Merge branch 'development' into hplin/check_energy_rebase

.gitmodules

@@ -1,7 +1,7 @@
 [submodule "ccpp-framework"]
         path          = ccpp_framework
         url           = https://github.com/NCAR/ccpp-framework
-        fxtag         = 2024-07-19-dev
+        fxtag         = 2024-11-07-dev
         fxrequired    = AlwaysRequired
 	fxDONOTUSEurl = https://github.com/NCAR/ccpp-framework
 [submodule "history"]
@@ -19,8 +19,8 @@
         fxDONOTUSEurl = https://github.com/MPAS-Dev/MPAS-Model.git
 [submodule "ncar-physics"]
         path          = src/physics/ncar_ccpp
-	url           = https://github.com/jimmielin/atmospheric_physics
-	fxtag         = 7b188e35
+	url           = https://github.com/ESCOMP/atmospheric_physics
+	fxtag         = e7a599f4bb1533f7cdcd8723b1f864e11578e96c
         fxrequired    = AlwaysRequired
         fxDONOTUSEurl = https://github.com/ESCOMP/atmospheric_physics
 [submodule "ccs_config"]

cime_config/cam_autogen.py

@@ -392,7 +392,7 @@ def generate_registry(data_search, build_cache, atm_root, bldroot,
                                    gen_fort_indent, source_mods_dir, atm_root,
                                    logger=_LOGGER, schema_paths=data_search,
                                    error_on_no_validate=True)
-            retcode, reg_file_list, ic_names = retvals
+            retcode, reg_file_list, ic_names, registry_constituents = retvals
             # Raise error if gen_registry failed:
             if retcode != 0:
                 emsg = "ERROR:Unable to generate CAM data structures from {}, err = {}"
@@ -406,14 +406,15 @@ def generate_registry(data_search, build_cache, atm_root, bldroot,
         # Save build details in the build cache
         reg_file_paths = [x.file_path for x in reg_file_list if x.file_path]
         build_cache.update_registry(gen_reg_file, registry_files, dycore,
-                                    reg_file_paths, ic_names)
+                                    reg_file_paths, ic_names, registry_constituents)
     else:
         # If we did not run the registry generator, retrieve info from cache
         reg_file_paths = build_cache.reg_file_list()
         ic_names = build_cache.ic_names()
+        registry_constituents = build_cache.constituents()
     # End if
 
-    return genreg_dir, do_gen_registry, reg_file_paths, ic_names
+    return genreg_dir, do_gen_registry, reg_file_paths, ic_names, registry_constituents
 
 ###############################################################################
 def generate_physics_suites(build_cache, preproc_defs, host_name,
@@ -443,7 +444,8 @@ def generate_physics_suites(build_cache, preproc_defs, host_name,
     suite_search         = [source_mods_dir, atm_suites_path, atm_test_suites_path]
     # Find all scheme metadata files, organized by scheme name
     atm_schemes_path = os.path.join(atm_phys_top_dir, "schemes")
-    source_search    = [source_mods_dir, atm_schemes_path]
+    atm_test_schemes_path = os.path.join(atm_phys_top_dir, "test", "test_schemes")
+    source_search    = [source_mods_dir, atm_schemes_path, atm_test_schemes_path]
     all_scheme_files = _find_metadata_files(source_search, find_scheme_names)
 
     # Find the SDFs specified for this model build
@@ -657,7 +659,7 @@ def generate_physics_suites(build_cache, preproc_defs, host_name,
 ###############################################################################
 def generate_init_routines(build_cache, bldroot, force_ccpp, force_init,
                            source_mods_dir, gen_fort_indent,
-                           cap_database, ic_names):
+                           cap_database, ic_names, registry_constituents):
 ###############################################################################
     """
     Generate the host model initialization source code files
@@ -695,8 +697,8 @@ def generate_init_routines(build_cache, bldroot, force_ccpp, force_init,
         #   within write_init_files (so that write_init_files can be the place
         #   where the source include files are stored).
         source_paths = [source_mods_dir, _REG_GEN_DIR]
-        retmsg = write_init_files(cap_database, ic_names, init_dir,
-                                  _find_file, source_paths,
+        retmsg = write_init_files(cap_database, ic_names, registry_constituents,
+                                  init_dir, _find_file, source_paths,
                                   gen_fort_indent, _LOGGER)
 
