Merge tag 'ctsm5.1.dev147' into zerothtstep

Add sowing window input files Previously, one could run crops with either (a) sowing windows defined by the hemisphere-specific start and end dates on the paramfile or (b) prescribed sowing dates specified by input file stream_fldFileName_sdate. This PR replaces the latter with two new input files, stream_fldFileName_swindow_start and stream_fldFileName_swindow_end.
olyson · Nov 1, 2023 · d5b007f · d5b007f
2 parents 0dfd901 + abc3c27
commit d5b007f
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diff --git a/.git-blame-ignore-revs b/.git-blame-ignore-revs
@@ -1,4 +1,5 @@
 # Ran python directory through black python formatter
+d229b5c6689efc4c2a6cef077515c4ccd5c18ff6
 4cd83cb3ee6d85eb909403487abf5eeaf4d98911
 0aa2957c1f8603c63fa30b11295c06cfddff44a5
 2cdb380febb274478e84cd90945aee93f29fa2e6
@@ -7,3 +8,14 @@ e44dc469439e02e9ee582dab274d890ebdfab104
 b88e1cd1b28e3609684c79a2ec0e88f26cfc362b
 51c102c5df2e0ef971b5f8eeeb477567899af63a
 7dacad70e74e2ec97f6492d4e7a3cb5dd498bcd7
+b771971e3299c4fa56534b93421f7a2b9c7282fd
+9de88bb57ea9855da408cbec1dc8acb9079eda47
+8bc4688e52ea23ef688e283698f70a44388373eb
+0a5a9e803b56ec1bbd6232eff1c99dbbeef25eb7
+810cb346f05ac1aabfff931ab1a2b7b584add241
+5933b0018f8e29413e30dda9b906370d147bad45
+# Ran SystemTests and python/ctsm through black python formatter
+5364ad66eaceb55dde2d3d598fe4ce37ac83a93c
+8056ae649c1b37f5e10aaaac79005d6e3a8b2380
+540b256d1f3382f4619d7b0877c32d54ce5c40b6
+8a168bb0895f4f2421608dd2589398e13a6663e6
diff --git a/.github/workflows/black.yml b/.github/workflows/black.yml
@@ -16,6 +16,22 @@ jobs:
              # Use options and version identical to the conda environment
              # Using pyproject.toml makes sure this testing is consistent with our python directory testing
              options: "--check --config python/pyproject.toml"
-             src:     "./python"
+             src: "./python"
              # Version should be coordinated with the ctsm_pylib conda environment under the python directory
              version: "22.3.0"
+          # Actions identical to above for each directory and source file we need to check (arrays aren't allowed for src: field)
+        - uses: psf/black@stable
+          with:
+             options: "--check --config python/pyproject.toml"
+             src: "./cime_config/SystemTests"
+             version: "22.3.0"
+        - uses: psf/black@stable
+          with:
+             options: "--check --config python/pyproject.toml"
+             src: "./cime_config/buildlib"
+             version: "22.3.0"
+        - uses: psf/black@stable
+          with:
+             options: "--check --config python/pyproject.toml"
+             src: "./cime_config/buildnml"
+             version: "22.3.0"
diff --git a/Externals.cfg b/Externals.cfg
@@ -34,7 +34,7 @@ hash = 34723c2
 required = True
 
 [ccs_config]
-tag = ccs_config_cesm0.0.64
+tag = ccs_config_cesm0.0.65
 protocol = git
 repo_url = https://github.com/ESMCI/ccs_config_cesm.git
 local_path = ccs_config
@@ -44,7 +44,7 @@ required = True
 local_path = cime
 protocol = git
 repo_url = https://github.com/ESMCI/cime
-tag = cime6.0.108
+tag = cime6.0.125
 required = True
 
 [cmeps]

diff --git a/Externals_CLM.cfg b/Externals_CLM.cfg
@@ -2,7 +2,7 @@
 local_path = src/fates
 protocol = git
 repo_url = https://github.com/NGEET/fates
-tag = sci.1.65.3_api.25.4.0
+tag = sci.1.68.0_api.28.0.0
 required = True
 
