Check initial value attribute(s) (#376)

Tag name (required for release branches):
Originator(s): peverwhee

Description (include the issue title, and the keyword ['closes',
'fixes', 'resolves'] followed by the issue number):

Adds logic to check the initial_value `dycore` attribute, if present,
against the dycore. Hopefully also will be "easy" to add additional
attributes in the future.

The logic is:
- Will pick the initial_value entry with the "most" attribute matches
(which, right now, just means it'll pick the default if the dycore
doesn't match other entries or if there are no dycore-specific entries)
- Will error if there is a "tie" (multiple entries have the same number
of attribute matches)

Describe any changes made to build system:
**M   src/data/generate_registry_data.py**
- check dycore attribute for initial_value, if present
- also update "dycore" to "dyn"

**M src/data/registry.xml**
- update "dycore" to "dyn"

**M src/data/registry_v1_0.xsd**
- update "dycore" to "dyn"

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  test/unit/python/sample_files/*.xml**
- add additional options for dycore initial_value attribute

**M test/unit/python/sample_files/*.F90**
- update expected files corresponding to .xml updates

**M test/unit/python/test_registry.py**
- change "dycore" to "dyn"

If there are new failures (compared 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: all PASS

derecho/gnu/aux_sima: all PASS

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:

Author: peverwhee

src/data/generate_registry_data.py

@@ -141,7 +141,7 @@ class VarBase:
     __pointer_type_str = "pointer"
 
     def __init__(self, elem_node, local_name, dimensions, known_types,
-                 type_default, units_default="", kind_default='',
+                 type_default, units_default="", kind_default='', dycore='',
                  protected=False, index_name='', local_index_name='',
                  local_index_name_str='', alloc_default='none',
                  tstep_init_default=False):
@@ -154,6 +154,7 @@ def __init__(self, elem_node, local_name, dimensions, known_types,
         self.__standard_name = elem_node.get('standard_name')
         self.__long_name = ''
         self.__initial_value = ''
+        self.__initial_value_match = 0
         self.__initial_val_vars = set()
         self.__ic_names = None
         self.__elements = []
@@ -183,7 +184,30 @@ def __init__(self, elem_node, local_name, dimensions, known_types,
             if attrib.tag == 'long_name':
                 self.__long_name = attrib.text
             elif attrib.tag == 'initial_value':
-                self.__initial_value = attrib.text
+                # Figure out if we should use this initial_value
+                #  If the number of matching attributes is greater than the
+                #  default or a previous match, pick this one
+                matches = 0
+                if not attrib.keys():
+                    self.__initial_value = attrib.text
+                # end if (no attributes, this is the default)
+                for att in attrib.keys():
+                    # Check each attribute (for now, this is only the dycore)
+                    if att == 'dyn':
+                        dycore_list = attrib.get('dyn').lower().split(',')
+                        if dycore in dycore_list:
+                            matches += 1
+                        # end if (dycore matches)
+                    # end if (check the dycore)
+                # end for
+                if matches == self.__initial_value_match and matches != 0:
+                    emsg = f"Unclear which initial_value to use for {local_name}. There are at least two configurations with {matches} matching attributes"
+                    raise CCPPError(emsg)
+                elif matches > self.__initial_value_match:
+                    # Use this initial_value (for now)
+                    self.__initial_value_match = matches
+                    self.__initial_value = attrib.text
+                # end if (number of matches)
             elif attrib.tag == 'ic_file_input_names':
                 #Separate out string into list:
                 self.__ic_names = [x.strip() for x in attrib.text.split(' ') if x]
@@ -488,16 +512,16 @@ class Variable(VarBase):
 ###############################################################################
     # pylint: disable=too-many-instance-attributes
     """Registry variable
-    >>> Variable(ET.fromstring('<variable kind="kind_phys" local_name="u" standard_name="east_wind" type="real" units="m s-1"><dimensions>ccpp_constant_one:horizontal_dimension:two</dimensions></variable>'), TypeRegistry(), VarDict("foo", "module", None), None) #doctest: +IGNORE_EXCEPTION_DETAIL
+    >>> Variable(ET.fromstring('<variable kind="kind_phys" local_name="u" standard_name="east_wind" type="real" units="m s-1"><dimensions>ccpp_constant_one:horizontal_dimension:two</dimensions></variable>'), TypeRegistry(), VarDict("foo", "module", None), 'se', None) #doctest: +IGNORE_EXCEPTION_DETAIL
     Traceback (most recent call last):
     CCPPError: Illegal dimension string, ccpp_constant_one:horizontal_dimension:two, in u, step not allowed.
-    >>> Variable(ET.fromstring('<variable kind="kind_phys" local_name="u" standard_name="east_wind" type="real" units="m s-1"><dims>horizontal_dimension</dims></variable>'), TypeRegistry(), VarDict("foo", "module", None), None) #doctest: +IGNORE_EXCEPTION_DETAIL
+    >>> Variable(ET.fromstring('<variable kind="kind_phys" local_name="u" standard_name="east_wind" type="real" units="m s-1"><dims>horizontal_dimension</dims></variable>'), TypeRegistry(), VarDict("foo", "module", None), 'se', None) #doctest: +IGNORE_EXCEPTION_DETAIL
     Traceback (most recent call last):
     CCPPError: Unknown Variable content, dims
-    >>> Variable(ET.fromstring('<variable kkind="kind_phys" local_name="u" standard_name="east_wind" type="real" units="m s-1"></variable>'), TypeRegistry(), VarDict("foo", "module", None), None) #doctest: +IGNORE_EXCEPTION_DETAIL
+    >>> Variable(ET.fromstring('<variable kkind="kind_phys" local_name="u" standard_name="east_wind" type="real" units="m s-1"></variable>'), TypeRegistry(), VarDict("foo", "module", None), 'se', None) #doctest: +IGNORE_EXCEPTION_DETAIL
     Traceback (most recent call last):
     CCPPError: Bad variable attribute, 'kkind', for 'u'
-    >>> Variable(ET.fromstring('<variable kind="kind_phys" local_name="u" standard_name="east_wind" type="real" units="m s-1" allocatable="target"><dimensions>horizontal_dimension vertical_dimension</dimensions></variable>'), TypeRegistry(), VarDict("foo", "module", None), None) #doctest: +IGNORE_EXCEPTION_DETAIL
+    >>> Variable(ET.fromstring('<variable kind="kind_phys" local_name="u" standard_name="east_wind" type="real" units="m s-1" allocatable="target"><dimensions>horizontal_dimension vertical_dimension</dimensions></variable>'), TypeRegistry(), VarDict("foo", "module", None), 'se', None) #doctest: +IGNORE_EXCEPTION_DETAIL
     Traceback (most recent call last):
     CCPPError: Dimension, 'vertical_dimension', not found for 'u'
     """
@@ -511,7 +535,7 @@ class Variable(VarBase):
                         "phys_timestep_init_zero", "standard_name",
                         "type", "units", "version"]
 
