Mwarusz/omega/submesoscale eddies by mwarusz · Pull Request #8 · mwarusz/E3SM

mwarusz · 2026-07-14T16:11:22Z

No description provided.

mwarusz · 2026-07-14T16:14:05Z

@copilot Please add user and developer documentation for the submesoscale eddy parametrization added in this PR in the same style as the documentation of other components in doc/userGuide and doc/devGuide.

Copilot · 2026-07-14T16:17:48Z

@copilot Please add user and developer documentation for the submesoscale eddy parametrization added in this PR in the same style as the documentation of other components in doc/userGuide and doc/devG...

Implemented in commit 409f413. I added new pages for both guides (components/omega/doc/userGuide/SubmesoEddies.md and components/omega/doc/devGuide/SubmesoEddies.md) and added them to the Omega docs toctrees in components/omega/doc/index.md.

mwarusz · 2026-07-14T16:39:25Z

@copilot In the developer docs please add more detail about inputs to the core methods of the SubmesoEddies class.

Copilot · 2026-07-14T16:41:23Z

@copilot In the developer docs please add more detail about inputs to the core methods of the SubmesoEddies class.

Implemented in commit 7cc031e. I expanded the developer guide with a new Core method inputs section in components/omega/doc/devGuide/SubmesoEddies.md covering the inputs and data dependencies for computeDenMixLayerDepth, computeBuoyGrad, and computeEddyVelocity.

mwarusz · 2026-07-14T19:55:32Z

@copilot Improve the wording of the developer docs without making substantial changes.

Copilot · 2026-07-14T19:57:07Z

@copilot Improve the wording of the developer docs without making substantial changes.

Updated with wording-only improvements in the developer docs, without substantial content changes. Addressed in commit b003252.

Copilot

Pull request overview

This PR introduces an optional submesoscale mixed-layer instability (MLI) parameterization (“SubmesoEddies”) to Omega, wiring it into the auxiliary-state transport velocity used by pseudo-thickness and tracer advection, and adds accompanying documentation, tests, and machine/build support updates.

Changes:

Add SubmesoEddies singleton (mixed-layer depth, buoyancy gradient, eddy velocity) and initialize/finalize it in the ocean driver lifecycle.
Introduce TransportAuxVars::NormalTransportVelocity and refactor tendencies to use transport velocity (base flow + optional submeso eddy-induced component).
Update test utilities (setScalar/setVectorEdge) and add a new unit test for SubmesoEddies, plus documentation and config defaults.

Reviewed changes

Copilot reviewed 73 out of 73 changed files in this pull request and generated 5 comments.

