Merge pull request #3673 from ekluzek/merge-b4bdev-20251219

Merge b4bdev 20251219

Author: ekluzek

.git-blame-ignore-revs

@@ -75,3 +75,4 @@ cdf40d265cc82775607a1bf25f5f527bacc97405
 49ad0f7ebe0b07459abc00a5c33c55a646f1e7e0
 ac03492012837799b7111607188acff9f739044a
 d858665d799690d73b56bcb961684382551193f4
+c0c6da391ee359f2765439426f3a2a4593a95343

WhatsNewInCTSM5.4.md

@@ -37,21 +37,23 @@ Changes to defaults for \`clm6\` physics:
 * See “Changes to FATES and the FATES parameter file” below.  
 * Namelist defaults change so that  
   * use\_c13/use\_c14 are on only for HistClm60Bgc compsets with CRUJRA2024 or CAM7 forcing; examples of when use\_c13/use\_c14 are now off include SSP and single-point compsets, as well as cases using older forcings, such as CAM6, GSWP3v1, Qian, and CRUv7  
-  * when use\_c13 or use\_c14 is on, turn on the corresponding time series file  
+  * when use\_c13 or use\_c14 is on, turn on the corresponding time series file  (responding to the CLM_CMIP_ERA flag)
+  * C13/C14 CMIP7 data is done using streams with new namelist variables (stream_*_atm_c13, stream_*_atm_c14)
   * irrigation is on for transient cases (1850-2000, 1850-2100, but not for clm4\_5).
 
 Changes for all physics versions:
 
 * Parameters updated: Added MIMICS parameter \`mimics\_fi\` (fraction of litter inputs that bypass litter pools, directly contributing to SOM) and updated other MIMICS parameters (https://github.com/ESCOMP/CTSM/pull/2365) to remove NPP control on turnover, fix density dependent control on turnover, add litterfall fluxes that bypass litter pools and contribute directly to soil organic matter.  
 * FATES parameter file updated: ([PR \#2965](https://github.com/ESCOMP/CTSM/pull/2965), [PR \#2904](https://github.com/ESCOMP/CTSM/pull/2904), [PR \#1344](https://github.com/NGEET/fates/pull/1344), [PR \#3087](https://github.com/ESCOMP/CTSM/pull/3087)). See “FATES parameter file” section below for details.  
 * New surface datasets and landuse timeseries files (see “surface datasets” section below).
+* CMIP7 C13/C14 atmospheric timeseries data
 
 ## Heads up
 
 * History tapes now split into two files from hX to hXi and hXa, where X is the tape number (e.g. h0i/h0a) and where "i" stands for history file containing instantaneous fields, while "a" stands for history file containing non-instantaneous fields. Details in the “history files” section below and in the PRs https://github.com/ESCOMP/ctsm/pull/2445 https://github.com/ESCOMP/MOSART/pull/117 https://github.com/ESCOMP/RTM/pull/61 and the corresponding issues.  
 * Adding time to 1d weighting fields in transient simulations PR https://github.com/ESCOMP/CTSM/pull/3328  
 * Regarding CMIP7 vs. CMIP6 inputs:  
-  * We supply only CMIP7 C13/C14 isotope datasets, so these get used regardless of CLM\_CMIP\_ERA setting.  
+  * C13/C14 isotope datasets are the new CMIP7 datasets using streams, while when CLM_CMIP_ERA==cmip6, the older cmip6 files are used
   * We supply only CMIP7 population density with clm6 physics in non-SSP cases, because the fire model is calibrated to that; conversely, we supply only CMIP6 population density for pre-clm6 physics and for SSP cases.  
   * We supply only CESM2 nitrogen deposition (ndep), so this gets used regardless of CLM\_CMIP\_ERA setting.  
   * For DATM we supply only CMIP6 aerosols.  
@@ -147,4 +149,3 @@ The former is calculated as a function of the latter and can be time-evolving de
 * ne30 with \`Clm60BgcCropCruJra\`: https://github.com/NCAR/LMWG_dev/issues/123 (123\_HIST\_popDens)  
 * ne30 SP https://github.com/NCAR/LMWG_dev/issues/126  
 * f09 SP https://github.com/NCAR/LMWG_dev/issues/127
-

