Construct an instance of an size-structured NPZD model.

This constructor builds a size-structured plankton model with two plankton functional types: phytoplankton (P) and zooplankton (Z), each of which can be specified to have any number of size classes (n_phyto and n_zoo). In addition to plankton, the constructor implements idealized detritus (D) and nutrient (N) cycling by default, although more complex N and D cycling can also be defined using the nutrient_dynamics and detritus_dynamics arguments.

During model construction, the size of each plankton determines photosynthetic growth rates, nutrient half saturation constants, predation rates, and optionally predator-prey assimilation and palatability values. Alternatively, if manually defined predator-prey assimilation and palatability values are desired, these can be defined using the palatability_matrix and assimilation_efficiency_matrix arguments.

Note that if non-default *_dynamics expressions are passed, the relevant *_args also need to be specified.

Arguments

• n_phyto: number of phytoplankton to include in the model
• n_zoo: number of zooplankton to include in the model
• phyto_diameters: dictionary from which n_phyto diameters can be computed or a list of values to use
• zoo_diameters: dictionary from which zoo diameters can be computed or a list of values to use
• nutrient_dynamics: expression describing how nutrients change over time, see Agate.Models.Tracers
• detritus_dynamics: expression describing how detritus evolves over time, see Agate.Models.Tracers
• phyto_dynamics: expression describing how phytoplankton grow, see Agate.Models.Tracers
• zoo_dynamics: expression describing how zooplankton grow, see Agate.Models.Tracers
• phyto_args: Dictionary of phytoplankton parameters, for default values see Agate.Models.Constructors.DEFAULT_PHYTO_ARGS
• zoo_args: Dictionary of zooplankton parameters, for default values see Agate.Models.Constructors.DEFAULT_ZOO_ARGS
• interaction_args: Dictionary of arguments from which a palatability and assimilation efficiency matrix between all plankton can be computed, for default values see Agate.Models.Constructors.DEFAULT_INTERACTION_ARGS
• bgc_args: biogeochemistry parameters related to nutrient and detritus, for default values see Agate.Models.Constructors.DEFAULT_BGC_ARGS
• palatability_matrix: optional palatability matrix passed as a NamedArray, if provided then interaction_args are not used to compute this
• assimilation_efficiency_matrix: optional assimilation efficiency matrix passed as a NamedArray, if provided then interaction_args are not used to compute this

define_tracer_functions(
    parameters,
    tracers;
    auxiliary_fields=[:PAR],
    helper_functions=nothing,
    sinking_tracers=nothing,
    grid=nothing,
    open_bottom=false,
) -> DataType

Create an Oceananigans.Biogeochemistry model type.

Arguments

• parameters: named sequence of values of the form ((<field name> = <default value>, ...)
• tracers: dictionary of the form (<name> => <expression>, ...)

Keywords

• auxiliary_fields: an iterable of auxiliary field variables, defaults to [:PAR,]
• helper_functions: optional path to a file of helper functions used in tracer expressions
• sinking_tracers: optional NamedTuple of sinking speeds (passed as positive values) of the form (<tracer name> = <speed>, ...)
• grid: optional Oceananigans grid object defining the geometry to build the model on, must be passed if sinking_tracers is defined
• open_bottom: indicates whether the sinking velocity should be smoothly brought to zero at the bottom to prevent the tracers leaving the domain, defaults to true, which means the bottom is open and the tracers leave (i.e., no slowing of velocity to 0 is applied)

Note that the field names defined in parameters can't be any of [:x, :y, :z, :t], as these are reserved for coordinates, and they must include all parameters used in the tracers expressions. The expressions must use methods that are either defined within this module or passed in the helper_functions file.

Example

parameters = (α=2 / 3, β=4 / 3, δ=1, γ=1)
tracers = Dict("R" => :(α * R - β * R * F), "F" => :(-γ * F + δ * R * F))
LV = define_tracer_functions(parameters, tracers)