Library

A fast and flexible modelling environment for modelling the coupled interactions between ocean biogeochemistry, carbonate chemistry, and physics.

Biogeochemistry(underlying_biogeochemistry;
                light_attenuation = nothing,
                sediment = nothing,
                particles = nothing,
                modifiers = nothing)

Construct a biogeochemical model based on underlying_biogeochemistry which may have a light_attenuation model, sediment, particles, and modifiers.

Keyword Arguments

• light_attenuation_model: light attenuation model which integrated the attenuation of available light
• sediment_model: slot for AbstractSediment
• particles: slot for BiogeochemicalParticles
• modifiers: slot for components which modify the biogeochemistry when the tendencies have been calculated or when the state is updated

ScaleNegativeTracers(; tracers, scalefactors = ones(length(tracers)), warn = false, invalid_fill_value = NaN)

Constructs a modifier to scale tracers so that none are negative. Use like:

modifier = ScaleNegativeTracers((:P, :Z, :N))
biogeochemistry = Biogeochemistry(...; modifier)

This method is better, though still imperfect, method to prevent numerical errors that lead to negative tracer values compared to ZeroNegativeTracers. Please see discussion in github.

Future plans include implement a positivity-preserving timestepping scheme as the ideal alternative.

~~If warn is true then scaling will raise a warning.~~

invalid_fill_value specifies the value to set the total cell content to if the total is less than 0 (meaning that total tracer conservation can not be enforced). If the value is set to anything other than NaN this scheme no longer conserves mass. While this may be useful to prevent spurious numerics leading to crashing care should be taken that the mass doesn't deviate too much.

This scheme is similar to that used by NEMO-PISCES, although they scale the tendency rather than the value, while other Earth system models simply set negative tracers to zero, for example NCAR's MARBL and NEMO-TOPAZ2, which does not conserve mass. More complicated schemes exist, for example ROMS-BECS uses an implicite-itterative approach where each component is updated in sequence to garantee mass conservation, possibly at the expense of numerical precision.

ScaleNegativeTracers(model::UnderlyingBiogeochemicalModel; warn = false)

Construct a modifier to scale the conserved tracers in model.

If warn is true then scaling will raise a warning.

ZeroNegativeTracers(; exclude = ())

Construct a modifier that zeroes any negative tracers excluding those listed in exclude.

conserved_tracers(model::UnderlyingBiogeochemicalModel)

Returns the names of tracers which together are conserved in model

redfield(i, j, k, val_tracer_name, bgc, tracers)

Returns the redfield ratio of tracer_name from bgc at i, j, k.

redfield(val_tracer_name, bgc)
redfield(val_tracer_name, bgc, tracers)

Returns the redfield ratio of tracer_name from bgc when it is constant across the domain.

Nutrient-Phytoplankton-Zooplankton-Detritus model of Kuhn et al. (2015).

Tracers

• Nutrients: N (mmol N/m³)
• Phytoplankton: P (mmol N/m³)
• Zooplankton: Z (mmol N/m³)
• Detritus: D (mmol N/m³)

Required submodels

• Photosynthetically available radiation: PAR (W/m²)

NutrientPhytoplanktonZooplanktonDetritus(; grid,
                                           initial_photosynthetic_slope::FT = 0.1953 / day, # 1/(W/m²)/s
                                           base_maximum_growth::FT = 0.6989 / day, # 1/s
                                           nutrient_half_saturation::FT = 2.3868, # mmol N/m³
                                           base_respiration_rate::FT = 0.066 / day, # 1/s/(mmol N / m³)
                                           phyto_base_mortality_rate::FT = 0.0101 / day, # 1/s/(mmol N / m³)
                                           maximum_grazing_rate::FT = 2.1522 / day, # 1/s
                                           grazing_half_saturation::FT = 0.5573, # mmol N/m³
                                           assimulation_efficiency::FT = 0.9116, 
                                           base_excretion_rate::FT = 0.0102 / day, # 1/s/(mmol N / m³)
                                           zoo_base_mortality_rate::FT = 0.3395 / day, # 1/s/(mmol N / m³)²
                                           remineralization_rate::FT = 0.1213 / day, # 1/s

                                           surface_photosynthetically_active_radiation = default_surface_PAR,
                                           light_attenuation_model::LA =
                                               TwoBandPhotosyntheticallyActiveRadiation(; grid,
                                                                                          surface_PAR = surface_photosynthetically_active_radiation),
                                           sediment_model::S = nothing,
            
                                           sinking_speeds = (P = 0.2551/day, D = 2.7489/day),
                                           open_bottom::Bool = true,

                                           scale_negatives = false,
                                                                                  
                                           particles::P = nothing,
                                           modifiers::M = nothing)

Construct a Nutrient-Phytoplankton-Zooplankton-Detritus (NPZD) biogeochemical model.

