Updates for ZM round 4 (#345)

Tag name (required for release branches): sima0_02_000zh
Originator(s): cacraig, peverley, nusbaume

Description (include the issue title, and the keyword ['closes',
'fixes', 'resolves'] followed by the issue number):
- No issue made
- Adds mods from various developers to get ZM to work properly in
CAM-SIMA

Describe any changes made to build system: N/A

Describe any changes made to the namelist: N/A

List any changes to the defaults for the input datasets (e.g. boundary
datasets): N/A

List all files eliminated and why: N/A

List all files added and what they do: N/A
A
cime_config/testdefs/testmods_dirs/cam/outfrq_zm_derecho/shell_commands
A cime_config/testdefs/testmods_dirs/cam/outfrq_zm_derecho/user_nl_cam
             - setup ZM regression test
             
A       src/physics/utils/ppgrid.F90
            - temporary file to use for backwards compatibility with CAM

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
             - update to get atmospheric_physics changes for ZM
            
M       cime_config/atm_in_paramgen.py
             - exit if namelist entry does not have a value
             
M       cime_config/testdefs/testlist_cam.xml
             - add test for ZM
             
M       src/data/physconst.meta
M       src/data/ref_pres.meta
             - updated CCPP standard names
             
M       src/data/registry.xml
             - add entries required for ZM
            
M       src/physics/ncar_ccpp
             - updated submodule
             
M       src/physics/utils/musica_ccpp_dependencies.F90
M       src/physics/utils/musica_ccpp_dependencies.meta
             - remove cloud_area_fraction 
            
M       src/physics/utils/phys_comp.F90
             - Add new dimension: number_of_ccpp_constituents
             
M       src/utils/time_manager.F90
             - add current_timestep_number as "mark_as_initialized"
            
M       test/unit/python/test_atm_in_paramgen.py
             - @nusbaume added unit test for new python code

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:
    - Added ZM test

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:

.gitmodules

@@ -20,7 +20,7 @@
 [submodule "ncar-physics"]
         path          = src/physics/ncar_ccpp
 	url           = https://github.com/ESCOMP/atmospheric_physics
-	fxtag         = 74e905b7a0ee5b2d2bfc3e3dd942eb9963398373
+	fxtag         = atmos_phys0_08_000
         fxrequired    = AlwaysRequired
         fxDONOTUSEurl = https://github.com/ESCOMP/atmospheric_physics
 [submodule "ccs_config"]

cime_config/atm_in_paramgen.py

@@ -1495,11 +1495,16 @@ def write(self, output_path):
                 # Write all variables within that group (sorted alphabetically):
                 for var in sorted(self._data[nml_group], key=var_sort_key):
                     #Extract variable value(s):
-                    val = self._data[nml_group][var]["values"].strip()
+                    val = self._data[nml_group][var]["values"]
 
-                    #If no value is set then move to the next variable:
+                    #Raise error if no value found:
                     if val is None:
-                        continue
+                        emsg = f"Namelist entry '{var}' is missing a "
+                        emsg += "valid/default 'value' element."
+                        raise AtmInParamGenError(emsg)
+                    else:
+                        #If value found then strip white space:
+                        val = val.strip()
                     #End if
 
                     #Extract variable type:

cime_config/testdefs/testlist_cam.xml

@@ -43,6 +43,15 @@
       <option name="comment">Test for Moist Held-Suarez (TJ2016) physics (physics_after_coupler group)</option>
     </options>
   </test>
+  <test compset="FPHYStest" grid="ne3pg3_ne3pg3_mg37" name="SMS_Ln2" testmods="cam/outfrq_zm_derecho">
+    <machines>
+      <machine name="derecho" compiler="gnu" category="aux_sima"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:10:00</option>
+      <option name="comment">Test for Zhang McFarlane physics</option>
+    </options>
+  </test>
 
