API Reference

Base type for bulk weighting/mixing schemes that calculate weighted mixture of material properties such as conductivities or densities.

abstract type AbstractClosureRelation

Base type for prognostic variable closure relations for differential equations of the form:

\[\frac{\partial g(u)}{\partial t} = F(u)\]

where F represents the RHS tendency as a function of the state variable u, and g(u) is a closure or constitutive relation that maps u to the physical units matching the tendency. Common examples in soil hydrothermal modeling are temperature-enthalpy and saturation-pressure relations.

abstract type AbstractEnergyBalanceModel{NF} <: Terrarium.AbstractModel{NF}

Base type for surface energy balance models.

abstract type AbstractGroundModel{NF} <: Terrarium.AbstractModel{NF}

Base type for ground (e.g. soil and rock) models.

abstract type AbstractHydrologyModel{NF} <: Terrarium.AbstractModel{NF}

Base type for surface hydrology models.

AbstractLandModel <: AbstractModel

Base type for full land models which couple together multiple component models.

AbstractLandProcess{NF}

Base type for all land processes which define physics or parameterizations but are not standalone models.

abstract type AbstractModel{NF}

Base type for all models.

abstract type AbstractSnowModel{NF} <: Terrarium.AbstractModel{NF}

Base type for snow models.

abstract type AbstractSoilModel{NF} <: Terrarium.AbstractGroundModel{NF}

Base type for soil ground models.

Base type for time-stepper state caches.

abstract type AbstractVariable

Base type for state variable specification.

abstract type AbstractVegetationModel{NF} <: Terrarium.AbstractModel{NF}

Base type for vegetation/carbon models.

AuxiliaryVariable{VD<:VarDims} <: AbstractVariable

Represents an auxiliary (sometimes called "diagnostic") variable with the given name and dims on the spatial grid.

ColumnGrid{NF,RectGrid<:Grids.RectilinearGrid} <: AbstractLandGrid

Represents a set of laterally independent vertical columns with dimensions (x, y, z) where x is the column dimension, y=1 is constant, and z is the vertical axis.

struct ConstantSoilCarbonDenisty{NF} <: Terrarium.AbstractSoilBiogeochemistry{NF}

Naive implementation of soil biogeochemistry that just assumes there to be a constant organic content in all soil layers.

Properties:

• ρ_soc::Any: Soil organic carbon density [kg/m^3]

• ρ_org::Any: Pure organic matter density [kg/m^3]

• por_org::Any: Natural porosity of organic material

struct FieldInitializers{VarInits<:NamedTuple} <: Terrarium.AbstractInitializer

Initializer type that allows for direct specification of Field initializer functions.

Example:

initializer = FieldInitializers(:temperature => )

FieldInitializers(; vars...)

Creates a FieldInitializers for the given variables. The first value of the pair is the name of the state variable while the second value should be a Function or callable struct of the form f(x,y,z)::Real where z is the vertical coordinate, decreasing with depth.

Example:

initializer = FieldInitializers(
    temperature = (x,y,z) -> 0.01*abs(z) + exp(z)*sin(2π*z)
)

Simple forward Euler time stepping scheme.

struct GlobalRingGrid{NF, RingGrid<:SpeedyWeather.RingGrids.AbstractGrid, RectGrid<:Oceananigans.Grids.AbstractGrid} <: Terrarium.AbstractLandGrid{NF}

Convenience wrapper around ColumnGrid that defines the columns as points on a global RingGrid.

struct HomogeneousSoil{NF} <: Terrarium.AbstractStratigraphy{NF}

Represents a soil stratigraphy of well mixed material with homogeneous soil texture.

