v0.96.30

Oceananigans v0.96.30

Diff since v0.96.29

Merged pull requests:

• Fix Biharmonic Viscosity on Cubed-Sphere Grid (#3850) (@siddharthabishnu)
• Creates bottommost_active_node function (#4507) (@tomchor)
• Shuffle import order to clarify dependencies (#4530) (@glwagner)
• Implement ForcingOperation plus improvements to show (#4534) (@glwagner)
• Uncomment test block in test_dynamics.jl (#4542) (@glwagner)
• Don't search for missing bcs (#4545) (@navidcy)
• Ensure constancy preservation with nonlinear free surface (#4546) (@simone-silvestri)
• Correct diffusive dissipation for tuple of closures (#4548) (@simone-silvestri)
• Fix indexing issues for FieldTimeSeries (#4550) (@simone-silvestri)
• Add constructor for missing FieldBoundaryConditions (#4557) (@glwagner)
• (0.96.30) Fix vector rotation operation (#4560) (@simone-silvestri)

Closed issues:

• Biharmonic viscosity on Cubed-Sphere grid (#3849)
• Problems with new output readers (#4549)

v0.96.29

Oceananigans v0.96.29

Diff since v0.96.28

Merged pull requests:

• (0.96.29) Add adapt structure for BuoyancyForce (#4543) (@glwagner)

Closed issues:

• Docs aren't being created for all registered versions (#4413)

v0.96.28

Oceananigans v0.96.28

Diff since v0.96.27

Merged pull requests:

• Solving Poisson equation for p * dt instead of p (#4276) (@xkykai)
• Changes default AMD poincare coefficient (#4494) (@jagoosw)
• Add distributed reductions (#4497) (@navidcy)
• Clean up update_boundary_conditions! (#4503) (@glwagner)
• Fix some FieldTimeSeries indexing bugs (#4505) (@loisbaker)
• Use default prettyurls=true in docs build (#4520) (@navidcy)
• Fix a bug in the handshake macro (#4521) (@simone-silvestri)
• Improve variance dissipation computation (#4522) (@simone-silvestri)
• RK3 variance dissipation support (#4523) (@simone-silvestri)
• Re-zero immersed fields after creating plotting data (#4524) (@glwagner)
• FirstTimeStep: don't call update_state twice in a row (#4525) (@wsmoses)
• Don't time-step TKE unless warranted (add clock to CATKE and TKEDissipation) (#4526) (@glwagner)
• Fix warning message for set timestepper (#4528) (@simone-silvestri)
• Revert "Don't time-step TKE unless warranted (add clock to CATKE and … (#4533) (@wsmoses)
• Splitting substep_turbulent_kinetic_energy! into two kernels (#4536) (@jlk9)
• Fix VarianceDissipation docstring links (#4537) (@navidcy)
• Fix indentation in docs/make.jl (#4540) (@tomchor)

Closed issues:

• ConjugateGradientPoissonSolver fails to converge/is numerically unstable for extremely small timesteps (#4067)
• Simulation with ImmersedBoundary blows up on the first step, but only when when plotting a field first (#4519)

v0.96.27

Oceananigans v0.96.27

Diff since v0.96.26

Merged pull requests:

• Variance dissipation computation (#3877) (@simone-silvestri)
• Small improvements to PerturbationAdvectionOpenBoundaryCondition interface (#4394) (@tomchor)
• Fix incorrect type parameter count in ConformalCubedSpherePanel and ConformalCubedSpherePanelGrid definitions (#4500) (@siddharthabishnu)
• Fix out-of-bounds access in vorticity computation at halo boundaries on conformal cubed sphere panels (#4501) (@siddharthabishnu)
• Fill halo regions before interpolating rotated velocities (#4508) (@glwagner)
• Try to update_state during initalization for ReactantModel (#4509) (@glwagner)
• Add Bisits et al. 2025 (#4511) (@navidcy)
• Try running Langmuir turbulence example on GPU with higher resolution (#4512) (@glwagner)
• Add a warning if trying to launch a kernel with workspec () instead of throwing an error (#4514) (@simone-silvestri)
• Warn if using a Distributed architecture using a single rank (#4515) (@simone-silvestri)
• Update Project.toml (#4518) (@navidcy)

