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Box model

In this example we setup a LOBSTER biogeochemical model in a single box configuration. This example demonstrates:

  • How to setup OceanBioME's biogeochemical models as a stand-alone box model

Install dependencies

First we check we have the dependencies installed

using Pkg
pkg"add OceanBioME"

Model setup

Load the packages and setup the initial and forcing conditions

using OceanBioME, Oceananigans, Oceananigans.Units
using Oceananigans.Fields: FunctionField

const year = years = 365day

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

This is forced by a prescribed time-dependent photosynthetically available radiation (PAR)

PAR⁰(t) = 60 * (1 - cos((t + 15days) * 2π / year)) * (1 / (1 + 0.2 * exp(-((mod(t, year) - 200days) / 50days)^2))) + 2

const z = -10 # specify the nominal depth of the box for the PAR profile
PAR_func(t) = PAR⁰(t) * exp(0.2z) # Modify the PAR based on the nominal depth and exponential decay

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

Set up the model. Here, first specify the biogeochemical model, followed by initial conditions and the start and end times

model = BoxModel(; biogeochemistry = LOBSTER(grid; light_attenuation = PrescribedPhotosyntheticallyActiveRadiation(PAR)),
                   clock)

set!(model, NO₃ = 10.0, NH₄ = 0.1, P = 0.1, Z = 0.01)

simulation = Simulation(model; Δt = 5minutes, stop_time = 5years)

simulation.output_writers[:fields] = JLD2Writer(model, model.fields; filename = "box.jld2", schedule = TimeInterval(10days), overwrite_existing = true)

prog(sim) = @info "$(prettytime(time(sim))) in $(prettytime(simulation.run_wall_time))"

simulation.callbacks[:progress] = Callback(prog, IterationInterval(1000000))
Callback of prog on IterationInterval(1000000)

Run the model (should only take a few seconds)

@info "Running the model..."
run!(simulation)
[ Info: Running the model...
[ Info: Initializing simulation...
[ Info: 0 seconds in 0 seconds
┌ Warning: error ArgumentError("a group or dataset named grid is already present within this group") thrown when trying to serialize the grid at serialized/grid
└ @ Oceananigans.OutputWriters ~/.julia-oceananigans/packages/Oceananigans/41MiP/src/OutputWriters/jld2_writer.jl:234
[ Info:     ... simulation initialization complete (4.134 seconds)
[ Info: Executing initial time step...
[ Info:     ... initial time step complete (182.539 ms).
[ Info: Simulation is stopping after running for 25.931 seconds.
[ Info: Simulation time 1825 days equals or exceeds stop time 1825 days.

Load the output

times = FieldTimeSeries("box.jld2", "P").times

timeseries = NamedTuple{keys(model.fields)}(FieldTimeSeries("box.jld2", "$field")[1, 1, 1, :] for field in keys(model.fields))
(NO₃ = [10.0, 10.014166831970215, 9.95338249206543, 9.784919738769531, 9.375934600830078, 8.368718147277832, 6.369740009307861, 4.483834743499756, 2.825942039489746, 1.0725213289260864, 0.11781363934278488, 0.0055581084452569485, 0.000587504415307194, 0.00036966733750887215, 0.0003323778510093689, 0.00032169869518838823, 0.0003297854564152658, 0.0003561199700925499, 0.0004021570202894509, 0.0004714794922620058, 0.0005718325264751911, 0.0007220993866212666, 0.000976161623839289, 0.0015284680994227529, 0.0034679363016039133, 0.014730865135788918, 0.06833924353122711, 0.23592886328697205, 0.5924817323684692, 1.151922583580017, 1.880109190940857, 2.7274773120880127, 3.640096664428711, 4.565077304840088, 5.455395221710205, 6.273810863494873, 6.994857311248779, 7.603814125061035, 8.091344833374023, 8.437606811523438, 8.52462387084961, 7.639492988586426, 6.304966926574707, 4.981163501739502, 3.3960671424865723, 1.6185245513916016, 0.2977498173713684, 0.016796935349702835, 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And plot

using CairoMakie

fig = Figure(size = (1200, 1200), fontsize = 24)

axs = []
for (name, tracer) in pairs(timeseries)
    idx = (length(axs))
    push!(axs, Axis(fig[floor(Int, idx/2), Int(idx%2)], ylabel = "$name", xlabel = "Year", xticks=(0:10)))
    lines!(axs[end], times / year, tracer, linewidth = 3)
end

fig

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