Photosynthesis.jl

mutable struct C3Trait{FT}

Struct that contains the trait variables for C3 photosynthesis

Fields

• K_OCS::Any: Multiplier to derive internal conductance for OCS [mol μmol⁻¹]

• b₆f::Any: Total concentration of Cytochrome b₆f [μmol m⁻²]

• j_max25::Any: Maximal electron transport rate at 298.15 K [μmol m⁻² s⁻¹]

• r_d25::Any: Respiration rate at 298.15 K [μmol m⁻² s⁻¹]

• v_cmax25::Any: Maximal carboxylation rate at 298.15 K [μmol m⁻² s⁻¹]

mutable struct C4Trait{FT}

Struct that contains the trait variables for C4 photosynthesis

Fields

• K_OCS::Any: Multiplier to derive internal conductance for OCS [mol μmol⁻¹]

• r_d25::Any: Respiration rate at 298.15 K [μmol m⁻² s⁻¹]

• v_cmax25::Any: Maximal carboxylation rate at 298.15 K [μmol m⁻² s⁻¹]

• v_pmax25::Any: Maximal PEP carboxylation rate at 298.15 K [μmol m⁻² s⁻¹]

mutable struct C3State{FT}

Struct that contains the state variables for C3 photosynthesis (VJP model)

Fields

• EFF_1::Any: Coefficient 4.0/4.5 for NADPH/ATP requirement stochiometry, respectively

• EFF_2::Any: Coefficient 8.0/10.5 for NADPH/ATP requirement stochiometry, respectively

• k_npq_sus::Any: Sustained NPQ rate constant (for seasonal changes, default is zero)

mutable struct C4State{FT}

Struct that contains the state variables for C4 photosynthesis (VJP model)

Fields

• k_npq_sus::Any: Sustained NPQ rate constant (for seasonal changes, default is zero)

mutable struct LeafPhotosystemAuxil{FT}

Struct that contains the auxiliary variables for leaf photosynthesis

Fields

• a_c::Vector: RubisCO limited photosynthetic rate [μmol m⁻² s⁻¹]

• a_g::Vector: Gross photosynthetic rate [μmol m⁻² s⁻¹]

• a_i::Vector: Intermediate photosynthetic rate [μmol m⁻² s⁻¹]

• a_j::Vector: Light limited photosynthetic rate [μmol m⁻² s⁻¹]

• a_n::Vector: Net photosynthetic rate [μmol m⁻² s⁻¹]

• a_p::Vector: Product limited photosynthetic rate [μmol m⁻² s⁻¹]

• e2c::Vector: Electron to CO₂ coefficient

• f_psii::Any: Fraction of absorbed light used by PSII ETR

• j::Vector: Electron transport [μmol m⁻² s⁻¹]

• j_max::Any: Maximal electron transport rate at leaf temperature [μmol m⁻² s⁻¹]

• j_pot::Vector: Potential Electron Transport Rate [μmol m⁻² s⁻¹]

• j_psi::Vector: PSI electron transport rate after colimitation

• k_c::Any: RubisCO coefficient Kc [Pa]

• k_m::Any: Michaelis-Menten's coefficient [Pa]

• k_o::Any: RubisCO coefficient Ko [Pa]

• k_pep::Any: PEP coefficient Kpep [Pa]

• k_pep_clm::Any: PEP coefficient Kpep fro CLM (different algorithm) [Pa]

• k_q::Any: Maximal turnover rate of Cytochrome b₆f [e⁻ s⁻¹]

• γ_star::Any: CO₂ compensation point with the absence of Rd [Pa]

• r_d::Any: Respiration rate at leaf temperature [μmol m⁻² s⁻¹]

• v_cmax::Any: Maximal carboxylation rate at leaf temperature [μmol m⁻² s⁻¹]

• v_pmax::Any: Maximal PEP carboxylation rate at leaf temperature [μmol m⁻² s⁻¹]

• v_qmax::Any: Maximal Cytochrome b₆f activity [μmol e⁻ m⁻² s⁻¹]