         #Check that script ran properly:

cime_config/cam_build_cache.py

@@ -226,6 +226,7 @@ def __init__(self, build_cache):
         self.__kind_types = {}
         self.__reg_gen_files = []
         self.__ic_names = {}
+        self.__constituents = []
         if os.path.exists(build_cache):
             # Initialize build cache state
             _, cache = read_xml_file(build_cache)
@@ -252,6 +253,10 @@ def __init__(self, build_cache):
                             # end if
                             itext = clean_xml_text(item)
                             self.__ic_names[stdname].append(itext)
+                        elif item.tag == 'constituent_entry':
+                            stdname = item.get('standard_name')
+                            itext = clean_xml_text(item)
+                            self.__constituents.append(itext)
                         else:
                             emsg = "ERROR: Unknown registry tag, '{}'"
                             raise ValueError(emsg.format(item.tag))
@@ -313,7 +318,7 @@ def __init__(self, build_cache):
         # end if
 
     def update_registry(self, gen_reg_file, registry_source_files,
-                        dycore, reg_file_list, ic_names):
+                        dycore, reg_file_list, ic_names, constituents):
         """Replace the registry cache data with input data
         """
         self.__dycore = dycore
@@ -328,6 +333,7 @@ def update_registry(self, gen_reg_file, registry_source_files,
         # ic_names are the initial condition variable names from the registry,
         # and should already be of type dict:
         self.__ic_names = ic_names
+        self.__constituents = constituents
 
     def update_ccpp(self, suite_definition_files, scheme_files, host_files,
                     xml_files, namelist_meta_files, namelist_groups,
@@ -400,6 +406,10 @@ def write(self):
                 ic_entry.text = ic_name
             # end for
         # end for
+        for stdname in self.__constituents:
+            const_entry = ET.SubElement(registry, 'constituent_entry')
+            const_entry.text = stdname
+        # end for
         # CCPP
         ccpp = ET.SubElement(new_cache, 'CCPP')
         for sfile in self.__sdfs.values():
@@ -603,5 +613,9 @@ def ic_names(self):
         """Return a copy of the registry initial conditions dictionary"""
         return dict(self.__ic_names)
 
+    def constituents(self):
+        """Return a copy of the registry constituents list"""
+        return list(self.__constituents)
+
 #############
 # End of file

cime_config/cam_config.py

@@ -838,7 +838,7 @@ def generate_cam_src(self, gen_fort_indent):
         retvals = generate_registry(data_search, build_cache, self.__atm_root,
                                     self.__bldroot, source_mods_dir,
                                     dyn, gen_fort_indent)
-        reg_dir, force_ccpp, reg_files, ic_names = retvals
+        reg_dir, force_ccpp, reg_files, ic_names, registry_constituents = retvals
 
         #Add registry path to config object:
         reg_dir_desc = "Location of auto-generated registry code."
@@ -871,7 +871,7 @@ def generate_cam_src(self, gen_fort_indent):
         init_dir = generate_init_routines(build_cache, self.__bldroot,
                                           force_ccpp, force_init,
                                           source_mods_dir, gen_fort_indent,
-                                          capgen_db, ic_names)
+                                          capgen_db, ic_names, registry_constituents)
 
         #Add registry path to config object:
         init_dir_desc = "Location of auto-generated physics initialization code."

