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Published 20 hours ago • verified publisher icon CliMA

Add internal tide example in Docs

Open navidcy opened this issue 2 years ago • 22 comments

This is a simple example with immersed boundary.

https://github.com/CliMA/Oceananigans.jl/assets/7112768/b225a647-7f21-4dcc-8b12-1ae9d662d106

navidcy avatar Jun 03 '23 23:06 navidcy

This PR requires #3094. At the moment it includes the changes there but ideally we want to conclude the discussion in #3094 and merge that one before this.

Or perhaps use the split-explicit free surface?

navidcy avatar Jun 03 '23 23:06 navidcy

cc @djlikesdjs

navidcy avatar Jun 03 '23 23:06 navidcy

@navidcy can you please include the link to the docs preview page so that we see how it looks before approving?

tomchor avatar Jun 04 '23 00:06 tomchor

Could you build the docs locally?

Comment out all examples here https://github.com/CliMA/Oceananigans.jl/blob/72a2399394d60fa22d77dc51822d6175ffcf07e3/docs/make.jl#L30-L43 except the tide one and run:

$ rm -rf docs/build; rm -rf docs/src/generated; julia --project -e 'using Pkg; Pkg.instantiate()'; julia --project=docs/ -e 'using Pkg; Pkg.precompile()'; JULIA_DEBUG=Documenter julia --project=docs/ docs/make.jl

and then open, e.g., docs/build/generated/barotropic_tide.html.

If you even change https://github.com/CliMA/Oceananigans.jl/blob/72a2399394d60fa22d77dc51822d6175ffcf07e3/docs/make.jl#L141-L151 to doctest = false, strict = false and checkdocs = :none, it'll speed things even more.

(It took ~8 mins on my laptop.)

navidcy avatar Jun 04 '23 00:06 navidcy

Could you build the docs locally?

I know how to do it, but I didn't try. I thought the best practice was to set push_preview=true temporarily for docs changes like this one as per your first comment in https://github.com/CliMA/Oceananigans.jl/pull/2870.

But fair enough. I'll build and view them locally for review.

tomchor avatar Jun 04 '23 18:06 tomchor

Could you build the docs locally?

I know how do it, but I didn't try. I thought the best practice was to set push_preview=true temporarily for docs changes like this one as per your first comment in #2870.

But fair enough. I'll build and view them locally for review.

Thanks. It's quite cumbersome to delete the previews from the OceananigansDocumentation branch and thus I'm very reluctant doing it. Sorry :(

navidcy avatar Jun 04 '23 19:06 navidcy

So I tried with SplitExplicit and 1) it's much faster but 2) I see this very fast motion in the beginning...

Compare this

https://github.com/CliMA/Oceananigans.jl/assets/7112768/b098f251-0880-4ead-8f71-a3a5282540d4

with the animation at the top of this PR.

I suppose it's the gravity waves... Are they implicitly filtered out with the implicit free surface solver at the top?

navidcy avatar Jun 04 '23 22:06 navidcy

I think it would be clearer to call this "internal tide" or "barotropic tide over seamount". The point is not the barotropic tide, the point is to showcase the generation of internal waves.

glwagner avatar Jun 04 '23 22:06 glwagner

Agree! "Barotropic tide over seamount" is a good title or "Internal tide generation from seamount"

navidcy avatar Jun 04 '23 22:06 navidcy

So I tried with SplitExplicit and 1) it's much faster but 2) I see this very fast motion in the beginning...

Compare this

barotropic_tide_splitexplicit.mp4 with the animation at the top of this PR.

I suppose it's the gravity waves... Are they implicitly filtered out with the implicit free surface solver at the top?

Yeah, the implicit solver diffuses out all the gravity waves while the split explicit "resolves" them. You can also check out the validation case in validation/implicit_free_surface/geostrophic_adjustment_test.jl that shows quite some difference in the dynamics using the implicit solver vs split explicit solver

simone-silvestri avatar Jun 04 '23 22:06 simone-silvestri

Just for the future I think adding an example is a big deal so I think it might be best to discuss such an addition on an issue before submitting a PR.

glwagner avatar Jun 04 '23 23:06 glwagner

We can delete this validation test too after this: https://github.com/CliMA/Oceananigans.jl/blob/main/validation/immersed_boundaries/internal_tide.jl

glwagner avatar Jun 04 '23 23:06 glwagner

Just for the future I think adding an example is a big deal so I think it might be best to discuss such an addition on an issue before submitting a PR.