-    def __init__(self, var_node, known_types, vdict, logger):
+    def __init__(self, var_node, known_types, vdict, dycore, logger):
         # pylint: disable=too-many-locals
         """Initialize a Variable from registry XML"""
         local_name = var_node.get('local_name')
@@ -588,7 +612,7 @@ def __init__(self, var_node, known_types, vdict, logger):
         # Initialize the base class
         super().__init__(var_node, local_name,
                                        my_dimensions, known_types, ttype,
-                                       protected=protected)
+                                       dycore=dycore, protected=protected)
 
         for attrib in var_node:
             # Second pass, only process array elements
@@ -1090,7 +1114,7 @@ def __init__(self, ddt_node, known_types, var_dict, dycore):
                 varname = attrib.text
                 include_var = True
                 attrib_dycores = [x.strip().lower() for x in
-                                  attrib.get('dycore', default="").split(',')
+                                  attrib.get('dyn', default="").split(',')
                                   if x]
                 if attrib_dycores and (dycore not in attrib_dycores):
                     include_var = False
@@ -1226,6 +1250,7 @@ def __init__(self, file_node, known_types, dycore,
         self.__use_statements = []
         self.__generate_code = gen_code
         self.__file_path = file_path
+        self.__dycore = dycore
         for obj in file_node:
             if obj.tag in ['variable', 'array']:
                 self.add_variable(obj, logger)
@@ -1252,7 +1277,7 @@ def add_variable(self, var_node, logger):
         """Create a Variable from <var_node> and add to this File's
         variable dictionary"""
         newvar = Variable(var_node, self.__known_types, self.__var_dict,
-                          logger)
+                          self.__dycore, logger)
         self.__var_dict.add_variable(newvar)
 
     def add_ddt(self, newddt, logger=None):

