Merge b4bdev 20241220

bld/CLMBuildNamelist.pm

@@ -3395,7 +3395,7 @@ sub setup_logic_mineral_nitrogen_dynamics {
   #
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
-  my @vars = ( "freelivfix_slope_wet", "freelivfix_intercept" );
+  my @vars = ( "freelivfix_slope_wet", "freelivfix_intercept", "nfix_method" );
   if (  &value_is_true($nl_flags->{'use_cn'}) && &value_is_true($nl->get_value('use_fun')) ) {
     foreach my $var ( @vars ) {
        add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, $var,
@@ -3408,6 +3408,14 @@ sub setup_logic_mineral_nitrogen_dynamics {
        }
     }
   }
+
+  if (  &value_is_true($nl_flags->{'use_cn'}) && &value_is_true($nl->get_value('use_fun')) ) {
+    my $var = $nl->get_value('nfix_method');
+    if ( $var ne "'Houlton'" && $var ne "'Bytnerowicz'" ) {
+      $log->fatal_error("$var is incorrect entry for the namelist variable nfix_method; expected Houlton or Bytnerowicz");
+    }
+  }
+
 }
 
 

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -524,10 +524,10 @@ 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="clm6_0" >lnd/clm2/paramdata/ctsm60_params.c241017.nc</paramfile>
-<paramfile phys="clm5_1" >lnd/clm2/paramdata/ctsm51_params.c241017.nc</paramfile>
-<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c241017.nc</paramfile>
-<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c241017.nc</paramfile>
+<paramfile phys="clm6_0" >lnd/clm2/paramdata/ctsm60_params.c241119.nc</paramfile>
+<paramfile phys="clm5_1" >lnd/clm2/paramdata/ctsm60_params.c241119.nc</paramfile>
+<paramfile phys="clm5_0" >lnd/clm2/paramdata/clm50_params.c241119.nc</paramfile>
+<paramfile phys="clm4_5" >lnd/clm2/paramdata/clm45_params.c241119.nc</paramfile>
 
 <!-- ================================================================== -->
 <!-- FATES default parameter file                                       -->
@@ -1894,6 +1894,8 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/surfdata_1x1_NEON_TOOL_hist_2000_78pfts_c2
 <freelivfix_intercept use_fun=".true." use_cn=".true.">0.0117d00</freelivfix_intercept>
 <freelivfix_slope_wet use_fun=".true." use_cn=".true.">0.0006d00</freelivfix_slope_wet>
 
+<nfix_method>Houlton</nfix_method>
+
 <br_root>0.83d-06</br_root>
 
 <!-- Scalar of leaf respiration to vcmax (used for SP mode and with luna) (could vary with physics version) -->

bld/namelist_files/namelist_definition_ctsm.xml

@@ -388,6 +388,11 @@ Slope of free living Nitrogen fixation with annual ET
 Intercept of free living Nitrogen fixation with zero annual ET
 </entry>
 
+<entry id="nfix_method" type="char*25" category="clm_nitrogen"
+       group="clm_nitrogen" valid_values="Houlton,Bytnerowicz" value="Houlton" >
+Choice of nfix parameterization
+</entry>
+
 <entry id="use_undercanopy_stability" type="logical" category="clm_physics"
        group="canopyfluxes_inparm" valid_values="" >
 If TRUE use the undercanopy stability term used with CLM4.5 (Sakaguchi&amp;Zeng, 2008)

cime_config/testdefs/testmods_dirs/clm/ciso_cwd_hr/user_nl_clm

@@ -1,2 +1,2 @@
-paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm51_ciso_cwd_hr_params.c241017.nc'
+paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm60_ciso_cwd_hr_params.c241119.nc'
 hist_fincl1 = 'CWDC_HR','C13_CWDC_HR','C14_CWDC_HR','CWD_HR_L2','CWD_HR_L2_vr','CWD_HR_L3','CWD_HR_L3_vr'

cime_config/testdefs/testmods_dirs/clm/clm60_monthly_matrixcn_soilCN30/user_nl_clm

