Merge branch 'jgfouca/eamxx_consistent_names' into master (PR #7197)

First round of name convention enforcing in namelist_defaults_eamxx.xml

and YAML files.

Related to #7179

Avoid arbitrary capitalization of param names, use only when it really makes sense (like T for temperature).

Full list of XML renames:
* Scorpio -> scorpio
* Type -> type
* Averaging Type -> averaging_type
* Group -> group
* Sequential -> sequential
* Moisture -> moisture
* BfbHash -> bfb_hash
* cldFraction -> cld_fraction
* Filename -> filename
* MPI Ranks in Filename -> mpi_ranks_in_filename
* ML* -> ml_*
* testOnly -> test_only
* Frequency -> frequency
* Ckh -> coeff_kh
* Ckm -> coeff_km
* srf_emis_specifier_for_DMS -> srf_emis_specifier_for_dms
* srf_emis_specifier_for_SO2 -> srf_emis_specifier_for_so2

YAML renames:
* Remove mpi_ranks_in_filename
* column_conservation_checks_fail_handling_type Warning/Fatal -> warning/fatal
* disable_diagnostics and theta_hydrostatic_mode, False->false
* GLL -> gll
* PG2 -> pg2
* None -> none (physics_grid_rebalance)
* Homme -> homme
* All average_type values should be lowercase
* Max Snapshots Per File -> max_snapshots_per_file
* Fields -> fields
* Physics -> physics
* Field Names -> field_names
* Mesh Free -> mesh_free
* Restart -> restart. Restart Run -> restart_run
* Point Grid -> point_grid
* Checkpoint Control -> checkpoint_control
* Sub Name -> sub_name
* Grid Name -> grid_name. IO Grid Name -> io_grid_name
* SurfaceCouplingImporter -> surface_coupling_importer
* Dynamics -> dynamics
* physics gll -> physics_gll. physics pg2 -> physics_pg2

[BFB]

Author: jgfouca

components/eamxx/cime_config/eamxx_buildnml.py

@@ -587,8 +587,8 @@ def _create_raw_xml_file_impl(case, xml, filepath=None):
     ...         <enable_postcondition_checks type='logical'>true</enable_postcondition_checks>
     ...       </atm_proc_base>
     ...       <physics_proc_base inherit='atm_proc_base'>
-    ...         <Grid>Physics GLL</Grid>
-    ...         <Grid grid='ne4ne4'>Physics PG2</Grid>
+    ...         <Grid>physics_gll</Grid>
+    ...         <Grid grid='ne4ne4'>physics_pg2</Grid>
     ...       </physics_proc_base>
     ...       <atm_proc_group inherit="atm_proc_base">
     ...         <atm_procs_list>NONE</atm_procs_list>
@@ -617,7 +617,7 @@ def _create_raw_xml_file_impl(case, xml, filepath=None):
                     ('enable_postcondition_checks', True),
                     (   'P1',
                         OrderedDict([   ('prop1', 'hi'),
-                                        ('Grid', 'Physics PG2'),
+                                        ('Grid', 'physics_pg2'),
                                         ('number_of_subcycles', 1),
                                         ('enable_precondition_checks', True),
                                         ('enable_postcondition_checks', True)])),
@@ -940,7 +940,7 @@ def create_input_data_list_file(case,caseroot):
     with open(eamxx_xml_file, "r") as fd:
         eamxx_xml = ET.parse(fd).getroot()
 
-        scorpio = get_child(eamxx_xml,'Scorpio')
+        scorpio = get_child(eamxx_xml,'scorpio')
         out_files_xml = get_child(scorpio,"output_yaml_files",must_exist=False)
         #  out_files = out_files_xml.text.split(",") if (out_files_xml is not None and out_files_xml.text is not None) else []
         #  for fn in out_files:
@@ -1009,7 +1009,7 @@ def do_cime_vars_on_yaml_output_files(case, caseroot):
     with open(eamxx_xml_file, "r") as fd:
         eamxx_xml = ET.parse(fd).getroot()
 
-    scorpio = get_child(eamxx_xml,'Scorpio')
+    scorpio = get_child(eamxx_xml,'scorpio')
     out_files_xml = get_child(scorpio,"output_yaml_files",must_exist=False)
     out_files = out_files_xml.text.split(",") if (out_files_xml is not None and out_files_xml.text is not None) else []
 
