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Improve docstring example for seawater density #3398

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Dec 30, 2023
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Improve docstring example for seawater density #3398

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02b84c8
Improve docstring example for seawater density
glwagner Nov 29, 2023
b4e4d6f
Update seawater_buoyancy.jl
glwagner Nov 29, 2023
b5f4e7a
Update seawater_density.jl
glwagner Nov 29, 2023
2564c2d
fix doctest
navidcy Dec 3, 2023
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fix doctests
navidcy Dec 6, 2023
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fix doctests
navidcy Dec 7, 2023
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Merge branch 'main' into glwagner-patch-3
navidcy Dec 13, 2023
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Merge branch 'main' into glwagner-patch-3
navidcy Dec 29, 2023
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8 changes: 4 additions & 4 deletions src/BuoyancyModels/seawater_buoyancy.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -36,7 +36,7 @@ function Base.show(io::IO, b::SeawaterBuoyancy{FT}) where FT
print(io, "├── constant_salinity: ", b.constant_salinity, "\n")
end

print(io, "└── equation of state: ", summary(b.equation_of_state))
print(io, "└── equation_of_state: ", summary(b.equation_of_state))
end

"""
Expand Down Expand Up @@ -80,7 +80,7 @@ julia> using Oceananigans
julia> buoyancy = SeawaterBuoyancy(equation_of_state=teos10)
SeawaterBuoyancy{Float64}:
├── gravitational_acceleration: 9.80665
└── equation of state: BoussinesqEquationOfState{Float64}
└── equation_of_state: BoussinesqEquationOfState{Float64}
```

Buoyancy that depends only on salinity with temperature held at 20 degrees Celsius
Expand All @@ -90,7 +90,7 @@ julia> salinity_dependent_buoyancy = SeawaterBuoyancy(equation_of_state=teos10,
SeawaterBuoyancy{Float64}:
├── gravitational_acceleration: 9.80665
├── constant_temperature: 20
└── equation of state: BoussinesqEquationOfState{Float64}
└── equation_of_state: BoussinesqEquationOfState{Float64}
```

Buoyancy that depends only on temperature with salinity held at 35 psu
Expand All @@ -100,7 +100,7 @@ julia> temperature_dependent_buoyancy = SeawaterBuoyancy(equation_of_state=teos1
SeawaterBuoyancy{Float64}:
├── gravitational_acceleration: 9.80665
├── constant_salinity: 35
└── equation of state: BoussinesqEquationOfState{Float64}
└── equation_of_state: BoussinesqEquationOfState{Float64}
```
"""
function SeawaterBuoyancy(FT = Float64;
Expand Down
46 changes: 27 additions & 19 deletions src/Models/seawater_density.jl
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Expand Up @@ -55,16 +55,18 @@ Example
Compute a density `Field` using the `KernelFunctionOperation` returned from `seawater_density`

```jldoctest density
julia> using Oceananigans, Oceananigans.Models, SeawaterPolynomials.TEOS10
julia> using Oceananigans, SeawaterPolynomials.TEOS10

julia> grid = RectilinearGrid(CPU(), size=(32, 32), x=(0, 2π), y=(0, 2π), topology=(Periodic, Periodic, Flat))
32×32×1 RectilinearGrid{Float64, Periodic, Periodic, Flat} on CPU with 3×3×0 halo
├── Periodic x ∈ [3.60072e-17, 6.28319) regularly spaced with Δx=0.19635
├── Periodic y ∈ [3.60072e-17, 6.28319) regularly spaced with Δy=0.19635
└── Flat z
julia> using Oceananigans.Models: seawater_density

julia> tracers = (:S, :T)
(:S, :T)
julia> grid = RectilinearGrid(size=100, z=(-1000, 0), topology=(Flat, Flat, Bounded))
1×1×100 RectilinearGrid{Float64, Flat, Flat, Bounded} on CPU with 0×0×3 halo
├── Flat x
├── Flat y
└── Bounded z ∈ [-1000.0, 0.0] regularly spaced with Δz=10.0

julia> tracers = (:T, :S)
(:T, :S)

