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Merge pull request #2662 from adrifoster/merge-master-2024-0725
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Merge master 2024 0725
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@adrifoster
adrifoster authored Jul 25, 2024
2 parents 3de6f95 + 3839e4d commit 51067b0
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2 changes: 2 additions & 0 deletions .git-blame-ignore-revs
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Expand Up @@ -36,6 +36,7 @@ e096358c832ab292ddfd22dd5878826c7c788968
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2500534eb0a83cc3aff94b30fb62e915054030bf
78d05967c2b027dc9776a884716597db6ef7f57c
47839a77229c61555e3b8932927bb54cdc511b27
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6c6f57e948bfa31e60b383536cc21663fedb8b70
9660667b1267dcd4150889f5f39db540158be74a
665cf86102e09b4c4c5a140700676dca23bc55a9
1a49e547ba3c48fa483f9ae81a8f05adcd6b888c
045d90f1d80f713eb3ae0ac58f6c2352937f1eb0
12 changes: 6 additions & 6 deletions .gitmodules
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Expand Up @@ -28,31 +28,31 @@
[submodule "fates"]
path = src/fates
url = https://github.com/NGEET/fates
fxtag = sci.1.73.0_api.35.0.0
fxtag = sci.1.77.1_api.36.0.0
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

[submodule "cism"]
path = components/cism
url = https://github.com/ESCOMP/CISM-wrapper
fxtag = cismwrap_2_2_001
fxtag = cismwrap_2_2_002
fxrequired = ToplevelRequired
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
fxDONOTUSEurl = https://github.com/ESCOMP/CISM-wrapper

[submodule "rtm"]
path = components/rtm
url = https://github.com/ESCOMP/RTM
fxtag = rtm1_0_79
fxtag = rtm1_0_80
fxrequired = ToplevelRequired
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
fxDONOTUSEurl = https://github.com/ESCOMP/RTM

[submodule "mosart"]
path = components/mosart
url = https://github.com/ESCOMP/MOSART
fxtag = mosart1_0_49
fxtag = mosart1.1.02
fxrequired = ToplevelRequired
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
fxDONOTUSEurl = https://github.com/ESCOMP/MOSART
Expand All @@ -68,7 +68,7 @@ fxDONOTUSEurl = https://github.com/ESCOMP/mizuRoute
[submodule "ccs_config"]
path = ccs_config
url = https://github.com/ESMCI/ccs_config_cesm.git
fxtag = ccs_config_cesm0.0.106
fxtag = ccs_config_cesm1.0.0
fxrequired = ToplevelRequired
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
fxDONOTUSEurl = https://github.com/ESMCI/ccs_config_cesm.git
Expand All @@ -84,7 +84,7 @@ fxDONOTUSEurl = https://github.com/ESMCI/cime
[submodule "cmeps"]
path = components/cmeps
url = https://github.com/ESCOMP/CMEPS.git
fxtag = cmeps0.14.63
fxtag = cmeps0.14.77
fxrequired = ToplevelRequired
# Standard Fork to compare to with "git fleximod test" to ensure personal forks aren't committed
fxDONOTUSEurl = https://github.com/ESCOMP/CMEPS.git
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336 changes: 303 additions & 33 deletions bld/CLMBuildNamelist.pm
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93 changes: 71 additions & 22 deletions bld/namelist_files/namelist_defaults_ctsm.xml
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Expand Up @@ -47,11 +47,13 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
<clm_accelerated_spinup>off</clm_accelerated_spinup>

<!-- Spinup state for BGC -->
<spinup_state clm_accelerated_spinup="on" use_cn=".true." >2</spinup_state>
<spinup_state clm_accelerated_spinup="on" use_cn=".true." phys="clm4_5" >1</spinup_state>
<spinup_state clm_accelerated_spinup="on" use_fates=".true." >2</spinup_state>
<spinup_state clm_accelerated_spinup="on" use_fates=".true." phys="clm4_5" >1</spinup_state>
<spinup_state clm_accelerated_spinup="off" >0</spinup_state>
<spinup_state clm_accelerated_spinup="on" use_cn=".true." use_soil_matrixcn=".false.">2</spinup_state>
<spinup_state clm_accelerated_spinup="on" use_cn=".true." phys="clm4_5" use_soil_matrixcn=".false.">1</spinup_state>
<spinup_state clm_accelerated_spinup="on" use_fates=".true." use_soil_matrixcn=".false.">2</spinup_state>
<spinup_state clm_accelerated_spinup="on" use_fates=".true." phys="clm4_5" use_soil_matrixcn=".false.">1</spinup_state>
<spinup_state clm_accelerated_spinup="sasu" >0</spinup_state>
<spinup_state use_soil_matrixcn=".true." >0</spinup_state>
<spinup_state clm_accelerated_spinup="off" >0</spinup_state>

