Oceananigans.jl

## Oceananigans v0.113.6 [Diff since v0.113.5](https://github.com/CliMA/Oceananigans.jl/compare/v0.113.5...v0.113.6) **Merged pull requests:** - Fix indexing of `FieldTimeSeries` with `OnDisk` backend and specified `times` (#5515) (@matt-graham) - Add distributed benchmark pipeli

## Oceananigans v0.113.5 [Diff since v0.113.4](https://github.com/CliMA/Oceananigans.jl/compare/v0.113.4...v0.113.5) **Merged pull requests:** - Fix performance problems introduced by IMEX PR (#5921) (@simone-silvestri) - Interpolation for `TotallyInMemoryFTS` under Reactant (#59

## Oceananigans v0.113.4 [Diff since v0.113.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.113.3...v0.113.4) **Merged pull requests:** - Add FilteredTimeInterval: filtered output with pluggable kernels for JLD2, NetCDF and Zarr writers (#5971) (@enri66) - Introducing a TP

## Oceananigans v0.113.3 [Diff since v0.113.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.113.2...v0.113.3) **Merged pull requests:** - Add a single column parameter estimation example with Reactant and Enzyme (#5013) (@glwagner) - (0.113.3) Corrects particle stepping or

## Oceananigans v0.113.2 [Diff since v0.113.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.113.1...v0.113.2) **Merged pull requests:** - Thread model.clock, fields(model) through set!/interpolate! halo fills (#5866) (@aklocker42) - Add TracerReservoir: open boundary trace

## Oceananigans v0.113.1 [Diff since v0.113.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.113.0...v0.113.1) **Merged pull requests:** - Various minor improvements to the test suite (#5999) (@giordano) - Try to speed up `simulations` test group (#6017) (@giordano) - Remov

## Oceananigans v0.113.0 [Diff since v0.112.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.112.0...v0.113.0) ## Breaking changes - `NetCDFWriter`, `JLD2Writer`, and `ZarrWriter`: The `overwrite_existing` keyword argument has been renamed to `overwrite_files`. **Merged pul

## Oceananigans v0.112.0 [Diff since v0.111.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.111.0...v0.112.0) ## Breaking changes - This version bump captures #5924, which changes the UI for invoking bounded WENO advection and improves the bounds from 1D to 3D **Merged pul

## Oceananigans v0.111.0 [Diff since v0.110.20](https://github.com/CliMA/Oceananigans.jl/compare/v0.110.20...v0.111.0) ## Breaking changes - `Solvers.get_coefficient` methods for `VerticallyImplicit*Diagonal` has changed to accept only the complete list of arguments including adv

## Oceananigans v0.110.20 [Diff since v0.110.19](https://github.com/CliMA/Oceananigans.jl/compare/v0.110.19...v0.110.20) **Merged pull requests:** - implement an `IMEXFluxTimeDiscretization` for `FluxBoundaryCondition` (#5631) (@simone-silvestri) - Fix IsopycnalSkewSymmetricDiffu

## Oceananigans v0.110.18 [Diff since v0.110.17](https://github.com/CliMA/Oceananigans.jl/compare/v0.110.17...v0.110.18) **Merged pull requests:** - Read a FieldTimeSeries at a cell with a precomputed TimeInterpolator (#5886) (@xkykai) - (0.110.18) Center the longitude fold windo

## Oceananigans v0.110.19 [Diff since v0.110.18](https://github.com/CliMA/Oceananigans.jl/compare/v0.110.18...v0.110.19) **Merged pull requests:** - Make Zarr output CF interoperable; expand tests and benchmarks (#5610) (@glwagner) **Closed issues:** - Write CF-compliant Zarr out

## Oceananigans v0.110.17 [Diff since v0.110.16](https://github.com/CliMA/Oceananigans.jl/compare/v0.110.16...v0.110.17) **Merged pull requests:** - Read Field boundary conditions windowed to a plane at their own plane (#5881) (@giordano) - There are no method ambiguities in `Adv

## Oceananigans v0.110.16 [Diff since v0.110.15](https://github.com/CliMA/Oceananigans.jl/compare/v0.110.15...v0.110.16) **Merged pull requests:** - Explicit imports for OutputWriters module (#5862) (@navidcy) - Throw an error when file splitting limit is below metadata size (#58

## Oceananigans v0.110.15 [Diff since v0.110.14](https://github.com/CliMA/Oceananigans.jl/compare/v0.110.14...v0.110.15) **Merged pull requests:** - Open boundary conditions using `SplitExplicitFreeSurface` (#5351) (@simone-silvestri) - Update Oceananigans papers to docs (#5780)

## Oceananigans v0.110.14 [Diff since v0.110.13](https://github.com/CliMA/Oceananigans.jl/compare/v0.110.13...v0.110.14) **Merged pull requests:** - Documentation: FieldTimeSeries, FieldDataset and basic post-processing (#5789) (@erin-atkinson) - Add Unicode integral operators (#

## Oceananigans v0.110.13 [Diff since v0.110.12](https://github.com/CliMA/Oceananigans.jl/compare/v0.110.12...v0.110.13) **Merged pull requests:** - Reduce kernel launching overhead (#5774) (@jackdfranklin) - Adds adapt method for IsopycnalSkewSymmetricDiffusivity (#5785) (@jlk9)

## Oceananigans v0.110.12 [Diff since v0.110.11](https://github.com/CliMA/Oceananigans.jl/compare/v0.110.11...v0.110.12) **Merged pull requests:** - Support NetCDF output on any AbstractVerticalCoordinate (#5689) (@ewquon) - Fix scalar indexing of GPUs when resizing immersed boun

## Oceananigans v0.110.10 [Diff since v0.110.9](https://github.com/CliMA/Oceananigans.jl/compare/v0.110.9...v0.110.10) **Merged pull requests:** - Bump CUDA in /test (#5696) (@dependabot[bot]) - Remove type-instability in `buffer_*_parameters` (#5748) (@simone-silvestri) - Bugfix

## Oceananigans v0.110.11 [Diff since v0.110.10](https://github.com/CliMA/Oceananigans.jl/compare/v0.110.10...v0.110.11) **Merged pull requests:** - (0.110.11) Restores `update_state!` ordering for nonhydrostatic model (#5791) (@jagoosw)

## Oceananigans v0.110.9 [Diff since v0.110.8](https://github.com/CliMA/Oceananigans.jl/compare/v0.110.8...v0.110.9) **Merged pull requests:** - Add distributed tests for ConjugateGradientPoissonSolver (#5757) (@xkykai) - Reject FieldTimeSeries operands in AbstractOperations (#57

## Oceananigans v0.110.7 [Diff since v0.110.6](https://github.com/CliMA/Oceananigans.jl/compare/v0.110.6...v0.110.7) **Merged pull requests:** - Simplify Relaxation: drop ContinuousForcing dependency, add transform and Field targets (#5620) (@glwagner) - Add `ColumnwiseTridiagona

## Oceananigans v0.110.8 [Diff since v0.110.7](https://github.com/CliMA/Oceananigans.jl/compare/v0.110.7...v0.110.8) ## What's Changed * Remove type instability in `flattened_unique_values` by @simone-silvestri in https://github.com/CliMA/Oceananigans.jl/pull/5749 * Density-weigh

## Oceananigans v0.110.6 [Diff since v0.110.5](https://github.com/CliMA/Oceananigans.jl/compare/v0.110.5...v0.110.6) **Closed issues:** - Test velocity exchanges across the tripolar seam more thoroughly (#4488) - Add option for distributed computation to benchmark (#5579) - Type-

## Oceananigans v0.110.5 [Diff since v0.110.4](https://github.com/CliMA/Oceananigans.jl/compare/v0.110.4...v0.110.5) **Merged pull requests:** - Update on_architecture for MetalGPU to specifically target `StepRangeLen{FT, Float64, Float64}` (#5375) (@glwagner) - Add BFloat16 as s

## Oceananigans v0.110.3 [Diff since v0.110.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.110.2...v0.110.3) **Closed issues:** - `JLD2Writer(overwrite_existing=true)` behaves like iteration-level overwrite, not file-level overwrite (#5643)

## Oceananigans v0.110.4 [Diff since v0.110.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.110.3...v0.110.4) **Closed issues:** - `JLD2Writer(overwrite_existing=true)` behaves like iteration-level overwrite, not file-level overwrite (#5643) - Accidental emoji rendering in

## Oceananigans v0.110.2 [Diff since v0.110.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.110.1...v0.110.2) **Closed issues:** - `cell_diffusion_timescale` breaks for CATKE (#5641) - TripolarGrid face-coordinate generation appears incomplete at the north seam, yielding N

## Oceananigans v0.110.1 [Diff since v0.110.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.110.0...v0.110.1) **Merged pull requests:** - Allow set! to copy between reduced and windowed single-layer fields (#5652) (@glwagner) - Update Project.toml (#5653) (@glwagner) **Clo

## Oceananigans v0.110.0 [Diff since v0.109.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.109.2...v0.110.0) ## Breaking changes - `Open` boundary conditions were renamed to `NormalFlow`. `Value` now accepts a `scheme` (used to set up radiation boundary conditions for tra

## Oceananigans v0.109.2 [Diff since v0.109.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.109.1...v0.109.2) **Merged pull requests:** - Limit pass through to target extension for auto_extension (#5644) (@rafmudaf) - (0.109.2) Apply tracer open boundary conditions in `Non

## Oceananigans v0.109.1 [Diff since v0.109.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.109.0...v0.109.1) **Merged pull requests:** - Support tracers in `PerturbationAdvection` open boundary conditions (#5617) (@tomchor) - Regularize correctly `U` and `V` bc for a `Tri

## Oceananigans v0.108.1 [Diff since v0.108.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.108.0...v0.108.1) **Closed issues:** - Implement a ZarrOutputWriter (#3821) - Extend `NetCDFWriter` to support `TripolarGrid` and `MutableVerticalDiscretization` (#4332) - Makie ext

## Oceananigans v0.108.2 [Diff since v0.108.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.108.1...v0.108.2)

## Oceananigans v0.109.0 [Diff since v0.108.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.108.2...v0.109.0) ## Breaking changes - the syntax of `time_discretization` was changed ## What's Changed * Allow changing schedule from `TimeInterval` --> `IterationInterval` on pi

## Oceananigans v0.108.0 [Diff since v0.107.7](https://github.com/CliMA/Oceananigans.jl/compare/v0.107.7...v0.108.0) ## Breaking changes - When picking up a simulation from a checkpoint instead of using the Δt that was saved in the checkpoint, the simulation will use the Δt that

## Oceananigans v0.107.7 [Diff since v0.107.6](https://github.com/CliMA/Oceananigans.jl/compare/v0.107.6...v0.107.7) **Merged pull requests:** - Change behavior for halo metrics for a `TripolarGrid` + bugfix at `j == 1` (#5565) (@simone-silvestri) - Bugfix `actuations` for `TimeI

## Oceananigans v0.107.6 [Diff since v0.107.5](https://github.com/CliMA/Oceananigans.jl/compare/v0.107.5...v0.107.6) ## What's Changed * Allow `AveragedTimeInterval` with a `Dates` clock by @simone-silvestri in https://github.com/CliMA/Oceananigans.jl/pull/5562 * Update Chor et.

## Oceananigans v0.107.5 [Diff since v0.107.4](https://github.com/CliMA/Oceananigans.jl/compare/v0.107.4...v0.107.5) **Closed issues:** - Bug: Adapt.adapt_structure swaps north/south in CommunicationBuffers (#5422) - `interpolate!` fails silently on `Flat` topologies with explici

## Oceananigans v0.107.4 [Diff since v0.107.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.107.3...v0.107.4) **Merged pull requests:** - Bump actions/upload-artifact from 7.0.0 to 7.0.1 (#5507) (@dependabot[bot]) - Only allow CUDA.jl v5 in benchmarking environment (#5531)

## Oceananigans v0.107.2 [Diff since v0.107.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.107.1...v0.107.2) **Merged pull requests:** - Adapt to CUDA.jl v6 (#5458) (@giordano) - Explicit imports in `Advection` (#5523) (@giordano) - Resolve some ambiguities (#5524) (@gior

## Oceananigans v0.107.3 [Diff since v0.107.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.107.2...v0.107.3) **Merged pull requests:** - Append colon to `JULIA_DEPOT_PATH` (#5525) (@giordano) - Avoid use of at-doc macro inside structs (#5527) (@giordano) - Simplify defini

## Oceananigans v0.107.0 [Diff since v0.106.6](https://github.com/CliMA/Oceananigans.jl/compare/v0.106.6...v0.107.0) ## Breaking changes - https://github.com/CliMA/Oceananigans.jl/pull/5486 changed the structure of JLD2 and NetCDF output files, to allow for multiple grids, see ht

## Oceananigans v0.107.1 [Diff since v0.107.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.107.0...v0.107.1) 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

## Oceananigans v0.106.6 [Diff since v0.106.5](https://github.com/CliMA/Oceananigans.jl/compare/v0.106.5...v0.106.6) 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

## Oceananigans v0.106.5 [Diff since v0.106.4](https://github.com/CliMA/Oceananigans.jl/compare/v0.106.4...v0.106.5) 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

## Oceananigans v0.106.4 [Diff since v0.106.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.106.3...v0.106.4) **Merged pull requests:** - Switch biases to be enums rather than distinct types. (#5318) (@jackdfranklin) - Add a hydrostatic barotropic soliton case validation f

## Oceananigans v0.106.3 [Diff since v0.106.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.106.2...v0.106.3) **Merged pull requests:** - Partial cell conservation (#5356) (@simone-silvestri) - Add flow over hill validation using open boundaries and a hydrostatic model wit

## Oceananigans v0.106.2 [Diff since v0.106.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.106.1...v0.106.2) **Merged pull requests:** - (0.106.2) Refactor coriolis and add Triad scheme (#5383) (@simone-silvestri) - Shift the `RightFaceFolded` fold upwards by one row (#54

## Oceananigans v0.106.1 [Diff since v0.106.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.106.0...v0.106.1) **Merged pull requests:** - Add restart verification script (#5379) (@ewquon) - Reinvoke sharding tests and refactor Clock constructor for sharded grids (#5389) (@

## Oceananigans v0.106.0 [Diff since v0.105.4](https://github.com/CliMA/Oceananigans.jl/compare/v0.105.4...v0.106.0) ## Breaking changes - https://github.com/CliMA/Oceananigans.jl/pull/5355 changed the default file when restoring from a checkpointer. **Merged pull requests:** - A

## Oceananigans v0.105.5 [Diff since v0.105.4](https://github.com/CliMA/Oceananigans.jl/compare/v0.105.4...v0.105.5) 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

## Oceananigans v0.105.4 [Diff since v0.105.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.105.3...v0.105.4) **Merged pull requests:** - (0.105.4) Add basic tests for Reactant-Oceananigans correctness (#5093) (@glwagner) - Rename `JULIA_DEPOT_PATH` to the `.julia` for bui

## Oceananigans v0.105.3 [Diff since v0.105.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.105.2...v0.105.3) **Merged pull requests:** - (0.105.3) Fix interpolation of terms in chain horizontal derivatives for MutableVerticalDiscretization (#5339) (@glwagner) - Restructur

