Merge pull request #1016 from swensosc/heat_storage_biomass

Heat storage biomass

bld/CLMBuildNamelist.pm

@@ -2063,7 +2063,6 @@ sub error_if_set {
    }
 }
 
-
 #-------------------------------------------------------------------------------
 
 sub setup_logic_soilstate {
@@ -3676,6 +3675,11 @@ sub setup_logic_canopyfluxes {
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_undercanopy_stability' );
   add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'itmax_canopy_fluxes',
               'structure'=>$nl_flags->{'structure'});
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_biomass_heat_storage',
+              'use_fates'=>$nl_flags->{'use_fates'}, 'phys'=>$nl_flags->{'phys'} );
+  if ( &value_is_true($nl->get_value('use_biomass_heat_storage') ) && &value_is_true( $nl_flags->{'use_fates'}) ) {
+     $log->fatal_error('use_biomass_heat_storage can NOT be set to true when fates is on');
+  }
 }
 
 #-------------------------------------------------------------------------------

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -182,7 +182,6 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <use_bedrock phys="clm5_0"                     >.true.</use_bedrock>
 <use_bedrock phys="clm4_5"                     >.false.</use_bedrock>
 
-
 <!-- Rooting profile namelist defaults -->
 <rooting_profile_method_water  phys="clm5_1" >1</rooting_profile_method_water>
 <rooting_profile_method_water  phys="clm5_0" >1</rooting_profile_method_water>
@@ -312,6 +311,10 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <use_undercanopy_stability phys="clm5_0" >.false.</use_undercanopy_stability>
 <use_undercanopy_stability phys="clm4_5" >.true.</use_undercanopy_stability>
 
+<use_biomass_heat_storage  phys="clm5_1"                   >.true.</use_biomass_heat_storage>
+<use_biomass_heat_storage  phys="clm5_1" use_fates=".true.">.false.</use_biomass_heat_storage>
+<use_biomass_heat_storage                                  >.false.</use_biomass_heat_storage>
+
 <itmax_canopy_fluxes structure="standard">40</itmax_canopy_fluxes>
 <itmax_canopy_fluxes structure="fast"    >3</itmax_canopy_fluxes>
 
@@ -470,9 +473,9 @@ 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.c200905.nc</paramfile>
-<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c200905.nc</paramfile>
-<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c200905.nc</paramfile>
+<paramfile phys="clm5_1" >lnd/clm2/paramdata/ctsm51_params.c210112.nc</paramfile>
+<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c210112.nc</paramfile>
+<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c210112.nc</paramfile>
 
 <!-- ================================================================== -->
 <!-- FATES default parameter file                                       -->

bld/namelist_files/namelist_definition_ctsm.xml

@@ -331,6 +331,10 @@ Intercept of free living Nitrogen fixation with zero annual ET
 If TRUE use the undercanopy stability term used with CLM4.5 (Sakaguchi&Zeng, 2008)
 </entry>
 
+<entry id="use_biomass_heat_storage" type="logical" category="clm_physics"
+       group="canopyfluxes_inparm" valid_values="" >
+If TRUE, include biomass heat storage in canopy energy balance.
+
 <entry id="itmax_canopy_fluxes" type="integer" category="clm_physics"
        group="canopyfluxes_inparm">
 Max number of iterations used in subr. CanopyFluxes. For many years, 40 was the hardwired default value.

bld/unit_testers/build-namelist_test.pl

@@ -138,9 +138,9 @@ sub make_config_cache {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 1513;
+my $ntests = 1550;
 if ( defined($opts{'compare'}) ) {
-   $ntests += 1017;
+   $ntests += 1044;
 }
 plan( tests=>$ntests );
 