Gotcha!

But also happy to close the PR! I had made this example for a demo and I thought it might be useful.

navidcy avatar Jun 04 '23 23:06 navidcy

Just for the future I think adding an example is a big deal so I think it might be best to discuss such an addition on an issue before submitting a PR.

Gotcha!

But also happy to close the PR! I had made this example for a demo and I thought it might be useful.

I think we need more examples with immersed boundaries which was part of our motivation for doing the double gyre with bathymetry with @siddharthabishnu right? I was just also under the impression that we wanted to limit examples to keep the docs build relatively fast. (Or at least, until we had solved the problem with glacially slow docs builds, then we could afford to add more.) Maybe that has changed though, I'm not keeping track of the time it takes to build docs. It used to be 3h.

glwagner avatar Jun 04 '23 23:06 glwagner

Just for the future I think adding an example is a big deal so I think it might be best to discuss such an addition on an issue before submitting a PR.

Gotcha! But also happy to close the PR! I had made this example for a demo and I thought it might be useful.

I think we need more examples with immersed boundaries which was part of our motivation for doing the double gyre with bathymetry with @siddharthabishnu right? I was just also under the impression that we wanted to limit examples to keep the docs build relatively fast. (Or at least, until we had solved the problem with glacially slow docs builds, then we could afford to add more.) Maybe that has changed though, I'm not keeping track of the time it takes to build docs. It used to be 3h.

It's still 3hrs... :(

Recently there was some suggestions in slack about parallelizing the run of the examples in the doc built but I haven't tried it yet.

navidcy avatar Jun 04 '23 23:06 navidcy

Now animation looks like:

https://github.com/CliMA/Oceananigans.jl/assets/7112768/ddd57896-ae0d-45d1-a1f0-ac9b4bcb82f5

navidcy avatar Jun 05 '23 12:06 navidcy

Great example @navidcy

Do we want to mask the hill in the animations? (Especially since https://github.com/CliMA/Oceananigans.jl/pull/3092 isn't merged yet.) The top plot specifically keeps changing color where the hill is supposed to be, which might throw off some readers. This could probably be done with Makie.poly.

tomchor avatar Jun 05 '23 14:06 tomchor

Thanks!! I also find the rainbow mountain at top annoying. That’s what the mask_immersed! was trying to deal with.

navidcy avatar Jun 05 '23 19:06 navidcy

We can delete this validation test too after this: https://github.com/CliMA/Oceananigans.jl/blob/main/validation/immersed_boundaries/internal_tide.jl

The validation script includes a multi region example. Shall I still delete it? I could also clean it up and add toml files in the validation script directory (see #3076).

navidcy avatar Jun 05 '23 20:06 navidcy

We can delete this validation test too after this: https://github.com/CliMA/Oceananigans.jl/blob/main/validation/immersed_boundaries/internal_tide.jl

The validation script includes a multi region example. Shall I still delete it? I could also clean it up and add toml files in the validation script directory (see #3076).

Yeah, that's a random place for a multi region example.

glwagner avatar Jun 05 '23 21:06 glwagner

@navidcy I'm trying to add a drag flux to this example like we talked about in https://github.com/CliMA/Oceananigans.jl/issues/3148 but I'm getting an error that I can't figure out. Using u as an example, I'm trying to implement the BCs as

