Merge remote-tracking branch 'escomp/b4b-dev' into cesm3_0_beta05_sub…

…modules

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 +3408,7 @@ sub setup_logic_mineral_nitrogen_dynamics {
        }
     }
   }
+
 }
 
 
@@ -5208,6 +5209,7 @@ sub write_output_files {
   }
   push @groups, "clm_humanindex_inparm";
   push @groups, "cnmresp_inparm";
+  push @groups, "cnfun_inparm";
   push @groups, "photosyns_inparm";
   push @groups, "cnfire_inparm";
   push @groups, "cn_general";

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -524,10 +524,9 @@ 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="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_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 +1893,8 @@ 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="cnfun_inparm"
+       group="cnfun_inparm" 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: Tue 24 Dec 2024 03:43:01 PM 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 seems problematic at the moment
+
+
+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 12/24/2024 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