@@ -1,2 +1,2 @@
 use_soil_matrixcn = .true.
-paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm60_params_cn30.c241017.nc'
+paramfile = '$DIN_LOC_ROOT/lnd/clm2/paramdata/ctsm60_params_cn30.c241119.nc'

doc/ChangeLog

@@ -1,4 +1,88 @@
 ===============================================================
+Tag name: ctsm5.3.017
+Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
+Date: Fri 20 Dec 2024 11:31:36 AM MST
+One-line Summary: Merge b4b-dev
+
+Purpose and description of changes
+----------------------------------
+
+ #2869 Update temperature cost function for symbiotic Nfix in FUN
+
+
+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.]
+
+[ ] clm6_0
+
+[ ] clm5_0
+
+[ ] ctsm5_0-nwp
+
+[ ] clm4_5
+
+
+Bugs fixed
+----------
+List of CTSM issues fixed (include CTSM Issue # and description) [one per line]:
+ Resolves #2869
+
+Notes of particular relevance for users
+---------------------------------------
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
+ New namelist variable: nfix_method
+
+Changes made to namelist defaults (e.g., changed parameter values):
+ nfix_method default: Houlton
+ other available option: Bytnerowicz
+
+
+Testing summary:
+----------------
+
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - PASS
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- machine unavailable
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: No, but read caveat.
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: tests with ciso_cwd_hr testmods
+    - what platforms/compilers: all
+    - nature of change: irrelevant
+
+ Explanation:
+ "diff ctsm60_ciso_cwd_hr_params.c241119.asc ctsm60_params.c241119.asc"
+ differ ONLY in the value of ceta. The previous paramfile for ciso_cwd_hr
+ showed additional diffs, likely due to problems that we have seen before
+ when generating new paramfiles. The ciso_cwd_hr tests would not have shown
+ diffs had the previous paramfile been correct, so I only mention the diffs
+ here for the record.
+
+
+Other details
+-------------
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/2869
+
+===============================================================
+===============================================================
 Tag name: ctsm5.3.016
 Originator(s): jedwards and erik (Erik Kluzek,UCAR/TSS,303-497-1326)
 Date: Thu 19 Dec 2024 04:23:39 PM MST

doc/ChangeSum

@@ -1,5 +1,6 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.3.017   slevis 12/20/2024 Merge b4b-dev
        ctsm5.3.016     erik 12/19/2024 Rpointer files for restart now have the simulation date in the filename
        ctsm5.3.015     erik 12/18/2024 Update cdeps with cam7 nextsw cday changes
        ctsm5.3.014     erik 12/03/2024 Bring in several fixes for testing in the previous cesm3_0_beta03/04 tags

src/biogeochem/CNFUNMod.F90

@@ -26,7 +26,7 @@ module CNFUNMod
   use pftconMod                       , only : pftcon, npcropmin
   use decompMod                       , only : bounds_type
   use clm_varctl                      , only : use_nitrif_denitrif,use_flexiblecn
-    use CNSharedParamsMod               , only : use_matrixcn
+  use CNSharedParamsMod               , only : use_matrixcn
   use abortutils                      , only : endrun
   use CNVegstateType                  , only : cnveg_state_type
   use CNVegCarbonStateType            , only : cnveg_carbonstate_type
@@ -206,7 +206,7 @@ subroutine CNFUN(bounds,num_soilc, filter_soilc,num_soilp&
    use clm_time_manager, only : get_step_size_real, get_curr_date
    use clm_varpar      , only : nlevdecomp
    use clm_varcon      , only : secspday, smallValue, fun_period, tfrz, dzsoi_decomp, spval
-   use clm_varctl      , only : use_nitrif_denitrif
+   use clm_varctl      , only : use_nitrif_denitrif, nfix_method
    use PatchType       , only : patch
    use subgridAveMod   , only : p2c
    use pftconMod       , only : npcropmin
@@ -290,7 +290,7 @@ subroutine CNFUN(bounds,num_soilc, filter_soilc,num_soilp&
   real(r8)  :: litterfall_n(bounds%begp:bounds%endp)                 ! N loss based on the leafc to litter   (gN/m2)  
   real(r8)  :: litterfall_n_step(bounds%begp:bounds%endp,1:nstp)       ! N loss based on the leafc to litter   (gN/m2)
   real(r8)  :: litterfall_c_step(bounds%begp:bounds%endp,1:nstp)       ! N loss based on the leafc to litter   (gN/m2)
-  real(r8)  :: tc_soisno(bounds%begc:bounds%endc,1:nlevdecomp)       ! Soil temperature            (degrees Celsius)
+  real(r8)  :: tc_soisno(bounds%begc:bounds%endc,1:nlevdecomp)       ! Soil temperature                      (degrees Celsius)
   real(r8)  :: npp_remaining(bounds%begp:bounds%endp,1:nstp)         ! A temporary variable for npp_remaining(gC/m2) 
   real(r8)  :: n_passive_step(bounds%begp:bounds%endp,1:nstp)        ! N taken up by transpiration at substep(gN/m2)
   real(r8)  :: n_passive_acc(bounds%begp:bounds%endp)                ! N acquired by passive uptake          (gN/m2)
@@ -467,7 +467,6 @@ subroutine CNFUN(bounds,num_soilc, filter_soilc,num_soilp&
   real(r8) :: total_c_spent_retrans
   real(r8) :: total_c_accounted_retrans
 