@inline u_drag(x, y, t, u, v, w, p) = - p.cᵈ * u * √(u^2 + v^2 + w^2)
@inline u_drag(x, y, z, t, u, v, w, cᵈ) = u_drag(x, y, t, u, v, w, cᵈ)

u_drag_bc = FluxBoundaryCondition(u_drag, field_dependencies=(:u, :v, :w), parameters=(; cᵈ=1e-3))
boundary_conditions = (u = FieldBoundaryConditions(bottom=u_drag_bc),)

but when time-stepping the model I get

ERROR: LoadError: MethodError: no method matching field_arguments(::Int64, ::Int64, ::Int64, ::ImmersedBoundaryGrid{Float64, Periodic, Flat, Bounded, RectilinearGrid{Float64, Periodic, Flat, Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, CPU}, GridFittedBottom{OffsetArrays.OffsetMatrix{Float64, Matrix{Float64}}, Oceananigans.ImmersedBoundaries.CenterImmersedCondition}, Nothing, CPU}, ::NamedTuple{(:u, :v, :w, :b, :η), Tuple{Field{Face, Center, Center, Nothing, ImmersedBoundaryGrid{Float64, Periodic, Flat, Bounded, RectilinearGrid{Float64, Periodic, Flat, Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, CPU}, GridFittedBottom{OffsetArrays.OffsetMatrix{Float64, Matrix{Float64}}, Oceananigans.ImmersedBoundaries.CenterImmersedCondition}, Nothing, CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, FieldBoundaryConditions{BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Nothing, Nothing, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Oceananigans.BoundaryConditions.ContinuousBoundaryFunction{Face, Center, Nothing, Oceananigans.BoundaryConditions.LeftBoundary, typeof(u_drag), NamedTuple{(:cᵈ,), Tuple{Float64}}, Tuple{Symbol, Symbol, Symbol}, Tuple{Int64, Int64, Nothing}, Tuple{typeof(Oceananigans.Operators.identity4), typeof(Oceananigans.Operators.ℑxyᶠᶜᵃ), typeof(Oceananigans.Operators.ℑxᶠᵃᵃ)}}}, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing}}, Field{Center, Face, Center, Nothing, ImmersedBoundaryGrid{Float64, Periodic, Flat, Bounded, RectilinearGrid{Float64, Periodic, Flat, Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, CPU}, GridFittedBottom{OffsetArrays.OffsetMatrix{Float64, Matrix{Float64}}, Oceananigans.ImmersedBoundaries.CenterImmersedCondition}, Nothing, CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, FieldBoundaryConditions{BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Nothing, Nothing, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing}}, Field{Center, Center, Face, Nothing, ImmersedBoundaryGrid{Float64, Periodic, Flat, Bounded, RectilinearGrid{Float64, Periodic, Flat, Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, CPU}, GridFittedBottom{OffsetArrays.OffsetMatrix{Float64, Matrix{Float64}}, Oceananigans.ImmersedBoundaries.CenterImmersedCondition}, Nothing, CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, FieldBoundaryConditions{BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Nothing, Nothing, Nothing, Nothing, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing}}, Field{Center, Center, Center, Nothing, ImmersedBoundaryGrid{Float64, Periodic, Flat, Bounded, RectilinearGrid{Float64, Periodic, Flat, Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, CPU}, GridFittedBottom{OffsetArrays.OffsetMatrix{Float64, Matrix{Float64}}, Oceananigans.ImmersedBoundaries.CenterImmersedCondition}, Nothing, CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, FieldBoundaryConditions{BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Nothing, Nothing, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing}}, Field{Center, Center, Face, Nothing, ImmersedBoundaryGrid{Float64, Periodic, Flat, Bounded, RectilinearGrid{Float64, Periodic, Flat, Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, CPU}, GridFittedBottom{OffsetArrays.OffsetMatrix{Float64, Matrix{Float64}}, Oceananigans.ImmersedBoundaries.CenterImmersedCondition}, Nothing, CPU}, Tuple{Colon, Colon, UnitRange{Int64}}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, FieldBoundaryConditions{BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Nothing, Nothing, Nothing, Nothing, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing}}}}, ::Tuple{typeof(Oceananigans.Operators.identity4), typeof(Oceananigans.Operators.ℑxyᶠᶜᵃ), typeof(Oceananigans.Operators.ℑxᶠᵃᵃ)}, ::Tuple{Int64, Int64, Nothing})

Closest candidates are:
  field_arguments(::Any, ::Any, ::Any, ::Any, ::Any, ::Any, ::Tuple{T, T} where T)
   @ Oceananigans ~/repos/Oceananigans.jl/src/Utils/user_function_arguments.jl:4
  field_arguments(::Any, ::Any, ::Any, ::Any, ::Any, ::Any, ::Tuple{T, T, T} where T)
   @ Oceananigans ~/repos/Oceananigans.jl/src/Utils/user_function_arguments.jl:8
  field_arguments(::Any, ::Any, ::Any, ::Any, ::Any, ::Any, ::Tuple{Any})
   @ Oceananigans ~/repos/Oceananigans.jl/src/Utils/user_function_arguments.jl:1
  ...