   <!-- Derecho dycore tests -->
   <test compset="FKESSLER" grid="mpasa480_mpasa480" name="SMS_Ln9" testmods="cam/outfrq_kessler_mpas_derecho">

cime_config/testdefs/testmods_dirs/cam/outfrq_zm_derecho/shell_commands

@@ -0,0 +1 @@
+ ./xmlchange CAM_CONFIG_OPTS="--dyn none --physics-suites zhang_mcfarlane"

cime_config/testdefs/testmods_dirs/cam/outfrq_zm_derecho/user_nl_cam

@@ -0,0 +1,16 @@
+ncdata='/glade/campaign/cesm/community/amwg/sima_baselines/cam_sima_test_snapshots/cam_ne3pg3_ZM_snapshot_derecho_gnu_before_c20250116.nc'
+ncdata_check='/glade/campaign/cesm/community/amwg/sima_baselines/cam_sima_test_snapshots/cam_ne3pg3_ZM_snapshot_derecho_gnu_after_c20250116.nc'
+debug_output=0
+pver=32
+zmconv_momcd=.7D0
+zmconv_momcu=.7D0
+zmconv_num_cin=1
+hist_add_inst_fields;h1: ZMDT, ZMDQ, CAPE, FREQZM, CMFMC_DP, ZMMU, ZMMD, DLFZM, PCONVT, PCONVB, ZMFLXPRC, ZMFLXSNW
+hist_add_inst_fields;h1: ZMNTPRPD, ZMNTSNPD, ZMEIHEAT, PRECCDZM, PRECZ
+hist_add_inst_fields;h1: ZMUPGU, ZMUPGD, ZMVPGU, ZMVPGD, ZMICUU, ZMICUD, ZMICVU, ZMICVD
+hist_add_inst_fields;h1: EVAPTZM, FZSNTZM, EVSNTZM, EVAPQZM
+hist_add_inst_fields;h1: ZMMTU, ZMMTV, ZMMTT
+hist_add_inst_fields;h1: ZMDLIQ, ZMDICE
+hist_output_frequency;h1: 1*nstep
+hist_precision;h1: REAL64
+hist_max_frames;h1: 1

src/data/physconst.meta

@@ -25,7 +25,7 @@
   dimensions = ()
   protected = True
 [ cpliq ]
-  standard_name = specific_heat_of_liquid_water_at_20c
+  standard_name = specific_heat_of_liquid_water_at_constant_pressure
   long_name = Specific heat of fresh H2O
   units = J kg-1 K-1
   type = real | kind = kind_phys

src/data/ref_pres.meta

@@ -35,7 +35,7 @@
   dimensions = ()
   protected = True
 [ trop_cloud_top_lev ]
-  standard_name = index_of_pressure_at_troposhere_cloud_top
+  standard_name = vertical_layer_index_of_troposphere_cloud_top
   units = index
   type = integer
   dimensions = ()
@@ -65,7 +65,7 @@
   dimensions = ()
   protected = True
 [ nbot_molec ]
-  standard_name = index_of_pressure_at_bottom_of_molecular_diffusion
+  standard_name = vertical_layer_index_at_bottom_of_molecular_diffusion
   units = index
   type = integer
   dimensions = ()

src/data/registry.xml

@@ -491,5 +491,71 @@
       <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>
+
+    <!-- cam_in Variables -->
+    <variable local_name="landfrac"
+              standard_name="land_area_fraction"
+              units="fraction" type="real" kind="kind_phys"
+              allocatable="allocatable">
+      <dimensions>horizontal_dimension</dimensions>
+      <ic_file_input_names>landfrac cam_in_landfrac</ic_file_input_names>
+    </variable>
+
+    <!-- Zhang McFarlane (ZM) Variables -->
+    <variable local_name="pblh"
+              standard_name="atmosphere_boundary_layer_thickness"
+              units="m" type="real" kind="kind_phys"
+              allocatable="allocatable">
+      <dimensions>horizontal_dimension</dimensions>
+      <ic_file_input_names>pblh pbuf_pblh</ic_file_input_names>
+    </variable>
+    <variable local_name="tpert"
+              standard_name="convective_temperature_perturbation_due_to_pbl_eddies"
+              units="K" type="real" kind="kind_phys"
+              allocatable="allocatable">
+      <dimensions>horizontal_dimension</dimensions>
+      <ic_file_input_names>tpert pbuf_tpert</ic_file_input_names>
+    </variable>
+    <variable local_name="ql"
+              standard_name="in_cloud_water_vapor_mixing_ratio_wrt_moist_air_and_condensed_water_due_to_deep_convection"
+              units="kg kg-1" type="real" kind="kind_phys"
+              allocatable="allocatable">
+      <dimensions>horizontal_dimension vertical_layer_dimension</dimensions>
+      <ic_file_input_names>ICWMRDP pbuf_ICWMRDP</ic_file_input_names>
+    </variable>
+    <variable local_name="cldfrc"
+              standard_name="cloud_area_fraction"
+              units="fraction" type="real" kind="kind_phys"
+              allocatable="allocatable">
+      <dimensions>horizontal_dimension vertical_layer_dimension</dimensions>
+      <initial_value>0.7_kind_phys</initial_value>
+      <ic_file_input_names>CLD pbuf_CLD</ic_file_input_names>
+    </variable>
+    <variable local_name="domomtran"
+              standard_name="flag_for_momentum_transport_by_zhang_mcfarlane_deep_convection_scheme"
+              units="flag" type="logical"
+              access="protected" >
+      <initial_value>.true.</initial_value>
+    </variable>
+    <variable local_name="il1g"
+              standard_name="index_of_first_column_of_gathered_deep_convection_arrays"
+              units="index" type="integer"
+              access="protected" >
+      <initial_value>1</initial_value>
+    </variable>
+    <variable local_name="dpdry"
+              standard_name="air_pressure_thickness_of_dry_air_for_deep_convection_for_gathered_convective_columns"
+              units="hPa" type="real" kind="kind_phys"
+              allocatable="allocatable">
+      <dimensions>horizontal_dimension vertical_layer_dimension</dimensions>
+    </variable>
+    <variable local_name="fracis"
+              standard_name="fraction_of_water_insoluble_convectively_transported_species"
+              units="fraction" type="real" kind="kind_phys"
+              allocatable="allocatable"
+              access="protected" >
+      <dimensions>horizontal_dimension vertical_layer_dimension number_of_ccpp_constituents</dimensions>
+      <initial_value>1</initial_value>
+    </variable>
   </file>
 </registry>

