Version 1.0: North Atlantic Update - Tides, Curved Boundaries, Config, and More!😀🤯🥳 #193
Conversation
…CESM when parsing
Override min depth
Changes to make compatible with CESM
having mask table and layout no longer required
Fix layout requirements
fix typo in find replace
Replace minimum layers with min depth
…nt num After talking with Ashley, the find_MOM6_orientation will likely be removed
The function names for rectangular and sinmple boundaries were changed because the tides are a kind of boundary function, the old names now give a warning and call the correct function. GFDL had rough horizontal subsetting for the tpxo dataset (probably for efficiency?), implemented in setup_tides_rectangular_boundaries.
Collapsed the *_tidal_dims functions into the encode_tides function in segment, and add citing documentation to the docstrings for now.
…l-mom6 into croc_with_req_changes
OK, when is ready to review we can talk again? Huge PRs are harder to review though and take longer...
Each of the major features mentioned in the first comment sounds like could be a PR? Just a suggestion.. |
haha, sorry if I introduced this difficulty to devs |
…x __getattr__ bug (#24)
… + tests (#30) * Package type changes for CRR * Black Formatting * Change MOM Param * Change MOM_param to Work * black * Revert back to reg * Add tide boundary flexibility * Update Config to only vars * Update Write and Read Config for computer independence * Update Read/Write Config for Computer Independenc * Fix Change MOM Param Issues * Fix bug in __getattr__ and comment out matplotlib dependencies in demo * Package type changes for CRR * Black Formatting * Add Boundaries to Init part 1 * black formatting * Changing Boundary Def to __init__ pt 2 * Minor Bugs * Make Direction Dir a one-time calculation because keys() doesn't gaurentee order * Rearrange handling boundaries in __init__ to a boundary array and segments dict in the boundary functions ocean_state and tides * Clean * Improve commenting on setuop_ocean_state_boundaries * Fix bug in declaring number of OBC segments * Minor Big in override * Add boundaries to config
| @@ -1754,6 +2504,198 @@ def setup_run_directory( | |||
| 0, | |||
| ] | |||
| nml.write(self.mom_run_dir / "input.nml", force=True) | |||
| return | |||
|
|
|||
| def change_MOM_parameter( | |||
There was a problem hiding this comment.
I think this MOM parameter file stuff could get lifted out to a separate file?
There was a problem hiding this comment.
Hey Angus,
This would be a pretty big change. Any chance you would mind if we made this an issue instead and punted on it so we can get this PR out the door? I have no disagreements with this comment!
- Manish
|
Is this still being verified? I can't wait |
|
Thanks for prompting! @navidcy – I have something to run by you. The new features we want to demonstrate in an example notebook are a) tides, b) rotated grids and c) user can input own grid Using the existing Tasman example, we can add a couple of lines to generate the tidal forcing to tick off a. To tick off b and c I am creating an example rotated grid for the user to input. There is only one small difference between a user-inputted grid and a grid generated by this toolbox – so we are suggesting that we include a comment to explain this on the existing notebook rather than creating 2 separate example notebooks. Will this work for you? When I have it, I will upload the example notebook for everyone to comment. |
Yes, thank you, this should be very useful, I urgently need a tidal boundary to run a model |
Hi, you can use branch of the code as it currently is. It's stable for domains with boundaries parallel to lines of constant lat and lon, but has had issues on curved boundaries so far. That's what is holding up the merge, but if you need tides right now then no reason to wait for this |
- correct the first arg of a classmethod (from self to cls). - introduce optional write_to_file arg in setup_bathymetry. - introduce optional bathymetry obj arg in tidy_bathymetry.
…filenames. Similarly, add thickesses arg to _make_vgrid.
