):
+                            rundir = case.get_value("RUNDIR")
+                            for plumber in available_plumber_data:
+                                stream_datafiles += (
+                                    os.path.join(rundir, "inputdata", "atm", plumber)
+                                    + "\n"
+                                )
                         else:
                             _stream_datafiles = child.xml_element.text
                             _stream_datafiles = self._resolve_values(

diff --git a/cime_config/stream_definition_v2.0.xsd b/cime_config/stream_definition_v2.0.xsd
@@ -93,7 +93,8 @@
       <xs:simpleContent>
         <xs:extension base="xs:string">
           <xs:attribute name="model_grid" type="xs:string" />
-          <xs:attribute name="compset" type="xs:string" />
+	  <xs:attribute name="compset" type="xs:string" />
+	  <xs:attribute name="CLM_USRDAT_NAME" type="xs:string" />
         </xs:extension>
       </xs:simpleContent>
     </xs:complexType>

diff --git a/datm/atm_comp_nuopc.F90 b/datm/atm_comp_nuopc.F90
@@ -33,60 +33,44 @@ module cdeps_datm_comp
   use dshr_methods_mod , only : dshr_state_diagnose, chkerr, memcheck
   use dshr_strdata_mod , only : shr_strdata_type, shr_strdata_init_from_config, shr_strdata_advance
   use dshr_strdata_mod , only : shr_strdata_get_stream_pointer, shr_strdata_setOrbs
-  use dshr_mod         , only : dshr_model_initphase, dshr_init
+  use dshr_mod         , only : dshr_model_initphase, dshr_init, dshr_restart_write
   use dshr_mod         , only : dshr_state_setscalar, dshr_set_runclock, dshr_log_clock_advance
-  use dshr_mod         , only : dshr_mesh_init, dshr_check_restart_alarm
+  use dshr_mod         , only : dshr_mesh_init, dshr_check_restart_alarm, dshr_restart_read
   use dshr_mod         , only : dshr_orbital_init, dshr_orbital_update
   use dshr_dfield_mod  , only : dfield_type, dshr_dfield_add, dshr_dfield_copy
   use dshr_fldlist_mod , only : fldlist_type, dshr_fldlist_add, dshr_fldlist_realize
 
   use datm_datamode_core2_mod   , only : datm_datamode_core2_advertise
   use datm_datamode_core2_mod   , only : datm_datamode_core2_init_pointers
   use datm_datamode_core2_mod   , only : datm_datamode_core2_advance
-  use datm_datamode_core2_mod   , only : datm_datamode_core2_restart_write
-  use datm_datamode_core2_mod   , only : datm_datamode_core2_restart_read
 
   use datm_datamode_jra_mod     , only : datm_datamode_jra_advertise
   use datm_datamode_jra_mod     , only : datm_datamode_jra_init_pointers
   use datm_datamode_jra_mod     , only : datm_datamode_jra_advance
-  use datm_datamode_jra_mod     , only : datm_datamode_jra_restart_write
-  use datm_datamode_jra_mod     , only : datm_datamode_jra_restart_read
 
   use datm_datamode_clmncep_mod , only : datm_datamode_clmncep_advertise
   use datm_datamode_clmncep_mod , only : datm_datamode_clmncep_init_pointers
   use datm_datamode_clmncep_mod , only : datm_datamode_clmncep_advance
-  use datm_datamode_clmncep_mod , only : datm_datamode_clmncep_restart_write
-  use datm_datamode_clmncep_mod , only : datm_datamode_clmncep_restart_read
 
   use datm_datamode_cplhist_mod , only : datm_datamode_cplhist_advertise
   use datm_datamode_cplhist_mod , only : datm_datamode_cplhist_init_pointers
   use datm_datamode_cplhist_mod , only : datm_datamode_cplhist_advance
-  use datm_datamode_cplhist_mod , only : datm_datamode_cplhist_restart_write
-  use datm_datamode_cplhist_mod , only : datm_datamode_cplhist_restart_read
 
