clm4_5_18_r272

Bring in the latest version of FATES from NGEET/fates-release and the associated interface changes in CLM from NGEET/fates-clm. The new version is 1.4.1 for science and version 3.0 of the API updated from 1.3.0 for science and 1.0.0 for the API.
ESCOMP · Jan 25, 2018 · b837fc3 · b837fc3
1 parent 0052110
commit b837fc3
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diff --git a/SVN_EXTERNAL_DIRECTORIES b/SVN_EXTERNAL_DIRECTORIES
@@ -1,2 +1,2 @@
-src/fates      https://github.com/NCAR/fates-release/tags/fates_s1.3.0_a1.0.0_rev3
+src/fates      https://github.com/NCAR/fates-release/tags/fates_s1.4.1_a3.0.0_rev2
 tools/PTCLM    https://github.com/ESCOMP/ptclm/tags/PTCLM2_171216c
diff --git a/SVN_EXTERNAL_DIRECTORIES.standalone b/SVN_EXTERNAL_DIRECTORIES.standalone
@@ -1,4 +1,4 @@
 cime                               https://github.com/CESM-Development/cime/tags/clm4518/n02/cime5.4.0-alpha.03
 components/cism                    https://svn-ccsm-models.cgd.ucar.edu/glc/trunk_tags/cism2_1_40
-components/rtm			   https://github.com/ESCOMP/rtm/tags/rtm1_0_64
-components/mosart		   https://github.com/ESCOMP/mosart/tags/mosart1_0_29
+components/rtm			   https://github.com/ESCOMP/rtm/tags/rtm1_0_65
+components/mosart		   https://github.com/ESCOMP/mosart/tags/mosart1_0_30
diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
@@ -741,7 +741,7 @@ sub setup_cmdl_fates_mode {
 
       # The following variables may be set by the user and are compatible with use_fates
       # no need to set defaults, covered in a different routine
-      my @list  = (  "use_fates_spitfire", "use_vertsoilc", "use_century_decomp", "use_lch4" );
+      my @list  = (  "use_vertsoilc", "use_century_decomp", "use_lch4" );
       foreach my $var ( @list ) {
 	  if ( defined($nl->get_value($var))  ) {
 	      $nl_flags->{$var} = $nl->get_value($var);
@@ -754,15 +754,14 @@ sub setup_cmdl_fates_mode {
 	      }
 	  }
       }
-
-#      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_vertsoilc', 'use_fates'=>$nl_flags->{'use_fates'} );
-
-
     } else {
-	# we only dis-allow fates_spit_fire with non-fates runs
-       $var = "use_fates_spitfire";
-       if ( defined($nl->get_value($var)) ) {
-           $log->fatal_error("$var is being set, but can ONLY be set when -bgc fates option is used.");
+       # dis-allow fates specific namelist items with non-fates runs
+       my @list  = (  "use_fates_spitfire", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys", 
+                      "use_fates_inventory_init", "fates_inventory_ctrl_filename","use_fates_logging" );
+       foreach my $var ( @list ) {
+          if ( defined($nl->get_value($var)) ) {
+              $log->fatal_error("$var is being set, but can ONLY be set when -bgc fates option is used.\n");
+          }
        }
     }
   }
@@ -1244,14 +1243,14 @@ sub setup_cmdl_run_type {
   if (defined $opts->{$var}) {
     if ($opts->{$var} eq "default" ) {
       add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 
-                  'use_cndv'=>$nl_flags->{'use_cndv'} );
+                  'use_cndv'=>$nl_flags->{'use_cndv'}, 'use_fates'=>$nl_flags->{'use_fates'} );
     } else {
       my $group = $definition->get_group_name($var);
       $nl->set_variable_value($group, $var, quote_string( $opts->{$var} ) );
     }
   } else {
     add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 
-                  'use_cndv'=>$nl_flags->{'use_cndv'} );
+                  'use_cndv'=>$nl_flags->{'use_cndv'}, 'use_fates'=>$nl_flags->{'use_fates'} );
   }
   $nl_flags->{'clm_start_type'} = $nl->get_value($var);
 }
@@ -2339,7 +2338,7 @@ sub setup_logic_initial_conditions {
        }
     } else {
        foreach my $item ( "mask", "maxpft", "irrigate", "glc_nec", "use_crop", "use_cn", "use_cndv", 
-                          "use_nitrif_denitrif", "use_vertsoilc", "use_century_decomp"
+                          "use_nitrif_denitrif", "use_vertsoilc", "use_century_decomp", "use_fates"
                         ) {
           $settings{$item}    = $nl_flags->{$item};
        }
@@ -2381,7 +2380,8 @@ sub setup_logic_initial_conditions {
           } 
           add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $useinitvar,
                      'use_cndv'=>$nl_flags->{'use_cndv'}, 'phys'=>$physv->as_string(),
-                     'sim_year'=>$settings{'sim_year'}, 'nofail'=>1  );
+                     'sim_year'=>$settings{'sim_year'}, 'nofail'=>1, 
+                     'use_fates'=>$nl_flags->{'use_fates'} );
           $settings{$useinitvar} = $nl->get_value($useinitvar);
           if ( $try > 1 ) {
              my $group = $definition->get_group_name($useinitvar);
@@ -2390,7 +2390,8 @@ sub setup_logic_initial_conditions {
           if ( &value_is_true($nl->get_value($useinitvar) ) ) {
 
