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Megan CTSM#96

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rosiealice wants to merge 227 commits intoNorESMhub:noresmNorESMhub/CTSM:noresmfrom rosiealice:megan_cherrypick_ctsmrosiealice/ctsm:megan_cherrypick_ctsmCopy head branch name to clipboard

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Commits on Jun 21, 2023

• Document that fincl1 maps to 'h0' history file. And fexcl1.

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Commits on Aug 10, 2023

• Merge tag 'ctsm5.1.dev133' into hist_doc_bc

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Commits on Jun 26, 2024

• move from depricated shr_file to shr_log

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Commits on Aug 8, 2024

• add spellcheck in bld-nml-tester

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Commits on Aug 15, 2024

• updating fates default parameter file to api 36.1

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Commits on Aug 22, 2024

• add test, add warning

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• add spellcheck in bld-nml-tester

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Commits on Aug 29, 2024

• Merge tag 'ctsm5.2.027' into merge-master-20240828

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• Merge pull request ESCOMP#2733 from ekluzek/merge-master-20240828

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Commits on Sep 13, 2024

• Merge remote-tracking branch 'escomp/b4b-dev' into hs-uii-ssr

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• Ignore warnings in Hillslope tests.

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Commits on Sep 16, 2024

• Merge pull request #6 from samsrabin/hs-uii-ssr

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Commits on Sep 17, 2024

• Merge pull request ESCOMP#2703 from mvdebolskiy/hs-uii

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• Remove references to PTCLM/PTCLMmkdata.

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• Use double-backticks instead of double-hyphens in one instance.

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Commits on Sep 18, 2024

• Fix comments on urban thermal variables

  

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• Fix two hillslope error messages.

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• Move hillslope variables from fsurdat to hillslope_file.

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• Merge pull request ESCOMP#2765 from olyson/urbthermalcomment

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• Move how-to-make-mesh.md to the User's Guide; give extension .rst.

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• how-to-make-mesh: Markdown to RestructuredText.

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• Improve mesh_maker instructions.

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• Fix typo in mesh_plotter arg description.

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• mesh_plotter now stops if output file exists w/o --overwrite given.

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• Add --dpi option to mesh_plotter.

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• More reasonable marker sizes in mesh_plotter.

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Commits on Sep 19, 2024

• Convert I1850 hillslope 5x5_amazon tests to I2000.

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• Add non-serial HillslopeC 5x5_amazon test to hillslope suite.

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• Add issue reference to non-serial HillslopeC 5x5_amazon test.

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• Fix HillslopeC test in expected fails list.

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• Add mesh_plotter instructions.

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Commits on Sep 20, 2024

• UG: Fix path of example mksurfdata_esmf namelist.

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• Add double backticks in lots of places.

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• Add doc todo to replace missing figure.

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• Fix a title overline.

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• More formatting fixes.

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• Replace some :: with :.

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• Formatting fixes in wrf-nesting.rst.

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Commits on Sep 23, 2024

• Add --no-center-coords option.

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• Properly handle --outdir.

  samsrabin

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• Add tests to test_advanced_sys_mesh_plotter.py.

  samsrabin

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• Use os.path.join in test_advanced_sys_mesh_plotter.py.

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• Add dpi test to test_advanced_sys_mesh_plotter.py.

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• Format with black.

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• Add previous commit to .git-blame-ignore-revs.

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• Merge pull request ESCOMP#2772 from samsrabin/mesh-plotter-improvements

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Commits on Sep 24, 2024

• Update namelist_defaults_clm4_5.xml references.

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• namelist_defaults_|version|_tools.xml files no longer exist.

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• Fix namelist XML refs in what-are-the-clm-tools.rst.

  samsrabin

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• Specify path to create_newcase.

  samsrabin

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• Add TODOs to update refs to queryDefaultNamelist.pl.

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• Add TODOs to update refs to mksurfdata.pl.

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• Fix compset and add TODO to "Running with historical CO2 forcing."

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• TODO added in "Running with irrigation".

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• Add TODO about -bgc_spinup.

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• Add TODOs about mkprocdata_map.

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• Add TODOs about domain files not being needed in nuopc.

  samsrabin

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• Add TODO about updating "Observational Sites Datasets".

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• Merge branch 'b4b-dev' into docs-fixes-202409

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• Fix another namelist_definition_clm4_5.xml reference.

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• More double-backticks in "Spinup of |version|-BGC-Crop".

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• Remove User's Guide section about running w/ transient hist CO2.

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• Resolve a docs build warning.

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Commits on Sep 25, 2024

• PPE change to sa_leaf

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• Error in Hillslope/shell_commands if running on grid w/o a hillslope_file.

  samsrabin

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• Hillslope testmod: Add hillslope_file for 5x5_amazon.