Closed issues:

• Error running a distributed nonhydrostatic model on CPU (#4483)

v0.96.26

Oceananigans v0.96.26

Diff since v0.96.25

Merged pull requests:

• Include background tracer and velocities in closure tendency terms (#3646) (@glwagner)
• Resolve ambiguity when setting MultiRegionField with a number (#4489) (@siddharthabishnu)
• Refactor getbc interface (#4491) (@glwagner)
• Fix dot implementation (#4493) (@simone-silvestri)
• [docs] Use non-deprecated syntax for MPI.mpiexec (#4496) (@giordano)
• Add BoundaryConditionOperation (#4506) (@glwagner)
• Update Project.toml (#4510) (@glwagner)

Closed issues:

• Oceananigans on AMD GPUs (#1546)
• Having a domain that's periodic in the "gravity" direction doesn't work for gravity_unit_vector = NegativeZDirection() (#3290)
• Update syntax of MPI.mpiexec in docs (#4495)
• Refactor JRA55 to use the DataWrangling Metadata, Bounding_Box, etc functionality (#4498)

v0.96.25

Oceananigans v0.96.25

Diff since v0.96.24

Merged pull requests:

• Store computational coordinates in OrthogonalSphericalShellGrid for non-uniform conformal mappings (#4295) (@siddharthabishnu)
• ReactantExt: Fix conditional operator ordering (#4472) (@wsmoses)
• Interpret u, v within set! on OrthogonalSphericalShellGrid as an extrinsic vector by default (#4479) (@glwagner)
• Clean up LatitudeLongitudeGrid from rectilinear grid (#4480) (@tomchor)
• Update Fields.jl (#4481) (@glwagner)
• Reactant: fix catke type conversions (#4482) (@wsmoses)
• Add extrema(c::AbstractField) (#4484) (@Sbozzolo)
• Bump to 0.96.25 (#4486) (@glwagner)

v0.96.24

Oceananigans v0.96.24

Diff since v0.96.23

Merged pull requests:

• Some more fixing for polar BC (#4463) (@simone-silvestri)
• Add a constructor for LatitudeLongitudeGrid from RectilinearGrid (#4465) (@glwagner)
• Better arg name: size -> side (#4469) (@navidcy)
• Add Atkinson et al 2024 in papers list (#4471) (@navidcy)
• implement default vertical coordinate (#4474) (@glwagner)
• Fix show for MutableVerticalDiscretization (#4476) (@glwagner)
• Fix default auxiliary bc for y-Flat lat-lon grids (#4477) (@glwagner)
• Bump to 0.96.24 (#4478) (@glwagner)

Closed issues:

• BoundsError using WENO and stretched grids (#2717)
• Can't @show a grid with MutableVerticalDiscretization and vector interfaces on GPU (#4475)

v0.96.23

Oceananigans v0.96.23

Diff since v0.96.22

Merged pull requests:

• Add Distributed grids section in Grids tutorial (#3698) (@navidcy)
• support for active_cells_map in kernels (#3920) (@simone-silvestri)
• Fix Zstar-RK3 (#4362) (@simone-silvestri)
• Remove assumption about X/YFaceField on TripolarGrid by generalizing default_auxiliary_boundary_condition (#4368) (@glwagner)
• Export CATKE and k-ε (#4449) (@navidcy)
• Bugfix in RK3 previous fields (#4456) (@simone-silvestri)
• Bugfix BC default (#4457) (@simone-silvestri)
• Improve and test error handling for vertical level specification in grid construction (#4461) (@NoraLoose)
• Make NetCDFWriter work with PartialCellBottom grids (#4462) (@tomchor)

Closed issues:

