Arctic changes branch with Kattge in place of Leuning in LUNA

bld/CLMBuildNamelist.pm

@@ -1102,6 +1102,12 @@ sub setup_cmdl_spinup {
        $nl_flags->{'bgc_spinup'} = "off";
        $val = $defaults->get_value($var);
     }
+    # For AD spinup mode by default reseed dead plants
+    if ( $nl_flags->{$var} ne "off" ) {
+        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition,
+                    $defaults, $nl, "reseed_dead_plants", clm_accelerated_spinup=>$nl_flags->{$var},
+                    use_cn=>$nl_flags->{'use_cn'} );
+    }
   } else {
     if ( defined($nl->get_value("spinup_state")) ) {
        $log->fatal_error("spinup_state is accelerated (=1 or 2) which is for a BGC mode of CN or BGC," .
@@ -1616,6 +1622,11 @@ sub process_namelist_inline_logic {
   ##################################
   setup_logic_bgc_shared($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
 
+  ##################################
+  # namelist group: cnphenology
+  ##################################
+  setup_logic_cnphenology($opts,  $nl_flags, $definition, $defaults, $nl, $physv);
+
   #############################################
   # namelist group: soilwater_movement_inparm #
   #############################################
@@ -2685,6 +2696,24 @@ sub setup_logic_bgc_shared {
 
 #-------------------------------------------------------------------------------
 
+sub setup_logic_cnphenology {
+  my ($opts, $nl_flags, $definition, $defaults, $nl, $physv) = @_;
+
+  my @list  = (  "onset_thresh_depends_on_veg", "min_crtical_dayl_depends_on_lat" );
+  foreach my $var ( @list ) {
+    if (  &value_is_true($nl_flags->{'use_cn'}) ) {
+       add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var, 
+                   'phys'=>$physv->as_string(), 'use_cn'=>$nl_flags->{'use_cn'} );
+    } else {
+       if ( defined($nl->get_value($var)) ) {
+          $log->fatal_error("$var should only be set if use_cn is on");
+       }
+    }
+  }
+}
+
+#-------------------------------------------------------------------------------
+
 sub setup_logic_supplemental_nitrogen {
   #
   # Supplemental Nitrogen for prognostic crop cases

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -57,6 +57,10 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <spinup_state clm_accelerated_spinup="on"  use_fates=".true." phys="clm4_5" >1</spinup_state>
 <spinup_state clm_accelerated_spinup="off"                               >0</spinup_state>
 
+<!-- Reseeding of dead plants normally only done for AD spinup -->
+<reseed_dead_plants clm_accelerated_spinup="on" use_cn=".true.">.true.</reseed_dead_plants>
+<reseed_dead_plants                                            >.false.</reseed_dead_plants>
+
 <for_testing_run_ncdiopio_tests>.false.</for_testing_run_ncdiopio_tests>
 
 <!-- Set to .true. in namelist to write hist fields master list file -->
@@ -473,9 +477,9 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- The default filenames are given relative to the root directory
      for the CLM2 data in the CESM distribution -->
 <!-- Plant function types (relative to {csmdata}) -->
-<paramfile phys="clm5_1" >lnd/clm2/paramdata/ctsm51_params.c210208.nc</paramfile>
-<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c210208.nc</paramfile>
-<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c210208.nc</paramfile>
+<paramfile phys="clm5_1" >lnd/clm2/paramdata/ctsm51_params.c210305.nc</paramfile>
+<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c210217.nc</paramfile>
+<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c210217.nc</paramfile>
 
 <!-- ================================================================== -->
 <!-- FATES default parameter file                                       -->
@@ -549,6 +553,11 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <initial_seed_at_planting use_crop=".true." phys="clm5_0" >3.d00</initial_seed_at_planting>
 <initial_seed_at_planting use_crop=".true." phys="clm4_5" >1.d00</initial_seed_at_planting>
 
+<!-- CN Phenology -->
+<onset_thresh_depends_on_veg     use_cn=".true." phys="clm5_1" >.true.</onset_thresh_depends_on_veg>
+<min_crtical_dayl_depends_on_lat use_cn=".true." phys="clm5_1" >.true.</min_crtical_dayl_depends_on_lat>
+<onset_thresh_depends_on_veg                                   >.false.</onset_thresh_depends_on_veg>
+<min_crtical_dayl_depends_on_lat                               >.false.</min_crtical_dayl_depends_on_lat>
 
 <!-- turnover time modifications    -->
 <decomp_depth_efolding phys="clm4_5" >0.5</decomp_depth_efolding>

bld/namelist_files/namelist_definition_ctsm.xml

@@ -1096,6 +1096,18 @@ Initial seed Carbon to use at planting
 (only used when CN is on as well as crop)
 </entry>
 
