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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), each represented by n_phyto and n_zoo size classes.

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.

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

Keywords

  • n_phyto=2: number of phytoplankton size classes
  • n_zoo=2: number of zooplankton size classes
  • phyto_diameters=(1.5, 20.0, :log_splitting): diameter specification for phytoplankton
  • zoo_diameters=(20.0, 100.0, :log_splitting): diameter specification for zooplankton
  • parameters=(;): parameter overrides (validated against the DARWIN parameter set)
  • palatability_matrix=nothing: optional palatability matrix override. Must be an explicit rectangular matrix sized to the canonical interaction axes (n_consumer, n_prey) (for DARWIN defaults, (n_zoo, n_phyto)).
  • assimilation_matrix=nothing: optional assimilation matrix override. Must be an explicit rectangular matrix sized to the canonical interaction axes (n_consumer, n_prey) (for DARWIN defaults, (n_zoo, n_phyto)).
  • 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()
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