Oceananigans.jl - v0.87.3

Oceananigans v0.87.3

Diff since v0.87.2

Closed issues:

• Possible bug in computing Field(::KernelFunctionOperation) (#3232)

Merged pull requests:

• (0.87.3) BugFix for computing Field(::KernelFunctionOperation) (#3235) (@simone-silvestri)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] over 1 year ago

Oceananigans.jl - v0.87.2

Oceananigans v0.87.2

Diff since v0.87.1

Closed issues:

• Callable tridiagonal coefficients produces catastrophic loss of performance (#3047)
• Should reductions exclude peripheral_node? (#3064)
• Error only while debugging in VSCode (#3171)
• Generalization of OrthogonalSphericalShellGrid to be able to construct any grid with coords-metrics that vary in both i, j (#3200)
• LatitudeLongitudeGrid validation seems to be leaky (#3241)
• Add to the docs a better explanation about max_change and min_change of the TimeStepWizard (#3244)

Merged pull requests:

• (0.87.2) Bugfix CATKEVerticalDiffusivity locator functions + CATKE reformulation + other fixes (#3122) (@glwagner)
• Generalization of OrthogonalSphericalShellGrid to be able to construct any grid with coords-metrics that vary in both i, j (#3230) (@navidcy)
• Update dependencies (#3231) (@navidcy)
• Better validation for LatitudeLongitudeGrid + add test for sum(Azᶜᶜᵃ) ≈ 4πr² (#3240) (@navidcy)
• Fix latex rendering in Ocean wind and mixing example (#3243) (@navidcy)
• Provide a better explanation of the max_change and min_change of TimeStepWizard (#3245) (@iuryt)
• Add method for constants to field (#3247) (@glwagner)
• Update TimeStepWizard (#3248) (@iuryt)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] over 1 year ago

Oceananigans.jl - v0.87.1

Oceananigans v0.87.1

Diff since v0.87.0

Closed issues:

• Offline differential operators do not correctly apply boundary conditions (#3224)

Merged pull requests:

• (0.87.1) Make set! a little more ambitious (#3225) (@glwagner)
• getregion for KernelFunctionOperation (#3227) (@simone-silvestri)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] over 1 year ago

Oceananigans.jl - v0.87.0

Oceananigans v0.87.0

Diff since v0.86.0

Closed issues:

• Inconsistent advection from "different" velocities (#2928)
• Simple tests for correct halo filling + dynamics with the MultiRegion cubed sphere (#3020)
• Immersed boundary conditions invalidate all non-immersed BCs? (#3208)

Merged pull requests:

• Add ConformalCubedSphere grid via MultiRegion module (#2867) (@navidcy)
• Use latest Documenter + DocumenterCitations (#3186) (@navidcy)
• Fixes typo in Field docstring (#3192) (@tomchor)
• Fix admonition in Docs landing page (#3194) (@navidcy)
• Allow the default_bc to be a ContinuousBoundaryFunction (#3196) (@simone-silvestri)
• Toggle immersed differences with immersed_inactive_node (#3209) (@glwagner)
• Remove type instability in AB2/3 (#3213) (@milankl)
• (0.87.0) Fix advective forcing for upwind advection schemes (#3215) (@jagoosw)
• Fix typos (#3223) (@Sbozzolo)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] over 1 year ago

Oceananigans.jl - 🪃 v0.86.0

Oceananigans v0.86.0

Diff since v0.85.0

Closed issues:

• fkeep error for HydrostaticFreeSurfaceModel with a HeptadiagonalIterativeSolver (#3184)
• Integer division error in solve! on GPU (#3189)

Merged pull requests:

• CompatHelper: bump compat for PencilArrays to 0.19, (keep existing compat) (#3185) (@github-actions[bot])
• (0.86.0) Removes all support for <1.9 Julia versions (#3190) (@iuryt)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] almost 2 years ago

Oceananigans.jl - v0.85.0

Oceananigans v0.85.0

Diff since v0.84.1

Closed issues:

• ImmersedBoundaryCondition has the opposite convention of FieldBoundaryConditions (#3141)

Merged pull requests:

• (v0.85.0) Switching cells where fluxes are applied in ImmersedBoundaryCondition to match FieldBoundaryConditions' kwargs (#3142) (@simone-silvestri)
• Upgrade to Julia v1.9.2 (#3175) (@navidcy)
• Delete validation-pipeline.yml (#3176) (@glwagner)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] almost 2 years ago

Oceananigans.jl - v0.84.1

Oceananigans v0.84.1

Diff since v0.84.0

Closed issues:

• Running simulations with Clock{DateTime} (#2956)
• Dispatch fractional_x/y/z_index methods over various grid types? (#3156)
• specified_times_str(::SpecifiedTimes) (#3163)

Merged pull requests:

• Use julia v1.9 (#3100) (@navidcy)
• Bump compat entries for PencilFFTs and PencilArrays (#3121) (@navidcy)
• Fix issue with GL/CairoMakie not being able to compile on Apple's M1/2 chips (#3161) (@navidcy)
• Αdd CATKE paper in list of papers that used Oceananigans in the Docs (#3164) (@navidcy)
• Dispatch fractional_x/y/z_index methods over various grid types (#3165) (@navidcy)
• Restore netCDF output writer tests (#3167) (@navidcy)
• More docs built optimization (#3168) (@navidcy)
• Some simplifications in Docs/Simulations For GPUs (#3170) (@navidcy)
• Minor cleanup (#3172) (@navidcy)
• Add update_biogeochemical_state! to update_state! for hydrostatic free surface single column mode (#3173) (@jagoosw)
• (0.84.1) Fixes string generator for summary(::SpecifiedTimes) (#3174) (@glwagner)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] almost 2 years ago

Oceananigans.jl - 🚯 v0.84.0

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 vorticity_scheme, a vertical_scheme and an upwinding keyword argument. The divergence_scheme kwarg does not exist anymore as the divergence scheme is incorporated in the upwind kwarg (https://github.com/CliMA/Oceananigans.jl/pull/3091);

Highlights:

• NonhydrostaticModel now accepts grids that are stretched only in the x direction and only in the y direction, in addition to grids that stretched only in the z direction (https://github.com/CliMA/Oceananigans.jl/pull/3145);

Diff since v0.83.0

Closed issues:

• Calculate number of barotropic substeps on the fly using CFL criterion and current time-step (#2982)
• Allowing NonhydrostaticModel with grids that are irregular in either x or y (#3116)
• Passing compression to NetCDFOutputWriter does not reduce output file sizes (#3152)
• Making it easier to evolve tracers only after a certain time keeping them "frozen" until then (#3154)

Merged pull requests:

• (0.84.0) Improvement of vector invariant advection + various new implementations (#3091) (@simone-silvestri)
• Allowing NonhydrostaticModel with grids that are irregular in either x or y (#3111) (@tomchor)
• Use multiple processes to execute examples in make.jl (#3135) (@glwagner)
• Adaptive (CFL-based) time step in the SplitExplicit solver (#3145) (@simone-silvestri)
• Create dependabot.yml (#3149) (@navidcy)
• Fix typos in Docs (#3150) (@navidcy)
• More doc built optimizations -- run computationally expensive examples first (#3151) (@navidcy)
• (0.84.0) Fix NetCDFOutputWriter compression kwarg (#3153) (@Yixiao-Zhang)
• Update dependencies (#3155) (@navidcy)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] almost 2 years ago

Oceananigans.jl - v0.83.0

Oceananigans v0.83.0

Diff since v0.82.0

Closed issues:

• Error interpolating on an irregularly spaced grid (#2911)
• Can't reduce some KernelFunctionOperations on the GPU with ImmersedBoundaryGrid (#3140)

Merged pull requests:

• (v0.83.0) Fix error interpolating field on irregularly spaced grid (#2912) (@jagoosw)
• Three dimensional difference operators (#3127) (@simone-silvestri)
• Diffusivity docs (#3133) (@navidcy)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] almost 2 years ago

Oceananigans.jl - v0.82.0

Oceananigans v0.82.0

Diff since v0.81.1

Merged pull requests:

• (v0.82.0) Fixes inconsistent advection from "different" velocities (#3027) (@jagoosw)
• Fix few bugs + improve docstring of SplitExplicitFreeSurface (#3131) (@navidcy)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] almost 2 years ago

Oceananigans.jl - 🧰 v0.81.1

Oceananigans v0.81.1

Diff since v0.81.0

Closed issues:

• UniformStokesDrift would benefit from a parameters keyword (#2960)
• Simulation with tilted gravity and background buoyancy increases in total energy (#3036)
• NetCDFOutputWriter cannot find default_dimension_attributes for immersed boundary grids (#3069)
• Continuous boundary functions don't use grids' native coordinates (#3073)
• RegularCartesianGrid not defined (#3083)
• Find a way to recursively search for .nc/.jld2 files within the docs directory (#3112)
• Question about comparison with Veros (#3126)

Merged pull requests:

• Remove event system from KA and update to CUDA v4.1 (#2924) (@vchuravy)
• Update dependencies (#2966) (@navidcy)
• Add diffusive and viscous flux methods for tuples (#3057) (@tomchor)
• Better ShallowWaterScalarDiffusivity docs (#3063) (@navidcy)
• TwoDimensionalLeith for all grids (#3065) (@simone-silvestri)
• CompatHelper: add new compat entry for CUDA at version 4, (keep existing compat) (#3070) (@github-actions[bot])
• Fix default_dimension_attributes in NetCDFwriter to work with IBG (#3071) (@navidcy)
• Use grids' native coordinates in continuous BCs (#3074) (@navidcy)
• Reduce memory fetch for ContinuousBoundaryFunction BCs (#3077) (@navidcy)
• Fix bug in buoyancy implementation (#3079) (@glwagner)
• Better julia compat version message in Docs (#3084) (@navidcy)
• Double gyre (#3086) (@navidcy)
• Adds parameters keyword to UniformStokesDrift (#3096) (@tomchor)
• Updates dependencies (#3101) (@navidcy)
• Simplify implementation of SmagorinskyLilly + some other closure doc fixes (#3102) (@glwagner)
• Mention native coords in ScalarDiffusivity/ScalarBiharmonicDiffusivity docs (#3103) (@navidcy)
• Add "free surface" in the docs for set!(::HydrostaticFreeSurfaceModel) (#3105) (@navidcy)
• Minor updates in Docs/simulation_tips (#3106) (@navidcy)
• Fix small typo in tilted_bottom_boundary_layer.jl (#3107) (@tomchor)
• Small wording updates + missing `` added for correct rendering in horizontal convection example (#3108) (@jbisits)
• Ensure that all .jld2/.nc files are deleted before docs deployment (#3109) (@navidcy)
• Find output files recursively after a doc build (#3113) (@navidcy)
• Small improvements to the docs (#3115) (@tomchor)
• Extend BatchedTridiagonalSolver to all directions (#3117) (@tomchor)
• Fix units for vorticity in tilted BL example (#3118) (@navidcy)
• Initialize SplitExplicitFreeSurface with a CFL condition (#3124) (@simone-silvestri)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] almost 2 years ago

Oceananigans.jl - v0.81.0

Oceananigans v0.81.0

Diff since v0.80.0

Closed issues:

