🟥 v0.91.12

Oceananigans v0.91.12

Diff since v0.91.11

Merged pull requests:

• Remove space from doi url (#3734) (@navidcy)
• Fix CFL calculation on flat grids (#3737) (@ali-ramadhan)
• Remove tendency computation at model construction (#3741) (@simone-silvestri)
• Test N-tuple MultipleForcings and make them work on the GPU (#3743) (@ali-ramadhan)
• Bug in the vector rotation operator (#3744) (@simone-silvestri)
• Add node_names and others to ImmersedBoundaryGrid (#3746) (@glwagner)
• Fix auto_extension for short filenames (#3749) (@ali-ramadhan)
• (0.91.12) Fix non-optimal CATKE parameters (#3759) (@glwagner)

Closed issues:

• cell_advection_timescale (and CFL) does not account for Flat topologies (#3679)
• Error when trying to use MultipleForcings (#3736)
• Some problems with ImmersedBoundaryGrids (#3742)
• Should tests be run with julia --check-bounds=yes? (#3747)
• Out of bounds error in auto_extension if output writer filename is 4 characters or shorter (#3748)

v0.91.11

Oceananigans v0.91.11

Diff since v0.91.10

Merged pull requests:

• Nullify preferred axis for field arg (#3730) (@glwagner)
• Bugfix for #3731 (#3733) (@simone-silvestri)

Closed issues:

• Bug with Makie extension (#3727)
• Bug in interpolate!(target_fts::FieldTimeSeries, source_fts::FieldTimeSeries)? (#3731)

v0.91.10

Oceananigans v0.91.10

Diff since v0.91.9

Merged pull requests:

• Make it easier to build simple HydrostaticFreeSurfaceModels (#3620) (@glwagner)
• Bugfix in interpolate! for FieldTimeSeries (#3723) (@simone-silvestri)
• Make the quickstart a bit more fun (#3724) (@glwagner)
• Invoke mask_immersed_field! when converting args for Makie (#3725) (@glwagner)
• Bump patch release (#3729) (@navidcy)

Closed issues:

• Cleanup Doc Previews (#3726)

v0.91.9

Oceananigans v0.91.9

Diff since v0.91.8

Merged pull requests:

• Adds methods to mask_immersed_field! for BinaryOperations (#3683) (@jagoosw)
• Fixs fallback for AbstractContinuousFormBiogeochemistry (#3685) (@jagoosw)
• Restrict LatitudeLongitueGrid topologies (#3694) (@glwagner)
• Use the word "grid" in the grid tutorial (#3713) (@glwagner)
• Add extension feature for plotting fields when nodes are provided (#3715) (@glwagner)
• (0.91.9) Bumps patch number (#3722) (@jagoosw)

Closed issues:

• minimum_zspacing isn't working on the GPU (#3040)
• maximum(abs, v) doesn't work on GPU in Julia 1.10.0 with grid size larger than (10, 10, 10) (#3427)

v0.91.8

Oceananigans v0.91.8

Diff since v0.91.7

Merged pull requests:

• Add new constructor for KernelParameters (#3645) (@glwagner)
• The start of documentation 2.0 (#3673) (@glwagner)
• Add constructor for windowing nothing boundary conditions (#3688) (@glwagner)
• Distributed tridiagonal Fourier solver (#3689) (@simone-silvestri)
• Create a warning for using the NonhydrostaticModel on ImmersedBoundaryGrid and change the default treatment of hydrostatic pressure anomaly (#3692) (@glwagner)
• Go back to support BoundaryCondition(Classification, args...) (#3695) (@simone-silvestri)
• Disambiguate tracer fluxes on an immersed boundary (#3696) (@simone-silvestri)
• Make shading better in baroclinic_adjustment.jl (#3697) (@asinghvi17)
• Leverage Makie extension in quick start (#3700) (@glwagner)
• Add Chor & Wenegrat (2024) in papers using package list (#3706) (@navidcy)
• (0.91.8) bug fix release (#3709) (@simone-silvestri)

Closed issues:

• Outdated docs on background diffusivity/viscosity (#3649)
• view fails on a Field indexed from FieldTimeSeries (#3687)

v0.91.7

Oceananigans v0.91.7

Diff since v0.91.6

This PR implements the infrastructure for open boundaries in NonhydrostaticModels by differentiating the filling of halos for BoundaryCondition{Open} boundaries so they are not refilled after the pressure correction step, as this would result in the interior field becoming divergent. This means that if the boundary value is not known a priori (e.g. it depends on the interior values), then the condition will not be enforced exactly. However, since open boundary conditions are already unphysical, it was decided that this was the preferable non-physicality.

