v0.105.4

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)

v0.105.3

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)

v0.105.2

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)

v0.105.1

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)

v0.105.0

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)

v0.104.5

Oceananigans v0.104.5

Diff since v0.104.4

Merged pull requests:

• Bugfix in CATKE with RK3 v2 (#5269) (@simone-silvestri)
• Use FieldTimeSeries in tilted BBL example (with NetCDF output) (#5273) (@tomchor)
• Add test for PrescribedFreeSurface with PrescribedVelocityFields and ZStar (#5278) (@Copilot)
• Update NumericalEarth Slack link in README (#5279) (@glwagner)
• Changing rotation_angle to output in radians instead of degrees (#5280) (@jlk9)
• Validate indices for field time series (#5281) (@briochemc)
• Add new paper citation to Oceananigans section (#5284) (@navidcy)
• Fix equations rendering in split_explicit_timesteppers.jl (#5285) (@navidcy)
• (0.104.5) Use the default FloatType in TripolarGrid (#5288) (@simone-silvestri)
• Add new paper citation to Oceananigans documentation (#5293) (@navidcy)
• Add reference to Zhang et al. (2025) on Enceladus (#5294) (@navidcy)

Closed issues:

• OceananigansDocumentation repo is quite large due to SVGs (#5027)
• don't delete previews too fast (#5243)
• Absolute or relative imports? (#5290)

v0.104.4

Oceananigans v0.104.4

Diff since v0.104.3

Merged pull requests:

• Add the possibility for using fill_halo_regions! instead of extended halos for SplitExplicitFreeSurface (#4750) (@simone-silvestri)
• Do not explicitly step model.velocities for pressure_correction models (#5178) (@simone-silvestri)
• Support FFT planning for ConcreteRArray (#5246) (@dkytezab)
• (0.104.4) Guarantee conservation with an ImplicitFreeSurface (#5247) (@simone-silvestri)
• unpin reactant (#5253) (@wsmoses)
• Use WENO in the ocean mixing example (#5254) (@tomchor)
• Add pre-commit hook and explain how to use it (#5256) (@giordano)
• Always run Base.julia_cmd() in distributed tests (#5258) (@giordano)
• Create test-specific project (#5259) (@giordano)
• (0.104.4) Bugfix for DynamicSmagorinsky (improve check for restoration) (#5260) (@glwagner)
• Add support for RK3 in Reactant extension (#5261) (@dkytezab)
• Explicit imports in MultiRegion, and remove all imports in that module (#5262) (@giordano)

Closed issues:

• Problem with wind mixing and convection example (#5231)
• Support FFT tracing for ConcreteRArray (#5244)
• Reactant failing on buildkite (#5249)
• Dynamic Smagorinsky always produces zero values for eddy viscosity (#5257)
• Enter the Product Title Here (#5265)

v0.104.3

Oceananigans v0.104.3

Diff since v0.104.2

Merged pull requests:

