Tidal dissipation parameterisation

[minghangli-uni]

1. Summary:
Tidal dissipation parameterisation

What has changed?
config.yaml
manifests/input.yaml
testing/checksum/historical-3hr-checksum.json
MOM_input
I’ll update the files in docs/ after #556 and ACCESS-NRI/om3-scripts#53 have been merged.

Why was this done?
Ensures physically realistic deep ocean mixing, supports overturning circulation, and enhances model fidelity in long-term coupled simulations.

2. Issues Addressed:

• Parameterize impact of tides #457
• Address missing tidal related external files om3-scripts#52

3. Depedencies (e.g. on payu, model or om3-scripts)

This change requires changes to (note required version where true):

• payu:
• access-om3:
• om3-scripts:

4. Ad-hoc Testing

What ad-hoc testing was done? How are you convinced this change is correct (plots are good)?

5. CI Testing

• !test repro has been run

6. Reproducibility

Is this reproducible with the previous commit? (If not, why not?)

• Yes
• No - !test repro commit has been run.

7. Documentation

The docs folder has been updated with output from running the model?

• Yes
• N/A

A PR has been created for updating the documentation?

• Yes:
• N/A

8. Formatting

Changes to MOM_input have been copied from model output in docs/MOM_parameter_docs.short?

• Yes
• N/A

9. Merge Strategy

• Merge commit
• Rebase and merge
• Squash

[aekiss]

This matches GFDL-OM5 except that these non-default values are missing:

BBL_EFFIC = 0.01                !   [nondim] default = 0.2
                                ! The efficiency with which the energy extracted by bottom drag drives BBL
                                ! diffusion.  This is only used if BOTTOMDRAGLAW is true.
BBL_MIXING_AS_MAX = False       !   [Boolean] default = True
                                ! If true, take the maximum of the diffusivity from the BBL mixing and the other
                                ! diffusivities. Otherwise, diffusivity from the BBL_mixing is simply added.
USE_LOTW_BBL_DIFFUSIVITY = True !   [Boolean] default = False
                                ! If true, uses a simple, imprecise but non-coordinate dependent, model of BBL
                                ! mixing diffusivity based on Law of the Wall. Otherwise, uses the original BBL
                                ! scheme.
SIMPLE_TKE_TO_KD = True         !   [Boolean] default = False
                                ! If true, uses a simple estimate of Kd/TKE that will work for arbitrary
                                ! vertical coordinates. If false, calculates Kd/TKE and bounds based on exact
                                ! energetics for an isopycnal layer-formulation.

[aekiss]

Ignore my previous comment - these are set in #556

[aekiss]

LGTM, thanks @minghangli-uni

[minghangli-uni]

Thanks @aekiss ! Once the tidal forcing PR is merged, I’ll update config.yaml to include the tidal forcings as well. I’ll request another review tomorrow morning.

[minghangli-uni]

!test repro commit

[github-actions]

❌ The Bitwise Reproducibility Check Failed ❌

When comparing:

• 457-tide-parameterisation (checksums created using commit 82391a2), against
• dev-MC_25km_jra_ryf (checksums in commit 44d7453)

🔧 The new checksums will be committed to this PR, if they differ from what is on this branch.

Further information

The experiment can be found on Gadi at /scratch/tm70/repro-ci/experiments/access-om3-configs/82391a2034ebe54e568c88100ec78e60dc92695d, and the test results at https://github.com/ACCESS-NRI/access-om3-configs/runs/43509448898.

The checksums generated by this !test command are found in the testing/checksum directory of https://github.com/ACCESS-NRI/access-om3-configs/actions/runs/15456307844/artifacts/3264050232.

The checksums compared against are found here https://github.com/ACCESS-NRI/access-om3-configs/tree/44d7453b92323f930131485cab8f43910f872c10/testing/checksum

[dougiesquire]

!test repro commit

[dougiesquire]

(Regenerating checksums with the new 6 hour run length)

[github-actions]

❌ !test Command Failed ❌ See https://github.com/ACCESS-NRI/access-om3-configs/actions/runs/15457391027

[minghangli-uni]

❌ !test Command Failed ❌ See https://github.com/ACCESS-NRI/access-om3-configs/actions/runs/15457391027

Gadi is down unexpectedly....

[dougiesquire]

!test repro commit

[github-actions]

❌ The Bitwise Reproducibility Check Failed ❌

When comparing:

• 457-tide-parameterisation (checksums created using commit 13fc8d9), against
• dev-MC_25km_jra_ryf (checksums in commit 44d7453)

🔧 The new checksums will be committed to this PR, if they differ from what is on this branch.

Further information

The experiment can be found on Gadi at /scratch/tm70/repro-ci/experiments/access-om3-configs/13fc8d94e95b9aa6bf83cfe46be7dfd5b6056c6c, and the test results at https://github.com/ACCESS-NRI/access-om3-configs/runs/43513618115.