• Every exported name requires a docstring (#1133)
• More comprehensive contributors list? (#1519)
• Current implementation of dot(::Field, ::Field) is slow and allocates a lot (#2725)
• Solvers.initialize_matrix does not infer boundary conditions from template_field (#2882)
• Shallow water regression tests often fail on GPU (#2922)
• x/y/znode returns different things for different grids (#2978)
• Constants are sometimes defined twice (#2981)
• Issues connected to grid overhaul (spacings and nodes) (#3038)
• Move ShallowWaterModel to a different package? (#3049)
• Should we remove the year constant? (#3055)

Merged pull requests:

• Clean up methods for computing matrix that corresponds to linear_operation! used by MultigridSolver (#2885) (@navidcy)
• (v0.81.0) node(s) return native coordinates for grids + x/y/znode(s) -> distances & λ/φnode(s) -> degrees (#2979) (@navidcy)
• Update LICENSE (#3033) (@navidcy)
• Updates Docs/Buoyancy models and equation of state + update SeawaterPolynomials to v0.3.2 (#3035) (@jbisits)
• Remove Tullio dependency; take #2 and implement universally accurate CFL time-scale (#3037) (@simone-silvestri)
• Add .sqlite and .nsys-rep to .gitignore (#3044) (@navidcy)
• Avoid redefining R_Earth in the Coriolis module (#3046) (@navidcy)
• Remove swe regression + add warning in ShallowWaterModel (#3050) (@navidcy)
• (v0.81.0) Remove AlgebraicMultigrid + AMGX deps (#3052) (@navidcy)
• (v0.81.0) Remove year(s) from Units (#3059) (@glwagner)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 2 years ago

Oceananigans.jl - v0.80.0

Oceananigans v0.80.0

Diff since v0.79.6

Closed issues:

• Running with Posits as well as AbstractFloat. (#39)
• Implement Vreman SGS closure (#440)
• Verification tests comparing performance of different LES closures (#441)
• Field should subtype an array type for named axis behaviors? (#457)
• Each turbulence closure should probably have its own submodule (#521)
• Make sure Oceananigans is type stable (#552)
• Equatorial Rossby waves on a beta plane verification experiment (#640)
• Double gyre example (#678)
• 'Orlanski' open boundary condition (#833)
• Be careful of using end in forcing functions and boundary conditions (#838)
• 'ContinuedFlow' boundary condition (#848)
• Should we add multithreading benchmarks to README? (#900)
• Improving tracer budget tests (#942)
• Docs have "Model setup" but not "Simulation" (#946)
• README example is excessively large + README needs updating for current julia REPL look (#961)
• Evaluating volume-averages of functions of x, y, z, t with higher than first-order accuracy (#1011)
• Do we still need so much @hascuda? (#1043)
• "Computing tips" docs section for running on clusters with slurm, google cloud, etc... (#1045)
• Create a wiki with information / notes on how to setup buildkite for local testing? (#1046)
• Run Windows tests on GitHub Actions. (#1050)
• Upload coverage artifacts to Codecov from Buildkite. (#1052)
• Combine Diagnostics and OutputWriters docs page and add more AbstractOperations examples? (#1062)
• Benchmarking fully loaded simulations (#1089)
• 100% code coverage (#1100)
• Interactive/reactive examples with Pluto.jl (#1109)
• Interactive 3D visualization example with WGLMakie.jl (#1112)
• Check out where can we make use of Unitful.jl (#1116)
• Mixing data types and instantiated types in the user interface (#1119)
• State checker diagnostic (#1135)
• Example/tutorial on automating parameter exploration with Slurm? (#1137)
• More tutorials involving AbstractOperations + Output (#1143)
• Pedagogical improvements to the Langmuir turbulence example (#1146)
• Supporting non-zero or time-dependent wall-normal velocities (#1156)
• notebooks? (#1172)
• Positive preserving WENO scheme (#1173)
• Do TimeSteppers belong to Models, or to Simulations? (#1175)
• Stop assuming a default topology? (#1178)
• Print system info before running tests (#1180)
• Minor optimization: use convert rather than constructor to convert array type before output (#1182)
• linear stability calculator? (#1191)
• Grid in JLD2 files produced by JLD2OutputWriter is not sliced (#1194)
• Running Oceananigans with 2 threads allocates the most memory (#1218)
• Roadmap to version 1.0 (#1234)
• generalizing calculate_tendencies! ? (#1239)
• Change default advection scheme and halo size for grids, and add utilities for inferring needed halo sizes? (#1245)
• 4th order or higher for center differencing (#1265)
• Output writer schedules should be checkpointed (#1280)
• Error on invalid time interval + time window combinations for AveragedTimeInterval (#1288)
• Available Potential Energy (#1297)
• Extensive saving of model and simulation parameters in output metadata? (#1313)
• Create two new advection schemes: UpwindBiasedFirstOrder and CenterSixthOrder (#1320)
• Allow for computed fields diffusivities (#1327)
• implicit free-surface for ShallowWaterModel (#1378)
• Is convert_output for NamedTuple sufficiently general? (#1398)
• Examples should plot without using any Oceananigans functions (#1405)
• Convergence tests pipeline takes several hours to finish (#1420)
• What time attribute should Oceananigans use for NetCDF? (#1421)
• Document the parameters that users can change and their default values (#1427)
• Get rid of vertical integrals for IncompressibleModel (#1443)
• Modify test_dynamics.jl to includes tests for ShallowWaterModel (#1448)
• Test non-equal MPI domain decompositions soon (#1450)
• Profiling MPI and benchmarking strong + weak scaling (#1451)
• Check "model consistency" for users during model construction? (#1453)
• Separate Poisson solvers from main code (#1553)
• Generating conformal cubed sphere grids (#1586)
• Best way to interpolate cubed sphere grid to a regular lat-lon grid? (#1587)
• Boundary conditions cannot be enforced with closure = nothing (#1630)
• Keeping validation script up-to-date (#1634)
• "Dimension-aware" behavior of set! and interior with Flat directions? (#1655)
• benchmarks scripts cannot write CPU to GPU speedup table to html file due to ">" being in filename (#1672)
• Literate internal tide validation experiment? (#1694)
• Cannot construct GPU models on PowerPC architectures: ERROR: cfunction: closures are not supported on this platform (#1706)
• ShallowWaterModel.bathymetry? (#1712)
• Add a bathymetry test for ShallowWaterModel (#1716)
• What API should we implement for specifying fluxes across GridFittedImmersedBoundary? (#1720)
• New Benchmarks (#1722)
• ShallowWaterModel on Float32 (#1724)
• Direct 2D solves with FFT-based solver for rigid lid and implicit free surface (#1727)
• Aborting a simulation with NaNs without stacktraces (#1734)
• Test correctness / geometric consistency of VerticallyStretchedRectilinearGrid (#1756)
• Energy/enstrophy conserving schemes for Coriolis (#1818)
• Oceananigans is much slower when using relaxation forcing functions (#1827)
• An example with a non-trivial thermal-wind balance (#1846)
• Should examples be written so that the "part 2" (load output and plot/process) is independent of "part 1" (setup and run)? (#1850)
• Documentation v2.0 (#1852)
• Threaded benchmarks (#1861)
• Making all examples GPU-compatible (#1863)
• Many of the shallow water advection operators appear to be wrong (#1866)
• Poisson solver tests use CenterField to represent fields at Faces (#1867)
• Multi GPU scaling is very poor (#1882)
• Catching common performance / type inference issues with user functions (#1885)
• PTX compilation errors with GPU AbstractOperations (#1886)
• Enhance simulation Callback and model StateModifier utilities (#1895)
• Need to remove CUDA.allowscalar(true) because it's been deprecated (#1901)
• Refactoring Coriolis implementation and semantics (#1904)
• Utilities for benchmarking user-defined forcing, boundary conditions, and output calculation (#1918)
• Test for incompressibility in hydrostatic and non-hydrostatic models (#1934)
• More comprehensive testing for immersed boundaries (#1937)
• Need test for non-trivial fluxes along two boundaries (#1938)
• No need for free surface tendency with ImplicitFreeSurface (#1941)
• Arrays are not correctly extruded when broadcasting with fields (#1942)
• scalings for the distributed models (#1948)
• NaNChecker should only check a field in prognostic_fields(model), not all fields(model) (#1960)
• Cleaning up tests for efficiency (#1990)
• Add method to AveragedField to prescribed averaged dimensions with names, e.g., dims = (:x, :y) (#2006)
• Do we need separate MultiCPU and MultiGPU architectures? (#2020)
• Trigonometric functions may be causing slowdown on a simulation when running on GPUs (#2034)
• Should we test also models run with tuple of closures and/or using different models? (#2047)
• Simplify way users have access to grid metrics (#2058)
• Better name for the "underlying grid" for ImmersedBoundaryGrid (#2095)
• Encourage compiler to inline recursive closure tuple operators with "outer-inner" form (#2101)
• Pressure solver algorithm involves two superfluous fields (#2126)
• with_size for building new grids with similar domains and topologies but different resolutions (#2146)
• Emit warning when buoyancy.gravitational_acceleration != free_surface.gravitational_acceleration? (#2148)
• K-Profile Parametrization (#2149)
• Function interface for extracting properties from models (#2156)
• Helpful error when using an invalid schedule in OutputWriters, Diagnostics, and Callbacks (#2180)
• Variable grid spacing in horizontal dimension (x or y) causes NonhydrostaticModel instantiation to fail (#2191)
• HydrostaticFreeSurface model on a grid with Flat z (#2198)
• 32-bit indices for decreased GPU register pressure (#2202)
• Move FieldTimeSeriesCollector to Oceananigans? (#2216)
• Testing problem (#2222)
• Try harder to transfer boundary conditions to derived fields? (#2233)
• Simplifying notation for difference and interpolation operators (#2236)
• Automagically wrap AbstractOperation and Reduction in Field inside OutputWriters? (#2242)
• Move barotropic mode calculation to update_state!? (#2244)
• Serialize ImmersedBoundaryGrid by converting immersed boundary functions to arrays? (#2245)
• Export Horizontal and Vertical diffusivity isotropies from top-level? (#2254)
• Need test for (Cu)Array of IsopycnalSkewSymmetricDiffusivity closures (#2258)
• Possibly changing calculation of solid_interface function (#2263)
• Support Field(loc, op) for specifying AbstractOperation location (#2270)
• Improvements to stretched WENO5 API and new method validate_advection (#2271)
• Implementing Li et al's "theory wave" surface wave model (#2290)
• Convenience constructors for 1 and 2D grids? (#2292)
• Why is solid_interface used for reducing immersed fields? (#2293)
• interpolate Field fails on stretched grids (#2300)
• ImmesedBoundaryGrids with Flat dimensions don't work (#2301)
• Can we build examples separately from makedocs? (#2309)
• Teach AbstractOperations.validate_grid about ZeroField and ConstantField (#2311)
• Reorganizing examples in the docs (#2326)
• Passing parameters for nested boundary functions (nested task error: UndefKeywordError: keyword argument not assigned) (#2336)
• NetCDFOutputWriter should have mode = "c" as default? (#2339)
• Friendlier syntax for KernelFunctionOperation? (#2340)
• Can't use single ScalarDiffusivity(; κ) when κ isa AbstractArray (#2342)
• Usability concerns and possible improvements for MultiArch (#2349)
• Do we need a place to document experimental features? (#2355)
• Interface for closures (and other model terms) that introduce auxiliary prognostic variables (#2422)
• Benchmarking scripts for immersed boundaries and immersed boundary conditions (#2452)
• Modular and unified user interface for advection schemes (#2454)
• Add examples for setting initial conditions with Arrays on the docs (CPU and GPU) (#2457)
• Oceananigans "wiki" for hosting practical usage information (#2470)
• Is the finite volume discretization of the barotropic pressure gradient correct? (#2475)
• Change FieldTimeSeries to behave like 1D vector? (#2492)
• Tests for OffsetArrays-Field broadcasts (#2501)
• Biogeoceananigans.jl (#2512)
• Error in visualize_barotropic_gyre.jl in validation exps (#2542)
• Advection in ShallowWaterModel (#2615)
• Bug in DiagonallyDominantPreconditioner (#2668)
• Incremental compilation warning for next_stream() (#2676)
• Near global quarter degree validation experiment is broken (#2690)
• Failed to compile PTX code ... uses too much parameter space (#2700)
• Callback with SpecifiedTimes also gets called in iteration 0 (#2719)
• Issues with heuristic_workgroup (#2828)
• (Abstract) reductions don't play well with other operations (#2856)
• Validation script for flow over immersed hills fails in bottom_drag case (#2860)
• Initially quasi-quiescent stably stratified simulations develop instabilies and eventually blow up (#2935)
• README images broken (#2947)
• Heat flux sign incorrect in mixing and convection example (#2959)
• Ambiguous halo size error in HydrostaticFreeSurfaceModel (#2983)
• need to update docstring in netcdf_output_writer.jl (#2986)
• 10-100x slowdown on CPU after upgrade to KernelAbstractions 0.8 (due to type inference failure?) (#2996)
• Fill velocity halos correctly on the MultiRegion cubed sphere (#3021)
• Kernel compilation error in model with forcing + auxiliary_fields on GPU (#3025)