Keyword Arguments

• grid: (required) the geometry to build the model on, required to calculate sinking
• initial_photosynthetic_slope, ..., remineralization_rate: NPZD parameter values
• surface_photosynthetically_active_radiation: function (or array in the future) for the photosynthetically available radiation at the surface, should be shape f(x, y, t)
• light_attenuation_model: light attenuation model which integrated the attenuation of available light
• sediment_model: slot for AbstractSediment
• sinking_speed: named tuple of constant sinking, of fields (i.e. ZFaceField(...)) for any tracers which sink (convention is that a sinking speed is positive, but a field will need to follow the usual down being negative)
• open_bottom: should the sinking velocity be smoothly brought to zero at the bottom to prevent the tracers leaving the domain
• scale_negatives: scale negative tracers?
• particles: slot for BiogeochemicalParticles
• modifiers: slot for components which modify the biogeochemistry when the tendencies have been calculated or when the state is updated

Example

julia> using OceanBioME

julia> using Oceananigans

julia> grid = RectilinearGrid(size=(20, 30), extent=(200, 200), topology=(Bounded, Flat, Bounded));

julia> model = NutrientPhytoplanktonZooplanktonDetritus(; grid)
NutrientPhytoplanktonZooplanktonDetritus{Float64} model, with (:P, :D) sinking 
 Light attenuation: Two-band light attenuation model (Float64)
 Sediment: Nothing
 Particles: Nothing
 Modifiers: Nothing

The Lodyc-DAMTP Ocean Biogeochemical Simulation Tools for Ecosystem and Resources (LOBSTER) model.

Tracers

• Nitrates: NO₃ (mmol N/m³)
• Ammonia: NH₄ (mmol N/m³)
• Phytoplankton: P (mmol N/m³)
• Zooplankton: Z (mmol N/m³)
• Small (slow sinking) particulate organic matter: sPOM (mmol N/m³)
• Large (fast sinking) particulate organic matter: bPOM (mmol N/m³)
• Dissolved organic matter: DOM (mmol N/m³)

Optional tracers

Carbonate chemistry

• Dissolved inorganic carbon: DIC (mmol C/m³)
• Alkalinity: Alk (meq/m³)

Oxygen chemistry

• Oxygen: O₂ (mmol O₂/m³)

Variable redfield

• Small (slow sinking) particulate organic matter carbon content: sPOC (mmol C/m³)
• Large (fast sinking) particulate organic matter carbon content: bPOC (mmol C/m³)
• Dissolved organic matter carbon content: DOC (mmol C/m³)
• When this option is enabled then the usual sPOM and bPOM change to sPON and bPON as they explicitly represent the nitrogen contained in the particulate matter

Required submodels

• Photosynthetically available radiation: PAR (W/m²)

For optional tracers:

• Temperature: T (ᵒC)
• Salinity: S (‰)

LOBSTER(; grid,
          phytoplankton_preference::FT = 0.5,
          maximum_grazing_rate::FT = 9.26e-6, # 1/s
          grazing_half_saturation::FT = 1.0, # mmol N/m³
          light_half_saturation::FT = 33.0, # W/m² (?)
          nitrate_ammonia_inhibition::FT = 3.0,
          nitrate_half_saturation::FT = 0.7, # mmol N/m³
          ammonia_half_saturation::FT = 0.001, # mmol N/m³
          maximum_phytoplankton_growthrate::FT = 1.21e-5, # 1/s
          zooplankton_assimilation_fraction::FT = 0.7,
          zooplankton_mortality::FT = 2.31e-6, # 1/s/mmol N/m³
          zooplankton_excretion_rate::FT = 5.8e-7, # 1/s
          phytoplankton_mortality::FT = 5.8e-7, # 1/s
          small_detritus_remineralisation_rate::FT = 5.88e-7, # 1/s
          large_detritus_remineralisation_rate::FT = 5.88e-7, # 1/s
          phytoplankton_exudation_fraction::FT = 0.05,
          nitrification_rate::FT = 5.8e-7, # 1/s
          ammonia_fraction_of_exudate::FT = 0.75, 
          ammonia_fraction_of_excriment::FT = 0.5,
          ammonia_fraction_of_detritus::FT = 0.0,
          phytoplankton_redfield::FT = 6.56, # mol C/mol N
          organic_redfield::FT = 6.56, # mol C/mol N
          phytoplankton_chlorophyll_ratio::FT = 1.31, # g Chl/mol N
          organic_carbon_calcate_ratio::FT = 0.1, # mol CaCO₃/mol C
          respiration_oxygen_nitrogen_ratio::FT = 10.75, # mol O/molN
          nitrification_oxygen_nitrogen_ratio::FT = 2.0, # mol O/molN
          slow_sinking_mortality_fraction::FT = 0.5, 
          fast_sinking_mortality_fraction::FT = 0.5,
          dissolved_organic_breakdown_rate::FT = 3.86e-7, # 1/s
          zooplankton_calcite_dissolution::FT = 0.3,