Properties:

• texture::CryoGrid.Soils.SoilTexture{NF, NF, NF} where NF: Material composition of mineral soil componnet

The inverse quadratic (or "quadratic parallel") bulk thermal conductivity formula (Cosenza et al. 2003):

\[k = [\sum_{i=1}^N θᵢ\sqrt{kᵢ}]^2\]

Cosenza, P., Guérin, R., and Tabbagh, A.: Relationship between thermal conductivity and water content of soils using numerical modelling, European Journal of Soil Science, 54, 581–588, https://doi.org/10.1046/j.1365-2389.2003.00539.x, 2003.

struct LUEPhotosynthesis{NF} <: Terrarium.AbstractPhotosynthesis

Photosynthesis implementation from PALADYN (Willeit 2016) for C3 PFTs following the general light use efficiency model described in Haxeltine and Prentice 1996.

Authors: Maha Badri and Matteo Willeit

Properties:

• τ25::Any: Value of τ at 25°C

• Kc25::Any: Value of Kc at 25°C

• Ko25::Any: Value of Ko at 25°C

• q10_τ::Any: q10 for temperature-sensitive parameter τ

• q10_Kc::Any: q10 for temperature-sensitive parameter Kc

• q10_Ko::Any: q10 for temperature-sensitive parameter Ko

• α_leaf::Any: Leaf albedo in PAR range [-]

• cq::Any: Conversion factor for solar radiation at 550 nm from J/m² to mol/m² [mol/J]

• k_ext::Any: Extinction coefficient for radiation through vegetation [-]

• α_a::Any: Fraction of PAR assimilated at ecosystem level, relative to leaf level [-]

• t_CO2_high::Any: Parameter, PFT specific [°C]

• t_CO2_low::Any: Parameter, PFT specific [°C]

• t_photos_high::Any: Parameter, PFT specific [°C]

• t_photos_low::Any: Parameter, PFT specific [°C]

• α_C3::Any: Intrinsic quantum efficiency of CO2 uptake in C3 plants [mol/mol]

• C_mass::Any: Atomic mass of carbon [gC/mol]

• θ_r::Any: Shape parameter [-]

• day_length::Any: Day length [h/day]

• sec_day::Any: Seconds per day [s/day]

struct MedlynStomatalConductance{NF} <: Terrarium.AbstractStomatalConductance

Stomatal conductance implementation from PALADYN (Willeit 2016) following the optimal stomatal conductance model (Medlyn et al. 2011).

Authors: Maha Badri and Matteo Willeit

Properties:

• g1::Any: Parameter in optimal stomatal conductance formulation, Lin et al. 2015 [-], PFT specific

Namespace <: AbstractVariable

Represents a new variable namespace, typically from a subcomponent of the model. It is (currently) assumed that tha name of the namesapce corresponds to a property defined on the model type.

struct PALADYNAutotrophicRespiration{NF} <: Terrarium.AbstractAutotrophicRespiration

Autotrophic respiration implementation from PALADYN (Willeit 2016).

Authors: Maha Badri and Matteo Willeit

Properties:

• cn_sapwood::Any: Sapwood parameter

• cn_root::Any: Root parameter

• aws::Any: Ratio of total to respiring stem carbon, Cox 2001, PFT specific [-]

struct PALADYNCarbonDynamics{NF} <: Terrarium.AbstractVegetationCarbonDynamics

Vegetation carbon dynamics implementation following PALADYN (Willeit 2016) but considering only the sum of the vegetation carbon pools. The subsequent splitting into Cleaf, Cstem, C_root is not implemented for now.

Authors: Maha Badri

Properties:

• SLA::Any: Specific leaf area (Kattge et al. 2011) [m²/kgC], PFT specific

• awl::Any: Allometric coefficient, modified from Cox 2001 to account for bwl=1 [kgC/m²], PFT specific

• LAI_min::Any: Minimum Leaf Area Index modified from Clark et al. 2011 [m²/m²], PFT specific

• LAI_max::Any: Maximum Leaf Area Index modified from Clark et al. 2011 [m²/m²], PFT specific

• γL::Any: Leaf turnover rate (Kattge et al. 2011) [1/year], PFT specific

• γR::Any: Root turnover rate [1/year], PFT specific

• γS::Any: Stem turnover rate modified from Clark et al. 2011 [1/year], PFT specific

struct PALADYNPhenology{NF} <: Terrarium.AbstractPhenology

Vegetation phenology implementation from PALADYN (Willeit 2016).

