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CliMA · May 31, 2024 · 0e2b645 · 0e2b645
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diff --git a/examples/OceananigansSingleColumnSimulation/run_single_column_simulation.jl b/examples/OceananigansSingleColumnSimulation/run_single_column_simulation.jl
@@ -4,21 +4,29 @@ using CLIMAParameters
 # In a "real" use case, we recommend implementing setups in source code.
 include("single_column_simulation.jl")
 
-parameters = CLIMAParameters.create_toml_dict(Float64,
-                                              override_file = "my_parameters.toml",
-                                              default_file = "default_parameters.toml",
-                                              dict_type = "name")
-
-parameters = CLIMAParameters.get_parameter_values!(parameters, "gravitational_acceleration", "Ocean")
+parameters = CLIMAParameters.create_toml_dict(
+    Float64,
+    override_file = "my_parameters.toml",
+    default_file = "default_parameters.toml",
+    dict_type = "name",
+)
+
+parameters = CLIMAParameters.get_parameter_values!(
+    parameters,
+    "gravitational_acceleration",
+    "Ocean",
+)
 parameters = NamedTuple(parameters...)
 
 output_filename = "single_column_simulation.jld2"
-simulation = single_column_simulation(; parameters..., output_filename,
-                                      initial_buoyancy_frequency = 1e-5)
+simulation = single_column_simulation(;
+    parameters...,
+    output_filename,
+    initial_buoyancy_frequency = 1e-5,
+)
 
 @info "Running a simulation on \n $(simulation.model.grid)..."
 
 run!(simulation)
 
 include("visualize_single_column_simulation.jl")
-
diff --git a/examples/OceananigansSingleColumnSimulation/single_column_simulation.jl b/examples/OceananigansSingleColumnSimulation/single_column_simulation.jl
@@ -1,4 +1,4 @@
-using Oceananigans  
+using Oceananigans
 using Oceananigans.Units
 using SeawaterPolynomials
 using SeawaterPolynomials.TEOS10: TEOS10EquationOfState
@@ -7,61 +7,66 @@ using CLIMAParameters
 using Printf
 
 using Oceananigans.TurbulenceClosures.CATKEVerticalDiffusivities:
-    CATKEVerticalDiffusivity,
-    MixingLength,
-    TurbulentKineticEnergyEquation
-
+    CATKEVerticalDiffusivity, MixingLength, TurbulentKineticEnergyEquation
+
 function single_column_simulation(;
     # Grid / domain parameters
-    architecture                                       = CPU(),
-    Nz                                                 = 64,
-    Lz                                                 = 256,
-    floating_point_type                                = Float64,
+    architecture = CPU(),
+    Nz = 64,
+    Lz = 256,
+    floating_point_type = Float64,
     # Output
-    output_fields                                      = (:u, :v, :T, :S, :e),
-    output_schedule                                    = TimeInterval(10minutes),
-    output_filename                                    = "single_column_simulation.jld2",
+    output_fields = (:u, :v, :T, :S, :e),
+    output_schedule = TimeInterval(10minutes),
+    output_filename = "single_column_simulation.jld2",
     # Boundary conditions
-    surface_heat_flux                                  = 200,
-    surface_zonal_momentum_flux                        = -0.2,
-    surface_meridional_momentum_flux                   = 0.0,
+    surface_heat_flux = 200,
+    surface_zonal_momentum_flux = -0.2,
+    surface_meridional_momentum_flux = 0.0,
     # Ocean physical parameters
-    ocean_reference_density                            = 1020,
-    ocean_heat_capacity                                = 3991,
-    gravitational_acceleration                         = 9.81,
-    coriolis_parameter                                 = 1e-4,
+    ocean_reference_density = 1020,
+    ocean_heat_capacity = 3991,
+    gravitational_acceleration = 9.81,
+    coriolis_parameter = 1e-4,
     # CATKE parameters
-    catke_surface_distance_coefficient                 = 2.4,
-    catke_tracer_convective_mixing_length_coefficient  = 1.5,
-    catke_tracer_convective_penetration_coefficient    = 0.2,
-    catke_tke_convective_mixing_length_coefficient     = 1.2,
-    catke_sheared_convection_coefficient               = 0.14,
-    catke_low_Ri_momentum_shear_mixing_coefficient     = 0.19,
-    catke_high_Ri_momentum_shear_mixing_coefficient    = 0.086,
-    catke_low_Ri_tracer_shear_mixing_coefficient       = 0.2,
-    catke_high_Ri_tracer_shear_mixing_coefficient      = 0.045,
-    catke_low_Ri_tke_shear_mixing_coefficient          = 1.9,
-    catke_high_Ri_tke_shear_mixing_coefficient         = 0.57,
-    catke_stability_function_width                     = 0.45,
-    catke_stability_function_threshold_Ri              = 0.47,
-    catke_low_Ri_dissipation_shear_length_coefficient  = 1.1,
+    catke_surface_distance_coefficient = 2.4,
+    catke_tracer_convective_mixing_length_coefficient = 1.5,
+    catke_tracer_convective_penetration_coefficient = 0.2,
+    catke_tke_convective_mixing_length_coefficient = 1.2,
+    catke_sheared_convection_coefficient = 0.14,
+    catke_low_Ri_momentum_shear_mixing_coefficient = 0.19,
+    catke_high_Ri_momentum_shear_mixing_coefficient = 0.086,
+    catke_low_Ri_tracer_shear_mixing_coefficient = 0.2,
+    catke_high_Ri_tracer_shear_mixing_coefficient = 0.045,
+    catke_low_Ri_tke_shear_mixing_coefficient = 1.9,
+    catke_high_Ri_tke_shear_mixing_coefficient = 0.57,
+    catke_stability_function_width = 0.45,
+    catke_stability_function_threshold_Ri = 0.47,
+    catke_low_Ri_dissipation_shear_length_coefficient = 1.1,
     catke_high_Ri_dissipation_shear_length_coefficient = 0.37,
-    catke_dissipation_convective_length_coefficient    = 0.88,
-    catke_surface_tke_shear_flux_coefficient           = 1.1,
-    catke_surface_tke_convective_flux_coefficient      = 4.0,
-    catke_minimum_turbulent_kinetic_energy             = 1e-6,
+    catke_dissipation_convective_length_coefficient = 0.88,
+    catke_surface_tke_shear_flux_coefficient = 1.1,
+    catke_surface_tke_convective_flux_coefficient = 4.0,
+    catke_minimum_turbulent_kinetic_energy = 1e-6,
     # Initial conditions
-    initial_salinity                                   = 35,
-    initial_surface_temperature                        = 20,
-    initial_turbulent_kinetic_energy                   = 1e-6,
+    initial_salinity = 35,
+    initial_surface_temperature = 20,
+    initial_turbulent_kinetic_energy = 1e-6,
     # Simulation parameters
-    stop_time                                          = 8days,
-    time_step                                          = 10minutes,
-    initial_buoyancy_frequency                         = 1e-6)
+    stop_time = 8days,
+    time_step = 10minutes,
+    initial_buoyancy_frequency = 1e-6,
+)
 
