Add Crocus snowpack/glacier model to WRF-Hydro (#607)

* Add Crocus to Noah-MP
* Move lat lon in snowcro since they are not used
* Move max SWE limit to a parameter in MPTABLE.
* Fix energy NAs over large snowpacks due to very small numbers being rounded to 0, so number/number=NA instead of 1. Switched to an if statement.
* Add swe_limit into crocus specific calls
* Add outputs (flow from glacier snow or glacier ice)
* Add crocus outputs to retro config.
* Move a series of files that module_snowcro.F needs to the surfex directory for a cleaner build, and modify Makefile as necessary
* Move a series of files from Land_models/NoahMP/phys directory into a subdirectory and update the Makefile paths to those files and include the new surfex subdirectory
* Increase max SWE in glacier module to 5m to match standard snow model max value.
* Remove swe max limit.
* Add Aubreys changes for energy balance
* Add option to add visible albedo map
* Add possibility to read visible ice albedo from netcdf file
* Add Crocus namelist to end of namelist.hrldas
* Crocus: Set the ldasOutDict numLev to the act_lev input from the namelist file
* Crocus: crocus can be turned off and on with crocus_opt
* Crocus: code cleanup and formatting
* Crocus: if vis_icealb is not present, set it to NaN
* Crocus: removed dev comments and reformatted code
* Crocus: Trude fix of SNOW being updated, rather than SNEQVOXY
* Crocus: bug fix, certain values needed to be reset while iterating over array
* Crocus: Trude fix for when snowthickness becomes zero in the top layer
* Crocus: bugfix to albedo output. Code from Trude Eidhammer
* Bugfix: ALBSND and ALBSNI should be undefined when NOAHMP_SFLX isn't called. Fixes some output file differences

Co-authored-by: Trude Eidhammer <trude@ucar.edu>
Co-authored-by: Aubrey Dugger <adugger@ucar.edu>
Co-authored-by: Ryan Cabell <rcabell@ucar.edu>

trunk/NDHMS/Land_models/NoahMP/IO_code/Makefile

@@ -1,4 +1,4 @@
-# Makefile 
+# Makefile
 #
 .SUFFIXES:
 .SUFFIXES: .o .F
@@ -20,13 +20,13 @@ NoahMP : $(OBJS_NoahMP) $(OBJS)
 module_NoahMP_hrldas_driver.o: module_NoahMP_hrldas_driver.F ../../../HYDRO_drv/module_HYDRO_drv.o ../../../Data_Rec/module_namelist.o ../../../Data_Rec/module_RT_data.o
 	@echo ""
 	$(COMPILERF90) $(CPPINVOKE) $(CPPFLAGS) $(CPPHRLDAS) -o $(@) -c $(F90FLAGS) $(FREESOURCE) $(MODFLAG) -I. \
-	-I../phys -I../Utility_routines -I../../../mod $(NETCDFMOD) $(*).F
+	-I../phys -I../phys/surfex -I../Utility_routines -I../../../mod $(NETCDFMOD) $(*).F
 	@echo ""
 
 main_hrldas_driver.o: ../../../OrchestratorLayer/orchestrator.o main_hrldas_driver.F
 	@echo ""
 	$(COMPILERF90) $(CPPINVOKE) $(CPPFLAGS) $(CPPHRLDAS) -o $(@) -c $(F90FLAGS) $(LDFLAGS) $(FREESOURCE) -I ../MPP -I. \
-	-I../phys -I../Utility_routines -I../../../mod -I../../../MPP -I../data_structures $(NETCDFMOD) $(*).F
+	-I../phys -I../phys/surfex -I../Utility_routines -I../../../mod -I../../../MPP -I../data_structures $(NETCDFMOD) $(*).F
 #	$(COMPILERF90) -o $(@) -c $(F90FLAGS) $(FREESOURCE) -I ../MPP -I. \
 #	-I../phys -I../Utility_routines $(NETCDFMOD) $(*).f90
 	@echo ""

trunk/NDHMS/Land_models/NoahMP/phys/Makefile

@@ -1,35 +1,33 @@
-# Makefile 
+# Makefile
 #
-.SUFFIXES:
-.SUFFIXES: .o .F
-
 include ../user_build_options
 
-OBJS = \
-	module_sf_noahmpdrv.o \
-	module_sf_noahmplsm.o \
-	module_sf_noahmp_glacier.o \
-	module_sf_noahmp_groundwater.o
-
+SRCS := $(wildcard *.F)
+OBJS := $(SRCS:%.F=%.o)
+SUR_SRCS := $(wildcard surfex/*.F)
+SUR_OBJS := $(SUR_SRCS:%.F=%.o)
 CPPHRLDAS = -D_HRLDAS_OFFLINE_
 
-all:	$(OBJS)
+all: $(OBJS)
 
-.F.o:
+%.o:%.F
 	@echo ""
-	$(COMPILERF90) $(CPPINVOKE) $(CPPFLAGS) $(CPPHRLDAS) -o $(@) -c -I../Utility_routines $(F90FLAGS) $(LDFLAGS) $(FREESOURCE) $(*).F
+	$(COMPILERF90) $(CPPINVOKE) $(CPPFLAGS) $(CPPHRLDAS) -o $(@) -c -I../Utility_routines -Isurfex $(F90FLAGS) $(LDFLAGS) $(FREESOURCE) $(*).F
 	@echo ""
 
+surfex/%.o:
+	$(MAKE) --directory=surfex/
+
 #
 # Dependencies:
 #
-module_sf_noahmpdrv.o:	module_sf_noahmplsm.o module_sf_noahmp_glacier.o module_sf_noahmp_groundwater.o
+module_sf_noahmpdrv.o:	module_sf_noahmplsm.o module_sf_noahmp_glacier.o module_sf_noahmp_groundwater.o module_snowcro.o
 module_sf_noahmp_groundwater.o: module_sf_noahmplsm.o
+module_snowcro.o: $(SUR_OBJS)
 
 #
 # This command cleans up object (etc) files:
 #
-
 clean:
+	$(MAKE) clean --directory=surfex
 	$(RM) *.o *.mod *.stb *~
-

trunk/NDHMS/Land_models/NoahMP/phys/surfex/Makefile

@@ -0,0 +1,31 @@
+#
+# Makefile
+#
+
+include ../../user_build_options
+SRCS := $(wildcard *.F)
+OBJS := $(SRCS:%.F=%.o)
+CPPHRLDAS = -D_HRLDAS_OFFLINE_
+
+all: $(OBJS)
+
+%.o:%.F
+	@echo ""
+	$(COMPILERF90) $(CPPINVOKE) $(CPPFLAGS) $(CPPHRLDAS) -o $@ -c -I../Utility_routines \
+	   $(F90FLAGS) $(LDFLAGS) $(FREESOURCE) $<
+	@echo ""
+
+#
+# Dependencies:
+#
+mode_snow3l.o: modd_snow_par.o modd_csts.o modd_snow_metamo.o
+mode_thermos.o: modd_csts.o modd_snow_par.o
+mode_surf_coefs.o: modd_surf_atm.o mode_thermos.o
+ini_csts.o: modd_csts.o
+
+
+#
+# This command cleans up object (etc) files:
+#
+clean:
+	$(RM) *.o *.mod *.stb *~