Authors: Maha Badri and Matteo Willeit

Properties:

struct PALADYNVegetationDynamics{NF} <: Terrarium.AbstractVegetationDynamics

Vegetation dynamics implementation following PALADYN (Willeit 2016) for a single PFT based on the Lotka–Volterra approach.

Authors: Maha Badri

Properties:

• ν_seed::Any: Vegetation seed fraction [-]

• γv_min::Any: Minimum vegetation disturbance rate [1/year]

struct PhysicalConstants{NF}

A collection of general physical constants that do not (usually) need to be varied in parameter calibration.

PrescribedHydraulics{NF} <: AbstractSoilHydraulicProperties

Represents a simple case where soil hydraulic properties are directly prescribed to constant values. This is mostly provided just for testing, although it may be useful in certain cases where direct measurements of hydraulic properites are available.

Properties:

• cond_sat::Any: Hydraulic conductivity at saturation [m/s]

• porosity::Any: Prescribed soil porosity [-]

• field_capacity::Any: Prescribed field capacity [-]

• wilting_point::Any: Prescribed wilting point [-]

struct SURFEXHydraulics{NF} <: Terrarium.AbstractSoilHydraulicProperties{NF}

SURFEX parameterization of mineral soil porosity (Masson et al. 2013).

struct Simulation{Model<:Terrarium.AbstractModel, TimeStepperCache<:Terrarium.AbstractTimeStepperCache, StateVars<:Terrarium.AbstractStateVariables} <: Terrarium.AbstractSimulation

Represents the state of a "simulation" for a given model. A simulation is here defined as a particular choice of model in conjunction with values for all state variables (including the Clock) and any necessary state caches for the time-stepper.

struct SoilEnergyBalance{NF, HeatOperator<:Terrarium.AbstractHeatOperator, ThermalProps<:(SoilThermalProperties{NF})} <: Terrarium.AbstractSoilEnergyBalance{NF}

Standard implementation of the soil energy balance accounting for freezing and thawing of pore water/ice.

Properties:

• operator::Terrarium.AbstractHeatOperator: Heat transport operator

• thermal_properties::SoilThermalProperties: Soil thermal properties

struct SoilHeatCapacities{NF}

Properties:

• water::Any

• ice::Any

• air::Any

• mineral::Any

• organic::Any

struct SoilHydrology{NF, SoilWaterFluxes<:Terrarium.AbstractSoilWaterFluxes, SoilHydraulicProperties<:Terrarium.AbstractSoilHydraulicProperties{NF}, FC<:FreezeCurves.FreezeCurve} <: Terrarium.AbstractSoilHydrology{NF}

Properties:

• fluxes::Terrarium.AbstractSoilWaterFluxes: Soil water flux scheme

• hydraulic_properties::Terrarium.AbstractSoilHydraulicProperties: Soil hydraulic properties parameterization

• freezecurve::FreezeCurves.FreezeCurve: Soil freezing and water retention curve(s) from FreezeCurves.jl

struct SoilModel{NF, GridType<:Terrarium.AbstractLandGrid{NF}, Stratigraphy<:Terrarium.AbstractStratigraphy, SoilEnergy<:Terrarium.AbstractSoilEnergyBalance, SoilHydrology<:Terrarium.AbstractSoilHydrology, Biogeochemistry<:Terrarium.AbstractSoilBiogeochemistry, Constants<:PhysicalConstants{NF}, BoundaryConditions<:Terrarium.AbstractBoundaryConditions, Initializer<:Terrarium.AbstractInitializer, TimeStepper<:Terrarium.AbstractTimeStepper} <: Terrarium.AbstractSoilModel{NF}

General implementation of a 1D column model of soil energy, water, and carbon transport.