 [externals_description]

diff --git a/bld/CLMBuildNamelist.pm b/bld/CLMBuildNamelist.pm
diff --git a/bld/namelist_files/namelist_defaults_ctsm.xml b/bld/namelist_files/namelist_defaults_ctsm.xml
@@ -67,8 +67,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <for_testing_use_repr_structure_pool>.false.</for_testing_use_repr_structure_pool>
 <for_testing_no_crop_seed_replenishment>.false.</for_testing_no_crop_seed_replenishment>
 
-<!-- Set to .true. in namelist to write hist fields master list file -->
-<hist_master_list_file>.false.</hist_master_list_file>
+<!-- Set to .true. in namelist to write file with all history fields -->
+<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>
@@ -146,7 +146,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <!-- Supplmental Nitrogen mode -->
 <suplnitro use_cn=".true." >NONE</suplnitro>
-<suplnitro use_fates=".true." >NONE</suplnitro>
+<suplnitro use_fates=".true." >ALL</suplnitro>
 
 <!-- Albedo for glaciers -->
 <albice phys="clm5_1" >0.50,0.30</albice>
@@ -213,7 +213,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <zetamaxstable               use_biomass_heat_storage=".true." >2.0d00</zetamaxstable>
 <zetamaxstable phys="clm4_5"                                   >2.0d00</zetamaxstable>
 <zetamaxstable phys="clm5_0"                                   >0.5d00</zetamaxstable>
-<zetamaxstable phys="clm5_1"                                   >0.5d00</zetamaxstable>
+<zetamaxstable phys="clm5_1" z0param_method="ZengWang2007" >0.5d00</zetamaxstable>
+<zetamaxstable phys="clm5_1" z0param_method="Meier2022" >2.0d00</zetamaxstable>
 
 <!-- atm2lnd defaults -->
 <repartition_rain_snow phys="clm5_1" >.true.</repartition_rain_snow>
@@ -324,6 +325,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <itmax_canopy_fluxes structure="standard">40</itmax_canopy_fluxes>
 <itmax_canopy_fluxes structure="fast"    >3</itmax_canopy_fluxes>
 
+
 <!-- Canopy hydrology namelist defaults -->
 <use_clm5_fpi                 phys="clm5_1" >.true.</use_clm5_fpi>
 <interception_fraction        phys="clm5_1" >1.0</interception_fraction>
@@ -493,7 +495,16 @@ 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.25.4.0_12pft_c230327.nc</fates_paramfile>
+<fates_paramfile>lnd/clm2/paramdata/fates_params_api.25.5.0_12pft_c230628.nc</fates_paramfile>
+
+<!-- ================================================================== -->
+<!-- Default surface roughness parameterization                         -->
+<!-- ================================================================== -->
+
+<z0param_method>ZengWang2007</z0param_method>
+
+<use_z0m_snowmelt z0param_method="Meier2022" >.true.</use_z0m_snowmelt>
+<use_z0m_snowmelt >.false.</use_z0m_snowmelt>
 
 <!-- ========================================================================================  -->
 <!-- clm 5.0 BGC nitrogen model                                                                -->
@@ -510,6 +521,7 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <use_luna phys="clm5_0"  >.true.</use_luna>
 <use_luna phys="clm5_0"  use_fates=".true." >.false.</use_luna>
 <use_luna phys="clm4_5"  >.false.</use_luna>
+<use_luna phys="clm4_5"  use_fates=".true." >.false.</use_luna>
 
 <!-- Flexible CN options -->
 <MM_Nuptake_opt             use_flexibleCN=".true." >.true.</MM_Nuptake_opt>
@@ -562,6 +574,8 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 <min_critical_dayl_method         use_cn=".true." phys="clm5_1" >DependsOnLat</min_critical_dayl_method>
 <onset_thresh_depends_on_veg                                    >.false.</onset_thresh_depends_on_veg>
 <min_critical_dayl_method                                       >Constant</min_critical_dayl_method>
+<generate_crop_gdds                                             >.false.</generate_crop_gdds>
+<use_mxmat                                                      >.true.</use_mxmat>
 