Merged pull requests:

• Creates functions for grid spacings (#2842) (@tomchor)
• Horizontal regridding and stabilizing CATKE features (#2881) (@glwagner)
• Simplify user interface for KernelFunctionOperation (#2964) (@glwagner)
• Fixes typo in abstract_scalar_biharmonic_diffusivity_closure.jl (#2968) (@tomchor)
• Fix docs rendering in Model setup/Forcing (#2971) (@navidcy)
• Fix rendering in numerical_implementation/turbulence_colsures.md (#2976) (@jbisits)
• More informative message when user provides smaller halo size than ImmersedBoundraryGrid requires (#2984) (@navidcy)
• Fix show(io, ::KernelFunctionOperation) (#2987) (@navidcy)
• Flips sign for gravity_unit_vector to match its description (attempt #2) (#2990) (@tomchor)
• Completely overhaul grid utils + min_Δx/y/z -> minimum_spacing + move x/y/zspacing to Grids (#2991) (@navidcy)
• Update resting_stratified_bumpy_ocean.jl (#2993) (@francispoulin)
• Update contributing.md to use main not master (#2994) (@glwagner)
• Time-averaged eddy diffusivities for RiBasedVerticalDiffusivity (#2995) (@glwagner)
• Fix bug in precondition! for DiagonallyDominantPreconditioner (#3011) (@glwagner)
• Delete validation/near_global_lat_lon directory (#3012) (@glwagner)
• Make OnDisk backend minimally usable (#3014) (@glwagner)
• Homogenize interface for initializing Simulation, schedules, etc (#3015) (@glwagner)
• Stabilizing CATKE for three-dimensional runs on ImmersedBoundaryGrid (#3016) (@glwagner)
• Increase halo size in flow_over_hills.jl (#3019) (@glwagner)
• Check for NaNs in prognostic_fields not fields (#3023) (@glwagner)
• Fixes CPU slowdown with KernelAbstractions >= v0.8 (#3026) (@simone-silvestri)
• Brings back SWE regression (#3028) (@navidcy)
• Bugfix in initialize! (#3029) (@simone-silvestri)
• Fix performance on CPU after upgrade to KernelAbstractions 0.8; issue #2996 (#3030) (@simone-silvestri)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 2 years ago

Oceananigans.jl - 🔬 v0.79.6

Oceananigans v0.79.6

Diff since v0.79.5

Closed issues:

• Unexpected behavior when interpolating? (#2969)

Merged pull requests:

• Adds an interface for inserting biogeochemistry models into Oceananigans models (#2802) (@glwagner)
• Clean up ImmersedBoundaries module (#2932) (@glwagner)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 2 years ago

Oceananigans.jl - 📼 v0.79.5

Oceananigans v0.79.5

Diff since v0.79.4

Closed issues:

• Bugfix in hydrostatic spherical coriolis (#2929)
• Docstring needed for ShallowWaterScalarDiffusivity (#2939)
• Nonhydrostatic pressure solver does not accept a horizontally irregular grid. (#2940)
• Clock's parameter and gravitational acceleration in shallow water model are both T (#2954)

Merged pull requests:

• Bugfix in heuristic workgroup (#2843) (@glwagner)
• Docstring for ShallowWaterScalarDiffusivity (#2941) (@navidcy)
• \textit{...} -> *...* for correct rendering in boundary_conditions.md (#2944) (@jbisits)
• Fixes calculation of diffusive CFL for LES with Tuple closures (#2945) (@tomchor)
• Informative error message for non-regularly spaced grids in NonhydrostaticModel (#2946) (@navidcy)
• Return zero for closure == nothing (#2951) (@tomchor)
• Convert docstring example to doctest (#2952) (@navidcy)
• Added another parameter for gravitational acceleration (#2955) (@dhruvbhagtani)
• Fix bug in hydrostatic spherical Coriolis (#2957) (@navidcy)
• Some updates in Docs/Simulations tips (#2958) (@navidcy)
• Add a note about default lat-lon topologies (#2961) (@navidcy)
• Changes "heating" to "cooling" in ocean wind mixing and convection example comment (#2962) (@jagoosw)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 2 years ago

Oceananigans.jl - v0.79.4

Oceananigans v0.79.4

Diff since v0.79.3

Closed issues:

• Are cells "wet", "dry", "active", or "inactive"? (#2833)
• Problems with NonTraditionalBetaPlane (#2876)
• WetCell -> ActiveCell ? (#2880)
• problems using the seawater equation of state (#2916)
• Type instability in hydrostatic_spherical_coriolis.jl? (#2925)
• Different results from identical tracers when using NetCDFOutputWriter (#2931)
• Use of similar in conditional_operations.jl (#2942)

Merged pull requests:

• Bugfix for non traditional beta plane (#2877) (@simone-silvestri)
• Parallel and Serial Split Explicit Free Surface (#2888) (@simone-silvestri)
• Make construct_regionally handle multiple return values (#2909) (@glwagner)
• Fixes diffusivity() for Smagorinsky-Lilly closure (#2913) (@tomchor)
• Refactor of some stretched rectilinear grid tests (#2917) (@tomchor)
• Changes wet/dry to active/inactive (#2918) (@navidcy)
• Update deps (#2919) (@navidcy)
• Update TimeStepWizard docs (#2920) (@navidcy)
• Fix broken wiki link on README (#2923) (@navidcy)
• Avoid type instability in HydrostaticSphericalCoriolis (#2926) (@navidcy)
• Temporarily disable ShallowWater GPU regression test (#2927) (@simone-silvestri)
• Don't conflate the status of a sliced field with its parent field (#2933) (@glwagner)
• Small changes to tilted bottom boundary layer example (#2934) (@tomchor)
• Brings back ShallowWater regression test (#2937) (@navidcy)
• Make it easier to restart a simulation from a checkpoint with additional passive tracers (#2938) (@tomchor)
• Better momentum advection message (#2943) (@glwagner)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 2 years ago

Oceananigans.jl - v0.79.3

Oceananigans v0.79.3

Diff since v0.79.2

Closed issues:

• Updating CUDAKernels to v0.4? (#2799)
• Error when writing Fields reduced over 3 dimensions to NetCDF (#2857)
• device kernel image is invalid error when running relatively complex simulation on GPUs (#2869)

Merged pull requests:

• Fixes writing of 3d-reduced Fields to NetCDF (#2865) (@tomchor)
• Upgrade KernelAbstractions to 0.8 (#2899) (@vchuravy)
• Removes diffusivity calculation from DiffusivityFields() for Smagorinsky closure (#2908) (@tomchor)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 2 years ago

Oceananigans.jl - v0.79.2

Oceananigans v0.79.2

Diff since v0.79.1

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 (#2884)

Merged pull requests:

• Improve function names and comments in Lagrangian particle update (#2685) (@glwagner)
• Changes to naming in the TurbulenceClosures module (#2752) (@tomchor)
• Improve immersed boundary performance (#2817) (@simone-silvestri)
• Use Julia v1.8.5 (#2862) (@navidcy)
• CubedSphere grid construction + tests (#2871) (@navidcy)
• Adds get_face() method for FunctionField (#2875) (@tomchor)
• Defines some binary operations with ZeroField (#2883) (@tomchor)
• Correct filename for internal wave movie (#2886) (@navidcy)
• Better DistributedFFTBasedPoissonSolver docstring (#2887) (@navidcy)
• Change default output array type for JLD2OutputWriter to Array{Float64} (#2890) (@glwagner)
• Better show for impenetrable boundary condition (#2894) (@navidcy)
• Fix in lat-lon grid Δy metric (#2897) (@navidcy)
• Some docstring fixes/enhancements + Code cleanup (#2903) (@navidcy)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 2 years ago

Oceananigans.jl - v0.79.1

Oceananigans v0.79.1

Diff since v0.79.0

Merged pull requests:

• Add metric calculation in the face grid of the cubed sphere + general clean up of CubedSphere code (#2836) (@navidcy)
• Upgrade Makie (#2853) (@navidcy)
• Added @inline to value/gradient fill halo functions (#2858) (@jagoosw)
• Increased interpolate speed (#2859) (@jagoosw)
• Fixes display() of LinearEquationOfState (#2861) (@tomchor)
• Update CATKE numerics and implement MEWSVerticalDiffusivity for mesoscale interfacial form stress (#2864) (@glwagner)
• Don't push docs preview (#2870) (@navidcy)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] over 2 years ago

Oceananigans.jl - ⛽️ v0.79.0

Oceananigans v0.79.0

Diff since v0.78.6

Merged pull requests:

• New vector invariant scheme (#2852) (@simone-silvestri)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] over 2 years ago

Oceananigans.jl - 🫣 v0.78.6

Oceananigans v0.78.6

Diff since v0.78.5

Merged pull requests:

• Fix bug loading netcdf (#2847) (@navidcy)
• Add three papers using Oceananigans to list (#2848) (@ali-ramadhan)
• Drop compat entry for KernelAbstractions 0.8 (#2849) (@navidcy)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] over 2 years ago

Oceananigans.jl - 🐞 v0.78.5

Oceananigans v0.78.5

Diff since v0.78.4

Merged pull requests:

• Fix bug when throwing exception during grid validation (#2845) (@ali-ramadhan)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] over 2 years ago

Oceananigans.jl - 👊 v0.78.4

Oceananigans v0.78.4

Diff since v0.78.3

Merged pull requests:

• Bump version 0.78.4 (#2846) (@glwagner)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] over 2 years ago

