construct(; kw...) -> bgc

Construct a size-structured NiPiZD ecosystem model.

The NiPiZD 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 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.

Keywords

• n_phyto=2: number of phytoplankton size classes
• n_zoo=2: number of zooplankton size classes
• phyto_diameters=(2, 10, :log_splitting): diameter specification for phytoplankton
• zoo_diameters=(20, 100, :linear_splitting): diameter specification for zooplankton
• parameters=(;): parameter overrides (validated against the NiPiZD 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 NiPiZD 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 NiPiZD 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. (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()