Photosynthesis

SIFParameters{FT<:AbstractFloat}

The required parameters for the SIF parameterisation Lee et al, 2015. Global Change Biology 21, 3469-3477, doi:10.1111/gcb.12948.

• kf: The rate coefficient for florescence, unitless

• kd_p1: Parameter used to compute the rate coefficient for heat loss in dark-adapted conditions, Tol et al. 2014, unitless

• kd_p2: Parameter used to compute the rate coefficient for heat loss in dark-adapted conditions, Tol et al. 2014, unitless

• min_kd: Parameter used to compute the rate coefficient for heat loss in dark-adapted conditions, Tol et al. 2014, unitless

• kn_p1: Parameter used to compute the rate coefficient for heat loss in light-adapted conditions, Lee et al 2013 (unitless)

• kn_p2: Parameter used to compute the rate coefficient for heat loss in light-adapted conditions, Lee et al 2013 (unitless)

• kp: Rate coefficient for photochemical quenching

• kappa_p1: Slope of line relating leaf-level fluorescence to spectrometer-observed fluorescence as a function of Vcmax 25. Lee et al 2015.

• kappa_p2: Intercept of line relating leaf-level fluorescence to spectrometer-observed fluorescence as a function of Vcmax 25. Lee et al 2015.

FarquharParameters{
    FT<:AbstractFloat,
    MECH <: Union{FT, ClimaCore.Fields.Field},
    VC <: Union{FT, ClimaCore.Fields.Field},
}

The required parameters for the Farquhar photosynthesis model.

• Vcmax25: Vcmax at 25 °C (mol CO2/m^2/s)

• Γstar25: Γstar at 25 °C (mol/mol)

• Kc25: Michaelis-Menten parameter for CO2 at 25 °C (mol/mol)

• Ko25: Michaelis-Menten parameter for O2 at 25 °C (mol/mol)

• ΔHkc: Energy of activation for CO2 (J/mol)

• ΔHko: Energy of activation for oxygen (J/mol)

• ΔHVcmax: Energy of activation for Vcmax (J/mol)

• ΔHΓstar: Energy of activation for Γstar (J/mol)

• ΔHJmax: Energy of activation for Jmax (J/mol)

• ΔHRd: Energy of activation for Rd (J/mol)

• To: Reference temperature equal to 25 degrees Celsius (K)

• oi: Intercelluar O2 concentration (mol/mol); taken to be constant

• ϕ: Quantum yield of photosystem II (Bernacchi, 2003; unitless)

• θj: Curvature parameter, a fitting constant to compute J, unitless

• f: Constant factor appearing the dark respiration term, equal to 0.015.

• sc: Sensitivity to low water pressure, in the moisture stress factor, (Pa^{-1}) [Tuzet et al. (2003)]

• pc: Reference water pressure for the moisture stress factor (Pa) [Tuzet et al. (2003)]

• is_c3: Photosynthesis mechanism: 1.0 indicates C3, 0.0 indicates C4

OptimalityFarquharParameters{FT<:AbstractFloat}

The required parameters for the optimality Farquhar photosynthesis model. Currently, only C3 photosynthesis is supported.

• is_c3: Photosynthesis mechanism: C3 only

• Γstar25: Γstar at 25 °C (mol/mol)

• Kc25: Michaelis-Menten parameter for CO2 at 25 °C (mol/mol)

• Ko25: Michaelis-Menten parameter for O2 at 25 °C (mol/mol)

• ΔHkc: Energy of activation for CO2 (J/mol)

• ΔHko: Energy of activation for oxygen (J/mol)

• ΔHVcmax: Energy of activation for Vcmax (J/mol)

• ΔHΓstar: Energy of activation for Γstar (J/mol)

• ΔHJmax: Energy of activation for Jmax (J/mol)

• ΔHRd: Energy of activation for Rd (J/mol)

• To: Reference temperature equal to 25 degrees Celsius (K)

• oi: Intercellular O2 concentration (mol/mol); taken to be constant

• ϕ: Quantum yield of photosystem II (Bernacchi, 2003; unitless)

• θj: Curvature parameter, a fitting constant to compute J, unitless

• f: Constant factor appearing the dark respiration term, equal to 0.015.

• sc: Fitting constant to compute the moisture stress factor (Pa^{-1})

• pc: Fitting constant to compute the moisture stress factor (Pa)

• c: Constant describing cost of maintaining electron transport (unitless)

arrhenius_function(T::FT, To::FT, R::FT, ΔH::FT)

Computes the Arrhenius function at temperature T given the reference temperature To=298.15K, the universal gas constant R, and the energy activation ΔH.

See Table 11.5 of G. Bonan's textbook, Climate Change and Terrestrial Ecosystem Modeling (2019).

intercellular_co2(ca::FT, Γstar::FT, medlyn_factor::FT) where{FT}

Computes the intercellular CO2 concentration (mol/mol) given the atmospheric concentration (ca, mol/mol), the CO2 compensation (Γstar, mol/mol), and the Medlyn factor (unitless).

co2_compensation(Γstar25::FT,
                 ΔHΓstar::FT,
                 T::FT,
                 To::FT,
                 R::FT) where {FT}

Computes the CO2 compensation point (Γstar), in units of mol/mol, as a function of its value at 25 °C (Γstar25), a constant energy of activation (ΔHΓstar), a standard temperature (To), the unversal gas constant (R), and the temperature (T).