<!-- Reseeding of dead plants normally only done for AD spinup -->
<reseed_dead_plants clm_accelerated_spinup="on" use_cn=".true.">.true.</reseed_dead_plants>
Expand All @@ -66,7 +68,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
<hist_fields_list_file>.false.</hist_fields_list_file>

<!-- In accelerated spinup mode reduce the amount of history output -->
<hist_empty_htapes clm_accelerated_spinup="on">.true.</hist_empty_htapes>
<hist_empty_htapes clm_accelerated_spinup="on" >.true.</hist_empty_htapes>
<hist_empty_htapes clm_accelerated_spinup="sasu">.true.</hist_empty_htapes>
<hist_fincl1 clm_accelerated_spinup="on" use_cn=".true." use_cndv=".true."
>'TOTECOSYSC','TOTECOSYSN','TOTSOMC','TOTSOMN','TOTVEGC','TOTVEGN','TLAI','GPP','NPP','TWS','TSAI','HTOP','HBOT'</hist_fincl1>
<hist_fincl1 clm_accelerated_spinup="on" use_cn=".true."
Expand All @@ -75,8 +78,18 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
>'TOTSOMC','TOTSOMN','TLAI','GPP','NPP','TWS'</hist_fincl1>
<hist_fincl1 clm_accelerated_spinup="on" use_cn=".false."
>'TLAI','TWS'</hist_fincl1>
<hist_nhtfrq clm_accelerated_spinup="on">-8760</hist_nhtfrq>
<hist_mfilt clm_accelerated_spinup="on">20</hist_mfilt>
<hist_fincl1 clm_accelerated_spinup="sasu" use_cn=".true." use_cndv=".true."
>'TOTECOSYSC','TOTECOSYSN','TOTSOMC','TOTSOMN','TOTVEGC','TOTVEGN','TLAI','GPP','NPP','TWS','TSAI','HTOP','HBOT'</hist_fincl1>
<hist_fincl1 clm_accelerated_spinup="sasu" use_cn=".true."
>'TOTECOSYSC','TOTECOSYSN','TOTSOMC','TOTSOMN','TOTVEGC','TOTVEGN','TLAI','GPP','CPOOL','NPP','TWS'</hist_fincl1>
<hist_fincl1 clm_accelerated_spinup="sasu" use_fates=".true."
>'TOTSOMC','TOTSOMN','TLAI','GPP','NPP','TWS'</hist_fincl1>
<hist_fincl1 clm_accelerated_spinup="sasu" use_cn=".false."
>'TLAI','TWS'</hist_fincl1>
<hist_nhtfrq clm_accelerated_spinup="on" >-8760</hist_nhtfrq>
<hist_nhtfrq clm_accelerated_spinup="sasu">-8760</hist_nhtfrq>
<hist_mfilt clm_accelerated_spinup="on" >20</hist_mfilt>
<hist_mfilt clm_accelerated_spinup="sasu">20</hist_mfilt>

<!-- Root and stem acclimation (could depend on the physics version) -->
<rootstem_acc >.false.</rootstem_acc>
Expand Down Expand Up @@ -124,9 +137,10 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
<crop_fsat_equals_zero>.false.</crop_fsat_equals_zero>

<!-- MEGAN model -->
<megan >1</megan>
<megan clm_accelerated_spinup="on" >0</megan>
<megan configuration="nwp" >0</megan>
<megan >1</megan>
<megan clm_accelerated_spinup="on" >0</megan>
<megan clm_accelerated_spinup="sasu">0</megan>
<megan configuration="nwp" >0</megan>

<!-- Supplmental Nitrogen mode -->
<suplnitro use_cn=".true." >NONE</suplnitro>
Expand Down Expand Up @@ -499,7 +513,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
<!-- FATES default parameter file -->
<!-- ================================================================== -->