-
   !------end of not_use_nitrif_denitrif------!
   !--------------------------------------------------------------------
   !------------
@@ -495,9 +494,10 @@ subroutine CNFUN(bounds,num_soilc, filter_soilc,num_soilp&
   !  fixers, 2 for non fixers. This will become redundant with the
   !   'fixer' parameter if it works. 
 
+  character(len=32) :: subname = 'CNFUN'
   !--------------------------------------------------------------------
   !---------------------------------
-  associate(ivt                    => patch%itype                                          , & ! Input:   [integer  (:) ]  p
+  associate(ivt                 => patch%itype                                          , & ! Input:   [integer  (:) ]  p
          leafcn                 => pftcon%leafcn                                        , & ! Input:   leaf C:N (gC/gN)
          season_decid           => pftcon%season_decid                                  , & ! Input:   binary flag for seasonal
          ! -deciduous leaf habit (0 or 1)
@@ -507,6 +507,9 @@ subroutine CNFUN(bounds,num_soilc, filter_soilc,num_soilp&
          b_fix                  => pftcon%b_fix                                         , & ! Input:   A BNF parameter
          c_fix                  => pftcon%c_fix                                         , & ! Input:   A BNF parameter
          s_fix                  => pftcon%s_fix                                         , & ! Input:   A BNF parameter
+         nfix_tmin              => pftcon%nfix_tmin                                     , & ! Input:   A BNF parameter
+         nfix_topt              => pftcon%nfix_topt                                     , & ! Input:   A BNF parameter
+         nfix_tmax              => pftcon%nfix_tmax                                     , & ! Input:   A BNF parameter
          akc_active             => pftcon%akc_active                                    , & ! Input:   A mycorrhizal uptake
          !  parameter
          akn_active             => pftcon%akn_active                                    , & ! Input:   A mycorrhizal uptake
@@ -522,10 +525,10 @@ subroutine CNFUN(bounds,num_soilc, filter_soilc,num_soilp&
          perecm                 => pftcon%perecm                                        , & ! Input:   The fraction of ECM
          ! -associated PFT 
          grperc                 => pftcon%grperc                                        , & ! Input:   growth percentage
-         fun_cn_flex_a           => pftcon%fun_cn_flex_a                                , & ! Parameter a of FUN-flexcn link code (def 5)
-         fun_cn_flex_b           => pftcon%fun_cn_flex_b                                , & ! Parameter b of FUN-flexcn link code (def 200)
-         fun_cn_flex_c           => pftcon%fun_cn_flex_c                                , & ! Parameter b of FUN-flexcn link code (def 80)         
-         FUN_fracfixers          => pftcon%FUN_fracfixers                               , & ! Fraction of C that can be used for fixation.    
+         fun_cn_flex_a          => pftcon%fun_cn_flex_a                                 , & ! Parameter a of FUN-flexcn link code (def 5)
+         fun_cn_flex_b          => pftcon%fun_cn_flex_b                                 , & ! Parameter b of FUN-flexcn link code (def 200)
+         fun_cn_flex_c          => pftcon%fun_cn_flex_c                                 , & ! Parameter b of FUN-flexcn link code (def 80)
+         FUN_fracfixers         => pftcon%FUN_fracfixers                                , & ! Fraction of C that can be used for fixation.
          leafcn_offset          => cnveg_state_inst%leafcn_offset_patch                 , & ! Output:
          !  [real(r8)  (:)]  Leaf C:N used by FUN
          plantCN                => cnveg_state_inst%plantCN_patch                       , & ! Output:  [real(r8)  (:)]  Plant
@@ -1041,42 +1044,50 @@ subroutine CNFUN(bounds,num_soilc, filter_soilc,num_soilp&
          npp_to_nonmyc_nh4(:)        = 0.0_r8
          npp_to_fixation(:)          = 0.0_r8
          npp_to_retrans(:)           = 0.0_r8
-
-
-
+
          unmetDemand              = .TRUE.
          plant_ndemand_pool_step(p,istp)   = plant_ndemand_pool(p)    * permyc(p,istp) 
          npp_remaining(p,istp)             = availc_pool(p)           * permyc(p,istp)
 
