Merge pull request ESCOMP#3124 from slevis-lmwg/merge-master-20250509

slevis-lmwg · web-flow · commit 3df302f27c9b · 2025-05-09T14:33:35.000-07:00
Merge master 20250509
diff --git a/.gitmodules b/.gitmodules
@@ -28,7 +28,7 @@
 [submodule "fates"]
 path = src/fates
 url = https://github.com/NGEET/fates
-fxtag = sci.1.82.3_api.39.0.0
+fxtag = sci.1.83.1_api.39.0.0
 fxrequired = AlwaysRequired
 # Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
 fxDONOTUSEurl = https://github.com/NGEET/fates
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -781,10 +781,9 @@ This option is older than the luhdata options and may be depricated at some poin
 </entry>
 
 <entry id="fates_electron_transport_model" type="char*256" category="physics"
-        group="elm_inparm" valid_values="FvCB1980,JohnsonBerry2021" value="FvCB1980">
+        group="clm_inparm" valid_values="FvCB1980,JohnsonBerry2021" value="FvCB1980">
 Set the FATES electron transport model to either Johnson-Berry 2021 or
   Farquhar von Caemmerer and Berry 1980 (FvCB1980).
-
 </entry>
 
 <entry id="fates_radiation_model" type="char*256" category="physics"
diff --git a/cime_config/testdefs/ExpectedTestFails.xml b/cime_config/testdefs/ExpectedTestFails.xml
@@ -245,10 +245,10 @@
     </phase>
   </test>
 
-  <test name="PEM_D_Ld20.f10_f10_mg37.I2000Clm50FatesRs.derecho_gnu.clm-FatesColdSeedDisp">
-    <phase name="COMPARE_base_modpes">
+  <test name="PEM_D_Ld20.5x5_amazon.I2000Clm50FatesRs.derecho_gnu.clm-FatesColdSeedDisp">
+    <phase name="RUN">
       <status>FAIL</status>
-      <issue>FATES#1089</issue>
+      <issue>#3097</issue>
     </phase>
   </test>
 
diff --git a/cime_config/testdefs/testlist_clm.xml b/cime_config/testdefs/testlist_clm.xml
@@ -3236,6 +3236,15 @@
       <option name="comment">Ensure functionality of the tree damage option in FATES</option>
     </options>
   </test>
+  <test name="ERS_D_Ld20" grid="f45_f45_mg37" compset="I2000Clm60FatesRs" testmods="clm/FatesColdElecTransJB">
+    <machines>
+      <machine name="derecho" compiler="gnu" category="fates"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment">Ensure functionality of the JohnsonBerry2021 option in FATES</option>
+    </options>
+  </test>
   <test name="ERI_D_Ld20" grid="f45_f45_mg37" compset="I2000Clm50FatesRs" testmods="clm/FatesColdTwoStream">
     <machines>
       <machine name="derecho" compiler="intel" category="fates"/>
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm
@@ -8,7 +8,7 @@ use_fates_tree_damage = .true.
 hist_ndens = 1
 hist_fincl1       = 'FATES_TLONGTERM',
 'FATES_TGROWTH','FATES_SEEDS_IN_GRIDCELL_PF','FATES_SEEDS_OUT_GRIDCELL_PF','FATES_NCL_AP',
-'FATES_NPATCH_AP','FATES_VEGC_AP','FATES_SECONDARY_ANTHRODISTAGE_AP','FATES_SECONDARY_AREA_AP',
+'FATES_NPATCH_AP','FATES_VEGC_AP','FATES_SECONDARY_AREA_ANTHRO_AP','FATES_SECONDARY_AREA_AP',
 'FATES_FUEL_AMOUNT_APFC','FATES_STOREC_TF_USTORY_SZPF','FATES_STOREC_TF_CANOPY_SZPF',
 'FATES_CROWNAREA_CLLL','FATES_ABOVEGROUND_MORT_SZPF',
 'FATES_ABOVEGROUND_PROD_SZPF','FATES_NPLANT_SZAP','FATES_NPLANT_CANOPY_SZAP',
@@ -56,5 +56,7 @@ hist_fincl1       = 'FATES_TLONGTERM',
 'FATES_PARSUN_CL','FATES_PARSHA_CL','FATES_LAISUN_CLLL','FATES_LAISHA_CLLL','FATES_LAISUN_CLLLPF',
 'FATES_LAISHA_CLLLPF','FATES_PARPROF_DIR_CLLLPF','FATES_PARPROF_DIF_CLLLPF','FATES_LAISUN_CL','FATES_LAISHA_CL',
 'FATES_PARPROF_DIR_CLLL','FATES_PARPROF_DIF_CLLL','FATES_NET_C_UPTAKE_CLLL','FATES_CROWNFRAC_CLLLPF',
-'FATES_LBLAYER_COND_AP','FATES_STOMATAL_COND_AP','FATES_TLONGTERM','FATES_PRIMARY_AREA_AP','FATES_NPP_LU',
-'FATES_GPP_LU'
+'FATES_LBLAYER_COND_AP','FATES_STOMATAL_COND_AP','FATES_TLONGTERM','FATES_PRIMARY_AREA_AP','FATES_NPP_LU','FATES_GPP_LU',
+'FATES_SEED_BANK_PF','FATES_UNGERM_SEED_BANK_PF','FATES_SEEDLING_POOL_PF','FATES_SEEDS_IN_PF','FATES_SEEDS_IN_LOCAL_PF',
+'FATES_SAPWOOD_AREA_SZPF','FATES_CANOPYAREA','FATES_NCL','FATES_PATCHAREA','FATES_PRIMARY_AREA','FATES_SCORCH_HEIGHT_PF',
+'FATES_SECONDARY_AREA_ANTHRO','FATES_SECONDARY_AREA','FATES_ZSTAR'
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdElecTransJB/include_user_mods b/cime_config/testdefs/testmods_dirs/clm/FatesColdElecTransJB/include_user_mods
@@ -0,0 +1 @@
+../FatesCold
diff --git a/cime_config/testdefs/testmods_dirs/clm/FatesColdElecTransJB/user_nl_clm b/cime_config/testdefs/testmods_dirs/clm/FatesColdElecTransJB/user_nl_clm
@@ -0,0 +1 @@
+fates_electron_transport_model='JohnsonBerry2021'
diff --git a/doc/ChangeLog b/doc/ChangeLog
@@ -1,4 +1,162 @@
 ===============================================================
+Tag name: ctsm5.3.043
+Originator(s): slevis (Samuel Levis,UCAR/TSS,303-665-1310)
+Date: Fri 09 May 2025 12:28:17 PM MDT
+One-line Summary: Merge b4b-dev
+
+Purpose and description of changes
+----------------------------------
+
+ Updates to the b4b-dev branch since its last merge to master (PRs #3091 #3092), as shown by git log:
+
+ - Merge pull request Update docs infrastructure #2809 from samsrabin/update-docs-builder-2
+   Update docs infrastructure
+ - Merge pull request Update externals to cesm3_0_alpha06c #3106 from ekluzek/update_to_alpha06c
+   Update externals to cesm3_0_alpha06c
+ - Merge pull request User control over snow thermal conductivity scheme over glaciers #3072 from wwieder/JordanGlacier
+   User control over snow thermal conductivity scheme over glaciers
+
+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 #2818 Update doc-builder
+Resolves #3098 st-archive issues in ctsm5.3.041
+Resolves #3071 Opt to use Jordan1991 over glacier land
+Resolves #3080 Lake snow thermal conductivity hard coded to Jordan
+
+Notes of particular relevance for users
+---------------------------------------
+Changes to CTSM's user interface (e.g., new/renamed XML or namelist variables):
+ Introduce user control over snow thermal conductivity scheme over glaciers
+
+Changes to documentation:
+ #2809 updates docs infrastructure
+
+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: No
+
+Other details
+-------------
+List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
+ #3106 updates submodules to cesm3_0_alpha06c
+
+Pull Requests that document the changes (include PR ids):
+ https://github.com/ESCOMP/ctsm/pull/3123
+
+===============================================================
+===============================================================
