Version 1.0: North Atlantic Update - Tides, Curved Boundaries, Config, and More!😀🤯🥳 #193
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…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
| @@ -129,7 +129,7 @@ def test_quadrilateral_areas(lat, lon, true_area): | |||
| ], | |||
| ) | |||
| def test_rectangular_hgrid(lat, lon): | |||
| assert isinstance(rectangular_hgrid(lat, lon), xr.Dataset) | |||
| assert isinstance(generate_rectangular_hgrid(lat, lon), xr.Dataset) | |||
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The args are reversed in the test compared to the method definition
Probably doesn't matter for this test, but it might create confusion to users/developers.
Yes it's a huge PR! We did have this broken down into smaller PRs on the CROCODILE fork, which we reviewed and merged one by one over the last couple of months. Unfortunately these PRs might not be useful for us to break up this big one any more, because we did need to do a lot of merging given that @manishvenu and I were working in parallel on several changes. It's still in draft state for now while we polish it (build on the Is there a way you suggest that we break up the PR? Since we did a huge overhaul of the entire codebase, it's kind of hard to separate some of the changes! |
…up_run_directory (#20) * Package type changes for CRR * Black Formatting * Change MOM Param * Change MOM_param to Work * black * Remvoe premade_run_dir_arg * Remove init * Black * Update MOM_param_test * Clean
* include DataReader class * within __getattr__ read data files * bug * update demo with plots * typo
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
| except: | ||
| raise ValueError( | ||
| "Invalid Input. Tidal constituent {} is not supported.".format(tc) | ||
| ) |
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There'll be a few of these, but catch only the exception you're looking for here. I guess in this case it's a KeyError?
| list_of_ints = [] | ||
| for tc in tidal_constituents: | ||
| try: | ||
| list_of_ints.append(tidal_constituents_tpxo_dict[tc]) | ||
| except: | ||
| raise ValueError( | ||
| "Invalid Input. Tidal constituent {} is not supported.".format(tc) | ||
| ) | ||
|
|
||
| return list_of_ints |
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| list_of_ints = [] | |
| for tc in tidal_constituents: | |
| try: | |
| list_of_ints.append(tidal_constituents_tpxo_dict[tc]) | |
| except: | |
| raise ValueError( | |
| "Invalid Input. Tidal constituent {} is not supported.".format(tc) | |
| ) | |
| return list_of_ints | |
| try: | |
| constituent_indices = [constituent_map[tc] for tc in tidal_constituents] | |
| except KeyError as e: | |
| raise ValueError(f"Invalid tidal constituent: {e.args[0]}") | |
| return constituent_indices |
| try: | ||
| expt.longitude_extent = tuple(config_dict["longitude_extent"]) | ||
| expt.latitude_extent = tuple(config_dict["latitude_extent"]) | ||
| except: | ||
| expt.longitude_extent = None | ||
| expt.latitude_extent = None |
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| try: | |
| expt.longitude_extent = tuple(config_dict["longitude_extent"]) | |
| expt.latitude_extent = tuple(config_dict["latitude_extent"]) | |
| except: | |
| expt.longitude_extent = None | |
| expt.latitude_extent = None | |
| try: | |
| expt.longitude_extent = tuple(config_dict["longitude_extent"]) | |
| expt.latitude_extent = tuple(config_dict["latitude_extent"]) | |
| except KeyError: | |
| expt.longitude_extent = None | |
| expt.latitude_extent = None |
Check that extents are correct length?
| try: | ||
| expt.date_range = config_dict["date_range"] | ||
| expt.date_range[0] = dt.datetime.strptime( | ||
| expt.date_range[0], "%Y-%m-%d %H:%M:%S" | ||
| ) | ||
| expt.date_range[1] = dt.datetime.strptime( | ||
| expt.date_range[1], "%Y-%m-%d %H:%M:%S" | ||
| ) | ||
| except: | ||
| expt.date_range = None |
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Maybe KeyError for the path where expt.date_range = None, but if you handle IndexError separately you can warn/error on the incorrect range input.
