Oceananigans v0.110.8

Diff since v0.110.7

What's Changed

• Remove type instability in flattened_unique_values by @simone-silvestri in #5749
• Density-weighted (mass-flux) adaptive implicit vertical advection by @glwagner in #5733

Full Changelog: v0.110.7...v0.110.8

Oceananigans v0.110.7

Diff since v0.110.6

Merged pull requests:

• Simplify Relaxation: drop ContinuousForcing dependency, add transform and Field targets (#5620) (@glwagner)
• Add ColumnwiseTridiagonalPreconditioner for the CG Poisson solver (#5650) (@xkykai)

Oceananigans v0.110.6

Diff since v0.110.5

Closed issues:

• Test velocity exchanges across the tripolar seam more thoroughly (#4488)
• Add option for distributed computation to benchmark (#5579)
• Type-unstable ifelse over tuples in interpolating_time_indices(::Clamp, …) (mixed Int/Float64 slot) (#5731)

What's Changed

• Bump actions/checkout from 6 to 7 by @dependabot[bot] in #5720
• node returns the physical znode (not the reference rnode) on mutable vertical grids by @glwagner in #5723
• Add interpolate(f, …): map source values through f before blending by @glwagner in #5726
• Make Clock adapt recursive by @Pangoraw in #5725
• Fix type instability in interpolating_time_indices(::Clamp, …) by @xkykai in #5732
• Allow kernel functions with fewer indices for KernelFunctionOperation at reduced locations by @simone-silvestri in #5659
• Bugfix type inference of Clock types by @simone-silvestri in #5738
• Immersed boundary as a plain OffsetArray by @simone-silvestri in #5737
• Fast interpolate! from a LambertConformalConicGrid source by @glwagner in #5727
• Add a memory allocation test by @simone-silvestri in #5739
• Update papers using Oceananigans list and fix mismatched DOI links by @navidcy in #5741
• Extend zstar to allow mass fluxes by @simone-silvestri in #5592
• Remove looping over tuple of fields by @simone-silvestri in #5743
• Update UpwindBiased function default type by @glwagner in #5747
• Allow Flat-z (2D) TripolarGrid via z = nothing by @glwagner in #5728
• Fix error reading FieldTimeSeries from NetCDF by @tomchor in #5684
• Fix boxing of large args inputs by @simone-silvestri in #5746
• Remove type instability from the extract_field_time_series function by @simone-silvestri in #5740
• Dk/add distributed benchmark by @vopikamm in #5591
• Fix tripolar reductions by @simone-silvestri in #5099
• Fix instabilities in the launch! function by @simone-silvestri in #5745

Full Changelog: v0.110.5...v0.110.6

Oceananigans v0.110.5

Diff since v0.110.4

Merged pull requests:

• Update on_architecture for MetalGPU to specifically target StepRangeLen{FT, Float64, Float64} (#5375) (@glwagner)
• Add BFloat16 as supported float type (#5476) (@Pangoraw)
• Bump codecov/codecov-action from 6 to 7 (#5674) (@dependabot[bot])
• Add tracer budget closure test (#5679) (@navidcy)
• Better show for RotatedLatitudeLongitudeGrid and LambertConformalConicGrid (#5709) (@navidcy)
• [CI] Upload docs build directory as an artifact (#5710) (@giordano)
• Add Reactant == for LatitudeLongitudeGrid (#5711) (@dkytezab)
• Remove convert type piracy from Reactant extension (#5713) (@giordano)
• Bump project version from 0.110.4 to 0.110.5 (#5721) (@glwagner)

Closed issues:

• Custom validate_grid for Reactant + LatLon (#5668)
• Treatment of bathymetry in ShallowWaterModels (#5712)

Oceananigans v0.110.4

Diff since v0.110.3

Closed issues:

• JLD2Writer(overwrite_existing=true) behaves like iteration-level overwrite, not file-level overwrite (#5643)
• Accidental emoji rendering in docstrings (#5685)

Oceananigans v0.110.3

Diff since v0.110.2

Closed issues:

• JLD2Writer(overwrite_existing=true) behaves like iteration-level overwrite, not file-level overwrite (#5643)

Oceananigans v0.110.2

Diff since v0.110.1

Closed issues:

• cell_diffusion_timescale breaks for CATKE (#5641)
• TripolarGrid face-coordinate generation appears incomplete at the north seam, yielding NaNs in rotation_angle / intrinsic_vector (#5665)

What's Changed

• Add inactive_nodes to NetCDFWriter's gather_immersed_boundary by @tomchor in #5658
• Update Diagnostics.cell_diffusion_timescale method for vertically-implicit treatment by @navidcy in #5642
• Add ::Nothing methods to avoid type piracy in other packages by @navidcy in #5661
• Fix misleading docstring descriptions by @tomchor in #5664
• Reset clock to stage 1 not 0 by @simone-silvestri in #5672
• Use the correct function to compute the rotation angle by @simone-silvestri in #5677
• define *_domain methods for an OSSG by @simone-silvestri in #5673
• Fix inaccurate defaults/descriptions in user-facing docstrings by @tomchor in #5662
• Fix wrong/stale signatures in developer-facing docstrings by @tomchor in #5663
• Pin cuda 6.1 by @simone-silvestri in #5681
• Update citation for Atkinson and Grisouard's paper. by @navidcy in #5683
• Update Buildkite pipeline for the new JuliaGPU cluster by @maleadt in #5678
• Use DocStringExtension's TYPEDSIGNATURES for default-free docstring signatures by @tomchor in #5680
• (0.110.2) Fix reading reduced fields from NetCDF as FieldTimeSeries by @tomchor in #5682

Full Changelog: v0.110.1...v0.110.2

Oceananigans v0.110.1

Diff since v0.110.0

Merged pull requests:

• Allow set! to copy between reduced and windowed single-layer fields (#5652) (@glwagner)
• Update Project.toml (#5653) (@glwagner)

Closed issues:

• Passive tracers are not conserved on tripolar grid (#4466)

Oceananigans v0.110.0

Diff since v0.109.2

Breaking changes

• Open boundary conditions were renamed to NormalFlow. Value now accepts a scheme (used to set up radiation boundary conditions for tracers). See #5648 for details

Merged pull requests:

• Add target_transport to PerturbationAdvection for per-boundary transport control (#5479) (@tomchor)
• add zarr writer and chunk size as option to io benchmark (#5638) (@vopikamm)
• (0.110.0) Rename Open → NormalFlow and add a scheme to Value (#5648) (@glwagner)

Closed issues:

• Add scheme slot to Value (Value{MS}) and migrate PerturbationAdvection's Center-field path (#5647)

Oceananigans v0.109.2

Diff since v0.109.1

Merged pull requests:

• Limit pass through to target extension for auto_extension (#5644) (@rafmudaf)
• (0.109.2) Apply tracer open boundary conditions in NonhydrostaticModel (#5646) (@tomchor)