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)

🏍️ v0.90.12

Oceananigans v0.90.12

Diff since v0.90.11

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 grid coordinates and metrics in a single pass (#3488) (@siddharthabishnu)
• Default partition in Distributed (#3496) (@simone-silvestri)
• Add support for AbstractArray Forcing (#3498) (@glwagner)
• Allow interpolation on Distributed architectures (#3499) (@simone-silvestri)
• Revisit SplitExplicitFreeSurface user-interface and Docs + use SplitExplicitFreeSurface as the default when appropriate (#3503) (@navidcy)
• Enhance immersed boundary grid docs (#3505) (@navidcy)
• Adds last_Δt to Clock (#3508) (@jagoosw)
• Allow testing of just a single file (#3511) (@navidcy)
• File splitting in NetCDFOutputWriter when max_filesize is exceeded (#3512) (@josuemtzmo)
• (0.90.12) Bugfix for SpitExplicitFreeSurface on MultiRegionGrids and make SpitExplicitFreeSurface the default + don't allow more halos than interior points (#3514) (@navidcy)
• Generalize file splitting for output writers (#3515) (@glwagner)
• Add Chen et al. 2024 (#3517) (@navidcy)
• Don't ship docs with Manifest (#3521) (@navidcy)
• Tests for splitting output files using TimeInterval (#3523) (@josuemtzmo)
• Add interpolation for fields on ImmersedBoundaryGrids (#3524) (@simone-silvestri)
• Friendlier KH example for GPU (#3528) (@navidcy)
• Minor bug fix so that Δzᶜᶜᶜ(... , ibg::PCBIBG) works for grids with flat dims (#3530) (@navidcy)
• Add a bottom boundary layer example using CATKE (#3531) (@glwagner)
• Add info about models that support BackgroundFields (#3532) (@navidcy)
• Automatically try to reshape arrays when encountering DimensionMismatch (#3535) (@glwagner)
• Fix examples in ConformalCubedSphereGrid docs and convert to doctests (#3539) (@navidcy)
• Use adaptive timestep in two-dimensional turbulence example (#3540) (@navidcy)
• Update climacommon to 2024_04_05 (#3541) (@Sbozzolo)
• Show methods display information about the advection scheme(s) (#3542) (@navidcy)
• Bump julia-actions/setup-julia from 1 to 2 (#3544) (@dependabot[bot])

Closed issues:

• Splitting NetCDF output with NetCDFOutputWriter (#2967)
• PGC FreeSurface solver hardcodes 3 halo points and breaks if not (#3093)
• Fill velocity halos in a single pass for ConformalCubedSphereGrid (#3201)
• Some issue(s) with SplitExplicitFreeSurface (#3238)
• Default free surface solver: SplitExplicit or Implicit (#3289)
• Slow initialization after updating to v0.90.0 (#3381)
• Warnings regarding loop not unrolled when constructing model (#3494)
• What if we just wanna run one test file? (#3507)
• Change the default free-surface solver for MultiRegionGrids to SplitExplicitFreeSurface (#3513)
• Grid's halo size can exceed its interior (#3516)
• Remove Manifest.toml from docs (#3520)
• Scalar Indexing is not allowed on GPU array (KH instability) (#3522)
• Should have an option to apply Forcing only at specific nodes? (#3525)
• Compare ImmersedBoundary with tilted geometry (#3526)
• show for models should display the advection scheme too (#3534)
• bottom_heights from the immersed boundary method don't look right with a coarse grid (#3537)
• 2D turbulence example is outputting NaNs (#3538)

📺 v0.90.11

Oceananigans v0.90.11

Diff since v0.90.10

Merged pull requests:

• Add internal tide example in Docs (#3132) (@navidcy)
• (0.90.11) Tests for a distributed Immersed boundary grid + fix some on_architecture bugs (#3487) (@simone-silvestri)
• Remove few @unrolls that sneaked in with #3404 (#3501) (@navidcy)
• Show method for HydrostaticFreeSurfaceModel summarizes advection schemes (#3504) (@navidcy)

Closed issues:

• Creating a new doc example with drag on immersed boundaries (#3148)
• show method for HydrostaticFreeSurfaceModel does not show the advection scheme (#3197)
• Bugs in the Tilted Bottom Boundary Layer Example Code (#3412)