Show a summary per file

File	Description
components/omega/test/ocn/TendencyTermsTest.cpp	Update test lambdas to match new `setScalar`/`setVectorEdge` functor signatures.
components/omega/test/ocn/TendenciesTest.cpp	Update test setup calls to pass `nullptr` ZCoord and updated functor signatures.
components/omega/test/ocn/SubmesoEddiesTest.cpp	New unit test exercising mixed-layer depth, buoyancy gradient, and eddy velocity.
components/omega/test/ocn/OceanTestCommon.h	Extend `setScalar`/`setVectorEdge` to pass element indices and optional Z-coordinates.
components/omega/test/ocn/HorzOperatorsTest.cpp	Update operator tests for new `setScalar`/`setVectorEdge` signatures.
components/omega/test/ocn/ForcingTest.cpp	Update forcing tests for new `setScalar`/`setVectorEdge` signatures.
components/omega/test/ocn/AuxiliaryVarsTest.cpp	Update aux-var tests for new `setScalar`/`setVectorEdge` signatures.
components/omega/test/ocn/AuxiliaryStateTest.cpp	Update aux-state test init to pass `nullptr` ZCoord and updated signatures.
components/omega/test/CMakeLists.txt	Adjust test command and add SubmesoEddies test; MPI arg formatting changes.
components/omega/src/timeStepping/ForwardBackwardStepper.cpp	Pass tracer array into pseudo-thickness tendency computation.
components/omega/src/ocn/Tendencies.h	Extend pseudo-thickness tendency API to accept tracer array.
components/omega/src/ocn/Tendencies.cpp	Use `AuxState` helpers for pseudo-thickness/tracer aux, and switch to transport velocity for advection operators.
components/omega/src/ocn/SubmesoEddies.h	New submesoscale eddy parameterization interface (+ `linearInterp`).
components/omega/src/ocn/SubmesoEddies.cpp	New implementation and IO field definitions for submeso diagnostics.
components/omega/src/ocn/OceanInit.cpp	Initialize `SubmesoEddies` during module init.
components/omega/src/ocn/OceanFinal.cpp	Destroy `SubmesoEddies` during finalization.
components/omega/src/ocn/auxiliaryVars/TransportAuxVars.h	New aux-var container for normal transport velocity.
components/omega/src/ocn/auxiliaryVars/TransportAuxVars.cpp	Register/unregister `NormalTransportVelocity` field with IO metadata.
components/omega/src/ocn/AuxiliaryState.h	Add `TransportAux` member and new compute methods for transport/pseudo-thickness/tracer aux.
components/omega/src/ocn/AuxiliaryState.cpp	Compute and apply submeso eddy-induced velocity into `NormalTransportVelocity`; refactor aux computations.
components/omega/src/CMakeLists.txt	Remove `stdc++fs` linkage (commented out).
components/omega/OmegaBuild.cmake	Allow skipping CIME config in standalone build via `OMEGA_SKIP_CIME`.
components/omega/machines/nocime/workmac-clang.cmake	New “nocime” machine preset for a mac clang/mpich-style build.
components/omega/machines/nocime/pm-gpu-gcc.env	New nocime env module file.
components/omega/machines/nocime/pm-gpu-gcc.cmake	New nocime cmake preset.
components/omega/machines/nocime/pm-cpu-intel.env	New nocime env module file.
components/omega/machines/nocime/pm-cpu-intel.cmake	New nocime cmake preset.
components/omega/machines/nocime/pm-cpu-gcc.env	New nocime env module file.
components/omega/machines/nocime/pm-cpu-gcc.cmake	New nocime cmake preset.
components/omega/machines/nocime/liczydlo-gpu-amdclang.cmake	New nocime cmake preset.
components/omega/machines/nocime/liczydlo-cpu-gcc.cmake	New nocime cmake preset.
components/omega/machines/nocime/liczydlo-cpu-amdclang.cmake	New nocime cmake preset.
components/omega/machines/nocime/frontier-gpu-amdclang.env	New nocime env module file.
components/omega/machines/nocime/frontier-gpu-amdclang.cmake	New nocime cmake preset.
components/omega/machines/nocime/frontier-cpu-gcc.env	New nocime env module file.
components/omega/machines/nocime/frontier-cpu-gcc.cmake	New nocime cmake preset.
components/omega/machines/nocime/frontier-cpu-amdclang.env	New nocime env module file.
components/omega/machines/nocime/frontier-cpu-amdclang.cmake	New nocime cmake preset.
components/omega/machines/nocime/chrysalis-intel.env	New nocime env module file.
components/omega/machines/nocime/chrysalis-intel.cmake	New nocime cmake preset.
components/omega/machines/nocime/blake-pvc-intel.env	New nocime env module file.
components/omega/machines/nocime/blake-pvc-intel.cmake	New nocime cmake preset.
components/omega/machines/nocime/blake-h100-gcc.env	New nocime env module file.
components/omega/machines/nocime/blake-h100-gcc.cmake	New nocime cmake preset.
components/omega/machines/nocime/blake-cpu-polaris.env	New nocime env module file.
components/omega/machines/nocime/blake-cpu-polaris.cmake	New nocime cmake preset.
components/omega/machines/nocime/blake-cpu-intel.env	New nocime env module file.
components/omega/machines/nocime/blake-cpu-intel.cmake	New nocime cmake preset.
components/omega/machines/nocime/blake-cpu-gcc.env	New nocime env module file.
components/omega/machines/nocime/blake-cpu-gcc.cmake	New nocime cmake preset.
components/omega/machines/nocime/aurora-gpu-intel.env	New nocime env module file.
components/omega/machines/nocime/aurora-gpu-intel.cmake	New nocime cmake preset.
components/omega/machines/cime/pm-gpu-nvidiagpu.cmake	New CIME-backed machine preset.
components/omega/machines/cime/pm-gpu-gnugpu.cmake	New CIME-backed machine preset.
components/omega/machines/cime/pm-cpu-nvidia.cmake	New CIME-backed machine preset.
components/omega/machines/cime/pm-cpu-intel.cmake	New CIME-backed machine preset.
components/omega/machines/cime/pm-cpu-gnu.cmake	New CIME-backed machine preset.
components/omega/machines/cime/frontier-gnu.cmake	New CIME-backed machine preset.
components/omega/machines/cime/frontier-craygnu.cmake	New CIME-backed machine preset.
components/omega/machines/cime/frontier-craygnu-mphipcc.cmake	New CIME-backed machine preset.
components/omega/machines/cime/frontier-craycray.cmake	New CIME-backed machine preset.
components/omega/machines/cime/frontier-craycray-mphipcc.cmake	New CIME-backed machine preset.
components/omega/machines/cime/chrysalis-intel.cmake	New CIME-backed machine preset.
components/omega/machines/cime/chrysalis-gnu.cmake	New CIME-backed machine preset.
components/omega/machines/cime/aurora-ifxgpu.cmake	New CIME-backed machine preset.
components/omega/machines/cime/aurora-ifx.cmake	New CIME-backed machine preset.
components/omega/external/CMakeLists.txt	Adjust GSW-C build flags, adding a Darwin-specific shared-library link mode.
components/omega/doc/userGuide/SubmesoEddies.md	New user documentation for configuration and diagnostics.
components/omega/doc/devGuide/SubmesoEddies.md	New developer documentation describing algorithms and APIs.
components/omega/doc/index.md	Add SubmesoEddies docs to Sphinx toctrees.
components/omega/configs/Default.yml	Add default `Omega:Submeso` configuration block.

