Running ocean_simulation with closure being a tuple of closures which includes CATKE throws initialization error due to tracer :e missing.

[xkykai]

Here's a MWE:

using Oceananigans
using ClimaOcean
using OrthogonalSphericalShellGrids
using CUDA

z_faces = exponential_z_faces(Nz=40, depth=6000)

Nx = 360
Ny = 180
Nz = length(z_faces) - 1

grid = TripolarGrid(CPU();
                    size = (Nx, Ny, Nz),
                    halo = (7, 7, 7),
                    z = z_faces, 
                    north_poles_latitude = 55,
                    first_pole_longitude = 70)

bottom_height = regrid_bathymetry(grid; 
                                  minimum_depth = 10,
                                  interpolation_passes = 5,
                                  major_basins = 3,
                                  dir = "./scratch")

CUDA.@allowscalar interior(bottom_height)[isnan.(bottom_height)] .= 0;
grid = ImmersedBoundaryGrid(grid, GridFittedBottom(bottom_height))

closure = (Oceananigans.TurbulenceClosures.IsopycnalSkewSymmetricDiffusivity(κ_skew = 1000.0, κ_symmetric = 1000.0), 
           ClimaOcean.OceanSimulations.default_ocean_closure())
ocean = ocean_simulation(grid; closure)

which throws

ERROR: ArgumentError: Tracers must contain :e to represent turbulent kinetic energy for `CATKEVerticalDiffusivity`.
Stacktrace:
  [1] with_tracers
    @ C:\Users\xinle\.julia\packages\Oceananigans\IsF1o\src\TurbulenceClosures\turbulence_closure_implementations\TKEBasedVerticalDiffusivities\catke_vertical_diffusivity.jl:123 [inlined]
  [2] #22
    @ .\none:0 [inlined]
  [3] iterate
    @ .\generator.jl:47 [inlined]
  [4] collect_to!(dest::Vector{…}, itr::Base.Generator{…}, offs::Int64, st::Int64)
    @ Base .\array.jl:892
  [5] collect_to_with_first!
    @ .\array.jl:870 [inlined]
  [6] collect
    @ .\array.jl:844 [inlined]
  [7] _totuple
    @ .\tuple.jl:425 [inlined]
  [8] Tuple
    @ .\tuple.jl:391 [inlined]
  [9] with_tracers(tracers::Tuple{…}, closure_tuple::Tuple{…})
    @ Oceananigans.TurbulenceClosures C:\Users\xinle\.julia\packages\Oceananigans\IsF1o\src\TurbulenceClosures\closure_tuples.jl:74
 [10] HydrostaticFreeSurfaceModel(; grid::ImmersedBoundaryGrid{…}, clock::Clock{…}, momentum_advection::VectorInvariant{…}, tracer_advection::FluxFormAdvection{…}, buoyancy::SeawaterBuoyancy{…}, coriolis::HydrostaticSphericalCoriolis{…}, free_surface::SplitExplicitFreeSurface{…}, tracers::Tuple{…}, forcing::@NamedTuple{…}, closure::Tuple{…}, boundary_conditions::@NamedTuple{…}, particles::Nothing, biogeochemistry::Nothing, velocities::Nothing, pressure::Nothing, diffusivity_fields::Nothing, auxiliary_fields::@NamedTuple{})
    @ Oceananigans.Models.HydrostaticFreeSurfaceModels C:\Users\xinle\.julia\packages\Oceananigans\IsF1o\src\Models\HydrostaticFreeSurfaceModels\hydrostatic_free_surface_model.jl:175
 [11] ocean_simulation(grid::ImmersedBoundaryGrid{…}; Δt::Float64, closure::Tuple{…}, free_surface::SplitExplicitFreeSurface{…}, reference_density::Int64, rotation_rate::Float64, gravitational_acceleration::Float64, bottom_drag_coefficient::ClimaOcean.OceanSimulations.Default{…}, forcing::@NamedTuple{}, coriolis::HydrostaticSphericalCoriolis{…}, momentum_advection::VectorInvariant{…}, tracer_advection::FluxFormAdvection{…}, verbose::Bool)
    @ ClimaOcean.OceanSimulations C:\Users\xinle\.julia\packages\ClimaOcean\l5TH1\src\OceanSimulations\OceanSimulations.jl:122
 [12] top-level scope
    @ c:\Users\xinle\MIT\NN_global_simulation\global_simulation copy.jl:30
Some type information was truncated. Use `show(err)` to see complete types.

The issue is https://github.com/CliMA/ClimaOcean.jl/blob/cd2677b91b4f1a6469fda9ded13f937333760997/src/OceanSimulations/OceanSimulations.jl#L116C1-L120C8 does not allow for closure being a tuple.

Suggested change could be either checking for whether closure is a tuple eg.

    tracers = (:T, :S)
    if closure isa Tuple
        for clo in closure
            if clo isa CATKEVerticalDiffusivity
                tracers = tuple(tracers..., :e)
                tracer_advection = (; T = tracer_advection, S = tracer_advection, e = nothing)
            end
        end
    else
        if closure isa CATKEVerticalDiffusivity
            tracers = tuple(tracers..., :e)
            tracer_advection = (; T = tracer_advection, S = tracer_advection, e = nothing)
        end
    end

or allowing the user to freely define tracers as a function argument.

[glwagner]

Oh that's silly that users can't add tracers on their own.

I think #123 put that in but that PR hasn't moved in a bit

[simone-silvestri]

should be closed with PR #222