Merge tag 'ctsm5.1.dev142' into hillslope_hydrology-ssr

b4b changes to Python scripts, history lists, tech note, and clm_time_manager. * Add system and unit tests for making fsurdat with all crops everywhere (ESCOMP#2081) * Rework master_list* files etc. (ESCOMP#2087) * Fixes to methane Tech Note (ESCOMP#2091) * Add is_doy_in_interval() function (ESCOMP#2158) * Avoid using subprocess.run() in FSURDATMODIFYCTSM (ESCOMP#2125) Closes issues: * Add unit test for making fsurdat with all crops everywhere (ESCOMP#2079) * Rework master_list_(no)?fates.rst? (ESCOMP#2083) * conda run -n can fail if a conda environment is already active (ESCOMP#2109) * conda fails to load for SystemTests (ESCOMP#2111)
samsrabin · Oct 4, 2023 · 595d95d · 595d95d
2 parents 5924c68 + 2e2434d
commit 595d95d
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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.1.66.1_api.25.5.0
+tag = sci.1.67.2_api.27.0.0
 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>
@@ -495,6 +497,15 @@ attributes from the config_cache.xml file (with keys converted to upper-case).
 
 <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>
@@ -1138,6 +1152,8 @@ 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.">
@@ -1677,6 +1693,11 @@ 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>
@@ -2718,4 +2739,14 @@ 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>
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -799,9 +799,9 @@ SNICAR (SNow, ICe, and Aerosol Radiative model) optical data file name
 SNICAR (SNow, ICe, and Aerosol Radiative model) snow aging data file name
 </entry>
 
-<entry id="hist_master_list_file" type="logical" category="history"
+<entry id="hist_fields_list_file" type="logical" category="history"
        group="clm_inparm" valid_values="" value=".false.">
-If TRUE, write master field list to separate file for documentation purposes
+If TRUE, write list of all output fields to separate file for documentation purposes
 </entry>
 
 <entry id="hist_avgflag_pertape" type="char*10(10)" category="history"
@@ -1125,20 +1125,20 @@ Toggle to turn on the 1-year grain product pool in the crop model
 </entry>
 
 <entry id="baset_mapping" type="char*20" category="physics"
-       group="crop" valid_values="constant,varytropicsbylat" value="constant">
+       group="crop_inparm" valid_values="constant,varytropicsbylat" value="constant">
 Type of mapping to use for base temperature for prognostic crop model
 constant = Just use baset from the PFT parameter file
 varytropicsbylat = Vary the tropics by latitude 
 </entry>
 
 <entry id="baset_latvary_slope" type="real" category="physics"
-       group="crop" valid_values="" value="0.4d00">
+       group="crop_inparm" valid_values="" value="0.4d00">
 Only used when baset_mapping == varytropicsbylat
 Slope with latitude in degrees to vary tropical baset by
 </entry>
 
 <entry id="baset_latvary_intercept" type="real" category="physics"
-       group="crop" valid_values="" value="12.0d00">
+       group="crop_inparm" valid_values="" value="12.0d00">
 Only used when baset_mapping == varytropicsbylat
 Intercept at zero latitude to add to baset from the PFT parameter file
 </entry>
@@ -1164,6 +1164,16 @@ Phenology onset depends on the vegetation type
 (only used when CN is on)
 </entry>
 
+<entry id="generate_crop_gdds" type="logical" category="physics"
+        group="cnphenology" valid_values="" value=".false.">
+Set to .true. in order to override crop harvesting logic and to instead harvest the day before the next sowing date. Used to generate growing-degree day outputs that can be used with an external script to generate new GDD requirement ("cultivar") files.
+</entry>
+
+<entry id="use_mxmat" type="logical" category="physics"
+        group="cnphenology" valid_values="" value=".true.">
+Set to .false. in order to ignore crop PFT parameter for maximum growing season length (mxmat). Must be set to .false. when generate_crop_gdds is .true.
+</entry>
+
 <entry id="min_critical_dayl_method" type="char*25" category="physics"
        group="cnphenology" valid_values="Constant,DependsOnLat,DependsOnVeg,DependsOnLatAndVeg">
 Method for determining what the minimum critical day length for seasonal decidious leaf offset depends on
@@ -1840,6 +1850,41 @@ Mapping method from LAI input file to the model resolution
     copy     = copy using the same indices
 </entry>
 
