alpha-ctsm5.4.CMIP7.15.ctsm5.3.082: Update the alpha54 branch to ctsm5.3.082

bld/CLMBuildNamelist.pm

@@ -3753,8 +3753,12 @@ sub setup_logic_c_isotope {
   #
   my ($opts, $nl_flags, $definition, $defaults, $nl) = @_;
 
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_c13', 'bgc_mode'=>$nl_flags->{'bgc_mode'}, 'phys'=>$nl_flags->{'phys'});
-  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_c14', 'bgc_mode'=>$nl_flags->{'bgc_mode'}, 'phys'=>$nl_flags->{'phys'});
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_c13', 
+              'bgc_mode'=>$nl_flags->{'bgc_mode'}, 'phys'=>$nl_flags->{'phys'},
+              'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'}, ssp_rcp=>$nl_flags->{'ssp_rcp'} );
+  add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_c14', 
+              'bgc_mode'=>$nl_flags->{'bgc_mode'}, 'phys'=>$nl_flags->{'phys'},
+              'lnd_tuning_mode'=>$nl_flags->{'lnd_tuning_mode'}, ssp_rcp=>$nl_flags->{'ssp_rcp'} );
   my $use_c13 = $nl->get_value('use_c13');
   my $use_c14 = $nl->get_value('use_c14');
   if ( $nl_flags->{'bgc_mode'} ne "sp" && $nl_flags->{'bgc_mode'} ne "fates" ) {
@@ -3767,7 +3771,7 @@ sub setup_logic_c_isotope {
       }
     }
     if ( &value_is_true($use_c14) ) {
-      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_c14_bombspike', 'bgc_mode'=>$nl_flags->{'bgc_mode'}, 'phys'=>$nl_flags->{'phys'});
+      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_c14_bombspike', 'use_c14'=>$use_c14 );
       my $use_c14_bombspike = $nl->get_value('use_c14_bombspike');
       if ( &value_is_true($use_c14_bombspike) ) {
          add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'atm_c14_filename',
@@ -3781,7 +3785,7 @@ sub setup_logic_c_isotope {
       }
     }
     if ( &value_is_true($use_c13) ) {
-      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_c13_timeseries', 'bgc_mode'=>$nl_flags->{'bgc_mode'}, 'phys'=>$nl_flags->{'phys'});
+      add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'use_c13_timeseries', 'use_c13'=>$use_c13 );
       my $use_c13_timeseries = $nl->get_value('use_c13_timeseries');
       if ( &value_is_true($use_c13_timeseries) ) {
          add_default($opts, $nl_flags->{'inputdata_rootdir'}, $definition, $defaults, $nl, 'atm_c13_filename',

bld/namelist_files/namelist_defaults_ctsm.xml

@@ -115,11 +115,22 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <use_c14>.false.</use_c14>
 <use_c13_timeseries>.false.</use_c13_timeseries>
 <use_c14_bombspike>.false.</use_c14_bombspike>
-
-<use_c13 phys="clm6_0" bgc_mode="bgc" >.true.</use_c13>
-<use_c14 phys="clm6_0" bgc_mode="bgc" >.true.</use_c14>
-<use_c13_timeseries phys="clm6_0" bgc_mode="bgc" >.true.</use_c13_timeseries>
-<use_c14_bombspike phys="clm6_0" bgc_mode="bgc" >.true.</use_c14_bombspike>
+<!-- Turn timeseries on if Carbon isotopes are on -->
+<use_c13_timeseries use_c13=".true.">.true.</use_c13_timeseries>
+<use_c14_bombspike use_c14=".true.">.true.</use_c14_bombspike>
+
+<!-- Turn Carbon isotopes on for clm6_0 physics with BGC on with CRUJRA or CAM7 forcing and for historical period-->
+<!-- NOTE: Have Carbon isotopes off for older physics as those earlier versions were run that way. 
+       They can only be on for BGC compsets (NOT SP or FATES).
+
+       Also, we configured the defaults the following ways:
+       - On only for CRUJRA2024 or CAM7 forcing because that is how the CESM3.0 clm6_0 simulations were run
+       - In contrast to above, it's turned off for other forcing options as we haven't run simulations with those configurations
+      - It's also only turned on for Historical periods and NOT future scenarios because we don't have CMIP7 data for them -->
+<use_c13 phys="clm6_0" bgc_mode="bgc" lnd_tuning_mode="clm6_0_CRUJRA2024" ssp_rcp="hist">.true.</use_c13>
+<use_c14 phys="clm6_0" bgc_mode="bgc" lnd_tuning_mode="clm6_0_CRUJRA2024" ssp_rcp="hist">.true.</use_c14>
+<use_c13 phys="clm6_0" bgc_mode="bgc" lnd_tuning_mode="clm6_0_cam7.0" ssp_rcp="hist">.true.</use_c13>
+<use_c14 phys="clm6_0" bgc_mode="bgc" lnd_tuning_mode="clm6_0_cam7.0" ssp_rcp="hist">.true.</use_c14>
 