@@ -837,6 +837,11 @@ sub make_config_cache {
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
                                      phys=>"clm5_0",
                                    },
+     "useFATESWbMH"              =>{ options=>"-bgc fates -envxml_dir . -no-megan",
+                                     namelst=>"use_biomass_heat_storage=.true.",
+                                     GLC_TWO_WAY_COUPLING=>"FALSE",
+                                     phys=>"clm5_1",
+                                   },
      "createcropFalse"           =>{ options=>"-bgc bgc -envxml_dir . -no-megan",
                                      namelst=>"create_crop_landunit=.false.",
                                      GLC_TWO_WAY_COUPLING=>"FALSE",
@@ -1413,22 +1418,30 @@ sub make_config_cache {
   &cleanup();
   # Run FATES mode for several resolutions and configurations
   my $clmoptions = "-bgc fates -envxml_dir . -no-megan";
-  my @clmres = ( "1x1_brazil", "5x5_amazon", "10x15", "1.9x2.5" );
+  my @clmres = ( "1x1_brazil", "5x5_amazon", "4x5", "1.9x2.5" );
   foreach my $res ( @clmres ) {
-     $options = "-res $res";
-     my @edoptions = ( "-use_case 2000_control", "", "-namelist \"&a use_lch4=.true.,use_nitrif_denitrif=.true./\"", "-clm_accelerated_spinup on" );
+     $options = "-res $res -clm_start_type cold";
+     my @edoptions = ( "-use_case 2000_control", 
+                       "-use_case 1850_control", 
+                       "", 
+                       "-namelist \"&a use_lch4=.true.,use_nitrif_denitrif=.true./\"", 
+                       "-clm_accelerated_spinup on" 
+                     );
      foreach my $edop (@edoptions ) {
+        if ( $res eq "5x5_amazon" && ($edop =~ /1850_control/) ) {
+           next;
+        }
         &make_env_run( );
         eval{ system( "$bldnml $options $clmoptions $edop  > $tempfile 2>&1 " ); };
         is( $@, '', "$options $edop" );
-        $cfiles->checkfilesexist( "$options $edop", $mode );
+        $cfiles->checkfilesexist( "$options $clmoptions $edop", $mode );
         $cfiles->shownmldiff( "default", "standard" );
         if ( defined($opts{'compare'}) ) {
-           $cfiles->doNOTdodiffonfile( "$tempfile", "$options $edop", $mode );
-           $cfiles->comparefiles( "$options $edop", $mode, $opts{'compare'} );
+           $cfiles->doNOTdodiffonfile( "$tempfile", "$options $clmoptions $edop", $mode );
+           $cfiles->comparefiles( "$options $clmoptions $edop", $mode, $opts{'compare'} );
         }
         if ( defined($opts{'generate'}) ) {
-           $cfiles->copyfiles( "$options $edop", $mode );
+           $cfiles->copyfiles( "$options $clmoptions $edop", $mode );
         }
         &cleanup();
      }

cime_config/config_compsets.xml

@@ -144,6 +144,11 @@
     <science_support grid="f19_g17"/>
   </compset>
 
+  <compset>
+    <alias>I1850Clm51BgcCrop</alias>
+    <lname>1850_DATM%GSWP3v1_CLM50%BGC-CROP_SICE_SOCN_MOSART_SGLC_SWAV</lname>
+  </compset>
+
   <compset>
     <alias>I1850Clm51Sp</alias>
     <lname>1850_DATM%GSWP3v1_CLM51%SP_SICE_SOCN_MOSART_SGLC_SWAV</lname>
@@ -238,6 +243,12 @@
     <science_support grid="f19_g17"/>
   </compset>
 
