Upgrading to atmos_phys0_07_001 #187
Merged
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
…ants (#152) Originator(s): @boulderdaze Summary (include the keyword ['closes', 'fixes', 'resolves'] and issue number): - Update extraterrestrial flux in TUV-x prior to calculating rate constants - Closes #97 Describe any changes made to the namelist: N/A List all files eliminated and why: ``` D test/musica/tuvx/configs/ts1_tsmlt.json ``` We have moved the MUSICA configuration to [CAM-SIMA Chemistry Data](https://github.com/NCAR/cam-sima-chemistry-data) repository List all files added and what they do: ``` A schemes/musica/tuvx/musica_ccpp_tuvx_extraterrestrial_flux.F90 A test/musica/tuvx/test_tuvx_extraterrestrial_flux.F90 A to_be_ccppized/ccpp_tuvx_utils.F90 ``` List all existing files that have been modified, and describe the changes: ``` M schemes/musica/micm/musica_ccpp_micm.F90 M schemes/musica/musica_ccpp.F90 M schemes/musica/musica_ccpp.meta M schemes/musica/tuvx/musica_ccpp_tuvx.F90 M schemes/musica/tuvx/musica_ccpp_tuvx_surface_albedo.F90 M schemes/musica/tuvx/musica_ccpp_tuvx_temperature.F90 M schemes/musica/tuvx/musica_ccpp_tuvx_util.F90 M schemes/musica/tuvx/musica_ccpp_tuvx_wavelength_grid.F90 M test/CMakeLists.txt M test/docker/Dockerfile.musica M test/docker/Dockerfile.musica.no_install M test/musica/CMakeLists.txt M test/musica/test_musica_api.F90 M test/musica/tuvx/CMakeLists.txt ``` List any test failures: N/A Is this a science-changing update? New physics package, algorithm change, tuning changes, etc? No --------- Co-authored-by: Matt Dawson <[email protected]>
…156) Originator(s): @boulderdaze Summary (include the keyword ['closes', 'fixes', 'resolves'] and issue number): - Simplify deallocation of multiple objects associated with the TUV-x - Closes #155 Describe any changes made to the namelist: N/A List all files eliminated and why: ``` D schemes/musica/tuvx/musica_ccpp_tuvx_util.F90 ``` Moved the deallocation helper function to schemes/musica/tuvx/musica_ccpp_tuvx.F90 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/tuvx/musica_ccpp_tuvx.F90 ``` List any test failures: N/A Is this a science-changing update? New physics package, algorithm change, tuning changes, etc? No --------- Co-authored-by: Matt Dawson <[email protected]>
Originator(s): @jimmielin Summary (include the keyword ['closes', 'fixes', 'resolves'] and issue number): Fixes #159. b4b changes to include errmsg, errflg in the check_energy schemes 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>`) ``` Add errmsg, errflg (or set when not previously set) in check_energy schemes. M schemes/check_energy/check_energy_chng.F90 M schemes/check_energy/check_energy_fix.F90 M schemes/check_energy/check_energy_fix.meta M schemes/check_energy/check_energy_gmean/check_energy_gmean.F90 M schemes/check_energy/check_energy_gmean/check_energy_gmean.meta M schemes/check_energy/check_energy_save_teout.F90 M schemes/check_energy/check_energy_save_teout.meta M schemes/check_energy/check_energy_zero_fluxes.F90 M schemes/check_energy/check_energy_zero_fluxes.meta M schemes/check_energy/dycore_energy_consistency_adjust.F90 M schemes/check_energy/dycore_energy_consistency_adjust.meta ``` List any test failures: N/A Is this a science-changing update? New physics package, algorithm change, tuning changes, etc? No
Originator(s): @boulderdaze Summary (include the keyword ['closes', 'fixes', 'resolves'] and issue number): - Add an automated checker that validates the MUSICA meta data against the CCPP standard names - Closes #120 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: ``` M doc/NamesNotInDictionary.txt M schemes/musica/musica_ccpp_namelist.xml M test/docker/Dockerfile.musica M test/docker/Dockerfile.musica.no_install M test/musica/CMakeLists.txt ``` List any test failures: N/A Is this a science-changing update? New physics package, algorithm change, tuning changes, etc? No --------- Co-authored-by: Matt Dawson <[email protected]>
Originator(s): peverwhee Summary (include the keyword ['closes', 'fixes', 'resolves'] and issue number): Adds the `apply_constituent_tendencies` scheme to `utilties/physics_tendency_updaters.F90`. - Replaces dadadj_apply_qv_tendency in the dadadj suite. Describe any changes made to the namelist: None List all files eliminated and why: D schemes/dry_adiabatic_adjust/dadadj_apply_qv_tendency.F90 D schemes/dry_adiabatic_adjust/dadadj_apply_qv_tendency.meta - remove now-unnecessary temporary water vapor state update scheme List all files added and what they do: none 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/dry_adiabatic_adjust/dadadj.meta - add `constituent = True` metadata property to tendency variable M schemes/utilities/physics_tendency_updaters.F90 M schemes/utilities/physics_tendency_updaters.meta - add new `apply_constituent_tendencies` scheme M test/test_suites/suite_dry_adiabatic_adjust.xml - replace temporary tendency updater scheme with new one List any test failures: none - Confirmed no differences found with ne5 run of dadadj (compared to snapshots) on derecho Is this a science-changing update? New physics package, algorithm change, tuning changes, etc? No --------- Co-authored-by: Courtney Peverley <[email protected]>
Adds the calculation of cloud optical properties to TUV-x for photolysis rate constant calculations. The algorithm is adapted from a post-calculation modification of photolysis rate constants calculated by the lookup version of TUV-x in CAM to account for the effects of clouds, [here](https://github.com/ESCOMP/CAM/blob/47dd341f83afc1e1faf28fd4cb6e463629db4c19/src/chemistry/mozart/mo_photo.F90#L949-L965) closes #100 Adds a few more Valgrind suppressions for minor memory leaks during initialization functions in 2 tests (9 and 72 bytes). We will look into these, but they are expected to go away as TUV-x is moved out of Fortran.