Oceananigans.jl - 🦃 v0.78.3

Oceananigans v0.78.3

Diff since v0.78.2

Closed issues:

• Adding Immersed Boundary Capabilities (#1036)
• GPU and CPU Profiling (#1912)
• Improvements to CATKEVerticalDiffusivity (#2450)
• Error for maximum(::Field{Face, Center, Center}) on GPU (#2744)
• Cleanup? (#2810)
• test_matrix_poisson_solver.jl very slow on GPU (#2813)
• Compatibility with DrWatson.jl (#2829)
• Error setting boundary_conditions for Field (#2837)
• Saving NC files on Power9 (#2840)

Merged pull requests:

• Fixes bug in error for validate_index (#2824) (@tomchor)
• Use AMGX v0.1.3 + drop @ifhasamgx (#2825) (@navidcy)
• Speed up matrix Poisson solver test + minor code cleanup (#2826) (@navidcy)
• Fixing a small bug in VerticallyImplicitTimeDiscretization vertical momentum fluxes (#2830) (@simone-silvestri)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] over 2 years ago

Oceananigans.jl - 🫂 v0.78.2

Oceananigans v0.78.2

Diff since v0.78.1

Closed issues:

• Potentially a race condition? (#2809)
• Dangerous behavior with @inbounds within for loop over 1:lenght(ξ::OffSetArray) (#2815)

Merged pull requests:

• Better docstrings for sparse utility functions in Solvers (#2808) (@navidcy)
• Fix wrong looping over indices of OffsetArray (#2816) (@navidcy)
• Simplify the baroclinic adjustment example (#2819) (@navidcy)
• Fix race condition affecting HydrostaticFreeSurfaceModel with isnothing(free_surface) (#2821) (@glwagner)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] over 2 years ago

Oceananigans.jl - 🐏 v0.78.1

Oceananigans v0.78.1

Diff since v0.78.0

Closed issues:

• Seeing only partial function index from Documenter (#599)
• Plotting recipes (#1115)
• Incorrect warning about simulations running forever in Simulation constructor (#1124)
• Friendly "getting started" section that encompasses installation + running examples for new users? (#1149)
• Bottom boundary layer example / tutorial? (#1183)
• Need more tests for single_column_model_mode and slice_ensemble_model_mode (#2219)
• Multigrid iterative pressure solver implementation (#2267)
• Halo warning asks users for more halo points than required (#2277)
• GPU + no-slip BC (#2530)
• Can't use GradientBoundaryCondition on the GPU (#2709)
• Reproducibility issue in LES results (#2766)
• State callbacks (#2772)
• Parallel simulations using multiple nodes/MPI (#2787)
• Increasing memory use on GPUs with recent versions (#2794)
• update_state! for HydrostaticFreeSurfaceModel seems that overwrites itself? (#2800)
• Why does this package have a Manifest.toml? (#2806)
• Unnecessary barrier in ab2_step_velocities!? (#2811)
• Unnecessary barrier definition? (#2812)

Merged pull requests:

• State callbacks (#2773) (@jagoosw)
• Adds benchmark for free surface solvers on lat-lon immersed boundary + triply-bounded Poisson bench/validation script (#2784) (@elise-palethorpe)
• Fixes typo in Callback() docstring (#2785) (@tomchor)
• CATKE and GM in a near-global 1 degree simulation + updates Ri-based vertical diffusivity (#2786) (@glwagner)
• Fix warning on IB boundary condition docs (#2789) (@tomchor)
• Update list of papers using Oceananigans (#2791) (@navidcy)
• Remove extra memory allocations of output_construction (#2797) (@simone-silvestri)
• Delete some benchmarks that were done on archaic Oceananigans v0.34.0 (#2803) (@navidcy)
• Fix docstring/doctest for required_halo_size (#2804) (@navidcy)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] over 2 years ago

Oceananigans.jl - 🚣🏻‍♀️ v0.78.0

Oceananigans v0.78.0

Diff since v0.77.5

Closed issues:

• Question regarding a doctest that involves rand (#2702)
• Auxiliary fields not directly available to tracer forcing functions (#2730)
• Advection for the Flat Direction Momentum Equation Seems Missing (#2742)
• Error running on GPUs using CUDA>=3.10 (#2756)
• Cannot fill halos during NonhydrostaticModel construction when specifying some boundary conditions (#2768)

Merged pull requests:

• Bump Julia to v1.8 (#2701) (@navidcy)
• Ignore halos and immersed cells in calculating shallow water advection time-scale (#2721) (@glwagner)
• BC and Immersed Reductions for Sliced Fields (#2740) (@simone-silvestri)
• Fix flat advective fluxes (#2757) (@navidcy)
• Enforce capitalizations in bib entry (#2758) (@navidcy)
• Typo in ConsecutiveIterations (#2759) (@simone-silvestri)
• Cleanup unused type variables (#2761) (@simone-silvestri)
• Fix some docstrings (#2762) (@navidcy)
• CompatHelper: bump compat for MPI to 0.20, (keep existing compat) (#2767) (@github-actions[bot])
• Only BoundaryConditions as default_boundary_conditions (#2769) (@simone-silvestri)
• Bugfix in implicit free surface (#2774) (@simone-silvestri)
• Update dependencies (#2775) (@navidcy)
• CompatHelper: bump compat for SeawaterPolynomials to 0.3, (keep existing compat) (#2777) (@github-actions[bot])
• Bump SeawaterPolynomials to v0.3.0 (#2779) (@navidcy)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] over 2 years ago

Oceananigans.jl - 🛷 v0.77.5

Oceananigans v0.77.5

Diff since v0.77.4

Closed issues:

• Definition of length(grid) is not consistent with Julia definition (#1253)
• Error in num_prod? (#2747)

Merged pull requests:

• Add direct access to auxiliary fields for forcing functions (#2733) (@jagoosw)
• Updates the near_global_quarter_degree.jl validation script (#2743) (@navidcy)
• Fix CenterField docstring (#2745) (@navidcy)
• Bug fix for general interpolation (#2746) (@simone-silvestri)
• Fix bug in num_prod (#2749) (@navidcy)
• Fixed bug in Callback summary (#2750) (@jagoosw)
• Add multigrid preconditioned for the heptadiagonal solver (#2753) (@elise-palethorpe)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] over 2 years ago

Oceananigans.jl - 🎒 v0.77.4

Oceananigans v0.77.4

Diff since v0.77.3

Closed issues:

• Strange behavior in filling halos in GridFittedBottom -- does it matter? (#2739)

Merged pull requests:

• Wet point Coriolis scheme and bugfix in GM tapering (#2729) (@simone-silvestri)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] over 2 years ago

Oceananigans.jl - 🐿 v0.77.3

Oceananigans v0.77.3

Diff since v0.77.2

Closed issues:

• Zero-ed initial guess to preconditioner for CG solver improves performance compared to using previous z (#2655)
• Add GPU functionality to Multigrid solver (#2657)
• Potential bug introduced either in immersed boundaries or at PGC (or somewhere else)? (#2708)
• maximum(::Field) not working on GPU (#2727)
• Volume integral of buoyancy variance changed between v0.71.6 and v0.72.4 (#2735)

Merged pull requests:

• Preconditioning CG solver with Multigrid (#2654) (@elise-palethorpe)
• Add GPU functionality to Multigrid solver (#2688) (@elise-palethorpe)
• Update dependencies (#2695) (@navidcy)
• Add test for implicit free surface with immersed boundary (#2712) (@navidcy)
• Slightly reorganizes dependencies in tests (#2715) (@tomchor)
• Fix notation k̂ -> ẑ (#2716) (@navidcy)
• Fix bullet points in Docs/Model setup/Boundary conditions (#2731) (@navidcy)
• Fix examples is CFL docstrings (#2732) (@navidcy)
• Correct computation for buoyancy dissipation rate, χ_diff + demonstrate Integral (#2734) (@navidcy)
• Reduces allocations for Multigrid solver on CPU: Multilevel structure only created when required (#2736) (@elise-palethorpe)
• CompatHelper: add new compat entry for AMGX at version 0.1, (keep existing compat) (#2738) (@github-actions[bot])

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] over 2 years ago

Oceananigans.jl - 🥼 v0.77.2

Oceananigans v0.77.2

Diff since v0.77.1

Closed issues:

• Potential bug introduced either in immersed boundaries or at PGC (or somewhere else)? (#2708)

Merged pull requests:

• Improves plotting in tilted bottom boundary layer example (#2704) (@tomchor)
• Set TagBot lookback to 3 days (#2707) (@navidcy)
• Fix location of Integrated areas derivatives in the PCG solver (#2710) (@simone-silvestri)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] over 2 years ago

Oceananigans.jl - 🌔 v0.77.1

Oceananigans v0.77.1

Diff since v0.77.0

Closed issues:

• Strange behaviour of Lagrangian Particles near top of domain (#2681)

Merged pull requests:

• Update benchmarks.md (#2680) (@pitmonticone)
• Fixed Lagrangian Particle boundary condition enforcement issue #2681 (#2682) (@jagoosw)
• Small bugfix (#2687) (@simone-silvestri)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] over 2 years ago

Oceananigans.jl - v0.77.0

Oceananigans v0.77.0

Diff since v0.76.8

Closed issues:

• Adding Lagrangian particles to a nonuniform grid (#2395)

Merged pull requests:

• High-order advection stencils, overhaul of boundary treatment, and bugfix in advection reconstruction (#2603) (@simone-silvestri)
• [WIP] Advection Refactor (#2642) (@simone-silvestri)
• Multi Dimensional Advection scheme (#2643) (@simone-silvestri)
• Revamp of LagrangianParticles (#2658) (@simone-silvestri)
• ImplicitFreeSurface default in HydrostaticFreeSurfaceModel (#2674) (@simone-silvestri)
• small bugfix in multi-region (#2675) (@simone-silvestri)
• Fix a few typos in README, docs and docstrings (#2679) (@pitmonticone)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] almost 3 years ago

Oceananigans.jl - v0.76.8

Oceananigans v0.76.8

Diff since v0.76.7

Closed issues:

• Form of viscosity in ShallowWaterModel (#2403)
• Add example for FieldBoundaryConditions on an ImmersedBoundaryGrid (#2631)
• ShallowWaterModel only filling in one halo point (#2650)
• Sign error in Docs/Numerical implementation/Pressure decomposition (#2653)
• Is there a typo in Docs/Numerical implementation/Pressure decomposition in ∇p → ∇p_non + ∇ₕp_hyd? (#2656)
• Can't create averaged Field while specifying scratch space (#2659)
• Leith closure not working on GPU() (#2660)
• ERROR: MethodError: no method matching initarray! on Julia v1.8.0-rc1 (#2663)
• Scaling ShallowWaterModel causes static issue (#2671)

Merged pull requests:

• Add example for FieldBoundaryConditions on an ImmersedBoundaryGrid (#2632) (@navidcy)
• Update several Docs sections + docstrings (#2639) (@elise-palethorpe)
• Viscous term for Shallow Water model (#2645) (@simone-silvestri)
• Change CUDA.query (deprecated) -> CUDA.isdone (#2649) (@navidcy)
• Bugfix for DiscreteDiffusionFunction + passes prognostic + auxiliary fields to forcing functions (#2651) (@simone-silvestri)
• Diffusivity for Leith (#2661) (@simone-silvestri)
• Fixes to Gent McWilliams parametrization (#2664) (@simone-silvestri)
• initarray! julia 1.8 (#2666) (@simone-silvestri)
• Fix RiBasedVerticalDiffusivity docstring (#2670) (@navidcy)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] almost 3 years ago