Minor changes ahead of CrocoDash-visualCaseGen integration
|
Hi @navidcy
Note that the new package does not include the ability to create hgrid.nc for curvilinear and rotated domains, you need to BYO. I have created one notebook that demonstrates BYO domain and tidal forcing, which I am running with an example rotated + curvilinear h_grid.nc. Do you have suggestions for how the rotated/curvilinear h_grid should be delivered for testing the pull request? It is currently on the crocodile docker and we are discussing if this should be imported to the testing suite for the COSIMA regional mom6. I can also email you (or the pull request reviewer) a copy or put it online somewhere |
I think it's great to modify slightly the current example for a. and then include another one for b and c.! (sorry for the slack; I was on break and slowly catching up!) |
|
@helenmacdonald and others, when this PR is ready for review ping me (and @angus-g?)? |
Thanks! |
|
@helenmacdonald, I'm a bit confused: you have a different PR? isn't this the PR we are referring to? |
|
Sorry @navidcy I should have clarified. I am working on an example notebook for Manish to pull into the crocodile-CESM:main to then be added to this pull request. From the perspective of cosima:main there will only be 1 pull request. |
|
Gotcha |
… tracers, add proper body tide parameters, add MOM6's angle calculation. (#33) * Add GFDL Rotation Code and minor tides debugging in setup_run_directory The GFDL rotation code was commented out🙈 * Black * Actual Angle Change * Minor Clean * Add First Regridding Option * More tidal changes * Change default tides to use all constituents in TPXO allowed in MOM6 * Fix Tests * Start of Angle Calc * Blacl * Rand * Clean up testing (#37) * Remove extra directories created * Black * Clean up created dirs * Rand * Keith Method Step 1, add t-point boundaries to coords() * Start implementing alternative angles approaches... * Set up rotational method framework * Add h, t, and change default mom6_angle_calc to regional * black * Fred Angle Calc * Black * Black 2 * Keith Method * Tidal Rotational Methods Completed * Finish rotational methods for velocity_tracers * Combine the grid_rotation_calc for fred_pseudo and mom6 general (keiths) * Move rotation/angle functions to a different file * Doesn't make sense to use rot method in expt because the regrid methods are in segment right now. Something to discuss and then add * Clean up the keith method to use the regridding func add_secondary_dimension * Add angle_calc to docs * Main Page Link for now... * Start testing setup * Change func name for consistency * Minor Commenting * Minor Commenting * Black * Redo Auto Docs * Start of testing * Test until curved grid generation comes in * Bug * Test_Rotation Changes * Adjust Docker Path * Testing Framework Trial 1 * Docker Docs * Test Cleaning * Change name of docker docs * Adjust docker image to crocodile one * Step 1: Setup Framework Tidal Regridding Nans/LandMask BugFix * Finish setting up masking framework * Clean up process of masking * Regridding Testing except for the mask functions * First round testing w/o mask tests * First Round Testing Completed * Minor Clean * MOM6 Angle Calculation (#34) * Start of Angle Calc * Blacl * Rand * Rand * Keith Method Step 1, add t-point boundaries to coords() * Start implementing alternative angles approaches... * Set up rotational method framework * Add h, t, and change default mom6_angle_calc to regional * black * Fred Angle Calc * Black * Black 2 * Keith Method * Tidal Rotational Methods Completed * Finish rotational methods for velocity_tracers * Combine the grid_rotation_calc for fred_pseudo and mom6 general (keiths) * Move rotation/angle functions to a different file * Doesn't make sense to use rot method in expt because the regrid methods are in segment right now. Something to discuss and then add * Clean up the keith method to use the regridding func add_secondary_dimension * Add angle_calc to docs * Main Page Link for now... * Start testing setup * Change func name for consistency * Minor Commenting * Minor Commenting * Black * Redo Auto Docs * Start of testing * Test until curved grid generation comes in * Bug * Test_Rotation Changes * Adjust Docker Path * Testing Framework Trial 1 * Docker Docs * Test Cleaning * Change name of docker docs * Adjust docker image to crocodile one * Step 1: Setup Framework Tidal Regridding Nans/LandMask BugFix * Finish setting up masking framework * Revert "Finish setting up masking framework" This reverts commit 9287030. * Revert "Step 1: Setup Framework Tidal Regridding Nans/LandMask BugFix" This reverts commit a2b961a. * respond to alper comments * Docs changes * Seg Fault Issue Pt1 * Disable threading * Just single threading * Clean up testing * Remove Single Threading * Add back single threading * Spelling Mistake * Zero Out Attempt * Black + Add Mask to Regrid_vt * Zero Out Corner + 3 Cell * Update Land Mask Tests * Fix Bathy NTiles Issue * Minor Cleaning + Variable Renaming * minor changes ahead of visualCaseGen integration in CrocoDash: - correct the first arg of a classmethod (from self to cls). - introduce optional write_to_file arg in setup_bathymetry. - introduce optional bathymetry obj arg in tidy_bathymetry. * Mirro GFDL NWA12-Cobalt a bit more and add diag table date adjustment * Black * Add aiohttp and copernicusmarine dependencies * add hgrid_path and vgrid_path args to __init__ to allow non-standard filenames. Similarly, add thickesses arg to _make_vgrid. * black reformatting * Update Initial Condition + Alternate Rotation Function * Rename get_glorys_rect to get_glorys * Move RM6 to logging over print statements, but still report regional_mom6 to stdout * Formatting * Fix logging bug * Revert RM6 Logging * Formatting * Alper Review Comments Pt1 * Relative Imports * Revert "Relative Imports" This reverts commit 15d8d36. * Check if the ESMF warning is the issue in the tests failure * Add Rotational Methods function * Small Adj to Docs' --------- Co-authored-by: alperaltuntas <[email protected]>
* First Round outside of OBC String making and strptime dates * Completed Review Comments * Black * Minor Bug Catch
Authors: @ashjbarnes, @manishvenu
Description:
Ashley and I worked together to add a few features to RM6. While we get the changes ready to merge with the main COSIMA branch, please check out this draft with a list of the changes below.
Major Features:
Minor Features:
Breaking Changes (for backwards compatibility):
Documentation Changes:
Co-authored-by: @ashjbarnes
this PR closes #184 , #168 , and also #55 in a roundabout way since user now specifies which boundaries they want, and the MOM inputs are adjusted accordingly.
Before merging, need to resolve the following:
Outstanding Questions:
regridding.pyandrotation.py). Do we want to switch over RM6 to use python logging instead of print statements? Currently, we would prefer that but open it up to opinions.