## Oceananigans v0.105.2 [Diff since v0.105.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.105.1...v0.105.2) **Merged pull requests:** - Add random seeds to examples for reproducible results (#5312) (@tomchor) - (0.105.2) Fix and test checkpointing with open-domain simula

## Oceananigans v0.105.1 [Diff since v0.105.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.105.0...v0.105.1) **Merged pull requests:** - Enable `AveragedSpecifiedTimes` to be used in output writers (#4876) (@xkykai) - Fix lock-exchange example (#5248) (@simone-silvestri)

## Oceananigans v0.105.0 [Diff since v0.104.5](https://github.com/CliMA/Oceananigans.jl/compare/v0.104.5...v0.105.0) ## 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 #527

## Oceananigans v0.104.5 [Diff since v0.104.4](https://github.com/CliMA/Oceananigans.jl/compare/v0.104.4...v0.104.5) **Merged pull requests:** - Bugfix in CATKE with RK3 v2 (#5269) (@simone-silvestri) - Use FieldTimeSeries in tilted BBL example (with NetCDF output) (#5273) (@tomc

## Oceananigans v0.104.4 [Diff since v0.104.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.104.3...v0.104.4) **Merged pull requests:** - Add the possibility for using `fill_halo_regions!` instead of extended halos for `SplitExplicitFreeSurface` (#4750) (@simone-silvestri)

## Oceananigans v0.104.3 [Diff since v0.104.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.104.2...v0.104.3) **Merged pull requests:** - Extend FFTBasedPoissonSolver to work on AMDGPU (#4593) (@navidcy) - Do not pass `CommunicationBuffers` as `clock` to BC (#5063) (@Mikol

## Oceananigans v0.104.2 [Diff since v0.104.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.104.1...v0.104.2) **Merged pull requests:** - Problems with TimeStepWizard and ImmersedBoundaryGrid on MetalGPU (#4990) (@alesok) - Fix halo-edge interpolation and column depth for

## Oceananigans v0.104.1 [Diff since v0.104.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.104.0...v0.104.1) **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) (@

## Oceananigans v0.104.0 [Diff since v0.103.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.103.1...v0.104.0) ## Breaking changes - The `grid` is now an argument in model constructors instead of keyword argument (https://github.com/CliMA/Oceananigans.jl/pull/5087). For exa

## Oceananigans v0.103.1 [Diff since v0.103.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.103.0...v0.103.1) **Merged pull requests:** - Lock Exchange Example (#4968) (@surbhidhiman) - Update docs for turbulence closures (#5069) (@glwagner) - Update references in index.md

## Oceananigans v0.103.0 [Diff since v0.102.5](https://github.com/CliMA/Oceananigans.jl/compare/v0.102.5...v0.103.0) ## Breaking changes - This PR changes the interface for using turbulence closures that have prognostic tracers. Instead of adding these tracers manually, the trace

## Oceananigans v0.102.5 [Diff since v0.102.4](https://github.com/CliMA/Oceananigans.jl/compare/v0.102.4...v0.102.5) **Merged pull requests:** - Extending `DistributedField` and `DistributedFFTBasedPoissonSolver` functionality to allow for distributed FFT preconditioner for `Conj

## Oceananigans v0.102.4 [Diff since v0.102.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.102.3...v0.102.4) **Merged pull requests:** - Generalize bounded WENO advection (#5002) (@glwagner) - Fix flaky test: `test_chunked_abstraction` (#5038) (@ali-ramadhan) - Support ve

## Oceananigans v0.102.3 [Diff since v0.102.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.102.2...v0.102.3) **Merged pull requests:** - Explicit imports in more modules (#5015) (@giordano) - (v0.102.3) Fix NetCDF outputs on vertically stretched lat-lon grids, test non-hy

## Oceananigans v0.102.2 [Diff since v0.102.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.102.1...v0.102.2) **Merged pull requests:** - SphericalCoriolis which supports nonhydrostatic and hydrostatic formulations (#4695) (@francispoulin) - Fix `clock` argument in `TriadI

## Oceananigans v0.102.1 [Diff since v0.102.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.102.0...v0.102.1) **Merged pull requests:** - Add a test for CATKE with DateTime clock and fix (#4885) (@glwagner) - Oceananigans-local FFTW num threads setting (#4958) (@milankl) -

## Oceananigans v0.102.0 [Diff since v0.101.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.101.3...v0.102.0) ## Breaking changes - This release fixes the non-standard style of `BuoyancyField`, which is renamed to `buoyancy_field` - It also adds ExplicitImports to testing

## Oceananigans v0.101.3 [Diff since v0.101.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.101.2...v0.101.3) **Merged pull requests:** - Make `nodes()` return the correct indices when passed a `view` of a `Field` (#4814) (@tomchor) - Refactor the buffer system and add met

## Oceananigans v0.101.2 [Diff since v0.101.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.101.1...v0.101.2) **Merged pull requests:** - Try reusing the julia path for distributed tests (#4783) (@simone-silvestri) - Change regularize_forcing to materialize_forcing, plus r

## Oceananigans v0.101.1 [Diff since v0.101.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.101.0...v0.101.1) **Merged pull requests:** - Add missing method for `ReactantState` architecture (#4931) (@simone-silvestri) - Don't materialize gradients by default (#4933) (@glwa

## Oceananigans v0.101.0 [Diff since v0.100.7](https://github.com/CliMA/Oceananigans.jl/compare/v0.100.7...v0.101.0) ## Breaking changes - Breaking changes in exported Smagorinsky utilities. Previously we exported the "Coefficient" objects, but the public interface is supposed to

## Oceananigans v0.100.7 [Diff since v0.100.6](https://github.com/CliMA/Oceananigans.jl/compare/v0.100.6...v0.100.7) **Merged pull requests:** - (0.100.7) Update Oceananigans to use non-uniform conformal cubed sphere grid from CubedSphere.jl (#4724) (@siddharthabishnu) - Add new

## Oceananigans v0.100.6 [Diff since v0.100.5](https://github.com/CliMA/Oceananigans.jl/compare/v0.100.5...v0.100.6) **Merged pull requests:** - Docs, Examples, and Validation for the XESMF extension (#4823) (@navidcy) - Add missing import when extending `FieldBoundaryConditions`

## Oceananigans v0.100.4 [Diff since v0.100.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.100.3...v0.100.4) **Merged pull requests:** - Clean up unnecessary splatting and allow `fields` to be passed in the implicit solver (#4383) (@simone-silvestri) - Implement MixedBoun

## Oceananigans v0.100.5 [Diff since v0.100.4](https://github.com/CliMA/Oceananigans.jl/compare/v0.100.4...v0.100.5) **Merged pull requests:** - (0.100.5) Fix outputting index-reduced fields like the free surface height (#4567) (@ali-ramadhan) - Add fields to `implicit_step!` in

## Oceananigans v0.100.3 [Diff since v0.100.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.100.2...v0.100.3) **Merged pull requests:** - Move defaults to central location for gravitational acceleration, rotation rate, and planet radius (#4833) (@glwagner) - Fix `mt` probl

## Oceananigans v0.100.2 [Diff since v0.100.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.100.1...v0.100.2) **Merged pull requests:** - (0.100.2) Refactor checkpointing restoring + set particles from checkpointing only if they exist (#4749) (@simone-silvestri)

## Oceananigans v0.100.1 [Diff since v0.100.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.100.0...v0.100.1) **Merged pull requests:** - Eliminate GridMetricOperation and create node metrics (#4805) (@glwagner) - (0.100.1) Set CUDA.jl compatibility to v5.9+ (#4824) (@ali-

## Oceananigans v0.100.0 [Diff since v0.99.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.99.2...v0.100.0) ## Breaking changes - https://github.com/CliMA/Oceananigans.jl/pull/4672 renamed: - `ExponentialCoordinate` to `ExponentialDiscretization` - `ConstantToStretchedCoor

## Oceananigans v0.99.2 [Diff since v0.99.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.99.1...v0.99.2) Add new extension for XESMF.jl that allows conservative regridding for `CenterField`s. **Merged pull requests:** - (0.99.2) Add XESMF.jl extension to use xESMF to comp

## Oceananigans v0.99.1 [Diff since v0.99.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.99.0...v0.99.1) **Merged pull requests:** - Remove misleading benchmark scripts (#4787) (@glwagner) - Removing Reactant extension method for materialize_immersed_boundary (#4789) (@jl

## Oceananigans v0.99.0 [Diff since v0.98.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.98.1...v0.99.0) ## Breaking changes - `HeptadiagonalSolver` no longer supported **Merged pull requests:** - Remove the `HeptadiagonalSolver` (#4386) (@simone-silvestri) - Sets last_Δt

## Oceananigans v0.98.1 [Diff since v0.98.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.98.0...v0.98.1) **Merged pull requests:** - Regularize auxiliary boundary conditions (#4722) (@glwagner) - Remove support for MultiRegionObject split on different devices (#4738) (@si

## Oceananigans v0.98.0 [Diff since v0.97.8](https://github.com/CliMA/Oceananigans.jl/compare/v0.97.8...v0.98.0) ## Breaking changes - new interface for `OpenBoundaryCondition`s where a new kwarg `scheme` specified as `OpenBoundaryCondition(scheme = ...)` specifies the numerical

## Oceananigans v0.97.8 [Diff since v0.97.7](https://github.com/CliMA/Oceananigans.jl/compare/v0.97.7...v0.97.8) **Merged pull requests:** - RK3 CATKE Implementation (#4705) (@simone-silvestri) - Informative error when using LagrangianParticles on Distributed archs (#4709) (@navi

## Oceananigans v0.97.7 [Diff since v0.97.6](https://github.com/CliMA/Oceananigans.jl/compare/v0.97.6...v0.97.7) **Merged pull requests:** - Move storage space to from `MutableVerticalDiscretization` to `ZStarCoordinate` (#4686) (@simone-silvestri) - Fix some inference problems i

## Oceananigans v0.97.6 [Diff since v0.97.5](https://github.com/CliMA/Oceananigans.jl/compare/v0.97.5...v0.97.6) **Merged pull requests:** - `NonhydrostaticModel` on a `LatitudeLongitudeGrid` (#4654) (@simone-silvestri) - Fix distributed HydrostaticFreeSurfaceModel test that seem

## Oceananigans v0.97.4 [Diff since v0.97.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.97.3...v0.97.4) **Merged pull requests:** - Fix a couple of typos in `grids.md` (#4667) (@tomchor) - (0.97.4) Speed up reductions and remove inference problems in Field constructor (#

## Oceananigans v0.97.5 [Diff since v0.97.4](https://github.com/CliMA/Oceananigans.jl/compare/v0.97.4...v0.97.5) **Merged pull requests:** - (0.97.5) Enforce mass-conservation inside domains with Radiation OpenBoundaryConditions (#4627) (@tomchor)

## Oceananigans v0.97.3 [Diff since v0.97.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.97.2...v0.97.3) **Merged pull requests:** - Fix boundary conditions with general vertical coordinate (#4651) (@simone-silvestri) - CompatHelper: bump compat for AMDGPU in [weakdeps] t

## Oceananigans v0.97.2 [Diff since v0.97.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.97.1...v0.97.2) **Merged pull requests:** - Docs for Generalized vertical coordinate (+ discrete implementation) + ZStar vertical coordinate for HydrostaticFreeSurfaceModel (#4588) (@

## Oceananigans v0.97.1 [Diff since v0.97.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.97.0...v0.97.1) **Merged pull requests:** - @allowscalar when indexing `FieldTimeSeries` times on the GPU (#4652) (@simone-silvestri) - add mailmap (#4657) (@vchuravy)

## Oceananigans v0.97.0 [Diff since v0.96.35](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.35...v0.97.0) ## Breaking changes - CUDA-related functionality moved into an extension. Using CUDA-enabled GPU now requires loading CUDA.jl package, e.g., ```Julia using Oceananig

## Oceananigans v0.96.35 [Diff since v0.96.34](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.34...v0.96.35) **Merged pull requests:** - Don't initialize callback every time_step (#4212) (@glwagner) - Fix saveproperty! for a `ConstantField` (#4393) (@simone-silvestri) - A

## Oceananigans v0.96.34 [Diff since v0.96.33](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.33...v0.96.34) **Merged pull requests:** - Fix the problem that particles may be out of bounds when velocity is too large (#3349) (@Yixiao-Zhang) - Introduce closure_constant int

## Oceananigans v0.96.33 [Diff since v0.96.32](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.32...v0.96.33) **Merged pull requests:** - Integrate cubed sphere functionality with halo filling and core infrastructure updates (#4538) (@siddharthabishnu) - fix mean pressure

## Oceananigans v0.96.32 [Diff since v0.96.31](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.31...v0.96.32) **Merged pull requests:** - (0.96.32) Fix `zspacing()` for `PartialCellBottom` immersed boundaries and add tests for `ImmersedGrid`s (#4572) (@tomchor) - Fix a cou

## Oceananigans v0.96.31 [Diff since v0.96.30](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.30...v0.96.31) **Merged pull requests:** - Call `compute!` in constructor for `ComputedField` (#4531) (@glwagner) - Generalize assumed_field_location, plus allow FourierTridiagon

## Oceananigans v0.96.30 [Diff since v0.96.29](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.29...v0.96.30) **Merged pull requests:** - Fix Biharmonic Viscosity on Cubed-Sphere Grid (#3850) (@siddharthabishnu) - Creates `bottommost_active_node` function (#4507) (@tomchor

## Oceananigans v0.96.29 [Diff since v0.96.28](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.28...v0.96.29) **Merged pull requests:** - (0.96.29) Add adapt structure for BuoyancyForce (#4543) (@glwagner) **Closed issues:** - Docs aren't being created for all registered v

## Oceananigans v0.96.28 [Diff since v0.96.27](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.27...v0.96.28) **Merged pull requests:** - Solving Poisson equation for `p * dt` instead of `p` (#4276) (@xkykai) - Changes default AMD poincare coefficient (#4494) (@jagoosw) -

## Oceananigans v0.96.27 [Diff since v0.96.26](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.26...v0.96.27) **Merged pull requests:** - Variance dissipation computation (#3877) (@simone-silvestri) - Small improvements to `PerturbationAdvectionOpenBoundaryCondition` inter

## Oceananigans v0.96.26 [Diff since v0.96.25](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.25...v0.96.26) **Merged pull requests:** - Include background tracer and velocities in closure tendency terms (#3646) (@glwagner) - Resolve ambiguity when setting MultiRegionFiel

## Oceananigans v0.96.25 [Diff since v0.96.24](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.24...v0.96.25) **Merged pull requests:** - Store computational coordinates in OrthogonalSphericalShellGrid for non-uniform conformal mappings (#4295) (@siddharthabishnu) - Reacta

## Oceananigans v0.96.24 [Diff since v0.96.23](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.23...v0.96.24) **Merged pull requests:** - Some more fixing for polar BC (#4463) (@simone-silvestri) - Add a constructor for LatitudeLongitudeGrid from RectilinearGrid (#4465) (@