Stacktrace:
  [1] user_function_arguments
    @ ~/repos/Oceananigans.jl/src/Utils/user_function_arguments.jl:31 [inlined]
  [2] getbc
    @ ~/repos/Oceananigans.jl/src/BoundaryConditions/continuous_boundary_function.jl:129 [inlined]
  [3] apply_z_bottom_bc!
    @ ~/repos/Oceananigans.jl/src/BoundaryConditions/apply_flux_bcs.jl:125 [inlined]
  [4] macro expansion
    @ ~/repos/Oceananigans.jl/src/BoundaryConditions/apply_flux_bcs.jl:81 [inlined]
  [5] cpu__apply_z_bcs!
    @ ~/.julia/packages/KernelAbstractions/lhhMo/src/macros.jl:276 [inlined]
  [6] cpu__apply_z_bcs!(__ctx__::KernelAbstractions.CompilerMetadata{KernelAbstractions.NDIteration.StaticSize{(250, 1)}, KernelAbstractions.NDIteration.NoDynamicCheck, CartesianIndex{2}, Nothing, KernelAbstractions.NDIteration.NDRange{2, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, KernelAbstractions.NDIteration.StaticSize{(250, 1)}, Nothing, Nothing}}, Gc::Field{Face, Center, Center, Nothing, ImmersedBoundaryGrid{Float64, Periodic, Flat, Bounded, RectilinearGrid{Float64, Periodic, Flat, Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, CPU}, GridFittedBottom{OffsetArrays.OffsetMatrix{Float64, Matrix{Float64}}, Oceananigans.ImmersedBoundaries.CenterImmersedCondition}, Nothing, CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, FieldBoundaryConditions{BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Nothing, Nothing, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing}}, loc::Tuple{Face, Center, Center}, grid::ImmersedBoundaryGrid{Float64, Periodic, Flat, Bounded, RectilinearGrid{Float64, Periodic, Flat, Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, CPU}, GridFittedBottom{OffsetArrays.OffsetMatrix{Float64, Matrix{Float64}}, Oceananigans.ImmersedBoundaries.CenterImmersedCondition}, Nothing, CPU}, bottom_bc::BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Oceananigans.BoundaryConditions.ContinuousBoundaryFunction{Face, Center, Nothing, Oceananigans.BoundaryConditions.LeftBoundary, typeof(u_drag), NamedTuple{(:cᵈ,), Tuple{Float64}}, Tuple{Symbol, Symbol, Symbol}, Tuple{Int64, Int64, Nothing}, Tuple{typeof(Oceananigans.Operators.identity4), typeof(Oceananigans.Operators.ℑxyᶠᶜᵃ), typeof(Oceananigans.Operators.ℑxᶠᵃᵃ)}}}, top_bc::BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, args::Tuple{Clock{Float64}, NamedTuple{(:u, :v, :w, :b, :η), Tuple{Field{Face, Center, Center, Nothing, ImmersedBoundaryGrid{Float64, Periodic, Flat, Bounded, RectilinearGrid{Float64, Periodic, Flat, Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, CPU}, GridFittedBottom{OffsetArrays.OffsetMatrix{Float64, Matrix{Float64}}, Oceananigans.ImmersedBoundaries.CenterImmersedCondition}, Nothing, CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, FieldBoundaryConditions{BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Nothing, Nothing, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Oceananigans.BoundaryConditions.ContinuousBoundaryFunction{Face, Center, Nothing, Oceananigans.BoundaryConditions.LeftBoundary, typeof(u_drag), NamedTuple{(:cᵈ,), Tuple{Float64}}, Tuple{Symbol, Symbol, Symbol}, Tuple{Int64, Int64, Nothing}, Tuple{typeof(Oceananigans.Operators.identity4), typeof(Oceananigans.Operators.ℑxyᶠᶜᵃ), typeof(Oceananigans.Operators.