 <!-- use additional stress deciduous onset trigger    -->
 <constrain_stress_deciduous_onset phys="clm4_5" >.false.</constrain_stress_deciduous_onset>
@@ -1126,6 +1140,8 @@ lnd/clm2/surfdata_map/release-clm5.0.30/surfdata_C24_hist_78pfts_CMIP6_simyr2000
 lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_0.9x1.25_hist_78pfts_CMIP6_simyr2000_c190214.nc</fsurdat>
 <fsurdat hgrid="1.9x2.5"   sim_year="2000" use_crop=".true." use_vichydro=".false.">
 lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_1.9x2.5_hist_78pfts_CMIP6_simyr2000_c190304.nc</fsurdat>
+<fsurdat hgrid="hcru_hcru"   sim_year="2000">
+lnd/clm2/surfdata_map/release-clm5.0.18/surfdata_360x720cru_78pfts_CMIP6_simyr2000_c170824.nc</fsurdat>
 <fsurdat hgrid="0.125x0.125"  sim_year="2000" use_crop=".true." >
 lnd/clm2/surfdata_map/release-clm5.0.24/surfdata_0.125x0.125_hist_78pfts_CMIP6_simyr2005_c190624.nc</fsurdat>
 <fsurdat hgrid="10x15"     sim_year="2000" use_crop=".true." use_vichydro=".false.">
@@ -1539,8 +1555,24 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
 
 <!-- SNICAR (SNow, ICe, and Aerosol Radiative model) datasets -->
 <!--  ***********  Resolution independent:   ***********  -->
-<fsnowoptics >lnd/clm2/snicardata/snicar_optics_5bnd_c090915.nc</fsnowoptics>
-<fsnowaging  >lnd/clm2/snicardata/snicar_drdt_bst_fit_60_c070416.nc</fsnowaging>
+<fsnowaging>lnd/clm2/snicardata/snicar_drdt_bst_fit_60_c070416.nc</fsnowaging>
+
+<snicar_numrad_snw>5</snicar_numrad_snw>
+
+<fsnowoptics snicar_numrad_snw="480">lnd/clm2/snicardata/snicar_optics_480bnd_c012422.nc</fsnowoptics>
+<fsnowoptics snicar_numrad_snw="5"  >lnd/clm2/snicardata/snicar_optics_5bnd_c013122.nc</fsnowoptics>
+
+<snicar_snw_shape phys="clm5_1">hexagonal_plate</snicar_snw_shape>
+<snicar_snw_shape phys="clm5_0">sphere</snicar_snw_shape>
+<snicar_snw_shape phys="clm4_5">sphere</snicar_snw_shape>
+
+<use_snicar_frc>.false.</use_snicar_frc>
+<snicar_solarspec    >mid_latitude_winter</snicar_solarspec>
+<snicar_dust_optics  >sahara</snicar_dust_optics>
+<snicar_snodst_intmix>.false.</snicar_snodst_intmix>
+<snicar_snobc_intmix >.false.</snicar_snobc_intmix>
+<snicar_use_aerosol  >.true.</snicar_use_aerosol>
+<do_sno_oc           >.false.</do_sno_oc>
 
 <!-- Nitrogen deposition streams namelist defaults -->
 <stream_year_first_ndep phys="clm4_5"  use_cn=".true." sim_year_range="1850-2100"  >2015</stream_year_first_ndep>
@@ -1665,10 +1697,16 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
 <lai_mapalgo  hgrid="1x1_asphaltjungleNJ" >nn</lai_mapalgo>
 <lai_mapalgo  hgrid="5x5_amazon"          >nn</lai_mapalgo>
 
+<!-- crop calendar streams namelist defaults -->
+<stream_year_first_cropcal  >1850</stream_year_first_cropcal>
+<stream_year_last_cropcal   >2100</stream_year_last_cropcal>
+<model_year_align_cropcal   >1850</model_year_align_cropcal>
+
 <!-- lightning streams namelist defaults -->
 
