Oceananigans v0.106.3

Diff since v0.106.2

Merged pull requests:

• Partial cell conservation (#5356) (@simone-silvestri)
• Add flow over hill validation using open boundaries and a hydrostatic model with implicit surface (#5359) (@tomchor)
• Remove initialization_update_state! and clean up initialization (#5420) (@glwagner)
• Fix typo in Simulation tips docs (#5425) (@glwagner)
• Relieve memory in unit tests (#5428) (@simone-silvestri)
• Fix formatting and citation errors in index.md (#5430) (@navidcy)
• Bump minor version from 0.106.2 to 0.106.3 (#5431) (@simone-silvestri)

Oceananigans v0.106.2

Diff since v0.106.1

Merged pull requests:

• (0.106.2) Refactor coriolis and add Triad scheme (#5383) (@simone-silvestri)
• Shift the RightFaceFolded fold upwards by one row (#5408) (@simone-silvestri)
• Extend TabulatedFunction to support 4D and 5D interpolation (#5417) (@glwagner)

Oceananigans v0.106.1

Diff since v0.106.0

Merged pull requests:

• Add restart verification script (#5379) (@ewquon)
• Reinvoke sharding tests and refactor Clock constructor for sharded grids (#5389) (@glwagner)
• Improve serial tripolar grid fold tests (#5405) (@briochemc)
• Temporarily drop Benchmark section from Docs + delete legacy_benchmarks (#5412) (@briochemc)
• Fix issue downstream in Reactant on 1.12 (#5415) (@dkytezab)
• Reinstate Docs/Benchmarks (#5419) (@navidcy)
• Small improvements to the benchmarking pipeline (#5421) (@giordano)

Oceananigans v0.106.0

Diff since v0.105.4

Breaking changes

• #5355 changed the default file when restoring from a checkpointer.

Merged pull requests:

• Add benchmarking package with earth_ocean case (#5317) (@glwagner)
• Rework support for reduction operations on Metal GPU to avoid materialization of the interior (#5329) (@alesok)
• (0.106) Log checkpoint file and mtime when restoring simulations (#5355) (@taimoorsohail)
• (0.105.5) Fix initialize_closure_fields!() use with DynamicSmagorinsky (#5366) (@tomchor)
• Fix section rendering that includes greek LaTeX characters in the documentation (#5380) (@navidcy)
• Bump julia-actions/cache from 2 to 3 (#5382) (@dependabot[bot])
• Propose fix some typos (#5385) (@jeis4wpi)
• Reduce number of ambiguities (#5390) (@giordano)
• Explicit imports in Grids (#5391) (@giordano)
• Load XESFM after Oceananigans (#5393) (@giordano)
• Add new paper reference to Oceananigans documentation (#5395) (@navidcy)
• Fix formatting of reference list in index.md (#5397) (@navidcy)
• Fix typo with density perturbation in docs (#5398) (@navidcy)
• Fix the reference list in the Langmuir example (#5400) (@navidcy)
• (0.105.5) Add unit test for zero momentum flux at immersed peripheral nodes (#5402) (@tomchor)
• Implement ReactantCore.materialize_traced_array for Field (#5409) (@Pangoraw)
• Revise citation for De Abreu and Timmermans (#5411) (@navidcy)
• Remove Oceananigans compact from Project.toml in benchmarks (#5414) (@simone-silvestri)

Closed issues:

• Lagrangian-averaged DynamicSmagorinsky producing zero values for eddy viscosity (again) (#5365)
• Some incorrect formatting in the docs (#5377)
• Langmuir example includes all reference list from the Docs (#5399)
• T_forcing and S_forcing do not receive the expected values (#5407)

Oceananigans v0.105.5

Diff since v0.105.4

This release has been identified as a backport.
Automated changelogs for backports tend to be wildly incorrect.
Therefore, the list of issues and pull requests is hidden.

