Ocean/moc streamfunction am

src/Makefile.in.ACME

@@ -41,7 +41,6 @@ RM = rm -f
 CPP = cpp -P -traditional
 FC=$(MPIFC)
 CC=$(MPICC)
-CXX=$(MPICXX)
 NETCDF=$(NETCDF_PATH)
 PNETCDF=$(PNETCDF_PATH)
 PIO=$(EXEROOT)/pio
@@ -71,7 +70,7 @@ all:
 	@echo $(CPPINCLUDES)
 	@echo $(FCINCLUDES)
 	( $(MAKE) mpas RM="$(RM)" CPP="$(CPP)" NETCDF="$(NETCDF)" PNETCDF="$(PNETCDF)" \
-	  PIO="$(PIO)" FC="$(FC)" CC="$(CC)" CXX="$(CXX)" SFC="$(SFC)" SCC="$(SCC)" \
+	  PIO="$(PIO)" FC="$(FC)" CC="$(CC)" SFC="$(SFC)" SCC="$(SCC)" \
 	  CPPFLAGS="$(CPPFLAGS)" CPPINCLUDES="$(CPPINCLUDES)" FCINCLUDES="$(FCINCLUDES)" \
 	  FFLAGS="$(FFLAGS)" CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" )
 
@@ -83,7 +82,7 @@ mpas: externals frame ops dycore drver
 	ar ru lib$(COMPONENT).a $(DRIVER)/*.o
 
 externals:
-	( cd external; $(MAKE) FC="$(FC)" SFC="$(SFC)" CC="$(CC)" CXX="$(CXX)" SCC="$(SCC)" FFLAGS="$(FFLAGS)" CFLAGS="$(CFLAGS)" CPP="$(CPP)" NETCDF="$(NETCDF)" CORE="$(CORE)" ezxml-lib )
+	( cd external; $(MAKE) FC="$(FC)" SFC="$(SFC)" CC="$(CC)" SCC="$(SCC)" FFLAGS="$(FFLAGS)" CFLAGS="$(CFLAGS)" CPP="$(CPP)" NETCDF="$(NETCDF)" CORE="$(CORE)" ezxml-lib )
 
 drver: externals frame ops dycore
 	( cd $(DRIVER); $(MAKE) CPPFLAGS="$(CPPFLAGS)" CPPINCLUDES="$(CPPINCLUDES)" FREEFLAGS="$(FREEFLAGS)" all ) 

src/Makefile.in.CESM

@@ -41,7 +41,6 @@ RM = rm -f
 CPP = cpp -P -traditional
 FC=$(MPIFC)
 CC=$(MPICC)
-CXX=$(MPICXX)
 NETCDF=$(NETCDF_PATH)
 PNETCDF=$(PNETCDF_PATH)
 PIO=$(EXEROOT)/pio
@@ -71,7 +70,7 @@ all:
 	@echo $(CPPINCLUDES)
 	@echo $(FCINCLUDES)
 	( $(MAKE) mpas RM="$(RM)" CPP="$(CPP)" NETCDF="$(NETCDF)" PNETCDF="$(PNETCDF)" \
-	  PIO="$(PIO)" FC="$(FC)" CC="$(CC)" CXX="$(CXX)" SFC="$(SFC)" SCC="$(SCC)" \
+	  PIO="$(PIO)" FC="$(FC)" CC="$(CC)" SFC="$(SFC)" SCC="$(SCC)" \
 	  CPPFLAGS="$(CPPFLAGS)" CPPINCLUDES="$(CPPINCLUDES)" FCINCLUDES="$(FCINCLUDES)" \
 	  FFLAGS="$(FFLAGS)" CFLAGS="$(CFLAGS)" LDFLAGS="$(LDFLAGS)" )
 
@@ -83,7 +82,7 @@ mpas: externals frame ops dycore drver
 	ar ru lib$(COMPONENT).a $(DRIVER)/*.o
 
 externals:
-	( cd external; $(MAKE) FC="$(FC)" SFC="$(SFC)" CC="$(CC)" CXX="$(CXX)" SCC="$(SCC)" FFLAGS="$(FFLAGS)" CFLAGS="$(CFLAGS)" CPP="$(CPP)" NETCDF="$(NETCDF)" CORE="$(CORE)" ezxml-lib )
+	( cd external; $(MAKE) FC="$(FC)" SFC="$(SFC)" CC="$(CC)" SCC="$(SCC)" FFLAGS="$(FFLAGS)" CFLAGS="$(CFLAGS)" CPP="$(CPP)" NETCDF="$(NETCDF)" CORE="$(CORE)" ezxml-lib )
 
 drver: externals frame ops dycore
 	( cd $(DRIVER); $(MAKE) CPPFLAGS="$(CPPFLAGS)" CPPINCLUDES="$(CPPINCLUDES)" FREEFLAGS="$(FREEFLAGS)" all ) 

src/core_ocean/.gitignore

@@ -1,6 +1,8 @@
 # Ignore all cvmix code.
 cvmix
 .cvmix_all
+BGC
+.BGC_all
 .*.zip
 
 # Ignore processed registry files.

src/core_ocean/Makefile

@@ -2,11 +2,12 @@
 
 
 OCEAN_SHARED_INCLUDES = -I$(PWD)/../framework -I$(PWD)/../external/esmf_time_f90 -I$(PWD)/../operators
-OCEAN_SHARED_INCLUDES += -I$(PWD)/shared -I$(PWD)/analysis_members -I$(PWD)/cvmix -I$(PWD)/mode_forward -I$(PWD)/mode_analysis
+OCEAN_SHARED_INCLUDES += -I$(PWD)/BGC -I$(PWD)/shared -I$(PWD)/analysis_members -I$(PWD)/cvmix -I$(PWD)/mode_forward -I$(PWD)/mode_analysis -I$(PWD)/mode_init
 