              add_default($opts,  $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, "init_interp_attributes",
-                        'sim_year'=>$settings{'sim_year'}, 'use_cndv'=>$nl_flags->{'use_cndv'},
+                        'sim_year'=>$settings{'sim_year'}, 'use_cndv'=>$nl_flags->{'use_cndv'}, 
+                        'glc_nec'=>$nl_flags->{'glc_nec'}, 'use_fates'=>$nl_flags->{'use_fates'},
                         'use_cn'=>$nl_flags->{'use_cn'}, 'nofail'=>1 );
              my $attributes_string = remove_leading_and_trailing_quotes($nl->get_value("init_interp_attributes"));
              foreach my $pair ( split( /\s/, $attributes_string) ) {
@@ -3679,8 +3680,23 @@ sub setup_logic_fates {
     my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
 
     if ($physv->as_long() >= $physv->as_long("clm4_5") && &value_is_true( $nl_flags->{'use_fates'})  ) {
- 	add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_fates_spitfire', 'use_fates'=>$nl_flags->{'use_fates'} );
         add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'fates_paramfile', 'phys'=>$nl_flags->{'phys'});
+        my @list  = (  "use_fates_spitfire", "use_fates_planthydro", "use_fates_ed_st3", "use_fates_ed_prescribed_phys", 
+                       "use_fates_inventory_init", "use_fates_logging" );
+        foreach my $var ( @list ) {
+ 	  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 'use_fates'=>$nl_flags->{'use_fates'} );
+        }
+        my $var = "use_fates_inventory_init";
+        if ( defined($nl->get_value($var))  ) {
+           if ( &value_is_true($nl->get_value($var)) ) {
+              $var = "fates_inventory_ctrl_filename";
+              if ( ! defined($nl->get_value($var))  ) {
+                 $log->fatal_error("$var is required when use_fates_inventory_init is set" );
+              } elsif ( ! -f "$nl->get_value($var)" ) {
+                 $log->fatal_error("$var does NOT point to a valid filename" );
+              }
+           }
+        }
     }
 }
 

diff --git a/bld/namelist_files/namelist_defaults_clm4_5.xml b/bld/namelist_files/namelist_defaults_clm4_5.xml
@@ -347,8 +347,11 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <paramfile phys="clm5_0">lnd/clm2/paramdata/clm5_params.c171117.nc</paramfile>
 <paramfile phys="clm4_5">lnd/clm2/paramdata/clm_params.c170913.nc</paramfile>
 