 <!-- Carbon isotope concentration files -->
 <atm_c13_filename use_c13=".true." use_c13_timeseries=".true." ssp_rcp="hist"     >lnd/clm2/isotopes/atm_delta_C13_CMIP6_1850-2015_yearly_v2.0_c190528.nc</atm_c13_filename>
@@ -141,6 +152,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <!-- Irrigation default (Note, the use-cases also set this) -->
 <irrigate                                                             >.false.</irrigate>
 <irrigate               use_cndv=".false."  sim_year_range="1850-2100">.true.</irrigate>
+<irrigate phys="clm6_0" use_cndv=".false."  sim_year_range="1850-2000">.true.</irrigate>
 <irrigate phys="clm4_5" use_cndv=".false."  sim_year_range="1850-2100">.false.</irrigate>
 
 <!-- Saturation excess runoff for crops  -->
@@ -2282,8 +2294,7 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/surfdata_1x1_NEON_TOOL_hist_2000_78pfts_c2
 <stream_year_first_popdens use_fates=".true." sim_year="constant" sim_year_range="1000-1004" >2000</stream_year_first_popdens>
 <stream_year_last_popdens  use_fates=".true." sim_year="constant" sim_year_range="1000-1004" >2000</stream_year_last_popdens>
 
-<stream_fldfilename_popdens hgrid="0.5x0.5"   use_cn=".true." phys="clm6_0" >lnd/clm2/firedata/clmforc.Li_2025_CMIP7_SSP3CMIP6_hdm_0.5x0.5_simyr1850-2100_c250717.nc</stream_fldfilename_popdens>
-<stream_fldfilename_popdens hgrid="0.5x0.5"   use_cn=".true."               >lnd/clm2/firedata/clmforc.Li_2017_HYDEv3.2_CMIP6_hdm_0.5x0.5_AVHRR_simyr1850-2016_c180202.nc</stream_fldfilename_popdens>
+<stream_fldfilename_popdens hgrid="0.5x0.5"   use_cn=".true." >lnd/clm2/firedata/clmforc.Li_2025_CMIP7_hdm_0.5x0.5_simyr1850-2025_c251013.nc</stream_fldfilename_popdens>
 <stream_fldfilename_popdens hgrid="0.5x0.5"   use_cn=".true." ssp_rcp="SSP1-1.9" >lnd/clm2/firedata/clmforc.Li_2018_SSP1_CMIP6_hdm_0.5x0.5_AVHRR_simyr1850-2100_c181205.nc
 </stream_fldfilename_popdens>
 <stream_fldfilename_popdens hgrid="0.5x0.5"   use_cn=".true." ssp_rcp="SSP1-2.6" >lnd/clm2/firedata/clmforc.Li_2018_SSP1_CMIP6_hdm_0.5x0.5_AVHRR_simyr1850-2100_c181205.nc
@@ -2301,8 +2312,7 @@ lnd/clm2/surfdata_esmf/NEON/ctsm5.3.0/surfdata_1x1_NEON_TOOL_hist_2000_78pfts_c2
 <stream_fldfilename_popdens hgrid="0.5x0.5"   use_cn=".true." ssp_rcp="SSP5-3.4" >lnd/clm2/firedata/clmforc.Li_2018_SSP5_CMIP6_hdm_0.5x0.5_AVHRR_simyr1850-2100_c181205.nc
 </stream_fldfilename_popdens>
 