          surface_photosynthetically_active_radiation = default_surface_PAR,

          light_attenuation_model::LA =
              TwoBandPhotosyntheticallyActiveRadiation(; grid, 
                                                         surface_PAR = surface_photosynthetically_active_radiation),
          sediment_model::S = nothing,

          carbonates::Bool = false,
          oxygen::Bool = false,
          variable_redfield::Bool = false,

          sinking_speeds = (sPOM = 3.47e-5, bPOM = 200/day),
          open_bottom::Bool = true,

          scale_negatives = false,

          particles::P = nothing,
          modifiers::M = nothing)

Construct an instance of the LOBSTER biogeochemical model.

Keyword Arguments

• grid: (required) the geometry to build the model on, required to calculate sinking
• phytoplankton_preference, ..., dissolved_organic_breakdown_rate: LOBSTER parameter values
• surface_photosynthetically_active_radiation: funciton (or array in the future) for the photosynthetically available radiation at the surface, should be shape f(x, y, t)
• light_attenuation_model: light attenuation model which integrated the attenuation of available light
• sediment_model: slot for AbstractSediment
• carbonates, oxygen, and variable_redfield: include models for carbonate chemistry and/or oxygen chemistry and/or variable redfield ratio dissolved and particulate organic matter
• sinking_speed: named tuple of constant sinking, of fields (i.e. ZFaceField(...)) for any tracers which sink (convention is that a sinking speed is positive, but a field will need to follow the usual down being negative)
• open_bottom: should the sinking velocity be smoothly brought to zero at the bottom to prevent the tracers leaving the domain
• scale_negatives: scale negative tracers?
• particles: slot for BiogeochemicalParticles
• modifiers: slot for components which modify the biogeochemistry when the tendencies have been calculated or when the state is updated

Example

julia> using OceanBioME

julia> using Oceananigans

julia> grid = RectilinearGrid(size=(3, 3, 30), extent=(10, 10, 200));

julia> model = LOBSTER(; grid)
LOBSTER{Float64} with carbonates ❌, oxygen ❌, variable Redfield ratio ❌ and (:sPOM, :bPOM) sinking 
 Light attenuation: Two-band light attenuation model (Float64)
 Sediment: Nothing
 Particles: Nothing
 Modifiers: Nothing

Sugar kelp model of Broch and Slagstad (2012) and updated by Broch et al. (2013), Fossberg et al. (2018), and Broch et al. (2019).

Prognostic properties

• Area: A (dm²)
• Nitrogen reserve: N (gN/gSW)
• Carbon reserve: C (gC/gSW)

Tracer dependencies

• Nitrates: NO₃ (mmol N/m³)
• Photosynthetically available radiation: PAR (einstein/m²/day)

Optional

• Ammonia: NH₄ (mmol N/m³)