## Oceananigans v0.96.23 [Diff since v0.96.22](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.22...v0.96.23) **Merged pull requests:** - Add Distributed grids section in Grids tutorial (#3698) (@navidcy) - support for active_cells_map in kernels (#3920) (@simone-silvestri

## Oceananigans v0.96.22 [Diff since v0.96.21](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.21...v0.96.22) **Merged pull requests:** - Add a performance benchmark pipeline (#4375) (@simone-silvestri) - Improve z-star tracer conservation tests (#4403) (@NoraLoose) - Fuse

## Oceananigans v0.96.21 [Diff since v0.96.20](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.20...v0.96.21) **Merged pull requests:** - Implement an interface for writing output with Simulation (#4271) (@glwagner) - Remove trailing white spaces in code (#4304) (@tomchor)

## Oceananigans v0.96.20 [Diff since v0.96.19](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.19...v0.96.20) **Merged pull requests:** - Replace IncompleteLU.jl by KrylovPreconditioners.jl (#3789) (@amontoison) - Interface to Krylov.jl solvers (#4041) (@amontoison) - Test

## Oceananigans v0.96.19 [Diff since v0.96.18](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.18...v0.96.19) **Merged pull requests:** - Correctly account for field names in `ContinuousBoundaryFunctions` (#4008) (@simone-silvestri) - Zstar test that actually test conserva

## Oceananigans v0.96.17 [Diff since v0.96.16](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.16...v0.96.17) **Merged pull requests:** - Massive clean up for conditional operations (#3794) (@glwagner) - Use polar criteria to build PolarBoundaryCondition (#4350) (@glwagner

## Oceananigans v0.96.18 [Diff since v0.96.17](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.17...v0.96.18) **Merged pull requests:** - Correcting split explicit barotropic velocities (#4355) (@simone-silvestri) - (0.96.18) Update Project.toml (#4356) (@simone-silvestri)

## Oceananigans v0.96.15 [Diff since v0.96.14](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.14...v0.96.15) **Merged pull requests:** - More fixes for z sharding on vertically Flat grids (#4338) (@glwagner) - Throw an error when the partitioning seems wrong (#4339) (@glw

## Oceananigans v0.96.16 [Diff since v0.96.15](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.15...v0.96.16) **Merged pull requests:** - Build sharded coordinates on the CPU (#4343) (@simone-silvestri) - fix: sharding dropped on LatLon Grid (#4344) (@avik-pal) - Fix alloc

## Oceananigans v0.96.13 [Diff since v0.96.12](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.12...v0.96.13) **Merged pull requests:** - fix: create the grid directly on device (#4334) (@avik-pal) - Bump 0.96.13 (#4335) (@glwagner)

## Oceananigans v0.96.14 [Diff since v0.96.13](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.13...v0.96.14) **Merged pull requests:** - Fix a memory allocation issues (#4336) (@simone-silvestri) - (0.96.14) Support Flat vertical dir: `sharded_z` for z::Nothing (#4337) (@

## Oceananigans v0.96.12 [Diff since v0.96.11](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.11...v0.96.12) **Merged pull requests:** - Pad Center fields on BoundedTopology so that all `Fields` have identical horizontal size (#4144) (@glwagner) - Increment run_wall_time

## Oceananigans v0.96.11 [Diff since v0.96.10](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.10...v0.96.11) **Merged pull requests:** - Fix broken doctests (#4315) (@glwagner) - Removes warning from implicit-explicit RK3 (#4317) (@jagoosw) - Sharding on a rectilinear gri

## Oceananigans v0.96.10 [Diff since v0.96.9](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.9...v0.96.10) **Merged pull requests:** - (0.96.10) Fix bug when masking CATKE during time-stepping (#4314) (@glwagner) **Closed issues:** - EKE is zero with [some] CATKE configs

## Oceananigans v0.96.8 [Diff since v0.96.7](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.7...v0.96.8) **Merged pull requests:** - Rm hardcoded Float32 in VerticalScalarDiffusivity (#4309) (@glwagner) - Bump to 0.96.8 (#4310) (@glwagner)

## Oceananigans v0.96.9 [Diff since v0.96.8](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.8...v0.96.9) **Merged pull requests:** - Use default FloatType to build Reactant clock (#4308) (@glwagner) - Bump to 0.96.9 (#4311) (@glwagner)

## Oceananigans v0.96.7 [Diff since v0.96.6](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.6...v0.96.7) **Merged pull requests:** - Replaces greek capital N with latin N in variable names... (#4297) (@navidcy) - Fix some broken tests (#4299) (@simone-silvestri) - Swap ar

## Oceananigans v0.96.6 [Diff since v0.96.5](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.5...v0.96.6) **Merged pull requests:** - Export spacings operators near where they are defined (#4280) (@glwagner) - Reinstate sharding tests (#4281) (@simone-silvestri) - Fixes fo

## Oceananigans v0.96.4 [Diff since v0.96.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.3...v0.96.4) **Merged pull requests:** - [Reactant] Materialize traced array (#4270) (@wsmoses) - Sharding for LatitudeLongitudeGrid and extend Distributed methods for `Distributed

## Oceananigans v0.96.5 [Diff since v0.96.4](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.4...v0.96.5) **Merged pull requests:** - Add validation for `condition` kwarg in `ConditionalOperation` (#4266) (@navidcy) - Reactant in weak deps (#4283) (@simone-silvestri) - Rea

## Oceananigans v0.96.3 [Diff since v0.96.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.2...v0.96.3) **Merged pull requests:** - Implement Distributed{<:ReactantState} (#4200) (@glwagner) - Support `BoussinesqEquationOfState` in `NetCDFWriter` (#4252) (@jbisits) - Gen

## Oceananigans v0.96.2 [Diff since v0.96.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.1...v0.96.2) **Merged pull requests:** - feat: Distributed Reactant (#4246) (@avik-pal) - Try to make LatitudeLongitudeGrid traceable (#4259) (@glwagner) - Bump to 0.96.2 (#4263) (

## Oceananigans v0.96.1 [Diff since v0.96.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.96.0...v0.96.1) **Merged pull requests:** - Add section in the docs for reduced operations (#4235) (@navidcy) - Reactant: add make_tracer for grid (#4242) (@wsmoses) - find_time_index

## Oceananigans v0.96.0 [Diff since v0.95.29](https://github.com/CliMA/Oceananigans.jl/compare/v0.95.29...v0.96.0) ## Breaking changes This breaking release overhauls `NetCDFOutputWriter` (which is now called `NetCDFWriter`) and moves it to an extension. From now on scripts that

## Oceananigans v0.95.29 [Diff since v0.95.28](https://github.com/CliMA/Oceananigans.jl/compare/v0.95.28...v0.95.29) **Merged pull requests:** - Capture `Clock.stage` with a type parameter (#4226) (@jumerckx) - Add adapt for TimeInterpolator (#4227) (@wsmoses) - Convert TimeInter

## Oceananigans v0.95.28 [Diff since v0.95.27](https://github.com/CliMA/Oceananigans.jl/compare/v0.95.27...v0.95.28) **Merged pull requests:** - CompatHelper: add new compat entry for ConstructionBase in [weakdeps] at version 1, (keep existing compat) (#4184) (@github-actions[bot

## Oceananigans v0.95.27 [Diff since v0.95.26](https://github.com/CliMA/Oceananigans.jl/compare/v0.95.26...v0.95.27) **Merged pull requests:** - Refactor vertical vorticity to return operation rather than Field (#3340) (@glwagner) - [Reactant] feat: support new Reactant runtime I

## Oceananigans v0.95.26 [Diff since v0.95.25](https://github.com/CliMA/Oceananigans.jl/compare/v0.95.25...v0.95.26) **Merged pull requests:** - Tests on tartarus (#4139) (@simone-silvestri) - Adding a distributed tripolar grid (#4204) (@simone-silvestri) - Add a gpu test for the

## Oceananigans v0.95.24 [Diff since v0.95.23](https://github.com/CliMA/Oceananigans.jl/compare/v0.95.23...v0.95.24) **Merged pull requests:** - Use default FloatType in Centered advection (#4193) (@glwagner) - Fix bug in active-weighted interpolation (#4195) (@glwagner) - Change

## Oceananigans v0.95.25 [Diff since v0.95.24](https://github.com/CliMA/Oceananigans.jl/compare/v0.95.24...v0.95.25) **Merged pull requests:** - Tripolar grid in Oceananigans (only serial) (#3913) (@simone-silvestri) - (0.95.25) bump minor version (#4203) (@simone-silvestri)

## Oceananigans v0.95.22 [Diff since v0.95.21](https://github.com/CliMA/Oceananigans.jl/compare/v0.95.21...v0.95.22) **Merged pull requests:** - Bugfix in distributed fill halos (#3714) (@simone-silvestri) - Fix the docstring for `ImmersedBoundaryGrid` (#4174) (@glwagner) - Add n

## Oceananigans v0.95.23 [Diff since v0.95.22](https://github.com/CliMA/Oceananigans.jl/compare/v0.95.22...v0.95.23) **Merged pull requests:** - Fill halos after the update step (#4186) (@simone-silvestri) - Fix the `euler` keyword in `time_step!(sim::ReactantSimulation)` (#4191)

## Oceananigans v0.95.21 [Diff since v0.95.20](https://github.com/CliMA/Oceananigans.jl/compare/v0.95.20...v0.95.21) **Merged pull requests:** - Lagrangian Smagorinsky for 2D flows (#4009) (@simone-silvestri) - Set a default Clock depending on the grid (#4096) (@glwagner) - Expos

## Oceananigans v0.95.20 [Diff since v0.95.18](https://github.com/CliMA/Oceananigans.jl/compare/v0.95.18...v0.95.20) **Merged pull requests:** - Add support for ZStar in RK3 (#4156) (@simone-silvestri) - Formatting of the `store_*!` functions (#4164) (@simone-silvestri) - Maybe f

## Oceananigans v0.95.19 [Diff since v0.95.18](https://github.com/CliMA/Oceananigans.jl/compare/v0.95.18...v0.95.19) **Merged pull requests:** - Add support for ZStar in RK3 (#4156) (@simone-silvestri) - Remove if-statement from tridiagonal solver sweep (#4170) (@glwagner) - Bump

## Oceananigans v0.95.18 [Diff since v0.95.17](https://github.com/CliMA/Oceananigans.jl/compare/v0.95.17...v0.95.18) **Merged pull requests:** - Clean up immersed boundary interface (#4140) (@simone-silvestri) - Update spatial_operators.md (#4153) (@briochemc) - Clean up of activ

## Oceananigans v0.95.15 [Diff since v0.95.14](https://github.com/CliMA/Oceananigans.jl/compare/v0.95.14...v0.95.15) **Merged pull requests:** - Expanded interpolation utilities (#4146) (@glwagner) - Implement `time_step!(sim::Simulation, Δt)` (#4148) (@glwagner) - New reactant f

## Oceananigans v0.95.16 [Diff since v0.95.15](https://github.com/CliMA/Oceananigans.jl/compare/v0.95.15...v0.95.16) **Merged pull requests:** - (0.95.15) Fix bugs in ReactantExt for OrthogonalSphericalShellGrid (#4151) (@glwagner) - Bump to 0.95.16 (#4155) (@glwagner)

## Oceananigans v0.95.17 [Diff since v0.95.16](https://github.com/CliMA/Oceananigans.jl/compare/v0.95.16...v0.95.17) **Merged pull requests:** - Add method to `maximum_numeric_diffusivity` for `DiscreteDiffusionFunction` (#4101) (@jbisits) - Add more UnaryOperations with @unary (

## Oceananigans v0.95.13 [Diff since v0.95.12](https://github.com/CliMA/Oceananigans.jl/compare/v0.95.12...v0.95.13) **Merged pull requests:** - Fix some `FieldTimeSeries` bugs (#4086) (@simone-silvestri) - Implement RotatedLatitudeLongitudeGrid (#4108) (@glwagner) - Add warning

## Oceananigans v0.95.14 [Diff since v0.95.13](https://github.com/CliMA/Oceananigans.jl/compare/v0.95.13...v0.95.14) **Merged pull requests:** - Adds a pertubation advection open boundary matching scheme (#3977) (@jagoosw) - More README info about citing and model development pap

## Oceananigans v0.95.12 [Diff since v0.95.11](https://github.com/CliMA/Oceananigans.jl/compare/v0.95.11...v0.95.12) **Merged pull requests:** - Make the `OceananigansReactantExt` depend explicitly on KA (#4093) (@glwagner) - Allow schedules to use different float types (#4097) (

## Oceananigans v0.95.11 [Diff since v0.95.10](https://github.com/CliMA/Oceananigans.jl/compare/v0.95.10...v0.95.11) **Merged pull requests:** - Fix default Clock.time to Float64 (#4089) (@glwagner) - Add Fan et al. (2024) and Bhadouriya et al. (2025) in papers list + brings back

## Oceananigans v0.95.10 [Diff since v0.95.9](https://github.com/CliMA/Oceananigans.jl/compare/v0.95.9...v0.95.10) **Merged pull requests:** - Add a few more Reactant unit tests + test Reactant extension via github actions (#4082) (@glwagner) - Drop the downloads stats badges (#4

## Oceananigans v0.95.9 [Diff since v0.95.8](https://github.com/CliMA/Oceananigans.jl/compare/v0.95.8...v0.95.9) **Merged pull requests:** - `Field` Stokes shear and tendency with `UniformStokesDrift` (#2320) (@glwagner) - add a unit test for background flux divergence and clean

## Oceananigans v0.95.8 [Diff since v0.95.7](https://github.com/CliMA/Oceananigans.jl/compare/v0.95.7...v0.95.8) **Merged pull requests:** - More generalization of tuples (#4049) (@wsmoses) - Fix bug in validation of `MutableVerticalDiscretization()` (#4050) (@tomchor) - Disambig

## Oceananigans v0.95.7 [Diff since v0.95.6](https://github.com/CliMA/Oceananigans.jl/compare/v0.95.6...v0.95.7) **Merged pull requests:** - (0.95.7) Yet another ZStar implementation (#3956) (@simone-silvestri) - Allows properties of `StaticVerticalCoordinate` to have different t

## Oceananigans v0.95.6 [Diff since v0.95.5](https://github.com/CliMA/Oceananigans.jl/compare/v0.95.5...v0.95.6) **Merged pull requests:** - Correct `tupled_halo_filling` for distributed fields (#4017) (@simone-silvestri) - Support interpolating onto `Windowed` fields (#4021) (@s

## Oceananigans v0.95.4 [Diff since v0.95.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.95.3...v0.95.4) **Merged pull requests:** - Allow FieldTimeSeries to load data split across multiple files (#3976) (@glwagner) - Avoid flux computations when not needed in the `Isopyc

## Oceananigans v0.95.5 [Diff since v0.95.4](https://github.com/CliMA/Oceananigans.jl/compare/v0.95.4...v0.95.5)

## Oceananigans v0.95.3 [Diff since v0.95.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.95.2...v0.95.3) **Merged pull requests:** - (0.95.3) Reset model clock and skip `time_step!`ing if next actuation time is tiny (#3606) (@tomchor) - Add parameter to epsilon equation s