-<stream_fldfilename_popdens hgrid="0.5x0.5"   use_fates=".true." phys="clm6_0" >lnd/clm2/firedata/clmforc.Li_2025_CMIP7_SSP3CMIP6_hdm_0.5x0.5_simyr1850-2100_c250717.nc</stream_fldfilename_popdens>
-<stream_fldfilename_popdens hgrid="0.5x0.5"   use_fates=".true."               >lnd/clm2/firedata/clmforc.Li_2017_HYDEv3.2_CMIP6_hdm_0.5x0.5_AVHRR_simyr1850-2016_c180202.nc</stream_fldfilename_popdens>
+<stream_fldfilename_popdens hgrid="0.5x0.5"   use_fates=".true." >lnd/clm2/firedata/clmforc.Li_2025_CMIP7_hdm_0.5x0.5_simyr1850-2025_c251013.nc</stream_fldfilename_popdens>
 <stream_fldfilename_popdens hgrid="0.5x0.5"   use_fates=".true." ssp_rcp="SSP1-1.9" >lnd/clm2/firedata/clmforc.Li_2018_SSP1_CMIP6_hdm_0.5x0.5_AVHRR_simyr1850-2100_c181205.nc
 </stream_fldfilename_popdens>
 <stream_fldfilename_popdens hgrid="0.5x0.5"   use_fates=".true." ssp_rcp="SSP1-2.6" >lnd/clm2/firedata/clmforc.Li_2018_SSP1_CMIP6_hdm_0.5x0.5_AVHRR_simyr1850-2100_c181205.nc

