Merge branch 'bartgol/eamxx/namelist-change' (PR #7577)

Allows users to change the list of processes in the "overall eamxx atm process group".

[BFB]

Author: bartgol

components/eamxx/cime_config/eamxx_buildnml.py

@@ -577,14 +577,16 @@ def _create_raw_xml_file_impl(case, xml, filepath=None):
     ...     <selectors/>
     ...     <generated_files/>
     ...     <atmosphere_processes_defaults>
-    ...         <atm_procs_list type="array(string)">P1,P2</atm_procs_list>
     ...         <atm_proc_base>
     ...             <prop1>zero</prop1>
     ...         </atm_proc_base>
     ...         <atm_proc_group inherit="atm_proc_base">
     ...             <atm_procs_list>NONE</atm_procs_list>
     ...             <prop2>one</prop2>
     ...         </atm_proc_group>
+    ...         <eamxx inherit="atm_proc_group">
+    ...             <atm_procs_list>P1,P2</atm_procs_list>
+    ...         </eamxx>
     ...         <P1 inherit="atm_proc_base">
     ...             <prop1>two</prop1>
     ...         </P1>
@@ -596,7 +598,7 @@ def _create_raw_xml_file_impl(case, xml, filepath=None):
     >>> import xml.etree.ElementTree as ET
     >>> defaults = ET.fromstring(xml)
     >>> generated = _create_raw_xml_file_impl(case,defaults)
-    >>> d = convert_to_dict(get_child(generated,'atmosphere_processes'))
+    >>> d = convert_to_dict(get_child(generated,'eamxx'))
     >>> import pprint
     >>> pp = pprint.PrettyPrinter(indent=4)
     >>> pp.pprint(d)
@@ -610,18 +612,20 @@ def _create_raw_xml_file_impl(case, xml, filepath=None):
     >>> xml = '''
     ... <namelist_defaults>
     ...     <selectors>
-    ...       <selector name="grid" case_env="ATM_GRID"/>
+    ...         <selector name="grid" case_env="ATM_GRID"/>
     ...     </selectors>
     ...     <generated_files/>
     ...     <atmosphere_processes_defaults>
-    ...         <atm_procs_list type="array(string)">P1,P2</atm_procs_list>
     ...         <atm_proc_base>
     ...             <prop1>zero</prop1>
     ...         </atm_proc_base>
     ...         <atm_proc_group inherit="atm_proc_base">
     ...             <atm_procs_list>NONE</atm_procs_list>
     ...             <prop2>one</prop2>
     ...         </atm_proc_group>
+    ...         <eamxx inherit="atm_proc_group">
+    ...             <atm_procs_list>P1,P2</atm_procs_list>
+    ...         </eamxx>
     ...         <P1 inherit="atm_proc_base">
     ...             <prop1>two</prop1>
     ...             <prop1 grid='ne4ne4'>two_selected</prop1>
@@ -634,7 +638,7 @@ def _create_raw_xml_file_impl(case, xml, filepath=None):
     >>> import xml.etree.ElementTree as ET
     >>> defaults = ET.fromstring(xml)
     >>> generated = _create_raw_xml_file_impl(case,defaults)
-    >>> d = convert_to_dict(get_child(generated,'atmosphere_processes'))
+    >>> d = convert_to_dict(get_child(generated,'eamxx'))
     >>> import pprint
     >>> pp = pprint.PrettyPrinter(indent=4)
     >>> pp.pprint(d)
@@ -652,12 +656,14 @@ def _create_raw_xml_file_impl(case, xml, filepath=None):
     ...     </selectors>
     ...     <generated_files/>
     ...     <atmosphere_processes_defaults>
-    ...       <atm_procs_list type="array(string)">P1,P2</atm_procs_list>
     ...       <atm_proc_base>
     ...         <number_of_subcycles constraints='gt 0'>1</number_of_subcycles>
     ...         <enable_precondition_checks type='logical'>true</enable_precondition_checks>
     ...         <enable_postcondition_checks type='logical'>true</enable_postcondition_checks>
     ...       </atm_proc_base>
+    ...       <eamxx inherit="atm_proc_group">
+    ...         <atm_procs_list>P1,P2</atm_procs_list>
+    ...       </eamxx>
     ...       <physics_proc_base inherit='atm_proc_base'>
     ...         <Grid>physics_gll</Grid>
     ...         <Grid grid='ne4ne4'>physics_pg2</Grid>
@@ -678,7 +684,7 @@ def _create_raw_xml_file_impl(case, xml, filepath=None):
     >>> import xml.etree.ElementTree as ET
     >>> defaults = ET.fromstring(xml)
     >>> generated = _create_raw_xml_file_impl(case,defaults)
-    >>> d = convert_to_dict(get_child(generated,'atmosphere_processes'))
+    >>> d = convert_to_dict(get_child(generated,'eamxx'))
     >>> import pprint
     >>> pp = pprint.PrettyPrinter(indent=4)
     >>> pp.pprint(d)
@@ -721,15 +727,16 @@ def _create_raw_xml_file_impl(case, xml, filepath=None):
         # 4. Expand any CIME var that appears inside XML nodes text
         expand_cime_vars(xml,case)
 