   use datm_datamode_era5_mod    , only : datm_datamode_era5_advertise
   use datm_datamode_era5_mod    , only : datm_datamode_era5_init_pointers
   use datm_datamode_era5_mod    , only : datm_datamode_era5_advance
-  use datm_datamode_era5_mod    , only : datm_datamode_era5_restart_write
-  use datm_datamode_era5_mod    , only : datm_datamode_era5_restart_read
 
   use datm_datamode_gefs_mod    , only : datm_datamode_gefs_advertise
   use datm_datamode_gefs_mod    , only : datm_datamode_gefs_init_pointers
   use datm_datamode_gefs_mod    , only : datm_datamode_gefs_advance
-  use datm_datamode_gefs_mod    , only : datm_datamode_gefs_restart_write
-  use datm_datamode_gefs_mod    , only : datm_datamode_gefs_restart_read
 
   use datm_datamode_cfsr_mod    , only : datm_datamode_cfsr_advertise
   use datm_datamode_cfsr_mod    , only : datm_datamode_cfsr_init_pointers
   use datm_datamode_cfsr_mod    , only : datm_datamode_cfsr_advance
-  use datm_datamode_cfsr_mod    , only : datm_datamode_cfsr_restart_write
-  use datm_datamode_cfsr_mod    , only : datm_datamode_cfsr_restart_read
 
   use datm_datamode_simple_mod  , only : datm_datamode_simple_advertise
   use datm_datamode_simple_mod  , only : datm_datamode_simple_init_pointers
   use datm_datamode_simple_mod  , only : datm_datamode_simple_advance
-  use datm_datamode_simple_mod  , only : datm_datamode_simple_restart_write
-  use datm_datamode_simple_mod  , only : datm_datamode_simple_restart_read
 
   implicit none
   private ! except
@@ -157,7 +141,6 @@ module cdeps_datm_comp
   integer                      :: idt                                 ! integer model timestep
   logical                      :: diagnose_data = .true.
   integer          , parameter :: main_task   = 0                   ! task number of main task
-  character(len=*) , parameter :: rpfile        = 'rpointer.atm'
 #ifdef CESMCOUPLED
   character(*)     , parameter :: modName       = "(atm_comp_nuopc)"
 #else
@@ -479,7 +462,7 @@ subroutine InitializeRealize(gcomp, importState, exportState, clock, rc)
     if (ChkErr(rc,__LINE__,u_FILE_u)) return
 
     ! Run datm
-    call datm_comp_run(importstate, exportstate, current_ymd, current_tod, current_mon, &
+    call datm_comp_run(gcomp, importstate, exportstate, current_ymd, current_tod, current_mon, &
          orbEccen, orbMvelpp, orbLambm0, orbObliqr, restart_write=.false., rc=rc)
     if (ChkErr(rc,__LINE__,u_FILE_u)) return
 
@@ -561,7 +544,7 @@ subroutine ModelAdvance(gcomp, rc)
 
     ! Run datm
     call ESMF_TraceRegionEnter('datm_run')
-    call datm_comp_run(importstate, exportstate, next_ymd, next_tod, mon, &
+    call datm_comp_run(gcomp, importstate, exportstate, next_ymd, next_tod, mon, &
          orbEccen, orbMvelpp, orbLambm0, orbObliqr, restart_write,  rc)
     if (ChkErr(rc,__LINE__,u_FILE_u)) return
     call ESMF_TraceRegionExit('datm_run')
@@ -579,14 +562,15 @@ subroutine ModelAdvance(gcomp, rc)
   end subroutine ModelAdvance
 
   !===============================================================================
-  subroutine datm_comp_run(importState, exportState, target_ymd, target_tod, target_mon, &
+  subroutine datm_comp_run(gcomp, importState, exportState, target_ymd, target_tod, target_mon, &
        orbEccen, orbMvelpp, orbLambm0, orbObliqr, restart_write, rc)
-
+    use nuopc_shr_methods, only : shr_get_rpointer_name
     ! ----------------------------------
     ! run method for datm model
     ! ----------------------------------
 
