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

.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"]

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."

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

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"""

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>