101 calculate no photolysis rate constants #183
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Pull ZM 0.5 timestep removal into main
Replace original, locally-developed license with Apache 2.0 license.
Bring in new directory structure from development
Upgrading to atmos_phys0_06_000
Tag name (The PR title should also include the tag name): `atmos_phys0_07_000` Originator(s): @jimmielin List all `development` PR URLs included in this PR and a short description of each: * #141 by @mattldawson @boulderdaze * #147 by @peverwhee * #144 by @mwaxmonsky * #151 by @mattldawson * #145 by @jimmielin List all test failures: N/A
boulderdaze
requested changes
Jan 7, 2025
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Right now there's a memory leak, but I found out that you can pair valgrind with gdb to identify leaks as the process is running.
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Originator(s): Cheryl Craig Tag: atmos_phys0_08_000 Summary (include the keyword ['closes', 'fixes', 'resolves'] and issue number): Add ccpp'ized ZM - closes #66 Describe any changes made to the namelist: A schemes/zhang_mcfarlane/zm_convr_namelist.xml - namelist template for ZM List all files eliminated and why: N/A List all files added and what they do: A schemes/cloud_fraction/cloud_fraction_fice.F90 A schemes/cloud_fraction/cloud_fraction_fice.meta - Bring in the cloud_fraction_fice portion of the cloud_fraction CAM code and CCPP'ize it A schemes/sima_diagnostics/zm_diagnostics.F90 A schemes/sima_diagnostics/zm_diagnostics.meta - Add the main ZM diagnostics A schemes/sima_diagnostics/zm_convr_tendency_diagnostics.F90 A schemes/sima_diagnostics/zm_convr_tendency_diagnostics.meta A schemes/sima_diagnostics/zm_evap_tendency_diagnostics.F90 A schemes/sima_diagnostics/zm_evap_tendency_diagnostics.meta A schemes/sima_diagnostics/zm_momtran_tendency_diagnostics.F90 A schemes/sima_diagnostics/zm_momtran_tendency_diagnostics.meta A schemes/sima_diagnostics/zm_tendency_diagnostics.F90 A schemes/sima_diagnostics/zm_tendency_diagnostics.meta - Add ZM tendency diagnostics for each ZM component A schemes/utilities/to_be_ccppized_temporary.F90 A schemes/utilities/to_be_ccppized_temporary.meta - Add a temporary routine to house init methods which aren't being run with to_be_ccppized code. - Add a call to wv_sat_init A schemes/zhang_mcfarlane/set_deep_conv_fluxes_to_general.F90 A schemes/zhang_mcfarlane/set_deep_conv_fluxes_to_general.meta A schemes/zhang_mcfarlane/set_general_conv_fluxes_to_deep.F90 A schemes/zhang_mcfarlane/set_general_conv_fluxes_to_deep.meta - Add interstitials to move variables back and forth from the ZM deep variables to general variables for the ZM routine which is used in shallow convection as well A test/test_suites/suite_zhang_mcfarlane.xml - Suite to test ZM A to_be_ccppized/error_messages.F90 A to_be_ccppized/namelist_utils.F90 A to_be_ccppized/wv_sat_methods.F90 A to_be_ccppized/wv_saturation.F90 - Add methods which ZM requires, but are not being CCPP-ized at this point in time List all existing files that have been modified, and describe the changes: (Helpful git command: git diff --name-status development...<your_branch_name>) M doc/ChangeLog M doc/NamesNotInDictionary.txt - updated with ZM names M schemes/zhang_mcfarlane/zm_conv_convtran.F90 M schemes/zhang_mcfarlane/zm_conv_convtran.meta M schemes/zhang_mcfarlane/zm_conv_evap.F90 M schemes/zhang_mcfarlane/zm_conv_evap.meta M schemes/zhang_mcfarlane/zm_conv_momtran.F90 M schemes/zhang_mcfarlane/zm_conv_momtran.meta M schemes/zhang_mcfarlane/zm_convr.F90 M schemes/zhang_mcfarlane/zm_convr.meta - Further refinements needed to CCPP'ize ZM M suites/suite_cam7.xml - Add ZM routines to CAM7 List any test failures: Is this a science-changing update? New physics package, algorithm change, tuning changes, etc? - CCPP'ized ZM which was a package which already existed in CAM --------- Co-authored-by: Jesse Nusbaumer <[email protected]> Co-authored-by: Haipeng Lin <[email protected]> Co-authored-by: mwaxmonsky <[email protected]>