ℑxᶠᵃᵃ)}}}, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing}}, Field{Center, Face, Center, Nothing, ImmersedBoundaryGrid{Float64, Periodic, Flat, Bounded, RectilinearGrid{Float64, Periodic, Flat, Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, CPU}, GridFittedBottom{OffsetArrays.OffsetMatrix{Float64, Matrix{Float64}}, Oceananigans.ImmersedBoundaries.CenterImmersedCondition}, Nothing, CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, FieldBoundaryConditions{BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Nothing, Nothing, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing}}, Field{Center, Center, Face, Nothing, ImmersedBoundaryGrid{Float64, Periodic, Flat, Bounded, RectilinearGrid{Float64, Periodic, Flat, Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, CPU}, GridFittedBottom{OffsetArrays.OffsetMatrix{Float64, Matrix{Float64}}, Oceananigans.ImmersedBoundaries.CenterImmersedCondition}, Nothing, CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, FieldBoundaryConditions{BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Nothing, Nothing, Nothing, Nothing, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing}}, Field{Center, Center, Center, Nothing, ImmersedBoundaryGrid{Float64, Periodic, Flat, Bounded, RectilinearGrid{Float64, Periodic, Flat, Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, CPU}, GridFittedBottom{OffsetArrays.OffsetMatrix{Float64, Matrix{Float64}}, Oceananigans.ImmersedBoundaries.CenterImmersedCondition}, Nothing, CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, FieldBoundaryConditions{BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Nothing, Nothing, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing}}, Field{Center, Center, Face, Nothing, ImmersedBoundaryGrid{Float64, Periodic, Flat, Bounded, RectilinearGrid{Float64, Periodic, Flat, Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, CPU}, GridFittedBottom{OffsetArrays.OffsetMatrix{Float64, Matrix{Float64}}, Oceananigans.ImmersedBoundaries.CenterImmersedCondition}, Nothing, CPU}, Tuple{Colon, Colon, UnitRange{Int64}}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, FieldBoundaryConditions{BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Nothing, Nothing, Nothing, Nothing, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing}}}}, Nothing, Buoyancy{BuoyancyTracer, Oceananigans.Grids.NegativeZDirection}})
    @ Oceananigans.BoundaryConditions ./none:0
  [7] __thread_run(tid::Int64, len::Int64, rem::Int64, obj::KernelAbstractions.Kernel{KernelAbstractions.CPU, KernelAbstractions.NDIteration.StaticSize{(250, 1)}, KernelAbstractions.NDIteration.StaticSize{(250, 1)}, typeof(Oceananigans.BoundaryConditions.cpu__apply_z_bcs!)}, ndrange::Nothing, iterspace::KernelAbstractions.NDIteration.NDRange{2, KernelAbstractions.NDIteration.StaticSize{(1, 1)}, KernelAbstractions.NDIteration.StaticSize{(250, 1)}, Nothing, Nothing}, args::Tuple{Field{Face, Center, Center, Nothing, ImmersedBoundaryGrid{Float64, Periodic, Flat, Bounded, RectilinearGrid{Float64, Periodic, Flat, Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, CPU}, GridFittedBottom{OffsetArrays.OffsetMatrix{Float64, Matrix{Float64}}, Oceananigans.ImmersedBoundaries.CenterImmersedCondition}, Nothing, CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, FieldBoundaryConditions{BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Nothing, Nothing, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing}}, Tuple{Face, Center, Center}, ImmersedBoundaryGrid{Float64, Periodic, Flat, Bounded, RectilinearGrid{Float64, Periodic, Flat, Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, CPU}, GridFittedBottom{OffsetArrays.OffsetMatrix{Float64, Matrix{Float64}}, Oceananigans.ImmersedBoundaries.CenterImmersedCondition}, Nothing, CPU}, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Oceananigans.BoundaryConditions.ContinuousBoundaryFunction{Face, Center, Nothing, Oceananigans.BoundaryConditions.LeftBoundary, typeof(u_drag), NamedTuple{(:cᵈ,), Tuple{Float64}}, Tuple{Symbol, Symbol, Symbol}, Tuple{Int64, Int64, Nothing}, Tuple{typeof(Oceananigans.Operators.identity4), typeof(Oceananigans.Operators.ℑxyᶠᶜᵃ), typeof(Oceananigans.Operators.