## Oceananigans v0.95.0 [Diff since v0.94.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.94.3...v0.95.0) **Merged pull requests:** - Correct `AveragedTimeInterval` to use actuations (#3721) (@liuchihl) - Adds momentum equation test for Enzyme extension (#3822) (@jlk9) - A

## Oceananigans v0.95.1 [Diff since v0.95.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.95.0...v0.95.1) **Merged pull requests:** - Fix horizontally `Flat` WENO advection (#3979) (@simone-silvestri) - Fix exported names from BuoyancyFormulations module (#3984) (@glwagner

## Oceananigans v0.95.2 [Diff since v0.95.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.95.1...v0.95.2) **Merged pull requests:** - (0.95.2) Bugfix in the Polar BC (#3985) (@simone-silvestri)

## Oceananigans v0.94.3 [Diff since v0.94.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.94.2...v0.94.3) **Merged pull requests:** - Reduce parameter space for velocity tendency kernels (#3924) (@simone-silvestri) - Leftover from split explicit refactor (#3931) (@simone-s

## Oceananigans v0.94.0 [Diff since v0.93.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.93.3...v0.94.0) **Merged pull requests:** - Implement scale-invariant dynamic Smagorinsky (#3642) (@tomchor) - Open halo filling on Windowed fields (#3834) (@simone-silvestri) - `stat

## Oceananigans v0.94.1 [Diff since v0.94.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.94.0...v0.94.1)

## Oceananigans v0.94.2 [Diff since v0.94.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.94.1...v0.94.2) **Merged pull requests:** - (0.94.2) Support interpolation from triple-Flat grids (#3928) (@glwagner)

## Oceananigans v0.93.3 [Diff since v0.93.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.93.2...v0.93.3) **Merged pull requests:** - Add test of enzyme flux bc (#3643) (@jlk9) - Fix docs for `VectorInvariant` and `WENOVectorInvariant` (#3866) (@navidcy) - Use on_architect

## Oceananigans v0.93.2 [Diff since v0.93.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.93.1...v0.93.2) **Merged pull requests:** - Topology-aware operators (#3268) (@simone-silvestri) - Allow `FieldTimeSeries` to pass keyword arguments to `jldopen` (#3739) (@ali-ramadha

## Oceananigans v0.93.0 [Diff since v0.92.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.92.2...v0.93.0) **Merged pull requests:** - Correct vorticity computation at the corners of cubed sphere panels (#3325) (@siddharthabishnu) - Fixes bug in `FlatExtrapolation` matching

## Oceananigans v0.93.1 [Diff since v0.93.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.93.0...v0.93.1) **Merged pull requests:** - Fix bug calling domain for LatitudeLongitudeGrid (#3871) (@glwagner)

## Oceananigans v0.92.2 [Diff since v0.92.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.92.1...v0.92.2) **Merged pull requests:** - Temporary support for OrthogonalSphericalShellGrid for MakieExt (#3824) (@glwagner) - Add papers using Oceananigans (#3861) (@navidcy) - Co

## Oceananigans v0.92.1 [Diff since v0.92.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.92.0...v0.92.1) **Merged pull requests:** - Bug in NetCDF output for curvilinear immersed grids (#3666) (@simone-silvestri) - Different advection schemes in different directions (#373

## Oceananigans v0.92.0 [Diff since v0.91.15](https://github.com/CliMA/Oceananigans.jl/compare/v0.91.15...v0.92.0) **Merged pull requests:** - (0.92.0) Make RungeKutta3 the default time-stepper for NonhydrostaticModel (#3580) (@glwagner) - Change default `hydrostatic_pressure_ano

## Oceananigans v0.91.15 [Diff since v0.91.14](https://github.com/CliMA/Oceananigans.jl/compare/v0.91.14...v0.91.15) **Merged pull requests:** - Add `ImmersedPressureSolver` with `FFTBasedPoissonSolver` as preconditioner for complex domains (#3188) (@xkykai) - Fix a bug in the ad

## Oceananigans v0.91.14 [Diff since v0.91.13](https://github.com/CliMA/Oceananigans.jl/compare/v0.91.13...v0.91.14) **Merged pull requests:** - Remove Immersed map from `Adapt`ing the `ImmersedBoundaryGrid` (#3690) (@simone-silvestri) - Supporting indexing a `FieldDataset` with

## Oceananigans v0.91.13 [Diff since v0.91.12](https://github.com/CliMA/Oceananigans.jl/compare/v0.91.12...v0.91.13) **Merged pull requests:** - Fix typo in the README (#3757) (@glwagner) - Bump compat entry for CubedSphere (#3763) (@navidcy) - Fix FieldTimeSeries interpolation f

## Oceananigans v0.91.12 [Diff since v0.91.11](https://github.com/CliMA/Oceananigans.jl/compare/v0.91.11...v0.91.12) **Merged pull requests:** - Remove space from doi url (#3734) (@navidcy) - Fix CFL calculation on flat grids (#3737) (@ali-ramadhan) - Remove tendency computation

## Oceananigans v0.91.10 [Diff since v0.91.9](https://github.com/CliMA/Oceananigans.jl/compare/v0.91.9...v0.91.10) **Merged pull requests:** - Make it easier to build simple HydrostaticFreeSurfaceModels (#3620) (@glwagner) - Bugfix in `interpolate!` for `FieldTimeSeries` (#3723)

## Oceananigans v0.91.11 [Diff since v0.91.10](https://github.com/CliMA/Oceananigans.jl/compare/v0.91.10...v0.91.11) **Merged pull requests:** - Nullify preferred axis for field arg (#3730) (@glwagner) - Bugfix for #3731 (#3733) (@simone-silvestri) **Closed issues:** - Bug with M

## Oceananigans v0.91.9 [Diff since v0.91.8](https://github.com/CliMA/Oceananigans.jl/compare/v0.91.8...v0.91.9) **Merged pull requests:** - Adds methods to `mask_immersed_field!` for `BinaryOperations` (#3683) (@jagoosw) - Fixs fallback for `AbstractContinuousFormBiogeochemistry

## Oceananigans v0.91.8 [Diff since v0.91.7](https://github.com/CliMA/Oceananigans.jl/compare/v0.91.7...v0.91.8) **Merged pull requests:** - Add new constructor for KernelParameters (#3645) (@glwagner) - The start of documentation 2.0 (#3673) (@glwagner) - Add constructor for win

## Oceananigans v0.91.6 [Diff since v0.91.5](https://github.com/CliMA/Oceananigans.jl/compare/v0.91.5...v0.91.6) **Merged pull requests:** - (0.91.6) Distributed FFTs using Oceananigans' inhouse DiscreteTransforms (#3279) (@simone-silvestri) - Add Downloads badges on README.md (#

## Oceananigans v0.91.7 [Diff since v0.91.6](https://github.com/CliMA/Oceananigans.jl/compare/v0.91.6...v0.91.7) This PR implements the infrastructure for open boundaries in `NonhydrostaticModel`s by differentiating the filling of halos for `BoundaryCondition{Open}` boundaries so

## Oceananigans v0.91.5 [Diff since v0.91.4](https://github.com/CliMA/Oceananigans.jl/compare/v0.91.4...v0.91.5) **Merged pull requests:** - Fix index calculation for Lagrangian particles in periodic directions (#3416) (@xkykai) - Support non-trivial horizontal coordinates for si

## Oceananigans v0.91.4 [Diff since v0.91.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.91.3...v0.91.4) **Merged pull requests:** - Remove performance-/precompilation-time harmful `@eval` (#3556) (@simone-silvestri) - Enzyme: try bump without tuple changes (#3618) (@wsmo

## Oceananigans v0.91.3 [Diff since v0.91.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.91.2...v0.91.3) **Merged pull requests:** - TKEDissipationVerticalDiffusivity (aka k-epsilon) turbulence closure (take 2) (#3605) (@glwagner) - `Adapt`ing all fields of the `Orthogona

## Oceananigans v0.91.2 [Diff since v0.91.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.91.1...v0.91.2) **Merged pull requests:** - Speedup constructing a `ConformalCubedSphereGrid` on GPU (#3579) (@navidcy) - (0.91.2) Remove instances of `previous_Δt` and fix a bug sett

## Oceananigans v0.91.1 [Diff since v0.91.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.91.0...v0.91.1) **Merged pull requests:** - Bugfix for `parent_index_range` (#3573) (@siddharthabishnu) - Passes `grid` argument to `NetCDFOutputWriter` (#3576) (@tomchor) - Enforce t

## Oceananigans v0.91.0 [Diff since v0.90.14](https://github.com/CliMA/Oceananigans.jl/compare/v0.90.14...v0.91.0) **Merged pull requests:** - Update climacommon to 2024_04_30 (#3571) (@Sbozzolo) - (0.91.0) Make hydrostatic pressure anomaly optional in `NonhydrostaticModel` (#357

## Oceananigans v0.90.14 [Diff since v0.90.13](https://github.com/CliMA/Oceananigans.jl/compare/v0.90.13...v0.90.14) **Merged pull requests:** - Fix `interpolator` for left side of periodic domain (#3549) (@jagoosw) - Extend operations for two `ZeroField`s (#3567) (@zhihua-zheng)

## Oceananigans v0.90.13 [Diff since v0.90.12](https://github.com/CliMA/Oceananigans.jl/compare/v0.90.12...v0.90.13) **Merged pull requests:** - Fix `RiBasedVerticalDiffusivity` (#3510) (@glwagner) - Add Whitley & Wenegrat 2024 (#3546) (@navidcy) - Alignment and minor changes (#3

## Oceananigans v0.90.12 [Diff since v0.90.11](https://github.com/CliMA/Oceananigans.jl/compare/v0.90.11...v0.90.12) **Merged pull requests:** - PCG uses provided `grid`'s halo size instead of hardcoding `halo = (3, 3, 1)` (#3094) (@navidcy) - Fill halos of conformal cubed sphere

## Oceananigans v0.90.11 [Diff since v0.90.10](https://github.com/CliMA/Oceananigans.jl/compare/v0.90.10...v0.90.11) **Merged pull requests:** - Add internal tide example in Docs (#3132) (@navidcy) - (0.90.11) Tests for a distributed Immersed boundary grid + fix some `on_architec

## Oceananigans v0.90.10 [Diff since v0.90.9](https://github.com/CliMA/Oceananigans.jl/compare/v0.90.9...v0.90.10) **Merged pull requests:** - Support `FunctionField` as a `Field.operand`, similar to `AbstractOperation` (#3228) (@glwagner) - Move distributed buildkite CI to the `

## Oceananigans v0.90.9 [Diff since v0.90.8](https://github.com/CliMA/Oceananigans.jl/compare/v0.90.8...v0.90.9) **Merged pull requests:** - Use Julia v1.10 for CI (#3403) (@navidcy) - Scaling improvement for the distributed `HydrostaticFreeSurfaceModel` (#3404) (@simone-silvestr

## Oceananigans v0.90.8 [Diff since v0.90.7](https://github.com/CliMA/Oceananigans.jl/compare/v0.90.7...v0.90.8) **Merged pull requests:** - (0.90.8) Rules for `Time` interpolation / extrapolation for FieldTimeSeries and `InterpolatedField` (#3450) (@glwagner) **Closed issues:**

## Oceananigans v0.90.7 [Diff since v0.90.6](https://github.com/CliMA/Oceananigans.jl/compare/v0.90.6...v0.90.7) **Merged pull requests:** - Some type stabilization to get a new gradient from Enzyme (#3360) (@glwagner) - Fixes error when reducing `Fields` with a `condition` on `I

## Oceananigans v0.90.5 [Diff since v0.90.4](https://github.com/CliMA/Oceananigans.jl/compare/v0.90.4...v0.90.5) **Merged pull requests:** - Change StokesDrift example in docs to a wavepacket moving with group velocity (#3425) (@navidcy) - Improve references/citations in docs + e

## Oceananigans v0.90.6 [Diff since v0.90.5](https://github.com/CliMA/Oceananigans.jl/compare/v0.90.5...v0.90.6) **Merged pull requests:** - Refactor `Fields.interpolate` to make sense for `Nothing` locations and `Flat` directions - take 2 (#3395) (@simone-silvestri) - Enhance do

## Oceananigans v0.90.4 Added three-dimensional implementation of Stokes drift. [Diff since v0.90.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.90.3...v0.90.4) **Merged pull requests:** - Fixes bug with pre-defining diffusivity fields (#3367) (@jagoosw) - (0.90.4) Implem

## Oceananigans v0.90.3 [Diff since v0.90.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.90.2...v0.90.3) **Merged pull requests:** - (0.90.3) Fix bug in adapting `ScalarDiffusivity` and `ScalarBiharmonicDiffusivity` (#3413) (@glwagner)

## Oceananigans v0.90.2 [Diff since v0.90.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.90.1...v0.90.2) **Merged pull requests:** - Default NaN-Checker for Particle Tracking models (#3376) (@simone-silvestri) - Add OceanBioME.jl paper (#3380) (@navidcy) - Updates `Relaxa

## Oceananigans v0.90.1 [Diff since v0.90.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.90.0...v0.90.1) **Merged pull requests:** - Non uniform partitioning for `Distributed` architectures (#3339) (@simone-silvestri) - Fix advection timescale calculation (#3362) (@zhihua

## Oceananigans v0.90.0 This version introduces a major change (https://github.com/CliMA/Oceananigans.jl/pull/3355) to the API for initial conditions, background fields, and boundary conditions based on functions on grids with `Flat` directions. When using functions, we previousl

## Oceananigans v0.89.3 [Diff since v0.89.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.89.2...v0.89.3) **Merged pull requests:** - FieldTimeSeries for time-dependent boundary condition (#3233) (@simone-silvestri) - Update dependencies + use Documenter v1 (#3310) (@navid

## Oceananigans v0.89.2 [Diff since v0.89.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.89.1...v0.89.2) **Merged pull requests:** - Tweak Distributed API (#3314) (@glwagner) - Add validation for array-based coordinates (#3319) (@navidcy) - Fix typo in `Face` -> `Center`

## Oceananigans v0.89.1 [Diff since v0.89.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.89.0...v0.89.1) **Merged pull requests:** - (0.89.1) Make maximum numeric diffusivity more generic for named tuples of diffusivity (#3274) (@jagoosw) - Add `indices` info in `show(io,

## Oceananigans v0.89.0 [Diff since v0.88.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.88.0...v0.89.0) **Merged pull requests:** - Remove type instability in WENO β calculation for Float32 (#3212) (@milankl) - Type stabilize offset_data (#3273) (@wsmoses) - Reorder comp

## Oceananigans v0.88.0 [Diff since v0.87.4](https://github.com/CliMA/Oceananigans.jl/compare/v0.87.4...v0.88.0) **Merged pull requests:** - (0.88.0) MPI communication and computation overlap in the `HydrostaticFreeSurfaceModel` and `NonhydrostaticModel` (#3125) (@simone-silvestr

## Oceananigans v0.87.4 [Diff since v0.87.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.87.3...v0.87.4) **Merged pull requests:** - Deal with x ⇆ y, λ ⇆ φ, etc when filling halos for metrics/coords in `ConformalCubedSphereGrid` (#3256) (@navidcy) - Rename `return_metrics