+KOKKOS_INLINE_FUNCTION Real linearInterp(Real x, Real y1, Real x1, Real y2,
+                                         Real x2) {
+   const Real A = (y1 - y2) / (x1 - x2);
+   const Real B = y1 - A * x1;
+   return (x1 == x2) ? y1 : A * x + B;
+}


+   // Replace with global constant when added
+   const Real Tiny = 1e-12_Real;
+
+   parallelForOuter(


+                     std::numeric_limits<Real>::min(), // min valid value
+                     std::numeric_limits<Real>::max(), // max valid value


  else()
    add_test(
      NAME ${test_name}
-      COMMAND ../omega_env.sh ./${exe_name}
+      COMMAND ./${exe_name}
    )


+set(OMEGA_GKLIB_ROOT "/Users/mwarusz/installs/gklib" CACHE STRING "")
+set(OMEGA_METIS_ROOT "/Users/mwarusz/installs/metis" CACHE STRING "")
+set(OMEGA_PARMETIS_ROOT "/Users/mwarusz/installs/parmetis" CACHE STRING "")


mwarusz added 3 commits July 14, 2026 10:07

Work

ba574b2

Allow passing vertical coord to setScalar and setVector

f77ff37

Update set helpers to also provide element indices

ef02d1c

Copilot started work on behalf of mwarusz July 14, 2026 16:14 View session

Copilot finished work on behalf of mwarusz July 14, 2026 16:18

Copilot started work on behalf of mwarusz July 14, 2026 16:39 View session

Copilot finished work on behalf of mwarusz July 14, 2026 16:41

mwarusz force-pushed the mwarusz/omega/submesoscale-eddies branch from 7cc031e to 409f413 Compare July 14, 2026 16:47

Copilot started work on behalf of mwarusz July 14, 2026 19:55 View session

Copilot finished work on behalf of mwarusz July 14, 2026 19:57

mwarusz force-pushed the mwarusz/omega/submesoscale-eddies branch from b003252 to b257c69 Compare July 14, 2026 19:59

mwarusz requested a review from Copilot July 14, 2026 19:59

Copilot started reviewing on behalf of mwarusz July 14, 2026 20:00 View session

Copilot AI reviewed Jul 14, 2026

View reviewed changes

mwarusz force-pushed the mwarusz/omega/submesoscale-eddies branch from b257c69 to 433bbe5 Compare July 14, 2026 21:02

mwarusz added 9 commits July 14, 2026 15:13

Add submesocale eddies

77bcdbd

Add a helper for computing pseudo-thickness equation aux

fde305e

Add a helper for computing tracer aux

9697685

Add TransportAuxVars

e3a3d6d

Add a function to compute transport velocity

56724f0

Compute and use transport velocity where needed

e83e8e2

Add computation of Brunt-Vaisala freq in vert aux

720c44e

Add submesoscale contribution to transport velocity

f79c65b

Define submeso parametrization fields

6638a83

mwarusz and others added 6 commits July 14, 2026 15:13

Incorporate some copilot suggestions

2d15c8d

Adapt submeso eddies test to fill value changes

324c326

Fix linear interpolation

729c63f

Use tiny value for minimum Brunt-Vaisala freq

a2f1afc

Add Omega user and developer docs for submesoscale eddies

42c410a

Add eddy velocity only for active layers

a3ea9d4

mwarusz force-pushed the mwarusz/omega/submesoscale-eddies branch from 433bbe5 to a3ea9d4 Compare July 14, 2026 21:13

mwarusz added 3 commits July 14, 2026 15:51

Use multiple ranks in submeso eddies test

163b552

Fix linting

99429ec

Add a workaround for CUDA extended lambda issue

339140a

mwarusz force-pushed the mwarusz/omega/submesoscale-eddies branch from 5a970d3 to 339140a Compare July 15, 2026 17:24

mwarusz added 2 commits July 15, 2026 13:53

Add a teamBarrier

edeb6d4

Cleanup unused variables

66d1f4d

Provide feedback

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Mwarusz/omega/submesoscale eddies#8

Mwarusz/omega/submesoscale eddies#8
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		std::numeric_limits<Real>::min(), // min valid value
		std::numeric_limits<Real>::max(), // max valid value

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mwarusz commented Jul 14, 2026

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