See Table 11.5 of G. Bonan's textbook, Climate Change and Terrestrial Ecosystem Modeling (2019).

rubisco_assimilation(is_c3::AbstractFloat, args...)

Calls the correct rubisco assimilation function based on the is_c3.

A is_c3 value of 1.0 corresponds to C3 photosynthesis and calls c3_rubisco_assimilation, while 0.0 corresponds to C4 photsynthesis and calls c4_rubisco_assimilation.

light_assimilation(is_c3::AbstractFloat, args...)

Calls the correct light assimilation function based on the is_c3.

A is_c3 value of 1.0 corresponds to C3 photosynthesis and calls c3_light_assimilation, while 0.0 corresponds to C4 photsynthesis and calls c4_light_assimilation.

max_electron_transport(Vcmax::FT) where {FT}

Computes the maximum potential rate of electron transport (Jmax), in units of mol/m^2/s, as a function of Vcmax at 25 °C (Vcmax25), a constant (ΔHJmax), a standard temperature (To), the unversal gas constant (R), and the temperature (T).

See Table 11.5 of G. Bonan's textbook, Climate Change and Terrestrial Ecosystem Modeling (2019).

electron_transport(APAR::FT,
                   Jmax::FT,
                   θj::FT,
                   ϕ::FT) where {FT}

Computes the rate of electron transport (J), in units of mol/m^2/s, as a function of the maximum potential rate of electron transport (Jmax), absorbed photosynthetically active radiation (APAR), an empirical "curvature parameter" (θj; Bonan Eqn 11.21) and the quantum yield of photosystem II (ϕ).

See Ch 11, G. Bonan's textbook, Climate Change and Terrestrial Ecosystem Modeling (2019).

net_photosynthesis(Ac::FT,
                   Aj::FT,
                   Rd::FT,
                   β::FT) where {FT}

Computes the total net carbon assimilation (An), in units of mol CO2/m^2/s, as a function of the Rubisco limiting factor (Ac), the electron transport limiting rate (Aj), dark respiration (Rd), and the moisture stress factor (β).

See Table 11.5 of G. Bonan's textbook, Climate Change and Terrestrial Ecosystem Modeling (2019).

optimalitymaxphotosynthetic_rates(APAR::FT, θj::FT, ϕ::FT, oi::FT, ci::FT, Γstar::FT, Kc::FT, Ko::FT)

Computes the photosynthesis rates Vcmax and Jmax in mol/m^2/s given absorbed photosynthetically active radiation (APAR), an empirical "curvature parameter" (θj; Bonan Eqn 11.21) the quantum yield of photosystem II (ϕ), the intercellular o2 content (oi), the intercellular CO2 concentration (ci), Γstar, and Kc and Ko.

See Smith et al. 2019.

moisture_stress(pl::FT,
                sc::FT,
                pc::FT) where {FT}

Computes the moisture stress factor (β), which is unitless, as a function of a constant (sc, 1/Pa), a reference pressure (pc, Pa), and the leaf water pressure (pl, Pa) .

See Eqn 12.57 of G. Bonan's textbook, Climate Change and Terrestrial Ecosystem Modeling (2019).

dark_respiration(Vcmax25::FT,
                 β::FT,
                 f::FT,
                 ΔHkc::FT,
                 T::FT,
                 To::FT,
                 R::FT) where {FT}

Computes dark respiration (Rd), in units of mol CO2/m^2/s, as a function of the maximum rate of carboxylation of Rubisco (Vcmax25), and the moisture stress factor (β), an empirical factor f is equal to 0.015, a constant (ΔHRd), a standard temperature (To), the unversal gas constant (R), and the temperature (T).

See Table 11.5 of G. Bonan's textbook, Climate Change and Terrestrial Ecosystem Modeling (2019).

compute_GPP(An::FT,
         K::FT,
         LAI::FT,
         Ω::FT) where {FT}

Computes the total canopy photosynthesis (GPP) as a function of the total net carbon assimilation (An), the extinction coefficient (K), leaf area index (LAI) and the clumping index (Ω).

MM_Kc(Kc25::FT,
      ΔHkc::FT,
      T::FT,
      To::FT,
      R::FT) where {FT}

Computes the Michaelis-Menten coefficient for CO2 (Kc), in units of mol/mol, as a function of its value at 25 °C (Kc25), a constant (ΔHkc), a standard temperature (To), the unversal gas constant (R), and the temperature (T).

See Table 11.5 of G. Bonan's textbook, Climate Change and Terrestrial Ecosystem Modeling (2019).

MM_Ko(Ko25::FT,
      ΔHko::FT,
      T::FT,
      To::FT,
      R::FT) where {FT}

Computes the Michaelis-Menten coefficient for O2 (Ko), in units of mol/mol, as a function of its value at 25 °C (Ko25), a constant (ΔHko), a standard temperature (To), the universal gas constant (R), and the temperature (T).

See Table 11.5 of G. Bonan's textbook, Climate Change and Terrestrial Ecosystem Modeling (2019).

compute_Vcmax(Vcmax25::FT,
       T::FT,
       To::FT,
       R::FT,
       ep5::FT) where {FT}

Computes the maximum rate of carboxylation of Rubisco (Vcmax), in units of mol/m^2/s, as a function of temperature (T), Vcmax at the reference temperature 25 °C (Vcmax25), the universal gas constant (R), and the reference temperature (To).

See Table 11.5 of G. Bonan's textbook, Climate Change and Terrestrial Ecosystem Modeling (2019).