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Merge pull request #708 from CliMA/kd/rb/ar/basic_SIF_refactor
Kd/rb/ar/basic sif refactor
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117
src/standalone/Vegetation/solar_induced_fluorescence.jl
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| export SIFParameters, Lee2015SIFModel | ||
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| abstract type AbstractSIFModel{FT} <: AbstractCanopyComponent{FT} end | ||
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| """ | ||
| 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. | ||
| $(DocStringExtensions.FIELDS) | ||
| """ | ||
| @kwdef struct SIFParameters{FT <: AbstractFloat} | ||
| "The rate coefficient for florescence, unitless" | ||
| kf::FT = FT(0.05) | ||
| "Parameter used to compute the rate coefficient for heat loss in dark-adapted conditions, Tol et al. 2014, unitless" | ||
| kd_p1::FT = FT(0.03) | ||
| "Parameter used to compute the rate coefficient for heat loss in dark-adapted conditions, Tol et al. 2014, unitless" | ||
| kd_p2::FT = FT(0.0273) | ||
| "Parameter used to compute the rate coefficient for heat loss in dark-adapted conditions, Tol et al. 2014, unitless" | ||
| min_kd::FT = FT(0.087) | ||
| "Parameter used to compute the rate coefficient for heat loss in light-adapted conditions, Lee et al 2013 (unitless)" | ||
| kn_p1::FT = FT(6.2473) | ||
| "Parameter used to compute the rate coefficient for heat loss in light-adapted conditions, Lee et al 2013 (unitless)" | ||
| kn_p2::FT = FT(0.5944) | ||
| "Rate coefficient for photochemical quenching" | ||
| kp::FT = FT(4.0) | ||
| "Slope of line relating leaf-level fluorescence to spectrometer-observed fluorescence as a function of Vcmax 25. Lee et al 2015." | ||
| kappa_p1::FT = FT(0.045) | ||
| "Intercept of line relating leaf-level fluorescence to spectrometer-observed fluorescence as a function of Vcmax 25. Lee et al 2015." | ||
| kappa_p2::FT = FT(7.85) | ||
| end | ||
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| Base.eltype(::SIFParameters{FT}) where {FT} = FT | ||
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| struct Lee2015SIFModel{FT, SP <: SIFParameters{FT}} <: AbstractSIFModel{FT} | ||
| parameters::SP | ||
| function Lee2015SIFModel{FT}() where {FT} | ||
| parameters = SIFParameters{FT}() | ||
| new{FT, typeof(parameters)}(parameters) | ||
| end | ||
| end | ||
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| ClimaLand.name(model::AbstractSIFModel) = :sif | ||
| ClimaLand.auxiliary_vars(model::Lee2015SIFModel) = (:SIF,) | ||
| ClimaLand.auxiliary_types(model::Lee2015SIFModel{FT}) where {FT} = (FT,) | ||
| ClimaLand.auxiliary_domain_names(::Lee2015SIFModel) = (:surface,) | ||
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| # 4 Solar Induced Fluorescence (SIF) | ||
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| # call function below inside photosynthesis.jl p | ||
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| """ | ||
| update_SIF!( | ||
| SIF::FT, | ||
| sif_model::Lee2015SIFModel, | ||
| APAR::FT, | ||
| Tc::FT, | ||
| Vcmax25::FT, | ||
| R::FT, | ||
| T_freeze::FT, | ||
| photosynthesis_parameters, | ||
| ) where {FT} | ||
| Updates observed SIF at 755 nm in W/m^2. Note that Tc is in Kelvin, and photo | ||
| synthetic rates are in mol/m^2/s, and APAR is in PPFD. | ||
| Lee et al, 2015. Global Change Biology 21, 3469-3477, doi:10.1111/gcb.12948 | ||
| """ | ||
| function update_SIF!( | ||
| SIF, | ||
| sif_model::Lee2015SIFModel, | ||
| APAR, | ||
| Tc, | ||
| Vcmax25, | ||
| R, | ||
| T_freeze, | ||
| photosynthesis_parameters, | ||
| ) | ||
| sif_parameters = sif_model.parameters | ||
| @. SIF = compute_SIF_at_a_point( | ||
| APAR, | ||
| Tc, | ||
| Vcmax25, | ||
| R, | ||
| T_freeze, | ||
| photosynthesis_parameters, | ||
| sif_parameters, | ||
| ) | ||
| end | ||
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| Base.broadcastable(m::SIFParameters) = tuple(m) | ||
| function compute_SIF_at_a_point( | ||
| APAR::FT, | ||
| Tc::FT, | ||
| Vcmax25::FT, | ||
| R::FT, | ||
| T_freeze::FT, | ||
| photosynthesis_parameters, | ||
| sif_parameters, | ||
| ) where {FT} | ||
| (; ΔHJmax, To, θj, ϕ) = photosynthesis_parameters | ||
| Jmax = max_electron_transport(Vcmax25, ΔHJmax, Tc, To, R) | ||
| J = electron_transport(APAR, Jmax, θj, ϕ) | ||
| (; kf, kd_p1, kd_p2, min_kd, kn_p1, kn_p2, kp, kappa_p1, kappa_p2) = | ||
| sif_parameters | ||
| kd = max(kd_p1 * (Tc - T_freeze) + kd_p2, min_kd) | ||
| x = 1 - J / Jmax | ||
| kn = (kn_p1 * x - kn_p2) * x | ||
| ϕp0 = kp / (kf + kp + kn) | ||
| ϕp = J / Jmax * ϕp0 | ||
| ϕf = kf / (kf + kd + kn) * (1 - ϕp) | ||
| κ = kappa_p1 * Vcmax25 * FT(1e6) + kappa_p2 # formula expects Vcmax25 in μmol/m^2/s | ||
| F = APAR * ϕf | ||
| SIF_755 = F / κ | ||
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| return SIF_755 | ||
| end |