cime_config/config_archive.xml

@@ -0,0 +1,27 @@
+<components version="2.0">
+
+  <comp_archive_spec compname="cam" compclass="atm">
+    <rest_file_extension>r</rest_file_extension>
+    <rest_file_extension>rh\d*</rest_file_extension>
+    <rest_file_extension>rs</rest_file_extension>
+    <hist_file_extension>h\d*.*\.nc$</hist_file_extension>
+    <hist_file_extension>i\..*\.nc$</hist_file_extension>
+    <hist_file_extension>e</hist_file_extension>
+    <rest_history_varname>nhfil</rest_history_varname>
+    <rpointer>
+      <rpointer_file>rpointer.atm$NINST_STRING</rpointer_file>
+      <rpointer_content>$CASE.cam$NINST_STRING.r.$DATENAME.nc </rpointer_content>
+    </rpointer>
+    <test_file_names>
+      <tfile disposition="copy">rpointer.atm</tfile>
+      <tfile disposition="copy">rpointer.atm_9999</tfile>
+      <tfile disposition="copy">casename.cam.r.1976-01-01-00000.nc</tfile>
+      <tfile disposition="copy">casename.cam.rh4.1976-01-01-00000.nc</tfile>
+      <tfile disposition="move">casename.cam.h0.1976-01-01-00000.nc</tfile>
+      <tfile disposition="ignore">casename.cam.h0.1976-01-01-00000.nc.base</tfile>
+      <tfile disposition="move">casename.cam_0002.e.postassim.1976-01-01-00000.nc</tfile>
+      <tfile disposition="move">casename.cam_0002.e.preassim.1976-01-01-00000.nc</tfile>
+      <tfile disposition="move">casename.cam.i.1976-01-01-00000.nc</tfile>
+    </test_file_names>
+  </comp_archive_spec>
+</components>

cime_config/config_component.xml

@@ -8,6 +8,7 @@
       CAM
     ===============
    -->
+    <desc atm="CAM70[%1PCT][%4xCO2][%CCTS][%CFIRE][%CVBSX][%PORT][%RCO2][%SCAM][%SDYN][%WCCM][%WCMD][%WCSC][%WCTS][%WXIE]">CAM cam7 physics:</desc>
     <desc atm="CAM60[%1PCT][%4xCO2][%CCTS][%CFIRE][%CVBSX][%PORT][%RCO2][%SCAM][%SDYN][%WCCM][%WCMD][%WCSC][%WCTS][%WXIE]">CAM cam6 physics:</desc>
     <desc atm="CAM50[%CCTS][%CLB][%PORT][%RCO2][%SCAM][%SDYN][%WCSC][%WCTS]"              >CAM cam5 physics:</desc>
     <desc atm="CAM40[%PORT][%RCO2][%SCAM][%SDYN][%TMOZ][%WXIE][%WXIED][%WCMD]"                   >CAM cam4 physics:</desc>
@@ -120,6 +121,7 @@
     <valid_values></valid_values>
     <default_value></default_value>
     <values match="last" modifier='additive'>
+      <value compset="_CAM70">--physics-suites cam7</value>
 <!--      <value compset="_CAM40">-phys cam4</value>
       <value compset="_CAM50">-phys cam5</value>
       <value compset="_CAM60">-phys cam6</value> -->

cime_config/config_compsets.xml

@@ -104,6 +104,11 @@
   <!-- CAM tested compsets -->
   <!-- ****************************** -->
 
+  <compset>
+    <alias>FCAM7</alias>
+    <lname>2000_CAM70_SLND_SICE_SOCN_SROF_SGLC_SWAV</lname>
+  </compset>
+
   <compset>
     <alias>F2010climo</alias>
     <lname>2010_CAM60_CLM50%SP_CICE%PRES_DOCN%DOM_MOSART_CISM2%NOEVOLVE_SWAV</lname>

cime_config/config_pes.xml

@@ -72,6 +72,43 @@
       </pes>
     </mach>
   </grid>
+  <grid name="a%ne3np4">
+    <mach name="any">
+      <pes pesize="any" compset="any">
+        <comment>none</comment>
+        <ntasks>
+          <ntasks_atm>24</ntasks_atm>
+          <ntasks_lnd>24</ntasks_lnd>
+          <ntasks_rof>24</ntasks_rof>
+          <ntasks_ice>24</ntasks_ice>
+          <ntasks_ocn>24</ntasks_ocn>
+          <ntasks_glc>24</ntasks_glc>
+          <ntasks_wav>24</ntasks_wav>
+          <ntasks_cpl>24</ntasks_cpl>
+        </ntasks>
+        <nthrds>
+          <nthrds_atm>1</nthrds_atm>
+          <nthrds_lnd>1</nthrds_lnd>
+          <nthrds_rof>1</nthrds_rof>
+          <nthrds_ice>1</nthrds_ice>
+          <nthrds_ocn>1</nthrds_ocn>
+          <nthrds_glc>1</nthrds_glc>
+          <nthrds_wav>1</nthrds_wav>
+          <nthrds_cpl>1</nthrds_cpl>
+        </nthrds>
+        <rootpe>
+          <rootpe_atm>0</rootpe_atm>
+          <rootpe_lnd>0</rootpe_lnd>
+          <rootpe_rof>0</rootpe_rof>
+          <rootpe_ice>0</rootpe_ice>
+          <rootpe_ocn>0</rootpe_ocn>
+          <rootpe_glc>0</rootpe_glc>
+          <rootpe_wav>0</rootpe_wav>
+          <rootpe_cpl>0</rootpe_cpl>
+        </rootpe>
+      </pes>
+    </mach>
+  </grid>
   <grid name="a%ne30" >
     <mach name="any">
       <pes pesize="any" compset="any">