Oceananigans.jl - 🐚 v0.76.7

Oceananigans v0.76.7

Diff since v0.76.6

Closed issues:

• Need actual doctstring for SpecifiedTimes (#2608)
• Need to document the available solver method options for ImplicitFreeSurface solvers (#2620)
• Need to check for constant depth before we use the FFTBasedPoissonSolver in HydrostaticFreeSurfaceModel? (#2626)
• Rename Poisson Solvers section in Docs? (#2637)
• Is calc_∇²! redundant in view of compute_∇²!? (#2638)

Merged pull requests:

• Partial cell immersed boundaries (#2306) (@francispoulin)
• Implements a multigrid solver for Poisson and implicit free surface equations on CPU (#2396) (@elise-palethorpe)
• Fields in viscosity operators (#2580) (@simone-silvestri)
• Add docstring for SpecifiedTimes (#2617) (@navidcy)
• Update package's dependencies (#2619) (@navidcy)
• Update ImplicitFreeSurface & HeptadiagonalIterativeSolver docstrings (#2621) (@navidcy)
• Add empty PR template (#2624) (@navidcy)
• Docs library cleanup (#2627) (@navidcy)
• Some updates in validation scripts: AveragedField() -> Field(Average()) (#2630) (@navidcy)
• Fix typo in Docs/Buoyancy models (#2633) (@navidcy)
• Small bugfix for ContinuousBoundaryFunction (#2634) (@simone-silvestri)
• Use predefined compute_∇²! instead of defining new calc_∇²! in test_matrix_poisson_solver.jl (#2640) (@navidcy)
• Rename Docs/Numerical Implementation/Poisson solvers section -> Elliptic solvers (#2641) (@navidcy)
• VectorInvariant as a default for HydrostaticFreeSurfaceModel with LatitudeLongitudeGrid (#2644) (@simone-silvestri)
• Minor changes in Langmuir and Ocean wind mixing examples (#2646) (@tomchor)
• Small change to 1D diffusion example (#2648) (@tomchor)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] almost 3 years ago

Oceananigans.jl - 🪡 v0.76.6

Oceananigans v0.76.6

Diff since v0.76.5

Closed issues:

• CUDA error with immersed boundary when running on GPU (#2479)
• Odd behavior using ImmersedBoundary while specifying scratch data for Field computation (#2581)
• closure not working in ShallowWaterModel (#2606)
• Can we have advection like terms in the forcing? (#2609)

Merged pull requests:

• Near global one degree setup (#2463) (@glwagner)
• Improve support for immersed boundaries with Flat (#2532) (@glwagner)
• CompatHelper: bump compat for DocStringExtensions to 0.9, (keep existing compat) (#2578) (@github-actions[bot])
• compute_at! for ConditionalOperation (#2582) (@glwagner)
• Update near_global_quarter_degree.jl (#2593) (@simone-silvestri)
• Update boundary_conditions.md (#2598) (@francispoulin)
• Updates for Docs/Physics section (#2599) (@navidcy)
• Drop SafeTestset from package dependency (#2601) (@navidcy)
• Fix ShallowWaterModel closure for tracers in the vector invariant form (#2607) (@francispoulin)
• Update ShallowWaterModel to use areas (#2612) (@francispoulin)
• Bump up PencilFFTs (#2613) (@navidcy)
• Adds back a fig in Docs/Model/Grids + example with Flat topology (#2614) (@navidcy)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] almost 3 years ago

Oceananigans.jl - ⛑ v0.76.5

Oceananigans v0.76.5

Diff since v0.76.4

Closed issues:

• Can't we have a 2D simulation on the sphere? (#2372)
• Does non hydrostatic model impose boundary conditions based on topology? (#2594)
• Unnecessary GPU check? (#2595)

Merged pull requests:

• Vector Invariant Formulation of the ShallowWaterModel (#2522) (@simone-silvestri)
• Check for CUDA-enabled device on grid construction rather than in model constructors (#2596) (@navidcy)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] almost 3 years ago

Oceananigans.jl - v0.76.4

Oceananigans v0.76.4

Diff since v0.76.3

Closed issues:

• Error using immersed boundary on GPUs with buoyancy tracer (#2558)
• Type Error using ImmersedBoundaries on GPU (#2563)
• Do we want a HorizontalDivergenceField? (#2575)
• using ∂x in a forcing function (#2586)
• Input validation for stretched grid dimensions breaks FieldTimeSeries (#2588)

Merged pull requests:

• Synchronous intra-device copy (#2547) (@simone-silvestri)
• Update PencilArrays (#2552) (@navidcy)
• Convert two_dimensional_turbulence.jl and internal_wave.jl literated examples in docs to use CairoMakie (#2553) (@navidcy)
• Adds tracer-specific diffusivity subsection to model_setup (#2554) (@tomchor)
• Convert more examples to plot with Makie (#2556) (@navidcy)
• Maximum-principle-satisfying WENO scheme (#2557) (@simone-silvestri)
• Regularize Number boundary conditions to eltype(grid) (#2559) (@glwagner)
• Completely trivial update to a comment about continguous CuArrays (#2561) (@glwagner)
• Eliminate Plots as dependency in Docs; use Makie (#2562) (@navidcy)
• Adapt for ImmersedBoundaryCondition (#2564) (@simone-silvestri)
• Adds with_halos to NetCDFOutputWriter's signature call in docstring (#2566) (@tomchor)
• One more one(grid) (#2567) (@glwagner)
• Implement lastindex for FieldTimeSeries (#2568) (@glwagner)
• Fix inconsistent behaviour in test_matrix_poisson_solver.jl (#2569) (@simone-silvestri)
• update near_global_quarter_degree.jl (#2570) (@francispoulin)
• Fixes small typo in Langmuir turbulence example (#2571) (@tomchor)
• Fix matrix solver test take 2 (#2572) (@simone-silvestri)
• small bugfix in Integral construction (#2573) (@simone-silvestri)
• Update dependencies (#2574) (@navidcy)
• Beautify examples a bit more (#2576) (@glwagner)
• To enable discrete functions on "ImmersedBoundaryConditions" (#2577) (@simone-silvestri)
• PreconditionedConjugateGradientSolver: fix docstring and show() method (#2583) (@navidcy)
• Fix admonition (#2585) (@navidcy)
• Bug fix in conditional advective_tracer_flux (#2587) (@simone-silvestri)
• Fix fatal interaction between FieldTimeSeries construction and input validation (#2589) (@glwagner)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] almost 3 years ago

Oceananigans.jl - 🪛 v0.76.3

Oceananigans v0.76.3

Diff since v0.76.2

Closed issues:

• Should we check the size of grids in stretched directions? (#2548)

Merged pull requests:

• Throws error when size of dimension is mismatched when constructing RectilinearGrid (#2550) (@tomchor)
• Fixes bug in IBM with Value or Gradient boundary conditions (#2551) (@tomchor)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] almost 3 years ago

Oceananigans.jl - ⛰️ v0.76.2

Oceananigans v0.76.2

Diff since v0.76.1

Closed issues:

• NetCDF: filename vs filepath (#2541)
• error in baroclinic_adjustment.jl (#2543)

Merged pull requests:

• Update CATKE parameters for new implicit time-stepping (#2461) (@glwagner)
• Permute PencilFFT temporary array dimensions (#2513) (@glwagner)
• Cosmetic improvement to checkpointer docs (#2531) (@glwagner)
• Support two-dimensional distributed FFT-based Poisson solves (#2536) (@glwagner)
• Make JLD2 look before leaping (#2537) (@glwagner)
• CompatHelper: add new compat entry for PencilArrays at version 0.16, (keep existing compat) (#2539) (@github-actions[bot])
• Update PencilArrays and PencilFFTs (#2544) (@github-actions[bot])
• Fixes WENO5(grid=grid) for immersed boundary grids (#2549) (@tomchor)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] almost 3 years ago

Oceananigans.jl - 🧂 v0.76.1

Oceananigans v0.76.1

Diff since v0.76.0

Closed issues:

• TEOS10 Equation of State: Depth vs Height (#2528)

Merged pull requests:

• Update dependency packages (#2447) (@navidcy)
• Update compat for SeawaterPolynomials (#2529) (@glwagner)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] almost 3 years ago

Oceananigans.jl - 🖥️ v0.76.0

Oceananigans v0.76.0

Diff since v0.75.3

Closed issues:

• Shared memory for GPU kernels (#442)
• NetCDFOutputWriter leaves file open if the constructor errors (#555)
• InterpolatedField for Lagrangian particle tracking, output on custom grids, and restoring from checkpoint to a new grid. (#975)
• Different advection schemes for velocities and tracers (#1015)
• Terrain-following coordinates anyone? (#1549)
• Connected topologies (#1582)
• Error from benchmark/test distributed nonhydrostatic model scripts (#2347)
• Why do we need a hack_cosd/hack_sind? (#2371)
• Oceananigans Port to AMDGPU (#2493)

Merged pull requests:

• Multi-region module for MPI-less multi-GPU computation (#2253) (@simone-silvestri)
• VerticallyImplicitTimeDiscretization for symmetric isoneutral diffusion (#2487) (@glwagner)
• AMDGPU Branch Initial Pull Request (#2494) (@matinraayai)
• Remove spurious extra calculate_diffusivities! (#2498) (@glwagner)
• Fix minor error in internal_wave.jl (#2500) (@glwagner)
• Update PencilFFTs and GPUArrays and fix DistributedFFTBasedPoissonSolver (#2502) (@glwagner)
• Update JLD2OutputWriter calls (#2504) (@navidcy)
• Fix url for section about papers citing Oceananigans (#2505) (@navidcy)
• Update CubedSpheres (#2506) (@jm-c)
• Remove vertical advection from vector invariant WENO (#2510) (@simone-silvestri)
• README tweak (#2514) (@glwagner)
• Drop direct dependency to GPUArrays and BenchmarkTools (#2518) (@navidcy)
• Add tests for computations on slices (#2521) (@glwagner)
• OutputWriters for MultiRegion (#2524) (@simone-silvestri)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] almost 3 years ago

Oceananigans.jl - 🛰 v0.75.3

Oceananigans v0.75.3

Diff since v0.75.2

Closed issues:

• Problem installing and using Oceananigans (#2480)

Merged pull requests:

• Implement the actually-Cox (aka the anti-anti-Cox) stencil for GM (#2481) (@glwagner)
• Remove redundant definition of diffusive_flux_z for divergence damping (#2482) (@glwagner)
• Pin MPICH_jll at 4.0.1 (#2486) (@glwagner)
• Fix docs url typo in README (#2491) (@navidcy)
• Biharmonic divergence damping (#2495) (@simone-silvestri)
• Drop MPICH_jll direct dependency (#2496) (@navidcy)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] almost 3 years ago

Oceananigans.jl - 🛴 v0.75.2

Oceananigans v0.75.2

Diff since v0.75.1

Closed issues:

• Minor problem with closure in show(io, :: NonhydrostaticModel)? (#2443)
• Smsm (#2466)
• Smsm (#2468)

