Merge master 2024 0725 #2662
Merged
Merge master 2024 0725 #2662
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This is a small changeset, which only adds the passing of a text based flag to FATES, that defines which soil decomposition method is active. This setting is needed by FATES, so that it can pass specific boundary conditions to CLM (and potentially ELM in the future). This change was necessitated because MIMICS requires a Nitrogen to lignin-carbon ratio in the litter flux, yet other decomposition schemes do not. Moreover, the generation of this boundary condition is not trivial, so it is worth it to avoid its computation if mimics is not on. This change should have NO impact on any tests. slevis resolved conflicts: cime_config/testdefs/ExpectedTestFails.xml cime_config/testdefs/testlist_clm.xml src/biogeochem/CNPhenologyMod.F90
Refactor NutrientCompetition / CNAllocation to provide hooks for AgSys Major refactor of NutrientCompetition / CNAllocation to provide hooks for AgSys crop model: separates the NutrientCompetition modules into pieces based on (1) consolidating duplicate code between the Clm45 and FlexibleCN versions, and (2) separating pieces that will vs. won't be used for crop patches when running with the upcoming AgSys crop model. I have restored the old CNAllocationMod, with some of the responsibilities that it used to have. (I'm not sure it's appropriate to have the calculation of gpp and maint resp in CNAllocationMod, but I left it there because it has always been combined with the allocation code, including back when we had a separate CNAllocationMod.) slevis resolved conflicts: src/biogeochem/CNDriverMod.F90 src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 src/biogeochem/NutrientCompetitionCLM45defaultMod.F90 slevis important note: To resolve conflicts in the third (ie, last) of the above files, I checked with Will Wieder, and we agreed to not maintain a clm45 version of matrixcn.
Get FATES and carbon_only test-suite tests to pass with MIMICS active To pass with MIMICS active, FATES and carbon_only tests need calculations of: ligninNratioAvg and annsum_npp_col, both currently declared and calculated in CNVegCarbonFluxType.F90. ligninNratioAvg is a function of leafc_to_litter_patch, frootc_to_litter_patch, soilbiogeochem_cwdc_col, soilbiogeochem_cwdn_col, soilbiogeochem_decomp_cascade_ctransfer_col. I got both FATES and carbon_only tests to pass by declaring local copies (in MIMICS) of ligninNratioAvg and annsum_npp_col. slevis resolved conflicts: src/biogeochem/CNVegCarbonFluxType.F90 src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90
First pass at getting fates-sp mode to run without soil BGC Bring in externals updates that include adding AWS as a supported machine. Add a FatesSP compset and user-mod directory. Turn soil-BGC off when running FatesSP. Replace PGI tests on izumi with nvhpc tests on cheyenne. Fix an issue with a particular gnu compiler version in ch4Mod.F90 in DEBUG mode. Add some more threading tests for Fates. Start adding a prescribed-LAI tests for FatesSp Add a file to setup a python environment in conda for the python testing. Set line length for black to same as pylint (100). Add some extra excludes for black to the pylint checking. Paths for CIME python code was changed, which required changes to some CTSM python code. slevis resolved conflicts: cime_config/testdefs/ExpectedTestFails.xml cime_config/testdefs/testlist_clm.xml src/biogeochem/CNCStateUpdate1Mod.F90
Update cime to fix DAE issue modify_neon issue When FatesSp is on, make soil_decomp None by default slevis resolved conflicts: cime_config/testdefs/ExpectedTestFails.xml
This set of changes 1) allows FATES to dictate the number of patches on the naturaly vegetated land unit and 2) is compatible with a version of FATES that updates the parameter file format (changes in parameter naming and parameter set). Efforts were made to adhere to the system of how patches are looped and loop bounds are defined. There is interaction with the reading of the surface file, which previously dictated all patch counts based on the number of PFTs in the file. FATES-SP and biogeography preserves the ability to use surface file weighting factors associated with PFTs and CFTs to drive area fractions in FATES. This change is motivated by FATES-side updates to the parameter file, which includes new settings where the user can control the number of primary "fates_maxpatch_primary" and secondary "fates_maxpatch_secondary" patches. Users should also be aware of a new namelist setting "use_fates_tree_damage" which defaults to false (inoperative). slevis resolved conflicts: bld/unit_testers/build-namelist_test.pl