cime_config/namelist_definition_cam.xml

@@ -104,10 +104,15 @@
       <value hgrid="8x16" ic_ymd="10101" nlev="26">${DIN_LOC_ROOT}/atm/cam/inic/gaus/cami_0000-01-01_8x16_L26_c030228.nc</value>
       <value hgrid="8x16" ic_ymd="901" nlev="26">${DIN_LOC_ROOT}/atm/cam/inic/gaus/cami_0000-09-01_8x16_L26_c030918.nc</value>
       <value hgrid="8x16" ic_ymd="10101" nlev="30">${DIN_LOC_ROOT}/atm/cam/inic/gaus/cami_0000-01-01_8x16_L30_c090102.nc</value>
+      <value dyn="se" hgrid="ne3np4" nlev="93" chem="trop_strat_mam5_ts4">${DIN_LOC_ROOT}/atm/cam/inic/se/FCts4MTHIST_ne3pg3_spinup02.cam.i.1980-01-01_c240702.nc</value>
       <value dyn="se" hgrid="ne3np4" ic_ymd="10101" nlev="32">${DIN_LOC_ROOT}/atm/cam/inic/se/cam6_QPC6_topo_ne3pg3_mg37_L32_01-01-31_c221214.nc</value>
-      <value dyn="se" hgrid="ne3np4" ic_ymd="901" nlev="32">${DIN_LOC_ROOT}/atm/cam/inic/se/CESM2.F2000climo.ne3np4.cam.i.0003-09-01-00000.nc</value>
+      <value dyn="se" hgrid="ne3np4" ic_ymd="901"   nlev="32">${DIN_LOC_ROOT}/atm/cam/inic/se/CESM2.F2000climo.ne3np4.cam.i.0003-09-01-00000.nc</value>
       <value dyn="se" hgrid="ne3np4" ic_ymd="10101" nlev="30">${DIN_LOC_ROOT}/atm/cam/inic/se/cami_0000-01-01_ne3np4_L30_c120315.nc</value>
+      <value dyn="se" hgrid="ne3np4" ic_ymd="901"   nlev="30">${DIN_LOC_ROOT}/atm/cam/inic/se/cami_0000-01-01_ne3np4_L30_c120315.nc</value>
       <value dyn="se" hgrid="ne3np4" ic_ymd="10101" nlev="26">${DIN_LOC_ROOT}/atm/cam/inic/se/cami_0000-01-01_ne3np4_L26_c120525.nc</value>
+      <value dyn="se" hgrid="ne3np4" ic_ymd="901"   nlev="26">${DIN_LOC_ROOT}/atm/cam/inic/se/cami_0000-01-01_ne3np4_L26_c120525.nc</value>
+      <value dyn="se" hgrid="ne3np4" ic_ymd="10101" nlev="58">${DIN_LOC_ROOT}/atm/cam/inic/se/cam6_QPC6_topo_ne3pg3_mg37_L58_01-01-31_c221214.nc</value>
+      <value dyn="se" hgrid="ne3np4" ic_ymd="10101" nlev="93">${DIN_LOC_ROOT}/atm/cam/inic/se/cam6_FMTHIST_ne3pg3_mg37_L93_79-02-01_c240517.nc</value>
       <value dyn="se" hgrid="ne5np4" ic_ymd="10101" nlev="30">${DIN_LOC_ROOT}/atm/cam/inic/homme/cami-mam3_0000-01_ne5np4_L30.140707.nc</value>
       <value dyn="se" hgrid="ne16np4" ic_ymd="10101" nlev="26">${DIN_LOC_ROOT}/atm/cam/inic/se/ape_topo_cam4_ne16np4_L26_c171020.nc</value>
       <value dyn="se" hgrid="ne16np4" ic_ymd="10101" nlev="30">${DIN_LOC_ROOT}/atm/cam/inic/se/ape_topo_cam4_ne16np4_L30_c171020.nc</value>