<fates_paramfile>lnd/clm2/paramdata/fates_params_api.35.0.0_12pft_c240326.nc</fates_paramfile>
<fates_paramfile>lnd/clm2/paramdata/fates_params_api.36.0.0_12pft_c240517.nc</fates_paramfile>

<!-- ================================================================== -->
<!-- Default surface roughness parameterization -->
Expand Down Expand Up @@ -611,13 +625,36 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
<hillslope_pft_distribution_method >Standard</hillslope_pft_distribution_method>
<hillslope_soil_profile_method >Uniform</hillslope_soil_profile_method>
<downscale_hillslope_meteorology >.true.</downscale_hillslope_meteorology>
<hillslope_fsat_equals_zero >.true.</hillslope_fsat_equals_zero>
<hillslope_fsat_equals_zero>.false.</hillslope_fsat_equals_zero>
<hillslope_fsat_equals_zero use_hillslope=".true.">.true.</hillslope_fsat_equals_zero>

<!-- Plant hydraulic stress -->
<use_hydrstress >.false.</use_hydrstress>
<use_hydrstress use_fates=".false." configuration="clm">.true.</use_hydrstress>
<use_hydrstress phys="clm4_5" use_fates=".false." configuration="clm">.false.</use_hydrstress>


<!-- CN Matrix options -->
<use_matrixcn>.false.</use_matrixcn>
<use_matrixcn clm_accelerated_spinup="sasu" use_fates=".false." bgc_mode="bgc" >.true.</use_matrixcn>

<use_soil_matrixcn>.false.</use_soil_matrixcn>
<use_soil_matrixcn clm_accelerated_spinup="sasu" use_fates=".false." soil_decomp_method="CENTURYKoven2013" >.true.</use_soil_matrixcn>

<hist_wrt_matrixcn_diag clm_accelerated_spinup="on" >.false.</hist_wrt_matrixcn_diag>
<hist_wrt_matrixcn_diag clm_accelerated_spinup="sasu" >.false.</hist_wrt_matrixcn_diag>
<hist_wrt_matrixcn_diag clm_accelerated_spinup="off" >.false.</hist_wrt_matrixcn_diag>
<spinup_matrixcn clm_accelerated_spinup="on" use_soil_matrixcn=".true.">.true.</spinup_matrixcn>
<spinup_matrixcn clm_accelerated_spinup="sasu" use_soil_matrixcn=".true.">.true.</spinup_matrixcn>
<spinup_matrixcn clm_accelerated_spinup="off" >.false.</spinup_matrixcn>
<nyr_forcing >1</nyr_forcing>
<nyr_forcing spinup_matrixcn=".true." use_soil_matrixcn=".true.">20</nyr_forcing>
<!-- for SASU spinup nyr_sasu will normally be set to nyr_forcing (slow mode spinup) -->
<nyr_sasu >1</nyr_sasu>
<iloop_avg >-999</iloop_avg>
<iloop_avg spinup_matrixcn=".true." use_soil_matrixcn=".true.">-999</iloop_avg>


<!-- General CN options -->
<!-- Turn this on all of the time, eventually this namelist item should be removed -->
<dribble_crophrv_xsmrpool_2atm use_crop=".true.">.true.</dribble_crophrv_xsmrpool_2atm>
Expand Down Expand Up @@ -1298,7 +1335,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
ic_ymd="20110101" sim_year="2000" do_transient_pfts=".false."
ic_tod="0" glc_nec="10" use_crop=".true." irrigate=".true."
lnd_tuning_mode="clm6_0_GSWP3v1"
>lnd/clm2/initdata_esmf/ctsm5.2/clmi.I2000Clm50BgcCrop.2011-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c240223.nc
>lnd/clm2/initdata_esmf/ctsm5.2/clmi.I2000Clm52BgcCrop.2000-01-01.1.9x2.5_gx1v7_gl4_simyr2000_c240515.nc
</finidat>


Expand Down Expand Up @@ -2013,14 +2050,17 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c
<!-- SSP5-RCP3.4 - relative to {csmdata}) -->
<!--- currently empty until needed, we can't test because of lack of ndep files for this SSP -->

<!-- Land Use Harmonization unified data sets for dynamic FATES land use change -->
<!-- Land Use Harmonization unified timeseries data sets for dynamic FATES land use change -->

<fluh_timeseries hgrid="4x5" sim_year_range="1850-2000" use_fates=".true."
>lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1850-2015_c231101.nc</fluh_timeseries>