bld/namelist_files/namelist_definition_ctsm.xml

@@ -220,6 +220,7 @@ Index of rooting profile for soil carbon
 
 Changes rooting profile from Zeng 2001 double exponential (0) to
 Jackson 1996 single exponential (1) to Koven uniform exponential (2).
+(REMOVE, NOT in the CODE)
 </entry>
 
 <entry id="rooting_profile_varindex_water" type="integer" category="clm_physics"
@@ -1071,10 +1072,16 @@ If TRUE, implies output data on a 2D latitude/longitude grid. False means
 output in 1D vector format.  One setting per history tape series.
 </entry>
 
+<entry id="hist_all_fields" type="logical" category="history"
+       group="clm_inparm" valid_values="" >
+If TRUE, indicates output ALL history fields on the primary tape.
+</entry>
+
 <entry id="hist_empty_htapes" type="logical" category="history"
        group="clm_inparm" valid_values="" >
 If TRUE, indicates do NOT output any default history fields (requires you to use
-hist_fincl* to set the exact output fields to use)..
+hist_fincl1 to set the exact output fields to use). Note only the
+primary tape has default history fields.
 </entry>
 
 <entry id="hist_fexcl1" type="char*64(1000)" category="history"
@@ -1209,6 +1216,8 @@ number of segments per clump for decomposition
 <entry id="pertlim" type="real" category="clm_physics"
        group="clm_inparm" valid_values="" >
 Perturbation limit when doing error growth test
+(EXPERIMENTAL, UNSUPPORTED, and UNTESTED!)
+(deprecated -- will be removed)
 </entry>
 
 <entry id="rest_flag" type="logical" category="clm_restart"
@@ -1231,7 +1240,8 @@ If TRUE, use explicit, time-varying AC adoption rate for air-conditioning flux a
 
 <entry id="urban_traffic" type="logical" category="clm_physics"
        group="clmu_inparm" valid_values="" >
-If TRUE, urban traffic flux will be activated (Currently NOT implemented).
+If TRUE, urban traffic flux will be activated
+(Currently NOT implemented).
 </entry>
 
 <entry id="building_temp_method" type="integer" category="clm_physics"
@@ -1357,6 +1367,7 @@ CLM Biogeochemistry mode : Carbon Nitrogen model (CN)
        group="clm_inparm" valid_values="" value=".false.">
 CLM Biogeochemistry mode : Carbon Nitrogen with Dynamic Global Vegetation Model (CNDV)
 (or CLM45BGCDV if phys=clm4_5, vsoilc_centbgc='on', and clm4me='on')
+(deprecated -- will be removed)
 </entry>
 
 <entry id="use_fun" type="logical" category="bgc"
@@ -1398,6 +1409,7 @@ Toggle to use 25 lake layers instead of 10
        group="clm_inparm" valid_values="" value=".false.">
 Toggle to turn on the VIC hydrologic parameterizations
 (vichydro=".true." is EXPERIMENTAL, UNSUPPORTED!)
+(deprecated -- will be removed)
 </entry>
 
 <entry id="use_crop" type="logical" category="physics"
@@ -2540,6 +2552,7 @@ If TRUE, add extra diagnostics for methane model to the history files
 Profile over which to distribute C and N coming from surface pools (leaves, stem, grain).
 </entry>
 
+
 <!-- some N cycle flags  -->
 <entry id="no_frozen_nitrif_denitrif" type="logical" category="clm_vertcn"
        group="clm_inparm" valid_values="" >
@@ -2749,6 +2762,7 @@ If TRUE, turn on methane biogeochemistry model for lake columns, using a simplif
 <entry id="usephfact" type="logical" category="clm_methane"
        group="ch4par_in" valid_values="" >
 If TRUE, apply a limitation to methane production based on the soil pH dataset.
+(EXPERIMENTAL, UNSUPPORTED, and UNTESTED!)
 </entry>
 