SLatissima(; architecture :: AR = CPU(),
             growth_rate_adjustment :: FT = 4.5,
             photosynthetic_efficiency :: FT = 4.15e-5 * 24 * 10^6 / (24 * 60 * 60),
             minimum_carbon_reserve :: FT = 0.01,
             structural_carbon :: FT = 0.2,
             exudation :: FT = 0.5,
             erosion :: FT = 0.22,
             saturation_irradiance :: FT = 90 * day/ (10 ^ 6),
             structural_dry_weight_per_area :: FT = 0.5,
             structural_dry_to_wet_weight :: FT = 0.0785,
             carbon_reserve_per_carbon :: FT = 2.1213,
             nitrogen_reserve_per_nitrogen :: FT = 2.72,
             minimum_nitrogen_reserve :: FT = 0.0126,
             maximum_nitrogen_reserve :: FT = 0.0216,
             growth_adjustment_2 :: FT = 0.039 / (2 * (1 - minimum_nitrogen_reserve / maximum_nitrogen_reserve)),
             growth_adjustment_1 :: FT = 0.18 / (2 * (1 - minimum_nitrogen_reserve / maximum_nitrogen_reserve)) - growth_adjustment_2,
             maximum_specific_growth_rate :: FT = 0.18,
             structural_nitrogen :: FT = 0.0146,
             photosynthesis_at_ref_temp_1 :: FT = 1.22e-3 * 24,
             photosynthesis_at_ref_temp_2 :: FT = 1.3e-3 * 24,
             photosynthesis_ref_temp_1 :: FT = 285.0,
             photosynthesis_ref_temp_2 :: FT = 288.0,
             photoperiod_1 :: FT = 0.85,
             photoperiod_2 :: FT = 0.3,
             respiration_at_ref_temp_1 :: FT = 2.785e-4 * 24,
             respiration_at_ref_temp_2 :: FT = 5.429e-4 * 24,
             respiration_ref_temp_1 :: FT = 285.0,
             respiration_ref_temp_2 :: FT = 290.0,
             photosynthesis_arrhenius_temp :: FT = (1 / photosynthesis_ref_temp_1 - 1 / photosynthesis_ref_temp_2) ^ -1 * log(photosynthesis_at_ref_temp_2 / photosynthesis_at_ref_temp_1),
             photosynthesis_low_temp :: FT = 271.0,
             photosynthesis_high_temp :: FT = 296.0,
             photosynthesis_high_arrhenius_temp :: FT = 1414.87,
             photosynthesis_low_arrhenius_temp :: FT = 4547.89,
             respiration_arrhenius_temp :: FT = (1 / respiration_ref_temp_1 - 1 / respiration_ref_temp_2) ^ -1 * log(respiration_at_ref_temp_2 / respiration_at_ref_temp_1),
             current_speed_for_0p65_uptake :: FT = 0.03,
             nitrate_half_saturation :: FT = 4.0,
             ammonia_half_saturation :: FT = 1.3,
             maximum_nitrate_uptake :: FT = 10 * structural_dry_weight_per_area * 24 * 14 / (10^6),
             maximum_ammonia_uptake :: FT = 12 * structural_dry_weight_per_area * 24 * 14 / (10^6),
             current_1 :: FT = 0.72,
             current_2 :: FT = 0.28,
             current_3 :: FT = 0.045,
             respiration_reference_A :: FT = 1.11e-4 * 24,
             respiration_reference_B :: FT = 5.57e-5 * 24,
             exudation_redfield_ratio :: FT = Inf,

             prescribed_velocity :: U = 0.1,

             #position
             x :: P = on_architecture(architecture, [0.0])
             y :: P = on_architecture(architecture, zeros(Float64, length(x))),
             z :: P = on_architecture(architecture, zeros(Float64, length(x))),

             #properties
             A :: P = on_architecture(architecture, ones(Float64, length(x)) * 30),
             N :: P = on_architecture(architecture, ones(Float64, length(x)) * 0.01),
             C :: P = on_architecture(architecture, ones(Float64, length(x)) * 0.1),

             #feedback
             nitrate_uptake :: P = on_architecture(architecture, zeros(Float64, length(x))),
             ammonia_uptake :: P = on_architecture(architecture, zeros(Float64, length(x))),
             primary_production :: P = on_architecture(architecture, zeros(Float64, length(x))),
             frond_exudation :: P = on_architecture(architecture, zeros(Float64, length(x))),
             nitrogen_erosion :: P = on_architecture(architecture, zeros(Float64, length(x))),
             carbon_erosion :: P = on_architecture(architecture, zeros(Float64, length(x))),

             custom_dynamics :: F = no_dynamics,

             scalefactor :: FT = 1.0,
             latitude :: FT = 57.5)

Keyword Arguments

• architecture: the architecture to adapt arrays to
• growth_rate_adjustment, ..., exudation_redfield_ratio: parameter values
• prescribed_velocity: functions for the relative velocity f(x, y, z, t)
• x,y and z: positions of the particles
• A, N, and C: area, nitrogen, and carbon reserves
• nitrate_uptake ... carbon_erosion: diagnostic values coupled to tracer fields
• custom_dynamics: place to add any function of form f!(particles, model, bgc, Δt)
• scalefactor: scalar scaling for tracer coupling
• latitude: model latitude for seasonal growth modulation

Light attenuation by chlorophyll as described by Karleskind et al. (2011) (implemented as twoBand) and Morel (1988).