+<entry id="onset_thresh_depends_on_veg" type="logical" category="physics"
+       group="cnphenology">
+Phenology onset depends on the vegetation type
+(only used when CN is on)
+</entry>
+
+<entry id="min_crtical_dayl_depends_on_lat" type="logical" category="physics"
+       group="cnphenology">
+The minimum critical day length for onset depends on latitude
+(only used when CN is on)
+</entry>
+
 <entry id="use_ozone" type="logical" category="physics"
        group="clm_inparm" valid_values="" value=".false.">
 Toggle to turn on ozone stress

bld/unit_testers/build-namelist_test.pl

@@ -138,7 +138,7 @@ sub make_config_cache {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 1551;
+my $ntests = 1552;
 if ( defined($opts{'compare'}) ) {
    $ntests += 1044;
 }
@@ -446,6 +446,11 @@ sub make_config_cache {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
+     "onset_threh w SP"          =>{ options=>" -envxml_dir . -bgc sp",
+                                     namelst=>"onset_thresh_depends_on_veg=.true.",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm5_1",
+                                   },
      "dribble_crphrv w/o CN"     =>{ options=>" -envxml_dir . -bgc sp",
                                      namelst=>"dribble_crophrv_xsmrpool_2atm=.true.",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",

doc/ChangeLog

@@ -1,4 +1,120 @@
 ===============================================================
+Tag name:  ctsm5.1.dev034
+Originator(s):  erik (Erik Kluzek,UCAR/TSS,303-497-1326)
+Date: Mon Apr 19 16:02:29 MDT 2021
+One-line Summary: Bring in Arctic changes to LUNA from Leah Birch
+
+Purpose and description of changes
+----------------------------------
+
+This is @lmbirch89 branch from #947 with the exception that Kattge is used in place of 
+Leuning in LUNA. Also the startup initial values in the luna bug fix branch #961 is 
+used in place of the updated values by @lmbirch89. The LUNA bug fixes have already come
+in, so these are some changes to improve arctic plants.
+
+We have addressed the issues in phenology and photosynthesis in the high latitudes. 
+Development was focused on PFT specific differences and we used observations to inform 
+model development. GPP is improved now such that the tundra is realistically less
+productive than the boreal forest.
+
+
+Significant changes to scientifically-supported configurations
+--------------------------------------------------------------
+
+Does this tag change answers significantly for any of the following physics configurations?
+(Details of any changes will be given in the "Answer changes" section below.)
+
+    [Put an [X] in the box for any configuration with significant answer changes.]
+
+[x] clm5_1
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed or introduced
+------------------------
+
+Issues fixed (include CTSM Issue #):
+   Fixes #807 -- Revisit PFT optical properties per Majasalmi and Bright (2019)
+   Fixes #1307 -- Turn on reseed_dead_plants when you start AD spinup mode
+
+Known bugs introduced in this tag (include issue #):
+  #1346 -- Use of floating point flag onset_thresh is confusing in CNPhenologyMod
+
+Notes of particular relevance for users
+---------------------------------------
+
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
+   New namelist items: onset_thresh_depends_on_veg and min_crtical_dayl_depends_on_lat
+
+Changes made to namelist defaults (e.g., changed parameter values):
+  reseed_dead_plants turned on when AD spinup mode turned on
+  onset_thresh_depends_on_veg and min_crtical_dayl_depends_on_lat turned on for clm5_1 physics
+
+Changes to the datasets (e.g., parameter, surface or initial files):
+  New parameter file (same as start used in PPE work) also has additional fields on it
+
+Notes of particular relevance for developers:
+---------------------------------------------
+NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide
+[Remove any lines that don't apply. Remove entire section if nothing applies.]
+
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+  As noted in #1346 some of the logic in CNPhenology in CNSeasonDecidPhenology is a bit confusing.
+   The soil layer used was put in CNSharedParameters and needed it's own subroutine to prevent circular dependencies.
+   There are new accumulator variables added that area always turned on even when not needed. Doing this
+   in a reasonable manner (without having lots of CNPhenology logic spilled into base types) would require
+   a refactoring of a better way to figure this out.
+
+Testing summary: regular
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    cheyenne - PASS
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    cheyenne - PASS
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    cheyenne ---- OK
+    izumi ------- OK
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Yes for clm5_1 physics
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: clm5_1
+    - what platforms/compilers: all
+    - nature of change: new climate
+
+   If this tag changes climate describe the run(s) done to evaluate the new
+   climate (put details of the simulations in the experiment database)
+       oleson -- clm50_ctsm10d089_2deg_GSWP3V1_lmbirch_wkattge_jmaxb1-0.17_slatopA_1850AD
+
+   URL for LMWG diagnostics output used to validate new climate:
+     http://webext.cgd.ucar.edu/I1850/clm50_ctsm10d089_2deg_GSWP3V1_lmbirch_wkattge_jmaxb1-0.17_slatopA_1850AD/
+
+
+Other details
+-------------
+Pull Requests that document the changes (include PR ids):  #990
+(https://github.com/ESCOMP/ctsm/pull)
+
+   #990 -- Arctic changes branch with Kattge in place of Leuning in LUNA
+
+===============================================================
+===============================================================
 Tag name:  ctsm5.1.dev033
 Originator(s): mvertens (Mariana Vertenstein), sacks (Bill Sacks)
 Date:  Sat Apr 10 16:42:06 MDT 2021

doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+  ctsm5.1.dev034     erik 04/19/2021 Bring in Arctic changes to LUNA from Leah Birch
   ctsm5.1.dev033 mvertens 04/10/2021 Remove unnecessary settings of nextsw_cday
   ctsm5.1.dev032 mvertens 04/10/2021 Fix bugs in co2 from atmosphere
   ctsm5.1.dev031 jedwards 04/10/2021 Update externals and fixes for nuopc threading