Properties:

• grid::Terrarium.AbstractLandGrid: Spatial grid type

• strat::Terrarium.AbstractStratigraphy: Stratigraphy of the soil

• energy::Terrarium.AbstractSoilEnergyBalance: Soil energy balance

• hydrology::Terrarium.AbstractSoilHydrology: Soil hydrology/water balance

• biogeochem::Terrarium.AbstractSoilBiogeochemistry: Soil biogeochemistry

• constants::PhysicalConstants: Physical constants

• boundary_conditions::Terrarium.AbstractBoundaryConditions: Boundary conditions

• initializer::Terrarium.AbstractInitializer: State variable initializer

• time_stepping::Terrarium.AbstractTimeStepper: Timestepping scheme

struct SoilThermalConductivities{NF}

Properties:

• water::Any

• ice::Any

• air::Any

• mineral::Any

• organic::Any

struct SoilThermalProperties{NF, CondWeighting}

Properties:

• cond::SoilThermalConductivities: Thermal conductivities for all constituents

• cond_bulk::Any: Thermal conductivity mixing scheme

• heatcap::SoilHeatCapacities: Thermal conductivities for all constituents

struct StateVariables{prognames, tendnames, auxnames, subnames, closurenames, ProgVars, TendVars, AuxVars, SubVars, Closures, ClockType} <: Terrarium.AbstractStateVariables

Container type for all Fields corresponding to state variables defined by a model. StateVariables partitions the fields into three categories: prognostic, tendencies, and auxiliary. Prognostic variables are those which characterize the state of the system and are assigned tendencies to be integrated by the timestepper. Auxiliary fields are additional state variables derived from the prognostic state variables but which are conditionally independent of their values at the previous time step given the current prognostic state. It is worth noting that tendencies are also treated internally as auxiliary variables; however, they are assigned their own category here since they need to be handled separately by the timestepping scheme.

TemperatureEnergyClosure

Defines the constitutive relationship between temperature and the internal energy, U, of the system, i.e:

\[U(T) = T\times C(T) - L_f \theta_{wi} (1 - F(T))\]

where T is temperature, C(T) is the temperature-dependent heat capacity, L_f is the volumetric latent heat of fusion, and F(T) is the constitutive relation between temperature and the unfrozen fraction of pore water. Note that this formulation implies that the zero

struct VegetationModel{NF, Photosynthesis<:Terrarium.AbstractPhotosynthesis, StomatalConducatance<:Terrarium.AbstractStomatalConductance, AutotrophicRespiration<:Terrarium.AbstractAutotrophicRespiration, CarbonDynamics<:Terrarium.AbstractVegetationCarbonDynamics, VegetationDynamics<:Terrarium.AbstractVegetationDynamics, Phenology<:Terrarium.AbstractPhenology, GridType<:Terrarium.AbstractLandGrid{NF}, Constants<:PhysicalConstants{NF}, BoundaryConditions<:Terrarium.AbstractBoundaryConditions, Initializer<:Terrarium.AbstractInitializer, TimeStepper<:Terrarium.AbstractTimeStepper} <: Terrarium.AbstractVegetationModel{NF}

Model for natural (unmanaged) vegetation processes for a single plant functional type (PFT). Multiple PFTs can be later handled with a TiledVegetationModel type that composes multiple VegetationModels with different parameters for each PFT.