Originator(s): peverwhee Summary (include the keyword ['closes', 'fixes', 'resolves'] and issue number): The sima_state_diagnostics scheme only output the "known" constituents. This PR adds history add and out field calls for ALL other constituents. I'm open to discussion about the diagnostic names for these! Describe any changes made to the namelist: n/a List all files eliminated and why: n/a List all files added and what they do: n/a List all existing files that have been modified, and describe the changes: (Helpful git command: `git diff --name-status development...<your_branch_name>`) M schemes/sima_diagnostics/sima_state_diagnostics.F90 - add "history_add_field" and "history_out_field" calls for constituents outside of the core expected ones. List any test failures: all CAM-SIMA tests pass Is this a science-changing update? New physics package, algorithm change, tuning changes, etc? no - diagnostics update
Originator(s): @boulderdaze Summary (include the keyword ['closes', 'fixes', 'resolves'] and issue number): - Closes #196 - Fixed bugs for the CAM-SIMA build Describe any changes made to the namelist: ``` M schemes/musica/musica_ccpp_namelist.xml -> Specified the path to directory for the configuration ``` List all files eliminated and why: N/A List all files added and what they do: N/A List all existing files that have been modified, and describe the changes: ``` M schemes/musica/musica_ccpp.F90 M schemes/musica/musica_ccpp.meta M schemes/musica/musica_ccpp_namelist.xml M schemes/musica/tuvx/musica_ccpp_tuvx.F90 M schemes/musica/tuvx/musica_ccpp_tuvx_surface_albedo.F90 M test/musica/test_musica_api.F90 ``` List any test failures: N/A Is this a science-changing update? New physics package, algorithm change, tuning changes, etc? No
…rmo_water_update) (#178) Originator(s): @jimmielin Summary (include the keyword ['closes', 'fixes', 'resolves'] and issue number): Closes #177, implementing thermo_water_update scheme to call cam_thermo_water_update. Describe any changes made to the namelist: N/A List all files eliminated and why: N/A List all files added and what they do: Implement thermo_water_update scheme A schemes/thermo_water_update/thermo_water_update.F90 A schemes/thermo_water_update/thermo_water_update.meta List all existing files that have been modified, and describe the changes: (Helpful git command: `git diff --name-status development...<your_branch_name>`) Include thermo_water_update scheme in CAM7 suite and simple physics suites M suites/suite_cam7.xml M suites/suite_kessler.xml M suites/suite_tj2016.xml List any test failures: Is this a science-changing update? New physics package, algorithm change, tuning changes, etc? Yes --------- Co-authored-by: Jesse Nusbaumer <[email protected]>
…name update (#169) Originator(s): @jimmielin Summary (include the keyword ['closes', 'fixes', 'resolves'] and issue number): * Fixes #161: Add check_energy related history output variables to check_energy_diagnostics * Fixes #166: Need to remove old CAM suite definition files * Fixes #176 (updates `teout` standard name to `vertically_integrated_total_energy_using_dycore_energy_formula_at_end_of_physics_timestep`) Companion PR in SIMA: ESCOMP/CAM-SIMA#339 Describe any changes made to the namelist: N/A List all files eliminated and why: ``` Fix #166 to remove old SDF files from scoping exercise D suites/suite_cam4.xml D suites/suite_cam6.xml D suites/suite_cam6_silhs.xml ``` List all files added and what they do: ``` Add global energy fixer diagnostics (teinp, teout, tefix, efix) A schemes/sima_diagnostics/check_energy_fix_diagnostics.F90 A schemes/sima_diagnostics/check_energy_fix_diagnostics.meta ``` List all existing files that have been modified, and describe the changes: (Helpful git command: `git diff --name-status development...<your_branch_name>`) ``` Move some developments to check_energy_fix_diagnostics so they can be called at right time. M schemes/sima_diagnostics/check_energy_diagnostics.F90 M schemes/sima_diagnostics/check_energy_diagnostics.meta Add call to check_energy_fix_diagnostics in schemes using global energy fixer: M suites/suite_adiabatic.xml M suites/suite_cam7.xml Update teout standard name M doc/NamesNotInDictionary.txt M schemes/check_energy/check_energy_chng.meta M schemes/check_energy/check_energy_gmean/check_energy_gmean.meta M schemes/check_energy/check_energy_save_teout.meta M schemes/sima_diagnostics/check_energy_diagnostics.F90 M schemes/sima_diagnostics/check_energy_diagnostics.meta M schemes/sima_diagnostics/check_energy_gmean_diagnostics.meta ``` List any test failures: N/A Is this a science-changing update? New physics package, algorithm change, tuning changes, etc? N/A (diagnostics change only)