src/data/registry.xml

@@ -349,7 +349,7 @@
               units="flag" type="logical">
       <long_name>flag indicating if dynamical core energy is not consistent with CAM physics and to perform adjustment of temperature and temperature tendency</long_name>
       <initial_value>.false.</initial_value>
-      <initial_value dycore="SE,MPAS">.true.</initial_value>
+      <initial_value dyn="SE,MPAS">.true.</initial_value>
     </variable>
     <!-- Timestep properties -->
     <variable local_name="is_first_timestep"
@@ -392,7 +392,7 @@
               standard_name="dycore_calculates_geopotential_using_logarithms"
               units="flag" type="logical" access="protected">
       <initial_value>.false.</initial_value>
-      <initial_value dycore="SE,FV">.true.</initial_value>
+      <initial_value dyn="SE,FV">.true.</initial_value>
     </variable>
     <ddt type="physics_state">
       <data>air_temperature</data>

src/data/registry_v1_0.xsd

@@ -96,7 +96,7 @@
 
   <xs:attribute name="access"                  type="access_type"/>
   <xs:attribute name="allocatable"             type="allocation_type"/>
-  <xs:attribute name="dycore"                  type="dycore_type"/>
+  <xs:attribute name="dyn"                     type="dycore_type"/>
   <xs:attribute name="extends"                 type="fortran_id_type"/>
   <xs:attribute name="kind"                    type="fortran_id_type"/>
   <xs:attribute name="local_name"              type="fortran_id_type"/>
@@ -130,7 +130,10 @@
   <xs:complexType name="initial_value">
     <xs:simpleContent>
       <xs:extension base="xs:string">
-        <xs:attribute ref="dycore" use="optional" default=""/>
+	<!--- If adding a new attribute, also modify generate_registry_data.py
+		to check the attribute
+	-->
+        <xs:attribute ref="dyn" use="optional" default=""/>
       </xs:extension>
     </xs:simpleContent>
   </xs:complexType>
@@ -192,7 +195,7 @@
   <xs:complexType name="data_type">
     <xs:simpleContent>
       <xs:extension base="standard_name_type">
-        <xs:attribute ref="dycore" use="optional" default=""/>
+        <xs:attribute ref="dyn" use="optional" default=""/>
       </xs:extension>
     </xs:simpleContent>
   </xs:complexType>

test/unit/python/sample_files/physics_types_complete.F90

@@ -29,7 +29,7 @@ module physics_types_complete
 !! \htmlinclude physics_base.html
   type, bind(C) :: physics_base
     ! ncol: Number of horizontal columns
-    integer                    :: ncol = 0
+    integer                    :: ncol = 1
     ! pver: Number of vertical layers
     integer                    :: pver = 0
   end type physics_base
@@ -197,7 +197,7 @@ subroutine allocate_physics_types_complete_fields(horizontal_dimension,
       phys_state%q(:,:,ix_cld_liq) = nan
     end if
     if (set_init_val) then
-      phys_state%ncol = 0
+      phys_state%ncol = 1
     end if
     if (set_init_val) then
       phys_state%pver = 0

test/unit/python/sample_files/reg_good_complete.xml

@@ -9,6 +9,8 @@
               units="count" type="integer" access="protected">
       <long_name>Number of horizontal columns</long_name>
       <initial_value>0</initial_value>
+      <initial_value dyn='SE'>1</initial_value>
+      <initial_value dyn='FV,MPAS'>2</initial_value>
     </variable>
     <variable local_name="pver" standard_name="vertical_layer_dimension"
               units="count" type="integer" access="protected">

test/unit/python/sample_files/reg_good_ddt.xml

@@ -31,9 +31,9 @@
       <initial_value>rair/cpair</initial_value>
     </variable>
     <ddt type="physics_state">
-      <data dycore="FV,EUL,SE">horizontal_dimension</data>
-      <data dycore="SE">latitude</data>
-      <data dycore="FV">longitude</data>
+      <data dyn="FV,EUL,SE">horizontal_dimension</data>
+      <data dyn="SE">latitude</data>
+      <data dyn="FV">longitude</data>
     </ddt>
     <variable local_name="phys_state"
               standard_name="physics_state_due_to_dynamics"

test/unit/python/sample_files/reg_good_mf.xml

@@ -31,9 +31,9 @@
       <initial_value>rair/cpair</initial_value>
     </variable>
     <ddt type="physics_state">
-      <data dycore="FV,EUL,SE">horizontal_dimension</data>
-      <data dycore="SE">latitude</data>
-      <data dycore="FV">longitude</data>
+      <data dyn="FV,EUL,SE">horizontal_dimension</data>
+      <data dyn="SE">latitude</data>
+      <data dyn="FV">longitude</data>
     </ddt>
     <variable local_name="phys_state"
               standard_name="physics_state_due_to_dynamics"

test/unit/python/sample_files/reg_good_simple.xml

@@ -7,6 +7,7 @@
               units="count" type="integer" access="protected">
       <long_name>Number of horizontal columns</long_name>
       <initial_value>0</initial_value>
+      <initial_value dyn="SE">1</initial_value>
     </variable>
     <variable local_name="latitude" standard_name="latitude"
               units="radians" type="real" kind="kind_phys"

test/unit/python/test_registry.py

@@ -85,7 +85,9 @@ def setUpClass(cls):
     def test_good_simple_registry(self):
         """Test that a good registry with only variables validates.
         Check that generate_registry_data.py generates good
-        Fortran and metadata files"""
+        Fortran and metadata files. Expectation is that the initial
+        value for ncol will be set to the default of 0 because there is no
+        dycore match"""
         # Setup test
         filename = os.path.join(_SAMPLE_FILES_DIR, "reg_good_simple.xml")
         out_source_name = "physics_types_simple"
@@ -607,6 +609,56 @@ def test_bad_registry_version(self):
         self.assertFalse(os.path.exists(out_meta))
         self.assertFalse(os.path.exists(out_source))
 
+    def test_registry_no_clear_initial_value(self):
+        """
+        Check that generate_registry_data.py throws the correct
+        error message when there is no clear "winner"
+        between the initial_value entries
+        """
+
+        # Setup test
+        infilename = os.path.join(_SAMPLE_FILES_DIR, "reg_good_simple.xml")
+        tree, root = read_xml_file(infilename)
+
+        # Open base XML file:
+        base_tree = ET.parse(infilename)
+        base_root = base_tree.getroot()
+
+        # Write new namelist entry with "bad" value:
+        initial_value_tie_string = \
+        """
+        <variable local_name="myvar" standard_name="variable_with_unclear_initial_value"
+                  units="count" type="integer" access="protected">
+           <long_name>Number of horizontal columns</long_name>
+           <initial_value>2</initial_value>
+           <initial_value dyn="SE">0</initial_value>
+           <initial_value dyn="SE">1</initial_value>
+        </variable>
+        """
+
+        initial_value_tie_entry = ET.fromstring(initial_value_tie_string)
+
+        # Add new namelist entry back to original namelist XML tree:
+        base_root[0].append(initial_value_tie_entry)
+
+        # Write out new, temporary XML namelist file for testing:
+        xml_test_fil = os.path.join(_TMP_DIR, "test_registry_initial_value_tie.xml")
+        base_tree.write(xml_test_fil, encoding="utf-8", xml_declaration=True)
+        filename = os.path.join(_TMP_DIR, "test_registry_initial_value_tie.xml")
+
+        # Attempt to generate registry:
+        with self.assertRaises(CCPPError) as cerr:
+            retcode, files, _ = gen_registry(filename, 'se', _TMP_DIR, 2,
+                                             _SRC_MOD_DIR, _CAM_ROOT,
+                                             loglevel=logging.ERROR,
+                                             error_on_no_validate=True)
+
+        # Check exception message
+        emsg = "Unclear which initial_value to use for myvar. "
+        emsg += "There are at least two configurations with 1 matching attributes"
+
+        self.assertEqual(emsg, str(cerr.exception))
+
     def test_missing_standard_name(self):
         """Test a registry with a missing standard name.
         Check that it does not validate and does not generate any
@@ -812,10 +864,10 @@ def test_duplicate_type(self):
                         new_ddt = ET.SubElement(obj, "ddt")
                         new_ddt.set("type", dtype)
                         data_elem = ET.SubElement(new_ddt, "data")
-                        data_elem.set("dycore", "EUL")
+                        data_elem.set("dyn", "EUL")
                         data_elem.text = 'latitude'
                         data_elem = ET.SubElement(new_ddt, "data")
-                        data_elem.set("dycore", "EUL")
+                        data_elem.set("dyn", "EUL")
                         data_elem.text = 'longitude'
                         break
                     # End if