Oceananigans v0.105.4

Diff since v0.105.3

Merged pull requests:

• (0.105.4) Add basic tests for Reactant-Oceananigans correctness (#5093) (@glwagner)
• Rename JULIA_DEPOT_PATH to the .julia for buildkite (#5368) (@tomchor)
• Use view instead of indexing in cpu_face_constructor_r (#5376) (@glwagner)
• Fix HydroStaticFreeSurfaceModel init for open boundary conditions with SplitExplicitFreeSurface (#5378) (@rafmudaf)

Closed issues:

• Bug with Reactant + Periodic BCs + ParallelTestRunner (#5208)

Oceananigans v0.105.3

Diff since v0.105.2

Merged pull requests:

• (0.105.3) Fix interpolation of terms in chain horizontal derivatives for MutableVerticalDiscretization (#5339) (@glwagner)
• Restructure AGENTS.md into multi-file agent configuration (#5350) (@glwagner)
• (0.105.2) Fix with_halo for a TripolarGrid (#5353) (@simone-silvestri)
• Fix typo SKR3 -> SRK3 (#5360) (@briochemc)
• Update papers section in index.md (#5362) (@navidcy)
• Add 9 missing papers to the reference list (#5363) (@glwagner)
• Add new reference to Zheng et al. (2025) in index (#5364) (@navidcy)
• Fix ContinuousForcing field index mismatch in HydrostaticFreeSurfaceModel (#5370) (@glwagner)
• Add dependency guardrail to Common Pitfalls (#5371) (@glwagner)

Closed issues:

• Reformulating continuous forcing in discrete form giving unexpected results (#5369)

Oceananigans v0.105.2

Diff since v0.105.1

Merged pull requests:

• Add random seeds to examples for reproducible results (#5312) (@tomchor)
• (0.105.2) Fix and test checkpointing with open-domain simulations with a radiation OpenBoundaryCondition (#5347) (@tomchor)

Closed issues:

• Tilted boundary layer example failing on docs (#5299)
• Refactor timestepping to better integrate paranoid update (#5300)
• delete symlinks and trigger again docs CI build on that commit (tagbot) (#5320)
• Stable docs page 404s (#5338)
• Picking up a simulation fails when the model has OpenBoundaryConditions with a non-trivial scheme (#5346)

Oceananigans v0.105.1

Diff since v0.105.0

Merged pull requests:

• Enable AveragedSpecifiedTimes to be used in output writers (#4876) (@xkykai)
• Fix lock-exchange example (#5248) (@simone-silvestri)
• Reduce method ambiguities by disambiguating ConstantField binary ops (#5313) (@glwagner)
• (0.105.1) Add density and gravity_wave_speed to PerturbationAdvection (#5314) (@glwagner)
• Add maybe_initialize_state! and simplify Reactant time stepper overrides (#5315) (@glwagner)
• Fix inability to raise Bounded topology with Reactant (#5322) (@dkytezab)
• Add citation for Gupta et al. on upper-ocean energetics (#5325) (@navidcy)
• Fix undefined variable free_surface inside error message (#5328) (@giordano)
• --check-bounds=auto for Reactant tests (#5331) (@dkytezab)
• Avoid topology-aware operators when filling halos in the SplitExplicitFreeSurface (#5332) (@simone-silvestri)
• Fix broken hard-coded URLs with @ref (#5335) (@briochemc)
• Enhance run! docstring (#5336) (@navidcy)
• Add bibtex entry for Wagner et al. 2021 (#5337) (@navidcy)

Closed issues:

• AverageSpecifiedTimes cannot be used (#4875)
• JLD2Writer does not create per-rank files when filename contains .jld2 extension (#5263)
• How does checkpointing happen after wall-time limit is reached? (#5291)

Oceananigans v0.105.0

Diff since v0.104.5

Breaking Changes

There are 12 commits on main since v0.104.5. Of these, 3 contain breaking changes:

1. compute_diffusivities! → compute_closure_fields! (PR #5274)

The function compute_diffusivities! has been renamed to compute_closure_fields! across the entire codebase. This is an exported symbol from TurbulenceClosures. Anyone who:

• Imports or calls compute_diffusivities! directly
• Extends compute_diffusivities! for a custom closure

will need to update to compute_closure_fields!.