-<fates_paramfile>lnd/clm2/paramdata/fates_params.c170331.nc</fates_paramfile>
+<!-- ================================================================== -->
+<!-- FATES default parameter file                                       -->
+<!-- ================================================================== -->
 
+<fates_paramfile>lnd/clm2/paramdata/fates_params_2troppftclones.c171018.nc</fates_paramfile>
 
 <!-- ========================================================================================  -->
 <!-- clm 5.0 BGC nitrogen model                                                                -->
@@ -449,21 +452,21 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <init_interp_sim_years>1850,2000</init_interp_sim_years>
 
 <!-- Interpolate from an initial condition file at startup? -->
-<use_init_interp  use_cndv=".false." sim_year="1850">.true.</use_init_interp>
-<use_init_interp  use_cndv=".false." sim_year="2000">.true.</use_init_interp>
-<use_init_interp                                    >.false.</use_init_interp>
+<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="1850">.true.</use_init_interp>
+<use_init_interp  use_cndv=".false." use_fates=".false." sim_year="2000">.true.</use_init_interp>
+<use_init_interp                                                        >.false.</use_init_interp>
 
 <!--
   Set attributes to find specific matching finidat files below
   Each of these settings will correspond to a specific finidat that is
   set up. If more finidat files are added you may need to add more of these.
   Or one specific file will be chosen over another.
 -->
-<init_interp_attributes sim_year="1850" use_cndv=".false."
+<init_interp_attributes sim_year="1850" use_cndv=".false." use_fates=".false."
 >hgrid=1.9x2.5 maxpft=79 mask=gx1v6 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.false. glc_nec=10
 </init_interp_attributes>
 
-<init_interp_attributes sim_year="2000" use_cndv=".false."
+<init_interp_attributes sim_year="2000" use_cndv=".false." use_fates=".false."
 >hgrid=1.9x2.5 maxpft=79 mask=gx1v6 use_cn=.true. use_nitrif_denitrif=.true. use_vertsoilc=.true. use_crop=.true. irrigate=.true. glc_nec=10
 </init_interp_attributes>
 
@@ -472,7 +475,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 -->
 
 <!-- File from Dave Lawrence for a spinup of 2-degree at 1850 with crop on -->
-<finidat hgrid="1.9x2.5"  maxpft="79"  mask="gx1v6" use_cn=".true." use_cndv=".false." 
+<finidat hgrid="1.9x2.5"  maxpft="79"  mask="gx1v6" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="18500101" use_nitrif_denitrif=".true." use_vertsoilc=".true." sim_year="1850"
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".false." use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.IGM1850GSWCLM50BGCCROP.0481-01-01.1.9x2.5_gx1v6_gl5_simyr1850_c170419.nc
@@ -483,12 +486,26 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 -->
 
 <!-- Present day crop spinup at 2-degree with irrigation on -->
-<finidat hgrid="1.9x2.5"    maxpft="79"  mask="gx1v6" use_cn=".true." use_cndv=".false." 
+<finidat hgrid="1.9x2.5"    maxpft="79"  mask="gx1v6" use_cn=".true." use_cndv=".false." use_fates=".false."
          ic_ymd="20110101" use_nitrif_denitrif=".true." use_vertsoilc=".true." sim_year="2000"
          ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."  use_init_interp=".true."
 >lnd/clm2/initdata_map/clmi.IGM2000GSWP3CLM50BGCCROPIRR.2011-01-01.1.9x2.5_gx1v6_gl5_simyr2000_c170419.nc
 </finidat>
 