Merged pull requests:

• Useful regression benchmark (#1214) (@ali-ramadhan)
• Support boundary conditions on immersed boundaries (#2437) (@glwagner)
• Adds HorizontalDivergenceFormulation for scalar diffusions (#2440) (@glwagner)
• Few beautifications in docstrings (#2458) (@navidcy)
• Few minor beauty fixes (#2459) (@navidcy)
• Better diffusivity closure show() (#2460) (@navidcy)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - ☎️ v0.75.1

Oceananigans v0.75.1

Diff since v0.75.0

Merged pull requests:

• Excise some examples and improve others (#2333) (@glwagner)
• More distributed validation scripts (#2348) (@glwagner)
• Enhancements to RiBasedVerticalDiffusivity (#2423) (@glwagner)
• Use Julia v1.6.6 LTS (#2446) (@navidcy)
• Move CATKE diffusivities to vertical cell interfaces (#2449) (@glwagner)
• Fix typos in Docs/Numerics/Poisson solvers (#2451) (@navidcy)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - 🎞 v0.75.0

Oceananigans v0.75.0

Diff since v0.74.2

Closed issues:

• problems in setting BoundaryConditions in ImmersedBoundary (#1730)
• Do we need @unroll in fill halo flux functions? (#2369)
• ValueBoundaryCondition fails with ImmersedBoundaryGrid (#2430)
• Should we add location to the export list? (#2438)
• Possible issue with distributed architecture (#2445)

Merged pull requests:

• Change default halo size to 3 in non-Flat directions (#2378) (@glwagner)
• Location-aware halo filling (#2441) (@glwagner)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - v0.74.2

Oceananigans v0.74.2

Diff since v0.74.1

Closed issues:

• Unneeded arch argument to fill_halo_regions? (#969)
• Helpful error message for incorrect usage of FieldBoundaryConditions (#1968)
• Running the distributed_nonhydrostatic_model_mpi.jl benchmark (#2433)

Merged pull requests:

• Adds flow_over_hills validation case (#2402) (@glwagner)
• Semi-implicit treatment of TKE dissipation for CATKE (#2426) (@glwagner)
• Updates distributed_nonhydrostatic_model_mpi.jl (#2432) (@tomchor)
• Updates output writers interface to append extension automatically (#2435) (@glwagner)
• Add location to export list (#2439) (@iuryt)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - 📸 v0.74.1

Oceananigans v0.74.1

Diff since v0.74.0

Closed issues:

• Specifying multiple forcings for a model field (#2136)

Merged pull requests:

• Adds MultipleForcings and AdvectiveForcing (#2389) (@glwagner)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - 🦕 v0.74.0

Oceananigans v0.74.0

Diff since v0.73.8

Closed issues:

• Inconsistency in output writers interface (#884)
• Errors in the output writers docs page (#2427)

Merged pull requests:

• Unifies interfaces in NetCDFOutputWriter, JLD2OutputWriter and Checkpointer (#2416) (@tomchor)
• JLD2OutputWriter: right now the indices have to be contiguous (#2428) (@syou83syou83)
• Mention the Climate Modeling Alliance in Project.toml and README (#2429) (@glwagner)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - v0.73.8

Oceananigans v0.73.8

Diff since v0.73.7

Closed issues:

• Can't reduce FieldTimeSeries with non-default indices (#2424)

Merged pull requests:

• FFT-based preconditioner for immersed rectilinear grids (#2412) (@glwagner)
• Proper reductions for FieldTimeSeries (#2425) (@glwagner)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - v0.73.7

Oceananigans v0.73.7

Diff since v0.73.6

Closed issues:

• Error while using ImmersedBoundaries on GPU (#2367)

Merged pull requests:

• Fix bug showing AbstractOperations (#2414) (@glwagner)
• Updates Benchmarks environment (#2417) (@glwagner)
• Some backward compatibility for FieldTimeSeries (#2419) (@glwagner)
• Bickley jet, continued (#2420) (@glwagner)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - v0.73.6

Oceananigans v0.73.6

Diff since v0.73.5

Closed issues:

• Bug in showing empty NamedTuple (#2398)

Merged pull requests:

• Implements RiBasedVerticalDiffusivity (#2379) (@glwagner)
• fix the show for nonhydrostatic model (#2399) (@simone-silvestri)
• Bug in vertical WENO topological conditional flux (#2400) (@simone-silvestri)
• Fancy show for NamedTuple of Field without being a type pirate (#2401) (@glwagner)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - v0.73.5

Oceananigans v0.73.5

Diff since v0.73.4

Closed issues:

• Fields() throws an error when indices keyword is used (#2391)

Merged pull requests:

• Fixes and tests Field(u::Field; indices) and Field(u::AbstractOperation; indices) (#2392) (@tomchor)
• Adds a paper that uses Oceananigans in Docs (#2393) (@navidcy)
• On architecture for immersed boundary (#2394) (@simone-silvestri)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - v0.73.4

Oceananigans v0.73.4

Diff since v0.73.3

Closed issues:

• Adding a Background field to Langmuir Turbulence example (#2382)

Merged pull requests:

• Adds Rossby Haurwitz and Spherical Bickley jet examples (#1570) (@sandreza)
• High order vector invariant advection (#2317) (@simone-silvestri)
• Update architecture in distributed benchmark scripts (#2338) (@johnryantaylor)
• Return field from compute!(field::ReducedComputedField) (#2380) (@glwagner)
• Number all equations in Docs/Timestepping section (#2381) (@navidcy)
• Improve Reduction docstring (#2387) (@glwagner)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - 🧀 v0.73.3

Oceananigans v0.73.3

Diff since v0.73.2

Merged pull requests:

• Fewer warnings from output writers (#2375) (@glwagner)
• Fix docstring alignment (#2376) (@navidcy)
• Fix bug for vertically-implicit diffusion with multiple vertically-implicit closures (#2377) (@glwagner)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - 🫑 v0.73.2

Oceananigans v0.73.2

Diff since v0.73.1

Closed issues:

• Output error messages to a file? (#2363)
• Better/more concise show() for reduction of binary operation? (#2364)

Merged pull requests:

• Add show for Reductions (#2365) (@navidcy)
• Denote which coordinate is lat and which is lon in show(io, ::LatitudeLongitudeGrid) (#2370) (@navidcy)
• Fix docstrings in OutputReaders module (#2373) (@navidcy)
• Update dissipation and surface TKE flux parameters for CATKE (#2374) (@glwagner)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - 🥓 v0.73.1

Oceananigans v0.73.1

Diff since v0.73.0

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)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - 🥕 v0.73.0

Oceananigans v0.73.0

Diff since v0.72.4

Closed issues:

• Possible inconsistency in the eddy definition of diffusivities/closures in the docs (#1277)
• Cleaning up TurbulenceClosures (especially those for large eddy simulation) (#1381)
• Can't use a function for ScalarDiffusivity while running on GPU? (#2359)

Merged pull requests:

• Better subtyping of AbstractScalarDiffusivity and misc TurbulenceClosures cleanup (#2295) (@glwagner)
• Update README to use latest syntax (#2357) (@navidcy)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - 🥨 v0.72.4

Oceananigans v0.72.4

Diff since v0.72.3

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 Turbulence Closure (#2337)

Merged pull requests:

• Serialize grids with CPU architecture (#2346) (@glwagner)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - 🥝 v0.72.3

Oceananigans v0.72.3

Diff since v0.72.2

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - 🥥 v0.72.2

Oceananigans v0.72.2

Diff since v0.72.1

Closed issues:

• GPU timestep tests are taking too long (#2325)

Merged pull requests:

• Adds a tilted bottom boundary layer validation example (#1498) (@tomchor)
• A more detailed session for installation instructions (#2312) (@tomchor)
• Split timestep tests (#2324) (@navidcy)
• Better show() method + fix docstring for convective adjustment (#2331) (@navidcy)
• CATKE becomes friendlier with Convective Adjustment (#2332) (@navidcy)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - 🪲 v0.72.1

Oceananigans v0.72.1

Diff since v0.72.0

Merged pull requests:

• Adds methods to make CATKE work better with other closures (#2328) (@navidcy)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - v0.72.0

Oceananigans v0.72.0

Diff since v0.71.6

Closed issues:

• Better documentation for diagnostics and abstract operations (#658)
• Convenience args for FieldSlicer (#1080)
• Add "scripting tips" section to the documentation? (#1127)
• Support interior(f, i, j, k) to create custom views into parent(f) with correct indexing (#1647)
• Reductions and broadcasting over AbstractOperations require 4-5x invocations to avoid recompilation on GPU and CPU (#2024)
• Index for Reduced fields (#2177)
• Reduntant Clock constructor? (#2323)

Merged pull requests:

• Field.indices for windowed output, reductions, diagnostics, and post-processing (#2246) (@glwagner)
• Quarter degree near global simulation (#2298) (@simone-silvestri)
• Update Docs authors (#2310) (@navidcy)
• Upgrade NCDatasets to 0.12 (#2313) (@github-actions[bot])
• Update Docs/Simulation tips (#2316) (@navidcy)
• Enhances docstrings for timesteppers (#2322) (@navidcy)
• Bump to 0.72.0 (#2327) (@glwagner)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - 🪰 v0.71.6

Oceananigans v0.71.6

Diff since v0.71.5

Merged pull requests:

• Fix inconsistent variable definition in ScalarDiffusivity constructor (#2288) (@navidcy)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - ♨️ v0.71.5

Oceananigans v0.71.5

Diff since v0.71.4

Closed issues:

• Use verbose names in LinearEquationOfState (#453)
• Typo in stratified Couette flow verification experiment (#597)
• Type checking of simulation.Δt should be done via dispatch (#724)
• We could get rid of some floating point rounding artifacts in grid ranges (#824)
• More user-friendly JLD2OutputWriter (#963)
• Potential performance improvement for upwind schemes (#987)
• A more chatty, more friendly Oceananigans (#1013)
• TendencyTermField (or something like it) for diagnosing exact tendency terms and fluxes (#1073)
• Use DataDeps.jl and store regression data outside of the repository? (#1086)
• Stop documenting types and only docstring constructors. (#1134)
• Implement Wicker and Skamarock (2002) advection schemes? (#1145)
• TimeStepWizard docs are incorrect (#1166)
• Pretty printing for named tuples of fields (#1256)
• "Biharmonic" diffusivity is a misnomer and docs are incorrect (#1279)
• Initial and boundary condition setting for a channel flow along y-direction (#1294)
• Linear Stability Calculator for ShallowWaterModel (#1310)
• add norm to supported functions (#1479)
• MultiCPU or MPI_CPU (#1502)
• Normalizing different Grids (#1506)
• Can AbstractOperations convert functions to FunctionField? (#1538)
• User interface for specifying stretched coordinates and curvilinear grids (#1551)
• set!() using function fails in Julia 1.6 GPU (#1555)
• Using BackgroundField is slower than I expected (#1564)
• Error while implementing Vertical stretched grid (#1571)
• Using vertically stretched grid with horizontal biharmonic diffusion (#1574)
• Should interior(field) return a view into parent(field)? (#1610)
• Combined ENO and WENO interpolation for "true" high-order advection stencils (#1705)
• RegularLatitudeLongitudeGrid topologies (#1823)
• Refactor examples to use FieldTimeSeries (#1871)
• Split-Explicit scheme for HydrostaticFreeSurfaceModel (#2012)
• Switching off non - required equations (#2046)
• Local definition of area sometimes is Δx? (#2285)
• Horizontal diffusivities seems to not work when one of horizontal dimensions is Flat (#2286)
• z_viscosity is wrong for HorizontalScalarDiffusivity (#2291)

