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Add biogeochemical interface to ocean_simulation #123

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Add biogeochemical interface to ocean_simulation #123

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a1fd5b9
added biogeochemistry kwarg and merge user boundary_conditions
Jul 31, 2024
fb2537b
add tracer kwarg and merge tracer_advection
Aug 1, 2024
95646da
pass through biogeochemistry
Aug 1, 2024
b51e727
try a different way to merge tracer_advection
Aug 7, 2024
7f97325
fix NamedTuple tracer_advection
Aug 7, 2024
f2a705b
if statement for boundary conditions merge
Aug 7, 2024
31b8f15
changed biogeochemistry default to nothing
Aug 7, 2024
b67ae79
Merge branch 'CliMA:main' into add-bgc
vtamsitt Aug 9, 2024
abbb510
Update src/OceanSimulations/OceanSimulations.jl
vtamsitt Aug 12, 2024
163e01a
update tracer_advection
Aug 12, 2024
b059186
boundary_conditions merge retaining defaults
Aug 16, 2024
a96b28c
Merge branch 'CliMA:main' into add-bgc
vtamsitt Aug 19, 2024
5012fb7
Merge branch 'main' into add-bgc
vtamsitt Aug 20, 2024
9cd5f7e
Merge branch 'main' into add-bgc
glwagner Aug 22, 2024
1fc667d
Merge branch 'main' into add-bgc
vtamsitt Sep 4, 2024
f1f0589
added biogeochemistry kwarg and merge user boundary_conditions
Jul 31, 2024
ba6ae1d
Merge branch 'main' into add-bgc
vtamsitt Sep 30, 2024
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15 changes: 13 additions & 2 deletions src/OceanSimulations/OceanSimulations.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,7 @@ default_tracer_advection() = TracerAdvection(WENO(; order = 7),
@inline u_immersed_bottom_drag(i, j, k, grid, clock, fields, μ) = @inbounds - μ * fields.u[i, j, k] * is_immersed_drag_u(i, j, k, grid) * spᶠᶜᶜ(i, j, k, grid, fields) / Δzᶠᶜᶜ(i, j, k, grid)
@inline v_immersed_bottom_drag(i, j, k, grid, clock, fields, μ) = @inbounds - μ * fields.v[i, j, k] * is_immersed_drag_v(i, j, k, grid) * spᶜᶠᶜ(i, j, k, grid, fields) / Δzᶜᶠᶜ(i, j, k, grid)


# TODO: Specify the grid to a grid on the sphere; otherwise we can provide a different
# function that requires latitude and longitude etc for computing coriolis=FPlane...
function ocean_simulation(grid; Δt = 5minutes,
Expand All @@ -63,6 +64,9 @@ function ocean_simulation(grid; Δt = 5minutes,
coriolis = HydrostaticSphericalCoriolis(; rotation_rate),
momentum_advection = default_momentum_advection(),
tracer_advection = default_tracer_advection(),
biogeochemistry = nothing,
tracers = (:T, :S),
boundary_conditions = NamedTuple(),
verbose = false)

# Set up boundary conditions using Field
Expand All @@ -78,6 +82,10 @@ function ocean_simulation(grid; Δt = 5minutes,
v = FieldBoundaryConditions(top = FluxBoundaryCondition(Jᵛ), bottom = v_bot_bc),
T = FieldBoundaryConditions(top = FluxBoundaryCondition(Jᵀ)),
S = FieldBoundaryConditions(top = FluxBoundaryCondition(Jˢ)))

if !isempty(boundary_conditions)
ocean_boundary_conditions = merge(ocean_boundary_conditions, boundary_conditions)
end

if grid isa ImmersedBoundaryGrid
Fu = Forcing(u_immersed_bottom_drag, discrete_form=true, parameters=bottom_drag_coefficient)
Expand All @@ -96,10 +104,12 @@ function ocean_simulation(grid; Δt = 5minutes,
momentum_advection = nothing
end

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tracers = (:T, :S)

if closure isa CATKEVerticalDiffusivity
tracers = tuple(tracers..., :e)
tracer_advection = (; T = tracer_advection, S = tracer_advection, e = nothing)
advection_value = tuple(fill(tracer_advection, length(tracers))...)
tracer_advection = (; zip(tracers,advection_value)...)
tracer_advection = merge(tracer_advection, (e = nothing,))
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Something along these lines might work too:

tracer_advection = NamedTuple(name => tracer_advection for name in tracers)
tracer_advection = merge(tracer_advection, (; e=nothing))

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@glwagner glwagner Aug 10, 2024 •
edited
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Also should we have something that checks if the user has already provided a named tuple? something like

if !(tracer_advection isa NamedTuple)
    # expand tracer_advection into a named tuple with `e=nothing`
end

That way people can experiment with also advecting TKE which may be useful.

cc @simone-silvestri

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@glwagner glwagner Aug 10, 2024 •
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Dictionaries also can be used which may be a little easier to understand:

tracer_advection = Dict{Symbol, Any}(name => tracer_advection for name in tracers)
tracer_advection[:e] = nothing
tracer_advection = NamedTuple(name => tracer_advection[name] for name in tracers)

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Thanks @glwagner for the suggestions

end

ocean_model = HydrostaticFreeSurfaceModel(; grid,
Expand All @@ -111,6 +121,7 @@ function ocean_simulation(grid; Δt = 5minutes,
free_surface,
coriolis,
forcing,
biogeochemistry,
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🚀

boundary_conditions = ocean_boundary_conditions)

ocean = Simulation(ocean_model; Δt, verbose)
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