Properties:

• grid::Terrarium.AbstractLandGrid: Spatial grid type

• photosynthesis::Terrarium.AbstractPhotosynthesis: Photosynthesis scheme

• stomatal_conductance::Terrarium.AbstractStomatalConductance: Stomatal conducantance scheme

• autotrophic_respiration::Terrarium.AbstractAutotrophicRespiration: Autotrophic respiration scheme

• phenology::Terrarium.AbstractPhenology: Phenology scheme

• carbon_dynamics::Terrarium.AbstractVegetationCarbonDynamics: Vegetation carbon pool dynamics

• vegetation_dynamics::Terrarium.AbstractVegetationDynamics: Vegetation population density or coverage fraction dynamics

• constants::PhysicalConstants: Physical constants

• boundary_conditions::Terrarium.AbstractBoundaryConditions: Boundary conditions

• initializer::Terrarium.AbstractInitializer: State variable initializer

• time_stepping::Terrarium.AbstractTimeStepper: Timestepping scheme

XY <: VarDims

Indicator type for variables that should be assigned a 2D (lateral only) field on their associated grid.

XYZ <: VarDims

Indicator type for variables that should be assigned a 3D field on their associated grid.

auxiliary(name, dims)

Convenience constructor method for AuxiliaryVariable.

compute_APAR(photo, swdown, LAI)

Computes absorbed PAR limited by the fraction of PAR assimilated at ecosystem level APAR [mol/m²/day], Eq. 62, PALADYN (Willeit 2016).

compute_Ag(photo, c_1, c_2, APAR, Vc_max, β)

Computes the daily gross photosynthesis Ag [gC/m²/day], Eqn 2, Haxeltine & Prentice 1996

compute_And(photo, c_1, c_2, APAR, Vc_max, β, Rd)

Computes the total daytime net photosynthesis And [gC/m²/day], Eqn 19, Haxeltine & Prentice 1996 + Eq. 65, PALADYN (Willeit 2016).

compute_C_veg_tend(vegcarbon_dynamics, LAI_b, NPP)

Computes the C_veg tendency based on NPP and the balanced Leaf Area Index LAI_b, Eq. 72, PALADYN (Willeit 2016)

compute_JE_JC(photo, c_1, c_2, APAR, Vc_max)

Computes the PAR-limited and the rubisco-activity-limited photosynthesis rates JE and JC [gC/m²/day], Eqn 3+5, Haxeltine & Prentice 1996.

compute_LAI(phenol, LAI_b)

Computes LAI, based on the balanced Leaf Area Index LAI_b:

compute_NPP(autoresp, GPP, Ra)

Computes Net Primary Productivity NPP as the difference between Gross Primary Production GPP and autotrophic respiration Ra in [kgC/m²/day].

compute_PAR(photo, swdown)

Computes NET Photosynthetically Active Radiation PAR [mol/m²/day].

compute_Ra(
    autoresp,
    vegcarbon_dynamics,
    T_air,
    Rd,
    phen,
    C_veg,
    GPP
)

Computes autotrophic respiration Ra as the sum of maintenance respiration Rm and growth respiration Rg in [kgC/m²/day].

compute_Rd(photo, Vc_max, β)

Computes the daily leaf respiration Rd [gC/m²/day], Eqn 10, Haxeltine & Prentice 1996 and Eq. 10 PALADYN (Willeit 2016).

compute_Rg(autoresp, GPP, Rm)

Computes growth respiration Rg in [kgC/m²/day].

compute_Rm(
    autoresp,
    vegcarbon_dynamics,
    T_air,
    Rd,
    phen,
    C_veg
)

Computes maintenance respiration Rm in [kgC/m²/day].

compute_Vc_max(
    photo,
    c_1,
    APAR,
    Kc,
    Ko,
    Γ_star,
    pres_i,
    pres_O2
)

Computes the maximum daily rate of net photosynthesis Vc_max [gC/m²/day], following the coordination hypothesis (acclimation), see Harrison 2021 Box 2. Note: this is not the same formula in PALADYN paper, this implementaion is taken from the code

compute_auxiliary!(state, model::AbstractModel)

Computes updates to all auxiliary variables based on the current prognostic state of the model.

compute_auxiliary!(idx, state, model, process, args)

compute_c1_c2(photo, T_air, Γ_star, Kc, Ko, pres_i, pres_O2)