+<!-- FATES on for 2000 -->
+<finidat hgrid="4x5"  maxpft="17"  mask="gx3v7" use_cn=".false." use_fates=".true."
+         ic_ymd="20000101"  use_nitrif_denitrif=".false." use_vertsoilc=".true." sim_year="2000"
+         ic_tod="0" glc_nec="10" use_crop=".false." irrigate=".true." use_init_interp=".false."
+>lnd/clm2/initdata_map/clmi.I2000Clm45Fates.0121-01-01.4x5_mgx3v7_simyr2000_c180122.nc
+</finidat>
+
+<finidat hgrid="1x1_brazil"  maxpft="17"  mask="navy" use_cn=".false." use_fates=".true."
+         ic_ymd="20000101"  use_nitrif_denitrif=".false." use_vertsoilc=".true." sim_year="2000"
+         ic_tod="0" glc_nec="0" use_crop=".false." irrigate=".true." use_init_interp=".false."
+>lnd/clm2/initdata_map/clmi.I2000Clm45Fates.0101-01-01.1x1_brazil_simyr2000_c180120.nc
+</finidat>
+
+
 <!-- for present day simulations - year 2000 -->
 <fsurdat hgrid="360x720cru"   sim_year="2000" use_crop=".false." irrigate=".true.">
 lnd/clm2/surfdata_map/surfdata_360x720cru_16pfts_Irrig_CMIP6_simyr2000_c170824.nc</fsurdat>
@@ -1004,6 +1021,7 @@ lnd/clm2/surfdata_map/surfdata_ne120np4_78pfts_CMIP6_simyr1850_c170824.nc</fsurd
 <create_crop_landunit     use_fates=".false.">.true.</create_crop_landunit>
 <create_crop_landunit     use_fates=".true." >.false.</create_crop_landunit>
 
+
 <!-- =========================================  -->
 <!-- Performance issues                         -->
 <!-- =========================================  -->
@@ -2299,6 +2317,12 @@ lnd/clm2/surfdata_map/surfdata_ne120np4_78pfts_CMIP6_simyr1850_c170824.nc</fsurd
 <use_lch4            bgc_mode="fates"  >.false.</use_lch4>
 <use_nitrif_denitrif bgc_mode="fates"  >.false.</use_nitrif_denitrif>
 
-<use_fates_spitfire    use_fates=".true.">.false.</use_fates_spitfire>
+<!-- ===== FATES DEFAULTS =========== -->
+<use_fates_spitfire            use_fates=".true.">.false.</use_fates_spitfire>
+<use_fates_planthydro          use_fates=".true.">.false.</use_fates_planthydro>
+<use_fates_ed_st3              use_fates=".true.">.false.</use_fates_ed_st3>
+<use_fates_ed_prescribed_phys  use_fates=".true.">.false.</use_fates_ed_prescribed_phys>
+<use_fates_logging             use_fates=".true.">.false.</use_fates_logging>
+<use_fates_inventory_init      use_fates=".true.">.false.</use_fates_inventory_init>
 
 </namelist_defaults>
diff --git a/bld/namelist_files/namelist_defaults_overall.xml b/bld/namelist_files/namelist_defaults_overall.xml
@@ -13,12 +13,14 @@ determine default values for namelists.
 -->
 
 <!-- Default CLM start-type -->
-<clm_start_type phys="clm4_5"                  >startup</clm_start_type>
-<clm_start_type phys="clm5_0"                  >startup</clm_start_type>
-<clm_start_type phys="clm5_0" use_cndv=".true.">arb_ic</clm_start_type>
-<clm_start_type phys="clm4_5" use_cndv=".true.">arb_ic</clm_start_type>
-<clm_start_type phys="clm4_0"                  >arb_ic</clm_start_type>
-<clm_start_type bgc_spinup="on"                >cold</clm_start_type> <!-- CLM 4.5 -->
+<clm_start_type phys="clm4_5"                   >startup</clm_start_type>
+<clm_start_type phys="clm5_0"                   >startup</clm_start_type>
+<clm_start_type phys="clm5_0" use_cndv=".true." >arb_ic</clm_start_type>
+<clm_start_type phys="clm4_5" use_cndv=".true." >arb_ic</clm_start_type>
+<clm_start_type phys="clm5_0" use_fates=".true.">arb_ic</clm_start_type>
+<clm_start_type phys="clm4_5" use_fates=".true.">arb_ic</clm_start_type>
+<clm_start_type phys="clm4_0"                   >arb_ic</clm_start_type>
+<clm_start_type bgc_spinup="on"                 >cold</clm_start_type> <!-- CLM 4.5 -->
 
 <!-- Default location of {csmdata} -->
 <csmdata>/fs/cgd/csm/inputdata</csmdata>

diff --git a/bld/namelist_files/namelist_definition_clm4_5.xml b/bld/namelist_files/namelist_definition_clm4_5.xml
@@ -582,15 +582,48 @@ set to 3 meaning branch.
 