• Extend FFTBasedPoissonSolver to work on AMDGPU (#4593) (@navidcy)
• Do not pass CommunicationBuffers as clock to BC (#5063) (@Mikolaj-A-Kowalski)
• F-point pivot fold zipper boundary for tripolar grids (#5094) (@briochemc)
• Fix Clock constructor preventing Nonhydrostatic model to run on MetalGPU (#5187) (@alesok)
• Support combining distributed output for FieldTimeSeries with Reduced directions (#5188) (@simone-silvestri)
• Fix typos in generalized vertical coordinates documentation (#5190) (@navidcy)
• Move benchmarks from GPU 1 to GPU 0 (#5193) (@simone-silvestri)
• Add docstrings back to NetCDFWriter (#5194) (@tomchor)
• Rearrange example scripts in make.jl (#5196) (@navidcy)
• Convert examples in docstrings to doctests (#5197) (@navidcy)
• Fix typo (#5198) (@navidcy)
• Fix formatting of urls in the docs (#5199) (@navidcy)
• Refine schedules documentation for clarity and consistency (#5201) (@navidcy)
• Fix callback in example within Docs/Checkpoint (#5202) (@navidcy)
• apply_regionally! on multi-region kernels (#5203) (@simone-silvestri)
• Fix test_complex_boundary_conditions on distributed CI (#5205) (@navidcy)
• Enhance checkpointing tests with closure::Tuple (#5209) (@navidcy)
• Zenodo: Add citation metadata for Oceananigans.jl (#5215) (@milankl)
• Add more docstrings for FieldTimeSeries (#5217) (@briochemc)
• Add support for OffsetArray in restore_prognostic_state! + minor variable name changes (#5218) (@taimoorsohail)
• Added support for combining FTS using multiple ranks where filename is an absolute path (#5221) (@taimoorsohail)
• Fix formatting of titles in oceananigans.bib (#5222) (@navidcy)
• Add friendlier error for wrong timestepper in model constructors (#5224) (@briochemc)
• Introduce distributed conservation tests and fix some bugs (#5225) (@simone-silvestri)
• Fix Distributed GPU unit tests (#5226) (@navidcy)
• Simplify distributed test pipeline (#5228) (@simone-silvestri)
• Implement TimeSeriesInterpolatedField and support FieldTimeSeries in PrescribedVelocityFields (#5233) (@glwagner)
• Use stage=1 in Clock constructor for ReactantGrid (#5236) (@jlk9)
• Jlk9/reactant clock stage 1 (#5241) (@jlk9)
• (0.104.3) Make FieldTimeSeries respect architecture when reading from NetCDF files (#5242) (@tomchor)
• Update Julia version requirement to 1.10 (#5245) (@briochemc)
• Pin reactant (#5250) (@simone-silvestri)
• [WIP] Update FieldTimeSeries NetCDF architecture handling (#5251) (@Copilot)

Closed issues:

• AMDGPU with NonhydrostaticModel? (#4591)
• Conservation with Distributed architecture and ZStarCoordinate not ensured (#5161)
• Nonhydrostatic model fails on MetalGPU due to Clock(::AbstractGrid) constructor (#5186)
• Calling HydrostaticFreeSurfaceModel with invalid timestepper = :RungeKutta3 throws unfriendly error. (#5192)
• restore_prognostic_state! not supported for OffsetArrays (#5212)
• BoundaryConditionOperation not compiling on GPU. (#5214)
• Unusual density fluctuations have been observed in submarine acoustic simulation. (#5219)
• Feature request: Prescribed velocity field time series (#5227)

v0.104.2

Oceananigans v0.104.2

Diff since v0.104.1

Merged pull requests:

• Problems with TimeStepWizard and ImmersedBoundaryGrid on MetalGPU (#4990) (@alesok)
• Fix halo-edge interpolation and column depth for extended conformal cubed sphere grids (#5060) (@siddharthabishnu)
• Simplify and test FTS boundary conditions (#5171) (@simone-silvestri)
• Delete unused maybe_enable_peer_access! function (#5173) (@giordano)
• Remove RungeKuttaScheme alias (#5174) (@giordano)
• Add new paper references to Docs (#5175) (@navidcy)
• (0.104.2) Add convenience method for 1D interpolation (#5182) (@glwagner)
• Update including parameter to use default properties (#5184) (@navidcy)

Closed issues:

• Run HydrostaticFreeSurfaceModel with ImmersedBoundaryGrid on MetalGPU (#4969)
• rename master to main in OceananigansDocumentation repo (#5160)
• Undefined references to switch_device! and sync_all_devices! in maybe_enable_peer_access! (#5170)

v0.104.1

Oceananigans v0.104.1

Diff since v0.104.0

Merged pull requests:

• Test that certain modules have exactly 0 ambiguities (#5115) (@giordano)
• Update Julia compat from version from 1.9 to 1.10 (#5163) (@navidcy)
• Fix ConditionalOperation method (#5165) (@simone-silvestri)
• Resolve many more issues identified by JETLS (#5166) (@giordano)
• Add a checkpointing method for constant fields (#5168) (@simone-silvestri)
• Resolve bug in binary_operation (#5169) (@simone-silvestri)

Closed issues:

• Bogus Oceananigans.AbstractOperations.ConditionalOperation method (#5154)
• Bogus methods in binary_operations.jl (#5167)