Merged pull requests:

• Fix missing tracer equation reference in Docs (#2280) (@navidcy)
• Small adjustment to Turbulence Closures section of docs (#2283) (@tomchor)
• Fix bug for horizontal diffusivity with Flat horizontal dimension + updates baroclinic adjustment validation script (#2284) (@navidcy)
• Update turbulence closures Docs section (#2287) (@navidcy)
• Better local variable name: area -> grid_metric (#2289) (@navidcy)
• Use verbose names in LinearEquationOfState (#2294) (@glwagner)
• Update friction velocity definition in stratified_couette_flow.jl (#2296) (@glwagner)
• Updates docstring for LatitudeLongitudeGrid (#2297) (@glwagner)
• Add show method for FieldTuple (#2299) (@glwagner)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - 🔆 v0.71.4

Oceananigans v0.71.4

Diff since v0.71.3

Merged pull requests:

• Improve miscellaneous show and summary (#2274) (@glwagner)
• Downbump to 0.71.4 (#2279) (@glwagner)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - ♛ v0.71.3

Oceananigans v0.71.3

Diff since v0.71.2

Closed issues:

• Is there a better word than isotropy to use for the new ScalarDiffusivity? (#2261)
• Explicit/Implicit names for time-discretizations are a bit vague? (#2264)
• Update on CATKE default parameter values? (#2272)

Merged pull requests:

• Initialize schedules at iteration 0 (#2268) (@glwagner)
• CATKE with an improved model for shear-driven mixing (#2273) (@glwagner)
• Changes to scalar (normal and biharmonic) diffusivity (#2276) (@simone-silvestri)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - ∰ v0.71.2

Oceananigans v0.71.2

Diff since v0.71.1

Closed issues:

• Euler time-stepping in the QuasiAdamsBashforth2TimeStepper is buggy --- a NaN will persist! (#2259)
• Is it worth considering a more general way to define the directions of ScalarDiffusivirty closures? (#2265)

Merged pull requests:

• Fix bug in QuasiAdamsBashforth2TimeStepper (#2260) (@navidcy)
• Adds a sentence to the Anisotropic diffusivity section of the docs (#2262) (@tomchor)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - ∯ v0.71.1

Oceananigans v0.71.1

Diff since v0.71.0

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - ✎ v0.71.0

Oceananigans v0.71.0

Diff since v0.70.5

Closed issues:

• Replace AnisotropicDiffusivity and AnisotropicBiharmonicDiffusivity with their curvilinear-friendly counterparts (#2113)
• TurbulenceClosures consolidation of diffusivities (#2239)
• Define Fields on immersed grids or underlying grids? (#2250)

Merged pull requests:

• Diffusivity refactor (#2247) (@simone-silvestri)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - 🪗 v0.70.5

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - 👔 v0.70.4

Oceananigans v0.70.4

Diff since v0.70.3

Merged pull requests:

• Subtle reformulation of CATKEVerticalDiffusivity (#2232) (@glwagner)
• Minor change to Ocean mixing and convection example (#2238) (@tomchor)
• Adds a paper using Oceanigans in docs (#2241) (@navidcy)
• Deploy docs with forcepush = true (#2243) (@navidcy)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - 👼 v0.70.3

Oceananigans v0.70.3

Diff since v0.70.2

Closed issues:

• CATKE with NonHydrostaticModel (#2229)

Merged pull requests:

• Fixes CATKE-in-a-tuple implementation and adds tests (#2225) (@glwagner)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - 🎹 v0.70.2

Oceananigans v0.70.2

Diff since v0.70.1

Merged pull requests:

• Saves actual solver_method name in ImplicitFreeSurface (not just :Default) (#2212) (@navidcy)
• Updates models' docstrings (#2230) (@navidcy)
• Adds longform option to prettytime (#2231) (@glwagner)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - 🥾 v0.70.1

Oceananigans v0.70.1

Diff since v0.70.0

Closed issues:

• Restarting a simulation using run!(simulation, pickup=true) fails for a HydrostaticFreeSurfaceModel (#2223)

Merged pull requests:

• Tries to generalize checkpointer to work for HydrostaticFreeSurfaceModel (#2224) (@glwagner)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - v0.70.0

Oceananigans v0.70.0

Diff since v0.69.5

Closed issues:

• Conditional fluxes for Biharmonic operator and Immersed Boundaries (#2209)

Merged pull requests:

• 3D spacing and derivatives (#2214) (@simone-silvestri)
• Bump version (#2221) (@simone-silvestri)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - 🚧 v0.69.5

Oceananigans v0.69.5

Diff since v0.69.4

Closed issues:

• Making options for NetCDF and JLD2 output writers more unified (#2217)

Merged pull requests:

• Fixes FFT solver constructor for an ensemble of slice models (#2220) (@glwagner)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - 🧸 v0.69.4

Oceananigans v0.69.4

Diff since v0.69.3

Closed issues:

• Derivatives and interpolation of ComputedFields is incorrect on boundaries (#1130)
• Oceananigans.short_show should really extend Base.summary (#1986)

Merged pull requests:

• Support for tuples with arrays of closures (#2215) (@glwagner)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - 🦿 v0.69.3

Oceananigans v0.69.3

Diff since v0.69.2

Closed issues:

• User interface to ConditionalOperand (#2188)
• Bug in show for column Hydrostatic models (#2210)

Merged pull requests:

• Changes to ConditionalOperation (#2200) (@simone-silvestri)
• quick fixes (#2201) (@simone-silvestri)
• Docstrings + bit of code formatting (#2203) (@navidcy)
• Generalize interpolate(field, x, y, z) (#2204) (@glwagner)
• Include diffusive_cfl in TimeStepWizard's docstring (#2205) (@tomchor)
• More fixes in docstrings (#2206) (@navidcy)
• Some operators needed for biharmonic diffusivity (#2207) (@simone-silvestri)
• Add show method for CATKE closure (#2208) (@navidcy)
• Only show free surface info when there is a free surface (#2211) (@navidcy)
• Fixes bug in TimeStepWizard's diffusive timescale calculation (#2213) (@tomchor)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - 🛍 v0.69.2

Oceananigans v0.69.2

Diff since v0.69.1

Closed issues:

• Averaging field when grid is stretched doesn't always work (#2189)
• Show free surface solver method in show(::IO, ::HydrostaticFreeSurfaceModels)? (#2197)

Merged pull requests:

• Defines more area and volume calculations in Operations (#2190) (@tomchor)
• Show free surface method/solver for HydrostaticFreeSurfaceModels (#2199) (@navidcy)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - 🚰 v0.69.1

Oceananigans v0.69.1

Diff since v0.69.0

Closed issues:

• regrid! is (a bit) more general than it advertises (#2194)

Merged pull requests:

• Update docs/docstrings (#2195) (@navidcy)
• Fixes FreeSurface constructor for SingleColumnGrid and adds a test (#2196) (@glwagner)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] about 3 years ago

Oceananigans.jl - 🥔 v0.69.0

Oceananigans v0.69.0

Diff since v0.68.7

Closed issues:

• Poisson solver tests on GPU still take too long (#2183)
• Mean of stretched dimension using WindowedSpatialAverage (#2185)

Merged pull requests:

• Split poisson solver tests (#2187) (@navidcy)
• Removes WindowedSpatialAverage (#2193) (@tomchor)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] over 3 years ago

Oceananigans.jl - 🪑 v0.68.7

Oceananigans v0.68.7

Diff since v0.68.6

Closed issues:

• Should the free_surface.implicit_step_solver.right_hand_side be a vector in HydrostaticFreeSurfaceModel with a matrix solver? (#2184)

Merged pull requests:

• Adds Split-Explicit to HydrostaticFreeSurfaceModel (#2013) (@sandreza)
• CompatHelper: bump compat for PencilFFTs to 0.13, (keep existing compat) (#2178) (@github-actions[bot])
• Cleanup in the implicit free surface tests + add matrix_implicit_free_surface_solver_tests (#2181) (@navidcy)
• Bump to 0.68.7 (#2182) (@navidcy)
• Change regridding criterion to check field size rather than grid size (#2186) (@glwagner)

Hydrosphere - Ocean Models - Julia
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Oceananigans.jl - 📬 v0.68.6

Oceananigans v0.68.6

Diff since v0.68.5

Closed issues:

• Should vertical spacings Δzᵃᵃᶜ and Δzᵃᵃᶠ depend on horizontal location? (#2049)
• bug in vertically implicit diffusion solver ? (#2065)
• Vertically-implicit diffusion needs to know about field location (or whether field is momentum or tracer) (#2116)
• Do we need Ax, Ay, Az and volume from Operators.jl? (#2158)

Merged pull requests:

• Fixes for implicit vertical diffusion with immersed boundaries (#2097) (@glwagner)
• Update packages (#2175) (@navidcy)

Hydrosphere - Ocean Models - Julia
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Oceananigans.jl - 🌐 v0.68.5

Oceananigans v0.68.5

Diff since v0.68.4

Closed issues:

• Refactor regrid! so that it works with non-flat x and y dimensions? (#2067)

Merged pull requests:

• Let regridding work on non-SingleColumnGrid + better total_length on Flat grids (#2174) (@glwagner)

Hydrosphere - Ocean Models - Julia
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Oceananigans.jl - 🧄 v0.68.4

Oceananigans v0.68.4

Diff since v0.68.3

Merged pull requests:

• Fixes bug inferring regular dimensions for Average (#2173) (@glwagner)

Hydrosphere - Ocean Models - Julia
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Oceananigans.jl - 👜 v0.68.3

Oceananigans v0.68.3

Diff since v0.68.2

Closed issues:

• Check boundary condition arrays are CuArrays if arch=GPU (#419)
• Differing syntax for output writers (#500)
• Method / abstraction for outputting timeseries (#502)
• Implicit time-stepping for diffusion? (#587)
• Sharing turbulence closures between compressible and incompressible models (#654)
• Easy to mess up when setting boundary conditions via model constructor (#721)
• Validation test: Abernathey et al 2011 (#774)
• Check for 'invalid' boundary conditions (#890)
• The all-knowing TimeStepWizard (#1087)
• Redesigning Simulation and run! (#1138)
• Use time index for JLD2OutputWriter instead of the iteration number? (#1491)
• One stop shop: Oceananigans.DataAnalysis through abstract operations (#1493)
• Immersed boundaries for tracers (#1548)
• More concise show(field::Field) that prints data (like show(a::Array)?) (#1612)
• Should we do something about exponentiation with Int64? (#1832)
• Horizontal convection with VerticallyStretchedRectilinearGrid (#1872)
• About unstructured grids (#1899)
• 7-10x performance difference between 2D models in "xy" versus "xz" (#1919)
• HydrostaticFreeSurfaceModel does not enforce halo correctness (#2041)
• Fixing AveragedField and implementing IntegratedField using GridMetricOperation (#2051)
• Using Base.summary instead of short_show and better show for grids and fields (#2064)
• Do we really need AbstractCPUArchitecture? (#2072)
• Should we have models infer the architecture from the grid? (#2089)
• Add parameters to Callback (#2127)
• Conflict betweenCUDA.device and Oceananigans.Architectures.device (#2159)

