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Agate.jl-NiPiZD model

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

Construct a size-structured NiPiZD ecosystem model.

The NiPiZD 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 NiPiZD factory includes idealized nutrient (N) and detritus (D) cycling. The returned biogeochemistry instance includes a photosynthetically active radiation (PAR) auxiliary field.

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].

Keywords

  • phyto_size_structure=(n=2, min_esd=2, max_esd=10, splitting=:log_splitting): phytoplankton size structure
  • zoo_size_structure=(n=2, min_esd=20, max_esd=100, splitting=:linear_splitting): zooplankton size structure
  • parameters=(;): parameter overrides (validated against the NiPiZD parameter set). Vector parameters may be supplied positionally, as partial NamedTuple overrides keyed by plankton class name, or as allometric definitions for diameter-indexed plankton vectors.
  • 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 architecture inference and default scalar-type selection
  • scalar_type=nothing: explicit runtime scalar type. When omitted, construction uses eltype(grid) or Float64 if no grid is supplied
  • arch=nothing: override the architecture (usually inferred from grid)
  • sinking_tracers=nothing: sinking speed overrides, e.g. (D = 2/day, P1 = 0.1/day, ...)
  • open_bottom=true: whether sinking tracers leave the domain

Returns

An Oceananigans.Biogeochemistry.AbstractContinuousFormBiogeochemistry instance.

Example

using Agate.Models: NiPiZD

bgc = NiPiZD.construct()

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

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

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