Merge tag 'ctsm5.1.dev143' into CESM3_dev

Zeroing of wood product fluxes on fates columns products are otherwise zero'd in a p2c() routine that is incompatible with fates. When wood product fluxes become available via fates, these routines will be updated. These fluxes were previously left as uninitialized, which was causing math issues on some compilers. Conflicts: bld/namelist_files/namelist_defaults_ctsm.xml test/tools/input_tests_master
ekluzek · Oct 16, 2023 · 62b63c3 · 62b63c3
2 parents e8dd1eb + 2aa34fe
commit 62b63c3
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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]
@@ -55,7 +55,7 @@ local_path = components/cmeps
 required = True
 
 [cdeps]
-tag = cdeps1.0.9
+tag = cdeps1.0.13
 protocol = git
 repo_url = https://github.com/ESCOMP/CDEPS.git
 local_path = components/cdeps

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.1.67.2_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
diff --git a/bld/namelist_files/namelist_definition_ctsm.xml b/bld/namelist_files/namelist_definition_ctsm.xml
@@ -764,9 +764,9 @@ 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"
@@ -1090,20 +1090,20 @@ 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>
@@ -1129,6 +1129,16 @@ 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
@@ -1813,6 +1823,41 @@ 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)                              -->
 <!-- ========================================================================================  -->
@@ -2000,9 +2045,9 @@ to use for methane model
 </entry>
 
 <entry id="light_res" type="char*10" category="default_settings"
-       group="default_settings" valid_values="none,360x720,94x192">
-Resolution of Lightning dataset to use for CN fire model
-(only applies when CN and the CN fire model are turned on)
+       group="default_settings" valid_values="none,360x720,106x174,94x192">
+Resolution of Lightning dataset to use for CN or FATES fire model
+(only applies when CN or FATES and the fire model is turned on)
 </entry>
 
 <entry id="chk_res" type="integer"  category="default_settings"
@@ -2028,7 +2073,7 @@ CLM run type.
 
 <entry id="res" type="char*30" category="default_settings"
        group="default_settings"  
-       valid_values="512x1024,360x720cru,128x256,64x128,48x96,94x192,0.23x0.31,0.47x0.63,0.9x1.25,1.9x2.5,2.5x3.33,4x5,10x15,0.125nldas2,5x5_amazon,1x1_vancouverCAN,1x1_mexicocityMEX,1x1_asphaltjungleNJ,1x1_brazil,1x1_urbanc_alpha,1x1_numaIA,1x1_smallvilleIA,0.25x0.25,0.5x0.5,3x3min,5x5min,10x10min,0.33x0.33,0.125x0.125,ne4np4,ne16np4,ne30np4.pg2,ne30np4.pg3,ne30np4,ne60np4,ne120np4,ne120np4.pg2,ne120np4.pg3,ne0np4CONUS.ne30x8,ne0np4.ARCTIC.ne30x4,ne0np4.ARCTICGRIS.ne30x8,ne240np4,1km-merge-10min,C24,C48,C96,C192,C384">
+       valid_values="512x1024,360x720cru,128x256,64x128,48x96,94x192,0.23x0.31,0.47x0.63,0.9x1.25,1.9x2.5,2.5x3.33,4x5,10x15,0.125nldas2,5x5_amazon,1x1_vancouverCAN,1x1_mexicocityMEX,1x1_asphaltjungleNJ,1x1_brazil,1x1_urbanc_alpha,1x1_numaIA,1x1_smallvilleIA,0.25x0.25,0.5x0.5,3x3min,5x5min,10x10min,0.33x0.33,0.125x0.125,ne3np4.pg3,ne4np4,ne5np4.pg3,ne16np4,ne16np4.pg3,ne30np4.pg2,ne30np4.pg3,ne30np4,ne60np4,ne120np4,ne120np4.pg2,ne120np4.pg3,ne0np4CONUS.ne30x8,ne0np4.ARCTIC.ne30x4,ne0np4.ARCTICGRIS.ne30x8,ne240np4,1km-merge-10min,C24,C48,C96,C192,C384,mpasa480,mpasa240,mpasa120,mpasa60,mpasa30,mpasa15">
 Horizontal resolutions
 Note: 0.25x0.25, 0.5x0.5, 5x5min, 10x10min, 3x3min, 1km-merge-10min and 0.33x0.33 are only used for CLM toolsI
 </entry> 
@@ -2757,6 +2802,24 @@ 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                                                    -->
 <!-- ========================================================================================  -->
@@ -2811,4 +2874,38 @@ 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>