Computes factor for light-limited assimilation c_1 and factor for RuBisCO-limited assimilation c_2, Eqs. C4+C5, PALADYN (Willeit 2016).

compute_f_deciduous(phenol)

Computes f_deciduous, a factor for smooth transition between evergreen and deciduous [-].

compute_phen(phenol)

Computes phen, the phenology factor [-].

compute_photosynthesis(
    photo,
    T_air,
    swdown,
    pres,
    co2,
    LAI,
    λc
)

Computes Gross Primary Production GPPin [kgC/m²/day] and leaf respiration Rd in [gC/m²/day]

compute_pres_i(photo, λc, pres_a)

Computes intercellular CO2 partial pressure [Pa], Eq. 67, PALADYN (Willeit 2016).

compute_resp10(autoresp)

Computes resp10

compute_tendencies!(state, model::AbstractModel)

Computes tendencies for all prognostic state variables for model stored in the given state.

compute_tendencies!(idx, state, model, process, args)

compute_vpd(T_air, q_air, pres)

Computes the vapor pressure deficit from air temperature, specific humidity, and surface pressure.

compute_Γ_star(photo, τ, pres_O2)

Computes the CO2 compensation point Γ_star, Eq. C6, PALADYN (Willeit 2016).

compute_Λ_loc(vegcarbon_dynamics, LAI_b)

Computes the local litterfall rate Λ_loc based on the balanced Leaf Area Index LAI_b (assuming evergreen PFTs), Eq. 75, PALADYN (Willeit 2016).

compute_β(photo)

Computes the soil-moisture limiting factor β, Eq. 66, PALADYN (Willeit 2016).

compute_γv(veg_dynamics)

Computes the disturbance rateγv, Eq. 80, PALADYN (Willeit 2016).

compute_λ_NPP(vegcarbon_dynamics, LAI_b)

Computes λ_NPP,a factor determining the partitioning of NPP between increase of vegetation carbon of the existing vegetated area and spreading of the given PFT based on the balanced Leaf Area Index LAI_b, Eq. 74, PALADYN (Willeit 2016).

compute_λc(stomcond, vpd)

Computes the ratio of leaf-internal and air CO2 concentration λc, derived from the optimal stomatal conductance model (Medlyn et al. 2011), Eq. 71, PALADYN (Willeit 2016).

compute_ν_star(veg_dynamics, ν)

Computes ν_star which is the maximum between the current vegetation fraction ν and the seed fraction ν_seed [-], to ensure that a PFT is always seeded.

compute_ν_tend(
    veg_dynamics,
    vegcarbon_dynamics,
    LAI_b,
    C_veg,
    ν
)

Computes the vegetation fraction tendency for a single PFT, Eq. 73, PALADYN (Willeit 2016).

create_field(var, init, bcs, grid, args; kwargs...)

Initializes a Field on grid for the variable, var, using the given initializer, init, and boundary conditions, bcs. Additional arguments are passed direclty to the Field constructor. The location of the Field is determined by the specified VarDims on var.

fastmap(f::F, iter::NamedTuple...) where {F}

Same as map for NamedTuples but with guaranteed type stability. fastmap is a @generated function which unrolls calls to f into a loop-free tuple construction expression. All named tuples must have the same keys but in no particular order. The returned NamedTuple

fastmap(f::F, iter::NTuple{N,Any}...) where {F,N}

Same as map for NTuples but with guaranteed type stability. fastmap is a @generated function which unrolls calls to f into a loop-free tuple construction expression.

get_boundary_conditions(model::AbstractModel)::AbstractBoundaryConditions

Returns the boundary conditions associated with this model.

get_dt(timestepper::AbstractTimeStepper)

Get the current timestep size for the time stepper.

get_field_boundary_conditions(bcs::AbstractBoundaryConditions, var::AbstractVariable)

Retrieve the Field boundary conditions for the corresponding variable. Defaults to returning nothing if no BC is defined.

get_field_grid(grid)