<!-- Land Use Harmonization static landuse x pft mapping data sets for FATES land use change -->
<flandusepftdat hgrid="4x5" use_fates=".true." >lnd/clm2/surfdata_map/fates-sci.1.77.0_api.36.0.0/fates_landuse_pft_map_4x5_240206.nc</flandusepftdat>

<!-- This one is just for testing until Issue #2304 is resolved -->
<fluh_timeseries hgrid="4x5" sim_year_range="constant" use_fates=".true."
>lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr1850-2015_c231101.nc</fluh_timeseries>
>lnd/clm2/surfdata_map/fates-sci.1.68.3_api.31.0.0_tools.1.0.1/LUH2_states_transitions_management.timeseries_4x5_hist_simyr0850-2015_c240216.nc</fluh_timeseries>

<!-- Fixation and Uptake of Nitrogen Model (FUN2.0) -->
<use_fun >.false.</use_fun>
Expand Down Expand Up @@ -2514,22 +2554,31 @@ lnd/clm2/surfdata_esmf/NEON/surfdata_1x1_NEON_TOOL_hist_78pfts_CMIP6_simyr2000_c

<!-- ===== FATES DEFAULTS =========== -->
<fates_spitfire_mode use_fates=".true.">0</fates_spitfire_mode>
<fates_harvest_mode use_fates=".true.">no_harvest</fates_harvest_mode>
<use_fates_planthydro use_fates=".true.">.false.</use_fates_planthydro>
<use_fates_tree_damage use_fates=".true.">.false.</use_fates_tree_damage>
<use_fates_cohort_age_tracking use_fates=".true.">.false.</use_fates_cohort_age_tracking>
<use_fates_ed_st3 use_fates=".true.">.false.</use_fates_ed_st3>
<use_fates_ed_prescribed_phys use_fates=".true.">.false.</use_fates_ed_prescribed_phys>
<use_fates_logging use_fates=".true.">.false.</use_fates_logging>
<use_fates_inventory_init use_fates=".true.">.false.</use_fates_inventory_init>
<use_fates_sp use_fates=".true.">.false.</use_fates_sp>
<use_fates_luh use_fates=".true.">.false.</use_fates_luh>
<use_fates_lupft use_fates=".true.">.false.</use_fates_lupft>
<use_fates_potentialveg use_fates=".true.">.false.</use_fates_potentialveg>
<use_fates_luh use_fates=".true." fates_harvest_mode="luhdata_area" >.true.</use_fates_luh>
<use_fates_luh use_fates=".true." fates_harvest_mode="luhdata_mass" >.true.</use_fates_luh>
<use_fates_luh use_fates=".true." use_fates_lupft=".true.">.true.</use_fates_luh>
<use_fates_luh use_fates=".true." use_fates_potentialveg=".true.">.true.</use_fates_luh>
<use_fates_luh use_fates=".true." >.false.</use_fates_luh>
<fates_parteh_mode use_fates=".true.">1</fates_parteh_mode>
<fates_seeddisp_cadence use_fates=".true.">0</fates_seeddisp_cadence>
<use_fates_nocomp use_fates=".true." use_fates_sp=".true." >.true.</use_fates_nocomp>
<use_fates_nocomp use_fates=".true." use_fates_lupft=".true.">.true.</use_fates_nocomp>
<use_fates_nocomp use_fates=".true." >.false.</use_fates_nocomp>
<use_fates_fixed_biogeog use_fates=".true." use_fates_sp=".true." >.true.</use_fates_fixed_biogeog>
<use_fates_fixed_biogeog use_fates=".true." use_fates_lupft=".true.">.true.</use_fates_fixed_biogeog>
<use_fates_fixed_biogeog use_fates=".true." >.false.</use_fates_fixed_biogeog>
<fates_history_dimlevel use_fates=".true.">2,2</fates_history_dimlevel>
<use_fates_nocomp use_fates=".true." use_fates_sp=".true.">.true.</use_fates_nocomp>
<use_fates_nocomp use_fates=".true." >.false.</use_fates_nocomp>
<use_fates_fixed_biogeog use_fates=".true." use_fates_sp=".true.">.true.</use_fates_fixed_biogeog>
<use_fates_fixed_biogeog use_fates=".true." >.false.</use_fates_fixed_biogeog>


<!-- ========================================= -->
<!-- Defaults for dynamic subgrid -->
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