CliMA/Oceananigans.jl: v0.40.0

Diff since v0.39.0

• Support for Flat dimensions. See the grid section of the model setup documentation for more details and examples.
• New advection schemes: UpwindBiasedThirdOrder and UpwindBiasedFifthOrder.
• Grid halos are automatically adjusted on model construction depending on advection scheme and turbulence closure used.
• Improved two-dimensional turbulence example.
• Fixed Langmuir turbulence example.
• Numerous bug fixes.

Closed issues:

• Only perform operations as needed depending on model dimension. (#35)
• Float32 tracer conservation test not actually Float32 (#487)
• Utilities for calculating buoyancy and density offline (#516)
• Floating point equality checking in 2D Leith (#535)
• Model not enforcing zero vertical shear at top and bottom (do we expect this?) (#540)
• Deepening mixed layer verification experiment (#547)
• NetCDFOutputWriter output does not include global attributes (#576)
• Incompressibility and pressure projection step test (#673)
• ERROR: LoadError: UndefVarError: SolutionBoundaryConditions not defined (#686)
• Cubic lattice grid with missing nodes (#743)
• An example with stable mixed layer depth? (#749)
• questions relating to Oceananigans.jl (#770)
• Possible bug in checkpointing? (#778)
• test Oceananigans returns CUDA error depsite being able to run examples on CPU and GPU (#788)
• Is any way to simulate the hydrodynamic behaviour of a bioreactor with Oceananigans.jl? (#830)
• Test failing on GPU (#882)
• Eliding differences, interpolation, and fill_halo_regions for Flat dimensions (#902)
• Stop simulation when output is NaN (#938)
• Model immediately turns to NaN after 1 time step when grid length is zero along Flat dimensions (#940)
• Model constructor should check that halos are big enough for chosen advection scheme and turbulence closure (#941)
• Bug(s) somewhere in UpwindBiasedThirdOrder left-biased interpolation functions (#986)
• Requiring Lz and Nz for two-dimensional grids is a bit counterintuitive (#1001)
• Langmuir example broken (#1004)
• Passing a Clock to restore_from_checkpoint gets overwritten by clock from checkpoint file (#1008)
• Cannot use Forcings with field_dependencies on GPU with Oceananigans v0.39.0 (#1010)

Merged pull requests:

• Fixes bug in UpwindBiasedThirdOrder advection scheme (#993) (@glwagner)
• Adds naive (non-WENO) fifth order advection scheme (#994) (@glwagner)
• Better two-dimensional turbulence Docs example (#1000) (@navidcy)
• More support for Flat dimensions (#1003) (@glwagner)
• Update langmuir_turbulence.jl (#1005) (@glwagner)
• Add Buildkite CI pipeline (#1006) (@ali-ramadhan)
• Fix bug in restore_from_checkpoint (#1009) (@ali-ramadhan)
• Adjust halos according to advection scheme and turbulence closure (#1012) (@glwagner)
• Adds adapt_structure for ContinuousForcing (#1016) (@glwagner)
• Add Dev in Docs versions menu (#1017) (@navidcy)
• Build and test but do not deploy docs on Buildkite (#1018) (@ali-ramadhan)
• Fixes tests with AveragedField and BuoyancyField (#1020) (@glwagner)
• Bump v0.40.0 (#1021) (@ali-ramadhan)