ℑxᶠᵃᵃ)}}}, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, Tuple{Clock{Float64}, NamedTuple{(:u, :v, :w, :b, :η), Tuple{Field{Face, Center, Center, Nothing, ImmersedBoundaryGrid{Float64, Periodic, Flat, Bounded, RectilinearGrid{Float64, Periodic, Flat, Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, CPU}, GridFittedBottom{OffsetArrays.OffsetMatrix{Float64, Matrix{Float64}}, Oceananigans.ImmersedBoundaries.CenterImmersedCondition}, Nothing, CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, FieldBoundaryConditions{BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Nothing, Nothing, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Oceananigans.BoundaryConditions.ContinuousBoundaryFunction{Face, Center, Nothing, Oceananigans.BoundaryConditions.LeftBoundary, typeof(u_drag), NamedTuple{(:cᵈ,), Tuple{Float64}}, Tuple{Symbol, Symbol, Symbol}, Tuple{Int64, Int64, Nothing}, Tuple{typeof(Oceananigans.Operators.identity4), typeof(Oceananigans.Operators.ℑxyᶠᶜᵃ), typeof(Oceananigans.Operators.ℑxᶠᵃᵃ)}}}, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing}}, Field{Center, Face, Center, Nothing, ImmersedBoundaryGrid{Float64, Periodic, Flat, Bounded, RectilinearGrid{Float64, Periodic, Flat, Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, CPU}, GridFittedBottom{OffsetArrays.OffsetMatrix{Float64, Matrix{Float64}}, Oceananigans.ImmersedBoundaries.CenterImmersedCondition}, Nothing, CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, FieldBoundaryConditions{BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Nothing, Nothing, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing}}, Field{Center, Center, Face, Nothing, ImmersedBoundaryGrid{Float64, Periodic, Flat, Bounded, RectilinearGrid{Float64, Periodic, Flat, Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, CPU}, GridFittedBottom{OffsetArrays.OffsetMatrix{Float64, Matrix{Float64}}, Oceananigans.ImmersedBoundaries.CenterImmersedCondition}, Nothing, CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, FieldBoundaryConditions{BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Nothing, Nothing, Nothing, Nothing, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing}}, Field{Center, Center, Center, Nothing, ImmersedBoundaryGrid{Float64, Periodic, Flat, Bounded, RectilinearGrid{Float64, Periodic, Flat, Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, CPU}, GridFittedBottom{OffsetArrays.OffsetMatrix{Float64, Matrix{Float64}}, Oceananigans.ImmersedBoundaries.CenterImmersedCondition}, Nothing, CPU}, Tuple{Colon, Colon, Colon}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, FieldBoundaryConditions{BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Nothing, Nothing, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing}}, Field{Center, Center, Face, Nothing, ImmersedBoundaryGrid{Float64, Periodic, Flat, Bounded, RectilinearGrid{Float64, Periodic, Flat, Bounded, Float64, Float64, Float64, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}, OffsetArrays.OffsetVector{Float64, StepRangeLen{Float64, Base.TwicePrecision{Float64}, Base.TwicePrecision{Float64}, Int64}}, CPU}, GridFittedBottom{OffsetArrays.OffsetMatrix{Float64, Matrix{Float64}}, Oceananigans.ImmersedBoundaries.CenterImmersedCondition}, Nothing, CPU}, Tuple{Colon, Colon, UnitRange{Int64}}, OffsetArrays.OffsetArray{Float64, 3, Array{Float64, 3}}, Float64, FieldBoundaryConditions{BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, BoundaryCondition{Oceananigans.BoundaryConditions.Periodic, Nothing}, Nothing, Nothing, Nothing, Nothing, BoundaryCondition{Oceananigans.BoundaryConditions.Flux, Nothing}}, Nothing, Oceananigans.Fields.FieldBoundaryBuffers{Nothing, Nothing, Nothing, Nothing}}}}, Nothing, Buoyancy{BuoyancyTracer, Oceananigans.Grids.NegativeZDirection}}}, dynamic::KernelAbstractions.NDIteration.NoDynamicCheck)

