merge in framework-update branch

Externals_CAM.cfg

@@ -2,7 +2,7 @@
 local_path = ccpp_framework
 protocol = git
 repo_url = https://github.com/peverwhee/ccpp-framework
-tag = CPF_0.2.050
+tag = CPF_0.2.054
 required = True
 
 [mpas]
@@ -17,7 +17,7 @@ required = True
 local_path = src/physics/ncar_ccpp
 protocol = git
 repo_url = https://github.com/ESCOMP/atmospheric_physics
-tag = atmos_phys0_01_000
+tag = atmos_phys0_02_002
 required = True
 
 [externals_description]

cime_config/buildlib

@@ -185,8 +185,9 @@ def _setup_mpas(case: Case) -> None:
 
     shutil.copytree(mpas_dycore_src_root, mpas_dycore_bld_root, copy_function=_copy2_as_needed, dirs_exist_ok=True)
     shutil.move(os.path.join(mpas_dycore_bld_root, "Makefile"), os.path.join(mpas_dycore_bld_root, "Makefile.CESM"))
-    _copy2_as_needed(os.path.normpath(os.path.join(mpas_dycore_src_root, os.pardir, os.pardir, "Makefile")), os.path.join(mpas_dycore_bld_root, "Makefile"))
-    _copy2_as_needed(os.path.normpath(os.path.join(mpas_dycore_src_root, os.pardir, os.pardir, "Makefile.in.CESM")), os.path.join(mpas_dycore_bld_root, "Makefile.in.CESM"))
+    _copy2_as_needed(os.path.normpath(os.path.join(mpas_dycore_src_root, os.pardir, os.pardir, "driver", "dyn_mpas_subdriver.F90")), os.path.join(mpas_dycore_bld_root, "driver"))
+    _copy2_as_needed(os.path.normpath(os.path.join(mpas_dycore_src_root, os.pardir, os.pardir, "Makefile")), mpas_dycore_bld_root)
+    _copy2_as_needed(os.path.normpath(os.path.join(mpas_dycore_src_root, os.pardir, os.pardir, "Makefile.in.CESM")), mpas_dycore_bld_root)
 
 def _copy2_as_needed(src: str, dst: str) -> None:
     """
@@ -199,6 +200,9 @@ def _copy2_as_needed(src: str, dst: str) -> None:
                 # `src` and `dst` are both files but their modification time or size differ.
                 # Example scenario: User modified some existing source code files.
                 shutil.copy2(src, dst)
+        elif os.path.isdir(dst) and os.path.isfile(os.path.join(dst, os.path.basename(src))):
+            dst = os.path.join(dst, os.path.basename(src))
+            _copy2_as_needed(src, dst)
         else:
             if os.path.isdir(dst) or os.path.isdir(os.path.dirname(dst)):
                 # `src` is a new file that does not exist at `dst`.

cime_config/cam_config.py

@@ -375,6 +375,10 @@ def __init__(self, case, case_log):
             # MPAS dynamical core relies on its upstream build infrastructure for compilation instead of CIME to take advantage of future upstream changes automatically.
             self.create_config("dyn_src_dirs", dyn_dirs_desc, ["mpas"],
                                valid_list_type="str")
+
+            # Add XML namelist definition file for MPAS dynamical core.
+            mpas_dyn_nml_path = os.path.normpath(os.path.join(cime_conf_path, os.pardir, "src", "dynamics", "mpas"))
+            self._add_xml_nml_file(mpas_dyn_nml_path, "namelist_definition_mpas_dycore.xml")
         elif dycore == "none":
             # Source code directories
             self.create_config("dyn_src_dirs", dyn_dirs_desc, ["none"],

src/control/cam_comp.F90

@@ -563,6 +563,7 @@ subroutine cam_register_constituents(cam_runtime_opts)
       integer                                        :: errflg
       character(len=512)                             :: errmsg
       type(ccpp_constituent_prop_ptr_t), pointer     :: const_props(:)
+      type(ccpp_constituent_properties_t), allocatable, target :: dynamic_constituents(:)
       character(len=*), parameter :: subname = 'cam_register_constituents: '
 
       ! Initalize error flag and message:
@@ -614,7 +615,7 @@ subroutine cam_register_constituents(cam_runtime_opts)
       !Combine host and physics constituents into a single
       !constituents object:
       call cam_ccpp_register_constituents(cam_runtime_opts%suite_as_list(),             &
-           host_constituents, errcode=errflg, errmsg=errmsg)
+           host_constituents, dynamic_constituents, errcode=errflg, errmsg=errmsg)
 
       if (errflg /= 0) then
          call endrun(subname//trim(errmsg), file=__FILE__, line=__LINE__)

src/data/physconst.meta

@@ -68,7 +68,7 @@
   dimensions = ()
   protected = True
 [ pref ]
-  standard_name = reference_pressure
+  standard_name = surface_reference_pressure
   units = Pa
   type = real | kind = kind_phys
   dimensions = ()

src/data/ref_pres.F90

@@ -173,7 +173,7 @@ subroutine ref_pres_init(pref_edge_in, pref_mid_in, num_pr_lev_in)
       ! pref_mid_in
       call mark_as_initialized("reference_pressure_in_atmosphere_layer")
       ! pref_mid_norm
-      call mark_as_initialized("reference_pressure_in_atmosphere_layer_normalized_by_reference_pressure")
+      call mark_as_initialized("reference_pressure_in_atmosphere_layer_normalized_by_surface_reference_pressure")
       ! ptop_ref
       call mark_as_initialized("air_pressure_at_top_of_atmosphere_model")
       ! num_pr_lev

src/data/ref_pres.meta

@@ -17,7 +17,7 @@
   dimensions = (vertical_layer_dimension)
   protected = True
 [ pref_mid_norm ]
-  standard_name = reference_pressure_in_atmosphere_layer_normalized_by_reference_pressure
+  standard_name = reference_pressure_in_atmosphere_layer_normalized_by_surface_reference_pressure
   units = 1
   type = real | kind = kind_phys
   dimensions = (vertical_layer_dimension)

src/data/registry.xml

@@ -106,7 +106,7 @@
     </variable>
     <variable local_name="rpdel"
               standard_name="reciprocal_of_air_pressure_thickness"
-              units="Pa" type="real" kind="kind_phys"
+              units="Pa-1" type="real" kind="kind_phys"
               allocatable="pointer">
       <dimensions>horizontal_dimension vertical_layer_dimension</dimensions>
       <ic_file_input_names>rpdel state_rpdel</ic_file_input_names>
@@ -260,7 +260,7 @@
       <ic_file_input_names>dvdt tend_dvdt</ic_file_input_names>
     </variable>
     <variable local_name="lagrangian_vertical"
-              standard_name="lagrangian_vertical_coordinate"
+              standard_name="do_lagrangian_vertical_coordinate"
               units="flag" type="logical" access="protected">
       <long_name>flag indicating if vertical coordinate is lagrangian</long_name>
       <initial_value>.false.</initial_value>
@@ -334,13 +334,13 @@
     </variable>
     <variable local_name="errcode"
               standard_name="ccpp_error_code"
-              units="flag" type="integer">
+              units="1" type="integer">
       <long_name>ccpp error code</long_name>
       <initial_value>0</initial_value>
     </variable>
     <variable local_name="errmsg"
               standard_name="ccpp_error_message"
-              units="1" type="character" kind="len=512">
+              units="none" type="character" kind="len=512">
       <long_name>ccpp error message</long_name>
       <initial_value>''</initial_value>
     </variable>
@@ -379,7 +379,7 @@
     </variable>
     <variable local_name="zvirv"
               standard_name="ratio_of_water_vapor_gas_constant_to_composition_dependent_dry_air_gas_constant_minus_one"
-              units="J kg-1 K-1" type="real" kind="kind_phys"
+              units="1" type="real" kind="kind_phys"
               allocatable="allocatable">
       <long_name>Composition-dependent ratio of water vapor to dry air gas constants minus one</long_name>
       <dimensions>horizontal_dimension vertical_layer_dimension</dimensions>

src/dynamics/mpas/Makefile.in.CESM

@@ -9,6 +9,7 @@ endif
 #
 
 export CP = cp -afv
+export LN = ln -fsv
 export MKDIR = mkdir -pv
 export RM = rm -frv
 