src/physics/utils/musica_ccpp_dependencies.F90

@@ -29,7 +29,6 @@ module musica_ccpp_dependencies
   real(kind_phys), allocatable, public, protected :: extraterrestrial_radiation_flux(:)
   real(kind_phys), allocatable, public, protected :: surface_albedo(:)
   real(kind_phys), allocatable, public, protected :: blackbody_temperature_at_surface(:)
-  real(kind_phys), allocatable, public, protected :: cloud_area_fraction(:,:)
 
   ! local parameters
   character(len=*), parameter :: module_name = '(musica_ccpp_dependencies)'
@@ -77,14 +76,9 @@ subroutine musica_ccpp_dependencies_init(horizontal_dimension, &
     call check_allocate(error_code, subroutine_name, &
                         'blackbody_temperature_at_surface(horizontal_dimension)', &
                         file=__FILE__, line=__LINE__)
-    allocate(cloud_area_fraction(horizontal_dimension, vertical_layer_dimension), stat=error_code)
-    call check_allocate(error_code, subroutine_name, &
-                        'cloud_area_fraction(horizontal_dimension, vertical_layer_dimension)', &
-                        file=__FILE__, line=__LINE__)
 
     surface_albedo(:) = 0.1_kind_phys
     blackbody_temperature_at_surface(:) = 292.3_kind_phys
-    cloud_area_fraction(:,:) = 0.7_kind_phys
     extraterrestrial_radiation_flux(:) = 1.0e14_kind_phys
     photolysis_wavelength_grid_interfaces = (/ &
       120.0e-9_kind_phys, &
@@ -194,4 +188,4 @@ subroutine musica_ccpp_dependencies_init(horizontal_dimension, &
 
   end subroutine musica_ccpp_dependencies_init
 
-end module musica_ccpp_dependencies
+end module musica_ccpp_dependencies

src/physics/utils/musica_ccpp_dependencies.meta

@@ -40,9 +40,3 @@
   units = K
   dimensions = (horizontal_dimension)
   protected = True
-[ cloud_area_fraction ]
-  standard_name = cloud_area_fraction
-  type = real | kind = kind_phys
-  units = fraction
-  dimensions = (horizontal_dimension,vertical_layer_dimension)
-  protected = True

src/physics/utils/phys_comp.F90

@@ -177,12 +177,13 @@ subroutine phys_init()
       use cam_thermo_formula,   only: cam_thermo_formula_init
       use physics_types,        only: allocate_physics_types_fields
       use cam_ccpp_cap,         only: cam_ccpp_physics_initialize
+      use cam_constituents,     only: num_advected
 
       call cam_thermo_init(columns_on_task, pver, pverp)
       call cam_thermo_formula_init()
 
       call allocate_physics_types_fields(columns_on_task, pver, pverp,        &
-           set_init_val_in=.true., reallocate_in=.false.)
+           num_advected, 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))

