Merge branch 'jinyuntang/lnd/betr' into next (PR #367)

This merge brings in BeTR to facilitate reactive transport based land BGC modeling in ALM. By default, BeTR is turned off. BeTR has been tested with simulations with different bgc configurations for about 10000 years, and some modules was evaluated analytically. The merge does not requires new parameter files nor affect any other existing land components. [BFB] LG-108 Conflicts: cime/machines-acme/env_mach_specific.edison components/clm/bld/CLMBuildNamelist.pm components/clm/bld/configure components/clm/src/biogeochem/CNCStateUpdate1Mod.F90 components/clm/src/biogeochem/CNCStateUpdate2Mod.F90 components/clm/src/biogeochem/CNCStateUpdate3Mod.F90 components/clm/src/biogeochem/CNCarbonFluxType.F90 components/clm/src/biogeochem/CNEcosystemDynMod.F90 components/clm/src/biogeochem/CNNStateUpdate1Mod.F90 components/clm/src/biogeochem/CNNStateUpdate2Mod.F90 components/clm/src/biogeochem/CNNStateUpdate3Mod.F90 components/clm/src/biogeochem/CNNitrogenFluxType.F90 components/clm/src/biogeochem/CNNitrogenStateType.F90 components/clm/src/biogeochem/CNPrecisionControlMod.F90 components/clm/src/biogeochem/CNStateType.F90 components/clm/src/main/clm_driver.F90 components/clm/src/main/clm_initializeMod.F90 components/clm/src/main/clm_varctl.F90 components/clm/src/main/controlMod.F90 components/clm/src/main/restFileMod.F90
E3SM-Project · Oct 24, 2015 · 4d29a66 · 4d29a66
2 parents 20e6611 + be0d6ed
commit 4d29a66
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diff --git a/cime/machines-acme/env_mach_specific.edison b/cime/machines-acme/env_mach_specific.edison
@@ -19,12 +19,12 @@ echo "DEBUG=$DEBUG"
 if (-e /opt/modules/default/init/csh) then
   source /opt/modules/default/init/csh
   module rm PrgEnv-intel
-  module rm PrgEnv-cray 
+  module rm PrgEnv-cray
   module rm PrgEnv-gnu
   module rm intel
   module rm cce
   module rm cray-parallel-netcdf
-  module rm cray-parallel-hdf5 
+  module rm cray-parallel-hdf5
   module rm pmi
   module rm cray-libsci
   module rm cray-mpich2
@@ -46,16 +46,16 @@ if ( $COMPILER == "intel" ) then
          module load esmf/6.2.0-defio-mpi-g
     else
          module load esmf/6.2.0-defio-mpi-O
-    endif  
-endif    
+    endif
+endif
 if ( $COMPILER == "cray" ) then
     module load PrgEnv-cray
     module switch cce      cce/8.3.7
 endif    
 if ( $COMPILER == "gnu" ) then
     module load PrgEnv-gnu
     module switch gcc       gcc/4.8.0
-endif    
+endif
 
 module load papi/5.3.2
 module swap craype craype/2.1.1

diff --git a/components/clm/bld/CLMBuildNamelist.pm b/components/clm/bld/CLMBuildNamelist.pm
@@ -217,6 +217,7 @@ OPTIONS
      -version                 Echo the SVN tag name used to check out this CLM distribution.
      -vichydro                Toggle to turn on VIC hydrologic parameterizations (default is off)
                               This turns on the namelist variable: use_vichydro
+     -betr_mode               Turn on betr model for tracer transport in soil. [on|off] default is off.
 
 
 Note: The precedence for setting the values of namelist variables is (highest to lowest):
@@ -278,6 +279,7 @@ sub process_commandline {
                envxml_dir            => ".",
                vichydro              => 0,
                maxpft                => "default",
+               betr_mode             => "default",               
              );
 
   GetOptions(
@@ -322,6 +324,7 @@ sub process_commandline {
              "maxpft=i"                  => \$opts{'maxpft'},
              "v|verbose"                 => \$opts{'verbose'},
              "version"                   => \$opts{'version'},
+             "betr_mode=s"               => \$opts{'betr_mode'},             
             )  or usage();
 
   # Give usage message.
@@ -641,6 +644,7 @@ sub process_namelist_commandline_options {
   setup_cmdl_dynamic_vegetation($opts, $nl_flags, $definition, $defaults, $nl, $physv);
   setup_cmdl_ed_mode($opts, $nl_flags, $definition, $defaults, $nl, $physv);
   setup_cmdl_vichydro($opts, $nl_flags, $definition, $defaults, $nl, $physv);
+  setup_cmdl_betr_mode($opts, $nl_flags, $definition, $defaults, $nl, $physv);  
 }
 
 #-------------------------------------------------------------------------------
@@ -762,6 +766,49 @@ sub setup_cmdl_ed_mode {
   }
 }
 
+#-------------------------------------------------------------------------------
+sub setup_cmdl_betr_mode {
+  #
+  # call this at least after crop check is called
+  #
+  my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
+
+  my $val;
+  my $var = "betr_mode";
+
+  $val = $opts->{$var};
+  $nl_flags->{'betr_mode'} = $val;
+
+  if ( $physv->as_long() == $physv->as_long("clm4_0") || $nl_flags->{'crop'} eq "on" ) {
+    if ( $nl_flags->{'ed_mode'} == 1 ) {
+       # ED is not a clm4_0 option and should not be used with crop and not with clm4_0
+       fatal_error("** Cannot turn betr mode on with crop or with clm4_0 physics.\n" );
+    }
+  } else {
+
+    $var = "use_betr";
+    $nl_flags->{$var} = ".false.";
+    if ($nl_flags->{'betr_mode'} eq "on") {
+      message("Using BETR (Reactive Transport).");
+      $val = ".true.";
+      $nl_flags->{$var} = $val;
+    }
+    if ( defined($nl->get_value($var)) && $nl->get_value($var) ne $val ) {
+      fatal_error("$var is inconsistent with the commandline setting of -betr_mode");
+    }
+    if ( $nl_flags->{$var} eq ".true." ) {
+      my $group = $definition->get_group_name($var);
+      $nl->set_variable_value($group, $var, $val);
+      if (  ! $definition->is_valid_value( $var, $val ) ) {
+        my @valid_values   = $definition->get_valid_values( $var );
+        fatal_error("$var has a value ($val) that is NOT valid. Valid values are: @valid_values\n");
+      }
+
+    }
+  }
+}
+
+
 #-------------------------------------------------------------------------------
 sub setup_cmdl_bgc {
   # BGC - alias for group of biogeochemistry related use_XXX namelists
@@ -2759,7 +2806,7 @@ sub write_output_files {
   } else {
     @groups = qw(clm_inparm ndepdyn_nml popd_streams light_streams lai_streams clm_canopyhydrology_inparm 
                  clm_soilhydrology_inparm dynamic_subgrid finidat_consistency_checks dynpft_consistency_checks 
-                 clmu_inparm clm_soilstate_inparm clm_pflotran_inparm );
+                 clmu_inparm clm_soilstate_inparm clm_pflotran_inparm betr_inparm);
     #@groups = qw(clm_inparm clm_canopyhydrology_inparm clm_soilhydrology_inparm 
     #             finidat_consistency_checks dynpft_consistency_checks);
     # Eventually only list namelists that are actually used when CN on

diff --git a/components/clm/bld/configure b/components/clm/bld/configure
@@ -645,7 +645,12 @@ sub write_filepath_cesmbld
 
 	# source directories under root
 	my @dirs = ( "main", 
-		     "biogeophys", 
+		     "betr",
+		     "betr/betr_math",
+		     "betr/betr_core",
+		     "betr/bgc_century",
+		     "betr/bgc_sminn",
+		     "biogeophys",
 		     "biogeochem", 
 		     "dyn_subgrid",
 		     "ED", 

diff --git a/components/clm/bld/namelist_files/namelist_definition_clm4_5.xml b/components/clm/bld/namelist_files/namelist_definition_clm4_5.xml
@@ -198,6 +198,11 @@ This downscaling is conservative.
 <default>Default: .true.</default>
 </entry>
 
+<entry id="use_betr" type="logical" category="physics"
+        group="clm_inparm" valid_values="" value=".false.">
+Toggle to turn on the BeTR
+(BETR = 'on' is EXPERIMENTAL NOT SUPPORTED!)
+</entry>
 
 <entry id="use_ed" type="logical" category="physics"
         group="clm_inparm" valid_values="" value=".false.">
@@ -1275,6 +1280,14 @@ reaches melting when ice is present with no snow layers. Represents puddling, ic
 Set to alblak values (0.6, 0.4) to keep albedo constant for ice-covered lakes without snow layers.
 </entry>
 
+<!-- ========================================================================================  -->
+<!-- namelist elements associated with the betr_initializeMod                                  -->
+<!-- ========================================================================================  -->
+<entry id="bgc_method" type="char*256" category="clm_betr"
+       group="betr_inparm" valid_values="" >
+Specify what bgc module will be used within the betr framework. 
+</entry>
+
 <!-- ========================================================================================  -->
 <!-- namelist elements associated with the Hydrology1Mod                                       -->
 <!-- ========================================================================================  -->

diff --git a/components/clm/bld/test_build_namelist/t/input/namelist_definition_clm4_5_test.xml b/components/clm/bld/test_build_namelist/t/input/namelist_definition_clm4_5_test.xml
@@ -1159,6 +1159,14 @@ reaches melting when ice is present with no snow layers. Represents puddling, ic
 Set to alblak values (0.6, 0.4) to keep albedo constant for ice-covered lakes without snow layers.
 </entry>
 
+<!-- ========================================================================================  -->
+<!-- namelist elements associated with the betr_initializeMod                                  -->
+<!-- ========================================================================================  -->
+<entry id="bgc_method" type="char*256" category="clm_betr"
+       group="betr_inparm" valid_values="" >
+Specify what bgc module will be used within the betr framework. 
+</entry>
+
 <!-- ========================================================================================  -->
 <!-- namelist elements associated with the Hydrology1Mod                                       -->
 <!-- ========================================================================================  -->

diff --git a/components/clm/bld/unit_testers/build-namelist_test.pl b/components/clm/bld/unit_testers/build-namelist_test.pl
@@ -507,6 +507,11 @@ sub make_env_run {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      conopts=>"-phys clm4_5",
                                    },
+     "useBETRContradict"           =>{ options=>"-betr_mode -envxml_dir .",
+                                     namelst=>"use_betr=.false.",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     conopts=>"-phys clm4_5",
+                                   },          
      "useEDContradict2"          =>{ options=>"-envxml_dir .",
                                      namelst=>"use_ed=.true.",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",

diff --git a/components/clm/src/betr/BGCReactionsFactoryMod.F90 b/components/clm/src/betr/BGCReactionsFactoryMod.F90
@@ -0,0 +1,76 @@
+module BGCReactionsFactoryMod
+  !
+  ! !DESCRIPTION:
+  !  factory to load the specific bgc reaction modules
+  !
+  ! History:
+  !  Created by Jinyun Tang, Oct 2, 2014
+  !
+  !
+  ! !USES:
+  !
+  use shr_kind_mod          , only : r8 => shr_kind_r8
+  use decompMod             , only : bounds_type
+  use shr_log_mod           , only : errMsg => shr_log_errMsg
+  implicit none
+  save
+  private
+  public ::  ctreate_bgc_reaction_type
+
+
+contains
+
+  function ctreate_bgc_reaction_type(method) result(bgc_reaction)
+    !
+    ! !DESCRIPTION:
+    ! create and return an object of bgc_reaction
+    !
+    ! !USES:
+    use BGCReactionsMod             , only : bgc_reaction_type
+    use BGCReactionsMockRunType     , only : bgc_reaction_mock_run_type
+    use BGCReactionsCenturyType     , only : bgc_reaction_CENTURY_type
+    use BGCReactionsCenturyCLMType  , only : bgc_reaction_CENTURY_clm_type
+    use BGCReactionsCenturyECAType  , only : bgc_reaction_CENTURY_ECA_type
+    use BGCReactionsSminNType       , only : bgc_reaction_sminn_type
+    use BGCReactionsCenturyCLM3Type , only : bgc_reaction_CENTURY_clm3_type
+    use BGCReactionsCenturyCLMOType , only : bgc_reaction_CENTURY_clmo_type
+    use abortutils                  , only : endrun
+    use clm_varctl                  , only : iulog
+    use tracer_varcon               , only : is_active_betr_bgc, do_betr_leaching
+
+    ! !ARGUMENTS:
+    class(bgc_reaction_type), allocatable :: bgc_reaction
+    character(len=*), intent(in)          :: method
+    character(len=*), parameter           :: subname = 'ctreate_bgc_reaction_type'
+
+    select case(trim(method))
+    case ("mock_run")
+       allocate(bgc_reaction, source=bgc_reaction_mock_run_type())
+    case ("century_bgc")
+       is_active_betr_bgc = .true.
+       allocate(bgc_reaction, source=bgc_reaction_CENTURY_type())
+    case ("century_bgcclm")
+       is_active_betr_bgc = .true.
+       allocate(bgc_reaction, source=bgc_reaction_CENTURY_clm_type())
+    case ("century_bgcECA")
+       is_active_betr_bgc = .true.
+       allocate(bgc_reaction, source=bgc_reaction_CENTURY_ECA_type())
+    case ("century_bgcclm3")
+       is_active_betr_bgc=.true.
+       allocate(bgc_reaction, source=bgc_reaction_CENTURY_clm3_type())
+    case ("century_bgcclmo")
+       is_active_betr_bgc=.true.
+       allocate(bgc_reaction, source=bgc_reaction_CENTURY_clmo_type())
+    case ("betr_sminn")
+       !this must be used together with clm45bgc
+       do_betr_leaching = .true.
+       allocate(bgc_reaction, source=bgc_reaction_sminn_type())
+       !case ("o18_istope")    ! on hold
+       !  allocate(bgc_reaction, source=bgc_reaction_O18ISO_type())
+    case default
+       write(iulog,*)subname //' ERROR: unknown method: ', method
+       call endrun(msg=errMsg(__FILE__, __LINE__))
+    end select
+  end function ctreate_bgc_reaction_type
+
+end module BGCReactionsFactoryMod