read in all possible constituents from file, not just build-time ones (…

…#301) Tag name (required for release branches): Originator(s): peverwhee Summary (include the keyword ['closes', 'fixes', 'resolves'] and issue number): - Updates to enable reading in data for runtime constituents Describe any changes made to build system: M cime_config/cam_autogen.py M cime_config/cam_build_cache.py M cime_config/cam_config.py - keep track of registry constituents Describe any changes made to the namelist: None List any changes to the defaults for the input datasets (e.g. boundary datasets): None List all files eliminated and why: None List all files added and what they do: None List all existing files that have been modified, and describe the changes: (Helpful git command: `git diff --name-status development...<your_branch_name>`) M src/data/generate_registry_data.py - create list of registry constituents to pass to write_init_files M src/data/write_init_files.py - handle constituents separately from other host variables; read/check ALL constituent variables, not just "required" ones M test/unit/test_*.py - update calling lists If there are new failures (compare to the `test/existing-test-failures.txt` file), have them OK'd by the gatekeeper, note them here, and add them to the file. If there are baseline differences, include the test and the reason for the diff. What is the nature of the change? Roundoff? derecho/intel/aux_sima: derecho/gnu/aux_sima: If this changes climate describe any run(s) done to evaluate the new climate in enough detail that it(they) could be reproduced: CAM-SIMA date used for the baseline comparison tests if different than latest: --------- Co-authored-by: Courtney Peverley <courtneyp@izumi.cgd.ucar.edu>
ESCOMP · Dec 2, 2024 · fd886c1 · fd886c1
1 parent e36d265
commit fd886c1
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Showing 29 changed files with 1,513 additions and 1,096 deletions.
diff --git a/.gitmodules b/.gitmodules
@@ -20,7 +20,7 @@
 [submodule "ncar-physics"]
         path          = src/physics/ncar_ccpp
 	url           = https://github.com/ESCOMP/atmospheric_physics
-	fxtag         = 045b630a8c3b41d90b6c006392c3907af762dd39
+	fxtag         = d46bb55e233e8f16b4e7a7b5a90352e99c7a5d72
         fxrequired    = AlwaysRequired
         fxDONOTUSEurl = https://github.com/ESCOMP/atmospheric_physics
 [submodule "ccs_config"]

diff --git a/cime_config/cam_autogen.py b/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:

diff --git a/cime_config/cam_build_cache.py b/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
diff --git a/cime_config/cam_config.py b/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."

diff --git a/src/data/air_composition.F90 b/src/data/air_composition.F90
@@ -346,8 +346,8 @@ subroutine air_composition_init()
             !
             ! CLDICE
             !
-         case('cloud_ice_water_mixing_ratio_wrt_moist_air_and_condensed_water')
-            call air_species_info('cloud_ice_water_mixing_ratio_wrt_moist_air_and_condensed_water', &
+         case('cloud_ice_mixing_ratio_wrt_moist_air_and_condensed_water')
+            call air_species_info('cloud_ice_mixing_ratio_wrt_moist_air_and_condensed_water', &
                                   ix, mw)
             thermodynamic_active_species_idx(icnst) = ix
             thermodynamic_active_species_cp (icnst) = cpice
@@ -408,7 +408,7 @@ subroutine air_composition_init()
             !
             ! GRAUQM
             !
-         case('graupel_water_mixing_ratio_wrt_moist_air_and_conedensed_water')
+         case('graupel_water_mixing_ratio_wrt_moist_air_and_condensed_water')
             call air_species_info('graupel_water_mixing_ratio_wrt_moist_air_and_condensed_water', &
                                   ix, mw)
             thermodynamic_active_species_idx(icnst) = ix

diff --git a/src/data/generate_registry_data.py b/src/data/generate_registry_data.py
@@ -1734,6 +1734,31 @@ def _create_ic_name_dict(registry):
     # end for
     return ic_name_dict
 
+###############################################################################
+def _create_constituent_list(registry):
+###############################################################################
+    """
+    Create a list of all constituents found in the registry.
+    To be used by write_init_files.py - need to keep track
+    of all constituent variables, not just ones required by
+    CCPP metadata, to handle runtime constituents
+    """
+    constituent_list = []
+    for section in registry:
+        if section.tag == 'file':
+            for obj in section:
+                if obj.tag == 'variable':
+                    if obj.get('constituent'):
+                        stdname = obj.get('standard_name')
+                        constituent_list.append(stdname)
+                    # end if (ignore non-constituents)
+                # end if (ignore other node types)
+            # end for
+        # end if (ignore other node types)
+    # end for
+    return constituent_list
+
+
 ###############################################################################
 def gen_registry(registry_file, dycore, outdir, indent,
                  src_mod, src_root, loglevel=None, logger=None,
@@ -1794,6 +1819,7 @@ def gen_registry(registry_file, dycore, outdir, indent,
         retcode = 1
         files = None
         ic_names = None
+        constituents = None
     else:
         library_name = registry.get('name')
         emsg = f"Parsing registry, {library_name}"
@@ -1803,9 +1829,10 @@ def gen_registry(registry_file, dycore, outdir, indent,
                                      src_root, reg_dir, indent, logger)
         # See comment in _create_ic_name_dict
         ic_names = _create_ic_name_dict(registry)
+        registry_constituents = _create_constituent_list(registry)
         retcode = 0 # Throw exception on error
     # end if
-    return retcode, files, ic_names
+    return retcode, files, ic_names, registry_constituents
 
 def main():
     """Function to execute when module called as a script"""

diff --git a/src/data/registry.xml b/src/data/registry.xml
@@ -445,5 +445,17 @@
       <dimensions>horizontal_dimension vertical_layer_dimension</dimensions>
       <ic_file_input_names>RAINQM cnst_RAINQM</ic_file_input_names>
     </variable>
+    <variable local_name="snowqm"
+              standard_name="snow_mixing_ratio_wrt_moist_air_and_condensed_water"
+              units="kg kg-1" type="real" constituent="true">
+      <long_name>snow mass mixing ratio with respect to moist air plus all airborne condensates</long_name>
+      <ic_file_input_names>SNOWQM cnst_SNOWQM</ic_file_input_names>
+    </variable>
+    <variable local_name="grauqm"
+              standard_name="graupel_water_mixing_ratio_wrt_moist_air_and_condensed_water"
+              units="kg kg-1" type="real" constituent="true">
+      <long_name>graupel mass mixing ratio with respect to moist air plus all airborne condensates</long_name>
+      <ic_file_input_names>GRAUQM cnst_GRAUQM</ic_file_input_names>
+    </variable>
   </file>
 </registry>