Retrieves the underlying numerical grid on which Fields are defined.

get_field_initializer(init, var)

Retrieves the initializer for the given variable var or returns nothing if not defined.

get_field_initializer(init::AbstractInitializer, var::AbstractVariable)

get_grid(model::AbstractModel)::AbstractGrid

Return the spatial grid associated with this model.

get_initializer(model::AbstractModel)::AbstractInitializer

Returns the initializer associated with this model.

get_npoints(spacing)

Return the number of vertical layers defined by this discretization.

get_spacing(spacing)

Return a Vector of vertical layer thicknesses according to the given discretization.

get_time_stepping(model::AbstractModel)::AbstractTimeStepper

Returns the time stepping scheme associated with this model.

heatcapacity(props, fracs)

Computes the bulk heat capacity of a finite volume from the given volumetric fractions.

initialize!(state, model::AbstractModel)
initialize!(state, model::AbstractModel, initializer::AbstractInitializer)

Calls initialize! on the model and its corresponding initializer. This method only needs to be implemented if initialization routines are necessary in addition to direct field/variable initializers.

Resets the simulation clock and calls initialize!(state, model) on the underlying model which should reset all state variables to their values as defiend by the model initializer.

Creates and initializes a Simulation for the given model with the given clock state. This method allocates all necessary Fields for the state variables and calls initialize!(sim). Note that this method is not type stable and should not be called in an Enzyme autodiff call.

is_adaptive(timestepper::AbstractTimeStepper)

Returns true if the given time stepper is adaptive, false otherwise.

merge_duplicates(values::Tuple)

Filters out duplicates from the given tuple. Note that this method is not type stable or allocation-free!

namespace(name)

Convenience constructor method for Namespace provided only for consistency.

organic_fraction(idx, state, bgc::ConstantSoilCarbonDenisty)

Calculate the soil organic carbon fraction at the given grid index. For ConstantSoilCarbonDenisty, this simply returns a constant parameter. Implementations of soil carbon dynamics would want to compute this based on the prognostic state of the carbon content/pool stored in the soil.

organic_fraction(bgc::ConstantSoilCarbonDenisty)

Calculate the organic solid fraction based on the prescribed SOC and natural porosity/density of the organic material.

organic_porosity(bgc::ConstantSoilCarbonDenisty)

Get the prescribed natural porosity of organic soil.

partial_pressure_CO2(pres, conc_co2)

Compute partial pressure of CO2 from surface pressure and CO2 concentration in Pa.

partial_pressure_O2(pres)

Compute partial pressure of oxygen from surface pressure in Pa.

prognostic(name, dims)

Convenience constructor method for PrognosticVariable.

run!(sim; steps, period, dt)

Run the simulation by steps or a period with dt timestep size (in seconds or Dates.Period).

thermalconductivity(props, fracs)

Computes the bulk thermal conductivity of a finite volume from the given volumetric fractions.

timestep!(state, model::AbstractModel, timestepper::AbstractTimeStepper, [dt = nothing])

Advance the model state by one time step, or by dt units of time.

Convenience dispatch for timestep! that forwards to timestep!(state, model, get_time_stepping(model), dt).

timestep!(sim)

Advance the simulation forward by one timestep with optional timestep size dt.

tuplejoin([x, y], z...)

Concatenates one or more tuples together.

vardims(::AbstractVariable)

Retrieves the grid dimensions on which this variable is defined.

variables(model::AbstractModel)

Return a Tuple of AbstractVariables (i.e. PrognosticVariable, AuxiliaryVariable, etc.) defined by the model. For models that consist of one or more sub-models, variables may optionally be grouped into namespaces by returning a NamedTuple where the keys correspond to the group names.

varname(::AbstractVariable)
varname(::AbstractClosureRelation)
varname(::Pair{Symbol})

Retrieves the name of the given variable or closure. For closure relations, varname should return the name of the variable returned by the closure relation.