doc/ChangeLog

@@ -1,4 +1,231 @@
 ===============================================================
+Tag name: ctsm5.3.082
+Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
+Date: Fri 24 Oct 2025 11:17:41 AM MDT
+One-line Summary: Update to CMIP7 population density file for non-SSP cases
+
+Purpose and description of changes
+----------------------------------
+
+ Update two lines in namelist_defaults_ctsm.xml.
+
+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 #3545 Update to official CMIP7 pop. density data
+
+Notes of particular relevance for users
+---------------------------------------
+Changes made to namelist defaults (e.g., changed parameter values):
+ Updated pop. density file for non-SSP cases.
+
+Changes to the datasets (e.g., parameter, surface or initial files):
+ Updated pop. density file for non-SSP cases.
+
+Testing summary:
+----------------
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: Yes
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: non-SSP
+    - what platforms/compilers: all
+    - nature of change: larger than roundoff/same climate
+
+Other details
+-------------
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/3563
+
+===============================================================
+===============================================================
+Tag name: ctsm5.3.081
+Originator(s): erik (Erik Kluzek,UCAR/TSS,303-497-1326)
+Date: Wed 22 Oct 2025 05:31:52 PM MDT
+One-line Summary: Change defaults for when Carbon isotopes are turned on, and turn on irrigate for Sp/Bgc cases for clm6_0 historical transient cases
+
+Purpose and description of changes
+----------------------------------
+
+Only turn C13/C14 for clm6_0 and BGC, and also require the DATM forcing to be CRUJRA2024 or CAM7 and for the historical period. So for example SSP compsets won't have C13/C14 on, single point compsets won't, or for using older forcing (like CAM6, or GSWP3v1, Qian, or CRUv7). Also whenever use_c13 or use_c14 is on turn on the corresponding time series file.
+
+Also change default for irrigate to on for historical SP/BGC cases.
+
+
+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]:
+   Fixes #3527 -- irrigation settings for control vs historical cases
+   Fixes #3551 -- Turn on relevent Carbon isotope time-series when use_c13/c14 is on
+   Some work on #3346 -- CMIP7 Carbon isotope data
+
+Notes of particular relevance for users
+---------------------------------------
+
+Caveats for users (e.g., need to interpolate initial conditions):
+   This just changes the defaults for when Carbon isotopes are turned on, to make it less often
+   Users can still turn it on by hand for the cases that they want.
+
+Changes made to namelist defaults (e.g., changed parameter values):
+   Carbon isotope timeseries files are turned on whenever use_c13/use_c14 is turned on so it uses
+   the historical
+   Turn irrigate on for clm6_0 historical
+   Carbon isotopes only turned on by default for clm6_0 when CRUJRA2024 or CAM7 forcing is used
+   and only for historical cases and not SSP's
+
+Testing summary: regular
+----------------
+ [PASS means all tests PASS; OK means tests PASS other than expected fails.]
+
+  build-namelist tests (if CLMBuildNamelist.pm has changed):
+
+    derecho - OK (differences in namelists are all as expected)
+
+  python testing (if python code has changed; see instructions in python/README.md; document testing done):
+
+    derecho - PASS
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+If the tag used for baseline comparisons was NOT the previous tag, note that here: previous
+
+
+Answer changes
+--------------
+
+Changes answers relative to baseline: HistClm60 compsets and tests with the ciso testmod
+
+  Summarize any changes to answers, i.e.,
+    - what code configurations: HistClm60Sp/HistClm60Bgc now with irriage on
+         cases with use_c13/use_c14 now have c13/c14 isotope timeseries files on
+    - what platforms/compilers: all
+    - nature of change (roundoff; larger than roundoff/same climate; new climate):
+      Carbon Isotopes -- are diagnostic and only change fields on history files
+           Cases that now have C13/C14 isotopes on now use timeseries files rather
+           than the default pre-industrial so change answers for C13/C14 fields 
+      Irrigate turned on for HistClm60Bgc/HistClm60Sp compsets will change answers 
+
+Other details
+-------------
+
+Pull Requests that document the changes (include PR ids):
+(https://github.com/ESCOMP/ctsm/pull)
+
+https://github.com/ESCOMP/CTSM/pull/3549
+
+===============================================================
+===============================================================
+Tag name: ctsm5.3.080
+Originator(s): samrabin (Sam Rabin, UCAR/TSS)
+Date: Thu Oct 16 13:41:08 MDT 2025
+One-line Summary: Merge b4b-dev to master
+
+Purpose and description of changes
+----------------------------------
+
+Merge b4b-dev to master. Includes these PRs:
+- [ESCOMP/CTSM Pull Request #3193: resolve issue #103: Example 1.7 typo by linniahawkins](https://github.com/ESCOMP/CTSM/pull/3193)
+- [ESCOMP/CTSM Pull Request #3518: Update of the leaching doc by jinmuluo](https://github.com/ESCOMP/CTSM/pull/3518)
+- [ESCOMP/CTSM Pull Request #3548: Finishing adding RC14_CANAIR history output by ekluzek](https://github.com/ESCOMP/CTSM/pull/3548)
+
+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 in the included PRs:
+- [ESCOMP/CTSM Issue #103: Example 1.7 typo](https://github.com/ESCOMP/CTSM/issues/103)
+- [ESCOMP/CTSM Issue #3488: Add RC14_CANAIR as optional to history output so that C14 time series data can be verified](https://github.com/ESCOMP/CTSM/issues/3488)
+- [ESCOMP/CTSM Issue #3490: Change history averaging of RC13_CANAIR and RC14_CANAIR so that zero's aren't averaged in](https://github.com/ESCOMP/CTSM/issues/3490)
+
+
+Notes of particular relevance for users
+---------------------------------------
+
+Changes to documentation:
+- Updated leaching documentation
+- Typo fix
+
+
+Testing summary:
+----------------
+
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+
+Other details
+-------------
+
+Pull Requests that document the changes (include PR ids):
+- [ESCOMP/CTSM Pull Request #3553: b4b-dev merge 2025-10-16 by samsrabin](https://github.com/ESCOMP/CTSM/pull/3553)
+
+===============================================================
+===============================================================
 Tag name: ctsm5.3.079
 Originator(s): samrabin (Sam Rabin, UCAR/TSS)
 Date: Mon Oct  6 21:41:11 MDT 2025