@@ -212,6 +217,7 @@
       <value hgrid="2.5x3.33">${DIN_LOC_ROOT}/atm/cam/topo/USGS-gtopo30_2.5x3.33_remap_c100204.nc</value>
       <value hgrid="4x5">${DIN_LOC_ROOT}/atm/cam/topo/USGS-gtopo30_4x5_remap_c050520.nc</value>
       <value hgrid="10x15">${DIN_LOC_ROOT}/atm/cam/topo/fv_10x15_nc0540_Nsw042_Nrs008_Co060_Fi001_20171220.nc</value>
+      <value hgrid="ne3np4">${DIN_LOC_ROOT}/atm/cam/topo/se/ne3np4_gmted2010_modis_bedmachine_nc0540_Laplace1000_noleak_20230717.nc</value>
       <value hgrid="ne5np4">${DIN_LOC_ROOT}/atm/cam/topo/se/ne5np4_nc3000_Co360_Fi001_MulG_PF_nullRR_Nsw064_20170515.nc</value>
       <value hgrid="ne16np4">${DIN_LOC_ROOT}/atm/cam/topo/se/ne16np4_nc3000_Co120_Fi001_PF_nullRR_Nsw084_20171012.nc</value>
       <value hgrid="ne30np4">${DIN_LOC_ROOT}/atm/cam/topo/se/ne30np4_nc3000_Co060_Fi001_PF_nullRR_Nsw042_20171020.nc</value>
@@ -223,6 +229,7 @@
       <value hgrid="ne60np4" npg="2">${DIN_LOC_ROOT}/atm/cam/topo/se/ne60pg2_nc3000_Co030_Fi001_PF_nullRR_Nsw021_20171014.nc</value>
       <value hgrid="ne120np4" npg="2">${DIN_LOC_ROOT}/atm/cam/topo/se/ne120pg2_nc3000_Co015_Fi001_PF_nullRR_Nsw010_20171012.nc</value>
       <value hgrid="ne240np4" npg="2">${DIN_LOC_ROOT}/atm/cam/topo/se/ne240pg2_nc3000_Co008_Fi001_PF_nullRR_Nsw005_20171014.nc</value>
+      <value hgrid="ne3np4" npg="3">${DIN_LOC_ROOT}/atm/cam/topo/se/ne3pg3_gmted2010_modis_bedmachine_nc0540_Laplace1000_noleak_20230209.nc</value>
       <value hgrid="ne5np4" npg="3">${DIN_LOC_ROOT}/atm/cam/topo/se/ne5pg3_nc3000_Co360_Fi001_MulG_PF_nullRR_Nsw064_20170516.nc</value>
       <value hgrid="ne16np4" npg="3">${DIN_LOC_ROOT}/atm/cam/topo/se/ne16pg3_nc3000_Co120_Fi001_PF_nullRR_Nsw084_20171012.nc</value>
       <value hgrid="ne30np4" npg="3">${DIN_LOC_ROOT}/atm/cam/topo/se/ne30pg3_nc3000_Co060_Fi001_PF_nullRR_Nsw042_20171014.nc</value>
@@ -256,6 +263,18 @@
       <value>UNSET_PATH</value>
     </values>
   </entry>
+  <entry id="ncdata_check_err">
+    <type>logical</type>
+    <category>initial_conditions</category>
+    <group>physics_nl</group>
+    <desc>
+      Flag to determine whether to endrun if the ncdata check fails.
+      Default: FALSE
+    </desc>
+    <values>
+      <value>.false.</value>
+    </values>
+  </entry>
   <entry id="min_difference">
     <type>real</type>
     <category>diagnostics</category>