Photosynthesis

Per refactored Photosynthesis module, the only things one need to know is the public function leaf_photosynthesis! and some construtors from ClimaCache. See the examples in the methods below for details about how to use the function. The steps for computing photosynthetic rates are

• Update temperature dependent variables using photosystem_temperature_dependence!
• Calculate electron transport rate using photosystem_electron_transport!
• Calculate RubisCO limited rate using rubisco_limited_rate!
• Calculate light limited rate using light_limited_rate!
• Calculate product limited rate using product_limited_rate!
• Calculate gross and net rates using colimit_photosynthesis!
• Update fluorescence related variables using photosystem_coefficients!

leaf_photosynthesis!(lf::Union{Leaf{FT}, Leaves2D{FT}}, air::AirLayer{FT}, g_lc::FT, ppar::FT, t::FT = lf.t) where {FT<:AbstractFloat}
leaf_photosynthesis!(lf::Leaves1D{FT}, air::AirLayer{FT}, g_lc::FT, ppar::FT, t::FT) where {FT<:AbstractFloat}

Updates leaf photosynthetic rates based on CO₂ partial pressure (for StomataModels.jl temporary use), given

• lf Leaf, Leaves1D, or Leaves2D type structure that stores biophysical, reaction center, and photosynthesis model structures
• air AirLayer structure for environmental conditions like O₂ partial pressure
• g_lc Leaf diffusive conductance to CO₂ in [mol m⁻² s⁻¹], default is leaf._g_CO₂
• ppar APAR used for photosynthesis
• t Leaf temperature in [K]

leaf_photosynthesis!(lf::Union{Leaf{FT}, Leaves1D{FT}, Leaves2D{FT}}, air::AirLayer{FT}, mode::Union{GCO₂Mode, PCO₂Mode}) where {FT<:AbstractFloat}

Updates leaf photosynthetic rates based on CO₂ partial pressure or CO₂ conductance, given

• lf Leaf, Leaves1D, or Leaves2D type structure that stores biophysical, reaction center, and photosynthesis model structures
• air AirLayer structure for environmental conditions like O₂ partial pressure
• mode GCO₂Mode or PCO₂Mode that uses CO₂ conductance or partial pressure to compute photosynthetic rates

Examples

leaf = Leaf{Float64}("C3");
air  = AirLayer{Float64}();
mode = PCO₂Mode();
leaf_photosynthesis!(leaf, air, mode);

leaf_photosynthesis!(spac::MonoElementSPAC{FT}, mode::Union{GCO₂Mode, PCO₂Mode}) where {FT<:AbstractFloat}
leaf_photosynthesis!(spac::Union{MonoMLGrassSPAC{FT}, MonoMLPalmSPAC{FT}, MonoMLTreeSPAC{FT}}, mode::Union{GCO₂Mode, PCO₂Mode}) where {FT<:AbstractFloat}

Updates leaf photosynthetic rates for SPAC, given

• spac MonoElementSPAC, MonoMLGrassSPAC, MonoMLPalmSPAC, or MonoMLTreeSPAC type SPAC
• mode GCO₂Mode or PCO₂Mode

temperature_correction(td::Arrhenius{FT}, t::FT; t_ref::FT = td.T_REF) where {FT<:AbstractFloat}
temperature_correction(td::ArrheniusPeak{FT}, t::FT; t_ref::FT = td.T_REF) where {FT<:AbstractFloat}
temperature_correction(td::Q10{FT}, t::FT; t_ref::FT = td.T_REF) where {FT<:AbstractFloat}
temperature_correction(td::Q10Peak{FT}, t::FT; t_ref::FT = td.T_REF) where {FT<:AbstractFloat}

Return the correction ratio for a temperature dependent variable, given

• td Arrhenius, ArrheniusPeak, Q10, or Q10Peak 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::Union{Arrhenius{FT}, ArrheniusPeak{FT}, Q10{FT}, Q10Peak{FT}}, t::FT; t_ref::FT = td.T_REF) where {FT<:AbstractFloat}