julia> eos = TEOS10EquationOfState()
BoussinesqEquationOfState{Float64}:
Expand All @@ -74,7 +76,7 @@ BoussinesqEquationOfState{Float64}:
julia> buoyancy = SeawaterBuoyancy(equation_of_state=eos)
SeawaterBuoyancy{Float64}:
├── gravitational_acceleration: 9.80665
└── equation of state: BoussinesqEquationOfState{Float64}
└── equation_of_state: BoussinesqEquationOfState{Float64}

julia> model = NonhydrostaticModel(; grid, buoyancy, tracers)
NonhydrostaticModel{CPU, RectilinearGrid}(time = 0 seconds, iteration = 0)
Expand All @@ -87,25 +89,31 @@ NonhydrostaticModel{CPU, RectilinearGrid}(time = 0 seconds, iteration = 0)

julia> set!(model, S = 34.7, T = 0.5)

julia> density_field = Field(seawater_density(model))
32×32×1 Field{Center, Center, Center} on RectilinearGrid on CPU
├── grid: 32×32×1 RectilinearGrid{Float64, Periodic, Periodic, Flat} on CPU with 3×3×0 halo
julia> density_operation = seawater_density(model)
KernelFunctionOperation at (Center, Center, Center)
├── grid: 1×1×100 RectilinearGrid{Float64, Flat, Flat, Bounded} on CPU with 0×0×3 halo
├── kernel_function: ρ (generic function with 2 methods)
└── arguments: ("BoussinesqEquationOfState{Float64}", "1×1×100 Field{Center, Center, Center} on RectilinearGrid on CPU", "1×1×100 Field{Center, Center, Center} on RectilinearGrid on CPU", "KernelFunctionOperation at (Center, Center, Center)")

julia> density_field = Field(density_operation)
1×1×100 Field{Center, Center, Center} on RectilinearGrid on CPU
├── grid: 1×1×100 RectilinearGrid{Float64, Flat, Flat, Bounded} on CPU with 0×0×3 halo
├── boundary conditions: FieldBoundaryConditions
│ └── west: Periodic, east: Periodic, south: Periodic, north: Periodic, bottom: Nothing, top: Nothing, immersed: ZeroFlux
│ └── west: Nothing, east: Nothing, south: Nothing, north: Nothing, bottom: ZeroFlux, top: ZeroFlux, immersed: ZeroFlux
├── operand: KernelFunctionOperation at (Center, Center, Center)
├── status: time=0.0
└── data: 38×38×1 OffsetArray(::Array{Float64, 3}, -2:35, -2:35, 1:1) with eltype Float64 with indices -2:35×-2:35×1:1
└── data: 1×1×106 OffsetArray(::Array{Float64, 3}, 1:1, 1:1, -2:103) with eltype Float64 with indices 1:1×1:1×-2:103
└── max=0.0, min=0.0, mean=0.0

julia> compute!(density_field)
32×32×1 Field{Center, Center, Center} on RectilinearGrid on CPU
├── grid: 32×32×1 RectilinearGrid{Float64, Periodic, Periodic, Flat} on CPU with 3×3×0 halo
1×1×100 Field{Center, Center, Center} on RectilinearGrid on CPU
├── grid: 1×1×100 RectilinearGrid{Float64, Flat, Flat, Bounded} on CPU with 0×0×3 halo
├── boundary conditions: FieldBoundaryConditions
│ └── west: Periodic, east: Periodic, south: Periodic, north: Periodic, bottom: Nothing, top: Nothing, immersed: ZeroFlux
│ └── west: Nothing, east: Nothing, south: Nothing, north: Nothing, bottom: ZeroFlux, top: ZeroFlux, immersed: ZeroFlux
├── operand: KernelFunctionOperation at (Center, Center, Center)
├── status: time=0.0
└── data: 38×38×1 OffsetArray(::Array{Float64, 3}, -2:35, -2:35, 1:1) with eltype Float64 with indices -2:35×-2:35×1:1
└── max=1027.7, min=1027.7, mean=1027.7
└── data: 1×1×106 OffsetArray(::Array{Float64, 3}, 1:1, 1:1, -2:103) with eltype Float64 with indices 1:1×1:1×-2:103
└── max=1032.38, min=1027.73, mean=1030.06
```

Values for `temperature`, `salinity` and `geopotential_height` can be passed to
Expand Down