src/physics/utils/ppgrid.F90

@@ -0,0 +1,24 @@
+
+module ppgrid
+
+!-----------------------------------------------------------------------
+!
+! Purpose:  USED ONLY FOR BACKWARDS COMPATIBILITY WITH CAM!!!!
+!           PLEASE DELETE ONCE NO LONGER NEEDED BY "to_be_ccppized"
+!           PHYSICS SCHEMES!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
+!           Thanks!
+!-----------------------------------------------------------------------
+
+  use physics_grid,     only: pcols => columns_on_task
+  use vert_coord,       only: pver => pver, pverp => pverp !WILL NEED TO CHANGE THESE NAMES TO
+                                                           !SOMETHING ELSE IN CAM-SIMA!
+
+  implicit none
+  private
+  save
+
+  public pcols
+  public pver
+  public pverp
+
+end module ppgrid

src/utils/time_manager.F90

@@ -84,6 +84,8 @@ subroutine timemgr_init( &
    ref_tod, stop_ymd, stop_tod, curr_ymd, curr_tod,      &
    perpetual_run, perpetual_ymd, initial_run)
 
+   use phys_vars_init_check, only: mark_as_initialized
+
    ! Initialize the time manager.
 
    ! Arguments
@@ -152,6 +154,8 @@ subroutine timemgr_init( &
       call timemgr_print()
    end if
 
+   call mark_as_initialized('current_timestep_number')
+
 end subroutine timemgr_init
 
 !===========================================================================

test/unit/python/test_atm_in_paramgen.py

@@ -11,7 +11,7 @@
 
 python test_atm_in_paramgen.py -v
 
-which will currently run 23 tests, all of which should pass.
+which will currently run 24 tests, all of which should pass.
 """
 
 #----------------------------------------
@@ -279,6 +279,76 @@ def test_namelist_from_xml_using_multi_attrs(self):
 
     #++++++++++++++++++++++++++++++++++++++++++++++++
 
+    def test_namelist_xml_bad_value_entry(self):
+
+        """
+        Check that AtmInParamGen throws the correct
+        error message when an XML namelist file
+        has an entry with a non-valid value.
+        """
+
+        # Create fake CIME case:
+        fcase = FakeCase()
+
+        # Create namelist attribute dictionary:
+        nml_attr_dict = {"bird" : "goose", "never_read" : "0"}
+
+        # Get XML file path to original sample file:
+        xml_base_fil = os.path.join(_SAMPLES_DIR, "test_simple_nml_def.xml")
+
+        # Open base XML file:
+        base_tree = ET.parse(xml_base_fil)
+        base_root = base_tree.getroot()
+
+        # Write new namelist entry with "bad" value:
+        bad_namelist_string = \
+        """
+        <entry id="bad_default_entry">
+          <type>integer</type>
+          <category>more_testing</category>
+          <group>please_fail</group>
+          <desc>
+            Let's make sure we don't have
+            a good default value
+            Default: None!
+          </desc>
+          <values>
+            <value never_read="1">3</value>
+            <value never_read="1" feel_lucky="1">5</value>
+          </values>
+        </entry>
+        """
+
+        bad_xml_entry = ET.fromstring(bad_namelist_string)
+
+        # Add new namelist entry back to original namelist XML tree:
+        base_root.append(bad_xml_entry)
+
+        # Write out new, temporary XML namelist file for testing:
+        xml_test_fil = os.path.join(_TMP_DIR, "test_bad_value_nml_def.xml")
+        base_tree.write(xml_test_fil, encoding="utf-8", xml_declaration=True)
+
+        # Create ParamGen object:
+        pg_test = AtmInParamGen.from_namelist_xml(xml_test_fil)
+
+        # Set all ParamGen namelist values:
+        pg_test.reduce_atm_in(fcase, nml_attr_dict)
+
+        # Set atm_in filename to write to (should never get to this point):
+        test_output = os.path.join(_TMP_DIR, "test_bad_xml_value_entry_in")
+
+        # Attempt to write namelist using ParamGen:
+        with self.assertRaises(AtmInParamGenError) as cerr:
+            pg_test.write(test_output)
+
+        # Check exception message
+        emsg =  "Namelist entry 'bad_default_entry' is missing"
+        emsg += " a valid/default 'value' element."
+
+        self.assertEqual(emsg, str(cerr.exception))
+
+    #++++++++++++++++++++++++++++++++++++++++++++++++
+
     def test_namelist_xml_missing_elems(self):
 
         """