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Low level API

Agate.Utils.define_tracer_functions — Function
define_tracer_functions(
    parameters,
    tracers;
    auxiliary_fields=[:PAR],
    helper_functions=nothing,
    sinking_velocities=nothing,
)

Create an Oceananigans.Biogeochemistry model type.

Arguments

  • parameters: NamedTuple of values of the form ((<field name> = <default value>, ...)
  • tracers: Dictionary of the form (<tracer name> => <tracer method 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_velocities: optional NamedTuple of constant sinking, of fields (i.e. ZFaceField(...)) for any tracers which sink returned by OceanBioME.Sediments: sinking_tracers.
Warning

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.

Warning

The tracer expressions must use methods that are either defined within this module or passed in the helper_functions file.

Example

using Agate

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)
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