Merge pull request #248 from kuanchihwang/staging/implement-dyn-readnl

Implement namelist reading and early initialization of MPAS dynamical core

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/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) $(@) .