 
          ! if (plant_ndemand_pool_step(p,istp) .gt. 0._r8) then   !
             !  plant_ndemand_pool_step > 0.0
-            
+
             do j = 1, nlevdecomp
                tc_soisno(c,j)          = t_soisno(c,j)  -   tfrz
+
                if(pftcon%c3psn(patch%itype(p)).eq.1)then
                  fixer=1
                else
                  fixer=0
                endif
-               costNit(j,icostFix)     = fun_cost_fix(fixer,a_fix(ivt(p)),b_fix(ivt(p))&
-               ,c_fix(ivt(p)) ,big_cost,crootfr(p,j),s_fix(ivt(p)),tc_soisno(c,j))
+
+               select case (nfix_method)
+               case ('Houlton')
+                 costNit(j,icostFix) = fun_cost_fix(fixer,&
+                         a_fix(ivt(p)),b_fix(ivt(p)),c_fix(ivt(p)),&
+                         big_cost,crootfr(p,j),s_fix(ivt(p)),tc_soisno(c,j))
+               case ('Bytnerowicz')  ! no acclimation calculation
+                 costNit(j,icostFix) = fun_cost_fix_Bytnerowicz_noAcc(fixer, &
+                         nfix_tmin(ivt(p)),nfix_topt(ivt(p)),nfix_tmax(ivt(p)), &
+                         big_cost,crootfr(p,j),s_fix(ivt(p)),tc_soisno(c,j))
+               case default
+                  write(iulog,*) subname//' ERROR: unknown nfix_method value: ', nfix_method
+                  call endrun(msg=errMsg(sourcefile, __LINE__))
+               end select
+
             end do
             cost_fix(p,1:nlevdecomp)      = costNit(:,icostFix)
 
 
             !--------------------------------------------------------------------
-            !------------
             !         If passive uptake is insufficient, consider fixation,
             !          mycorrhizal 
             !         non-mycorrhizal, storage, and retranslocation.
             !--------------------------------------------------------------------
-            !------------
             !--------------------------------------------------------------------
-            !------------
             !          Costs of active uptake.
             !--------------------------------------------------------------------
-            !------------
             !------Mycorrhizal Uptake Cost-----------------!
             do j = 1,nlevdecomp
                rootc_dens_step            = rootc_dens(p,j) *  permyc(p,istp)
@@ -1608,6 +1619,44 @@ real(r8) function fun_cost_fix(fixer,a_fix,b_fix,c_fix,big_cost,crootfr,s_fix, t
   end if    ! ends up with the fixer or non-fixer decision
 
