Add vertical mixing tendencies by hyungyukang · Pull Request #410 · E3SM-Project/Omega

hyungyukang · 2026-05-18T13:28:21Z

This PR adds the velocity and tracer vertical mixing tendency terms. The implicit vertical mixing is solved by using TriDiagDiffSolver and is applied once at the end of each time step.

Implemented implicit vertical mixing using TriDiagDiffSolver.
Added VertMixImplicit to VertMix.
Applied vertical mixing once at the end of each time step.
Note: Tangential velocity, which is required by ComputeGradRichardsonNum in VertMix, is temporarily handled in VertMix.

This PR includes #352 for testing purposes.

Checklist

hyungyukang · 2026-05-18T14:26:24Z

Testing

CTest unit tests

Machine: frontier
Compiler: craygnu, craygnu-mphipcc
Build type: Release
Result: All tests passed

Polaris `omega_pr` suite

Baseline workdir: /lustre/orion/cli115/proj-shared/hgkang/E3SM/OMEGA/Polaris/work/pr_suite/260518_09_vMix_PR/baseline_omega
Baseline build: /lustre/orion/cli115/proj-shared/hgkang/E3SM/OMEGA/Polaris/polaris_main/e3sm_submodules/Omega
PR build: /lustre/orion/cli115/proj-shared/hgkang/E3SM/OMEGA/Omega_hyun_vmixHook_2
PR workdir: /lustre/orion/cli115/proj-shared/hgkang/E3SM/OMEGA/Polaris/work/pr_suite/260518_09_vMix_PR/branch_omega
Machine: frontier
Partition: batch
Compiler: craygnu
Build type: Release
Log: /lustre/orion/cli115/proj-shared/hgkang/E3SM/OMEGA/Polaris/work/pr_suite/260518_09_vMix_PR/branch_omega/polaris_omega_pr.o4609310
Result: All tests passed

hyungyukang · 2026-05-18T14:57:15Z

Tested this branch using ocean/column/vmix_stable from E3SM-Project/polaris#435 and compared with MPAS-O.

Here are results of vmix_stable/forward:

Temperature at day 10:

Normal velocity at day 10:

hyungyukang · 2026-05-19T16:18:07Z

@katsmith133 ,
Here're figures of VertVisc and VertDiff (vertViscTopOfCell and vertDiffTopOfCell in MPAS-O, respectively):

VertVisc at day 10:

VertDiff at day 10

I will retest your branch with this test case since you've updated it.

katsmith133 · 2026-05-19T19:00:42Z

@katsmith133 , Here're figures of VertVisc and VertDiff (vertViscTopOfCell and vertDiffTopOfCell in MPAS-O, respectively):
...
I will retest your branch with this test case since you've updated it.

@hyungyukang, thanks for the plots! I doubt the updates I just made in #352 will result in any difference here, but doesn't hurt to check. Let me pull down this branch and take a look at things and see if anything pops out to me.

hyungyukang · 2026-06-04T17:15:31Z

Test results from column/vmix_stable/forward_no_vadv in Polaris is posted here: #352 (comment)

hyungyukang · 2026-06-04T17:21:46Z

I fixed the bugs related to non-flat bottom topography and ran the overflow test to compare Omega with MPAS-O. MPAS-O was slightly modified to exclude horizontal FCT, since it has not yet been implemented in Omega.

The results below show temperature at 6 hours.

cbegeman · 2026-06-18T20:28:54Z

@hyungyukang The PR doesn't include bottom drag in the implicit mixing, correct? So we will continue to use explicit bottom drag with implicit vmix?

hyungyukang · 2026-06-18T22:17:48Z

@hyungyukang The PR doesn't include bottom drag in the implicit mixing, correct? So we will continue to use explicit bottom drag with implicit vmix?

@cbegeman , Yes, the implicit bottom drag is not included in this PR. I plan to open a separate PR for it after this one is merged.