• η::Vector: ratio between JP700 and JP680

• η_c::Any: Coupling efficiency of cyclic electron flow [mol ATP mol⁻¹ e⁻]

• η_l::Any: Coupling efficiency of linear electron flow [mol ATP mol⁻¹ e⁻]

• ϕ_d::Vector: Heat dissipation yield

• ϕ_f::Vector: Fluorescence yield

• ϕ_n::Vector: Non-photochemical yield

• ϕ_p::Vector: Photochemical yield

• ϕ_f1::Vector: Fluorescence yield of PSI

• ϕ_f2::Vector: Fluorescence yield of PSII

• f_m::Any: Dark adapted yield (Kp=0)

• f_m′::Vector: Light adapted yield (Kp=0)

• f_o::Any: Dark-adapted fluorescence yield (Kp=max)

• f_o′::Vector: Light-adapted fluorescence yield in the dark (Kp=max)

• npq::Vector: Non-Photochemical quenching

• q_e::Vector: Energy quenching

• q_p::Vector: Photochemical quenching

• k_d::Any: Rate constant for thermal dissipation

• k_n::Vector: Reversible NPQ rate constant (initially zero)

• k_p::Vector: Rate constant for photochemistry

• ϕ_psi_max::Any: Maximal PS I photochemical yield

• ϕ_psii_max::Any: max PSII yield (knpq_rev = 0, all RC open)

• cache1::Vector

• cache2::Vector

• cache3::Vector

• cache4::Vector

• cache5::Vector

• cache6::Vector

• cache7::Vector

• cache8::Vector

• cache9::Vector

• cache0::Vector

mutable struct LeafPhotosystem{FT}

Struct that contains the fields for C3 photosynthesis

Fields

• trait::Union{Photosynthesis.C3Trait{FT}, Photosynthesis.C4Trait{FT}} where FT: Trait variables

• state::Union{Photosynthesis.C3State{FT}, Photosynthesis.C4State{FT}} where FT: State variables

• auxil::Photosynthesis.LeafPhotosystemAuxil: Auxilary variables

Method configuration for the Photosynthesis model

Hierarchy of AbstractTemperatureDependency:

• Arrhenius
• ArrheniusPeak
• ArrheniusPeak2
• Q10
• Q10Peak
• Q10PeakHT
• Q10PeakLTHT

An Arrhenius type struct using

\[Y_1 = Y_0 \cdot \exp \left( \dfrac{H_a}{R T_0} - \dfrac{H_a}{R T_1} \right)\]

An ArrheniusPeak type struct using

\[Y_1 = Y_0 \cdot \exp \left( \dfrac{H_a}{R T_0} - \dfrac{H_a}{R T_1} \right) \cdot \dfrac{ 1 + \exp \left( \dfrac{S_v T_0 - H_d}{R T_0} \right) } { 1 + \exp \left( \dfrac{S_v T_1 - H_d}{R T_1} \right) }\]

An ArrheniusPeak2 type struct using

\[Y_1 = Y_0 \cdot \min \left(1, \exp \left( \dfrac{H_a}{R T_0} - \dfrac{H_a}{R T_1} \right) \right) \cdot \min \left(1, \dfrac{ 1 + \exp \left( \dfrac{S_v T_0 - H_d}{R T_0} \right) } { 1 + \exp \left( \dfrac{S_v T_1 - H_d}{R T_1} \right) } \right)\]

A Q10 type struct using

\[Y_1 = Y_0 \cdot Q_{10} ^ \dfrac{T_1 - T_0}{10}\]

A Q10Peak type struct using

\[Y_1 = Y_0 \cdot Q_{10} ^ \dfrac{T_1 - T_0}{10} \cdot \dfrac{ 1 + \exp \left( \dfrac{S_v T_0 - H_d}{R T_0} \right) } { 1 + \exp \left( \dfrac{S_v T_1 - H_d}{R T_1} \right) }\]

A Q10PeakHT type struct using

\[Y_1 = Y_0 \cdot Q_{10} ^ \dfrac{T_1 - T_0}{10} \cdot \dfrac{ 1 } { 1 + \exp \left( S_H * (T_1 - T_H) \right) }\]

