API reference

Introspection

Agate.Introspection.model_summary — Function

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

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Agate.Introspection.describe — Function

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

Print a human-readable summary of bgc.

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

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Agate.Introspection.tracer_names — Function

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.

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Agate.Introspection.auxiliary_field_names — Function

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.

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Agate.Introspection.parameter_names — Function

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.

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Agate.Introspection.plankton_groups — Function

plankton_groups(bgc) -> NamedTuple

Return a NamedTuple mapping plankton group symbols to the tracer symbols in each group. The group and tracer order follows the constructed runtime tracer layout.

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Agate.Introspection.plankton_tracers — Function

plankton_tracers(bgc) -> Vector{Symbol}

Return all plankton tracer symbols as a flat vector in runtime group order.

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Agate.Introspection.plankton_diameters — Function

plankton_diameters(bgc) -> Vector

Return the equivalent spherical diameters for plankton tracers in the same order as plankton_tracers(bgc). Models without plankton diameter metadata return an empty vector.

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Agate.Introspection.nonplankton_tracers — Function

nonplankton_tracers(bgc) -> Vector{Symbol}

Return the tracer symbols that are not part of a plankton group.

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Agate.Introspection.tracer_groups — Function

tracer_groups(bgc) -> NamedTuple

Return a structural grouping summary of the constructed tracer layout.

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Agate.Introspection.interaction_matrix — Function

interaction_matrix(bgc, kind::Symbol) -> NamedTuple

Return an interaction matrix with consumer and prey labels.

Supported kind values are the available interaction matrix fields, such as :palatability and :assimilation. The returned NamedTuple contains kind, matrix, rows, columns, row_axis, and column_axis. Matrix orientation follows the runtime container: rows are consumers and columns are prey.

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Interaction matrix introspection

using Agate
using Agate.Introspection

bgc = Agate.Models.NiPiZD.construct()
pal = interaction_matrix(bgc, :palatability)

pal.rows     # consumer labels
pal.columns  # prey labels
pal.matrix   # consumer-by-prey matrix

Construction API

Agate.Manifests.export_manifest — Function

export_manifest(path, setup) -> path

Write an Agate model setup manifest to path as pretty-printed JSON.

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Agate.Manifests.construct_from_manifest — Function

construct_from_manifest(setup; grid=nothing, arch=nothing) -> bgc
construct_from_manifest(path::AbstractString; grid=nothing, arch=nothing) -> bgc

Reconstruct an Agate biogeochemistry object from an exported model setup.

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Agate.Configuration.PFTSpecification — Type

Container for plankton functional-type specifications.

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

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Agate.Factories.AbstractBGCFactory — Type

Abstract supertype for biogeochemical model factories.

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Agate.Equations.CompiledEquation — Type

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

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

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Agate.Construction.define_tracer_functions — Function

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.

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Plankton communities and size structure

Agate.Configuration.build_plankton_community — Function

Build a plankton community from a base community spec.

This helper updates the size structure for one or more plankton groups, leaving all other group fields intact. Size-class counts are inferred from explicit diameter vectors or read from structured size definitions.

The ordering of groups in the returned NamedTuple is the ordering of base (i.e. keys(base)).

Keywords

diameters=(; ...): optional per-group size-structure inputs, keyed by group symbol.

Accepted size-structure inputs

Each group size structure must define class diameters either as a generated range or as explicit values. Accepted public forms are:

(n=3, min_esd=1, max_esd=10, splitting=:log_splitting) for a generated range.
[1.0, 3.2, 10.0] for explicit class diameters.

Examples

community = build_plankton_community(base;
    diameters=(Z=zoo_size_structure, P=phyto_size_structure),
)

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