@@ -61,22 +62,29 @@ all:
 	@echo '    `make libmpas-clean ESM="CESM" LIBROOT="..."`'
 
 .PHONY: libmpas-prepare
-libmpas-prepare: libmpas-archiver-script.txt libmpas-no-physics libmpas-preview
+libmpas-prepare: libmpas-archiver-script.txt libmpas-no-physics libmpas-prefix-namelist-groups libmpas-preview
 
 # Combine multiple static libraries into `libmpas.a` via archiver/MRI script. This requires GNU or GNU-like archiver (`ar`) program.
 libmpas-archiver-script.txt:
-	@echo "create libmpas.a"       > $(@)
-	@echo "addlib libdycore.a"    >> $(@)
-	@echo "addlib libframework.a" >> $(@)
-	@echo "addlib libops.a"       >> $(@)
-	@echo "save"                  >> $(@)
-	@echo "end"                   >> $(@)
+	@echo "create libmpas.a"             > $(@)
+	@echo "addlib libdycore.a"          >> $(@)
+	@echo "addlib libframework.a"       >> $(@)
+	@echo "addlib libops.a"             >> $(@)
+	@echo "addmod dyn_mpas_subdriver.o" >> $(@)
+	@echo "save"                        >> $(@)
+	@echo "end"                         >> $(@)
 
 # Do not use built-in MPAS/WRF physics.
 .PHONY: libmpas-no-physics
 libmpas-no-physics:
 	@sed -E -i -e "s/^ *PHYSICS=.+$$/PHYSICS=/g" core_atmosphere/Makefile
 
+# Prefix `mpas_` to MPAS namelist groups to avoid naming collisions.
+.PHONY: libmpas-prefix-namelist-groups
+libmpas-prefix-namelist-groups:
+	@sed -E -i -e "s/(^ *< *nml_record.+name=)\"(mpas_)?(\w+)\"/\1\"mpas_\3\"/g" core_atmosphere/Registry.xml
+	@sed -E -i -e "s/(^ *< *nml_record.+name=)\"(mpas_)?(\w+)\"/\1\"mpas_\3\"/g" core_atmosphere/diagnostics/Registry_*.xml
+
 .PHONY: libmpas-preview
 libmpas-preview:
 	@echo "Previewing build options for $(LIBROOT)/libmpas.a:"
@@ -106,13 +114,21 @@ $(LIBROOT)/libmpas.a: libmpas.a
 	$(MKDIR) $(LIBROOT)
 	$(CP) $(<) $(@)
 
-libmpas.a: $(AUTOCLEAN_DEPS) dycore externals frame ops
+libmpas.a: $(AUTOCLEAN_DEPS) dycore externals frame ops subdrv
 	$(AR) $(ARFLAGS) < libmpas-archiver-script.txt
+	@find -P . -name "*.mod" -type f -exec $(LN) "{}" . ";"
 
 .PHONY: libmpas-clean
 libmpas-clean: clean
-	$(RM) $(LIBROOT)/libmpas.a libmpas.a
+	$(RM) $(LIBROOT)/libmpas.a libmpas.a *.mod *.o
 
 .PHONY: externals
 externals: $(AUTOCLEAN_DEPS)
 	( cd external; $(MAKE) FC="$(FC)" SFC="$(SFC)" CC="$(CC)" SCC="$(SCC)" FFLAGS="$(FFLAGS)" CFLAGS="$(CFLAGS)" CPP="$(CPP)" NETCDF="$(NETCDF)" CORE="$(CORE)" ezxml-lib )
+
+.PHONY: subdrv
+subdrv: driver/dyn_mpas_subdriver.o
+
+%.o: %.F90 dycore frame ops
+	( cd $(<D); $(FC) $(CPPFLAGS) $(FFLAGS) -c $(<F) $(CPPINCLUDES) $(FCINCLUDES) -I../framework -I../operators -I../core_$(CORE) )
+	$(LN) $(@) .