-all: shared libcvmix analysis_members
+all: shared libcvmix analysis_members libBGC
 	(cd mode_forward; $(MAKE) FCINCLUDES="$(FCINCLUDES) $(OCEAN_SHARED_INCLUDES)" all )
 	(cd mode_analysis; $(MAKE) FCINCLUDES="$(FCINCLUDES) $(OCEAN_SHARED_INCLUDES)" all )
+	(cd mode_init; $(MAKE) FCINCLUDES="$(FCINCLUDES) $(OCEAN_SHARED_INCLUDES)" all )
 	(cd driver; $(MAKE) FCINCLUDES="$(FCINCLUDES) $(OCEAN_SHARED_INCLUDES)" all )
 	if [ -e libdycore.a ]; then \
 		($(RM) libdycore.a) \
@@ -21,9 +22,11 @@ core_input_gen:
 	(cd default_inputs; $(NL_GEN) ../Registry_processed.xml namelist.ocean )
 	(cd default_inputs; $(NL_GEN) ../Registry_processed.xml namelist.ocean.forward mode=forward )
 	(cd default_inputs; $(NL_GEN) ../Registry_processed.xml namelist.ocean.analysis mode=analysis )
+	(cd default_inputs; $(NL_GEN) ../Registry_processed.xml namelist.ocean.init mode=init )
 	(cd default_inputs; $(ST_GEN) ../Registry_processed.xml streams.ocean stream_list.ocean. mutable )
 	(cd default_inputs; $(ST_GEN) ../Registry_processed.xml streams.ocean.forward stream_list.ocean.forward. mutable mode=forward )
 	(cd default_inputs; $(ST_GEN) ../Registry_processed.xml streams.ocean.analysis stream_list.ocean.analysis. mutable mode=analysis )
+	(cd default_inputs; $(ST_GEN) ../Registry_processed.xml streams.ocean.init stream_list.ocean.init. mutable mode=init )
 
 gen_includes:
 	$(CPP) $(CPPFLAGS) $(CPPINCLUDES) Registry.xml > Registry_processed.xml
@@ -33,11 +36,22 @@ gen_includes:
 post_build:
 	if [ ! -e $(ROOT_DIR)/default_inputs ]; then mkdir $(ROOT_DIR)/default_inputs; fi
 	cp default_inputs/* $(ROOT_DIR)/default_inputs/.
-	( cd $(ROOT_DIR)/default_inputs; for FILE in `ls -1`; do if [ ! -e ../$$FILE ]; then cp $$FILE ../.; fi; done )
+	( cp $(ROOT_DIR)/default_inputs/namelist.ocean $(ROOT_DIR)/namelist.ocean )
+	( cp $(ROOT_DIR)/default_inputs/namelist.ocean.forward $(ROOT_DIR)/namelist.ocean.forward )
+	( cp $(ROOT_DIR)/default_inputs/namelist.ocean.analysis $(ROOT_DIR)/namelist.ocean.analysis )
+	( cp $(ROOT_DIR)/default_inputs/namelist.ocean.init $(ROOT_DIR)/namelist.ocean.init )
+	( cp $(ROOT_DIR)/default_inputs/streams.ocean $(ROOT_DIR)/streams.ocean )
+	( cp $(ROOT_DIR)/default_inputs/streams.ocean.forward $(ROOT_DIR)/streams.ocean.forward )
+	( cp $(ROOT_DIR)/default_inputs/streams.ocean.analysis $(ROOT_DIR)/streams.ocean.analysis )
+	( cp $(ROOT_DIR)/default_inputs/streams.ocean.init $(ROOT_DIR)/streams.ocean.init )
 
 cvmix_source: get_cvmix.sh
 	(chmod a+x get_cvmix.sh; ./get_cvmix.sh)
-	(cd cvmix; make clean)
+	(cd cvmix)
+
+BGC_source: get_BGC.sh
+	(chmod a+x get_BGC.sh; ./get_BGC.sh)
+	(cd BGC)
 
 libcvmix: cvmix_source
 	if [ -d cvmix ]; then \
@@ -46,7 +60,14 @@ libcvmix: cvmix_source
 		(exit 1) \
 	fi
 
-shared: libcvmix
+libBGC: BGC_source
+	if [ -d BGC ]; then \
+		(cd BGC; make all FC="$(FC)" FCFLAGS="$(FFLAGS)" FINCLUDES="$(FINCLUDES)") \
+	else \
+		(exit 1) \
+	fi
+
+shared: libcvmix libBGC
 	(cd shared; $(MAKE) FCINCLUDES="$(FCINCLUDES) $(OCEAN_SHARED_INCLUDES)")
 
 analysis_members: libcvmix shared
@@ -56,8 +77,15 @@ clean:
 	if [ -d cvmix ]; then \
 		(cd cvmix; make clean) \
 	fi
+	if [ -d inc ]; then \
+		($(RM) -r inc) \
+	fi
+	if [ -d BGC ]; then \
+		(cd BGC; make clean) \
+	fi
 	(cd mode_forward; $(MAKE) clean)
 	(cd mode_analysis; $(MAKE) clean)
+	(cd mode_init; $(MAKE) clean)
 	(cd driver; $(MAKE) clean)
 	(cd analysis_members; $(MAKE) clean)
 	(cd shared; $(MAKE) clean)