Cannot run box model simulation with LOBSTER and scale_negatives = true

[ali-ramadhan]

MWE:

using CairoMakie
using Oceananigans
using Oceananigans.Units
using Oceananigans.Fields: FunctionField

using OceanBioME

const year = years = 365day

grid = BoxModelGrid()
clock = Clock(time = zero(grid))

PAR⁰(t) = 100 * (1 - cos((t + 150days) * 2π / year)) * (1 / (1 + 0.2 * exp(-((mod(t, year) - 200days) / 50days)^2))) + 2

const z = -10
PAR_func(t) = PAR⁰(t) * exp(0.2z)

PAR = FunctionField{Center, Center, Center}(PAR_func, grid; clock)

biogeochemistry = LOBSTER(;
    grid,
    light_attenuation_model = PrescribedPhotosyntheticallyActiveRadiation(PAR),
    carbonates = true,
    oxygen = true,
    variable_redfield = true,
    scale_negatives = false
)

model = BoxModel(; biogeochemistry, clock)

simulation = Simulation(model; Δt = 0.1, stop_time = 10)

run!(simulation)

errors with

ERROR: LoadError: type BoxModel has no field tracers
Stacktrace:
  [1] getproperty
    @ ./Base.jl:37 [inlined]
  [2] (::OceanBioME.var"#21#22"{BoxModel{RectilinearGrid{…}, OceanBioME.ContinuousBiogeochemistry{…}, @NamedTuple{…}, Vector{…}, @NamedTuple{…}, Oceananigans.TimeSteppers.RungeKutta3TimeStepper{…}, Clock{…}, @NamedTuple{}}})(tracer_name::Symbol)
    @ OceanBioME ./none:0
  [3] iterate
    @ ./generator.jl:47 [inlined]
  [4] collect(itr::Base.Generator{NTuple{7, Symbol}, OceanBioME.var"#21#22"{BoxModel{RectilinearGrid{…}, OceanBioME.ContinuousBiogeochemistry{…}, @NamedTuple{…}, Vector{…}, @NamedTuple{…}, Oceananigans.TimeSteppers.RungeKutta3TimeStepper{…}, Clock{…}, @NamedTuple{}}}})
    @ Base ./array.jl:834
  [5] _totuple(::Type{Tuple}, ::Base.Generator{NTuple{7, Symbol}, OceanBioME.var"#21#22"{BoxModel{RectilinearGrid{…}, OceanBioME.ContinuousBiogeochemistry{…}, @NamedTuple{…}, Vector{…}, @NamedTuple{…}, Oceananigans.TimeSteppers.RungeKutta3TimeStepper{…}, Clock{…}, @NamedTuple{}}}})
    @ Base ./tuple.jl:425
  [6] Tuple(itr::Base.Generator{NTuple{7, Symbol}, OceanBioME.var"#21#22"{BoxModel{RectilinearGrid{…}, OceanBioME.ContinuousBiogeochemistry{…}, @NamedTuple{…}, Vector{…}, @NamedTuple{…}, Oceananigans.TimeSteppers.RungeKutta3TimeStepper{…}, Clock{…}, @NamedTuple{}}}})
    @ Base ./tuple.jl:391
  [7] update_biogeochemical_state!(model::BoxModel{RectilinearGrid{…}, OceanBioME.ContinuousBiogeochemistry{…}, @NamedTuple{…}, Vector{…}, @NamedTuple{…}, Oceananigans.TimeSteppers.RungeKutta3TimeStepper{…}, Clock{…}, @NamedTuple{}}, scale::ScaleNegativeTracers{NTuple{…}, Vector{…}, Float64, Bool})
    @ OceanBioME ~/atdepth/OceanBioME.jl/src/Utils/negative_tracers.jl:136
  [8] update_biogeochemical_state!(bgc::OceanBioME.ContinuousBiogeochemistry{…}, model::BoxModel{…})
    @ OceanBioME ~/atdepth/OceanBioME.jl/src/OceanBioME.jl:153
  [9] update_state!(model::BoxModel{RectilinearGrid{…}, OceanBioME.ContinuousBiogeochemistry{…}, @NamedTuple{…}, Vector{…}, @NamedTuple{…}, Oceananigans.TimeSteppers.RungeKutta3TimeStepper{…}, Clock{…}, @NamedTuple{}}, callbacks::Vector{Any}; compute_tendencies::Bool)
    @ OceanBioME.BoxModels ~/atdepth/OceanBioME.jl/src/BoxModel/boxmodel.jl:99
 [10] update_state!(model::BoxModel{RectilinearGrid{…}, OceanBioME.ContinuousBiogeochemistry{…}, @NamedTuple{…}, Vector{…}, @NamedTuple{…}, Oceananigans.TimeSteppers.RungeKutta3TimeStepper{…}, Clock{…}, @NamedTuple{}}, callbacks::Vector{Any})
    @ OceanBioME.BoxModels ~/atdepth/OceanBioME.jl/src/BoxModel/boxmodel.jl:86
 [11] initialize!(sim::Simulation{BoxModel{…}, Float64, Float64, OrderedCollections.OrderedDict{…}, OrderedCollections.OrderedDict{…}, OrderedCollections.OrderedDict{…}})
    @ Oceananigans.Simulations ~/.julia/packages/Oceananigans/GXAdX/src/Simulations/run.jl:202
 [12] time_step!(sim::Simulation{BoxModel{…}, Float64, Float64, OrderedCollections.OrderedDict{…}, OrderedCollections.OrderedDict{…}, OrderedCollections.OrderedDict{…}})
    @ Oceananigans.Simulations ~/.julia/packages/Oceananigans/GXAdX/src/Simulations/run.jl:118
 [13] run!(sim::Simulation{BoxModel{…}, Float64, Float64, OrderedCollections.OrderedDict{…}, OrderedCollections.OrderedDict{…}, OrderedCollections.OrderedDict{…}}; pickup::Bool)
    @ Oceananigans.Simulations ~/.julia/packages/Oceananigans/GXAdX/src/Simulations/run.jl:102
 [14] run!(sim::Simulation{BoxModel{…}, Float64, Float64, OrderedCollections.OrderedDict{…}, OrderedCollections.OrderedDict{…}, OrderedCollections.OrderedDict{…}})
    @ Oceananigans.Simulations ~/.julia/packages/Oceananigans/GXAdX/src/Simulations/run.jl:91
 [15] top-level scope
    @ ~/atdepth/OceanBioME.jl/scale_negatives_error.jl:33
 [16] include(fname::String)
    @ Base.MainInclude ./client.jl:494
 [17] top-level scope
    @ REPL[4]:1
in expression starting at /home/alir/atdepth/OceanBioME.jl/scale_negatives_error.jl:33
Some type information was truncated. Use `show(err)` to see complete types.

but is fine with scale_negatives = false.

Sounds like the issue is that it should model.fields for the box model and model.tracers for Oceananigans.jl models.

cc @almacarolina @suki-atdepthmrv