Hillslope hydrology pre-merge changes #9

This necessitates nyrs_crop_active being changed from integer to real(r8).

Still won't work with use_crop false. FATES handles coarse woody debris separately, but I haven't added handling of that, so implicitly tillage just doesn't affect CWD.

Multiple active crop patches per column shouldn't be possible YET, but perhaps eventually it will be.

…dim name.

…illage_multipliers().

Add parameterization to allow excess ice in soil and subsidence Description: Parameterization for excess ice described in Lee et al. (2014): http://dx.doi.org/10.1088/1748-9326/9/12/124006 This code is a modified version of code provided by Lei Cai: https://github.com/lca041/ctsm/tree/clm5.0.dev92_exice Works only for the nuopc driver.

Add parameterization to allow excess ice in soil and subsidence Description: Parameterization for excess ice described in Lee et al. (2014): http://dx.doi.org/10.1088/1748-9326/9/12/124006 This code is a modified version of code provided by Lei Cai: https://github.com/lca041/ctsm/tree/clm5.0.dev92_exice Works only for the nuopc driver. # Conflicts: # bld/CLMBuildNamelist.pm # bld/namelist_files/namelist_defaults_ctsm.xml # bld/namelist_files/namelist_definition_ctsm.xml

FATES API update to facilitate fates refactor This updates a number of FATES type names and module use statements which correspond with a refactoring effort that moves FATES patches and cohorts into their own respective modules. With the FATES update is a minor science update, so there are changes to answers for FATES. This also incorporates a minor update to a more recent version of the ccs config external.

Between CropPhenology()and get_tillage_multipliers(). New function DaysPastPlanting() shared from CNPhenologyMod to TillageMod.

In default configuration, there's no difference. This is setting up for the specification of this depth as a namelist parameter. Partially-tilled layers not yet allowed.

Rename hist fields to track them down more easily Renaming history fields to make easier to find in lists, e.g. when using ncview. For example, litter fields like MET_LIT and STR_LIT will be LIT_MET and LIT_STR.

…-runmeans" This reverts commit b693456, reversing changes made to 574f3b2.

…-runmeans

This enables unit testing of this code.

…terfall().

Replaces hard-coded removedresidue_fraction.

I understood zisoi to give the bottom of each layer, but it actually gives the top.

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)

Refactor some max_patch_per_col and maxsoil_patches loops As explained in issue 2025, the old loop structure was out-of-date and needed a refactor, partly because use of max_patch_per_col was limited, partly to simplify the code and make it easier to read and understand, and partly to improve (even if slightly) model performance.

Merging 2156 2148 2233 2235 2237 2044 For details please see the individual PRs and/or the ChangeLog. Multiple contributors, as listed in the individual PRs and the ChangeLog. Answers change for 3 tests: ERS_Lm20_Mmpi-serial.1x1_smallvilleIA.I2000Clm50BgcCropQianRs.izumi_gnu.clm-cropMonthlyNoinitial BASELINE ctsm5.1.dev151: DIFF SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm51Bgc.izumi_nag.clm-default--clm-NEON-NIWO BASELINE ctsm5.1.dev151: DIFF SMS_Ld10_D_Mmpi-serial.CLM_USRDAT.I1PtClm51Bgc.izumi_nag.clm-NEON-MOAB--clm-PRISM BASELINE ctsm5.1.dev151: DIFF - The first is due to the bug fix in 2237; the diffs are in the fill patterns of 3 fields. - The second and third are due to the bug fix in 2044.

…unction

Use baset_latvary parameters Namelist parameters baset_latvary_slope and baset_latvary_intercept were never actually used, with values of 0.4 and 12 being hard-coded in the relevant subroutine instead. This PR fixes that, and also adds unit testing of a refactored function that uses them.

…p usersmod

Do not use Meier roughness by default, even with 5.1 ctsm5.1.dev155 had turned on Meier2022 surface roughness calculation by default for 5.1 compsets. Several bugs have recently emerged that were not caught by pre-merge testing, so this tag reverts that change. Thus, the ZengWang2007 method is default for all compsets again. # Conflicts: # src/biogeochem/DryDepVelocity.F90 # src/biogeophys/SurfaceAlbedoMod.F90

Various BFB fixes and updates Purpose/description of changes ------------------------------ the default comes in a later tag (slevis) Regular and python testing passed. Does not change answers relative to dev158.

…-dev' into subset_data_fix"" This reverts commit a059445.

Similarly rename its file.

A newer parameter file was generated that reduces the maximum number of fates patches for the default configuration. This avoids misalignment between the default surface datasets.

The wt_nat_patch array is allocated using surfpft bounds. While surfpft and natpft will typically match, this isn't the case for fates currently. As such the nag compiler will complain if the input array has lower bounds for its dimensions than the dummy argument bounds.

Resolves ESCOMP#2167. Affected scripts: * test_sys_mesh_modifier * test_sys_run_neon * regrid_ggcmi_shdates

…file.