     ! input/output variables
+    type(ESMF_GridComp)    , intent(inout)    :: gcomp
     type(ESMF_State)       , intent(inout) :: importState
     type(ESMF_State)       , intent(inout) :: exportState
     integer                , intent(in)    :: target_ymd       ! model date
@@ -601,6 +585,7 @@ subroutine datm_comp_run(importState, exportState, target_ymd, target_tod, targe
 
     ! local variables
     logical :: first_time = .true.
+    character(len=CL) :: rpfile        
     character(*), parameter :: subName = '(datm_comp_run) '
     !-------------------------------------------------------------------------------
 
@@ -613,7 +598,6 @@ subroutine datm_comp_run(importState, exportState, target_ymd, target_tod, targe
     !--------------------
 
     if (first_time) then
-
        ! Initialize dfields
        call datm_init_dfields(rc=rc)
        if (ChkErr(rc,__LINE__,u_FILE_u)) return
@@ -648,23 +632,14 @@ subroutine datm_comp_run(importState, exportState, target_ymd, target_tod, targe
 
        ! Read restart if needed
        if (restart_read .and. .not. skip_restart_read) then
+          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')
-             call datm_datamode_core2_restart_read(restfilm, inst_suffix, logunit, my_task, mpicom, sdat)
-          case('CORE_IAF_JRA')
-             call datm_datamode_jra_restart_read(restfilm, inst_suffix, logunit, my_task, mpicom, sdat)
-          case('CLMNCEP')
-             call datm_datamode_clmncep_restart_read(restfilm, inst_suffix, logunit, my_task, mpicom, sdat)
-          case('CPLHIST')
-             call datm_datamode_cplhist_restart_read(restfilm, inst_suffix, logunit, my_task, mpicom, sdat)
-          case('ERA5')
-             call datm_datamode_era5_restart_read(restfilm, inst_suffix, logunit, my_task, mpicom, sdat)
-          case('GEFS')
-             call datm_datamode_gefs_restart_read(restfilm, inst_suffix, logunit, my_task, mpicom, sdat)
-          case('CFSR')
-             call datm_datamode_cfsr_restart_read(restfilm, inst_suffix, logunit, my_task, mpicom, sdat)
-          case('SIMPLE')
-             call datm_datamode_simple_restart_read(restfilm, inst_suffix, logunit, my_task, mpicom, sdat)
+          case('CORE2_NYF','CORE2_IAF','CORE_IAF_JRA','CLMNCEP','CPLHIST','ERA5','GEFS','CFSR','SIMPLE')
+             call dshr_restart_read(restfilm, rpfile, logunit, my_task, mpicom, sdat, rc)
+             if (ChkErr(rc,__LINE__,u_FILE_u)) return
+          case default
+             call shr_sys_abort(subName//'datamode '//trim(datamode)//' not recognized')
           end select
        end if
 
@@ -727,33 +702,15 @@ subroutine datm_comp_run(importState, exportState, target_ymd, target_tod, targe
 