-        # 5. Grab the atmosphere_processes macro list, with all the defaults
+        # 5. Grab the atmosphere_processes_defaults node, with all the procs defaults
         atm_procs_defaults = get_child(xml,"atmosphere_processes_defaults",remove=True)
 
-        # 6. Get atm procs list
-        atm_procs_list = get_child(atm_procs_defaults,"atm_procs_list",remove=True)
+        # 6. Get eamxx atm procs list
+        eamxx_group = get_child(atm_procs_defaults,"eamxx",remove=True)
+        atm_procs_list = get_child(eamxx_group,"atm_procs_list",remove=True)
 
         # 7. Form the nested list of atm procs needed, append to atmosphere_driver section
         atm_procs = gen_atm_proc_group(atm_procs_list.text, atm_procs_defaults)
-        atm_procs.tag = "atmosphere_processes"
+        atm_procs.tag = "eamxx"
         xml.append(atm_procs)
 
         # 8. Apply all changes in the SCREAM_ATMCHANGE_BUFFER that do not alter

components/eamxx/cime_config/eamxx_buildnml_impl.py

@@ -502,7 +502,9 @@ def resolve_inheritance(root, elem):
                         for child in elem:
                             if child.tag==entry.tag:
                                 expect (att not in child.attrib.keys(),
-                                        f"Do not set '{att}' attribute when parent node already specifies it.")
+                                        f"Do not set '{att}' attribute when parent node already specifies it."
+                                        f" parent node: {parent.tag}\n"
+                                        f" child node : {entry.tag}")
                                 child.attrib[att] = parent_type
 
     for child in elem:

components/eamxx/cime_config/namelist_defaults_eamxx.xml

@@ -50,7 +50,7 @@ be lost if SCREAM_HACK_XML is not enabled.
       <sections>ctl_nl</sections>
     </file>
     <file name="data/scream_input.yaml" format="yaml">
-      <sections>driver_debug_options,driver_options,iop_options,atmosphere_processes,grids_manager,initial_conditions,scorpio,e3sm_parameters</sections>
+      <sections>driver_debug_options,driver_options,iop_options,eamxx,grids_manager,initial_conditions,scorpio,e3sm_parameters</sections>
     </file>
   </generated_files>
 
@@ -138,15 +138,6 @@ be lost if SCREAM_HACK_XML is not enabled.
 
   <atmosphere_processes_defaults>
 
-    <!--
-      List of atm procs. You can form processes groups by using parentheses,
-      or by giving the group a name, and adding a subsection that inherit
-      from atm_proc_group. atm_procs_list itself *must* represent a group,
-      so it must be of the form (a,b,...).
-      NOTE: *CANNOT* be changed.
-    -->
-    <atm_procs_list type="array(string)">sc_import,homme,physics,sc_export</atm_procs_list>
-
     <!-- Basic options for each atm process -->
     <atm_proc_base>
       <number_of_subcycles constraints="gt 0" doc="how many times to subcycle this atm process">1</number_of_subcycles>
@@ -173,6 +164,11 @@ be lost if SCREAM_HACK_XML is not enabled.
       <schedule_type valid_values="sequential">sequential</schedule_type>
     </atm_proc_group>
 
