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Agate.jl-DARWIN model

Agate.Models.DARWIN.construct — Function
construct(; kw...) -> bgc

Construct a simplified DARWIN-like, size-structured ecosystem model.

Info

This model is in active development and has not been validated against MITgcm-DARWIN.

Formulation

TRACERS:

∂t cⱼ = $Uⱼ$DIC - $Mⱼ$ + $Gⱼ$ - $gⱼ$

∂t DIC = ∑($Uⱼ$ DIC) + $R$DOC + $R$POC

∂t DIN = ∑($Uⱼ$DIC * $Qⱼ$N) + $R$DON + $R$PON

∂t PO4 = ∑($Uⱼ$DIC * $Qⱼ$P) + $R$DOP + $R$POP

∂t DOC = ∑($Mⱼ$DOC) + $g$DOC - $R$DOC

∂t DON = ∑($Mⱼ$DOC * $Qⱼ$N) + $g$DON - $R$DON

∂t DOP = ∑($Mⱼ$DOC * $Qⱼ$P) + $g$DOP - $R$DOP

∂t POC = ∑($Mⱼ$POC) + $g$POC - $R$POC

∂t PON = ∑($Mⱼ$POC * $Qⱼ$N) + $g$PON - $R$PON

∂t POP = ∑($Mⱼ$POC * $Qⱼ$P) + $g$POP - $R$POP

where:

  • $U$ = uptake
  • $R$ = remineralization
  • $M$ = mortality
  • $g, G$ = grazing losses and gains
  • $Q$ = plankton elemental ratios

TRAITS:

μmax, KR, gmax = a*Volume^b

palat = η/(1+($ratio$-$opt$)^2)^σ

where:

  • μmax = maximum photosynthetic growth
  • KR = nutrient half saturation
  • gmax = maximum predation rate
  • palat = palatability
  • $ratio$ = predator to prey size ratio (diameter)
  • $opt$ = predator to prey size optimum (diameter)
  • η = prey protection
  • σ = predator specificity

The DARWIN model contains two plankton groups: phytoplankton (P) and zooplankton (Z), with size classes defined by their size-structure inputs.

In addition to plankton, the default DARWIN factory includes elemental cycling tracers: dissolved inorganic carbon (DIC), dissolved inorganic nitrogen (DIN), phosphate (PO4), dissolved organic matter (DOC, DON, DOP), and particulate organic matter (POC, PON, POP).

During construction, plankton size (diameter) is used to resolve trait-based parameter vectors and interaction matrices (e.g. palatability and assimilation efficiency). You may override interaction matrices explicitly with palatability_matrix and/or assimilation_matrix.

Size-structure inputs may be a NamedTuple range, for example (n=3, min_esd=1, max_esd=10, splitting=:log_splitting), or an explicit diameter vector such as [1.0, 3.2, 10.0].

The returned biogeochemistry instance includes a photosynthetically active radiation (PAR) auxiliary field.

Keywords

  • phyto_size_structure=(n=2, min_esd=1.5, max_esd=20.0, splitting=:log_splitting): phytoplankton size structure

  • zoo_size_structure=(n=2, min_esd=20.0, max_esd=100.0, splitting=:log_splitting): zooplankton size structure

  • parameters=(;): parameter overrides (validated against the DARWIN parameter set). Vector parameters may be supplied positionally or as partial NamedTuple overrides keyed by plankton class name.

  • scalar_type=nothing: explicit runtime scalar type. When omitted, construction uses eltype(grid) or Float64 if no grid is supplied

  • palatability_matrix=nothing: optional palatability matrix override. Must be an explicit rectangular matrix sized to the canonical interaction axes (n_consumer, n_prey).

  • assimilation_matrix=nothing: optional assimilation matrix override. Must be an explicit rectangular matrix sized to the canonical interaction axes (n_consumer, n_prey)

  • grid=BoxModelGrid(): grid used for precision/architecture inference and sinking velocity fields

  • arch=nothing: override the architecture (usually inferred from grid)

  • sinking_tracers=nothing: sinking speed overrides, e.g. (POC = 10/day, ...)

  • open_bottom=true: whether sinking tracers leave the domain

Returns

An Oceananigans.Biogeochemistry.AbstractContinuousFormBiogeochemistry instance.

Example

using Agate.Models: DARWIN

bgc = DARWIN.construct()

Trait-style allometric parameter overrides may be supplied during construction:

using Oceananigans.Units: day
using Agate.Library.Allometry: AllometricParam, PowerLaw

bgc = DARWIN.construct(;
    parameters=(;
        maximum_growth_rate=AllometricParam(
            PowerLaw(); prefactor=2 / day, exponent=-0.15
        ),
    ),
)
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