- Implemented implicit vertical mixing using TriDiagDiffSolver. - Added applyVertMixImplicit to VertMix. - Applied vertical mixing once at the end of each time step. - Note: Tangential velocity is temporarily handled in VertMix.

katsmith133

My comments aren't super major, except for whether we want to split the vertical mixing stuff up in some way in anticipation of having multiple parameterizations.

katsmith133 · 2026-06-24T17:46:51Z

+   GradRichNumSmoothed = Array2DReal("GradRichNumSmoothed", Mesh->NCellsSize,
+                                     VCoord->NVertLayersP1);
+
+   // TODO: Temporary handling of TangentialVelocity


Is this temporary handling to be addressed in a later PR?

katsmith133 · 2026-06-24T17:52:37Z


 } // end defineIOFields

+// Apply implicit velocity vertical mixing


In MPAS-O we have several files for the vertical mixing. One that handles the below calculations and several that do the computation of the coefficients (either from KPP or something else). Do we want to follow that design choice here in Omega? I feel like it might be good, as we add more mixing parameterizations, to have them split off more? Thoughts @vanroekel?

Yes I think so. This is what I'm doing in the forthcoming KPP PR. It's its own class in its own file.

katsmith133 · 2026-06-25T20:58:47Z

+             0.5_Real * (VertVisc(JCell0, K + 1) + VertVisc(JCell1, K + 1)) /
+             (LocRhoSw * SpecVolEdgeTop);
+
+         G = DT * ViscAlphaEdgeTop / PseudoThickEdgeTop;


Do we want more descriptive names for these variables (D, H, and X)?

hyungyukang force-pushed the omega/vmix-hookup branch 5 times, most recently from 7503bfb to 72ab187 Compare May 27, 2026 13:54

hyungyukang mentioned this pull request May 28, 2026

Change shear mixing to LMD94 formulation and add ri smoothing #352

Merged

17 tasks

hyungyukang force-pushed the omega/vmix-hookup branch 3 times, most recently from fd950d6 to 5abe72c Compare June 2, 2026 01:07

katsmith133 self-requested a review June 3, 2026 15:35

hyungyukang force-pushed the omega/vmix-hookup branch from f280be8 to d272fbe Compare June 5, 2026 14:34

sbrus89 requested a review from mwarusz June 17, 2026 15:18

hyungyukang force-pushed the omega/vmix-hookup branch from d272fbe to f2a132f Compare June 18, 2026 18:56

cbegeman self-requested a review June 22, 2026 15:15

katsmith133 and others added 8 commits June 25, 2026 15:42

changes shear mixing to LMD94 formulation and adds ri smoothing

bc24c0a

changes gradrichnum, vertvisc, and vertdiff to nvertlayersp1 dim

210c429

Add ALE projection time intervals to time steppers

51bd3e1

Implement vertical mixing tendency

1c4c1d7

- Implemented implicit vertical mixing using TriDiagDiffSolver. - Added applyVertMixImplicit to VertMix. - Applied vertical mixing once at the end of each time step. - Note: Tangential velocity is temporarily handled in VertMix.

Update VertMixImplicit code and linting

4e82aba

Update codes and add comments

8f49721

Fix linting issues

ee102d2

Change LayerThick to PseudoThick in VertMix tend

3b62a0a

hyungyukang added 7 commits June 25, 2026 15:43

Fix bugs after rebase

b701c6c

Fix tridiag policy change in applyVertMix

bf2b961

Fix linting issue

0a1495e

Fix bugs after rebase

e375921

Fix GPU compile error

69f7847

Fix linting issue

05a2fdf

Fix bugs for non-flat bottom topography and minor updates

abbc5c2

hyungyukang force-pushed the omega/vmix-hookup branch from f2a132f to abbc5c2 Compare June 25, 2026 19:43

katsmith133 reviewed Jun 25, 2026

View reviewed changes


		} // end defineIOFields

		// Apply implicit velocity vertical mixing

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Testing

CTest unit tests

Polaris omega_pr suite

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hyungyukang commented May 18, 2026 •

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Polaris `omega_pr` suite

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