Add new register phase (#319)

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):

1. Adds call to new CCPP register phase brought in with framework PR
[#582](NCAR/ccpp-framework#582)
2. Uses the full error message returned from the exception handled when
xmllint is called (updated in framework PR
[#586](NCAR/ccpp-framework#586))
3. Adds `inverse_exner_function_wrt_surface_pressure` as possible input
variable name for exner for backwards compatibility with old converted
snapshots

closes #215 (add optional register phase)
closes #286 (Improve error message returned by XML linter)

Describe any changes made to build system: None

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  .gitmodules

- brings in new CCPP framework tag

M src/control/cam_comp.F90
M src/physics/utils/phys_comp.F90

- Adds call to new CCPP register phase in the generated cap

M src/data/generate_registry_data.py

- Uses full error message returned from xmllint

M src/data/registry.xml

- add backwards-compatible exner name


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: N/A

CAM-SIMA date used for the baseline comparison tests if different than
latest:

---------

Co-authored-by: Courtney Peverley <courtneyp@izumi.cgd.ucar.edu>

.gitmodules

@@ -1,7 +1,7 @@
 [submodule "ccpp-framework"]
         path          = ccpp_framework
         url           = https://github.com/NCAR/ccpp-framework
-        fxtag         = 2024-07-19-dev
+        fxtag         = 2024-10-31-dev
         fxrequired    = AlwaysRequired
 	fxDONOTUSEurl = https://github.com/NCAR/ccpp-framework
 [submodule "history"]

src/control/cam_comp.F90

@@ -86,6 +86,7 @@ subroutine cam_init(caseid, ctitle, model_doi_url,                         &
       use cam_initfiles,        only: cam_initfiles_open
       use dyn_grid,             only: model_grid_init
       use phys_comp,            only: phys_init
+      use phys_comp,            only: phys_register
       use dyn_comp,             only: dyn_init
 !      use cam_restart,          only: cam_read_restart
       use camsrfexch,           only: hub2atm_alloc, atm2hub_alloc
@@ -186,6 +187,10 @@ subroutine cam_init(caseid, ctitle, model_doi_url,                         &
       ! Open initial or restart file, and topo file if specified.
       call cam_initfiles_open()
 
+      ! Call CCPP physics register phase (must happen before
+      !   cam_register_constituents)
+      call phys_register()
+
       ! Initialize constituent information
       !    This will set the total number of constituents and the
       !    number of advected constituents.

src/data/generate_registry_data.py

@@ -1783,16 +1783,7 @@ def gen_registry(registry_file, dycore, outdir, indent,
                                     logger, schema_path=schema_dir,
                                     error_on_noxmllint=error_on_no_validate)
     except CCPPError as ccpperr:
-        cemsg = f"{ccpperr}".split('\n', maxsplit=1)[0]
-        if cemsg[0:12] == 'Execution of':
-            xstart = cemsg.find("'")
-            if xstart >= 0:
-                xend = cemsg[xstart + 1:].find("'") + xstart + 1
-                emsg += '\n' + cemsg[xstart + 1:xend]
-            # end if (else, just keep original message)
-        elif cemsg[0:18] == 'validate_xml_file:':
-            emsg += "\n" + cemsg
-        # end if
+        emsg += f"\n{ccpperr}"
         file_ok = False
     # end try
     if not file_ok:

src/data/registry.xml

@@ -154,7 +154,7 @@
               allocatable="pointer">
       <long_name>inverse exner function w.r.t. surface pressure (ps/p)^(R/cp)</long_name>
       <dimensions>horizontal_dimension vertical_layer_dimension</dimensions>
-      <ic_file_input_names>exner state_exner</ic_file_input_names>
+      <ic_file_input_names>exner state_exner inverse_exner_function_wrt_surface_pressure</ic_file_input_names>
     </variable>
     <variable local_name="zm"
               standard_name="geopotential_height_wrt_surface"

src/physics/utils/phys_comp.F90

@@ -10,6 +10,7 @@ module phys_comp
    private
 
    public :: phys_readnl
+   public :: phys_register
    public :: phys_init
    public :: phys_timestep_init
    public :: phys_run1
@@ -129,26 +130,14 @@ subroutine phys_readnl(nlfilename)
 
    end subroutine phys_readnl
 
-   subroutine phys_init()
-      use cam_abortutils,       only: endrun
-      use physics_grid,         only: columns_on_task
-      use vert_coord,           only: pver, pverp
-      use cam_thermo,           only: cam_thermo_init
-      use physics_types,        only: allocate_physics_types_fields
-      use cam_ccpp_cap,         only: cam_ccpp_physics_initialize
+   subroutine phys_register()
+      use cam_ccpp_cap,         only: cam_ccpp_physics_register
       use cam_ccpp_cap,         only: ccpp_physics_suite_part_list
+      use cam_abortutils,       only: endrun
 
       ! Local variables
       integer                    :: i_group
 
-      call cam_thermo_init(columns_on_task, pver, pverp)
-
-      call allocate_physics_types_fields(columns_on_task, pver, pverp,        &
-           set_init_val_in=.true., reallocate_in=.false.)
-      call cam_ccpp_physics_initialize(phys_suite_name)
-      if (errcode /= 0) then
-         call endrun('cam_ccpp_physics_initialize: '//trim(errmsg))
-      end if
       call ccpp_physics_suite_part_list(phys_suite_name, suite_parts,         &
            errmsg, errcode)
       if (errcode /= 0) then
@@ -158,11 +147,35 @@ subroutine phys_init()
       ! Confirm that the suite parts are as expected
       do i_group = 1, size(suite_parts)
          if (.not. any(suite_parts(i_group) == suite_parts_expect)) then
-            write(errmsg, *) 'phys_init: SDF suite groups MUST be ',             &
+            write(errmsg, *) 'phys_register: SDF suite groups MUST be ',      &
                 'ONLY `physics_before_coupler` and/or `physics_after_coupler`'
             call endrun(errmsg)
          end if
       end do
+      ! Call CCPP register phase
+      call cam_ccpp_physics_register(phys_suite_name)
+      if (errcode /= 0) then
+         call endrun('cam_ccpp_physics_register: '//trim(errmsg))
+      end if
+
+   end subroutine phys_register
+
+   subroutine phys_init()
+      use cam_abortutils,       only: endrun
+      use physics_grid,         only: columns_on_task
+      use vert_coord,           only: pver, pverp
+      use cam_thermo,           only: cam_thermo_init
+      use physics_types,        only: allocate_physics_types_fields
+      use cam_ccpp_cap,         only: cam_ccpp_physics_initialize
+
+      call cam_thermo_init(columns_on_task, pver, pverp)
+
+      call allocate_physics_types_fields(columns_on_task, pver, pverp,        &
+           set_init_val_in=.true., reallocate_in=.false.)
+      call cam_ccpp_physics_initialize(phys_suite_name)
+      if (errcode /= 0) then
+         call endrun('cam_ccpp_physics_initialize: '//trim(errmsg))
+      end if
 