First Commit of CN Matrix Solution: Start bringing in the use_matrixcn and use_soil_matrixcn control options for the Carbon/Nitrogen BGC model using the matrix solution methodology developed by Dr. Yiqi Luo and his EcoLab members: Drs. Xingjie Lu, Yuanyuan Huang and Zhengguang Du, at Northern Arizona University Work on Anomaly forcing for SSEP scenarios: Do some work on anomoly forcing for SSP scenarios. Update the script in tools/contrib to work with the latest data and replicate results of Keith Oleson and Sean Swenson. Add some test cases for it. Python Environment Management using Conda: More work on the manage_python_env script to setup the "ctsm_py" conda environment. This now works for UCAR machines (such as cheyenne and casper) as well as CGD machines (like izumi). This script can also be called for tools, and the test tools mechanism is now using it rather than ncar_pylib. ./manage_python_env SCAM Fix: Add checkimport method for CMEPS so that single-column case can work with SCAM, from Jim Edwards. Black Formatter for Python Code: Run "black" python code reformatter on all code under the "python" directory. Add the commits to .git-blame-ignore-revs so they can be ignored when "git blame" is used, if you add this to each clone where you want this to apply: git config blame.ignoreRevsFile .git-blame-ignore-revs You can do it for your worktrees, but since the file only applies to CTSM for ctsm5.1.dev100 and forward, you'll need to do it for each CTSM clone seperately. Also there is now a github action that checks that python code under the "python" subdirectory is black clean. If it's not the action will fail and send you an email about it. Make Map Data Fix: Simple fix from Sam Rabin. Fix for DISPLA on History Output: Fix from Keith Oleson to set history output for DISPLA (displa_patch) to zero when vegetation is buried by snow. slevis resolved conflicts: bld/CLMBuildNamelist.pm bld/namelist_files/namelist_defaults_ctsm.xml bld/unit_testers/build-namelist_test.pl cime_config/testdefs/testlist_clm.xml src/biogeochem/CNAllocationMod.F90 src/biogeochem/CNCStateUpdate1Mod.F90 src/biogeochem/CNDriverMod.F90 src/biogeochem/CNNStateUpdate1Mod.F90 src/biogeochem/CNPhenologyMod.F90 src/biogeochem/CNVegCarbonFluxType.F90 src/biogeochem/NutrientCompetitionCLM45defaultMod.F90 src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 slevis had to restore many other files for which git replaced the matrixcn mods with dev100's matrixcn stubs. slevis is testing the code with SMS_Ln9.ne30pg2_ne30pg2_mg17.I2000Clm50BgcCrop.cheyenne_intel.clm-clm50cam6LndTuningMode and getting a column cbalance error at the moment.
Use conda environment rather than ncar_pylib with the fsurdat_modifier system test Reason: ncar_pylib is going away soon. slevis resolved conflicts: bld/unit_testers/build-namelist_test.pl cime_config/testdefs/testlist_clm.xml src/soilbiogeochem/SoilBiogeochemCarbonStateType.F90
Get gross unrepresented land use transitions working in CLM5.1. This is additional optional data added to the landuse.timeseries files for transient simulations. The current landuse.timseries files have this data, but it's set to zero. This data will be part of the CTSM5.2 surface dataset (that is upcoming) and be on by default for clm5_3 physics. slevis resolved conflict: bld/unit_testers/build-namelist_test.pl
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. slevis resolved conflicts: bld/unit_testers/build-namelist_test.pl cime_config/buildnml src/biogeochem/CNVegCarbonFluxType.F90