+  <compset>
+     <alias>I1850Clm51Bgc</alias>
+     <lname>1850_DATM%GSWP3v1_CLM50%BGC_SICE_SOCN_MOSART_SGLC_SWAV</lname>
+   </compset>
+
+
   <compset>
      <alias>I1850Clm51SpNoAnthro</alias>
      <lname>1850_DATM%GSWP3v1_CLM51%SP-NOANTHRO_SICE_SOCN_MOSART_SGLC_SWAV</lname>

cime_config/testdefs/testlist_clm.xml

@@ -1973,12 +1973,13 @@ for ERS test as otherwise it won't work for a sub-day test (no need to run this
       <option name="wallclock">00:20:00</option>
     </options>
   </test>
-  <test name="SMS_D_Ld5" grid="f45_f45_mg37" compset="I2000Clm50Fates" testmods="clm/FatesColdDef">
+  <test name="SMS_D_Ld5" grid="f45_f45_mg37" compset="I2000Clm51Fates" testmods="clm/FatesColdDef">
     <machines>
       <machine name="cheyenne" compiler="intel" category="aux_clm"/>
     </machines>
     <options>
       <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Run a Fates test with latest Clm5_1</option>
     </options>
   </test>
   <test name="SMS_D_Lm6" grid="f45_f45_mg37" compset="I2000Clm45Fates" testmods="clm/FatesColdDef">

doc/ChangeLog

@@ -1,4 +1,133 @@
 ===============================================================
+Tag name:  ctsm5.1.dev021
+Originator(s):  erik (Erik Kluzek,UCAR/TSS,303-497-1326)
+Date: Tue Jan 12 20:21:52 MST 2021
+One-line Summary: Add option for biomass heat storage (BHS) to clm5_1 physics
+
+Purpose of changes
+------------------
+
+Add heat stored in biomass (for trees and shrubs) to the surface energy balance calculation. Add
+a switch for it and turn it on by default for clm5_1 physics. It's turned off for clm4_5, clm5_0
+physics and when FATES is turned on. Those cases are identical to before, answers only change
+when it's turned on.
+
+Papers describing BHS simulations:
+R. Meier, Davin, E., Swenson, S., Lawrence, D., and Schwaab, Jo. (2019). Biomass heat 
+storage dampens diurnal temperature variations
+in forests. Environmental Research Letters. 14. 084026. 10.1088/1748-9326/ab2b4e.
+
+S.C. Swenson, Burns, S. P., and Lawrence, D. M. ( 2019). The impact of biomass heat storage 
+on the canopy energy balance and atmospheric stability in the community land model, Journal 
+of Advances in Modeling Earth Systems, 11, 83– 98.
+https://doi.org/10.1029/2018MS001476
+
+
+Bugs fixed or introduced
+------------------------
+
+Issues fixed (include CTSM Issue #):
+   #342 --- set medlynslope to C4 appropriate value for millet and sorghum 
+             (had already been done for miscanthus and switchgrass)
+   #1246 -- Make spinup_factor_deadwood a variable rather than hardcoded constant
+
+Known bugs introduced in this tag (include github issue ID): 
+   #1247 -- FATES doesn't work with BHS
+
+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
+
+Notes of particular relevance for users
+---------------------------------------
+
+Caveats for users (e.g., need to interpolate initial conditions):
+    New variables are added on the restart files (stem/leaf biomass and stem Temp)
+    Testing didn't show this as a problem, but theoretically could require
+       updating initial conditions
+
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables): New compsets, new hist fields
+   I1850Clm51BgcCrop
+   I1850Clm51Bgc
+   History fields: AGSB, AGLB, FSH_STEM, DHDT_CANOPY, RAH1, RAH2, RAW1, RAW2, USTAR, UM, UAF, UM, UAF,
+       TAF, QAF, OBU, ZETA, VPD, num_iter, RB, TSTEM
+   DHSDT_CANOPY, TSTEM are default active
+
+Changes made to namelist defaults (e.g., changed parameter values): New use_biomass_heat_storage
+   New namelist item: use_biomass_heat_storage to turn on or off (by default only on for clm5_1
+   physics for both SP and BGC modes)
+
+Changes to the datasets (e.g., parameter, surface or initial files): New parameter datasets
+   All of the params files were updated. New terms were BHS parameters and taper
+   stocking is now set as "nstem" on the parameter file
+   taper is now on the parameter file
+
+Substantial timing or memory changes: Doesn't seem to
+   Only one short test failed the TPUTCOMP test
+   Longer tests were not significantly different
+
+Notes of particular relevance for developers: (including Code reviews and testing)
+---------------------------------------------
+NOTE: Be sure to review the steps in README.CHECKLIST.master_tags as well as the coding style in the Developers Guide
+
+Caveats for developers (e.g., code that is duplicated that requires double maintenance):
+   Setting of leaf/stem biomass should be refactored and removed from CanopyFluxes (as described in #1247)
+   There's a change in CNGapMortality that could change for DV when AD mode is on
+   Stability cap (zera) is different for BHS on than off
+
+Changes to tests or testing: New CLM51 FATES test
+
+CTSM testing: regular
+
+ [PASS means all tests PASS and OK means tests PASS other than expected fails.]
+
+  build-namelist tests:
+
+    cheyenne - OK (462 comparisons fail because of new namelist and params files)
+
+  python testing (see instructions in python/README.md; document testing done):
+
+    cheyenne -- PASS
+
+  regular tests (aux_clm):
+
+    cheyenne ---- OK
+    izumi ------- OK
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here:
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Yes!
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: clm5_1
+    - what platforms/compilers: all
+    - nature of change: new climate for tree and shrubs
+
+Detailed list of changes
+------------------------
+
+Pull Requests that document the changes (include PR ids):
+(https://github.com/ESCOMP/ctsm/pull)
+   #1016 -- Heat Storage biomass
+
+===============================================================
+===============================================================
 Tag name:  ctsm5.1.dev020
 Originator(s):  erik (Erik Kluzek,UCAR/TSS,303-497-1326)
 Date: Wed Dec 30 00:42:16 MST 2020

doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+  ctsm5.1.dev021     erik 01/12/2021 Add option for biomass heat storage (BHS) to clm5_1 physics
   ctsm5.1.dev020     erik 12/30/2020 Potential roundoff changes in preparation for bio-mass heat storage option
   ctsm5.1.dev019    sacks 12/19/2020 Fix ndep from coupler
   ctsm5.1.dev018   slevis 12/08/2020 Add ACTIVE (T/F) column to master hist fields table and alphabetize

src/biogeochem/CNDVLightMod.F90

@@ -72,8 +72,9 @@ subroutine Light(bounds, num_natvegp, filter_natvegp, &
          slatop        =>    pftcon%slatop                          , & ! Input:  specific leaf area at top of canopy, projected area basis (m2/gC)
          dsladlai      =>    pftcon%dsladlai                        , & ! Input:  dSLA/dLAI, projected area basis (m2/gC)           
          woody         =>    pftcon%woody                           , & ! Input:  woody patch or not                  
-         tree          =>    pftcon%tree                            , & ! Input:  tree patch or not                    
-
+         is_tree       =>    pftcon%is_tree                         , & ! Input:  tree patch or not
+         is_shrub      =>    pftcon%is_shrub                        , & ! Input:  shrub patch or not
+
          deadstemc     =>    cnveg_carbonstate_inst%deadstemc_patch , & ! Input:  [real(r8) (:) ]  (gC/m2) dead stem C                               
          leafcmax      =>    cnveg_carbonstate_inst%leafcmax_patch  , & ! Input:  [real(r8) (:) ]  (gC/m2) leaf C storage                            
 
@@ -132,11 +133,11 @@ subroutine Light(bounds, num_natvegp, filter_natvegp, &
          fpc_inc(p) = max(0._r8, fpcgrid(p) - fpcgrid_old)
 
          if (woody(ivt(p)) == 1._r8) then
-            if (tree(ivt(p)) == 1) then
+            if (is_tree(ivt(p))) then
                numtrees(g) = numtrees(g) + 1
                fpc_tree_total(g) = fpc_tree_total(g) + fpcgrid(p)
                fpc_inc_tree(g) = fpc_inc_tree(g) + fpc_inc(p)
-            else ! if shrubs
+            else if (is_shrub(ivt(p))) then
                fpc_shrub_total(g) = fpc_shrub_total(g) + fpcgrid(p)
             end if
          else    ! if grass
@@ -162,7 +163,7 @@ subroutine Light(bounds, num_natvegp, filter_natvegp, &
 