## Oceananigans v0.87.3 [Diff since v0.87.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.87.2...v0.87.3) **Closed issues:** - Possible bug in computing `Field(::KernelFunctionOperation)` (#3232) **Merged pull requests:** - (0.87.3) BugFix for computing `Field(::KernelFunc

## Oceananigans v0.87.2 [Diff since v0.87.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.87.1...v0.87.2) **Closed issues:** - `Callable` tridiagonal coefficients produces catastrophic loss of performance (#3047) - Should reductions exclude `peripheral_node`? (#3064) - Err

## Oceananigans v0.87.1 [Diff since v0.87.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.87.0...v0.87.1) **Closed issues:** - Offline differential operators do not correctly apply boundary conditions (#3224) **Merged pull requests:** - (0.87.1) Make `set!` a little more a

## Oceananigans v0.87.0 [Diff since v0.86.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.86.0...v0.87.0) **Closed issues:** - Inconsistent advection from "different" velocities (#2928) - Simple tests for correct halo filling + dynamics with the MultiRegion cubed sphere (#

## Oceananigans v0.86.0 [Diff since v0.85.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.85.0...v0.86.0) **Closed issues:** - `fkeep` error for `HydrostaticFreeSurfaceModel` with a `HeptadiagonalIterativeSolver` (#3184) - Integer division error in `solve!` on GPU (#3189)

## Oceananigans v0.85.0 [Diff since v0.84.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.84.1...v0.85.0) **Closed issues:** - `ImmersedBoundaryCondition` has the opposite convention of `FieldBoundaryConditions` (#3141) **Merged pull requests:** - (v0.85.0) Switching cells

## Oceananigans v0.84.1 [Diff since v0.84.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.84.0...v0.84.1) **Closed issues:** - Running simulations with `Clock{DateTime}` (#2956) - Dispatch `fractional_x/y/z_index` methods over various grid types? (#3156) - `specified_times

## Oceananigans v0.84.0 Breaking changes: - `compression` kwarg for `NetCDFOutputWriter` does not exist anymore and is now replaced by `deflatelevel` (https://github.com/CliMA/Oceananigans.jl/pull/3153); - `VectorInvariant` advection constructor changed. Now it accepts a `vortici

## Oceananigans v0.83.0 [Diff since v0.82.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.82.0...v0.83.0) **Closed issues:** - Error interpolating on an irregularly spaced grid (#2911) - Can't reduce some `KernelFunctionOperation`s on the GPU with `ImmersedBoundaryGrid` (#

## Oceananigans v0.82.0 [Diff since v0.81.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.81.1...v0.82.0) **Merged pull requests:** - (v0.82.0) Fixes inconsistent advection from "different" velocities (#3027) (@jagoosw) - Fix few bugs + improve docstring of `SplitExplicitF

## Oceananigans v0.81.1 [Diff since v0.81.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.81.0...v0.81.1) **Closed issues:** - `UniformStokesDrift` would benefit from a `parameters` keyword (#2960) - Simulation with tilted gravity and background buoyancy increases in total

## Oceananigans v0.81.0 [Diff since v0.80.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.80.0...v0.81.0) **Closed issues:** - Every exported name requires a docstring (#1133) - More comprehensive contributors list? (#1519) - Current implementation of `dot(::Field, ::Field

## Oceananigans v0.80.0 [Diff since v0.79.6](https://github.com/CliMA/Oceananigans.jl/compare/v0.79.6...v0.80.0) **Closed issues:** - Running with Posits as well as AbstractFloat. (#39) - Implement Vreman SGS closure (#440) - Verification tests comparing performance of different

## Oceananigans v0.79.6 [Diff since v0.79.5](https://github.com/CliMA/Oceananigans.jl/compare/v0.79.5...v0.79.6) **Closed issues:** - Unexpected behavior when interpolating? (#2969) **Merged pull requests:** - Adds an interface for inserting biogeochemistry models into Oceananiga

## Oceananigans v0.79.5 [Diff since v0.79.4](https://github.com/CliMA/Oceananigans.jl/compare/v0.79.4...v0.79.5) **Closed issues:** - Bugfix in hydrostatic spherical coriolis (#2929) - Docstring needed for `ShallowWaterScalarDiffusivity` (#2939) - Nonhydrostatic pressure solver d

## Oceananigans v0.79.4 [Diff since v0.79.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.79.3...v0.79.4) **Closed issues:** - Are cells "wet", "dry", "active", or "inactive"? (#2833) - Problems with `NonTraditionalBetaPlane` (#2876) - WetCell -> ActiveCell ? (#2880) - pro

## Oceananigans v0.79.3 [Diff since v0.79.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.79.2...v0.79.3) **Closed issues:** - Updating CUDAKernels to v0.4? (#2799) - Error when writing `Field`s reduced over 3 dimensions to NetCDF (#2857) - `device kernel image is invalid`

## Oceananigans v0.79.2 [Diff since v0.79.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.79.1...v0.79.2) **Closed issues:** - `calc_κᶜᶜᶜ()` is only defined for AMD and questions about its default behavior (#2751) - Animation in internal wave example isn't being displayed

## Oceananigans v0.79.1 [Diff since v0.79.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.79.0...v0.79.1) **Merged pull requests:** - Add metric calculation in the face grid of the cubed sphere + general clean up of CubedSphere code (#2836) (@navidcy) - Upgrade Makie (#285

## Oceananigans v0.78.6 [Diff since v0.78.5](https://github.com/CliMA/Oceananigans.jl/compare/v0.78.5...v0.78.6) **Merged pull requests:** - Fix bug loading `netcdf` (#2847) (@navidcy) - Add three papers using Oceananigans to list (#2848) (@ali-ramadhan) - Drop compat entry for K

## Oceananigans v0.79.0 [Diff since v0.78.6](https://github.com/CliMA/Oceananigans.jl/compare/v0.78.6...v0.79.0) **Merged pull requests:** - New vector invariant scheme (#2852) (@simone-silvestri)

## Oceananigans v0.78.5 [Diff since v0.78.4](https://github.com/CliMA/Oceananigans.jl/compare/v0.78.4...v0.78.5) **Merged pull requests:** - Fix bug when throwing exception during grid validation (#2845) (@ali-ramadhan)

## Oceananigans v0.78.4 [Diff since v0.78.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.78.3...v0.78.4) **Merged pull requests:** - Bump version 0.78.4 (#2846) (@glwagner)

## Oceananigans v0.78.3 [Diff since v0.78.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.78.2...v0.78.3) **Closed issues:** - Adding Immersed Boundary Capabilities (#1036) - GPU and CPU Profiling (#1912) - Improvements to CATKEVerticalDiffusivity (#2450) - Error for `maxi

## Oceananigans v0.78.2 [Diff since v0.78.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.78.1...v0.78.2) **Closed issues:** - Potentially a race condition? (#2809) - Dangerous behavior with `@inbounds` within for loop over `1:lenght(ξ::OffSetArray)` (#2815) **Merged pull

## Oceananigans v0.78.1 [Diff since v0.78.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.78.0...v0.78.1) **Closed issues:** - Seeing only partial function index from Documenter (#599) - Plotting recipes (#1115) - Incorrect warning about simulations running forever in Simu

## Oceananigans v0.78.0 [Diff since v0.77.5](https://github.com/CliMA/Oceananigans.jl/compare/v0.77.5...v0.78.0) **Closed issues:** - Question regarding a doctest that involves `rand` (#2702) - Auxiliary fields not directly available to tracer forcing functions (#2730) - Advectio

## Oceananigans v0.77.5 [Diff since v0.77.4](https://github.com/CliMA/Oceananigans.jl/compare/v0.77.4...v0.77.5) **Closed issues:** - Definition of `length(grid)` is not consistent with Julia definition (#1253) - Error in `num_prod`? (#2747) **Merged pull requests:** - Add direct

## Oceananigans v0.77.4 [Diff since v0.77.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.77.3...v0.77.4) **Closed issues:** - Strange behavior in filling halos in `GridFittedBottom` -- does it matter? (#2739) **Merged pull requests:** - Wet point Coriolis scheme and bugfi

## Oceananigans v0.77.3 [Diff since v0.77.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.77.2...v0.77.3) **Closed issues:** - Zero-ed initial guess to preconditioner for CG solver improves performance compared to using previous `z` (#2655) - Add GPU functionality to Multi

## Oceananigans v0.77.2 [Diff since v0.77.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.77.1...v0.77.2) **Closed issues:** - Potential bug introduced either in immersed boundaries or at PGC (or somewhere else)? (#2708) **Merged pull requests:** - Improves plotting in til

## Oceananigans v0.77.1 [Diff since v0.77.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.77.0...v0.77.1) **Closed issues:** - Strange behaviour of Lagrangian Particles near top of domain (#2681) **Merged pull requests:** - Update benchmarks.md (#2680) (@pitmonticone) - Fi

## Oceananigans v0.77.0 [Diff since v0.76.8](https://github.com/CliMA/Oceananigans.jl/compare/v0.76.8...v0.77.0) **Closed issues:** - Adding Lagrangian particles to a nonuniform grid (#2395) **Merged pull requests:** - High-order advection stencils, overhaul of boundary treatment

## Oceananigans v0.76.8 [Diff since v0.76.7](https://github.com/CliMA/Oceananigans.jl/compare/v0.76.7...v0.76.8) **Closed issues:** - Form of viscosity in `ShallowWaterModel` (#2403) - Add example for `FieldBoundaryConditions` on an `ImmersedBoundaryGrid` (#2631) - `ShallowWaterM

## Oceananigans v0.76.7 [Diff since v0.76.6](https://github.com/CliMA/Oceananigans.jl/compare/v0.76.6...v0.76.7) **Closed issues:** - Need actual doctstring for `SpecifiedTimes` (#2608) - Need to document the available solver method options for ImplicitFreeSurface solvers (#2620)

## Oceananigans v0.76.6 [Diff since v0.76.5](https://github.com/CliMA/Oceananigans.jl/compare/v0.76.5...v0.76.6) **Closed issues:** - CUDA error with immersed boundary when running on GPU (#2479) - Odd behavior using `ImmersedBoundary` while specifying scratch data for `Field` co

## Oceananigans v0.76.5 [Diff since v0.76.4](https://github.com/CliMA/Oceananigans.jl/compare/v0.76.4...v0.76.5) **Closed issues:** - Can't we have a 2D simulation on the sphere? (#2372) - Does non hydrostatic model impose boundary conditions based on topology? (#2594) - Unnecess

## Oceananigans v0.76.4 [Diff since v0.76.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.76.3...v0.76.4) **Closed issues:** - Error using immersed boundary on GPUs with buoyancy tracer (#2558) - Type Error using ImmersedBoundaries on GPU (#2563) - Do we want a `Horizontal

## Oceananigans v0.76.3 [Diff since v0.76.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.76.2...v0.76.3) **Closed issues:** - Should we check the size of grids in stretched directions? (#2548) **Merged pull requests:** - Throws error when size of dimension is mismatched w

## Oceananigans v0.76.2 [Diff since v0.76.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.76.1...v0.76.2) **Closed issues:** - `NetCDF`: filename vs filepath (#2541) - error in `baroclinic_adjustment.jl` (#2543) **Merged pull requests:** - Update CATKE parameters for new i

## Oceananigans v0.76.0 [Diff since v0.75.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.75.3...v0.76.0) **Closed issues:** - Shared memory for GPU kernels (#442) - `NetCDFOutputWriter` leaves file open if the constructor errors (#555) - `InterpolatedField` for Lagrangian

## Oceananigans v0.76.1 [Diff since v0.76.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.76.0...v0.76.1) **Closed issues:** - TEOS10 Equation of State: Depth vs Height (#2528) **Merged pull requests:** - Update dependency packages (#2447) (@navidcy) - Update compat for `S

## Oceananigans v0.75.3 [Diff since v0.75.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.75.2...v0.75.3) **Closed issues:** - Problem installing and using Oceananigans (#2480) **Merged pull requests:** - Implement the actually-Cox (aka the anti-anti-Cox) stencil for GM (#

## Oceananigans v0.75.2 [Diff since v0.75.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.75.1...v0.75.2) **Closed issues:** - Minor problem with `closure` in `show(io, :: NonhydrostaticModel)`? (#2443) - Smsm (#2466) - Smsm (#2468) **Merged pull requests:** - Useful regre

## Oceananigans v0.75.1 [Diff since v0.75.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.75.0...v0.75.1) **Merged pull requests:** - Excise some examples and improve others (#2333) (@glwagner) - More distributed validation scripts (#2348) (@glwagner) - Enhancements to `Ri

## Oceananigans v0.75.0 [Diff since v0.74.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.74.2...v0.75.0) **Closed issues:** - problems in setting `BoundaryConditions` in `ImmersedBoundary` (#1730) - Do we need `@unroll` in fill halo flux functions? (#2369) - `ValueBoundar

## Oceananigans v0.74.2 [Diff since v0.74.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.74.1...v0.74.2) **Closed issues:** - Unneeded `arch` argument to fill_halo_regions? (#969) - Helpful error message for incorrect usage of `FieldBoundaryConditions` (#1968) - Running t

## Oceananigans v0.74.1 [Diff since v0.74.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.74.0...v0.74.1) **Closed issues:** - Specifying multiple forcings for a model field (#2136) **Merged pull requests:** - Adds MultipleForcings and AdvectiveForcing (#2389) (@glwagner)

## Oceananigans v0.74.0 [Diff since v0.73.8](https://github.com/CliMA/Oceananigans.jl/compare/v0.73.8...v0.74.0) **Closed issues:** - Inconsistency in output writers interface (#884) - Errors in the output writers docs page (#2427) **Merged pull requests:** - Unifies interfaces i

## Oceananigans v0.73.8 [Diff since v0.73.7](https://github.com/CliMA/Oceananigans.jl/compare/v0.73.7...v0.73.8) **Closed issues:** - Can't reduce `FieldTimeSeries` with non-default indices (#2424) **Merged pull requests:** - FFT-based preconditioner for immersed rectilinear grid

## Oceananigans v0.73.7 [Diff since v0.73.6](https://github.com/CliMA/Oceananigans.jl/compare/v0.73.6...v0.73.7) **Closed issues:** - Error while using `ImmersedBoundaries` on GPU (#2367) **Merged pull requests:** - Fix bug showing AbstractOperations (#2414) (@glwagner) - Updates

## Oceananigans v0.73.6 [Diff since v0.73.5](https://github.com/CliMA/Oceananigans.jl/compare/v0.73.5...v0.73.6) **Closed issues:** - Bug in showing empty `NamedTuple` (#2398) **Merged pull requests:** - Implements RiBasedVerticalDiffusivity (#2379) (@glwagner) - fix the show for

## Oceananigans v0.73.5 [Diff since v0.73.4](https://github.com/CliMA/Oceananigans.jl/compare/v0.73.4...v0.73.5) **Closed issues:** - `Fields()` throws an error when `indices` keyword is used (#2391) **Merged pull requests:** - Fixes and tests `Field(u::Field; indices)` and `Fiel