 <entry id="vmax_oxid_unsat" type="real" category="clm_methane"

bld/unit_testers/build-namelist_test.pl

@@ -163,7 +163,7 @@ sub cat_and_create_namelistinfile {
 #
 # Figure out number of tests that will run
 #
-my $ntests = 3405;
+my $ntests = 3403;
 
 if ( defined($opts{'compare'}) ) {
    $ntests += 2061;

cime_config/testdefs/ExpectedTestFails.xml

@@ -62,6 +62,20 @@
   </test>
 
   <!-- aux_clm test suite failures -->
+  <test name="ERP_Ld9.f45_f45_mg37.I2000Clm50FatesRs.derecho_intel.clm-FatesColdAllVars">
+    <phase name="COMPARE_base_rest">
+      <status>FAIL</status>
+      <issue>#3660</issue>
+      <comment>Restart issues with default "inactive" fields added to history by hist_all_fields.</comment>
+    </phase>
+  </test>
+  <test name="ERP_P64x2_D_Ld3.f10_f10_mt232.IHistClm60BgcCropCrujra.derecho_gnu.clm-default--clm-all_outputs">
+    <phase name="COMPARE_base_rest">
+      <status>FAIL</status>
+      <issue>#3661</issue>
+      <comment>Restart issues with default "inactive" fields added to history by hist_all_fields.</comment>
+    </phase>
+  </test>
   <test name="MKSURFDATAESMF_P128x1.f10_f10_mg37.I1850Clm50BgcCrop.derecho_intel">
     <phase name="NLCOMP">
       <status>FAIL</status>

cime_config/testdefs/testlist_clm.xml

@@ -2125,6 +2125,15 @@
       <option name="comment">Among other extra outputs, ensure that writing the list of all history fields to a separate file does not cause failure</option>
     </options>
   </test>
+  <test name="ERP_P64x2_D_Ld3" grid="f10_f10_mt232" compset="IHistClm60BgcCropCrujra" testmods="clm/default--clm/all_outputs">
+    <machines>
+      <machine name="derecho" compiler="gnu" category="aux_clm"/>
+    </machines>
+    <options>
+      <option name="wallclock">00:20:00</option>
+      <option name="comment"  >Test writing all history fields</option>
+    </options>
+  </test>
   <test name="ERS_D_Ld3" grid="f10_f10_mg37" compset="I1850Clm50BgcCrop" testmods="clm/default">
     <machines>
       <machine name="derecho" compiler="intel" category="aux_clm"/>

