DARWIN · Agate.jl

Agate.jl-DARWIN model

Agate.Models.DARWIN.Constructor.construct — Function

construct(;
    n_phyto=2,
    n_zoo=2,
    phyto_diameters=Dict(
        "min_diameter" => 2, "max_diameter" => 10, "splitting" => "log_splitting"
    ),
    zoo_diameters=Dict(
        "min_diameter" => 20, "max_diameter" => 100, "splitting" => "linear_splitting"
    ),
    DIC_dynamics=DIC_geider_light,
    PO4_dynamics=PO4_geider_light,
    DIN_dynamics=DIN_geider_light,
    POC_dynamics=POC_default,
    DOC_dynamics=DOC_default,
    PON_dynamics=PON_default,
    DON_dynamics=DON_default,
    POP_dynamics=POP_default,
    DOP_dynamics=DOP_default,
    phyto_dynamics=phytoplankton_growth_two_nutrients_geider_light,
    zoo_dynamics=zooplankton_default,
    phyto_args=DEFAULT_PHYTO_ARGS,
    zoo_args=DEFAULT_ZOO_ARGS,
    interaction_args=DEFAULT_INTERACTION_ARGS,
    bgc_args=DEFAULT_BGC_ARGS,
    palatability_matrix=nothing,
    assimilation_efficiency_matrix=nothing,
    sinking_tracers=nothing,
    grid=BoxModelGrid(),
    open_bottom=true,
)

Construct an Agate.jl-DARWIN model abstract type.

Info

This model is in active development and has not been validated against MITgcm-DARWIN.

Formulation

TRACERS:

∂t cⱼ = $Uⱼ$DIC - $Mⱼ$ + $Gⱼ$ - $gⱼ$

∂t DIC = ∑($Uⱼ$ DIC) + $R$DOC + $R$POC

∂t DIN = ∑($Uⱼ$DIC * $Qⱼ$N) + $R$DON + $R$PON

∂t PO4 = ∑($Uⱼ$DIC * $Qⱼ$P) + $R$DOP + $R$POP

∂t DOC = ∑($Mⱼ$DOC) + $g$DOC - $R$DOC

∂t DON = ∑($Mⱼ$DOC * $Qⱼ$N) + $g$DON - $R$DON

∂t DOP = ∑($Mⱼ$DOC * $Qⱼ$P) + $g$DOP - $R$DOP

∂t POC = ∑($Mⱼ$POC) + $g$POC - $R$POC

∂t PON = ∑($Mⱼ$POC * $Qⱼ$N) + $g$PON - $R$PON

∂t POP = ∑($Mⱼ$POC * $Qⱼ$P) + $g$POP - $R$POP

where:

$U$ = uptake
$R$ = remineralization
$M$ = mortality
$g, G$ = grazing losses and gains
$Q$ = plankton elemental ratios

TRAITS:

μmax, KR, gmax = a*Volume^b

palat = η/(1+($ratio$-$opt$)^2)^σ

where:

μmax = maximum photosynthetic growth
KR = nutrient half saturation
gmax = maximum predation rate
palat = palatability
$ratio$ = predator to prey size ratio (diameter)
$opt$ = predator to prey size optimum (diameter)
η = prey protection
σ = predator specificity

This constructor builds an Agate.jl-DARWIN 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 dissolved inorganic carbon (DIC), particulate organic matter (POC, POP, PON), dissolved organic matter (DOC, DOP, DON) and two nutrients (DIN and PO4) cycling by default, although more complex elemental 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.

The type specification includes a photosynthetic active radiation (PAR) auxiliary field.