   end function fun_cost_fix
+
+
+!=========================================================================================
+  real(r8) function fun_cost_fix_Bytnerowicz_noAcc(fixer,nfix_tmin,nfix_topt,nfix_tmax,big_cost,crootfr,s_fix, tc_soisno)
+
+! Description:
+!   Calculate the cost of fixing N by nodules.
+! Code Description:
+!   This code is written to CTSM5.1 by Will Wieder 11/17/2022, modified for CLM6 11/01/2024
+
+  implicit none
+!--------------------------------------------------------------------------
+! Function result.
+!--------------------------------------------------------------------------
+! real(r8) , intent(out) :: cost_of_n   !!! cost of fixing N (kgC/kgN)
+!--------------------------------------------------------------------------
+  integer,  intent(in) :: fixer     ! flag indicating if plant is a fixer
+                                    ! 1=yes, otherwise no.
+  real(r8), intent(in) :: nfix_tmin ! As in Bytnerowicz et al. (2022)
+  real(r8), intent(in) :: nfix_topt ! As in Bytnerowicz et al. (2022)
+  real(r8), intent(in) :: nfix_tmax ! As in Bytnerowicz et al. (2022)
+  real(r8), intent(in) :: big_cost  ! an arbitrary large cost (gC/gN)
+  real(r8), intent(in) :: crootfr   ! fraction of roots for carbon that are in this layer
+  real(r8), intent(in) :: s_fix     ! Inverts the temperature function for a cost function
+  real(r8), intent(in) :: tc_soisno ! soil temperature (degrees Celsius)
+
+  if (fixer == 1 .and. crootfr > 1.e-6_r8 .and. tc_soisno > nfix_tmin .and. tc_soisno < nfix_tmax) then
+     fun_cost_fix_Bytnerowicz_noAcc  = (-1*s_fix) * 1._r8 / ( ((nfix_tmax-tc_soisno)/(nfix_tmax-nfix_topt))*&
+                                                            ( ((tc_soisno-nfix_tmin)/(nfix_topt-nfix_tmin))**&
+                                                              ((nfix_topt- nfix_tmin)/(nfix_tmax-nfix_topt)) ) )
+     fun_cost_fix_Bytnerowicz_noAcc = min(fun_cost_fix_Bytnerowicz_noAcc,big_cost)
+  else
+     fun_cost_fix_Bytnerowicz_noAcc = big_cost
+  end if    ! ends up with the fixer or non-fixer decision
+
+  end function fun_cost_fix_Bytnerowicz_noAcc
+!=========================================================================================
+
 !=========================================================================================
   real(r8) function fun_cost_active(sminn_layer,big_cost,kc_active,kn_active,rootc_dens,crootfr,smallValue)         
 

src/main/clm_varctl.F90

@@ -227,6 +227,8 @@ module clm_varctl
   !
   real(r8), public :: nfix_timeconst = -1.2345_r8 
 
+  character(len=25), public :: nfix_method  ! choice of nfix parameterization
+
   !----------------------------------------------------------
   ! Physics
   !----------------------------------------------------------

src/main/controlMod.F90

@@ -257,6 +257,8 @@ subroutine control_init(dtime)
          CNratio_floating, lnc_opt, reduce_dayl_factor, vcmax_opt, &
          CN_evergreen_phenology_opt, carbon_resp_opt
 
+    namelist /clm_nitrogen/ nfix_method
+
     namelist /clm_inparm/ use_soil_moisture_streams
 
     ! excess ice flag
@@ -882,6 +884,7 @@ subroutine control_spmd()
        call mpi_bcast (use_c13_timeseries,  1, MPI_LOGICAL, 0, mpicom, ier)
        call mpi_bcast (atm_c13_filename,  len(atm_c13_filename), MPI_CHARACTER, 0, mpicom, ier)
        call mpi_bcast (use_fun,            1, MPI_LOGICAL, 0, mpicom, ier)
+       call mpi_bcast (nfix_method, len(nfix_method), MPI_CHARACTER, 0, mpicom, ier)
     end if
 
     call mpi_bcast (perchroot, 1, MPI_LOGICAL, 0, mpicom, ier)