…st (#204) Originator(s): jimmielin Description (include issue title and the keyword ['closes', 'fixes', 'resolves'] and issue number): The FPHYStest test for Kessler in SIMA right now uses the same `suite_kessler.xml` as FKESSLER, which means it includes `physics_after_coupler` and other `check_energy` schemes we do not want to include in the FPHYStest test which should only be testing `kessler_tend`. This PR includes a new `suite_kessler_test.xml` that removes all the other schemes from the SDF and keeps only what we want to test, and consistent with how the snapshots are taken in CAM: ```fortran if (trim(cam_take_snapshot_before) == "kessler_tend") then call cam_snapshot_all_outfld(cam_snapshot_before_num, state, tend, cam_in, cam_out, pbuf) end if call kessler_tend(state, ptend, ztodt, pbuf) if ( (trim(cam_take_snapshot_after) == "kessler_tend") .and. & (trim(cam_take_snapshot_before) == trim(cam_take_snapshot_after))) then call cam_snapshot_ptend_outfld(ptend, lchnk) end if call physics_update(state, ptend, ztodt, tend) if (trim(cam_take_snapshot_after) == "kessler_tend") then call cam_snapshot_all_outfld(cam_snapshot_after_num, state, tend, cam_in, cam_out, pbuf) end if ``` List all namelist files that were added or changed: N/A List all files eliminated and why: N/A List all files added and what they do: ``` A test/test_suites/suite_kessler_test.xml - new kessler_test suite ``` List all existing files that have been modified, and describe the changes: (Helpful git command: `git diff --name-status development...<your_branch_name>`) N/A List all automated tests that failed, as well as an explanation for why they weren't fixed: N/A Is this an answer-changing PR? If so, is it a new physics package, algorithm change, tuning change, etc? Yes for FPHYStest kessler test If yes to the above question, describe how this code was validated with the new/modified features: BFB when using this suite
Originator(s): @mwaxmonsky Summary (include the keyword ['closes', 'fixes', 'resolves'] and issue number): Adds pbl_utils capability from CAM. Describe any changes made to the namelist: N/A List all files eliminated and why: N/A List all files added and what they do: M phys_utils/atmos_phys_pbl_utils.F90 - Transferred all functionality (except for `compute_radf(...)`) from ESCOMP/cam/src/physics/cam/pbl_utils.F90 M .github/workflows/unit-tests.yaml - Added phys_utils to code coverage. M test/unit-test/CMakeLists.txt M test/unit-test/tests/CMakeLists.txt M test/unit-test/tests/phys_utils/CMakeLists.txt M test/unit-test/tests/phys_utils/test_atmos_pbl_utils.pf - Creating CMake target library for `phys_utils` and adding sample unit tests. List all existing files that have been modified, and describe the changes: N/A (Helpful git command: `git diff --name-status development...<your_branch_name>`) List any test failures: N/A Is this a science-changing update? New physics package, algorithm change, tuning changes, etc? No --------- Co-authored-by: Jesse Nusbaumer <[email protected]>
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Closes #101
Also needed are these two PRs with the configuration files
There are a number of TODOs I still need to figure out, and I'm not really sure how to test this properly. The paper detailing the implemented algorithm doesn't seem to list individual values for Js, and I'm not sure what values they used for their extra terrestrial flux, but that could be a potential testing avenue if we thinks its worth me tracking down values from references.