TwoBandPhotosyntheticallyActiveRadiation(; grid, 
                                           water_red_attenuation::FT = 0.225, # 1/m
                                           water_blue_attenuation::FT = 0.0232, # 1/m
                                           chlorophyll_red_attenuation::FT = 0.037, # 1/(m * (mgChl/m³) ^ eʳ)
                                           chlorophyll_blue_attenuation::FT = 0.074, # 1/(m * (mgChl/m³) ^ eᵇ)
                                           chlorophyll_red_exponent::FT = 0.629,
                                           chlorophyll_blue_exponent::FT = 0.674,
                                           pigment_ratio::FT = 0.7,
                                           phytoplankton_chlorophyll_ratio::FT = 1.31,
                                           surface_PAR::SPAR = (x, y, t) -> 100 * max(0.0, cos(t * π / 12hours)))

Keyword Arguments

• grid: grid for building the model on
• water_red_attenuation, ..., phytoplankton_chlorophyll_ratio: parameter values
• surface_PAR: function (or array in the future) for the photosynthetically available radiation at the surface, which should be f(x, y, t) where x and y are the native coordinates (i.e. meters for rectilinear grids and latitude/longitude as appropriate)

Boundary conditions for air/sea and sediment flux.

Currently implemented:

• gasexchange (Wanninkhof, 1992)

  • Generic air-sea flux model described by Wanninkhof (1992) but only setup for CO₂ and O₂.
  • Forces the DIC and oxygen fields, and requires temp (in centigrade) and salinity, plus current DIC and ALK concentration.

• Sediments

  • Soetaert (Soetaert et al., 2000)
    • simple (integrated) sediment model described by Soetaert et al. (2000), where organic matter that sinks to the bottom is stored, decays into NO₃ and NH₄, and takes up O₂ in the process.
    • Extended to attribute the corresponding release of DIC.
    • Forced by O₂, NO₃, NH₄ and particle concentration in bottom cell.
  • Instant remineralisation
    • simple model from Aumont et al. (2015), where sinking organic matter is instantly remineralised and returned to the bottom cell
    • some fraction is stored permanently in the sediment at an efficiency given by Dunne et al. (2007)

GasExchange(; gas,
              schmidt_params::ScP = (CO₂ = (A=2073.1, B=125.62, C=3.6276, D=0.043219),
                               O₂ = (A=1953.4, B=128.0, C=3.9918, D=0.050091))[gas],
              solubility_params::βP = (CO₂ = (A₁=-60.2409, A₂=93.4517, A₃=23.3585, B₁=0.023517, B₂=-0.023656, B₃=0.0047036),
                                 O₂ = (A₁=-58.3877, A₂=85.8079, A₃=23.8439, B₁=-0.034892, B₂=0.015568, B₃=-0.0019387))[gas],
              ocean_density::FT = 1026, # kg/m³
              air_concentration::AC = (CO₂ = 413.4, O₂ = 9352.7)[gas], # ppmv, mmolO₂/m³ (20.95 mol O₂/mol air, 0.0224m^3/mol air)
              air_pressure::FT = 1.0, # atm
              average_wind_speed::FT = 10, # m/s
              field_dependencies = (CO₂ = (:DIC, :ALK), O₂ = (:OXY, ))[gas])

Construct an Oceananigans FluxBoundaryCondition for the exchange of gas with the relevant tracer (i.e., DIC for CO₂ and oxygen for O₂). Please see note for other gases.

Keyword arguments

• gas: (required) the gas to be exchanged, if :CO₂ or :O₂ are specified then all other settings may be infered
• schmidt_params : named tuple of parameters for calculating the Schmidt number using the parameterisation of Wanninkhof (1992)
• solubility_params : named tuple of parameters for calculating the solubility (for O₂ the Bunsen solubility and CO₂ K₀, see note)
• ocean_density : density of the ocean in kg/m³
• air_concentratio : concentration of the gas in air in relivant units (i.e. ppmv for CO₂ and mmol O₂/m³ for O₂), can also be a function of x, y, t, or a field
• air_pressure : air pressure in atm (only used for CO₂), can also be a function of x, y, t, or a field
• average_wind_speed : average wind speed at 10m used to calculate the gas transfer velocity by the Wanninkhof (1992) parameterisation
• field_dependencies : tracer fields that gas exchange depends on, if the defaults have different names in your model you can specify as long as they are in the same order
• pCO₂ : pCO₂ calculator

struct InstantRemineralisation

Hold the parameters and fields the simplest benthic boundary layer where organic carbon is assumed to remineralise instantly with some portion becoming N, and a fraction being permanently buried.