To allow more sophisticated boundary conditions this PR adds a matching_scheme property to the Open boundary classification, and as an example, a matching scheme named FlatExtrapolation is implemented.

Finally, it introduces update_boundary_condition!(boundary_condition, field, model) which can be dispatched on boundary_condition to allow more complex boundary conditions to be implemented (e.g. to compute the mean outflow at the boundary and store it in the condition).

Merged pull requests:

• (0.91.7) Open boundary conditions for NonhydrostaticModel (#3482) (@jagoosw)
• Implement Makie extension (#3686) (@glwagner)

Closed issues:

• Adding Makie extension (#3178)

v0.91.6

Oceananigans v0.91.6

Diff since v0.91.5

Merged pull requests:

• (0.91.6) Distributed FFTs using Oceananigans' inhouse DiscreteTransforms (#3279) (@simone-silvestri)
• Add Downloads badges on README.md (#3652) (@navidcy)
• Update number_type.md (#3671) (@simone-silvestri)
• Update time_step! docstring for AB2 (#3674) (@simone-silvestri)
• Eliminate extra docstrings for FunctionField (#3678) (@glwagner)

Closed issues:

• What's the point of neglecting the computation of tendencies when taking a time-step? (#3565)

v0.91.5

Oceananigans v0.91.5

Diff since v0.91.4

Merged pull requests:

• Fix index calculation for Lagrangian particles in periodic directions (#3416) (@xkykai)
• Support non-trivial horizontal coordinates for single column grids (#3627) (@glwagner)
• Conversion between "Intrinsic" and "Extrinsic" reference frame (#3631) (@simone-silvestri)
• CuArray times for Cyclical field time series (#3639) (@simone-silvestri)
• Add inlines for general interpolation (#3653) (@simone-silvestri)
• One-sided upwind reconstruction (#3658) (@simone-silvestri)
• Removing some advection schemes (#3659) (@simone-silvestri)
• (0.91.5) Tweak initialization procedure so that callback schedules work with checkpointed simulations (#3660) (@glwagner)
• Update unified memory array (#3665) (@simone-silvestri)
• Improvements for TracerAdvection's API (#3668) (@simone-silvestri)

Closed issues:

• Problem when starting from a checkpoint with AveragedTimeInteval (#2226)
• Do we need to refer to MITgcm manual for horizontal vs vertical diffusivity implementation? (#2282)
• LagrangianParticles get moved at the right of Periodic topology when it shouldn't be (#3415)
• Allow single column grids with a specific location (#3626)
• Segmentation Fault when trying to run a script (#3655)
• Post-Checkpoint Output Saving Interval Issue (#3657)
• Mem.free is deprecated (#3664)

v0.91.4

Oceananigans v0.91.4

Diff since v0.91.3

Merged pull requests:

• Remove performance-/precompilation-time harmful @eval (#3556) (@simone-silvestri)
• Enzyme: try bump without tuple changes (#3618) (@wsmoses)
• Make Base.axes(f::Field) type-inferable for windowed fields (#3624) (@glwagner)
• fill_halo_regions! for velocities in implicit free surface correctly (#3629) (@glwagner)
• Fix a bug for SpecifiedTimes time-step alignment (#3634) (@glwagner)
• Remove vestigial code (#3636) (@glwagner)
• Update list of papers using Oceananigans (#3641) (@navidcy)
• (0.91.4) Fix interpolations in off-diagonal components of strain-rate tensor (#3648) (@tomchor)

Closed issues:

• @eval considered harmful (#3555)
• Huge memory use of Average associated with compilation (#3621)

v0.91.3

Oceananigans v0.91.3

Diff since v0.91.2

Merged pull requests:

• TKEDissipationVerticalDiffusivity (aka k-epsilon) turbulence closure (take 2) (#3605) (@glwagner)
• Adapting all fields of the OrthogonalSphericalShellGrid (#3619) (@simone-silvestri)
• Fixes small typo in docs (#3623) (@tomchor)
• (0.91.3) Bump (#3633) (@glwagner)

Closed issues:

• Using LagrangianParticles with Flat topology hits wrong function dispatch when computing fractional indices (#3632)