A Q10PeakLTHT type struct using

\[Y_1 = Y_0 \cdot Q_{10} ^ \dfrac{T_1 - T_0}{10} \cdot \dfrac{ 1 }{ 1 + \exp \left( S_H * (T_1 - T_H) \right) } \cdot \dfrac{ 1 }{ 1 + \exp \left( S_L * (T_L - T_1) \right) }\]

temperature_correction(
            td::AbstractTemperatureDependency{FT},
            t::FT;
            t_ref::FT = td.T_REF
    ) where {FT}

Return the correction ratio for a temperature dependent variable, given

• td Arrhenius, ArrheniusPeak, ArrheniusPeak2, Q10, Q10Peak, Q10PeakHT, or Q10PeakLTHT type temperature dependency struture
• t Target temperature in K
• t_ref Reference temperature in K, default is td.T_REF (298.15 K)

temperature_corrected_value(td::AbstractTemperatureDependency{FT}, t::FT; t_ref::FT = td.T_REF) where {FT}

Return the temperature corrected value, given

• td Arrhenius, ArrheniusPeak, ArrheniusPeak2, Q10, Q10Peak, Q10PeakHT, or Q10PeakLTHT type temperature dependency struture
• t Target temperature in K
• t_ref Reference temperature in K, default is td.T_REF (298.15 K)

photosystem_temperature_dependence!(
            methods::PhotosynthesisMethods{FT},
            ps::LeafPhotosystem{FT},
            p_air::FT,
            t::FT) where {FT}

Update the temperature dependencies of C3 photosynthesis model, given

• methods PhotosynthesisMethods structure that contains rate constants, temperature dependency methods, colimitation methods, and model features
• ps LeafPhotosystem structure
• p_air Surface atmosphere pressure in Pa
• t Target temperature in K

Structure that stores rate constants for photosystems (do not split PSI and PSII)

Structure that stores rate constants for photosystem I

Structure that stores rate constants for photosystem II

photosystem_electron_transport!(
            methods::PhotosynthesisMethods{FT},
            ps::LeafPhotosystem{FT},
            ppar::Vector{FT},
            p_i::Union{FT,Vector{FT}};
            β::FT = FT(1)
    ) where {FT}

Update the electron transport rates, given

• methods PhotosynthesisMethods structure that contains rate constants, temperature dependency methods, colimitation methods, and model features
• ps LeafPhotosystem type struct
• ppar Absorbed photosynthetically active radiation in μmol m⁻² s⁻¹
• p_i Internal CO₂ partial pressure in Pa, used to compute etoc
• β Tuning factor to downregulate effective Vmax, Jmax, and Rd

Abstract type for photosynthesis rate calculation methods for Ac:

• AcMethodC3VcmaxPi
• AcMethodC4Vcmax

Method to compute rubisco-limited photosynthesis rate (Ac):

\[A_\text{c} = V_{\text{cmax}} \dfrac{(P_{\text{i}} - \Gamma)}{(P_{\text{i}} + K_{\text{m}})}\]

Method to compute rubisco-limited photosynthesis rate (Ac):

\[A_\text{c} = V_{\text{cmax}}\]

rubisco_limited_rate!(
            methods::PhotosynthesisMethods{FT},
            ps::LeafPhotosystem{FT},
            p_air::FT,
            p_co2::FT,
            g_lc::Vector{FT};
            β::FT = FT(1)
    ) where {FT}
rubisco_limited_rate!(
            methods::PhotosynthesisMethods{FT},
            ps::LeafPhotosystem{FT},
            p_i::Union{FT,Vector{FT}};
            β::FT = FT(1)
    ) where {FT}

Update the RubisCO limited photosynthetic rate, given

• methods PhotosynthesisMethods structure that contains rate constants, temperature dependency methods, colimitation methods, and model features
• ps LeafPhotosystem struct
• p_air Surface atmosphere pressure in Pa
• p_co2 Surface CO₂ partial pressure in Pa
• g_lc Leaf diffusive conductance to CO₂ in [mol m⁻² s⁻¹] (if appears in the function signature, it is meant for conductance mode)
• β Tuning factor to downregulate effective Vmax, Jmax, and Rd
• p_i Internal CO₂ partial pressure in Pa