## Oceananigans v0.73.4 [Diff since v0.73.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.73.3...v0.73.4) **Closed issues:** - Adding a Background field to Langmuir Turbulence example (#2382) **Merged pull requests:** - Adds Rossby Haurwitz and Spherical Bickley jet exampl

## Oceananigans v0.73.3 [Diff since v0.73.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.73.2...v0.73.3) **Merged pull requests:** - Fewer warnings from output writers (#2375) (@glwagner) - Fix docstring alignment (#2376) (@navidcy) - Fix bug for vertically-implicit diffu

## Oceananigans v0.73.2 [Diff since v0.73.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.73.1...v0.73.2) **Closed issues:** - Output error messages to a file? (#2363) - Better/more concise `show()` for reduction of binary operation? (#2364) **Merged pull requests:** - Add

## Oceananigans v0.73.1 [Diff since v0.73.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.73.0...v0.73.1) **Closed issues:** - Fill Halo not working in julia < 1.7 (#2358) **Merged pull requests:** - Bugfix in `fill_halo` for julia < 1.7 (#2362) (@simone-silvestri)

## Oceananigans v0.73.0 [Diff since v0.72.4](https://github.com/CliMA/Oceananigans.jl/compare/v0.72.4...v0.73.0) **Closed issues:** - Possible inconsistency in the eddy definition of diffusivities/closures in the docs (#1277) - Cleaning up TurbulenceClosures (especially those for

## Oceananigans v0.72.4 [Diff since v0.72.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.72.3...v0.72.4) **Closed issues:** - Serialize grid with `CPU` architecture? (#2179) - How to create and save field-derived fields (e.g Richardson Number) and how to use it for a Turb

## Oceananigans v0.72.2 [Diff since v0.72.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.72.1...v0.72.2) **Closed issues:** - GPU timestep tests are taking too long (#2325) **Merged pull requests:** - Adds a tilted bottom boundary layer validation example (#1498) (@tomcho

## Oceananigans v0.72.3 [Diff since v0.72.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.72.2...v0.72.3)

## Oceananigans v0.72.1 [Diff since v0.72.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.72.0...v0.72.1) **Merged pull requests:** - Adds methods to make CATKE work better with other closures (#2328) (@navidcy)

## Oceananigans v0.72.0 [Diff since v0.71.6](https://github.com/CliMA/Oceananigans.jl/compare/v0.71.6...v0.72.0) **Closed issues:** - Better documentation for diagnostics and abstract operations (#658) - Convenience args for FieldSlicer (#1080) - Add "scripting tips" section to t

## Oceananigans v0.71.6 [Diff since v0.71.5](https://github.com/CliMA/Oceananigans.jl/compare/v0.71.5...v0.71.6) **Merged pull requests:** - Fix inconsistent variable definition in `ScalarDiffusivity` constructor (#2288) (@navidcy)

## Oceananigans v0.71.5 [Diff since v0.71.4](https://github.com/CliMA/Oceananigans.jl/compare/v0.71.4...v0.71.5) **Closed issues:** - Use verbose names in LinearEquationOfState (#453) - Typo in stratified Couette flow verification experiment (#597) - Type checking of simulation.Δ

## Oceananigans v0.71.4 [Diff since v0.71.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.71.3...v0.71.4) **Merged pull requests:** - Improve miscellaneous show and summary (#2274) (@glwagner) - Downbump to 0.71.4 (#2279) (@glwagner)

## Oceananigans v0.71.3 [Diff since v0.71.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.71.2...v0.71.3) **Closed issues:** - Is there a better word than `isotropy` to use for the new ScalarDiffusivity? (#2261) - `Explicit`/`Implicit` names for time-discretizations are a

## Oceananigans v0.71.2 [Diff since v0.71.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.71.1...v0.71.2) **Closed issues:** - Euler time-stepping in the `QuasiAdamsBashforth2TimeStepper` is buggy --- a NaN will persist! (#2259) - Is it worth considering a more general way

## Oceananigans v0.71.0 [Diff since v0.70.5](https://github.com/CliMA/Oceananigans.jl/compare/v0.70.5...v0.71.0) **Closed issues:** - Replace `AnisotropicDiffusivity` and `AnisotropicBiharmonicDiffusivity` with their curvilinear-friendly counterparts (#2113) - `TurbulenceClosures

## Oceananigans v0.71.1 [Diff since v0.71.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.71.0...v0.71.1)

## Oceananigans v0.70.4 [Diff since v0.70.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.70.3...v0.70.4) **Merged pull requests:** - Subtle reformulation of `CATKEVerticalDiffusivity` (#2232) (@glwagner) - Minor change to Ocean mixing and convection example (#2238) (@tomc

## Oceananigans v0.70.3 [Diff since v0.70.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.70.2...v0.70.3) **Closed issues:** - CATKE with `NonHydrostaticModel` (#2229) **Merged pull requests:** - Fixes CATKE-in-a-tuple implementation and adds tests (#2225) (@glwagner)

## Oceananigans v0.70.2 [Diff since v0.70.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.70.1...v0.70.2) **Merged pull requests:** - Saves actual `solver_method` name in `ImplicitFreeSurface` (not just `:Default`) (#2212) (@navidcy) - Updates models' docstrings (#2230) (@

## Oceananigans v0.70.1 [Diff since v0.70.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.70.0...v0.70.1) **Closed issues:** - Restarting a simulation using `run!(simulation, pickup=true)` fails for a `HydrostaticFreeSurfaceModel` (#2223) **Merged pull requests:** - Tries

## Oceananigans v0.69.5 [Diff since v0.69.4](https://github.com/CliMA/Oceananigans.jl/compare/v0.69.4...v0.69.5) **Closed issues:** - Making options for NetCDF and JLD2 output writers more unified (#2217) **Merged pull requests:** - Fixes FFT solver constructor for an ensemble of

## Oceananigans v0.70.0 [Diff since v0.69.5](https://github.com/CliMA/Oceananigans.jl/compare/v0.69.5...v0.70.0) **Closed issues:** - Conditional fluxes for Biharmonic operator and Immersed Boundaries (#2209) **Merged pull requests:** - 3D spacing and derivatives (#2214) (@simone

## Oceananigans v0.69.4 [Diff since v0.69.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.69.3...v0.69.4) **Closed issues:** - Derivatives and interpolation of ComputedFields is incorrect on boundaries (#1130) - `Oceananigans.short_show` should really extend `Base.summary`

## Oceananigans v0.69.3 [Diff since v0.69.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.69.2...v0.69.3) **Closed issues:** - User interface to `ConditionalOperand` (#2188) - Bug in show for column Hydrostatic models (#2210) **Merged pull requests:** - Changes to `Conditi

## Oceananigans v0.69.2 [Diff since v0.69.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.69.1...v0.69.2) **Closed issues:** - Averaging field when grid is stretched doesn't always work (#2189) - Show free surface solver method in `show(::IO, ::HydrostaticFreeSurfaceModels

## Oceananigans v0.69.0 [Diff since v0.68.7](https://github.com/CliMA/Oceananigans.jl/compare/v0.68.7...v0.69.0) **Closed issues:** - Poisson solver tests on GPU still take too long (#2183) - Mean of stretched dimension using `WindowedSpatialAverage` (#2185) **Merged pull request

## Oceananigans v0.69.1 [Diff since v0.69.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.69.0...v0.69.1) **Closed issues:** - `regrid!` is (a bit) more general than it advertises (#2194) **Merged pull requests:** - Update docs/docstrings (#2195) (@navidcy) - Fixes `FreeSu

## Oceananigans v0.68.7 [Diff since v0.68.6](https://github.com/CliMA/Oceananigans.jl/compare/v0.68.6...v0.68.7) **Closed issues:** - Should the `free_surface.implicit_step_solver.right_hand_side` be a vector in `HydrostaticFreeSurfaceModel` with a matrix solver? (#2184) **Merged

## Oceananigans v0.68.6 [Diff since v0.68.5](https://github.com/CliMA/Oceananigans.jl/compare/v0.68.5...v0.68.6) **Closed issues:** - Should vertical spacings `Δzᵃᵃᶜ` and `Δzᵃᵃᶠ` depend on horizontal location? (#2049) - bug in vertically implicit diffusion solver ? (#2065) - Vert

## Oceananigans v0.68.5 [Diff since v0.68.4](https://github.com/CliMA/Oceananigans.jl/compare/v0.68.4...v0.68.5) **Closed issues:** - Refactor `regrid!` so that it works with non-flat `x` and `y` dimensions? (#2067) **Merged pull requests:** - Let regridding work on non-`SingleCo

## Oceananigans v0.68.3 [Diff since v0.68.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.68.2...v0.68.3) **Closed issues:** - Check boundary condition arrays are CuArrays if arch=GPU (#419) - Differing syntax for output writers (#500) - Method / abstraction for outputting

## Oceananigans v0.68.4 [Diff since v0.68.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.68.3...v0.68.4) **Merged pull requests:** - Fixes bug inferring regular dimensions for Average (#2173) (@glwagner)

## Oceananigans v0.68.2 [Diff since v0.68.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.68.1...v0.68.2) **Merged pull requests:** - Implements a `ConsecutiveIterations` schedule (#2100) (@glwagner) - Adds a correct simplified Inverse preconditioner (#2141) (@simone-silve

## Oceananigans v0.68.1 [Diff since v0.68.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.68.0...v0.68.1) **Closed issues:** - halo_size definition duplicated (#2129) - Return statement in a test seems incomplete (#2135) - GPU tests take way too long (#2139) **Merged pull

## Oceananigans v0.68.0 [Diff since v0.67.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.67.1...v0.68.0) **Closed issues:** - Coalescing `Field` definitions (#2052) - Error if using too low julia version? (#2142) - Why is `simulation.stop_iteration` not an integer? (#2144

## Oceananigans v0.67.1 [Diff since v0.67.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.67.0...v0.67.1) **Closed issues:** - `HydrostaticModel` should do something if the halo is too small (#2106) - Remove warning from `HydrostaticFreeSurfaceModel`? (#2111) - `length(gri

## Oceananigans v0.67.0 [Diff since v0.66.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.66.3...v0.67.0) **Closed issues:** - Should we store `architecture` in `grid`? (#1825) - Option for `NaNChecker` to exit with error (#2086) - Do we want to go triply-Bounded for `test

## Oceananigans v0.66.3 [Diff since v0.66.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.66.2...v0.66.3) **Closed issues:** - Gent-McWilliams mesoscale eddy flux parameterization (#1492) - Implementing a tensor diffusivity rotated into the isopycnal coordinate frame (#197

## Oceananigans v0.66.2 [Diff since v0.66.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.66.1...v0.66.2) **Closed issues:** - Weighted WENO stencils for stretched grids (#1704) - Default tracers and buoyancy model for `NonhydrostaticModel ` (#1984) - A stray `true`? (#202

## Oceananigans v0.66.1 [Diff since v0.66.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.66.0...v0.66.1) * Converts all simulation stop criteria to callbacks, including `NaNChecker` (`NaNChecker` no longer throws an error) **Merged pull requests:** - Convert stop criteria

## Oceananigans v0.66.0 [Diff since v0.65.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.65.0...v0.66.0) **Merged pull requests:** - Eliminate VerticallyStretched and Regular RectilinearGrid (#2050) (@simone-silvestri) - Some initial bits for tracer cell face vertical int

## Oceananigans v0.65.0 [Diff since v0.64.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.64.1...v0.65.0) * Generalizes `RegularLatitudeLongitudeGrid` to a `LatitudeLongitudeGrid` that is optionally stretched in any direction **Closed issues:** - Go back to more complex `V

## Oceananigans v0.64.1 [Diff since v0.64.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.64.0...v0.64.1) * Optimized and fixed algorithm for `fill_halo_regions!` via #2035. Previously, halos will filled simultaneously. Now they are filled serially, and periodic halos are

## Oceananigans v0.64.0 [Diff since v0.63.4](https://github.com/CliMA/Oceananigans.jl/compare/v0.63.4...v0.64.0) **Merged pull requests:** - New Simulation API: more callbacks, less "progress" (#1971) (@glwagner) - Updates simulation tips (#2029) (@tomchor) - Regression test for

## Oceananigans v0.63.4 [Diff since v0.63.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.63.3...v0.63.4) **Merged pull requests:** - Fixes grid equality for GPUs (#2030) (@tomchor) - Adding regression test to lat-lon grid (#2032) (@simone-silvestri)

## Oceananigans v0.63.3 [Diff since v0.63.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.63.2...v0.63.3) **Closed issues:** - Changing notation from "resolution" to "grid size" in grids show methods (#1927) - Does Stokes drift have two names in the docs? (#2007) - Picking

## Oceananigans v0.63.2 [Diff since v0.63.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.63.1...v0.63.2) This patch release fixes CUDA versions to a specific range, preventing Julia from installing the latest CUDA.jl version (which as of now contains a bug (see #1996)). T

## Oceananigans v0.63.1 [Diff since v0.63.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.63.0...v0.63.1) **Closed issues:** - Regriding enhancements (#1991) **Merged pull requests:** - Quality of life improvements for `FieldDataset` (#1903) (@ali-ramadhan) - Adds docstrin

## Oceananigans v0.63.0 [Diff since v0.62.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.62.2...v0.63.0) **Merged pull requests:** - Adds vertical regridding feature (#1987) (@navidcy)

## Oceananigans v0.62.2 [Diff since v0.62.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.62.1...v0.62.2) **Closed issues:** - Why is bottom drag multiplied by domain depth? (#1974) - Column stability for convective adjustment: `∂z_b > 0`, or `∂z_b >= 0`? (#1980) - About S

## Oceananigans v0.62.1 [Diff since v0.62.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.62.0...v0.62.1) **Closed issues:** - Issue with TimeStepWizard (#1946) - Warning about inflating halo size does not take into account `Flat` dimensions (#1956) - `PrescribedVelocityFi

## Oceananigans v0.62.0 [Diff since v0.61.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.61.3...v0.62.0) The `TKEBasedVerticalDiffusivity` was changed to `CATKEVerticalDiffusivity`, and the implementation was changed to use the "triple max" formulation. **Closed issues:**

## Oceananigans v0.61.3 [Diff since v0.61.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.61.2...v0.61.3)

## Oceananigans v0.61.2 [Diff since v0.61.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.61.1...v0.61.2) **Merged pull requests:** - Fixed mpi_shallow_water example (#1933) (@vnderlev) - Fix diffusive flux bug for immersed boundaries (#1935) (@whitleyv) - Unrestrict secon

## Oceananigans v0.61.1 [Diff since v0.61.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.61.0...v0.61.1) **Closed issues:** - Figures in "Convergence test" section of the docs are missing (#1212) - A more general `NonTraditionalFPlane` to match the upcoming tilted gravity

## Oceananigans v0.61.0 [Diff since v0.60.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.60.1...v0.61.0) **Merged pull requests:** - Nuke `restore_from_checkpoint` (#1893) (@glwagner) - Fix typo in Readme (#1897) (@navidcy) - Fix broken link in Readme (#1898) (@navidcy) -

