Merge branch 'wanggangsheng/lnd/alm-pflotran-bgc-rebase3' (PR #1649)

Migrate NGEE-Arctic CLM-PFLOTRAN to ACME Land Model through a
generic clm_interface

1. clm_interface_dataType consists of biogeochemistry (bgcType)
and thermal-hydrology (thType).
2. Rename namelist use_bgc_interface to use_clm_interface to
include bgc & th interfaces.
3. Data passing between ALM & clm_interface is implemented in
clm_interface_funcsMod.F90.
4. Data passing between clm_interface & PFLOTRAN is implemented in
clm_interface_pflotranMod.F90.
5. Global-scale ALM-PFLOTRAN-bgc coupled run is tested.
6. The clm_interface is extended to incorporate PLFOTRAN
thermal-hydrology in next step.
7. Add configuration for mach "cades" for alm-pflotran coupled run.
8. makefile: update "PETSC_LIB"-"variables" dir for
petsc-git-version 1a9d3c3.

[BFB]

Conflicts:
	components/clm/src/biogeochem/CNNStateUpdate1Mod.F90
	components/clm/src/biogeochem/CNNitrogenFluxType.F90
	components/clm/src/biogeochem/PStateUpdate1Mod.F90
	components/clm/src/biogeochem/PStateUpdate2Mod.F90
	components/clm/src/biogeochem/PStateUpdate3Mod.F90
	components/clm/src/biogeophys/HydrologyNoDrainageMod.F90
	components/clm/src/main/clm_initializeMod.F90
	components/clm/src/main/controlMod.F90

config/acme/machines/Makefile

@@ -251,8 +251,9 @@ ifeq ($(strip $(USE_PETSC)), TRUE)
     $(error PETSC_PATH must be defined when USE_PETSC is TRUE)
   endif
 
-  # Get the "PETSC_LIB" list an env var
-  include $(PETSC_PATH)/conf/variables
+  # Get the "PETSC_LIB" list an env var 
+  include $(PETSC_PATH)/lib/petsc/conf/variables
+
 endif
 
 # Set Trilinos info if it is being used
@@ -564,7 +565,7 @@ endif
 
 # Add PETSc libraries
 ifeq ($(strip $(USE_PETSC)), TRUE)
-  SLIBS += -L${LIB_PETSC} ${PETSC_LIB}
+  SLIBS += ${PETSC_LIB}
 endif
 
 # Add trilinos libraries; too be safe, we include all libraries included in the trilinos build,
@@ -904,7 +905,7 @@ cleanrof:
 	$(RM) -fr $(EXEROOT)/rof/obj
 
 cleanlnd:
-	$(RM) -f $(LIBROOT)/liblnd.a
+	$(RM) -f $(LIBROOT)/$(LNDLIB)
 	$(RM) -fr $(EXEROOT)/lnd/obj
 
 cleancsmshare:

config/acme/machines/config_compilers.xml

@@ -82,6 +82,18 @@ for mct, etc.
   <ADD_CPPDEFS MODEL="pop"> -D_USE_FLOW_CONTROL </ADD_CPPDEFS>
 </compiler>
 
+
+<!-- hacking of mach/compiler generated 'Macros.make' for coupling with pflotran -->
+<!-- ideally it should go with CLM configuration -->
+<compiler>
+  <ADD_FFLAGS  MODEL="clm"    CLM_PFLOTRAN_COUPLED="TRUE"> -I$(CLM_PFLOTRAN_SOURCE_DIR) </ADD_FFLAGS>
+  <ADD_CPPDEFS MODEL="clm"    CLM_PFLOTRAN_COUPLED="TRUE"> -DCLM_PFLOTRAN </ADD_CPPDEFS>
+  <ADD_CPPDEFS MODEL="clm"    CLM_PFLOTRAN_COUPLED="TRUE" CLM_PFLOTRAN_COLMODE="TRUE"> -DCOLUMN_MODE </ADD_CPPDEFS>
+  <ADD_LDFLAGS MODEL="driver" CLM_PFLOTRAN_COUPLED="TRUE"> -L$(CLM_PFLOTRAN_SOURCE_DIR) -lpflotran $(PETSC_LIB) </ADD_LDFLAGS>
+</compiler>
+<!-- end of hacking 'Macros.make' for coupling with pflotran -->
+
+
 <compiler COMPILER="ibm">
   <!-- http://publib.boulder.ibm.com/infocenter/comphelp/v7v91/index.jsp
  Notes:  (see xlf user's guide for the details)

config/acme/machines/config_machines.xml

@@ -1947,6 +1947,16 @@
           <command name="load">netcdf-hdf5parallel/4.3.3.1</command>
         </modules>
       </module_system>
+
+      <!-- for CLM-PFLOTRAN coupling, the PETSC_PATH must be defined specifically upon machines -->
+      <environment_variables>
+        <env name="PETSC_PATH" compiler="gnu" mpilib="openmpi">/software/user_tools/current/cades-ccsi/petsc4pf/openmpi-1.10-gcc-5.3</env>      
+       <!-- hack for PFLOTRAN coupling (this is a temporary solution, and user must manually edit it after case.setup)-->
+       <env name="CLM_PFLOTRAN_COUPLED">FALSE</env>
+       <env name="CLM_PFLOTRAN_COLMODE">FALSE</env>
+       <!-- dir for pflotran source code -->
+       <env name="CLM_PFLOTRAN_SOURCE_DIR">/lustre/or-hydra/cades-ccsi/$USER/models/pflotran-interface/src/clm-pflotran</env>
+      </environment_variables>       
 </machine>
 
 <machine MACH="titan">

config/acme/testmods_dirs/allactive/clm/bgcinterface/user_nl_clm

@@ -0,0 +1,2 @@
+use_clm_interface = .true.
+use_clm_bgc = .true.

scripts/lib/update_acme_tests.py

@@ -73,6 +73,7 @@
                              ("SMS_Ld4.f45_f45.ICLM45ED","clm-fates"),
                              ("ERS.f19_g16.I1850CLM45","clm-betr"),
                              ("ERS.f19_g16.I1850CLM45","clm-vst"),
+                             ("ERS.f09_g16.I1850CLM45CN","clm-bgcinterface"),
                               "ERS.ne11_oQU240.I20TRCLM45",
                               "ERS.f09_g16.IMCLM45BC")
                              ),