+<!-- ========================================================================================  -->
+<!-- cropcal_streams streams Namelist                                                          -->
+<!-- ========================================================================================  -->
+
+<!-- Crop calendars -->
+<entry id="stream_year_first_cropcal" type="integer" category="datasets"
+       group="cropcal_streams" valid_values="" >
+First year to loop over for crop calendar data
+</entry>
+
+<entry id="stream_year_last_cropcal" type="integer" category="datasets"
+       group="cropcal_streams" valid_values="" >
+Last year to loop over for crop calendar data
+</entry>
+
+<entry id="model_year_align_cropcal" type="integer" category="datasets"
+       group="cropcal_streams" valid_values="" >
+Simulation year that aligns with stream_year_first_cropcal value
+</entry>
+
+<entry id="stream_fldfilename_sdate" type="char*256(30)" category="datasets"
+       input_pathname="abs" group="cropcal_streams" valid_values="" >
+Filename of input stream data for sowing dates
+</entry>
+
+<entry id="stream_fldfilename_cultivar_gdds" type="char*256(30)" category="datasets"
+       input_pathname="abs" group="cropcal_streams" valid_values="" >
+Filename of input stream data for cultivar growing degree-day targets
+</entry>
+
+<entry id="stream_meshfile_cropcal" type="char*256" category="datasets"
+       input_pathname="abs" group="cropcal_streams" valid_values="" >
+Filename of input stream data for crop calendar inputs
+</entry>
+
 <!-- ========================================================================================  -->
 <!-- light_streams streams Namelist (when CN an CLM4_5 is active)                              -->
 <!-- ========================================================================================  -->
@@ -2778,6 +2823,24 @@ the related bulk quantities.
 If .true., run with water isotopes
 </entry>  
 
+<!-- ========================================================================================  -->
+<!-- Namelist options related to surface roughness                                             -->
+<!-- ========================================================================================  -->
+
+<entry id="z0param_method" type="char*64" category="clm_physics"
+       group="clm_inparm" valid_values="ZengWang2007,Meier2022" >
+Parameterization/parameters to use for surface roughness
+ZengWang2007: Zeng and Wang 2007
+Meier2022: Meier et al. in prep. 2022
+</entry>
+
+<entry id="use_z0m_snowmelt" type="logical" category="clm_physics"
+       group="clm_inparm" valid_values="" >
+If FALSE use constant snow z0m
+If TRUE use parameterization of snow z0m as a function of accumulated
+snow melt of Brock et al. (2006)
+</entry>
+
 <!-- ========================================================================================  -->
 <!-- Namelist options related to initInterp                                                    -->
 <!-- ========================================================================================  -->
@@ -2832,4 +2895,38 @@ use case.)
 
 </entry>
 
+<!-- ========================================================================================  -->
+<!-- Namelist options related to excess ice                                                    -->
+<!-- ========================================================================================  -->
+<entry id="use_excess_ice" type="logical" category="clm_physics"
+        group="clm_inparm" valid_values="" >
+If TRUE turn on the excess ice physics, (Lee et al., 2014; Cai et al., 2020)
+</entry>
+
+<entry id="use_excess_ice_streams" type="logical" category="clm_physics"
+        group="exice_streams" valid_values="" >
+If TRUE and use_excess_ice is TRUE, use the excess ice stream to determine the initial values of the excess ice field
+if FALSE and use_excess_ice is TRUE, expect excess ice to come from the initial conditions or restart file
+Expect to be FALSE is use_excess_ice is FALSE
+</entry>
+
+<entry id="stream_fldfilename_exice" type="char*256(30)" category="datasets"
+       input_pathname="abs" group="exice_streams" valid_values="" >
+Filename of input stream data for excess ice data
+</entry>
+
+<entry id="stream_meshfile_exice" type="char*256" category="datasets"
+       input_pathname="abs" group="exice_streams" valid_values="" >
+mesh filename of input stream data for excess ice
+</entry>
+
+<entry id="stream_mapalgo_exice" type="char*256" category="datasets"
+       group="exice_streams" valid_values="bilinear,nn,none" >
+Mapping method from excess ice input stream data to the model resolution
+    bilinear = bilinear interpolation
+    nn       = nearest neighbor
+    none     = no interpolation
+</entry>
+
+
 </namelist_definition>