2. New step_closure_prognostics! interface (PR #5274)

A new exported function step_closure_prognostics! is now called by every time stepper (AB2, RK3, SplitRK) between tick! and update_state!. Previously, prognostic closure
stepping (e.g., TKE equation) was entangled inside compute_diffusivities!. Now it's a separate call. This is breaking for:

• Custom closures with prognostic variables that previously stepped them inside compute_diffusivities! — they must now implement step_closure_prognostics! instead.
• Custom time steppers that don't call step_closure_prognostics!(model, Δt) after tick!.

3. New initialize_closure_fields! interface (PR #5274)

A new exported function initialize_closure_fields! is called during initialize! to set up closure fields when a simulation starts. Custom closures that previously did
initialization inside compute_diffusivities! need to move that logic here.

4. Struct renames (PR #5274)

• CATKEDiffusivityFields -> CATKEClosureFields

• TKEDissipationDiffusivityFields -> TKEDissipationClosureFields

  These are internal types but may be referenced by users doing checkpointing, custom closures, or diagnostics. Additionally, two fields were removed from both structs:

  • previous_compute_time — no longer needed
  • _skip_next_compute — no longer needed
  5. Removed update_previous_compute_time! (PR #5274)

  The internal function update_previous_compute_time! was deleted entirely (from CATKE). Code that called it will break.

  6. Kernel function argument rename: diffusivities → closure_fields (PR #5274)

  Throughout the internal kernel functions (tendency kernels in hydrostatic, nonhydrostatic, and shallow water models), the argument name diffusivities has been renamed to
  closure_fields. This is breaking for anyone who dispatches on or extends these internal kernel functions using keyword arguments or positional argument names.

  7. cell_diffusion_timescale signature change (PR #5274)

  The second argument in Diagnostics.cell_diffusion_timescale(closure, diffusivities, grid, clock, fields) was renamed from diffusivities to closure_fields. This affects
  anyone extending this diagnostic for custom closures.

Non-breaking changes (bug fixes, features, docs)

• PR #5298: VarianceDissipationComputations now uses transport_velocities for HydrostaticFreeSurfaceModel (bug fix)
• PR #5297: xnodes/ynodes/znodes on windowed Fields now correctly return windowed nodes; mask_immersed_field! respects windowed indices (bug fix)
• PR #5237: SplitRungeKutta3 added to Reactant extension (new feature, non-breaking)
• PR #5295: Internal variable rename θ_radians → θ (cosmetic, non-breaking)
• PR #5282: Docstring added to MutableVerticalDiscretization (docs only)
• PR #5234: Distributed grids docs fixes (docs only)
• PR #5302–#5306: Documentation/reference updates

Merged pull requests:

• Implement horizontal derivatives at constant z for MutableVerticalDiscretization (#5101) (@glwagner)
• Setup vitepress for the docs (#5159) (@lazarusA)
• Distributed grids docs small fixes (#5234) (@romanlee)
• Add split runge kutta to reactant extension (#5237) (@jlk9)
• Extend TabulatedFunction to support 2D and 3D interpolation. (#5240) (@glwagner)
• Allow FieldTimeSeries to be read from NetCDF without reading the original architecture (#5271) (@tomchor)
• (0.105.0) Implement interface for stepping closure prognostic variables (#5274) (@glwagner)
• Add docstring to MutableVerticalDiscretization (#5282) (@briochemc)
• Drop a leftover _radians (#5295) (@navidcy)
• Fix nodes and immersed masking for windowed fields (#5297) (@briochemc)
• Use the correct velocities in VarianceDissipationComputations (#5298) (@simone-silvestri)
• Update references in index.md (#5302) (@navidcy)
• [docs] Fix URL of paper (#5304) (@giordano)
• Add new paper reference to Oceananigans documentation (#5305) (@navidcy)
• Revise citation for Johnston et al. in references (#5306) (@navidcy)
• Add fields with non-default indices to Field tutorial (#5308) (@glwagner)
• Support boolean comparison operations on fields (#5309) (@glwagner)

Closed issues:

• Use Vitepress for documentation (#4891)
• Add fields with non-default indices to Field tutorial (#5206)
• Support boolean comparison operations on fields (>, <, >=, <=, ==) (#5307)