     # A single colunn grid
     FT = floating_point_type
-    grid = RectilinearGrid(architecture, FT, size=Nz, z=(-Lz, 0), topology=(Flat, Flat, Bounded))
+    grid = RectilinearGrid(
+        architecture,
+        FT,
+        size = Nz,
+        z = (-Lz, 0),
+        topology = (Flat, Flat, Bounded),
+    )
 
     # Surface boundary conditions
     ρ₀ = ocean_reference_density
@@ -84,11 +89,11 @@ function single_column_simulation(;
 
     # Build CATKE
     catke_mixing_length = MixingLength(
-        Cˢ   = catke_surface_distance_coefficient,
-        Cᶜc  = catke_tracer_convective_mixing_length_coefficient,
-        Cᶜe  = catke_tracer_convective_penetration_coefficient,
-        Cᵉc  = catke_tke_convective_mixing_length_coefficient,
-        Cˢᵖ  = catke_sheared_convection_coefficient,
+        Cˢ = catke_surface_distance_coefficient,
+        Cᶜc = catke_tracer_convective_mixing_length_coefficient,
+        Cᶜe = catke_tracer_convective_penetration_coefficient,
+        Cᵉc = catke_tke_convective_mixing_length_coefficient,
+        Cˢᵖ = catke_sheared_convection_coefficient,
         Cˡᵒu = catke_low_Ri_momentum_shear_mixing_coefficient,
         Cʰⁱu = catke_high_Ri_momentum_shear_mixing_coefficient,
         Cˡᵒc = catke_low_Ri_tracer_shear_mixing_coefficient,
@@ -97,29 +102,38 @@ function single_column_simulation(;
         Cʰⁱe = catke_high_Ri_tke_shear_mixing_coefficient,
         CRiᵟ = catke_stability_function_width,
         CRi⁰ = catke_stability_function_threshold_Ri,
-    ) 
+    )
 