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Commits on Sep 26, 2024

• Merge pull request ESCOMP#2770 from samsrabin/docs-fixes-202409

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• Merge tag 'ctsm5.2.029' into fates-api36.1

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• Merge tag 'ctsm5.3.0' into merge-b4bdev-20240926

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• Updated number of tests

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• Don't manually set meshfile in Hillslope tests.

  samsrabin

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• First draft ChangeLog/ChangeSum

  slevis-lmwg

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• Updated EXPECTED FAILUREs (I should have done this in ctsm5.3.0)

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Commits on Sep 27, 2024

• correct clm_demand option typo

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• Remove parallel 5x5_amazon test from expected fails.

  samsrabin

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• Rename 10x15 synthetic hillslope_file to include 10x15.

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• Add/edit comments about 5x5_amazon hillslope tests.

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• Remove parallel 5x5_amazon hillslope test from aux_clm.

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• Adding one more EXPECTED FAILURE

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• Merge pull request ESCOMP#2792 from slevis-lmwg/merge-b4bdev-20240926

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• Merge tag 'ctsm5.3.001' into merge-master-20240927

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• Merge pull request ESCOMP#2795 from slevis-lmwg/merge-master-20240927

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• Revert "Merge tag 'ctsm5.3.001' into b4b-dev"

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• Merge pull request ESCOMP#2796 from ESCOMP/revert-2795-merge-master-20240927

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• Merge tag 'ctsm5.3.002' into merge-master-20240927

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• Merge pull request ESCOMP#2797 from slevis-lmwg/merge-master-20240927

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• Fix clm-basic tests

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Commits on Sep 28, 2024

• Updates for my fix to take effect correctly

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• Small important correction

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Commits on Sep 30, 2024

• Merge branch 'b4b-dev' into shr_file_to_shr_log

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• Change testlist_clm ne30pg3_t061 tests to ne30pg3_t232

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• First commit for CESM3 tuning of the dust emission module by dmleung. 30 Sep 2024

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• Merge branch 'b4b-dev' into fix_clm-basic_tests

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• Merge pull request ESCOMP#2798 from slevis-lmwg/fix_clm-basic_tests

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• Allocate elevclass_o before use in mkglcmecMod.F90

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• Change testlist_clm C96_t061 test to C96_t232

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Commits on Oct 1, 2024

• Remove elevclass_o altogether because it is NOT used

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• dmleung deleted a few unused parameters and variables. 30 Sep 2024

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• Revert change to C96 test; will do later, when ccs_config gets updated

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• Merge pull request ESCOMP#2799 from slevis-lmwg/change_t061_to_t232

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• Merge branch 'b4b-dev' into alloc_elevclass_o

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• Add domain check for hillslope file.

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• Update 10x15 hillslope_file (now has LATIXY/LONGXY).

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• Improve use_init_interp+use_hillslope namelist warning.

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• Merge tag 'ctsm5.3.002' into hillslopes-off-fsurdat

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• Merge pull request ESCOMP#2804 from slevis-lmwg/alloc_elevclass_o

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• Call domain_clean() at end of check_domain_attributes().

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• Remove outdated comment/TODO.

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• Rename surfdata_domain to inputdata_domain.

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• Merge branch 'fix-namelist-tester' of github.com:mvdebolskiy/CTSM into fix-namelist-tester

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• Merge remote-tracking branch 'escomp/b4b-dev' into fix-namelist-tester

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• Correct the name of the hash to use in the checks that hash values are all set in fail, warn, and finidat tests

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• Merge pull request ESCOMP#2678 from mvdebolskiy/fix-namelist-tester

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• dmleung changed the values of the tuning parameters and added a new tuning factor for vegetation drag partition effect. Also a first attempt to modify the code for soil moisture effect on dust to a…

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• add shell call to generate fates hydro parameter file on the fly

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• dmleung renamed the tuning parameter for Okin's vegetation drag partition factor to dust_veg_drag_fact from dust_veg_part_fact. 1 Oct 2024

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• fix typo in fates hydro user_nl_clm

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Commits on Oct 2, 2024

• correct call typo to clm_demand for fateslanduse test mod

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• update default fates parameter files

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• Merge tag 'ctsm5.3.002' into fates-api36.1

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• update the gitmodules tag for fates

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Commits on Oct 3, 2024

• Getting a new set of tuning parameters for dust. dmleung 2 Oct 2024

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• add expected failure for FatesColdLandUse test mod

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• add new changelog entry

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• minor changelog update

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• update filename

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Commits on Oct 4, 2024

• Merge branch 'b4b-dev' into shr_file_to_shr_log-ssr

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• update fates tag to api36.1

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Commits on Oct 7, 2024

• update testing results for ctsm5.3.003

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• update changelog and changesum date/time for ctsm5.3.003

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• Merge pull request ESCOMP#2700 from rgknox/fates-api36.1

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• Revert this change as it changed answers for SMS_Ln9.ne30pg2_ne30pg2_mg17.I1850Clm50Sp.derecho_intel.clm-clm50cam6LndTuningMode--clm-nofireemis, unit tests and some other tests went back to identic…

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• Merge branch 'dustemis_tune4cesm3' of github.com:dmleung/CTSM into dustemis_tune4cesm3

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• Bump up wallclock time for one test.