## Oceananigans v0.60.1 [Diff since v0.60.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.60.0...v0.60.1) **Closed issues:** - Complex AbstractOperations cannot be computed on GPU (#1241) - Reformulate `TKEBasedVerticalDiffusivity` (#1695) - Kernel calls for AMD diffusivit

## Oceananigans v0.60.0 [Diff since v0.59.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.59.0...v0.60.0) - Rename `IncompressibleModel` to `NonhydrostaticModel`. **Closed issues:** - Boussinesq model vs incompressible model (#1620) - `Oceananigans.BoundaryConditions.Conti

## Oceananigans v0.59.0 [Diff since v0.58.9](https://github.com/CliMA/Oceananigans.jl/compare/v0.58.9...v0.59.0) - Major refactor of boundary conditions for fields. Boundary conditions for prognostic fields are now constructed with `FieldBoundaryConditions()`. Boundary conditions

## Oceananigans v0.58.9 [Diff since v0.58.8](https://github.com/CliMA/Oceananigans.jl/compare/v0.58.8...v0.58.9) **Closed issues:** - Tests for 'show' methods (#705) - periodic_advection.jl fails because it can't find WENO (#1271) - one_dimensional_advection_schemes.jl fails (#12

## Oceananigans v0.58.8 [Diff since v0.58.7](https://github.com/CliMA/Oceananigans.jl/compare/v0.58.7...v0.58.8) **Closed issues:** - Very different results for the dissipation with NetCDFOutputWriter using snapshots and time-averaged fields (#1517) - Hydrostatic pressure integra

## Oceananigans v0.58.7 [Diff since v0.58.6](https://github.com/CliMA/Oceananigans.jl/compare/v0.58.6...v0.58.7) * Fixes a bug (possibly a race condition) with `AveragedField` on the GPU **Closed issues:** - Output of `AveragedField` is sometimes wrong on the GPU (#1767) - `calcu

## Oceananigans v0.58.6 [Diff since v0.58.5](https://github.com/CliMA/Oceananigans.jl/compare/v0.58.5...v0.58.6) **Closed issues:** - cell_advection_timescale should dispatch on `Flat` topologies (#1309) - Can't build docs locally based on instructions in "Contributor's guide" (#

## Oceananigans v0.58.4 [Diff since v0.58.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.58.3...v0.58.4) **Closed issues:** - Adaptive time stepping for VerticallyStretchedRectilinearGrid( ) (#1741) - DiffusiveCFL doesn't work for VerticallyStretchedGrids with LES closure

## Oceananigans v0.58.5 [Diff since v0.58.4](https://github.com/CliMA/Oceananigans.jl/compare/v0.58.4...v0.58.5) - Removes manual manipulation of grid metrics in constructor for `VerticallyStretchedRectilinearGrid` that may have lowered the order of accuracy or invalidated some c

## Oceananigans v0.58.3 [Diff since v0.58.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.58.2...v0.58.3) **Closed issues:** - Cannot run examples within the Oceananigans environment (#1205) - using warning (#1636) - Update Performance Benchmarks in Docs and README (#1676)

## Oceananigans v0.58.2 [Diff since v0.58.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.58.1...v0.58.2) * Fixes an error in the sign of the flux divergences for `AnisotropicBiharmonicDiffusivity` **Closed issues:** - Basic Documentation for ShallowWaterModel? (#1460) - S

## Oceananigans v0.58.1 [Diff since v0.58.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.58.0...v0.58.1) **Merged pull requests:** - Replaces a leftover Julia 1.5 -> 1.6 (#1675) (@navidcy) - Changed -> to to in the benchmark scripts (#1678) (@francispoulin) - Fix `show` f

## Oceananigans v0.57.3 [Diff since v0.57.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.57.2...v0.57.3) * Preliminary implementation of `ImmersedBoundaryGrid` and `GridFittedBoundary`! **Closed issues:** - `show()` for VerticallyStretchedRectilinearGrId (#1637) - Docstri

## Oceananigans v0.58.0 [Diff since v0.57.3](https://github.com/CliMA/Oceananigans.jl/compare/v0.57.3...v0.58.0) * Oceananigans.jl now supports and requires Julia 1.6+. **Merged pull requests:** - Upgrade to Julia 1.6 (#1514) (@ali-ramadhan) - No need for explicit dependence on A

## Oceananigans v0.57.2 [Diff since v0.57.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.57.1...v0.57.2) * Adds `VerticallyImplicitTimeDiscretization` for `IsotropicDiffusivity`, `AnisotropicDiffusivity`, `HorizontallyCurvilinearAnisotropicDiffusivity`, `AnisotropicMinimu

## Oceananigans v0.57.0 [Diff since v0.56.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.56.0...v0.57.0) This update adds support for direct reductions of `AbstractOperations` using `Base.mapreducedim!`. This eliminates the need to calculate and store `AbstractOperations`

## Oceananigans v0.57.1 [Diff since v0.57.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.57.0...v0.57.1) This release pins `ArrayInterface` at 3.1.6 to circumvent an issue compiling `run!(simulation)` with 3.1.7. See * https://github.com/JuliaArrays/ArrayInterface.jl/issu

## Oceananigans v0.56.0 [Diff since v0.55.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.55.1...v0.56.0) **Breaking changes:** - `zF` kwarg for `VerticallyStretchedRectilinearGrid` is now called `z_faces` **Closed issues:** - `with_halo` throws an error for VerticallyStre

## Oceananigans v0.55.0 [Diff since v0.54.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.54.2...v0.55.0) * Tests and fixes for FFTBasedPoissonSolver for topologies with Flat dimensions (#1560) * Improved AbstractOperations that are much more likely to compile on the GPU,

## Oceananigans v0.55.1 [Diff since v0.55.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.55.0...v0.55.1) **Merged pull requests:** - Broadcasting for AbstractField, AbstractReducedField, and AbstractOperations (#1596) (@glwagner)

## Oceananigans v0.54.2 [Diff since v0.54.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.54.1...v0.54.2) **Closed issues:** - Equation numbering in docs broken (#528) - Add "GPU simulation tips" section to the docs (#1478) - General question: how to build laminar flow wit

## Oceananigans v0.54.1 [Diff since v0.54.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.54.0...v0.54.1) **Closed issues:** - Maintain a list of publications using Oceananigans in the docs? (#973) - Models with `Flat` dimensions still return NaN (#1023) - Bug when trying

## Oceananigans v0.54.0 [Diff since v0.53.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.53.2...v0.54.0) **Breaking changes**: * When constructing boundary conditions, use the long form constructors: `FluxBoundaryCondition(...)` instead of `BoundaryCondition(Flux, ...)` a

## Oceananigans v0.53.2 [Diff since v0.53.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.53.1...v0.53.2) **Closed issues:** - Ability to run in hydrostatic mode. (#72) - Upgrade to single/unified stretched vertical grid spacing 3D elliptic solver? (#211) - Setup with Diff

## Oceananigans v0.53.1 [Diff since v0.53.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.53.0...v0.53.1) **Closed issues:** - buildkite with Julia v1.5.4? (#1461) - cell_advection_timescale is only defined for `RegularRectilinearGrid` (#1465) - Error in update (#1468) **M

## Oceananigans v0.53.0 [Diff since v0.52.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.52.1...v0.53.0) **Closed issues:** - PrescribedVelocities type for tracer advection problems (#958) - TurbulenceClosures module needs to be cleaned up (#1002) - NaN error (#1432) - Ev

## Oceananigans v0.52.1 [Diff since v0.52.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.52.0...v0.52.1) Bug fixes for `RegularLatitudeLongitudeGrid` and `HydrostaticSphericalCoriolis`. **Closed issues:** - Define `minimum` and `maximum` for `Field` (#1117) - Rename `NonD

## Oceananigans v0.52.0 [Diff since v0.51.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.51.0...v0.52.0) * New `WindowedSpatialAverage` diagnostic for outputting averages of a subset of the domain by @tomchor! * Lots more stuff is now exported by Oceananigans so you shoul

## Oceananigans v0.51.0 [Diff since v0.50.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.50.0...v0.51.0) **Major features**: * Experimental support for immersed boundaries by @whitleyv! * Experimental support for `HydrostaticFreeSurfaceModel` on `RegularLatitudeLongitudeG

## Oceananigans v0.49.0 [Diff since v0.48.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.48.0...v0.49.0) Checkpoint release including documentation fixes and very experimental support for curvilinear grids, a vertically-stretched rectilinear grid, and a preconditioned con

## Oceananigans v0.50.0 [Diff since v0.49.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.49.0...v0.50.0) **Breaking changes**: Renames `RegularCartesianGrid` to `RegularRectilinearGrid` and `VerticallyStretchedCartesianGrid` to `VerticallyStretchedRectilinearGrid`. **Clos

## Oceananigans v0.48.0 [Diff since v0.47.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.47.1...v0.48.0) **Breaking changes**: * The `Oceananigans.SurfaceWaves` module has been renamed to `Oceananigans.StokesDrift` and the `IncompressibleModel` keyword argument `surface_w

## Oceananigans v0.47.0 [Diff since v0.46.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.46.1...v0.47.0) All topologies are now supported on CPUs and GPUs. In particular, `(Periodic, Bounded, Bounded)` channel simulations on the GPU are ~2x faster now. **Closed issues:**

## Oceananigans v0.47.1 [Diff since v0.47.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.47.0...v0.47.1) Update docs Grids section removing discussion about `Flat` topologies (since currently it's broken) and also removing discussion about restrictions for certain topolog

## Oceananigans v0.46.0 [Diff since v0.45.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.45.2...v0.46.0) **Breaking changes**: * The `Cell` location has been renamed to `Center` which is a clearer name for cell centers on the staggered grid. **Major features**: * Support

## Oceananigans v0.46.1 [Diff since v0.46.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.46.0...v0.46.1) **Merged pull requests:** - Revive examples and bump v0.46.1 (#1319) (@ali-ramadhan)

## Oceananigans v0.45.2 [Diff since v0.45.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.45.1...v0.45.2) **Closed issues:** - set! should enforce incompressibility when setting an initial condition for an Incompressible model (#1027) - Halos should be filled as part of `s

## Oceananigans v0.45.1 [Diff since v0.45.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.45.0...v0.45.1) **Closed issues:** - Kill simulation after a crash (#1196) - Do we need compat "^1.4" for OffsetArrays? (#1233) - Examples are NaNing out 😱 (#1247) - Run simulation ca

## Oceananigans v0.45.0 [Diff since v0.44.2](https://github.com/CliMA/Oceananigans.jl/compare/v0.44.2...v0.45.0) **This release fixes an important bug affecting GPU simulation with odd-sized wall-bounded dimensions.** **You should upgrade to Oceananigans v0.45.0 as soon as possib

## Oceananigans v0.44.2 [Diff since v0.44.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.44.1...v0.44.2) **Closed issues:** - Multiple warnings about "incremental compilation may be fatally broken for this module" (#537) - Change contributor's guide to ColPrac (#1044) - M

## Oceananigans v0.44.1 [Diff since v0.44.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.44.0...v0.44.1) * New example: Stratified Kelvin-Helmholtz instability with stability analysis! * Named tuple support for `NetCDFOutputWriter`. * Some bug fixes. **Closed issues:** -

## Oceananigans v0.44.0 [Diff since v0.43.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.43.0...v0.44.0) Adds support for "picking up" a simulation from a checkpoint via the keyword `pickup=true`, `pickup=checkpoint_iteration::Int` and `pickup=checkpont_filepath::String`

## Oceananigans v0.43.0 [Diff since v0.42.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.42.0...v0.43.0) Release notes: * Fixes a bug in `TwoDimensionalLeith` (PR #1073, issue #1034). Previously tests were being skipped due to extreme slowness. Now we run tests on GPU (bu

## Oceananigans v0.42.0 [Diff since v0.41.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.41.0...v0.42.0) Added support for time averaging to `NetCDFOutputWriter` and revamped how field slicing is done. **Breaking changes**: * `NetCDFOutputWriter` constructor: The `filenam

## Oceananigans v0.41.0 [Diff since v0.40.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.40.0...v0.41.0) Oceananigans.jl fully supports Julia 1.5 now! Major changes: * Support for setting background fields. See [background fields section of the model setup docs](https://c

## Oceananigans v0.40.0 [Diff since v0.39.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.39.0...v0.40.0) * Support for `Flat` dimensions. See the [grid section of the model setup documentation](https://clima.github.io/OceananigansDocumentation/v0.40.0/model_setup/grids/)

## Oceananigans v0.39.0 [Diff since v0.38.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.38.0...v0.39.0) * Overhauled interface for forcing functions. Instead of calling `ModelForcing` to set up model forcing functions, you should pass a named tuple of `Forcing` objects t

## Oceananigans v0.38.0 [Diff since v0.37.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.37.0...v0.38.0) * New experimental WENO-5 advection scheme for momentum and tracers. Use by passing `advection=WENO5()` when creating a model. See https://github.com/CliMA/Oceananigan

## Oceananigans v0.37.0 [Diff since v0.36.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.36.0...v0.37.0) * More empowered `Field` abstraction: - `AbstractReducedField` and concrete `ReducedField` for representing fields that are reduced along one or more dimensions. - `Av

## Oceananigans v0.36.0 [Diff since v0.35.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.35.0...v0.36.0) This release coincides with the publication of the Oceananigans.jl Journal of Open Source Software (JOSS) paper. Changelog: * Simplified boundary condition interface,

## Oceananigans v0.35.0 [Diff since v0.34.1](https://github.com/CliMA/Oceananigans.jl/compare/v0.34.1...v0.35.0) * Support for multithreaded CPU simulations! Set the number of threads via the `JULIA_NUM_THREADS` environment variable or via the `-t` flag in Julia 1.5+. * New `Ocea

## Oceananigans v0.34.1 [Diff since v0.34.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.34.0...v0.34.1) This is a bugfix release that disables CuArray scalar operations by default (to avoid surprise scalar operations that can cause huge slowdowns) and **fixes a related b

## Oceananigans v0.34.0 [Diff since v0.33.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.33.0...v0.34.0) This release adds some new features, fixes some bugs, and improves the API (so there are some breaking changes, listed below). Major changes: * Triply periodic models

## Oceananigans v0.33.0 [Diff since v0.32.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.32.0...v0.33.0) This release adds new features to the `NetCDFOutputWriter` and fixes some bugs. * The date the file was generated, the Julia version, and the Oceananigans version used

## Oceananigans v0.32.0 [Diff since v0.31.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.31.0...v0.32.0) **Everyone should stop using Oceananigans v0.31.0 and upgrade to this version. Oceananigans now requires Julia 1.4 or later.** This release fixes a major bug concernin

## Oceananigans v0.31.0 [Diff since v0.30.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.30.0...v0.31.0) This release fixes a major bug where you couldn't run GPU models so if you're using GPUs you should upgrade to this version. **Oceananigans.jl now requires Julia 1.4+.