However, if I use the same formulation on a NohydrostaticModel this works

julia> @inline u_drag(x, y, t, u, v, w, p) = - p.cᵈ * u * √(u^2 + v^2 + w^2)
u_drag (generic function with 2 methods)

julia> u_drag_bc = FluxBoundaryCondition(u_drag, field_dependencies=(:u, :v, :w), parameters=(; cᵈ=1e-3))
FluxBoundaryCondition: ContinuousBoundaryFunction u_drag at (Nothing, Nothing, Nothing)

julia> boundary_conditions = (u = FieldBoundaryConditions(bottom=u_drag_bc),);

julia> model = NonhydrostaticModel(; grid, boundary_conditions);

julia> time_step!(model, 1)

julia>

So whatever's happening probably has to do with the HydrostaticModel, which I'm really not familiar with unfortunately.

What do you prefer that I do?

tomchor avatar Aug 07 '23 04:08 tomchor

So whatever's happening probably has to do with the HydrostaticModel, which I'm really not familiar with unfortunately.

What do you prefer that I do?

the hydrostatic model does not have w as state variable... try removing w and see if all is good.

navidcy avatar Jan 16 '24 12:01 navidcy

I update the internal tide example. Let's merge this so we have an example with bathymetry in the docs?

The latest version of the movie is:

https://github.com/CliMA/Oceananigans.jl/assets/7112768/1bfdca5c-6d49-4101-9037-eadfacea6900

I'm not so sure about 979c2a7; is this a good idea?

cc @simone-silvestri, @glwagner

navidcy avatar Mar 07 '24 12:03 navidcy

Without https://github.com/CliMA/Oceananigans.jl/commit/979c2a7cd10c1f2054cad996622cafd2e3fb3ffa the movie looks like

https://github.com/CliMA/Oceananigans.jl/assets/7112768/5b199c8c-0faf-4e73-97bf-b03edd40bb25

with the mountain changing colors in the first plot. A bit annoying...

navidcy avatar Mar 07 '24 12:03 navidcy

with the mountain changing colors in the first plot. A bit annoying...

Can't we just plot a fixed-color shape on top on the mount on all panels? Makie.poly seems to be able to do that.

tomchor avatar Mar 07 '24 15:03 tomchor

Can't we just plot a fixed-color shape on top on the mount on all panels? Makie.poly seems to be able to do that.

We can.

We can also mask the output after we load it, e.g, via

using something like

using Oceananigans.ImmersedBoundaries: mask_immersed_field!

function mask_and_get_interior(φ_t, n; value=NaN)
    mask_immersed_field!(φ_t[n], value)
    return interior(φ_t[n], :, 1, :)
end

u′ₙ = @lift mask_and_get_interior(u′_t, $n)

which gives

https://github.com/CliMA/Oceananigans.jl/assets/7112768/a402bfcd-ef72-42d8-bbb9-97fb98be4fe3

But either of these solutions complicate the example a bit. Ideally, mask_immersed_field! should not be user-facing. And plotting a mountain on top of the mountain is a bit of a hack and would require a bit of explaining and justifying why we do that.

navidcy avatar Mar 07 '24 15:03 navidcy

But I wouldn't mind adding the post-processing masking step with the hope we can eliminate it when masking is enabled for OutputWriters; see https://github.com/CliMA/Oceananigans.jl/pull/3092

navidcy avatar Mar 07 '24 15:03 navidcy

I am in favor of not doing 979c2a7. It hardcodes a change in the source code that is only required for aesthetic reasons. I would wait for #3092 and in the meantime mask the output in the example

simone-silvestri avatar Mar 07 '24 15:03 simone-silvestri

I am in favor of not doing 979c2a7. It hardcodes a change in the source code that is only required for aesthetic reasons. I would wait for #3092 and in the meantime mask the output in the example

Deal, done

navidcy avatar Mar 07 '24 16:03 navidcy

The movie looks great and I'm happy to see this example coming to life!

One question I have is in the plot for stratification, at the very top. It looks like there is a black line and then there is a thin layer right below that. Anyone know what that is?

francispoulin avatar Mar 08 '24 12:03 francispoulin