Merged pull requests:

• More support for broadcasting to reduced fields (#2157) (@glwagner)
• Resolves conflict between CUDA.device and Oceananigans.Architectures.device (#2160) (@navidcy)
• Overhauls show and summary (#2161) (@glwagner)
• Add parameters to Callback (#2162) (@glwagner)
• Validate boundary conditions on Fields (#2163) (@glwagner)
• Change TMPDIR for CPU initialization on tartarus (#2164) (@glwagner)
• Update examples in README (#2168) (@navidcy)
• Rehabilitating validation/cubed_sphere_eddying_aquaplanet (#2170) (@christophernhill)
• OneField, ConstantField, and generalized ZeroField (#2171) (@glwagner)
• Bump to 0.68.3 (#2172) (@glwagner)

Hydrosphere - Ocean Models - Julia
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Oceananigans.jl - 🍧 v0.68.2

Oceananigans v0.68.2

Diff since v0.68.1

Merged pull requests:

• Implements a ConsecutiveIterations schedule (#2100) (@glwagner)
• Adds a correct simplified Inverse preconditioner (#2141) (@simone-silvestri)
• Small fix for single column model mode (#2152) (@glwagner)
• Cleans examples/shallow_water_Bickley_jet.jl (#2153) (@tomchor)
• Fixes BuoyancyField when isnothing(model.buoyancy) (#2155) (@glwagner)

Hydrosphere - Ocean Models - Julia
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Oceananigans.jl - 📿 v0.68.1

Oceananigans v0.68.1

Diff since v0.68.0

Closed issues:

• halo_size definition duplicated (#2129)
• Return statement in a test seems incomplete (#2135)
• GPU tests take way too long (#2139)

Merged pull requests:

• Removes architecture from ShallowWaterModel docstring (#2128) (@aramirezreyes)
• Fix compat annotation in Docs (#2132) (@ErikQQY)
• Fix return statement in test_matrix_poisson_solver.jl (#2137) (@navidcy)
• Use julia 1.6.5 (#2138) (@navidcy)
• Bugfix in reset!(sim) for AB2 timesteppers (#2147) (@glwagner)
• Split tests into smaller bits and pieces (take #2) (#2151) (@navidcy)

Hydrosphere - Ocean Models - Julia
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Oceananigans.jl - 🩳 v0.68.0

Oceananigans v0.68.0

Diff since v0.67.1

Closed issues:

• Coalescing Field definitions (#2052)
• Error if using too low julia version? (#2142)
• Why is simulation.stop_iteration not an integer? (#2144)

Merged pull requests:

• Matrix based implicit solver (#2105) (@simone-silvestri)
• Field major refactor: one Field to rule them all (#2121) (@glwagner)
• Add possible option to test with one file (#2122) (@christophernhill)
• CompatHelper: add new compat entry for IterativeSolvers at version 0.9, (keep existing compat) (#2123) (@github-actions[bot])
• CompatHelper: add new compat entry for IncompleteLU at version 0.2, (keep existing compat) (#2124) (@github-actions[bot])
• Print integer version of stop_iteration if value less than Inf (#2145) (@navidcy)
• Bug fix in stretched grid! (#2150) (@simone-silvestri)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] over 3 years ago

Oceananigans.jl - ✍🏽 v0.67.1

Oceananigans v0.67.1

Diff since v0.67.0

Closed issues:

• HydrostaticModel should do something if the halo is too small (#2106)
• Remove warning from HydrostaticFreeSurfaceModel? (#2111)
• length(grid::AbstractGrid) is unlike any other Base.length + some stray grid utils (#2115)

Merged pull requests:

• Check that grid halo is sufficiently large in HydrostaticFreeSurfaceModel constructor (#2108) (@glwagner)
• Removes warning from HydrostaticFreeSurfaceModel (#2112) (@navidcy)
• Remove length(::AbstractGrid) and tidies up grid-related utility functions (#2119) (@navidcy)
• Bump to 0.67.1 (#2120) (@glwagner)

Hydrosphere - Ocean Models - Julia
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Oceananigans.jl - 🏛️ v0.67.0

Oceananigans v0.67.0

Diff since v0.66.3

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_boundary_conditions_integration.jl? (#2091)
• Avoid updating hydrostatic pressure for Flat z dimensions (#2092)
• WENO5 is very different from other advection schemes (#2098)
• Method overwritten errors (#2102)
• Evaluation of ∇ ⋅ (H ∇η) for the implicit free surface conjugate gradient solver is incorrect with immersed boundaries (#2109)

Merged pull requests:

• "Near-global" latitude longitude realistic ocean setup (#2023) (@glwagner)
• from Architectures to Grids to Models (#2078) (@simone-silvestri)
• Allow NaNChecker.erroring (#2087) (@glwagner)
• AllSchedule for combining scheduling criteria and avoiding checkpointing with NaNs (#2088) (@glwagner)
• Avoid computing hydrostatic pressure when z is Flat (#2093) (@navidcy)
• a little change to run checkpointers with IBG (#2094) (@simone-silvestri)
• Add Solvers docstrings in Docs/Library + better docstring for ImplicitFreeSurface (#2096) (@navidcy)
• More tests for boundary conditions (#2103) (@navidcy)
• Remove duplicate size method redefinitions (#2104) (@navidcy)
• Quality-of-life improvement for grid constructors (#2110) (@glwagner)
• Even clearer show(io, ::AbstractGrid) (#2114) (@navidcy)
• Bump to 0.67.0 (#2117) (@glwagner)
• More useful defaults for TimeStepWizard (#2118) (@glwagner)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] over 3 years ago

Oceananigans.jl - 🧢 v0.66.3

Oceananigans v0.66.3

Diff since v0.66.2

Closed issues:

• Gent-McWilliams mesoscale eddy flux parameterization (#1492)
• Implementing a tensor diffusivity rotated into the isopycnal coordinate frame (#1972)

Merged pull requests:

• IsopycnalSkewSymmetricDiffusivity Closure (#1994) (@navidcy)
• Makes FieldBoundaryConditions mutable (#2063) (@glwagner)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] over 3 years ago

Oceananigans.jl - 🪲 v0.66.2

Oceananigans v0.66.2

Diff since v0.66.1

Closed issues:

• Weighted WENO stencils for stretched grids (#1704)
• Default tracers and buoyancy model for NonhydrostaticModel (#1984)
• A stray true? (#2027)
• Fill halo regions for PrescribedVelocityFields in HydrostaticFreeSurfaceModel (#2061)
• Warnings regarding Diagnostics.error_if_nan_in_field (#2068)
• Distributed Poisson Solver (#2074)
• RectilinearGrid broken? (#2077)
• Use Doctest filtering in doctests (#2080)

Merged pull requests:

• Changes default buoyancy model and tracers for nonhydrostatic model (#1989) (@tomchor)
• Stretched WENO and general improvement of WENO infrastructure (#2060) (@simone-silvestri)
• Fill halos when the prescribed velocity field is AbstractDataField (#2062) (@glwagner)
• Add regrid! in Docs (#2066) (@navidcy)
• Update Oceananigans.CubedSpheres to correctly import error_if_nan_in_field (#2069) (@navidcy)
• Remove GLMakie from docs/Project.toml (#2070) (@navidcy)
• Fix NaNChecker for cubed sphere (#2071) (@navidcy)
• Use Julia v1.6.4 in CI (#2075) (@navidcy)
• Fix SeawaterBuoyancy docstring (#2076) (@navidcy)
• small bug fix in Distributed Poisson Solver (#2079) (@simone-silvestri)
• Better alignment for show(io, ::AbstractGrid) (#2081) (@navidcy)
• Enhance docstrings + add models & modules in Docs/Appendix/Library (#2082) (@navidcy)
• Fix WENO5 doctest (#2083) (@navidcy)
• Stores run_wall_time in seconds and fixes bug (#2084) (@tomchor)
• More docstrings (#2085) (@navidcy)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] over 3 years ago

Oceananigans.jl - 😶‍🌫️ v0.66.1

Oceananigans v0.66.1

Diff since v0.66.0

• Converts all simulation stop criteria to callbacks, including NaNChecker (NaNChecker no longer throws an error)

Merged pull requests:

• Convert stop criteria to callbacks (#2048) (@glwagner)

Hydrosphere - Ocean Models - Julia
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Oceananigans.jl - ⚙️ v0.66.0

Oceananigans v0.66.0

Diff since v0.65.0

Merged pull requests:

• Eliminate VerticallyStretched and Regular RectilinearGrid (#2050) (@simone-silvestri)
• Some initial bits for tracer cell face vertical integrals (#2055) (@christophernhill)
• Add ConvectiveAdjustmentVerticalDiffusivity in Docs (#2056) (@navidcy)
• Minor enhancement to ocean mixing example (#2057) (@navidcy)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] over 3 years ago

Oceananigans.jl - 🐫 v0.65.0

Oceananigans v0.65.0

Diff since v0.64.1

• Generalizes RegularLatitudeLongitudeGrid to a LatitudeLongitudeGrid that is optionally stretched in any direction

Closed issues:

• Go back to more complex VerticallyStretchedGrid for ocean mixing example (#2043)

Merged pull requests:

• General Latitude Longitude grid with precomputed metrics (#2025) (@simone-silvestri)
• Some more master -> main renamings (#2044) (@navidcy)
• Changes vertical stretching function back in Ocean wind + convection example (#2045) (@tomchor)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] over 3 years ago

Oceananigans.jl - 🛖 v0.64.1

Oceananigans v0.64.1

Diff since v0.64.0

• Optimized and fixed algorithm for fill_halo_regions! via #2035. Previously, halos will filled simultaneously. Now they are filled serially, and periodic halos are filled last. In addition, periodic and flux halo filling for opposite sides are combined into a single kernel, reducing kernel launch overhead.

Closed issues:

• Increase ≈ tolerance to account for differences across GPU microarchitectures (#1179)
• Package description - oceanic library (#2017)

Merged pull requests:

• Halo optimization and solving the race condition on corner nodes (#2035) (@simone-silvestri)
• Complete implementation of HydrostaticFreeSurfaceModel regression test (#2036) (@glwagner)
• Bump to 0.64.1 (#2042) (@glwagner)

Hydrosphere - Ocean Models - Julia
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Oceananigans.jl - v0.64.0

Oceananigans v0.64.0

Diff since v0.63.4

Merged pull requests:

• New Simulation API: more callbacks, less "progress" (#1971) (@glwagner)
• Updates simulation tips (#2029) (@tomchor)
• Regression test for Hydrostatic free surface model (#2031) (@simone-silvestri)
• Bump down to 0.64.0 (#2038) (@glwagner)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] over 3 years ago

Oceananigans.jl - 🔧 v0.63.4

Oceananigans v0.63.4

Diff since v0.63.3

Merged pull requests:

• Fixes grid equality for GPUs (#2030) (@tomchor)
• Adding regression test to lat-lon grid (#2032) (@simone-silvestri)

Hydrosphere - Ocean Models - Julia
Published by github-actions[bot] over 3 years ago