The checksums generated by this !test command are found in the testing/checksum directory of https://github.com/ACCESS-NRI/access-om3-configs/actions/runs/15457830432/artifacts/3264505121.

The checksums compared against are found here https://github.com/ACCESS-NRI/access-om3-configs/tree/44d7453b92323f930131485cab8f43910f872c10/testing/checksum

[dougiesquire]

Thanks @minghangli-uni. Can you confirm that the bottom_roughness.nc and tideamp.nc are correct for this bathymetry:

/g/data/vk83/prerelease/configurations/inputs/access-om3/share/grids/global.25km/2025.05.15

[dougiesquire]

Also, I get U and V velocity truncations within the first month. Is that expected?

[minghangli-uni]

Thanks @minghangli-uni. Can you confirm that the bottom_roughness.nc and tideamp.nc are correct for this bathymetry:
/g/data/vk83/prerelease/configurations/inputs/access-om3/share/grids/global.25km/2025.05.15

From the histories, yes.

2025.05.15]$ ncdump -h bottom_roughness.nc 
netcdf bottom_roughness {
dimensions:
        yh = 1142 ;
        xh = 1440 ;
variables:
        float h2(yh, xh) ;
                h2:_FillValue = NaNf ;
                h2:long_name = "Polynomial-fit bottom roughness squared (h^2) per model grid cell following Jayne & Laurent (2001)" ;
                h2:units = "m^2" ;
        double lon(yh, xh) ;
                lon:_FillValue = NaN ;
                lon:long_name = "Longitude" ;
                lon:units = "degrees_east" ;
        double lat(yh, xh) ;
                lat:_FillValue = NaN ;
                lat:long_name = "Latitude" ;
                lat:units = "degrees_north" ;

// global attributes:
                :history = "Created by ml0072 (minghangli-uni) on 2025-06-05, using https://github.com/COSIMA/om3-scripts/blob/ac71efbe8bcf9aa9dd9608c5361bfb86f9110693/external_tidal_generation/generate_bottom_roughness_polyfit.py: mpirun -n $PBS_NCPUS python3 generate_bottom_roughness_polyfit.py --topo-file=/g/data/ik11/inputs/SYNBATH/SYNBATH.nc --hgrid-file=/g/data/vk83/prerelease/configurations/inputs/access-om3/mom/grids/mosaic/global.25km/2025.05.15/ocean_hgrid.nc --mask-file=/g/data/vk83/prerelease/configurations/inputs/access-om3/share/grids/global.25km/2025.05.15/ocean_mask.nc --chunk-lat=800 --chunk-lon=1600 --output=/g/data/vk83/prerelease/configurations/inputs/access-om3/mom/tidal_external_files/global.25km/2025.05.15/bottom_roughness.nc" ;

2025.05.15]$ ncdump -h tideamp.nc 
netcdf tideamp {
dimensions:
        yh = 1142 ;
        xh = 1440 ;
variables:
        double lon(yh, xh) ;
                lon:_FillValue = NaN ;
                lon:long_name = "Longitude" ;
                lon:units = "degrees_east" ;
        double lat(yh, xh) ;
                lat:_FillValue = NaN ;
                lat:long_name = "Latitude" ;
                lat:units = "degrees_north" ;
        float tideamp(yh, xh) ;
                tideamp:_FillValue = NaNf ;
                tideamp:regrid_method = "conservative_normed" ;
                tideamp:long_name = "Tidal velocity amplitude" ;
                tideamp:units = "m/s" ;
                tideamp:coordinates = "lat lon" ;

// global attributes:
                :history = "Created by ml0072 (minghangli-uni) on 2025-06-05, using https://github.com/COSIMA/om3-scripts/blob/b232b52b300e51e8d560be0345051083aa6f7fa0/external_tidal_generation/generate_tide_amplitude.py: python3 generate_tide_amplitude.py --hgrid-file=/g/data/vk83/prerelease/configurations/inputs/access-om3/mom/grids/mosaic/global.25km/2025.05.15/ocean_hgrid.nc --mask-file=/g/data/vk83/prerelease/configurations/inputs/access-om3/share/grids/global.25km/2025.05.15/ocean_mask.nc --method=conservative_normed --data-path=/g/data/ik11/inputs/TPXO10_atlas_v2 --output=/g/data/vk83/prerelease/configurations/inputs/access-om3/mom/tidal_external_files/global.25km/2025.05.15/tideamp.nc " ;

[minghangli-uni]

Also, I get U and V velocity truncations within the first month. Is that expected?

Did that occur on the second day? That should be fine though. Also you are using greater timesteps in this PR.

[dougiesquire]

Did that occur on the second day? That should be fine though.

I'll didn't check the day sorry (and I've since cleaned up the test run)

[dougiesquire]

Thanks @minghang!