+Tag name: ctsm5.3.042
+Originator(s): glemieux (Gregory Lemieux, LBNL, glemieux@lbl.gov)
+Date: Thu May  8 16:15:48 MDT 2025
+One-line Summary: Update FATES tag, tests and address namelist option bug
+
+Purpose and description of changes
+----------------------------------
+
+This pull request updates the FatesColdAllVars test list due to changes in the FATES
+history output associated with ngeet/fates#1252, which is coordinated with this update.
+A bug in which the incorrect control variable was being sent to FATES for a recently
+added namelist options has been addressed.  The NEON-FATES-NIWO tests have also been
+addressed through the update of the FATES tag which includes fixes brought in with
+ngeet/fates#1376.
+
+
+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]:
+- [Issue #3052: Update FatesColdAllVars history output with recent additions](https://github.com/ESCOMP/CTSM/issues/3052)
+- [Issue #3038: NEON-FATES-NIWO test in aux_clm fails RUN](https://github.com/ESCOMP/CTSM/issues/3038)
+- [Issue #3062: Incorrect value being set for FATES electron transport namelist option](https://github.com/ESCOMP/CTSM/issues/3062)
+
+Notes of particular relevance for developers:
+---------------------------------------------
+Changes to tests or testing:
+  The PEM seed dispersal test is now failing RUN, where it was previously failing COMPARE_base_modpes.
+  This has been added to the expected failures and has been documented in a new issue, [#3097](https://github.com/ESCOMP/CTSM/issues/3097).
+  This issue is associated with updates that came in previously with ctsm5.3.041.
+
+Testing summary:
+----------------
+  regular tests (aux_clm: https://github.com/ESCOMP/CTSM/wiki/System-Testing-Guide#pre-merge-system-testing):
+
+    derecho ----- OK
+    izumi ------- OK
+
+  fates tests: (give name of baseline if different from CTSM tagname, normally fates baselines are fates-<FATES TAG>-<CTSM TAG>)
+    derecho ----- OK
+    izumi ------- OK
+
+Notes:
+- All tests resulted in expected st_archive exception due to known issue [#3098](https://github.com/ESCOMP/CTSM/issues/3098)
+- Due to permission issues, the izumi aux_clm tests were run against ctsm5.3.040 baselines.  This was deemed acceptable since ctsm5.3.041 is a b4b tag
+Answer changes
+--------------
+
+Changes answers relative to baseline: Yes, but only for FATES tests
+  This is due to updating the fates tag which includes a number of bug fixes and science updates
+
+
+Other details
+-------------
+List any git submodules updated (cime, rtm, mosart, cism, fates, etc.):
+   fates: sci.1.82.3_api.39.0.0 -> sci.1.83.1_api.39.0.0
+
+Pull Requests that document the changes (include PR ids):
+(https://github.com/ESCOMP/ctsm/pull)
+https://github.com/ESCOMP/CTSM/pull/3058
+https://github.com/ESCOMP/CTSM/pull/3063
+https://github.com/NGEET/fates/pull/1252
+https://github.com/NGEET/fates/pull/1376
+
+===============================================================
+===============================================================
 Tag name: ctsm5.3.041
 Originator(s): samrabin (Sam Rabin, UCAR/TSS)
 Date: Fri Apr 25 08:02:37 MDT 2025
diff --git a/doc/ChangeSum b/doc/ChangeSum
@@ -1,5 +1,7 @@
 Tag                   Who      Date  Summary
 ============================================================================================================================
+       ctsm5.3.043   slevis 05/09/2025 Merge b4b-dev
+       ctsm5.3.042 glemieux 05/08/2025 Update FATES tag, tests and address namelist option bug
        ctsm5.3.041 samrabin 04/25/2025 Merge b4b-dev to master
        ctsm5.3.040 samrabin 04/15/2025 Update ctsm_pylib to 3.13.2
        ctsm5.3.039  afoster 04/14/2025 Create driver data structure for SP mode
diff --git a/src/fates b/src/fates
@@ -1 +1 @@
-Subproject commit 0f321cd8699475f97a4a4815536ca09b7e463f89
+Subproject commit fe782ba4f851f8c8bfac8a89607e7c05bd397553
diff --git a/src/utils/clmfates_interfaceMod.F90 b/src/utils/clmfates_interfaceMod.F90
@@ -612,9 +612,9 @@ subroutine CLMFatesGlobals2()
         call set_fates_ctrlparms('radiation_model',ival=pass_radiation_model)
 
         if (trim(fates_electron_transport_model) == 'FvCB1980') then
-           pass_radiation_model = 1
+           pass_electron_transport_model = 1
         else if (trim(fates_electron_transport_model) == 'JohnsonBerry2021') then
-           pass_radiation_model = 2
+           pass_electron_transport_model = 2
         end if
         call set_fates_ctrlparms('electron_transport_model',ival=pass_electron_transport_model)
 

Original file line number	Diff line number	Diff line change
`@@ -0,0 +1 @@`
	`1`	`+fates_electron_transport_model='JohnsonBerry2021'`