@@ -1027,10 +1027,10 @@ def do_cime_vars_on_yaml_output_files(case, caseroot):
     scream_input = yaml.load(open(scream_input_file,"r"),Loader=loader)
 
     # Determine the physics grid type for use in CIME-var substitution.
-    pgt = 'GLL'
+    pgt = 'gll'
     atm_grid = case.get_value('ATM_GRID')
     if '.pg' in atm_grid:
-        pgt = 'PG' + atm_grid[-1]
+        pgt = 'pg' + atm_grid[-1]
 
     for fn in out_files:
         # Get full name
@@ -1052,10 +1052,10 @@ def do_cime_vars_on_yaml_output_files(case, caseroot):
         # produces an output at t=0, which is not present in the restarted run, and
         # which also causes different timestamp in the file name.
         # Hence, change default output settings to perform a single AVERAGE step at the end of the run
-        if case.get_value("TESTCASE") in ["ERP", "ERS"] and content['Averaging Type'].upper()=="INSTANT":
+        if case.get_value("TESTCASE") in ["ERP", "ERS"] and content['averaging_type'].upper()=="INSTANT":
             hist_n = int(case.get_value("HIST_N",resolved=True))
             hist_opt = case.get_value("HIST_OPTION",resolved=True)
-            content['output_control']['Frequency'] = hist_n
+            content['output_control']['frequency'] = hist_n
             content['output_control']['frequency_units'] = hist_opt
             content['output_control']['skip_t0_output'] = True
             print ("ERS/ERP test with INSTANT output detected. Adjusting output control specs:\n")
@@ -1065,7 +1065,7 @@ def do_cime_vars_on_yaml_output_files(case, caseroot):
         # If frequency_units is not nsteps, verify that we don't request
         # a frequency faster than the model timestep
         if content['output_control']['frequency_units'] in ['nsecs','nmins','nhours']:
-            freq  = content['output_control']['Frequency']
+            freq  = content['output_control']['frequency']
             units = content['output_control']['frequency_units']
             dt_out = 1 if units=="nsecs" else 60 if units=="nmins" else 3600
             dt_out = dt_out*int(freq)
@@ -1074,18 +1074,18 @@ def do_cime_vars_on_yaml_output_files(case, caseroot):
             expect (dt_atm<=dt_out,
                    "Cannot have output frequency faster than atm timestep.\n"
                    f"   yaml file: {fn.strip()}\n"
-                   f"   Frequency: {freq}\n"
+                   f"   frequency: {freq}\n"
                    f"   frequency_units: {units}\n"
                    f"   ATM_NCPL: {case.get_value('ATM_NCPL')}\n"
-                   f" This yields dt_atm={dt_atm} > dt_output={dt_out}. Please, adjust 'Frequency' and/or 'frequency_units'\n")
+                   f" This yields dt_atm={dt_atm} > dt_output={dt_out}. Please, adjust 'frequency' and/or 'frequency_units'\n")
 
         ordered_dump(content, open(dst_yaml, "w"))
 
         output_yaml_files.append(dst_yaml)
 
     # Now update the output yaml files entry, and dump the new content
     # of the scream input to YAML file
-    scream_input["Scorpio"]["output_yaml_files"] = refine_type(",".join(output_yaml_files),"array(string)")
+    scream_input["scorpio"]["output_yaml_files"] = refine_type(",".join(output_yaml_files),"array(string)")
     with open(scream_input_file, "w") as fd:
         fd.write(
 """################################################################

components/eamxx/cime_config/eamxx_buildnml_impl.py

@@ -590,8 +590,8 @@ def gen_group_processes(ap_names_str, atm_procs_defaults):
 
         # Check if this pre-defined proc is itself a group, and, if so,
         # build all its sub-processes
-        ptype = get_child(proc, "Type", must_exist=False)
-        if ptype is not None and ptype.text=="Group":
+        ptype = get_child(proc, "type", must_exist=False)
+        if ptype is not None and ptype.text=="group":
             # This entry of the group is itself a group, with pre-defined
             # defaults. Let's add its entries to it
             sub_group_procs = get_child(proc, "atm_procs_list").text