Skip to content

Add biogeochemical interface to ocean_simulation #123

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Draft
wants to merge 17 commits into
base: main
Choose a base branch
from
Draft

Add biogeochemical interface to ocean_simulation #123

Changes from 8 commits
Commits
Show all changes
17 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
15 changes: 13 additions & 2 deletions src/OceanSimulations/OceanSimulations.jl
View file
Open in desktop
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

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,))
Copy link
Member

@glwagner glwagner Aug 10, 2024

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

Something along these lines might work too:

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

Copy link
Member

@glwagner glwagner Aug 10, 2024 •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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

Copy link
Member

@glwagner glwagner Aug 10, 2024 •
edited
Loading

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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)

Copy link
Author

@vtamsitt vtamsitt Aug 12, 2024

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

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,
Copy link
Member

@glwagner glwagner Aug 10, 2024

Choose a reason for hiding this comment

The reason will be displayed to describe this comment to others. Learn more.

🚀

boundary_conditions = ocean_boundary_conditions)

ocean = Simulation(ocean_model; Δt, verbose)
Expand Down