• Renaming NetCDFOutputWriter to NetCDFWriter (#3936)
• Ax, Ay and Az are negative in a Tripolar grid (#4318)
• NetCDFWriter doesn't work for PartialCellBottom grids (#4416)
• Reading .jld2 with FieldTimeSeries() errors under new Oceananigans version (#4454)
• Scalar indexing when outputting a slice with NetCDFWriter and GPUs (#4464)

v0.96.22

Oceananigans v0.96.22

Diff since v0.96.21

Merged pull requests:

• Add a performance benchmark pipeline (#4375) (@simone-silvestri)
• Improve z-star tracer conservation tests (#4403) (@NoraLoose)
• Fused multiply add (fma) in stencil operations (#4407) (@simone-silvestri)
• Remove stretched advection (#4411) (@simone-silvestri)
• Don't invoke comm buffers on non-distributed grids and move to DistributedComputations (#4414) (@glwagner)
• Fix summary for PartialCellBottom (#4425) (@tomchor)
• Add CATKE and GPU dycore paper references (#4426) (@navidcy)
• Update CATKE docstring (#4427) (@navidcy)
• Remove trailing spaces part 2 (#4429) (@navidcy)
• Remove trailing white spaces part 3 (#4430) (@tomchor)
• Add operators functions for reciprocals of metrics (#4431) (@simone-silvestri)
• Add newton_div utility for fast (but approximate) mixed-precision computation of divisions (#4432) (@glwagner)
• Ensure user diffusivity NamedTuple have correct ordering (#4437) (@glwagner)
• Use tuple instead of vector in tilted_bottom_boundary_layer.jl (#4439) (@simone-silvestri)
• Compute the difference between the latest main and the PR (#4440) (@simone-silvestri)
• (0.96.22) Make NetCDFWriter work with GPU grids with stretched dimensions (#4441) (@tomchor)
• Improve benchmarks yml (#4442) (@simone-silvestri)
• Making condition size mismatch error a bit more helpful (#4443) (@taimoorsohail)
• Add Souza et al. 2025 + reorder refs chronologically (#4444) (@navidcy)
• CompatHelper: add new compat entry for MuladdMacro at version 0.2, (keep existing compat) (#4445) (@github-actions[bot])
• Use vertical spacing reciprocal in implicit solver (#4447) (@simone-silvestri)
• Adding the possibility of having dynamical particles (#4448) (@simone-silvestri)

Closed issues:

• Tracer conservation is broken in ZStar with Julia 1.11.4 (#4340)
• Improve and Verify Z-Star Tracer Conservation Tests (#4395)
• NetCDFWriter scalar indexing error on GPU (#4397)
• Tilted BBL example not working on GPU (#4438)

v0.96.21

Oceananigans v0.96.21

Diff since v0.96.20

Merged pull requests:

• Implement an interface for writing output with Simulation (#4271) (@glwagner)
• Remove trailing white spaces in code (#4304) (@tomchor)
• Reduce turbulence closure tests cost (#4380) (@simone-silvestri)
• Minor cosmetic improvements to internal tide example (#4400) (@glwagner)
• Intersect indices in output_construction (#4401) (@glwagner)
• Clean up buildkite pipeline slightly (#4404) (@glwagner)
• Mask implicit linear coefficient if inside an immersed boundary (#4405) (@simone-silvestri)
• Further clean up the buildkite yml (#4408) (@glwagner)
• Fix rendering + reference default_checkpointed_properties in Checkpointer docstring (#4410) (@jbisits)
• Clean up extra code in test_turbulence_closures.jl (#4415) (@tomchor)
• Add link to docstring of ConditionalOperations in the docs for various reductions (#4418) (@navidcy)
• Support Krylov.jl v0.10 (#4419) (@amontoison)
• Fix adapt for TKEDissipationDiffusivityFields (#4421) (@wsmoses)
• Bump to 0.96.21 (#4424) (@glwagner)

Closed issues:

• Turbulence closure tests taking a very long time (#4379)
• AMDGPU CI (#4398)
• Simulation callback: Error encountered when updating u_s with time (#4422)