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• Merge tag 'ctsm5.3.003' into hillslopes-off-fsurdat

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• Remove include_user_mods from matrixcnOn testmod.

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Commits on Oct 8, 2024

• Merge branch 'shr_file_to_shr_log-ssr' into shr_file_to_shr_log

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• Change a test wallclock time to ensure it's what we want.

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• Merge pull request ESCOMP#2434 from samsrabin/hillslopes-off-fsurdat

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• Update ChangeLog and ChangeSum.

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• Make dust_moist_fact different for Leung and Zender, even though both are 1.0, and then have the duplicated line outside of the if statement

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• Merge pull request ESCOMP#2820 from samsrabin/hillslopes-off-fsurdat

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• Fix issue ESCOMP#2793

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• Merge pull request ESCOMP#2627 from jedwards4b/shr_file_to_shr_log

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• Merge pull request ESCOMP#2806 from olyson/eflxbuild

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• Merge tag 'ctsm5.3.004' into dustemis_tune4cesm3

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• Clm60 finidat updates for ne30, f09, f19 grids

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• Fix hillslope with use_init_interp warning test, by specifying the hillslope_file this fixes ESCOMP#2826

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• ne30 updates in response to Keith Oleson's review

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• f19 updates for test to pick up the correct finidat

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• Add more expected fails

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• Updates after Erik's reviewr; ne30 1979 does not work, yet

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• Correct mask for ne30pg3 1979 finidat file

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• Remove 2003 finidat settings for clm5_1/clm6_0 so will use 2000 files, handle 1979 finidat settings consistently for f09, f19, and ne30pg3

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• Add matrixcn test suite.

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• Final ChangeLog

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• Merge pull request ESCOMP#2788 from olyson/saleaf

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• Transfer the following parameters from namelist to parameter file:

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• Merge tag 'ctsm5.3.009' into merge-master-20241021

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• Make jmaxb0, wc2wjb0, r_mort pft-dimensioned

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• ncd_io not needed after all

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• Other variables not needed after all

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• Consistent naming of units

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• New versions of specialized parameter files

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• Reinstate SMS_Lm1.f10_f10_mg37.I1850Clm60Bgc.derecho_intel.clm-clm60_monthly_matrixcn_soilCN30

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• Merge branch 'b4b-dev' into b4b-dev_PPE2830-2831

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• Move read of jmaxb0,jmaxb1,wc2wjb0 from pftcon to LunaMod and r_mort to CNGapMortality

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• Final paths for parameter files

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• Merge pull request ESCOMP#2845 from olyson/b4b-dev_PPE2830-2831

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• Remove/replace refs to DATM_C*_YR_* variables

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• Remove some more DATM_C..._YR_...

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• Remove additional DATM_C..._YR_...

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• Replace outdated DATM_CPL_CASE with DATM_CPLHIST_CASE

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• Add warning box to MOAR User's Guide page.

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• Merge pull request ESCOMP#2852 from slevis-lmwg/rm_refs_to_datm_vars

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• Merge branch 'b4b-dev' into hist_doc_bc

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• Merge pull request ESCOMP#2866 from johnpaulalex/hist_doc_bc

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• build-namelist_test: Ensure cold starts w/ finidat are handled properly.

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• Ignore finidat for cold-start FATES runs.

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• Don't allow users to supply finidat for cold-start non-FATES runs.

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• adding izumi nag fails

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• changelog

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• Merge pull request ESCOMP#2872 from adrifoster/merge-b4bdev-20241108

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• added CTSM side variables for MEGAN_pft_index

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• spelling corrections

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• use FATES voc index in MEGAN calculations (implied mapping between FATES PFTs and HLM PFTs

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• debugging

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• turn off the -megan cant run with FATES- statement in bldnamelist

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• passing ci from FATES into MEGAN

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• Merge tag 'ctsm5.3.010' into fix-fates-cold-finidat

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• Merge branch 'feature/update_testlist' into rosiealice_CTSM/megan_cherrypick_ctsm

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• Add some tests to expected fail list.

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• Update ChangeLog and ChangeSum.

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• Merge pull request ESCOMP#2870 from samsrabin/fix-fates-cold-finidat

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• updated with new tests

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• updated fates megan tests

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• Merge branch 'rosiealice_CTSM/megan_cherrypick_ctsm' into feature/megan_cherrypick_ctsm_mvertens

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• Merge tag 'ctsm5.3.011' into feature/megan_cherrypick_ctsm_mvertens

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• updated several files to ctsm5.3.011

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• fixed some testing problems

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• updated fates pointer in .gitmodules

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• updated fates to have megan functionality

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• updates for megan functionality

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• Merge pull request #6 from mvertens/feature/megan_cherrypick_ctsm_mvertens

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