Merge pull request #2928 from slevis-lmwg/tmp-241219

Merge tmp-241219 branch to master

.gitmodules

@@ -28,7 +28,7 @@
 [submodule "fates"]
 path = src/fates
 url = https://github.com/NGEET/fates
-fxtag = sci.1.79.3_api.37.0.0
+fxtag = sci.1.80.4_api.37.0.0
 fxrequired = AlwaysRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NCAR/fates-release

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/ExpectedTestFails.xml

@@ -114,7 +114,7 @@
   </test>
 
   <test name="SMS_D.f10_f10_mg37.I2000Clm60BgcCrop.derecho_nvhpc.clm-crop">
-    <phase name="BUILD">
+    <phase name="SHAREDLIB_BUILD">
       <status>FAIL</status>
       <issue>#1733</issue>
     </phase>
@@ -556,6 +556,13 @@
     </phase>
   </test>
 
+  <test name="PVT_Lm3.f45_f45_mg37.I2000Clm50FatesCruRsGs.derecho_intel.clm-FatesLUPFT">
+    <phase name="RUN">
+      <status>FAIL</status>
+      <issue>#2919</issue>
+    </phase>
+  </test>
+
   <!-- Other submodule test list failures (MOSART, RTM, etc. -->
 
   <test name="SMS_Lh3.f10_f10_mg37.I2000Clm60Sp.derecho_intel.mosart-clmAccelSpinupIgnoreWarn">

cime_config/testdefs/testlist_clm.xml

@@ -1317,6 +1317,15 @@
       <option name="comment"  >Science support for I1850Clm50BgcCropCru at f19</option>
     </options>
   </test>
+  <test name="ERP_D_Ld5_P48x1" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/flexCN_FUN_BNF">
+    <machines>
+      <machine name="derecho" compiler="intel" category="aux_clm"/>
+      <machine name="izumi" compiler="nag" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+    </options>
+  </test>
   <test name="ERP_D_Ld5_P48x1" grid="f10_f10_mg37" compset="I2000Clm50BgcCru" testmods="clm/flexCN_FUN">
     <machines>
       <machine name="izumi" compiler="nag" category="aux_clm"/>

cime_config/testdefs/testmods_dirs/clm/FatesColdHydro/user_nl_clm

@@ -2,7 +2,6 @@ hist_mfilt        = 365
 hist_nhtfrq       = -24
 hist_empty_htapes = .true.
 use_fates_planthydro= .true.
-fates_paramfile = '$CASEROOT/fates_params_hydrograsstempfix.nc'
 hist_fincl1       = 'FATES_ERRH2O_SZPF', 'FATES_TRAN_SZPF',
 'FATES_SAPFLOW_SZPF', 'FATES_ITERH1_SZPF','FATES_ABSROOT_H2O_SZPF',
 'FATES_TRANSROOT_H2O_SZPF','FATES_STEM_H2O_SZPF','FATES_LEAF_H2O_SZPF',

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'

cime_config/testdefs/testmods_dirs/clm/flexCN_FUN_BNF/include_user_mods

@@ -0,0 +1 @@
+../flexCN_FUN

cime_config/testdefs/testmods_dirs/clm/flexCN_FUN_BNF/user_nl_clm

@@ -0,0 +1,2 @@
+ nfix_method = 'Bytnerowicz'
+