doc/ChangeSum

@@ -1,5 +1,8 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.3.082   slevis 10/24/2025 Update to CMIP7 population density file for non-SSP cases
+       ctsm5.3.081     erik 10/22/2025 Change defaults for when Carbon isotopes are turned on, and turn on irrigate for Sp/Bgc cases for clm6_0 historical transient cases
+       ctsm5.3.080 samrabin 10/16/2025 Merge b4b-dev to master
        ctsm5.3.079 samrabin 10/06/2025 Update submodules to match versions in cesm3_0_alpha07e
        ctsm5.3.078   slevis 10/03/2025 Merge b4b-dev to master
        ctsm5.3.077   rgknox 10/02/2025 Adjustment of timestep albedo filtering with FATES

doc/source/tech_note/External_Nitrogen_Cycle/CLM50_Tech_Note_External_Nitrogen_Cycle.rst

@@ -133,6 +133,45 @@ where :math:`{WS}_{tot\_soil}` (kgH\ :sub:`2`\ O m\ :sup:`-2`) is the total mass
 
    NF_{leached} =\min \left(NF_{leached} ,\frac{NS_{sminn} sf}{\Delta t} \right).
 
+Alternative way of evaluating the Leaching Losses of Nitrogen
+--------------------------------------------------------------
+
+The previous leaching mechanism is not designed for describing the vertical transport of :math:`{NO}_{3}^{-}` in soil, an alternative way to evaluate the vertical convective, diffusive, and dispersive of dissolved :math:`{NO}_{3}^{-}` in soil is provided in (:ref:`Luo et al. 2025 <Luoetal2025>`). 
+To obtain the vertical profile of soil mineral N after vertical movement of each timestep, the vertical transport equation is summarized in :eq:`22.20`.
+
+.. math::
+   :label: 22.20
+
+   \frac{\partial NS_{sminn}}{\partial t} = \frac{\partial J}{\partial z} + S
+
+where :math:`NS_{sminn} (gN m^{-3})` is the soil :math:`{NO}_{3}^{-}` concentration in each layer, :math:`J (gN m^{-2} s^{-1})` is the different vertical transport terms (:math:`J_{convective}, J_{diffusive}, J_{dispersive}`) between two soil layers, and :math:`S` is the sources or sinks fluxes.
+Different transport terms are explained below 
+
+.. math::
+   :label: 22.21
+
+   J_{convective} = sf \frac{SN_{sminn}q_{out}}{\theta} 
+
+where :math:`q_{out} (mH_{2}Os^{-1})` is the darcy flow of water, :math:`\theta (m^3H_{2}O m^{-3}soil)` is the soil water content.
+
+.. math::
+   :label: 22.22
+
+   J_{diffusive} = -D_{aq} \frac{\theta^{7/3}}{\phi^{2}} \frac{\partial SN_{sminn}}{ \partial z}
+
+where :math:`\partial SN_{sminn}/ \partial z` is the concentration gradient, :math:`D_{aq}` is the nitrate aqueous diffusion coefficient which is taken as :math:`1.7*10^{-9} m^{2}s^{-1}`, and :math:`\phi (m^3m^{-3})` is soil porosity.
+
+.. math::
+   :label: 22.23
+
+   J_{dispersive} = -D_{dis} \frac{\theta^{7/3}}{\phi^{2}} \frac{\partial SN_{sminn}}{ \partial z}
+
+where :math:`D_{dis}` is the dispersion coefficient, which equal to :math:`L_{dis} q_{out} \theta ^{-1}`, for simplicity reasons, :math:`L_{dis}` is taken as 0.1 meter.
+
+Finally, the classical convective-diffusion algorithm described in (:ref:`Patankar.2018 <Patankaretal2018>`) is used to discrete and solve the :math:`{NO}_{3}^{-}` vertical transport :eq:`22.20` in soils. 
+The advantage of this leaching mechanism is the soil :math:`{NO}_{3}^{-}` is able to move vertically (both upward or downward) with soil water movement, the mass of :math:`{NO}_{3}^{-}` reaches bedrock layer is finally taken as the  :math:`NF_{leached}`.
+
+
 Losses of Nitrogen Due to Fire
 -----------------------------------