API reference

model_summary(bgc) -> NamedTuple

Return a compact summary of a constructed biogeochemistry instance.

The returned NamedTuple contains:

• tracers::Vector{Symbol}
• auxiliary_fields::Vector{Symbol}
• parameters::Vector{Symbol}
• has_sinking_velocities::Bool

describe([io], bgc; verbose=false)

Print a human-readable summary of bgc.

Set verbose=true to print full tracer / parameter lists.

tracer_names(bgc) -> Vector{Symbol}

Return the ordered tracer symbols required by bgc.

This helper is intended for interactive inspection, so it materializes the underlying tracer-name tuple as a Vector{Symbol}.

The ordering matches Oceananigans / OceanBioME state-vector conventions.

auxiliary_field_names(bgc) -> Vector{Symbol}

Return the ordered auxiliary field symbols required by bgc.

Auxiliary fields are non-tracer state fields (for example, light or temperature) that appear in tracer tendencies.

parameter_names(bgc) -> Vector{Symbol}

Return the parameter keys available on bgc.parameters.

This list describes the resolved parameter fields available on the constructed biogeochemistry instance.

Container for plankton functional-type specifications.

PFTSpecification wraps a NamedTuple of per-PFT traits and descriptors.

Abstract supertype for biogeochemical model factories.

Wrap a callable tracer equation in a concrete, type-stable container.

CompiledEquation stores the kernel-callable function used for a single tracer tendency.

define_tracer_functions(parameters, tracers; auxiliary_fields=(:PAR,), tracer_index=nothing, sinking_velocities=nothing)

Create an AgateBGCFactory from compiled tracer equations.

tracers must be a NamedTuple that maps tracer names to CompiledEquation values. Each wrapped callable must accept the Oceananigans biogeochemistry kernel signature

f(bgc, x, y, z, t, tracers..., auxiliary_fields...)

Keyword arguments

• auxiliary_fields: ordered auxiliary values appended to the tracer argument list.
• tracer_index: explicit positional tracer index. When omitted, a scalar-only index is built from keys(tracers).
• sinking_velocities: optional prebuilt sinking-velocity fields stored on the resulting factory.