cime_config/testdefs/testmods_dirs/clm/FatesColdAllVars/user_nl_clm

@@ -6,57 +6,4 @@ fates_spitfire_mode = 1
 fates_history_dimlevel = 2,2
 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_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',
-'FATES_NPLANT_USTORY_SZAP','FATES_DDBH_CANOPY_SZAP','FATES_DDBH_USTORY_SZAP',
-'FATES_MORTALITY_CANOPY_SZAP','FATES_MORTALITY_USTORY_SZAP','FATES_NPLANT_SZAPPF',
-'FATES_NPP_APPF','FATES_VEGC_APPF','FATES_SCORCH_HEIGHT_APPF','FATES_GPP_SZPF',
-'FATES_GPP_CANOPY_SZPF','FATES_AUTORESP_CANOPY_SZPF','FATES_GPP_USTORY_SZPF',
-'FATES_AUTORESP_USTORY_SZPF','FATES_NPP_SZPF','FATES_LEAF_ALLOC_SZPF',
-'FATES_SEED_ALLOC_SZPF','FATES_FROOT_ALLOC_SZPF','FATES_BGSAPWOOD_ALLOC_SZPF',
-'FATES_BGSTRUCT_ALLOC_SZPF','FATES_AGSAPWOOD_ALLOC_SZPF','FATES_AGSTRUCT_ALLOC_SZPF',
-'FATES_STORE_ALLOC_SZPF','FATES_DDBH_SZPF','FATES_GROWTHFLUX_SZPF','FATES_GROWTHFLUX_FUSION_SZPF',
-'FATES_DDBH_CANOPY_SZPF','FATES_DDBH_USTORY_SZPF','FATES_BASALAREA_SZPF','FATES_VEGC_ABOVEGROUND_SZPF',
-'FATES_NPLANT_SZPF','FATES_NPLANT_ACPF','FATES_MORTALITY_BACKGROUND_SZPF','FATES_MORTALITY_HYDRAULIC_SZPF',
-'FATES_MORTALITY_CSTARV_SZPF','FATES_MORTALITY_IMPACT_SZPF','FATES_MORTALITY_WILDFIRE_SZPF',
-'FATES_MORTALITY_WILDFIRE_CROWN_SZPF','FATES_MORTALITY_WILDFIRE_CAMBIAL_SZPF','FATES_MORTALITY_TERMINATION_SZPF',
-'FATES_MORTALITY_LOGGING_SZPF','FATES_MORTALITY_FREEZING_SZPF','FATES_MORTALITY_SENESCENCE_SZPF',
-'FATES_MORTALITY_AGESCEN_SZPF','FATES_MORTALITY_AGESCEN_ACPF','FATES_MORTALITY_CANOPY_SZPF',
-'FATES_M3_MORTALITY_CANOPY_SZPF','FATES_M3_MORTALITY_USTORY_SZPF',
-'FATES_STOREC_CANOPY_SZPF','FATES_LEAFC_CANOPY_SZPF','FATES_LAI_CANOPY_SZPF','FATES_CROWNAREA_CANOPY_SZPF',
-'FATES_CROWNAREA_USTORY_SZPF','FATES_NPLANT_CANOPY_SZPF','FATES_MORTALITY_USTORY_SZPF','FATES_STOREC_USTORY_SZPF',
-'FATES_LEAFC_USTORY_SZPF','FATES_LAI_USTORY_SZPF','FATES_NPLANT_USTORY_SZPF','FATES_CWD_ABOVEGROUND_DC',
-'FATES_CWD_BELOWGROUND_DC','FATES_CWD_ABOVEGROUND_IN_DC','FATES_CWD_BELOWGROUND_IN_DC',
-'FATES_CWD_ABOVEGROUND_OUT_DC','FATES_CWD_BELOWGROUND_OUT_DC','FATES_YESTCANLEV_CANOPY_SZ',
-'FATES_YESTCANLEV_USTORY_SZ','FATES_VEGC_SZ','FATES_DEMOTION_RATE_SZ','FATES_PROMOTION_RATE_SZ',
-'FATES_SAI_CANOPY_SZ','FATES_M3_MORTALITY_CANOPY_SZ','FATES_M3_MORTALITY_USTORY_SZ','FATES_SAI_USTORY_SZ',
-'FATES_NPP_CANOPY_SZ','FATES_NPP_USTORY_SZ','FATES_TRIMMING_CANOPY_SZ','FATES_TRIMMING_USTORY_SZ',
-'FATES_CROWNAREA_CANOPY_SZ','FATES_CROWNAREA_USTORY_SZ','FATES_LEAFCTURN_CANOPY_SZ','FATES_FROOTCTURN_CANOPY_SZ',