 <entry id="use_fates" type="logical" category="physics"
         group="clm_inparm" valid_values="" value=".false.">
-Toggle to turn on the ED
-(ED = 'on' is EXPERIMENTAL NOT SUPPORTED!)
+Toggle to turn on the FATES model
+(use_fates= '.true.' is EXPERIMENTAL NOT SUPPORTED!)
 </entry>
 
 <entry id="use_fates_spitfire" type="logical" category="physics"
         group="clm_inparm" valid_values="" value=".false.">
-Toggle to turn on spit fire (only relevant if ED is being used).
+Toggle to turn on spitfire module for modeling fire (only relevant if FATES is being used).
 </entry>
 
+<entry id="use_fates_logging" type="logical" category="physics"
+        group="clm_inparm" valid_values="" value=".false.">
+Toggle to turn on the logging module (only relevant if FATES is being used).
+</entry>
+
+<entry id="use_fates_planthydro" type="logical" category="physics"
+        group="clm_inparm" valid_values="" value=".false.">
+Toggle to turn on plant hydraulics (only relevant if FATES is on).
+(use_fates_planthydro=".true." is EXPERIMENTAL NOT SUPPORTED! Nor is it Tested!)
+</entry>
+
+<entry id="use_fates_ed_st3" type="logical" category="physics"
+        group="clm_inparm" valid_values="" value=".false.">
+Toggle to turn on Static Stand Structure Mode (only relevant if FATES is being used).
+(use_fates_ed_st3=".true." is EXPERIMENTAL NOT SUPPORTED! Nor is it Tested!)
+</entry>
+
+<entry id="use_fates_ed_prescribed_phys" type="logical" category="physics"
+        group="clm_inparm" valid_values="" value=".false.">
+Toggle to turn on prescribed physiology (only relevant if FATES is being used).
+</entry>
+
+<entry id="use_fates_inventory_init" type="logical" category="physics"
+        group="clm_inparm" valid_values="" value=".false.">
+Toggle to turn on inventory initialization to startup FATES (only relevant if FATES is being used).
+(use_fates_inventory_init=".true." is EXPERIMENTAL NOT SUPPORTED! Nor is it Tested!)
+</entry>
+
+<entry id="fates_inventory_ctrl_filename" type="char*256" category="datasets"
+       input_pathname="abs" group="clm_inparm" valid_values="" >
+Full pathname to the inventory initialization control file.
+(Required, if use_fates_inventory_init=T)
+</entry>
 
 <entry id="use_luna" type="logical" category="physics"
         group="clm_inparm" valid_values="" value=".false.">
@@ -871,13 +904,13 @@ Maximum nitrification rate constant (1/s)
 <entry id="use_vertsoilc" type="logical" category="bgc"
        group="clm_inparm" valid_values="" value=".false.">
 Turn on vertical soil carbon.
-Requires the CN or ED model to work (either CN or CNDV).
+Requires the CN or FATES model to work (either CN or CNDV).
 </entry>
 
 <entry id="use_century_decomp" type="logical" category="bgc"
        group="clm_inparm" valid_values="" value=".false.">
 Use parameters for decomposition from the CENTURY Carbon model
-Requires the CN or ED model to work (either CN or CNDV).
+Requires the CN or FATES model to work (either CN or CNDV).
 </entry>
 
 <entry id="use_extralakelayers" type="logical" category="physics"