Individuals

The effects of individuals can be modelled in OceanBioME. We have implemented this through custom dynamics in the Lagrangian Particle tracking feature of Oceananigans. We have extended these functionalities to make it easier to implement "active" particles which interact with the tracers. We have then implemented a model of sugar kelp which can be followed as an example of using this functionality.

To setup particles first create a particle biogeochemistry, e.g.:

struct GrowingParticles{FT}
    nutrients_half_saturation :: FT
end

We then need to add some methods to tell OceanBioME what properties this particle has, and what tracers it interacts with:

import OceanBioME.Particles: required_particle_fields, required_tracers, coupled_tracers

required_particle_fields(::GrowingParticles) = (:S, )
required_tracers(::GrowingParticles) = (:N, )
coupled_tracers(::GrowingParticles) = (:N, )

coupled_tracers (generic function with 3 methods)

So our model is going to track the Size of the particles and take up Nutrients. Now we need to how this growth happens. The forcing functions should be of the form (particles::ParticleBiogeochemistry)(::Val{:PROPERTY}, t, required_particle_fields..., required_tracers...), so in this example:

(p::GrowingParticles)(::Val{:S}, t, S, N) = N / (N + p.nutrient_half_saturation)
(p::GrowingParticles)(::Val{:N}, t, S, N) = - N / (N + p.nutrient_half_saturation)

We can then create an instance of this particle model using BiogeochemicalParticles, and set their initial position and size:

using OceanBioME, Oceananigans

Lx, Ly, Lz = 100, 100, 100
grid = RectilinearGrid(; size = (8, 8, 8), extent = (Lx, Ly, Lz))

particles = BiogeochemicalParticles(10; grid, biogeochemistry = GrowingParticles(0.5))

set!(particles, S = 0.1, x = rand(10) * Lx, y = rand(10) * Ly, z = rand(10) * Lz)

We can then put these into a compatible biogeochemical model, for example:

biogeochemistry = NPZD(; grid, particles)

NutrientPhytoplanktonZooplanktonDetritus{Float64} model, with (:P, :D) sinking 
 Light attenuation: Two-band light attenuation model (Float64)
 Sediment: Nothing
 Particles: 10 BiogeochemicalParticles with Main.GrowingParticles{Float64}
 Modifiers: Nothing