Originator(s): peverwhee Summary (include the keyword ['closes', 'fixes', 'resolves'] and issue number): Adds new (non-portable) initialize_constituents scheme (.F90 and .meta). This scheme will be used to instantiate all constituents in the file (used to validate schemes that need the full constituent array but do not modify all of the individual constituents). Added to new "test_schemes" directory. 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: A test/test_schemes/initialize_constituents.F90 A test/test_schemes/initialize_constituents.F90 - add initialize_constituents scheme List all existing files that have been modified, and describe the changes: (Helpful git command: git diff --name-status development...<your_branch_name>) List any test failures: none Is this a science-changing update? New physics package, algorithm change, tuning changes, etc? No --------- Co-authored-by: Courtney Peverley <[email protected]>
Originator(s): peverwhee Summary (include the keyword ['closes', 'fixes', 'resolves'] and issue number): Add state and tend diagnostics schemes to the test TJ2016 schemes so that the tests will create history files. Also fix the tendency units for wind variables. Describe any changes made to the namelist: none List all files eliminated and why: none List all files added and what they do: none List all existing files that have been modified, and describe the changes: (Helpful git command: `git diff --name-status development...<your_branch_name>`) M test/test_schemes/suite_tj2016_sfc_pbl_hs.xml M test/test_schemes/suite_tj2016_precip.xml - Add state and tend diagnostic schemes M schemes/tj2016/tj2016_sfc_pbl_hs.meta - fix wind tendency units List any test failures: none Is this a science-changing update? New physics package, algorithm change, tuning changes, etc? no.
Originator(s): peverwhee Summary (include the keyword ['closes', 'fixes', 'resolves'] and issue number): Update units of "radians" to "rad" to adhere to SI unit conventions closes #172 Describe any changes made to the namelist: none List all files eliminated and why: none List all files added and what they do: none 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/held_suarez/held_suarez_1994.meta M schemes/tj2016/tj2016_sfc_pbl_hs.meta M schemes/tropopause_find/tropopause_find.meta - update units List any test failures: none Is this a science-changing update? New physics package, algorithm change, tuning changes, etc? no.
Adds the calculation of solar zenith angle and Earth-Sun distance needed as inputs to TUV-x. closes #163 closes #164 Both calculations required functions that are currently in shared code in CAM [here](https://github.com/ESCOMP/CESM_share/blob/f6f31fd61cb8f80aee97311fcca64b3e26b0202c/src/shr_orb_mod.F90#L736-L814) and [here](https://github.com/ESCOMP/CESM_share/blob/f6f31fd61cb8f80aee97311fcca64b3e26b0202c/src/shr_orb_mod.F90#L110-L159) that I put in a modified form in the `to_be_ccppized/` folder. @nusbaume @peverwhee - if there is a better way to handle these functions, let me know and I can update the PR. Requires an update to CAM-SIMA that is in review to make certain variables available through CCPP (ESCOMP/CAM-SIMA#325) After more discussion, the plan is to use the shared functions in CAM-SIMA and pass the outputs through CCPP. So, this PR will be put in draft until this issue is finished: ESCOMP/CAM-SIMA#328 A related draft PR to CAM-SIMA has been added (ESCOMP/CAM-SIMA#337) and will be un-drafted once this PR is merged in.
Fixes ESCOMP/CAM-SIMA#308 Requires a companion PR in CAM-SIMA to update the standard name of `tropp_slices` there as well: ESCOMP/CAM-SIMA#329
Uses units of `fraction` for surface albedo in meta data. Also, uses `rad` instead of `radians` in metadata. closes #180
…dles (#185) Originator(s): peverwhee Summary (include the keyword ['closes', 'fixes', 'resolves'] and issue number): Removes water_species property from instantiate call for water vapor mixing ratio species (as air_composition will set those). We may run into this issue again at some point for the water vapor number concentration variables, but hopefully by then we'll have metadata properties for setting that! can supersede ESCOMP/CAM-SIMA#342 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 test/test_schemes/initialize_constituents.F90 - remove water_species property from instantiate call List any test failures: all expected tests pass Is this a science-changing update? New physics package, algorithm change, tuning changes, etc? no
nusbaume
approved these changes
Dec 30, 2024
cacraigucar
added a commit
to cacraigucar/atmospheric_physics
that referenced
this pull request
Jan 13, 2025
Upgrading to atmos_phys0_07_001 (ESCOMP#187)
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.
Tag name (The PR title should also include the tag name):
atmos_phys0_07_001Originator(s): @jimmielin
List all
developmentPR URLs included in this PR and a short description of each:List all test failures: N/A