     catke_tke_equation = TurbulentKineticEnergyEquation(
         CˡᵒD = catke_low_Ri_dissipation_shear_length_coefficient,
         CʰⁱD = catke_high_Ri_dissipation_shear_length_coefficient,
-        CᶜD  = catke_dissipation_convective_length_coefficient,
+        CᶜD = catke_dissipation_convective_length_coefficient,
         Cᵂu★ = catke_surface_tke_shear_flux_coefficient,
         CᵂwΔ = catke_surface_tke_convective_flux_coefficient,
     )
-
-    closure = CATKEVerticalDiffusivity(FT,
-                                       minimum_turbulent_kinetic_energy = catke_minimum_turbulent_kinetic_energy,
-                                       mixing_length = catke_mixing_length,
-                                       turbulent_kinetic_energy_equation = catke_tke_equation)
-
-    coriolis = FPlane(FT, f=coriolis_parameter)
-    equation_of_state = TEOS10EquationOfState(FT, ; reference_density=ocean_reference_density)
-    buoyancy = SeawaterBuoyancy(FT; equation_of_state, gravitational_acceleration)
-
-    model = HydrostaticFreeSurfaceModel(; grid, closure, coriolis, buoyancy,
-                                        tracers = (:T, :S, :e),
-                                        boundary_conditions = (; T=T_bcs, u=u_bcs, v=v_bcs))
-
+
+    closure = CATKEVerticalDiffusivity(
+        FT,
+        minimum_turbulent_kinetic_energy = catke_minimum_turbulent_kinetic_energy,
+        mixing_length = catke_mixing_length,
+        turbulent_kinetic_energy_equation = catke_tke_equation,
+    )
+
+    coriolis = FPlane(FT, f = coriolis_parameter)
+    equation_of_state =
+        TEOS10EquationOfState(FT, ; reference_density = ocean_reference_density)
+    buoyancy =
+        SeawaterBuoyancy(FT; equation_of_state, gravitational_acceleration)
+
+    model = HydrostaticFreeSurfaceModel(;
+        grid,
+        closure,
+        coriolis,
+        buoyancy,
+        tracers = (:T, :S, :e),
+        boundary_conditions = (; T = T_bcs, u = u_bcs, v = v_bcs),
+    )
+
     # Initial condition
     T₀ = initial_surface_temperature
     S₀ = initial_salinity
@@ -131,21 +145,24 @@ function single_column_simulation(;
     dTdz = N² / (α * g)
     Tᵢ(z) = T₀ + dTdz * z
     Sᵢ(z) = S₀
-    set!(model, S=Sᵢ, T=Tᵢ, e=initial_turbulent_kinetic_energy)
+    set!(model, S = Sᵢ, T = Tᵢ, e = initial_turbulent_kinetic_energy)
 
-    simulation = Simulation(model; Δt=time_step, stop_time)
+    simulation = Simulation(model; Δt = time_step, stop_time)
 
     model_fields = fields(model)
     outputs = NamedTuple(name => model_fields[name] for name in output_fields)
 
-    simulation.output_writers[:fields] = JLD2OutputWriter(model, outputs;
-                                                          schedule = output_schedule,
-                                                          filename = output_filename,
-                                                          overwrite_existing = true)
+    simulation.output_writers[:fields] = JLD2OutputWriter(
+        model,
+        outputs;
+        schedule = output_schedule,
+        filename = output_filename,
+        overwrite_existing = true,
+    )
 
-    progress(sim) = @info string("Iter: ", iteration(sim), " t: ", prettytime(sim))
+    progress(sim) =
+        @info string("Iter: ", iteration(sim), " t: ", prettytime(sim))
     simulation.callbacks[:progress] = Callback(progress, IterationInterval(100))
 
     return simulation
 end
-
diff --git a/examples/OceananigansSingleColumnSimulation/visualize_single_column_simulation.jl b/examples/OceananigansSingleColumnSimulation/visualize_single_column_simulation.jl
@@ -12,9 +12,13 @@ times = ut.times
 z = znodes(ut)
 
 fig = Figure()
-axu = Axis(fig[2, 1], xlabel="Velocities (m s⁻¹)", ylabel="z (m)")
-axT = Axis(fig[2, 2], xlabel="Temperature (ᵒC)", ylabel="z (m)")
-axe = Axis(fig[2, 3], xlabel="Turbulent kinetic energy (m² s⁻²)", ylabel="z (m)")
+axu = Axis(fig[2, 1], xlabel = "Velocities (m s⁻¹)", ylabel = "z (m)")
+axT = Axis(fig[2, 2], xlabel = "Temperature (ᵒC)", ylabel = "z (m)")
+axe = Axis(
+    fig[2, 3],
+    xlabel = "Turbulent kinetic energy (m² s⁻²)",
+    ylabel = "z (m)",
+)
 
 Nt = length(times)
 n = Observable(Nt)
@@ -27,16 +31,15 @@ vn = @lift interior(vt[$n], 1, 1, :)
 Tn = @lift interior(Tt[$n], 1, 1, :)
 en = @lift interior(et[$n], 1, 1, :)
 
-lines!(axu, un, z, label="u")
-lines!(axu, vn, z, label="v")
+lines!(axu, un, z, label = "u")
+lines!(axu, vn, z, label = "v")
 lines!(axT, Tn, z)
 lines!(axe, en, z)
 
 xlims!(axu, -0.1, 0.1)
 xlims!(axT, 19, 20)
 xlims!(axe, -1e-5, 4e-4)
 
-record(fig, "single_column_simulation.mp4", 1:Nt, framerate=24) do nn
+record(fig, "single_column_simulation.mp4", 1:Nt, framerate = 24) do nn
     n[] = nn
 end
-