          ! light competition
 
-         if (woody(ivt(p))==1._r8 .and. tree(ivt(p))==1._r8) then
+         if (woody(ivt(p))==1._r8 .and. is_tree(ivt(p))) then
 
             if (fpc_tree_total(g) > fpc_tree_max) then
 
@@ -200,7 +201,7 @@ subroutine Light(bounds, num_natvegp, filter_natvegp, &
 
             end if
 
-         else if (woody(ivt(p))==1._r8 .and. tree(ivt(p))==0._r8) then ! shrub
+         else if (woody(ivt(p))==1._r8 .and. is_shrub(ivt(p))) then ! shrub
 
             if (fpc_shrub_total(g) > fpc_shrub_max(g)) then
 

src/biogeochem/CNDVType.F90

@@ -97,7 +97,7 @@ subroutine InitAllocate(this, bounds)
     use shr_infnan_mod , only : nan => shr_infnan_nan, assignment(=)
     use clm_varpar     , only : maxveg
     use pftconMod      , only : allom1s, allom2s, allom1, allom2, allom3, reinickerp
-    use pftconMod      , only : ntree, nbrdlf_dcd_brl_shrub
+    use pftconMod      , only : nbrdlf_dcd_brl_shrub
     use pftconMod      , only : pftcon
     !
     ! !ARGUMENTS:
@@ -148,7 +148,7 @@ subroutine InitAllocate(this, bounds)
        dgv_ecophyscon%allom2(m)        = allom2
        dgv_ecophyscon%allom3(m)        = allom3
        ! modification for shrubs by X.D.Z
-       if (m > ntree .and. m <= nbrdlf_dcd_brl_shrub ) then 
+       if (pftcon%is_shrub(m)) then 
           dgv_ecophyscon%allom1(m) = allom1s
           dgv_ecophyscon%allom2(m) = allom2s
        end if

src/biogeochem/CNFireBaseMod.F90

@@ -24,7 +24,7 @@ module CNFireBaseMod
   use atm2lndType                        , only : atm2lnd_type
   use CNDVType                           , only : dgvs_type
   use CNVegStateType                     , only : cnveg_state_type
-  use CNVegCarbonStateType               , only : cnveg_carbonstate_type
+  use CNVegCarbonStateType               , only : cnveg_carbonstate_type, spinup_factor_deadwood
   use CNVegCarbonFluxType                , only : cnveg_carbonflux_type
   use CNVegNitrogenStateType             , only : cnveg_nitrogenstate_type
   use CNVegNitrogenFluxType              , only : cnveg_nitrogenflux_type
@@ -441,7 +441,7 @@ subroutine CNFireFluxes (this, bounds, num_soilc, filter_soilc, num_soilp, filte
    !
    ! !USES:
    use clm_time_manager     , only: get_step_size_real,get_days_per_year,get_curr_date
-   use clm_varctl           , only: use_cndv, spinup_state
+   use clm_varctl           , only: use_cndv
    use clm_varcon           , only: secspday
    use pftconMod            , only: nc3crop
    use dynSubgridControlMod , only: run_has_transient_landcover
@@ -718,10 +718,7 @@ subroutine CNFireFluxes (this, bounds, num_soilc, filter_soilc, num_soilp, filte
         ! apply this rate to the patch state variables to get flux rates
         ! biomass burning
         ! carbon fluxes
-        m = 1._r8
-        if (spinup_state == 2) then
-           m = 10._r8
-        end if
+        m = spinup_factor_deadwood
 
         m_leafc_to_fire(p)               =  leafc(p)              * f * cc_leaf(patch%itype(p))
         m_leafc_storage_to_fire(p)       =  leafc_storage(p)      * f * cc_other(patch%itype(p))