Return the temperature corrected value, given

• td Arrhenius, ArrheniusPeak, Q10, or Q10Peak 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!(psm::C3CytochromeModel{FT}, air::AirLayer{FT}, t::FT) where {FT<:AbstractFloat}
photosystem_temperature_dependence!(psm::C3VJPModel{FT}, air::AirLayer{FT}, t::FT) where {FT<:AbstractFloat}
photosystem_temperature_dependence!(psm::C4VJPModel{FT}, air::AirLayer{FT}, t::FT) where {FT<:AbstractFloat}

Update the temperature dependencies of C3 photosynthesis model, given

• psm C3CytochromeModel, C3VJPModel, or C4VJPModel structure for photosynthesis model
• air AirLayer structure for environmental conditions like O₂ partial pressure
• t Target temperature in K

∂R∂T(leaf::Leaf{FT}) where {FT<:AbstractFloat}
∂R∂T(leaves::Leaves1D{FT}) where {FT<:AbstractFloat}
∂R∂T(leaves::Leaves2D{FT}) where {FT<:AbstractFloat}

Return the marginal increase in respiration rate per temperature, given

• leaf Leaf type leaf
• leaves Leaves1D or Leaves2D type leaf

photosystem_electron_transport!(psm::C3CytochromeModel{FT}, rc::CytochromeReactionCenter{FT}, ppar::FT, p_i::FT; β::FT = FT(1)) where {FT<:AbstractFloat}
photosystem_electron_transport!(psm::C3VJPModel{FT}, rc::VJPReactionCenter{FT}, ppar::FT, p_i::FT; β::FT = FT(1)) where {FT<:AbstractFloat}
photosystem_electron_transport!(psm::C4VJPModel{FT}, rc::VJPReactionCenter{FT}, ppar::FT, p_i::FT; β::FT = FT(1)) where {FT<:AbstractFloat}

Update the electron transport rates, given

• psm C3CytochromeModel, C3VJPModel, or C4VJPModel type C3 photosynthesis model
• rc CytochromeReactionCenter or VJPReactionCenter type photosynthesis system reaction center
• 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

This function supports two types of calculations:

• Calculate the rate from internal CO₂
• Calculate the rate from CO₂ conductance by solving a quadratic function

rubisco_limited_rate!(psm::Union{C3CytochromeModel{FT},C3VJPModel{FT}}, p_i::FT; β::FT = FT(1)) where {FT<:AbstractFloat}
rubisco_limited_rate!(psm::C4VJPModel{FT}, p_i::FT; β::FT = FT(1)) where {FT<:AbstractFloat}

Update the RubisCO limited photosynthetic rate, given

• psm C3CytochromeModel, C3VJPModel, or C4VJPModel structure for photosynthesis model
• p_i Internal CO₂ partial pressure in Pa
• β Tuning factor to downregulate effective Vmax, Jmax, and Rd

rubisco_limited_rate!(psm::Union{C3CytochromeModel{FT}, C3VJPModel{FT}}, air::AirLayer{FT}, g_lc::FT; β::FT = FT(1)) where {FT<:AbstractFloat}
rubisco_limited_rate!(psm::C4VJPModel{FT}, air::AirLayer{FT}, g_lc::FT; β::FT = FT(1)) where {FT<:AbstractFloat}

Update the RubisCO limited photosynthetic rate in conductance mode, given

• psm C3CytochromeModel, C3VJPModel, or C4VJPModel structure for photosynthesis model
• air AirLayer structure for environmental conditions like O₂ partial pressure
• g_lc Leaf diffusive conductance to CO₂ in [mol m⁻² s⁻¹]
• β Tuning factor to downregulate effective Vmax, Jmax, and Rd

This function supports two types of calculations:

• Calculate the rate from internal CO₂
• Calculate the rate from CO₂ conductance by solving a quadratic function

light_limited_rate!(psm::Union{C3CytochromeModel{FT}, C4VJPModel{FT}}) where {FT<:AbstractFloat}
light_limited_rate!(psm::C3VJPModel{FT}) where {FT<:AbstractFloat}

Update the electron transport limited photosynthetic rate, given

• psm C3CytochromeModel, C3VJPModel, or C4VJPModel structure for C3 photosynthesis model

light_limited_rate!(psm::C3CytochromeModel{FT}, rc::CytochromeReactionCenter{FT}, air::AirLayer{FT}, g_lc::FT; β::FT = FT(1)) where {FT<:AbstractFloat}
light_limited_rate!(psm::C3VJPModel{FT}, rc::VJPReactionCenter{FT}, air::AirLayer{FT}, g_lc::FT; β::FT = FT(1)) where {FT<:AbstractFloat}
light_limited_rate!(psm::C4VJPModel{FT}, rc::VJPReactionCenter{FT}, air::AirLayer{FT}, g_lc::FT; β::FT = FT(1)) where {FT<:AbstractFloat}