     ! Write restarts if needed
     if (restart_write) then
+       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')
-          call datm_datamode_core2_restart_write(case_name, inst_suffix, target_ymd, target_tod, &
-               logunit, my_task, sdat)
-       case('CORE_IAF_JRA')
-          call datm_datamode_jra_restart_write(case_name, inst_suffix, target_ymd, target_tod, &
-               logunit, my_task, sdat)
-       case('CLMNCEP')
-          call datm_datamode_clmncep_restart_write(case_name, inst_suffix, target_ymd, target_tod, &
-               logunit, my_task, sdat)
-       case('CPLHIST')
-          call datm_datamode_cplhist_restart_write(case_name, inst_suffix, target_ymd, target_tod, &
-               logunit, my_task, sdat)
-       case('ERA5')
-          call datm_datamode_era5_restart_write(case_name, inst_suffix, target_ymd, target_tod, &
-               logunit, my_task, sdat)
-       case('GEFS')
-          call datm_datamode_gefs_restart_write(case_name, inst_suffix, target_ymd, target_tod, &
-               logunit, my_task, sdat)
+       case('CORE2_NYF','CORE2_IAF','CORE_IAF_JRA','CLMNCEP','CPLHIST','ERA5','GEFS','CFSR','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
-       case('CFSR')
-          call datm_datamode_cfsr_restart_write(case_name, inst_suffix, target_ymd, target_tod, &
-               logunit, my_task, sdat)
-          if (ChkErr(rc,__LINE__,u_FILE_u)) return
-       case('SIMPLE')
-          call datm_datamode_simple_restart_write(case_name, inst_suffix, target_ymd, target_tod, &
-               logunit, my_task, sdat)
+       case default
+          call shr_sys_abort(subName//'datamode '//trim(datamode)//' not recognized')
        end select
     end if
 

diff --git a/datm/cime_config/buildnml b/datm/cime_config/buildnml
@@ -141,11 +141,16 @@ def _create_namelists(case, confdir, inst_string, infile, nmlgen, data_list_path
     available_neon_data = None
     if 'CLM_USRDAT' in model_grid:
         config['model_grid'] = 'CLM_USRDAT'
-        neonsite = case.get_value("NEONSITE")
-        if neonsite:
-            config['neon'] = "True"
-            # download and use the listing.csv file to determine data availablity
-            available_neon_data = _get_neon_data_availability(case, neonsite)
+        if 'NEON' in clm_usrdat_name:
+            neonsite = case.get_value("NEONSITE")
+            if neonsite:
+                config['neon'] = "True"
+                # download and use the listing.csv file to determine data availablity
+                available_neon_data = _get_neon_data_availability(case, neonsite)
+        if 'PLUMBER2' in clm_usrdat_name:
+            plumber2site = case.get_value('PLUMBER2SITE')
+            if plumber2site:
+                config['plumber'] = "True"
     else:
         config['model_grid'] = model_grid
 
@@ -194,6 +199,8 @@ def _create_namelists(case, confdir, inst_string, infile, nmlgen, data_list_path
         streamlist.append(clm_usrdat_name+"_PRECIP."+neonsite)
     if  clm_usrdat_name == 'NEON':
         streamlist.append(clm_usrdat_name+".NEON_PRECIP."+neonsite)   
+    if clm_usrdat_name == 'PLUMBER2':
+        streamlist.append(clm_usrdat_name+"."+plumber2site)
 
     bias_correct = nmlgen.get_value("bias_correct")
     if bias_correct is not None:

diff --git a/datm/cime_config/config_component.xml b/datm/cime_config/config_component.xml
@@ -298,6 +298,15 @@
     <desc>starting year to loop data over</desc>
   </entry>
 
+  <entry id="DATM_YR_START_FILENAME">
+    <type>integer</type>
+    <valid_values></valid_values>
+    <default_value>9999</default_value>
+    <group>run_component_datm</group>
+    <file>env_run.xml</file>
+    <desc>Start year listed in PLUMBER2 filenames for certain datm_modes. Currently only used in PLUMBER2; leave as the default value (9999) for other cases.</desc>
+  </entry>
+
   <entry id="DATM_YR_END">
     <type>integer</type>
     <valid_values></valid_values>

diff --git a/datm/cime_config/namelist_definition_datm.xml b/datm/cime_config/namelist_definition_datm.xml
@@ -40,6 +40,9 @@
       <value datm_mode="1PT" model_grid="CLM_USRDAT" neon="True">
         NEON.$NEONSITE
       </value>
+      <value datm_mode="1PT" model_grid="CLM_USRDAT" neon="True">
+        PLUMBER2.$PLUMBER2SITE
+      </value>
       <value datm_mode="1PT" model_grid="CLM_USRDAT">
         CLM_USRDAT.$CLM_USRDAT_NAME
       </value>