Abstract type for photosynthesis rate calculation methods for Aj:

• AjMethodC3JmaxPi
• AjMethodC3VqmaxPi
• AjMethodC4JPSII

Method to compute electron transport-limited photosynthesis rate (Aj):

\[A_\text{j} = \dfrac{J}{4} \dfrac{(P_{\text{i}} - \Gamma)}{(P_{\text{i}} + 2 \Gamma)}\]

Method to compute electron transport-limited photosynthesis rate (Aj) using cytochrome b6f:

\[J = \dfrac{J_{\text{PSI}}}{\eta} A_{\text{j}} = \dfrac{J}{4} \dfrac{(P_{\text{i}} - \Gamma)}{(P_{\text{i}} + 2 \Gamma)}\]

Method to compute electron transport-limited photosynthesis rate (Aj) using cytochrome b6f:

\[Aj = \dfrac{J}{6}\]

light_limited_rate!(
            methods::PhotosynthesisMethods{FT},
            ps::LeafPhotosystem{FT},
            p_air::FT,
            p_co2::FT,
            g_lc::Vector{FT};
            β::FT = FT(1)
    ) where {FT}
light_limited_rate!(
            ps::LeafPhotosystem{FT}
    ) where {FT}

Update the electron transport limited photosynthetic rate, given

• methods PhotosynthesisMethods structure that contains rate constants, temperature dependency methods, colimitation methods, and model features
• ps LeafPhotosystem struct
• p_air Surface atmosphere pressure in Pa
• p_co2 Surface CO₂ partial pressure in Pa
• g_lc Leaf diffusive conductance to CO₂ in [mol m⁻² s⁻¹] (if appears in the function signature, it is meant for conductance mode)
• β Tuning factor to downregulate effective Vmax, Jmax, and Rd

Abstract type for photosynthesis rate calculation methods for Ap:

• ApMethodC3Inf
• ApMethodC3Vcmax
• ApMethodC4VcmaxPi
• ApMethodC4VpmaxPi

Method to compute product-limited photosynthesis rate (Ap) from Vcmax:

\[A_{\text{p}} = \dfrac{V_{\text{cmax}}}{2}\]

Method for models without TPU limitation:

\[A_{\text{p}} = \infty\]

Method to compute product-limited photosynthesis rate (Ap) from Vcmax:

\[A_{\text{p}} = k \cdot V_{\text{cmax}} \cdot P_{\text{i}}\]

Method to compute product-limited photosynthesis rate (Ap) from Vpmax:

\[A_{\text{p}} = V_{\text{pmax}} \dfrac{P_{\text{i}}}{(P_{\text{i}} + K_{\text{pep}})}\]

product_limited_rate!(
            methods::PhotosynthesisMethods{FT},
            ps::LeafPhotosystem{FT},
            p_air::FT,
            p_co2::FT,
            g_lc::Vector{FT};
            β::FT = FT(1)
    ) where {FT}
product_limited_rate!(
            methods::PhotosynthesisMethods{FT},
            ps::LeafPhotosystem{FT},
            p_i::Union{FT,Vector{FT}};
            β::FT = FT(1)
    ) where {FT}

Update the product limited photosynthetic rate, given

• methods PhotosynthesisMethods structure that contains rate constants, temperature dependency methods, colimitation methods, and model features
• ps LeafPhotosystem struct
• p_air Surface atmosphere pressure in Pa
• p_co2 Surface CO₂ partial pressure in Pa
• g_lc Leaf diffusive conductance to CO₂ in [mol m⁻² s⁻¹] (if appears in the function signature, it is meant for conductance mode)
• β Tuning factor to downregulate effective Vmax, Jmax, and Rd
• p_i Internal CO₂ partial pressure in Pa

Hierarchy of AbstractColimit

• MinimumColimit
• QuadraticColimit
• SerialColimit
• SquareColimit

Empty structure to indicate minimum colimitation: x = min(x₁, x₂)