Update the electron transport limited photosynthetic rate in conductance mode, given

• psm C3CytochromeModel, C3VJPModel, or C4VJPModel structure for C3 photosynthesis model
• rc CytochromeReactionCenter or VJPReactionCenter type photosynthesis system reaction center
• air AirLayer structure for environmental conditions like O₂ partial pressure
• g_lc Leaf diffusive conductance to CO₂ in [mol m⁻² s⁻¹]
• β Tuning factor to downregulate effective Vmax, Jmax, and Rd

This function supports two types of calculations:

• Calculate the rate from internal CO₂
• Calculate the rate from CO₂ conductance by solving a quadratic function

product_limited_rate!(psm::Union{C3CytochromeModel{FT}, C3VJPModel{FT}}, p_i::FT; β::FT = FT(1)) where {FT<:AbstractFloat}
product_limited_rate!(psm::C4VJPModel{FT}, p_i::FT; β::FT = FT(1)) where {FT<:AbstractFloat}

Update the product limited photosynthetic rate, given

• psm C3CytochromeModel, C3VJPModel, or C4VJPModel structure for C3 photosynthesis model
• p_i Internal CO₂ partial pressure in Pa, not used in this method
• β Tuning factor to downregulate effective Vmax, Jmax, and Rd

product_limited_rate!(psm::Union{C3CytochromeModel{FT}, C3VJPModel{FT}}, air::AirLayer{FT}, g_lc::FT; β::FT = FT(1)) where {FT<:AbstractFloat}
product_limited_rate!(psm::C4VJPModel{FT}, air::AirLayer{FT}, g_lc::FT; β::FT = FT(1)) where {FT<:AbstractFloat}

Update the electron transport limited photosynthetic rate in conductance mode, given

• psm C3CytochromeModel, C3VJPModel, or C4VJPModel structure for C3 photosynthesis model
• air AirLayer structure for environmental conditions like O₂ partial pressure, not used in this method
• g_lc Leaf diffusive conductance to CO₂ in [mol m⁻² s⁻¹], not used in this method
• β Tuning factor to downregulate effective Vmax, Jmax, and Rd

colimit_photosynthesis!(psm::Union{C3CytochromeModel{FT}, C3VJPModel{FT}, C4VJPModel{FT}}; β::FT = FT(1)) where {FT<:AbstractFloat}

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

• psm C3CytochromeModel, C3VJPModel, or C4VJPModel type photosynthesis model
• β Tuning factor to downregulate effective Vmax, Jmax, and Rd (default is 1)

colimited_rate(a_1::FT, a_2::FT, colim::MinimumColimit{FT}) where {FT<:AbstractFloat}
colimited_rate(a_1::FT, a_2::FT, colim::QuadraticColimit{FT}) where {FT<:AbstractFloat}
colimited_rate(a_1::FT, a_2::FT, colim::SerialColimit{FT}) where {FT<:AbstractFloat}
colimited_rate(a_1::FT, a_2::FT, colim::SquareColimit{FT}) where {FT<:AbstractFloat}

Return the minimum of two rates, given

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

photosystem_coefficients!(psm::C3CytochromeModel{FT}, rc::CytochromeReactionCenter{FT}, ppar::FT; β::FT = FT(1)) where {FT<:AbstractFloat}
photosystem_coefficients!(psm::Union{C3VJPModel{FT}, C4VJPModel{FT}}, rc::VJPReactionCenter{FT}, ppar::FT; β::FT = FT(1)) where {FT<:AbstractFloat}

Update the rate constants and coefficients in reaction center, given

• psm C3CytochromeModel, C3VJPModel, or C4VJPModel type photosynthesis model
• rc CytochromeReactionCenter or VJPReactionCenter type photosynthesis system reaction center
• ppar Absorbed photosynthetically active radiation in μmol m⁻² s⁻¹
• β Tuning factor to downregulate effective Vmax, Jmax, and Rd