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
DIC_dynamics: expression describing how DIC changes over time, see Agate.Models.Tracers
PO4_dynamics: expression describing how PO4 changes over time, see Agate.Models.Tracers
DIN_dynamics: expression describing how DIN changes over time, see Agate.Models.Tracers
POC_dynamics: expression describing how POC changes over time, see Agate.Models.Tracers
DOC_dynamics: expression describing how DOC changes over time, see Agate.Models.Tracers
PON_dynamics: expression describing how PON changes over time, see Agate.Models.Tracers
DON_dynamics: expression describing how DON changes over time, see Agate.Models.Tracers
POP_dynamics: expression describing how POP changes over time, see Agate.Models.Tracers
DOP_dynamics: expression describing how DOP changes 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 DARWIN.DEFAULT_PHYTO_ARGS
zoo_args: Dictionary of zooplankton parameters, for default values see DARWIN.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 DARWIN.DEFAULT_INTERACTION_ARGS
bgc_args: biogeochemistry parameters related to nutrient and detritus, for default values see DARWIN.DEFAULT_BGC_ARGS
palatability_matrix: optional palatability matrix passed as an Array, if provided then interaction_args are not used to compute this
assimilation_efficiency_matrix: optional assimilation efficiency matrix passed as an Array, if provided then interaction_args are not used to compute this
sinking_tracers: optional NamedTuple of sinking speeds (passed as positive values) of the form (<tracer name expressed as symbol> = <speed>, ...)
grid: optional Oceananigans grid object defining the geometry to build the model on, must be passed if sinking_tracers is defined, defaults to BoxModelGrid
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)

Example

using Agate.Constructors: DARWIN

darwin_2p_2z = DARWIN.construct()
darwin_2p_2z_model_obj = darwin_2p_2z()

source

Agate.Models.DARWIN.Constructor.instantiate — Function

instantiate(
    bgc_type;
    n_phyto=2,
    n_zoo=2,
    phyto_diameters=Dict(
        "min_diameter" => 2, "max_diameter" => 10, "splitting" => "log_splitting"
    ),
    zoo_diameters=Dict(
        "min_diameter" => 20, "max_diameter" => 100, "splitting" => "linear_splitting"
    ),
    phyto_args=DEFAULT_PHYTO_ARGS,
    zoo_args=DEFAULT_ZOO_ARGS,
    interaction_args=DEFAULT_INTERACTION_ARGS,
    bgc_args=DEFAULT_BGC_ARGS,
    palatability_matrix=nothing,
    assimilation_efficiency_matrix=nothing,
    sinking_tracers=nothing,
    grid=BoxModelGrid(),
    open_bottom=true,
)

A function to instantiate an object of bgc_type returned by DARWIN.construct().

The type specifies the number of phytoplankton and zooplankton in the model and includes default parameter values. The instantiate method is used to override the default values of any of the model parameters or plankton diameters.

Tip

Changing the parameter values of an existing DARWIN model type using instantiate() is useful in dynamic programming contexts such as for loops.

Arguments

bgc_type: subtype of Oceananigans.Biogeochemistry returned by DARWIN.construct() with a specified number of phytoplankton and zooplankton

Keywords

phyto_diameters: dictionary from which phyto diameters can be computed or a list of values to use (as many as the model expects)
zoo_diameters: dictionary from which zoo diameters can be computed or a list of values to use (as many as the model expects)
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 DARWIN.DEFAULT_PHYTO_ARGS
zoo_args: Dictionary of zooplankton parameters, for default values see DARWIN.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 DARWIN.DEFAULT_INTERACTION_ARGS
bgc_args: Dictionary of constant parameters used in growth functions (i.e., not size dependant plankton parameters as well as biogeochemistry parameters related to nutrient and detritus, for default values see DARWIN.DEFAULT_CONSTANT_ARGS
palatability_matrix: optional palatability matrix passed as an Array, if provided then interaction_args are not used to compute this
assimilation_efficiency_matrix: optional assimilation efficiency matrix passed as an Array, if provided then interaction_args are not used to compute this
sinking_tracers: optional NamedTuple of sinking speeds (passed as positive values) of the form (<tracer name expressed as symbol> = <speed>, ...)
grid: optional Oceananigans grid object defining the geometry to build the model on, must be passed if sinking_tracers is defined, defaults to BoxModelGrid
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)

Example

using Agate.Constructors: DARWIN

darwin_2p_2z = DARWIN.construct()

# change some parameter values
phyto_args = deepcopy(DARWIN.DEFAULT_PHYTO_ARGS)
phyto_args["allometry"]["maximum_growth_rate"]["a"] = 2
darwin_2p_2z_model_obj = DARWIN.instantiate(darwin_2p_2z; phyto_args=phyto_args)

source