Various BFB fixes and updates Purpose/description of changes ------------------------------ the default comes in a later tag (slevis) Regular and python testing passed. Does not change answers relative to dev158.

…ipliers.

Various BFB fixes and updates Purpose/description of changes ------------------------------ the default comes in a later tag (slevis) Regular and python testing passed. Does not change answers relative to dev158.

…ne at the model resolution and sim_year_range

…ssue ESCOMP#2304 is resolved

Add FATES land use change module to pass LUH2 data to FATES

FATES landuse version 1 This tag enables FATES to utilize the state and transitions data from the Land Use Harmonization (https://luh.umd.edu/) data sets. This data has been preprocessed using tooling provided by FATES via a separate pull request (FATES#1032). A new module has been added to the dyn_subgrid directory that largely adapts the dynHarvest module to import and read this minimially processed data, which is data is passed to fates.

Refactor 20-year running means of crop GDD accumulation Three variables track the 20-year running mean of GDD accumulation (base temperatures 0, 8, and 10°C) during the "growing season" (April through September in the Northern Hemisphere, October through March in the Southern Hemisphere). This update refactors those to use accumulMod, resolving overly-strong weighting of the first few years after a crop becomes active.

Improvements to processing of crop calendar files (v2) In python/ctsm/crop_calendars/, process_ggcmi_shdates.py and regrid_ggcmi_shdates.py are used to convert the raw GGCMI crop calendar files into CTSM-compatible versions. This update fixes some bugs, removes dependencies on the nco utilities, enables the use of surface datasets as template files (in addition to the existing ability to use CTSM output files), and standardizes things for consistency with other CTSM Python tools.

Improvements to processing of crop calendar files In python/ctsm/crop_calendars/, process_ggcmi_shdates.py and regrid_ggcmi_shdates.py are used to convert the raw GGCMI crop calendar files into CTSM-compatible versions. This update fixes some bugs, removes dependencies on the nco utilities, enables the use of surface datasets as template files (in addition to the existing ability to use CTSM output files), and standardizes things for consistency with other CTSM Python tools.

See ESCOMP#2310: NEON tests sometimes fail (ESCOMP#2310)

(cherry picked from commit 142c2c1)

Makes no changes, but I realized the cherry-pick I did before won't let Github recognize that this is up-to-date with the tillage branch.

…paramfile

Adds capability for cropland soil tillage and post-harvest residue removal. Tillage: This PR brings in the tillage code written by Sam Levis and Michael Graham and used in Graham et al. (2021, ERL, doi:10.1088/1748-9326/abe6c6). Low- and high-intensity tillage here work by increasing the decomposition rate of different soil carbon pools. These "decomposition multipliers" vary based on soil pool and how long it's been since the crop was planted; they are set with new paramfile variables till_decompk_multipliers and mimics_till_decompk_multipliers. Note that tillage is off by default. Residue removal: Adds a parameter hat represents what fraction of post-harvest crop residues (stems and leaves) should be removed to the crop product pool rather than being transferred to litter.

Fates two stream API

…slope_hydrology-ssr

Compatibility and tests for FATES 2-Stream This set of changes enables compatibility and testing for FATES two-stream radiation scattering. Two stream radiation is selected by setting the FATES parameter file variable fates_rad_mod = 2. This is an alternative to Norman radiation. The FATES default radiation model will continue to be Norman for the time being, but is expected to transition to two-stream in the near future.

This ensures that any methods added in the future are handled here.

…mods.

This logical array, where .true. will prevent individual gridcells from being collapsed. Includes unit testing.

For the Uniform and DominantPftLowland values of hillslope_pft_distribution_method

Squash-"merge" of hillslope_hydrology-functionize_linear into hillslope_hydrology-ssr3

…ion.

(The latter 2 have no theme; they are intended to exercise all options.) * HillslopeFromFile * HillslopeC * HillslopeD

Suites aux_clm and hillslope: * ERP_D_P64x2_Ld10.f10_f10_mg37.I2000Clm51Bgc.derecho_intel.clm-Hillslope * SMS_D_Mmpi-serial_Ld5.5x5_amazon.I1850Clm51Bgc.derecho_gnu.clm-HillslopeC * SMS_D_Ld3.f10_f10_mg37.I2000Clm51Bgc.izumi_nag.clm-HillslopeD Suite hillslope: * SMS_D_Ld3.f10_f10_mg37.I1850Clm51Bgc.derecho_intel.clm-HillslopeFromFile

Commits on Sep 12, 2023

arguments and hist call updates

rgknox committed Sep 12, 2023

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Commits on Sep 21, 2023

Updated temporary two-stream fates branch

rgknox committed Sep 21, 2023

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Commits on Dec 27, 2023

Updated test nl with updated fates history

rgknox committed Dec 27, 2023

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Hillslope hydrology pre-merge changes #9

Hillslope hydrology pre-merge changes #9

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