 <light_res    use_cn=".false."                     >none</light_res>
 <light_res    use_cn=".true." fire_method="nofire" >none</light_res>
+<light_res    use_cn=".true." neon=".true."        >106x174</light_res>
 <light_res    use_cn=".true." phys="clm4_5"        >94x192</light_res>
 <light_res    use_cn=".true." phys="clm5_0"        >94x192</light_res>
 <light_res    use_cn=".true." phys="clm5_1"        >360x720</light_res>
@@ -1679,12 +1717,18 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
 <light_res    use_fates=".true." fates_spitfire_mode="3" >360x720</light_res>
 <light_res    use_fates=".true." fates_spitfire_mode="4" >360x720</light_res>
 <light_res    use_fates=".true." fates_spitfire_mode="5" >360x720</light_res>
+<light_res    use_fates=".true." fates_spitfire_mode="2" neon=".true.">106x174</light_res>
+<light_res    use_fates=".true." fates_spitfire_mode="3" neon=".true.">106x174</light_res>
+<light_res    use_fates=".true." fates_spitfire_mode="4" neon=".true.">106x174</light_res>
+<light_res    use_fates=".true." fates_spitfire_mode="5" neon=".true.">106x174</light_res>
 
 <stream_year_first_lightng >0001</stream_year_first_lightng>
 <stream_year_last_lightng  >0001</stream_year_last_lightng>
 
 <stream_fldfilename_lightng hgrid="94x192"    >atm/datm7/NASA_LIS/clmforc.Li_2012_climo1995-2011.T62.lnfm_Total_c140423.nc</stream_fldfilename_lightng>
 <stream_meshfile_lightng    hgrid="94x192"    >atm/datm7/NASA_LIS/clmforc.Li_2012_climo1995-2011.T62_ESMFmesh_cdf5_110621.nc</stream_meshfile_lightng>
+<stream_fldfilename_lightng hgrid="106x174"   >atm/datm7/NASA_LIS/clmforc.Li_2016_climo1995-2013.360x720.lnfm_Total_NEONarea_c210625.nc</stream_fldfilename_lightng>
+<stream_meshfile_lightng    hgrid="106x174"   >atm/datm7/NASA_LIS/ESMF_MESH.Li_2016.360x720.NEONarea_cdf5_c221104.nc</stream_meshfile_lightng>
 <stream_fldfilename_lightng hgrid="360x720"   >atm/datm7/NASA_LIS/clmforc.Li_2016_climo1995-2013.360x720.lnfm_Total_c160825.nc</stream_fldfilename_lightng>
 <stream_meshfile_lightng    hgrid="360x720"   >atm/datm7/NASA_LIS/clmforc.Li_2016_climo1995-2013.360x720_ESMFmesh_cdf5_150621.nc</stream_meshfile_lightng>
 
@@ -2670,6 +2714,7 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
 <use_fates_inventory_init      use_fates=".true.">.false.</use_fates_inventory_init>
 <use_fates_sp                  use_fates=".true.">.false.</use_fates_sp>
 <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."                      >.false.</use_fates_nocomp>
@@ -2699,4 +2744,14 @@ use_crop=".true.">lnd/clm2/surfdata_map/ctsm5.1.dev052/landuse.timeseries_mpasa1
 
 <init_interp_method>general</init_interp_method>
 
+<!-- =========================================  -->
+<!-- Defaults for excess ice                    -->
+<!-- =========================================  -->
+
+<use_excess_ice>.false.</use_excess_ice>
+
+<stream_fldfilename_exice use_excess_ice=".true.">lnd/clm2/paramdata/exice_init_0.125x0.125_c20220516.nc</stream_fldfilename_exice>
+<stream_meshfile_exice    use_excess_ice=".true.">lnd/clm2/paramdata/exice_init_0.125x0.125_ESMFmesh_cdf5_c20220802.nc</stream_meshfile_exice>
+<stream_mapalgo_exice     use_excess_ice=".true.">bilinear</stream_mapalgo_exice>
+
 </namelist_defaults>