## Oceananigans v0.30.0 [Diff since v0.29.0](https://github.com/CliMA/Oceananigans.jl/compare/v0.29.0...v0.30.0) **Closed issues:** - Support for a full equation of state for seawater (TEOS-10?) (#692) - topology(grid) returns instantiated types while location(field) returns unin

## Oceananigans v0.29.0 [Diff since v0.28.0](https://github.com/climate-machine/Oceananigans.jl/compare/v0.28.0...v0.29.0) This release adds a `TEOS10` nonlinear equation of state and fixes some bugs. **Closed issues:** - TimeStepWizard should probably be defined in Simulation.jl

## Oceananigans v0.28.0 [Diff since v0.27.2](https://github.com/climate-machine/Oceananigans.jl/compare/v0.27.2...v0.28.0) This release refactors the grid implementation so that the coordinate arrays `xC`, `yC`, `zC`, `xF`, `yF`, and `zF` have nodal points within the halo regions

## Oceananigans v0.27.2 [Diff since v0.27.1](https://github.com/climate-machine/Oceananigans.jl/compare/v0.27.1...v0.27.2) - Fixes a bug with the zeros function so we can compute `HorizontalAverage`s on the GPU. **Closed issues:** - Bug in zeros function (#719) - `progress(simula

## Oceananigans v0.27.1 [Diff since v0.27.0](https://github.com/climate-machine/Oceananigans.jl/compare/v0.27.0...v0.27.1) **Merged pull requests:** - Fix has_velocities again (#708) (@glwagner) - Consistent Field API again (#709) (@glwagner)

## Oceananigans v0.27.0 [Diff since v0.26.0](https://github.com/climate-machine/Oceananigans.jl/compare/v0.26.0...v0.27.0) Breaking changes: - in `FieldBoundaryConditions(grid, location)`, the argument `location` is now be a 3-tuple of _uninstantiated_ types, eg: `(Face, Cell, Ce

## Oceananigans v0.26.0 [Diff since v0.25.2](https://github.com/climate-machine/Oceananigans.jl/compare/v0.25.2...v0.26.0) Some breaking changes: * Function signatures for boundary condition functions and forcing functions have been simplified. * The `model.parameters` field has

## Oceananigans v0.25.2 [Diff since v0.25.1](https://github.com/climate-machine/Oceananigans.jl/compare/v0.25.1...v0.25.2) **Closed issues:** - Abstraction for "equation" for performance, code clarity, memory footprint reduction, and powerful user interface (#259) **Merged pull r

## Oceananigans v0.25.1 [Diff since v0.25.0](https://github.com/climate-machine/Oceananigans.jl/compare/v0.25.0...v0.25.1) **Closed issues:** - Pretty printing for model structs. (#26) - Grid should encode whether positive means east, north, etc. (#50) - Iterate over a node list

## Oceananigans v0.25.0 [Diff since v0.24.2](https://github.com/climate-machine/Oceananigans.jl/compare/v0.24.2...v0.25.0) **Closed issues:** - Integrate opening and closing of Netcdf outputwriters in simulation loop (#650) - Netcdf output writer does not respect the clobber keyw

## Oceananigans v0.24.2 [Diff since v0.24.1](https://github.com/climate-machine/Oceananigans.jl/compare/v0.24.1...v0.24.2) **Closed issues:** - Model constructor is slightly mangled (#647) - Method redefinition warnings (#655) - Register Oceananigans v0.24.1 (#657) - Unexpected S

## Oceananigans v0.24.1 [Diff since v0.24.0](https://github.com/climate-machine/Oceananigans.jl/compare/v0.24.0...v0.24.1) **Closed issues:** - Register Oceananigans v0.24.0 (#646) - Getting timestep from simulation class is cumbersome (#648) - Method redefinition warnings (#655)

## Oceananigans v0.24.0 [Diff since v0.23.0](https://github.com/climate-machine/Oceananigans.jl/compare/v0.23.0...v0.24.0) **Closed issues:** - Storing boundary conditions inside fields (#606) - Register Oceananigans v0.23.0 (#638) **Merged pull requests:** - Upgrade fields to st

## Oceananigans v0.23.0 [Diff since v0.22.0](https://github.com/climate-machine/Oceananigans.jl/compare/v0.22.0...v0.23.0) **Closed issues:** - More modular and reproducible 3D plotting script (#203) - Make checkpointer more memory efficient (#416) - Checkpointer warning if prope

## Oceananigans v0.22.0 [Diff since v0.21.0](https://github.com/climate-machine/Oceananigans.jl/compare/v0.21.0...v0.22.0) **Closed issues:** - Make progress statements a part of `time_step!` (#432) - Use `FT` for "floating point type" (#446) - 'Simulation' type for managing time

## Oceananigans v0.21.0 [Diff since v0.20.0](https://github.com/climate-machine/Oceananigans.jl/compare/v0.20.0...v0.21.0) **Closed issues:** - Notation for non-traditional f-plane is obscure (#616) **Merged pull requests:** - Fixes off-by-one indexing error in hydrostatic pressu

## [v0.20.0](https://github.com/climate-machine/Oceananigans.jl/tree/v0.20.0) (2020-01-31) [Diff since v0.19.0](https://github.com/climate-machine/Oceananigans.jl/compare/v0.19.0...v0.20.0) **Closed issues:** - `TemperatureBuoyancy` for evolving temperature without salinity (#581

## [v0.19.0](https://github.com/climate-machine/Oceananigans.jl/tree/v0.19.0) (2020-01-14) [Diff since v0.18.1](https://github.com/climate-machine/Oceananigans.jl/compare/v0.18.1...v0.19.0) **Closed issues:** - Conflicting identifiers (#563) - Ranges are `Float64` even if `FT=Flo

## [v0.18.1](https://github.com/climate-machine/Oceananigans.jl/tree/v0.18.1) (2020-01-04) [Diff since v0.18.0](https://github.com/climate-machine/Oceananigans.jl/compare/v0.18.0...v0.18.1) **Closed issues:** - We should get rid of the `BoundaryConditions` alias (#582) - Switch t

## [v0.18.0](https://github.com/climate-machine/Oceananigans.jl/tree/v0.18.0) (2019-12-19) [Diff since v0.17.0](https://github.com/climate-machine/Oceananigans.jl/compare/v0.17.0...v0.18.0) **Major features:** - Major improvements to documentation. - Submission to Journal of Open

## [v0.17.0](https://github.com/climate-machine/Oceananigans.jl/tree/v0.17.0) (2019-12-12) [Diff since v0.16.0](https://github.com/climate-machine/Oceananigans.jl/compare/v0.16.0...v0.17.0) **Main features:** - Model setup documentation - General-purpose batched tridiaginal solve

## [v0.16.0](https://github.com/climate-machine/Oceananigans.jl/tree/v0.16.0) (2019-12-02) [Diff since v0.15.0](https://github.com/climate-machine/Oceananigans.jl/compare/v0.15.0...v0.16.0) **Main feature:** - Finite volume operators. **Closed issues:** - Multiple warnings about

**Main features:** - Multiple turbulence closures per tracer (#517) - Anisotropic biharmonic diffusivity closure (#518) - Craik-Leibovich terms and surface waves effects (#519) - BoundaryFunction wrapper for simple boundary condition functions (#513) - Start splitting code into s

## [v0.14.1](https://github.com/climate-machine/Oceananigans.jl/tree/v0.14.1) (2019-10-25) [Diff since v0.14.0](https://github.com/climate-machine/Oceananigans.jl/compare/v0.14.0...v0.14.1) **Merged pull requests:** - Bump version 0.14.1 (#507) ([ali-ramadhan](https://github.com/

## [v0.14.0](https://github.com/climate-machine/Oceananigans.jl/tree/v0.14.0) (2019-10-24) [Diff since v0.13.0](https://github.com/climate-machine/Oceananigans.jl/compare/v0.13.0...v0.14.0) **Main features:** - Support for abstract operations to define new diagnostics and equatio

## [v0.13.0](https://github.com/climate-machine/Oceananigans.jl/tree/v0.13.0) (2019-10-23) [Diff since v0.12.0](https://github.com/climate-machine/Oceananigans.jl/compare/v0.12.0...v0.13.0) **Main feature:** - The `k` index (used for indexing the vertical level in 3D arrays) now

## [v0.12.0](https://github.com/climate-machine/Oceananigans.jl/tree/v0.12.0) (2019-10-22) [Diff since v0.11.1](https://github.com/climate-machine/Oceananigans.jl/compare/v0.11.1...v0.12.0) **Main features:** - Support for specifying 0-2 active tracers and an arbitrary number of

## [v0.11.1](https://github.com/climate-machine/Oceananigans.jl/tree/v0.11.1) (2019-10-15) [Diff since v0.11.0](https://github.com/climate-machine/Oceananigans.jl/compare/v0.11.0...v0.11.1) **Main features:** - Stratified Couette flow verification experiment. - Much improved exam

## [v0.11.0](https://github.com/climate-machine/Oceananigans.jl/tree/v0.11.0) (2019-09-19) [Diff since v0.10.1](https://github.com/climate-machine/Oceananigans.jl/compare/v0.10.1...v0.11.0) **Main feature:** - Massive API cleanup and stabilization! **Closed issues:** - New abstra

## [v0.10.1](https://github.com/climate-machine/Oceananigans.jl/tree/v0.10.1) (2019-09-09) [Diff since v0.10.0](https://github.com/climate-machine/Oceananigans.jl/compare/v0.10.0...v0.10.1) **Main feature:** - Bug fixes for diffusivisty halo regions and `Value`/`Gradient` boundar

## [v0.10.0](https://github.com/climate-machine/Oceananigans.jl/tree/v0.10.0) (2019-08-29) [Diff since v0.9.5](https://github.com/climate-machine/Oceananigans.jl/compare/v0.9.5...v0.10.0) **Main feature:** - New and more correct turbulence closures. **Closed issues:** - Switch fr

## [v0.9.4](https://github.com/climate-machine/Oceananigans.jl/tree/v0.9.4) (2019-08-28) [Diff since v0.9.3](https://github.com/climate-machine/Oceananigans.jl/compare/v0.9.3...v0.9.4) **Main features:** * Model checkpointing via the `Checkpointer` output writer. * Verbose and ma

## [v0.9.5](https://github.com/climate-machine/Oceananigans.jl/tree/v0.9.5) (2019-08-28) [Diff since v0.9.4](https://github.com/climate-machine/Oceananigans.jl/compare/v0.9.4...v0.9.5) **Main feature:** - Horizontal average diagnostic and we kind of decided on what diagnostics sh

## [v0.9.3](https://github.com/climate-machine/Oceananigans.jl/tree/v0.9.3) (2019-08-09) [Diff since v0.9.2](https://github.com/climate-machine/Oceananigans.jl/compare/v0.9.2...v0.9.3) **Main feature:** - A sophisticated and efficient `set!` function for setting field to specific

## [v0.9.2](https://github.com/climate-machine/Oceananigans.jl/tree/v0.9.2) (2019-08-07) [Diff since v0.9.1](https://github.com/climate-machine/Oceananigans.jl/compare/v0.9.1...v0.9.2) **Closed issues:** - Register Oceananigans v0.9.1 (#331) **Merged pull requests:** - Kernel for

## [v0.9.1](https://github.com/climate-machine/Oceananigans.jl/tree/v0.9.1) (2019-08-05) [Diff since v0.9.0](https://github.com/climate-machine/Oceananigans.jl/compare/v0.9.0...v0.9.1) **Main bug fix:** - Value/Dirchlet boundary conditions are properly imposed. **Closed issues:**

## [v0.9.0](https://github.com/climate-machine/Oceananigans.jl/tree/v0.9.0) (2019-07-31) [Diff since v0.8.0](https://github.com/climate-machine/Oceananigans.jl/compare/v0.8.0...v0.9.0) **Main feature:** - Turbulence closures for large-eddy simulation (constant Smagorinsky and ani

## [v0.8.0](https://github.com/climate-machine/Oceananigans.jl/tree/v0.8.0) (2019-06-30) [Diff since v0.7.0](https://github.com/climate-machine/Oceananigans.jl/compare/v0.7.0...v0.8.0) **Main features:** - Dynamic launch configuration for GPU kernels (by @maleadt at GPU hackathon

## [v0.7.0](https://github.com/climate-machine/Oceananigans.jl/tree/v0.7.0) (2019-06-28) [Diff since v0.6.2](https://github.com/climate-machine/Oceananigans.jl/compare/v0.6.2...v0.7.0) **Main features:** - Support for channel geometries. - Wizard utility for adaptive time steppin

## [v0.6.2](https://github.com/climate-machine/Oceananigans.jl/tree/v0.6.2) (2019-06-05) [Diff since v0.6.1](https://github.com/climate-machine/Oceananigans.jl/compare/v0.6.1...v0.6.2) **Closed issues:** - Register Oceananigans v0.6.1 (#269) **Merged pull requests:** - No more sc

## [v0.6.0](https://github.com/climate-machine/Oceananigans.jl/tree/v0.6.0) (2019-06-04) [Diff since v0.5.4](https://github.com/climate-machine/Oceananigans.jl/compare/v0.5.4...v0.6.0) **Main features:** - Halo regions to enforce the doubly periodic boundary conditions. - Flow is

## [v0.6.1](https://github.com/climate-machine/Oceananigans.jl/tree/v0.6.1) (2019-06-04) [Diff since v0.6.0](https://github.com/climate-machine/Oceananigans.jl/compare/v0.6.0...v0.6.1) **Closed issues:** - CPU example in README.md fails (#267) - Register Oceananigans v0.6.0 (#265

**What's new** * Velocity field is now divergence-free to machine precision during time stepping. #161 #228 #229 * Fixed bug in how the Coriolis term was calculated. #215 @jm-c * Internal wave test and example. #229 @glwagner * Incompressibility test #226 * Analytic solution reco

**What's new** * Updated versions of CUDA dependencies. * Free convection, wind stress, and mixed layer seasonal cycle examples. * Added actual CPU and GPU examples to README and documentation. * Updated 3D contourf plotting script to also plot vertical profile diagnostics. * New

**What's new** * Model is ~5x faster! Buoyancy update kernel was taking quadratic time when it should have been linear. #169 #172 * NaN checker diagnostic. #38 #170 * Oceananigans.jl is a real package now! #142

Tons of improvements! We need more frequent releases. **What's new** * Parameterized abstractions that work on CPU and GPU architectures. * Flashy boundary conditions API. @glwagner * Fourth-order tracer advection scheme. @mukund-gupta * Much faster GPU compile times thanks to fi

**Features** * Operators were rewritten to act on individual volume elements (i.e. element-wise) which allowed the time stepping loop to be rewritten to loop over all volume elements and generically run on CPU and GPU architectures using [GPUifyLoops.jl](https://github.com/vchura

**Features** * Main struct is now the `Model` instead of the `Problem`. It should be neater too. * Support for no-slip boundary conditions at the top and bottom. * Boundary condition information stored in a `BoundaryConditions` struct. * Abstract output writer (checkpoints and wr

* High-level abstractions for the grid, fields, field sets, constant collections, equation of state, and spectral solver parameters. * Model code has been refactored so that all operators now modify the fields in place and no memory allocation occurs during time stepping. * FFTs

* Ocean model works! * Nonhydrostatic algorithm including quasi-spectral solver work and do not blow the model up! * Numerous examples run as expected in 2D and 3D. * More tests need to be run, and the code needs to be cleaned up.