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)

v0.91.2

Oceananigans v0.91.2

Diff since v0.91.1

Merged pull requests:

• Speedup constructing a ConformalCubedSphereGrid on GPU (#3579) (@navidcy)
• (0.91.2) Remove instances of previous_Δt and fix a bug setting last_Δt in RK3 (#3595) (@glwagner)
• Change TimeInterval to avoid roundoff error issue plus some cleanup (#3616) (@glwagner)
• Compute third stage time-step for RK3 in a way that reduces the accumulation of error (#3617) (@glwagner)

v0.91.1

Oceananigans v0.91.1

Diff since v0.91.0

Merged pull requests:

• Bugfix for parent_index_range (#3573) (@siddharthabishnu)
• Passes grid argument to NetCDFOutputWriter (#3576) (@tomchor)
• Enforce total buoyancy flux BC in tilted geometry example (#3581) (@hdrake)
• (0.91.1) CATKE numerics: discretely correct shear production, split-explicit TKE substepping (#3585) (@glwagner)
• Add PartialCellBottom to the export list on ImmersedBoundaries (#3589) (@iuryt)
• Implement Scan, generalizing Reduction to accumulating scans like cumsum! (#3590) (@glwagner)
• Fix typo in callbacks example (#3591) (@navidcy)
• Add four more parameters for shear turbulence in unstable stratification (#3600) (@glwagner)
• Jlk9/enzyme constructor any test (#3603) (@jlk9)
• Remove GKSwstype: "100" from buildkite environment variables (#3604) (@glwagner)
• Update climacommon to 2024_05_27 (#3608) (@Sbozzolo)
• Update deps (#3610) (@navidcy)

Closed issues:

• Bug in determination of indices of parent array by parent_index_range (#3572)
• Forcing functions that depend on internal model fields besides velocities and tracers (#3582)
• Typo in docs on callbacks (#3583)
• boundary condition and output questions (#3612)
• Potential 'output_writers' saving bug? (#3614)

v0.91.0

Oceananigans v0.91.0

Diff since v0.90.14

Merged pull requests:

• Update climacommon to 2024_04_30 (#3571) (@Sbozzolo)
• (0.91.0) Make hydrostatic pressure anomaly optional in NonhydrostaticModel (#3574) (@glwagner)
• Allow creating a ConformalCubedSphereGrid on GPU (#3575) (@navidcy)
• Make the 3D stokes drift validation case even better (#3578) (@glwagner)

Closed issues:

• bug with background fields? (#3364)

📸 v0.90.14

Oceananigans v0.90.14

Diff since v0.90.13

Merged pull requests:

• Fix interpolator for left side of periodic domain (#3549) (@jagoosw)
• Extend operations for two ZeroFields (#3567) (@zhihua-zheng)

Closed issues:

• Interpolation over periodic dimension returns strange result? (#3114)

v0.90.13

Oceananigans v0.90.13

Diff since v0.90.12

Merged pull requests:

• Fix RiBasedVerticalDiffusivity (#3510) (@glwagner)
• Add Whitley & Wenegrat 2024 (#3546) (@navidcy)
• Alignment and minor changes (#3548) (@navidcy)
• Fix bug when using Lagrangian particles on Flat topologies (#3550) (@Jamie-Hilditch)
• Update deps (#3553) (@navidcy)
• Fix typo in doc @ref in one_dimensional_diffusion.jl (#3554) (@Datseris)
• Bugfix on FieldTimeSeries interpolation (#3558) (@simone-silvestri)
• Adding tracer advection in a Single column model (#3559) (@simone-silvestri)
• (0.90.13) Bump version (#3562) (@glwagner)

Closed issues:

• Example/tutorial on checkpointing (#1136)
• GridFittedBottom.immersed_condition needs to be documented (#2905)
• Problematic behavior of the RiBasedVerticalDiffusivity (#3283)
• Lagrangian particles on Flat topology (#3545)
• Noise below the mixed layer when using AnisotropicMinimumDissipation (#3560)