    end subroutine phys_init
 

test/unit/sample_files/reg_bad_xml.xml

@@ -0,0 +1,110 @@
+<?xml version="1.0" encoding="UTF-8"?>
+
+<registry name="cam_registry" version="1.0">
+  <file name="physics_types_complete" type="module">
+    <use module="ccpp_kinds" reference="kind_phys"/>
+    <use module="physconst" reference="rair"/>
+    <use module="physconst" reference="cpair"/>
+    <variable local_name="ncol" standard_name="horizontal_dimension"
+              units="count" type="integer" access="protected">
+      <long_name>Number of horizontal columns</long_name>
+      <initial_value>0</initial_value>
+    </variable>
+    <variable local_name="pver" standard_name="vertical_layer_dimension"
+              units="count" type="integer" access="protected">
+      <long_name>Number of vertical layers</long_name>
+      <initial_value>0</initial_value>
+    </variable>
+    <variable local_name="ix_qv"
+              standard_name="index_of_water_vapor_specific_humidity"
+              units="count" type="integer">
+      <initial_value>1</initial_value>
+    </variable>
+    <variable local_name="ix_cld_liq"
+              standard_name="index_of_cloud_liquid_water_mixing_ratio_of_moist_air"
+              units="count" type="integer">
+      <initial_value>2</initial_value>
+    </variable>
+    <variable local_name="latitude" standard_name="latitude"
+              units="radians" type="real" kind="kind_phys"
+              allocatable="pointer" access="protected">
+      <dimensions>horizontal_dimension</dimensions>
+      <ic_file_input_name>lat</ic_file_input_name>
+    </variable>
+    <variable local_name="longitude" standard_name="longitude"
+              units="radians" type="real" kind="kind_phys"
+              allocatable="pointer" access="protected">
+      <dimensions>horizontal_dimension</dimensions>
+      <ic_file_input_names>lon</ic_file_input_names>
+    </variable>
+    <variable local_name="u" standard_name="x_wind"
+              units="m s-1" type="real" kind="kind_phys"
+              allocatable="pointer" access="protected">
+      <dimensions>horizontal_dimension vertical_layer_dimension</dimensions>
+      <ic_file_input_names>u_wind</ic_file_input_names>
+    </variable>
+    <variable local_name="v" standard_name="y_wind"
+              units="m s-1" type="real" kind="kind_phys"
+              allocatable="pointer" access="protected">
+      <dimensions>horizontal_dimension vertical_layer_dimension</dimensions>
+      <ic_file_input_names>v_wind</ic_file_input_names>
+    </variable>
+    <variable local_name="param_val_var"
+              standard_name="made_up_param_variable"
+              units="count" type="integer" allocatable="parameter">
+              <initial_value>42</initial_value>
+    </variable>
+    <variable local_name="standard_var"
+              standard_name="standard_non_ddt_variable"
+              units="K" type="real" phys_timestep_init_zero="true">
+              <ic_file_input_names>stand_var</ic_file_input_names>
+    </variable>
+    <variable local_name="cappav"
+              standard_name="composition_dependent_ratio_of_dry_air_gas_constant_to_specific_heat_at_constant_pressure"
+              units="1" type="real" kind="kind_phys"
+              allocatable="allocatable">
+      <long_name>Composition-dependent ratio of dry air gas constant to specific heat at constant pressure</long_name>
+      <dimensions>horizontal_dimension vertical_layer_dimension</dimensions>
+      <initial_value>1 + rair/cpair - rair * 2</initial_value>
+    </variable>
+    <array local_name="q" standard_name="constituent_mixing_ratio"
+              units="kg kg-1"
+              type="real" kind="kind_phys"
+              allocatable="pointer">
+      <dimensions>horizontal_dimension vertical_layer_dimension
+      number_of_constituents</dimensions>
+      <element standard_name="water_vapor_specific_humidity"
+               index_name="index_of_water_vapor_specific_humidity"
+               index_pos="number_of_constituents">
+               <ic_file_input_names>Q Q_snapshot</ic_file_input_names>
+      </element>
+      <element standard_name="cloud_liquid_water_mixing_ratio_of_moist_air"
+               index_name="index_of_cloud_liquid_water_mixing_ratio_of_moist_air"
+               index_pos="number_of_constituents">
+               <ic_file_input_names>CLDLIQ CLDLIQ_snapshot</ic_file_input_names>
+      </element>
+    </array>
+    <ddt type="physics_base" bindC="true">
+      <data>horizontal_dimension</data>
+      <data>vertical_layer_dimension</data>
+    </ddt>
+    <ddt type="model_wind">
+      <data>x_wind</data>
+      <data>y_wind</data>
+    </ddt>
+    <variable local_name="wind" standard_name="model_wind"
+              units="None" type="model_wind" />
+    <ddt type="physics_state" extends="physics_base">
+      <data>latitude</data>
+      <data>longitude</data>
+      <data>model_wind</data>
+      <data>constituent_mixing_ratio</data>
+    </ddt>
+    <variable local_name="phys_state"
+              standard_name="physics_state_due_to_dynamics"
+              units="None" type="physics_state" phys_timestep_init_zero="true">
+      <long_name>Physics state variables updated by dynamical core</long_name>
+    </variable>
+  </file>
+  <metadata_file>$SRCROOT/test/unit/sample_files/ref_pres.meta</metadata_file>
+</registry>

test/unit/test_registry.py

@@ -42,6 +42,7 @@
 from generate_registry_data import gen_registry
 from generate_registry_data import metadata_file_to_files, TypeRegistry
 from framework_env import CCPPFrameworkEnv
+from parse_source import CCPPError
 # pylint: enable=wrong-import-position
 
 ###############################################################################
@@ -116,6 +117,25 @@ def test_good_simple_registry(self):
         self.assertTrue(filecmp.cmp(out_source, in_source, shallow=False),
                         msg=amsg)
 
+    def test_bad_registry_xml(self):
+        """Test that the full error messages from xmllint is returned"""
+        # Setup test
+        filename = os.path.join(_SAMPLE_FILES_DIR, "reg_bad_xml.xml")
+        out_name = "physics_types_bad"
+        # Try to generate the 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)
+        # end with
+        expected_error = "reg_bad_xml.xml:32: element ic_file_input_name: Schemas validity error : Element 'ic_file_input_name': This element is not expected. Expected is one of ( initial_value, ic_file_input_names )."
+        split_exception = str(cerr.exception).split('\n')
+        amsg = f"Test failure: exception raised is {len(split_exception)} lines long and is expected to be 4"
+        self.assertEqual(len(split_exception), 4, msg=amsg)
+        # Check that the full xmllint message was returned
+        self.assertTrue(split_exception[2].endswith(expected_error))
+
     def test_good_ddt_registry(self):
         """Test code and metadata generation from a good registry with a DDT.
         Check that generate_registry_data.py generates good