Structure to indicate quadratic colimitation (contains field CURVATURE): θ⋅x² - (x₁ + x₂)⋅x + x₁x₂ = 0

Empty structure to indicate serial colimitation: x = 1 / (1/x₁ + 1/x₂)

Empty structure to indicate square colimitation: x = x₁⋅x₂ / sqrt(x₁² + x₂²)

colimited_rate(
            a_1::FT,
            a_2::FT,
            colim::AbstractColimit{FT}
    ) where {FT}

Return the minimum of two rates, given

• a_1 Rate 1
• a_2 Rate 2
• colim MinimumColimit, QuadraticColimit, SerialColimit, or SquareColimit type struct

colimited_rate!(
            a_1::Union{FT,Vector{FT}},
            a_2::Vector{FT},
            a_i::Vector{FT},
            colim::AbstractColimit{FT}
    ) where {FT}

Colimit the rates, given

• a_1 Rate 1
• a_2 Rate 2
• a_i Intermediate rate (overwritten)
• colim MinimumColimit, QuadraticColimit, SerialColimit, or SquareColimit type struct

colimit_photosynthesis!(
            methods::PhotosynthesisMethods{FT},
            ps::LeafPhotosystem{FT};
            β::FT = FT(1)
    ) where {FT}

Colimit the photosynthesis by rubisco-, light-, and product-limited photosynthetic rates, given

• methods PhotosynthesisMethods structure that contains rate constants, temperature dependency methods, colimitation methods, and model features
• ps LeafPhotosystem type photosynthesis model
• β Tuning factor to downregulate effective Vmax, Jmax, and Rd (default is 1)

Module that defines fluorescence methods used in leaf photosynthesis modeling:

Structure that stores van der Tol et al. (2013) fluorescence model parameters.

• van der Tol et al. (2013) Models of fluorescence and photosynthesis for interpreting measurements of solar-induced chlorophyll fluorescence

Structure that stores modified Han et al. (2022) fluorescence model parameters.

• Han et al. (2022) The physiological basis for estimating photosynthesis from Chla fluorescence

Structure that stores original Han et al. (2022) fluorescence model parameters.

• Han et al. (2022) The physiological basis for estimating photosynthesis from Chla fluorescence

Structure for the C3 Cytochrome fluorescence model.

photosystem_coefficients!(
            methods::PhotosynthesisMethods{FT},
            ps::LeafPhotosystem{FT},
            ppar::Vector{FT};
            β::FT = FT(1)
    ) where {FT}

Update the rate constants and coefficients in reaction center, given

• methods PhotosynthesisMethods structure that contains rate constants, temperature dependency methods, colimitation methods, and model features
• ps LeafPhotosystem type struct
• ppar Absorbed photosynthetically active radiation in μmol m⁻² s⁻¹
• β Tuning factor to downregulate effective Vmax, Jmax, and Rd

photosynthesis!(
            methods::PhotosynthesisMethods{FT},
            ps::LeafPhotosystem{FT},
            p_air::FT,
            p_co2::FT,
            ppar::Vector{FT},
            t::FT,
            g_lc::Vector{FT}
    ) where {FT}
photosynthesis!(
            methods::PhotosynthesisMethods{FT},
            ps::LeafPhotosystem{FT},
            p_air::FT,
            ppar::Vector{FT},
            t::FT,
            p_i::Union{FT,Vector{FT}}
    ) where {FT}

Update the photosynthesis rate, given

• methods PhotosynthesisMethods structure that contains rate constants, temperature dependency methods, colimitation methods, and model features
• ps LeafPhotosystem struct
• p_air Surface atmosphere pressure in Pa
• p_co2 Surface CO₂ partial pressure in Pa
• ppar Vector of photosynthetically active radiation
• t Leaf temperature in K
• g_lc Leaf diffusive conductance to CO₂ in [mol m⁻² s⁻¹] (if appears in the function signature, it is meant for conductance mode)
• p_i Vector of intercellular CO₂ partial pressures