Burial efficiency from Dunne et al. (2007).

InstantRemineralisation(; grid,
    burial_efficiency_constant1::FT = 0.013,
    burial_efficiency_constant2::FT = 0.53,
    burial_efficiency_half_saturation::FT = 7)

Return a single-layer instant remineralisaiton model for NPZD bgc models.

Example

using OceanBioME, Oceananigans, OceanBioME.Sediments

grid = RectilinearGrid(size=(3, 3, 30), extent=(10, 10, 200))

sediment_model = InstantRemineralisation(; grid)

struct SimpleMultiG

Hold the parameters and fields for a simple "multi G" single-layer sediment model. Based on the Level 3 model described by Soetaert et al. (2000).

SimpleMultiG(; grid
               fast_decay_rate = 2/day,
               slow_decay_rate = 0.2/day,
               fast_redfield = 0.1509,
               slow_redfield = 0.13,
               fast_fraction = 0.74,
               slow_fraction = 0.26,
               refactory_fraction = 0.1,
               nitrate_oxidation_params = on_architecture(architecture(grid), [- 1.9785, 0.2261, -0.0615, -0.0289, - 0.36109, - 0.0232]),
               denitrification_params = on_architecture(architecture(grid), [- 3.0790, 1.7509, 0.0593, - 0.1923, 0.0604, 0.0662]),
               anoxic_params = on_architecture(architecture(grid), [- 3.9476, 2.6269, - 0.2426, -1.3349, 0.1826, - 0.0143]),
               solid_dep_params = on_architecture(architecture(grid), [0.233, 0.336, 982.0, - 1.548]))

Return a single-layer "multi G" sediment model (SimpleMultiG) on grid, where parameters can be optionally specified.

The model is a single layer (i.e. does not include porous diffusion) model with three classes of sediment organic matter which decay at three different rates (fast, slow, refactory). The nitrification/denitrification/anoxic mineralisation fractions default to the parameterisation of Soetaert et al. 2000; doi:10.1016/S0012-8252(00)00004-0.

This model has not yet been validated or compared to observational data. The variety of degridation processes is likely to be strongly dependent on oxygen availability (see https://bg.copernicus.org/articles/6/1273/2009/bg-6-1273-2009.pdf) so it will therefore be important to also thoroughly validate the oxygen model (also currently limited).

Example

julia> using OceanBioME, Oceananigans, OceanBioME.Sediments

julia> grid = RectilinearGrid(size=(3, 3, 30), extent=(10, 10, 200));

julia> sediment_model = SimpleMultiG(; grid)
┌ Warning: Sediment models are an experimental feature and have not yet been validated.
└ @ OceanBioME.Boundaries.Sediments ~/OceanBioME.jl/src/Boundaries/Sediments/simple_multi_G.jl:102
[ Info: This sediment model is currently only compatible with models providing NH₄, NO₃, O₂, and DIC.
Single-layer multi-G sediment model (Float64)

Integrate biogeochemical models on a single point

BoxModel(; biogeochemistry::B,
           forcing = NamedTuple(),
           timestepper = :RungeKutta3,
           clock::C = Clock(0.0, 0, 1),
           prescribed_fields::PF = (:T, :PAR))

Constructs a box model of a biogeochemistry model. Once this has been constructed you can set initial condiitons by set!(model, X=1.0...) and then run!(model).

Keyword Arguments

• biogeochemistry: (required) an OceanBioME biogeochemical model, most models must be passed a grid which can be set to BoxModelGrid for box models
• forcing: NamedTuple of additional forcing functions for the biogeochemical tracers to be integrated
• timestepper: Timestepper to integrate model
• clock: Oceananigans clock to keep track of time
• prescribed_fields: Tuple of fields names (Symbols) which are not integrated but provided in forcing as a function of time with signature f(t)

set!(model::BoxModel; kwargs...)

Set the values for a BoxModel

Arguments

• model - the model to set the arguments for

Keyword Arguments

• variables and value pairs to set

Store previous source terms before updating them.