+    <!-- The list of atm processes for the atm as a whole -->
+    <eamxx inherit="atm_proc_group">
+      <atm_procs_list>sc_import,homme,physics,sc_export</atm_procs_list>
+    </eamxx>
+
     <!-- Surface coupling (import and export) -->
     <sc_import inherit="atm_proc_base"/>
     <sc_export inherit="atm_proc_base">

components/eamxx/cime_config/testdefs/testmods_dirs/eamxx/internal_diagnostics_level/shell_commands

@@ -1,2 +1,2 @@
-$CIMEROOT/../components/eamxx/scripts/atmchange ANY::internal_diagnostics_level=1 atmosphere_processes::internal_diagnostics_level=0 -b
+$CIMEROOT/../components/eamxx/scripts/atmchange ANY::internal_diagnostics_level=1 eamxx::internal_diagnostics_level=0 -b
 ./xmlchange POSTRUN_SCRIPT="$CIMEROOT/../components/eamxx/scripts/check-hashes-ers"

components/eamxx/cime_config/testdefs/testmods_dirs/eamxx/small_kernels/shell_commands

@@ -1,2 +1,2 @@
 ./xmlchange --append SCREAM_CMAKE_OPTIONS='SCREAM_SMALL_KERNELS On'
-$CIMEROOT/../components/eamxx/scripts/atmchange ANY::internal_diagnostics_level=1 atmosphere_processes::internal_diagnostics_level=0 -b
+$CIMEROOT/../components/eamxx/scripts/atmchange ANY::internal_diagnostics_level=1 eamxx::internal_diagnostics_level=0 -b

components/eamxx/cime_config/testdefs/testmods_dirs/eamxx/small_kernels_p3/shell_commands

@@ -1,2 +1,2 @@
 ./xmlchange --append SCREAM_CMAKE_OPTIONS='SCREAM_P3_SMALL_KERNELS On'
-$CIMEROOT/../components/eamxx/scripts/atmchange ANY::internal_diagnostics_level=1 atmosphere_processes::internal_diagnostics_level=0 -b
+$CIMEROOT/../components/eamxx/scripts/atmchange ANY::internal_diagnostics_level=1 eamxx::internal_diagnostics_level=0 -b

components/eamxx/cime_config/testdefs/testmods_dirs/eamxx/small_kernels_shoc/shell_commands

@@ -1,2 +1,2 @@
 ./xmlchange --append SCREAM_CMAKE_OPTIONS='SCREAM_SHOC_SMALL_KERNELS On'
-$CIMEROOT/../components/eamxx/scripts/atmchange ANY::internal_diagnostics_level=1 atmosphere_processes::internal_diagnostics_level=0 -b
+$CIMEROOT/../components/eamxx/scripts/atmchange ANY::internal_diagnostics_level=1 eamxx::internal_diagnostics_level=0 -b

components/eamxx/src/control/atmosphere_driver.cpp

@@ -235,7 +235,7 @@ void AtmosphereDriver::create_atm_processes()
   // Create the group of processes. This will recursively create the processes
   // tree, storing also the information regarding parallel execution (if needed).
   // See AtmosphereProcessGroup class documentation for more details.
-  auto& atm_proc_params = m_atm_params.sublist("atmosphere_processes");
+  auto& atm_proc_params = m_atm_params.sublist("eamxx");
   atm_proc_params.rename("EAMxx");
   atm_proc_params.set("logger",m_atm_logger);
   m_atm_process_group = std::make_shared<AtmosphereProcessGroup>(m_atm_comm,atm_proc_params);

components/eamxx/src/control/tests/ad_tests.yaml

@@ -9,7 +9,7 @@ initial_conditions:
   V: [2.0, 3.0]
   Z: "A"
 
-atmosphere_processes:
+eamxx:
   atm_procs_list: [dummy1, dummy2, dummy3]
   schedule_type: sequential
 

components/eamxx/tests/multi-process/dynamics_physics/homme_shoc_cld_p3_rrtmgp/input.yaml

@@ -23,7 +23,7 @@ initial_conditions:
   hetfrz_contact_nucleation_tend: 0.1
   hetfrz_deposition_nucleation_tend: 0.1
 
-atmosphere_processes:
+eamxx:
   atm_procs_list: [homme,physics]
   schedule_type: sequential
   homme: