Megan CTSM

.git-blame-ignore-revs

@@ -51,3 +51,4 @@ aa04d1f7d86cc2503b98b7e2b2d84dbfff6c316b
 1a49e547ba3c48fa483f9ae81a8f05adcd6b888c
 045d90f1d80f713eb3ae0ac58f6c2352937f1eb0
 753fda3ff0147837231a73c9c728dd9ce47b5997
+f112ba0bbf96a61d5a4d354dc0dcbd8b0c68145c

.gitmodules

@@ -27,8 +27,8 @@
 #
 [submodule "fates"]
 path = src/fates
-url = https://github.com/NGEET/fates
-fxtag = sci.1.78.2_api.36.0.0
+url = https://github.com/NorESMhub/fates
+fxtag = sci.1.78.3_api.36.1.0_noresm_v1
 fxrequired = AlwaysRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NCAR/fates-release
@@ -64,7 +64,7 @@ fxtag = cesm-coupling.n02_v2.1.2
 fxrequired = ToplevelRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
-        
+
 [submodule "ccs_config"]
 path = ccs_config
 url = https://github.com/NorESMhub/ccs_config_noresm.git

bld/CLMBuildNamelist.pm

@@ -978,7 +978,7 @@ sub setup_cmdl_bgc {
   # Set soil matrix (which is needed later for spinup)
   $var = "use_soil_matrixcn";
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
-              , 'use_fates'=>$nl_flags->{'use_fates'}, 
+              , 'use_fates'=>$nl_flags->{'use_fates'},
               , 'soil_decomp_method'=>$nl_flags->{'soil_decomp_method'},
               , 'phys'=>$nl_flags->{'phys'}, clm_accelerated_spinup=>$nl_flags->{'clm_accelerated_spinup'} );
   if ( &value_is_true($nl->get_value($var)) ) {
@@ -1214,7 +1214,7 @@ sub setup_cmdl_spinup {
   if ( &value_is_true($nl_flags->{'use_cn'}) ) {
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition,
                 $defaults, $nl, "spinup_state", clm_accelerated_spinup=>$nl_flags->{'clm_accelerated_spinup'},
-                use_cn=>$nl_flags->{'use_cn'}, use_fates=>$nl_flags->{'use_fates'}, 
+                use_cn=>$nl_flags->{'use_cn'}, use_fates=>$nl_flags->{'use_fates'},
                 use_soil_matrixcn=>$nl_flags->{"use_soil_matrixcn"} );
     if ( $nl->get_value("spinup_state") ne 0 ) {
        $nl_flags->{'bgc_spinup'} = "on";
@@ -2588,12 +2588,9 @@ sub setup_logic_initial_conditions {
   my $finidat = $nl->get_value($var);
   $nl_flags->{'excess_ice_on_finidat'} = "unknown";
   if ( $nl_flags->{'clm_start_type'} =~ /cold/ ) {
-    if (defined $finidat ) {
-      $log->warning("setting $var (either explicitly in your user_nl_clm or by doing a hybrid or branch RUN_TYPE)\n is incomptable with using a cold start" .
+    if (defined $finidat && !&value_is_true(($nl->get_value('use_fates')))) {
+      $log->fatal_error("setting $var (either explicitly in your user_nl_clm or by doing a hybrid or branch RUN_TYPE)\n is incompatible with using a cold start" .
               " (by setting CLM_FORCE_COLDSTART=on)." );
-      $log->warning("Overridding input $var file with one specifying that this is a cold start from arbitrary initial conditions." );
-      my $group = $definition->get_group_name($var);
-      $nl->set_variable_value($group, $var, "' '" );
     }
     add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl,
                 $var, 'val'=>"' '", 'no_abspath'=>1);
@@ -2756,6 +2753,12 @@ SIMYR:    foreach my $sim_yr ( @sim_years ) {
         $log->fatal_error("$useinitvar is being set for you but a $var was not found, so $useinitvar, init_interp_attributes, and finidat must not be set correctly for this configuration in the namelist_default file" );
      }
   }
+
+  # this check has to be here and not earlier since use_init_interp is set here and hillslope is already set above in setup_logic_hillslope
+  if ( &value_is_true($nl->get_value($useinitvar)) && value_is_true($nl->get_value("use_hillslope")) ) {
+     $log->warning("WARNING: You have set use_hillslope while $useinitvar is TRUE.\n This means all hillslope columns in a gridcell will read identical values from initial conditions, even if the initial conditions (finidat) file has hillslope information. If you are sure you want this behaviour, add -ignore_warnings to CLM_BLDNML_OPTS.")
+  }
+
 } # end initial conditions
 
 #-------------------------------------------------------------------------------
@@ -3596,17 +3599,6 @@ sub setup_logic_luna {
   if ( &value_is_true($nl->get_value('lnc_opt') ) && not &value_is_true( $nl_flags->{'use_cn'}) ) {
      $log->fatal_error("Cannot turn lnc_opt to true when bgc=sp" );
   }
-  my $var = "jmaxb1";
-  if ( &value_is_true( $nl_flags->{'use_luna'} ) ) {
-     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
-                 'use_luna'=>$nl_flags->{'use_luna'} );
-  }
-  my $val = $nl->get_value($var);
-  if ( ! &value_is_true( $nl_flags->{'use_luna'} ) ) {
-     if ( defined($val) ) {
-        $log->fatal_error("Cannot set $var when use_luna is NOT on" );
-     }
-  }
 }
 
 #-------------------------------------------------------------------------------
@@ -3630,6 +3622,10 @@ sub setup_logic_hillslope {
   if ( (! &value_is_true($use_hillslope)) && &value_is_true($use_hillslope_routing) ) {
       $log->fatal_error("Cannot turn on use_hillslope_routing when use_hillslope is off\n" );
   }
+  my $hillslope_file = $nl->get_value('hillslope_file');
+  if ( &value_is_true($use_hillslope) && ( ! defined($hillslope_file) ) ) {
+    $log->fatal_error("You must provide hillslope_file if use_hillslope is .true.\n" );
+  }
 }
 
 #-------------------------------------------------------------------------------
@@ -4152,12 +4148,8 @@ sub setup_logic_megan {
     add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'megan_factors_file');
   }
   if ( defined($nl->get_value('megan_specifier')) ||
-         defined($nl->get_value('megan_factors_file')) ) {
+       defined($nl->get_value('megan_factors_file')) ) {
     check_megan_spec( $opts, $nl, $definition );
-    if ( &value_is_true( $nl_flags->{'use_fates'} ) ) {
-      $log->warning("MEGAN can NOT be on when FATES is also on.\n" .
-                    "   Use the '-no-megan' option when '-bgc fates' is activated");
-    }
   }
 }
 
@@ -4516,8 +4508,6 @@ sub setup_logic_canopyhydrology {
   #
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'interception_fraction' );
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'maximum_leaf_wetted_fraction' );
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_clm5_fpi' );
 }
 
@@ -4536,7 +4526,6 @@ sub setup_logic_snowpack {
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'wind_dependent_snow_density');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'snow_overburden_compaction_method');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'lotmp_snowdensity_method');
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'upplim_destruct_metamorph');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_snow');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_snow_glc');
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'reset_snow_glc_ela');
@@ -4973,7 +4962,7 @@ sub setup_logic_exice {
   # excess ice streams, must be set before initial conditions
   #
   my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_excess_ice', 'phys'=>$physv->as_string()); 
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_excess_ice', 'phys'=>$physv->as_string());
   my $use_exice = $nl->get_value( 'use_excess_ice' );
   # Put use_exice into nl_flags so can be referenced later
   if ( value_is_true($use_exice) ) {