diff --git a/datm/cime_config/stream_definition_datm.xml b/datm/cime_config/stream_definition_datm.xml
@@ -42,6 +42,8 @@
   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)
   ERA5                  = ERA5 intra-annual year forcing
+  NEON                  = Run with forcing from NEON tower data
+  PLUMBER2              = Run with forcing from PLUMBER2 tower data
   SIMPLE                = Namelist-configurable, constant datm forcing for simple experiments
   CPLHIST               = Streams for lnd or ocn/ice forcing used for spinup
 
@@ -342,6 +344,50 @@
     <stream_readmode>single</stream_readmode>
   </stream_entry>
 
+
+  <!-- ===================================  -->
+  <!-- datm_mode PLUMBER2.$PLUMBER2SITE      -->
+  <!-- ===================================  -->
+
+  <stream_entry name="PLUMBER2.$PLUMBER2SITE">
+    <stream_meshfile>
+      <meshfile>none</meshfile>
+    </stream_meshfile>
+    <stream_datafiles>
+      <file first_year="$DATM_YR_START" last_year="$DATM_YR_END">$DIN_LOC_ROOT/atm/datm7/CLM1PT_data/PLUMBER2/${PLUMBER2SITE}/CLM1PT_data/CTSM_DATM_${PLUMBER2SITE}_${DATM_YR_START_FILENAME}-${DATM_YR_END}.nc</file>
+    </stream_datafiles>
+    <stream_datavars>
+      <var>ZBOT   Sa_z</var>
+      <var>TBOT   Sa_tbot</var>
+      <var>QBOT   Sa_shum</var>
+      <var>WIND   Sa_wind</var>
+      <var>PRECTmms   Faxa_precn</var>
+      <var>FSDS   Faxa_swdn</var>
+      <var>PSRF   Sa_pbot</var>
+      <var>FLDS   Faxa_lwdn</var>
+    </stream_datavars>
+    <stream_lev_dimname>null</stream_lev_dimname>
+    <stream_mapalgo>
+      <mapalgo>none</mapalgo>
+    </stream_mapalgo>
+    <stream_vectors>null</stream_vectors>
+    <stream_year_align>$DATM_YR_ALIGN</stream_year_align>
+    <stream_year_first>$DATM_YR_START</stream_year_first>
+    <stream_year_last>$DATM_YR_END</stream_year_last>
+    <stream_offset>0</stream_offset>
+    <stream_tintalgo>
+      <tintalgo>linear</tintalgo>
+    </stream_tintalgo>
+    <stream_taxmode>
+      <taxmode               >cycle</taxmode>
+      <taxmode compset="HIST">limit</taxmode>
+    </stream_taxmode>
+    <stream_dtlimit>
+      <dtlimit>1.5</dtlimit>
+    </stream_dtlimit>
+    <stream_readmode>single</stream_readmode>
+  </stream_entry>
+
   <!-- ===================================  -->
   <!-- datm_mode CLMGSWP3v1                 -->
   <!-- ===================================  -->
@@ -4313,6 +4359,7 @@
     </stream_taxmode>
     <stream_dtlimit>
       <dtlimit>1.5</dtlimit>
+      <dtlimit CLM_USRDAT_NAME="PLUMBER2">30</dtlimit>
     </stream_dtlimit>
     <stream_readmode>single</stream_readmode>
   </stream_entry>
@@ -4852,6 +4899,7 @@
     </stream_taxmode>
     <stream_dtlimit>
       <dtlimit>1.5</dtlimit>
+      <dtlimit CLM_USRDAT_NAME="PLUMBER2">30</dtlimit>
     </stream_dtlimit>
     <stream_readmode>single</stream_readmode>
   </stream_entry>