Soil Biogeochemistry

SoilCO2Model

A model for simulating the production and transport of CO₂ in the soil with dynamic source and diffusion terms.

• parameters: the parameter set

• domain: the soil domain, using ClimaCore.Domains

• boundary_conditions: the boundary conditions, of type AbstractBoundaryConditions

• sources: A tuple of sources, each of type AbstractSource

• driver: Drivers

SoilCO2ModelParameters{FT <: AbstractFloat, PSE}

A struct for storing parameters of the SoilCO2Model.

• P_sfc: Pressure at the surface of the soil (Pa)

• D_liq: Diffusivity of soil C substrate in liquid (unitless)

• ν: Soil porosity (m³ m⁻³)

• θ_a100: Air-filled porosity at soil water potential of -100 cm H₂O (~ 10 Pa)

• D_ref: Diffusion coefficient for CO₂ in air at standard temperature and pressure (m² s⁻¹)

• b: Absolute value of the slope of the line relating log(ψ) versus log(θ) (unitless)

• α_sx: Pre-exponential factor (kg C m-3 s-1)

• Ea_sx: Activation energy (J mol-1)

• kM_sx: Michaelis constant (kg C m-3)

• kM_o2: Michaelis constant for O2 (m3 m-3)

• O2_a: Volumetric fraction of O₂ in the soil air, dimensionless

• D_oa: Diffusion coefficient of oxygen in air, dimensionless

• p_sx: Fraction of soil carbon that is considered soluble, dimensionless

• earth_param_set: Physical constants used Clima-wide

MicrobeProduction{FT} <: AbstractCarbonSource{FT}

Struct for the microbe production of CO2, appearing as a source term in the differential equation.

SoilCO2FluxBC <: AbstractSoilCO2BC

A container holding the CO2 flux boundary condition, which is a function f(p,t), where p is the auxiliary state vector.

SoilCO2StateBC <: AbstractSoilCO2BC

A container holding the CO2 state boundary condition (kg CO2 m−3), which is a function f(p,t), where p is the auxiliary state vector.

AbstractSoilDriver

An abstract type for drivers of soil CO2 production. These are soil temperature, soil moisture, root carbon, soil organic matter and microbe carbon. All varying in space (horizontally and vertically) and time.

SoilDrivers

A container which passes in the soil drivers to the biogeochemistry model. These drivers are either of type Prescribed (for standalone mode) or Prognostic (for running with a prognostic model for soil temp and moisture).

• met: Soil temperature and moisture drivers - Prescribed or Prognostic

• soc: Soil SOM driver - Prescribed only

PrescribedMet <: AbstractSoilDriver

A container which holds the prescribed functions for soil temperature and moisture.

This is meant for use when running the biogeochemistry model in standalone mode, without a prognostic soil model.

• temperature: The temperature of the soil, of the form f(z::FT,t::FT) where FT <: AbstractFloat

• volumetric_liquid_fraction: Soil moisture, of the form f(z::FT,t::FT) FT <: AbstractFloat

PrescribedSOC <: AbstractSoilDriver

A container which holds the prescribed function for soil organic carbon

This is meant for use when running the biogeochemistry model without a soil organic carbon model.

• soil_organic_carbon: Carbon content of soil organic matter, of the form f(z::FT,t::FT) where FT <: AbstractFloat

volumetric_air_content(θ_w::FT,
                       params::SoilCO2ModelParameters{FT}
                       ) where {FT}

Computes the volumetric air content (θ_a) in the soil, which is related to the total soil porosity (ν) and volumetric soil water content (θ_w = θ_l+θ_i).

co2_diffusivity(
                T_soil::FT,
                θ_w::FT,
                params::SoilCO2ModelParameters{FT}
                ) where {FT}

Computes the diffusivity of CO₂ within the soil (D).

First, D0 is computed using the temperature within the soil (T_soil in K) and pressure at the surface of the soil (P_sfc in Pa), using reference values of T_ref and P_ref (273 K and 101325 Pa). Here, θ_a is the volumetric air content and θ_a100 is the volumetric air content at a soil water potential of 100cm, and b is the pore size distribution of the soil.

microbe_source(T_soil::FT,
               θ_l::FT,
               Csom::FT,
               params::SoilCO2ModelParameters{FT}
               ) where {FT}

Computes the CO₂ production in the soil by microbes, in depth and time (kg C / m^3/s), using the Dual Arrhenius Michaelis Menten model (Davidson et al., 2012).

soil_moisture(driver::PrescribedMet, p, Y, t, z)

Returns the soil moisture at location (z) and time (t) for the prescribed soil case.

soil_moisture(driver::PrognosticSoil, p, Y, t, z)

Returns the volumetric liquid fraction, computed by the soil model from the prognostic liquid and ice fractions.

soil_temperature(driver::PrescribedMet, p, Y, t, z)

Returns the soil temperature at location (z) and time (t) for the prescribed soil case.

soil_temperature(driver::PrognosticSoil, p, Y, t, z)

Returns the prognostic soil temperature.

soil_som_C(driver::PrescribedSOC, p, Y, t, z)

Returns the carbon soil organic matter (SOM) at location (z) and time (t) for the prescribed soil case.