Migration of FATES to share normal soil BGC call sequence and functionality This set of changes enables the normal soil biogeochemistry that is used for CN, to be used for FATES as well. FATES had been using a simplified subset of soil biogeochemistry in its own module. This change required coordination of litter flux and methane boundary conditions from FATES to CLM. CNVEG datastructures were given trivial allocation (of size one on index zero) to prevent inappropriate use of CNVEG datastructures while FATES is active. Note that now the carbon balance checking for the soil is now active when FATES is active. Various accomodations have also been put in place to enable nitrogen cycling between the two models. slevis resolved conflicts: bld/unit_testers/build-namelist_test.pl src/biogeochem/CNCStateUpdate1Mod.F90 src/biogeochem/CNDriverMod.F90 src/biogeochem/CNVegCarbonStateType.F90 src/biogeochem/CNVegNitrogenStateType.F90 src/biogeochem/CNVegetationFacade.F90 src/soilbiogeochem/SoilBiogeochemCarbonFluxType.F90 src/soilbiogeochem/SoilBiogeochemLittVertTranspMod.F90 src/soilbiogeochem/SoilBiogeochemNStateUpdate1Mod.F90 src/soilbiogeochem/SoilBiogeochemNitrogenFluxType.F90 src/soilbiogeochem/SoilBiogeochemNitrogenStateType.F90
because I updated 2 local copies of cn-matrix_v3 at the same time
Used this one for testing: SMS_D.1x1_brazil.I1850Clm51BgcCrop.cheyenne_gnu.clm-mimics_matrixcn
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. slevis resolved conflicts UNTESTED: bld/unit_testers/build-namelist_test.pl cime_config/testdefs/testlist_clm.xml src/biogeochem/CNPhenologyMod.F90 src/biogeochem/CNVegNitrogenFluxType.F90 src/biogeochem/NutrientCompetitionFlexibleCNMod.F90 AND I will still look for potential additional inconsistencies that I may need to resolve
because I updated 2 parallel local copies of cn-matrix_v3
This matches the corresponding fates tag that also impliments using this file
…tracer_test_v2 Relax tolerance for truncating small snocan values in CanopyFluxes
Relax tolerance for truncating small snocan values in CanopyFluxes See the PR ESCOMP#2457 for details.
Relax tolerance for truncating small snocan values in CanopyFluxes See the PR ESCOMP#2457 for details.
FATES land use v2 API update (CTSM-side)
slevis resolved conflicts: bld/unit_testers/build-namelist_test.pl
use_matrixcn and use_soil_matrixcn are coming in as default .false.
Merging ctsm5.2.014
ERS_D.f19_g17.I1850Clm50BgcCrop.izumi_nag.clm-ciso_monthly_matrixcn_spinup failed during the build because a namelist variable needed renaming
Update submodule tags to pass runoff from CISM to ROF as per issue ESCOMP#2590
Update submodule tags to pass runoff from cism to rof - Update MOSART, CMEPS, and CISM so CISM runoff goes to ROF rather than CTSM - Update RTM with fix needed for Paleo LGM work Contributors: @mvertens, @jedwards4b, @billsacks, @Katetc, @ekluzek, @slevis-lmwg Fixes ESCOMP#2590 Update CMEPS/MOSART/CISM/RTM tags Fixes ESCOMP/RTM#50 Likely wrong RTM river flux to MOM6 within cesm2_3_beta17 Differences in namelist 'mosart_inparm': missing variable: 'do_rtmflood' missing variable: 'finidat_rtm' missing variable: 'frivinp_rtm' missing variable: 'rtmhist_fexcl1' missing variable: 'rtmhist_fexcl2' missing variable: 'rtmhist_fexcl3' missing variable: 'rtmhist_fincl1' missing variable: 'rtmhist_fincl2' missing variable: 'rtmhist_fincl3' missing variable: 'rtmhist_mfilt' missing variable: 'rtmhist_ndens' missing variable: 'rtmhist_nhtfrq' found extra variable: 'budget_frq' found extra variable: 'fexcl1' found extra variable: 'fexcl2' found extra variable: 'fexcl3' found extra variable: 'fincl1' found extra variable: 'fincl2' found extra variable: 'fincl3' found extra variable: 'finidat' found extra variable: 'frivinp' found extra variable: 'mfilt' found extra variable: 'mosart_euler_calc' found extra variable: 'mosart_tracers' found extra variable: 'ndens' found extra variable: 'nhtfrq' found extra variable: 'use_halo_option' Changes answers - what code configurations: mosart and rtm - what platforms/compilers: all - nature of change: mosart roundoff; rtm larger than roundoff due to bug fix; the latter also affects bgc variables We are ignoring strange diffs from baseline in two tests in variable FATES_TRANSITION_MATRIX_LULU as explained in issue ESCOMP#2656.
slevis-lmwg
approved these changes
Jul 25, 2024
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
Merging in latest master