-'FATES_STORECTURN_CANOPY_SZ','FATES_STRUCTCTURN_CANOPY_SZ','FATES_SAPWOODCTURN_CANOPY_SZ','FATES_SEED_PROD_CANOPY_SZ',
-'FATES_LEAF_ALLOC_CANOPY_SZ','FATES_FROOT_ALLOC_CANOPY_SZ','FATES_SAPWOOD_ALLOC_CANOPY_SZ','FATES_STRUCT_ALLOC_CANOPY_SZ',
-'FATES_SEED_ALLOC_CANOPY_SZ','FATES_STORE_ALLOC_CANOPY_SZ','FATES_LEAFCTURN_USTORY_SZ','FATES_FROOTCTURN_USTORY_SZ',
-'FATES_STORECTURN_USTORY_SZ','FATES_STRUCTCTURN_USTORY_SZ','FATES_SAPWOODCTURN_USTORY_SZ',
-'FATES_SEED_PROD_USTORY_SZ','FATES_LEAF_ALLOC_USTORY_SZ','FATES_FROOT_ALLOC_USTORY_SZ','FATES_SAPWOOD_ALLOC_USTORY_SZ',
-'FATES_STRUCT_ALLOC_USTORY_SZ','FATES_SEED_ALLOC_USTORY_SZ','FATES_STORE_ALLOC_USTORY_SZ','FATES_CROWNAREA_CANOPY_CD',
-'FATES_CROWNAREA_USTORY_CD','FATES_NPLANT_CDPF','FATES_NPLANT_CANOPY_CDPF','FATES_NPLANT_USTORY_CDPF',
-'FATES_M3_CDPF','FATES_M11_SZPF','FATES_M11_CDPF','FATES_MORTALITY_CDPF','FATES_M3_MORTALITY_CANOPY_CDPF',
-'FATES_M3_MORTALITY_USTORY_CDPF','FATES_M11_MORTALITY_CANOPY_CDPF','FATES_M11_MORTALITY_USTORY_CDPF',
-'FATES_MORTALITY_CANOPY_CDPF','FATES_MORTALITY_USTORY_CDPF','FATES_DDBH_CDPF','FATES_DDBH_CANOPY_CDPF',
-'FATES_DDBH_USTORY_CDPF','FATES_VEGC_SZPF','FATES_LEAFC_SZPF','FATES_FROOTC_SZPF','FATES_SAPWOODC_SZPF',
-'FATES_STOREC_SZPF','FATES_REPROC_SZPF','FATES_NPP_AP','FATES_GPP_AP','FATES_RDARK_USTORY_SZ',
-'FATES_LSTEMMAINTAR_USTORY_SZ','FATES_CROOTMAINTAR_USTORY_SZ','FATES_FROOTMAINTAR_USTORY_SZ','FATES_GROWAR_USTORY_SZ',
-'FATES_MAINTAR_USTORY_SZ','FATES_RDARK_CANOPY_SZ','FATES_CROOTMAINTAR_CANOPY_SZ','FATES_FROOTMAINTAR_CANOPY_SZ',
-'FATES_GROWAR_CANOPY_SZ','FATES_MAINTAR_CANOPY_SZ','FATES_LSTEMMAINTAR_CANOPY_SZ','FATES_AUTORESP_SZPF',
-'FATES_GROWAR_SZPF','FATES_MAINTAR_SZPF','FATES_RDARK_SZPF','FATES_AGSAPMAINTAR_SZPF','FATES_BGSAPMAINTAR_SZPF',
-'FATES_FROOTMAINTAR_SZPF','FATES_PARSUN_CLLL','FATES_PARSHA_CLLL','FATES_PARSUN_CLLLPF','FATES_PARSHA_CLLLPF',
-'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_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'
+hist_all_fields = .true.

cime_config/testdefs/testmods_dirs/clm/SaveHistFieldList/user_nl_clm

@@ -1 +1,3 @@
 hist_fields_list_file = .true.
+hist_wrtch4diag = .true.
+calc_human_stress_indices = 'ALL'

cime_config/testdefs/testmods_dirs/clm/all_outputs/README

@@ -0,0 +1 @@
+This test mod turns on outputting of all history fields.

cime_config/testdefs/testmods_dirs/clm/all_outputs/user_nl_clm

@@ -0,0 +1,3 @@
+calc_human_stress_indices = 'ALL'
+hist_all_fields = .true.
+hist_wrtch4diag = .true.