| if mom_input_folder is None: | ||
| mom_input_folder = Path(os.path.join("mom_run", "from_config")) | ||
| if mom_run_folder is None: | ||
| mom_run_folder = Path(os.path.join("mom_input", "from_config")) |
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| if mom_input_folder is None: | |
| mom_input_folder = Path(os.path.join("mom_run", "from_config")) | |
| if mom_run_folder is None: | |
| mom_run_folder = Path(os.path.join("mom_input", "from_config")) | |
| if mom_input_folder is None: | |
| mom_input_folder = Path("mom_run" / "from_config") | |
| if mom_run_folder is None: | |
| mom_run_folder = Path("mom_input" / "from_config") |
or just e.g. "mom_input/from_config"
| if seg == "south": | ||
| index_str = '"J=0,I=0:N' | ||
| elif seg == "north": | ||
| index_str = '"J=N,I=N:0' | ||
| elif seg == "west": | ||
| index_str = '"I=0,J=N:0' | ||
| elif seg == "east": | ||
| index_str = '"I=N,J=0:N' |
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Would be a little cleaner as a dictionary
| key_DATA = key_start + "_DATA" | ||
| file_num_obc = str( | ||
| self.find_MOM6_rectangular_orientation(seg) | ||
| ) # 1,2,3,4 for rectangular boundaries, BUT if we have less than 4 segments we use the index to specific the number, but keep filenames as if we had four boundaries | ||
| MOM_override_dict[key_DATA][ | ||
| "value" | ||
| ] = f'"U=file:forcing_obc_segment_00{file_num_obc}.nc(u),V=file:forcing_obc_segment_00{file_num_obc}.nc(v),SSH=file:forcing_obc_segment_00{file_num_obc}.nc(eta),TEMP=file:forcing_obc_segment_00{file_num_obc}.nc(temp),SALT=file:forcing_obc_segment_00{file_num_obc}.nc(salt)' | ||
| if with_tides: | ||
| MOM_override_dict[key_DATA]["value"] = ( | ||
| MOM_override_dict[key_DATA]["value"] | ||
| + f',Uamp=file:tu_segment_00{file_num_obc}.nc(uamp),Uphase=file:tu_segment_00{file_num_obc}.nc(uphase),Vamp=file:tu_segment_00{file_num_obc}.nc(vamp),Vphase=file:tu_segment_00{file_num_obc}.nc(vphase),SSHamp=file:tz_segment_00{file_num_obc}.nc(zamp),SSHphase=file:tz_segment_00{file_num_obc}.nc(zphase)"' | ||
| ) | ||
| else: | ||
| MOM_override_dict[key_DATA]["value"] = ( | ||
| MOM_override_dict[key_DATA]["value"] + '"' | ||
| ) |
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Would be a bit clearer to build up the value string outside of the dictionary, then only set it at the end.
Should also split the really long lines, i.e.
obc_string = (
f",Uamp=file:tu_segment_00{file_num_obc}.nc(uamp),"
f"Uphase=file:tu_segment_00{file_num_obc}.nc(uphase),"
f"Vamp=file:tu_segment_00{file_num_obc}.nc(vamp),"
f"Vphase=file:tu_segment_00{file_num_obc}.nc(vphase),"
f"SSHamp=file:tz_segment_00{file_num_obc}.nc(zamp),"
f"SSHphase=file:tz_segment_00{file_num_obc}.nc(zphase)"'
)| str(self.date_range[0].year) | ||
| + ", " | ||
| + str(self.date_range[0].month) | ||
| + ", " | ||
| + str(self.date_range[0].day) | ||
| ) |
| for key in MOM_override_dict.keys(): | ||
| if type(MOM_override_dict[key]) == dict: | ||
| MOM_override_dict[key]["override"] = True |
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| for key in MOM_override_dict.keys(): | |
| if type(MOM_override_dict[key]) == dict: | |
| MOM_override_dict[key]["override"] = True | |
| for key, val in MOM_override_dict.items(): | |
| if isinstance(val, dict): | |
| MOM_override_dict[key]["override"] = True |
| @@ -1754,6 +2504,198 @@ def setup_run_directory( | |||
| 0, | |||
| ] | |||
| nml.write(self.mom_run_dir / "input.nml", force=True) | |||
| return | |||
|
|
|||
| def change_MOM_parameter( | |||
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I think this MOM parameter file stuff could get lifted out to a separate file?
|
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!) |
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@helenmacdonald and others, when this PR is ready for review ping me (and @angus-g?)? |
Thanks! |
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@helenmacdonald, I'm a bit confused: you have a different PR? isn't this the PR we are referring to? |
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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. |
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Gotcha |
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: