ClimaCache

Environmental Conditions

ClimaCache.AirLayer — Type

mutable struct AirLayer{FT<:AbstractFloat}

Structure that stores air layer information

Fields

Z::AbstractFloat: Mean height of the layer [m]
ΔZ::AbstractFloat: Layer thickness [m]
P_AIR::AbstractFloat: Atmospheric pressure [Pa]
p_CO₂::AbstractFloat: CO₂ partial pressure [Pa]
p_H₂O::AbstractFloat: H₂O partial pressure [Pa]
t::AbstractFloat: Temperature [K]
wind::AbstractFloat: Wind speed [m s⁻¹]
e::AbstractFloat: Total energy within the air layer [J m⁻²]
n_CO₂::AbstractFloat: Mole of CO₂ per surface area [mol m⁻²]
n_H₂O::AbstractFloat: Mole of H₂O per surface area [mol m⁻²]
∂e∂t::AbstractFloat: Marginal increase in total energy [J m⁻² s⁻¹]
∂CO₂∂t::AbstractFloat: Marginal increase in total moles of CO₂ [mol m⁻² s⁻¹]
∂H₂O∂t::AbstractFloat: Marginal increase in total moles of H₂O [mol m⁻² s⁻¹]

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ClimaCache.Meteorology — Type

mutable struct Meteorology{FT<:AbstractFloat}

Structure that stores meteorological information

Fields

rain::AbstractFloat: Precipitation in form of rain (before interception) [mol m⁻²]
snow::AbstractFloat: Precipitation in form of snow (before interception) [mol m⁻²]
t_air::AbstractFloat: Air temperature as the boundary condition for canopy airspace [K]
t_precip::AbstractFloat: Precipitation temperature [K]

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ClimaCache.AbstractSoilVC — Type

abstract type AbstractSoilVC{FT<:AbstractFloat}

Hierarchy of AbstractSoilVC:

BrooksCorey
VanGenuchten

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ClimaCache.BrooksCorey — Type

mutable struct BrooksCorey{FT<:AbstractFloat} <: ClimaCache.AbstractSoilVC{FT<:AbstractFloat}

Brooks Corey soil parameters

Fields

K_MAX::AbstractFloat: Maximum soil hydraulic conductivity at 25 °C [mol m⁻¹ s⁻¹ MPa⁻¹]
B::AbstractFloat: Soil b
TYPE::String: Soil type
Ψ_SAT::AbstractFloat: Potential at saturation [MPa]
Θ_SAT::AbstractFloat: Saturated soil volumetric water content
Θ_RES::AbstractFloat: Residual soil volumetric water content

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ClimaCache.VanGenuchten — Type

mutable struct VanGenuchten{FT<:AbstractFloat} <: ClimaCache.AbstractSoilVC{FT<:AbstractFloat}

van Genuchten soil parameters

Fields

K_MAX::AbstractFloat: Maximum soil hydraulic conductivity at 25 °C [mol m⁻¹ s⁻¹ MPa⁻¹]
N::AbstractFloat: Soil n is Measure of the pore-size distribution
TYPE::String: Soil type
α::AbstractFloat: Soil α is related to the inverse of the air entry suction, α > 0
Θ_RES::AbstractFloat: Residual soil volumetric water content
Θ_SAT::AbstractFloat: Saturated soil volumetric water content
M::AbstractFloat: Soil m = 1 - 1/n

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ClimaCache.VanGenuchten — Method

VanGenuchten{FT}(name::String) where {FT<:AbstractFloat}

Constructor for VanGenuchten, given

name Soil type name, need to be Sand, Loamy Sand, Sandy Loam, Loam (default), Sandy Clay Loam, Silt Loam, Silt, Clay Loam, Silty Clay Loam, Sandy Clay, Silty Clay, and Clay.

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ClimaCache.AbstractSoilAlbedo — Type

abstract type AbstractSoilAlbedo{FT<:AbstractFloat}

Hierarchy of AbstractSoilAlbedo:

BroadbandSoilAlbedo
HyperspectralSoilAlbedo

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ClimaCache.BroadbandSoilAlbedo — Type

mutable struct BroadbandSoilAlbedo{FT<:AbstractFloat} <: ClimaCache.AbstractSoilAlbedo{FT<:AbstractFloat}

Structure for broadband soil albedo

Fields

ρ_LW::AbstractFloat: Reflectance for longwave radiation
α_CLM::Bool: Whether to use CLM soil albedo scheme
e_net_diffuse::AbstractFloat: Net diffuse radiation at top soil [W m⁻²]
e_net_direct::AbstractFloat: Net direct radiation at top soil [W m⁻²]
r_net_lw::AbstractFloat: Net longwave energy absorption [W m⁻²]
r_net_sw::AbstractFloat: Net shortwave energy absorption [W m⁻²]
ρ_sw::Vector{FT} where FT<:AbstractFloat: Reflectance for shortwave radiation (for PAR and NIR)

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ClimaCache.HyperspectralSoilAlbedo — Type

mutable struct HyperspectralSoilAlbedo{FT<:AbstractFloat} <: ClimaCache.AbstractSoilAlbedo{FT<:AbstractFloat}

Structure for hyperspectral soil albedo

Fields

DATASET::String: File path to the Netcdf dataset
DIM_NIR::Int64: Number of wavelength bins for NIR
DIM_WL::Int64: Number of wavelength bins
α_CLM::Bool: Whether to use CLM soil albedo scheme
MAT_ρ::Matrix{FT} where FT<:AbstractFloat: A matrix of characteristic curves
ρ_LW::AbstractFloat: Reflectance for longwave radiation
e_net_diffuse::Vector{FT} where FT<:AbstractFloat: Net diffuse radiation at top soil [mW m⁻² nm⁻¹]
e_net_direct::Vector{FT} where FT<:AbstractFloat: Net direct radiation at top soil [mW m⁻² nm⁻¹]
r_net_lw::AbstractFloat: Net longwave energy absorption [W m⁻²]
r_net_sw::AbstractFloat: Net shortwave energy absorption [W m⁻²]
ρ_sw::Vector{FT} where FT<:AbstractFloat: Reflectance for shortwave radiation
_tmp_vec_nir::Vector{FT} where FT<:AbstractFloat: Cache variable with length of NIR
_weight::Vector{FT} where FT<:AbstractFloat: Weights of the four characteristic curves
_ρ_sw::Vector{FT} where FT<:AbstractFloat: Cache variable to store ρPAR and ρNIR (a segmented curve)
_θ::AbstractFloat: Last soil moisture used to compute albedo

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ClimaCache.SoilLayer — Type

mutable struct SoilLayer{FT<:AbstractFloat}

Structure for soil layer

Fields

CP::AbstractFloat: Specific heat capacity of soil [J K⁻¹ kg⁻¹]
Λ_THERMAL::AbstractFloat: Soil thermal conductivity [W m⁻¹ K⁻¹]
ρ::AbstractFloat: Dry soil density [kg m⁻³]
VC::Union{ClimaCache.BrooksCorey{FT}, ClimaCache.VanGenuchten{FT}} where FT<:AbstractFloat: Soil moisture retention curve
ZS::Vector{FT} where FT<:AbstractFloat: Depth boundaries [m]
Z::AbstractFloat: Mean depth [m]
ΔZ::AbstractFloat: Layer thickness [m]
t::AbstractFloat: Temperature [K]
e::AbstractFloat: Total stored energy per volume [J m⁻³]
θ::AbstractFloat: Soil water content
∂e∂t::AbstractFloat: Marginal increase in energy [W m⁻²]
∂θ∂t::AbstractFloat: Marginal increase in soil water content [s⁻¹]
k::AbstractFloat: Soil hydraulic conductance per area [mol m⁻² s⁻¹ MPa⁻¹]
ψ::AbstractFloat: Matric potential [MPa]
_cp::AbstractFloat: Combined specific heat capacity of soil [J K⁻¹ kg⁻¹]
_λ_thermal::AbstractFloat: Combined soil thermal conductance [W m⁻² K⁻¹]

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ClimaCache.Soil — Type

mutable struct Soil{FT<:AbstractFloat}

Structure for Soil

Fields

DIM_SOIL::Int64: Dimension of soil layers
AREA::AbstractFloat: Total area of the soil [m²]
COLOR::Int64: Color class as in CLM
ZS::Vector{FT} where FT<:AbstractFloat: Soil layers boundaries
ALBEDO::Union{ClimaCache.BroadbandSoilAlbedo{FT}, ClimaCache.HyperspectralSoilAlbedo{FT}} where FT<:AbstractFloat: Albedo related structure
LAYERS::Array{ClimaCache.SoilLayer{FT}, 1} where FT<:AbstractFloat: Soil layers
runoff::AbstractFloat: Surface runoff due to heavy precipitation during the time step [mol m⁻²]
_k::Vector{FT} where FT<:AbstractFloat: Soil hydraulic conductance between layers per area [mol m⁻² s⁻¹ MPa⁻¹]
_q::Vector{FT} where FT<:AbstractFloat: Flux between layers per area [mol m⁻² s⁻¹]
_q_thermal::Vector{FT} where FT<:AbstractFloat: Thermal flux between layers per area [mol m⁻² s⁻¹]
_δt::Vector{FT} where FT<:AbstractFloat: Soil temperature difference between layers [MPa]
_δψ::Vector{FT} where FT<:AbstractFloat: Soil metric potential difference between layers [MPa]
_λ_thermal::Vector{FT} where FT<:AbstractFloat: Soil thermal conductance between layers per area [W m⁻² K⁻¹]

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

Fields

T_REF::AbstractFloat: Reference temperature [K]
VAL_REF::AbstractFloat: Uncorrected vakye at reference temperature
ΔHA::AbstractFloat: Activation energy
ΔHD::AbstractFloat: Deactivation energy
ΔSV::AbstractFloat: Entropy factor

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ClimaCache.Q10 — Type

mutable struct Q10{FT<:AbstractFloat} <: ClimaCache.AbstractTemperatureDependency{FT<:AbstractFloat}

A Q10 type struct using

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

Fields

Q_10::AbstractFloat: Power of Q10 correction
T_REF::AbstractFloat: Reference temperature [K]
VAL_REF::AbstractFloat: Uncorrected vakye at reference temperature

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ClimaCache.Q10Peak — Type

mutable struct Q10Peak{FT<:AbstractFloat} <: ClimaCache.AbstractTemperatureDependency{FT<:AbstractFloat}

A Q10Peak type struct using

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

Fields

Q_10::AbstractFloat: Power of Q10 correction
T_REF::AbstractFloat: Reference temperature [K]
VAL_REF::AbstractFloat: Uncorrected vakye at reference temperature
ΔHD::AbstractFloat: Deactivation energy
ΔSV::AbstractFloat: Entropy factor

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ClimaCache.AbstractLeaf — Type

abstract type AbstractLeaf{FT<:AbstractFloat}

Abstract type for leaf

Hierarchy of the AbstractLeaf

Leaf
Leaves1D
Leaves2D

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ClimaCache.Leaf — Type

mutable struct Leaf{FT<:AbstractFloat} <: ClimaCache.AbstractLeaf{FT<:AbstractFloat}

Structure to save leaf parameters. This structure is meant for leaf level research and canopy radiative transfer scheme without sunlit and shaded partitioning (ppar and ppar-dependent variables).

Fields

APAR_CAR::Bool: Whether APAR absorbed by carotenoid is counted as PPAR
CP::AbstractFloat: Specific heat capacity of leaf [J K⁻¹ kg⁻¹]
G_LIMITS::Vector{FT} where FT<:AbstractFloat: Minimal and maximum stomatal conductance for H₂O at 25 °C [mol m⁻² s⁻¹]
WIDTH::AbstractFloat: Leaf width [m]
BIO::Union{ClimaCache.BroadbandLeafBiophysics{FT}, ClimaCache.HyperspectralLeafBiophysics{FT}} where FT<:AbstractFloat: AbstractLeafBiophysics type leaf biophysical parameters
HS::ClimaCache.LeafHydraulics: LeafHydraulics type leaf hydraulic system
PRC::Union{ClimaCache.CytochromeReactionCenter{FT}, ClimaCache.VJPReactionCenter{FT}} where FT<:AbstractFloat: AbstractReactionCenter type photosynthesis reaction center
PSM::Union{ClimaCache.C3CytochromeModel{FT}, ClimaCache.C3VJPModel{FT}, ClimaCache.C4VJPModel{FT}} where FT<:AbstractFloat: AbstractPhotosynthesisModel type photosynthesis model
SM::ClimaCache.AbstractStomataModel: Stomatal model
g_CO₂_b::AbstractFloat: Boundary leaf diffusive conductance to CO₂ [mol m⁻² s⁻¹]
ppar::AbstractFloat: Absorbed photosynthetically active radiation used for photosynthesis [μmol m⁻² s⁻¹]
t::AbstractFloat: Current leaf temperature
e::AbstractFloat: Total stored energy per area [J m⁻²]
g_H₂O_s::AbstractFloat: Stomatal conductance to water vapor [mol m⁻² s⁻¹]
∂e∂t::AbstractFloat: Marginal increase in energy [W m⁻²]
∂g∂t::AbstractFloat: Marginal increase of conductance per time [mol m⁻² s⁻²]
a_gross::AbstractFloat: Gross photosynthetic rate [μmol m⁻² s⁻¹]
a_net::AbstractFloat: Net photosynthetic rate [μmol m⁻² s⁻¹]
_cp::AbstractFloat: Combined specific heat capacity of leaf per area [J K⁻¹ m⁻²]
_g_CO₂::AbstractFloat: Total leaf diffusive conductance to CO₂ [mol m⁻² s⁻¹]
_p_CO₂_i::AbstractFloat: Leaf internal CO₂ partial pressure [Pa]
_p_CO₂_s::AbstractFloat: Leaf surface CO₂ partial pressure [Pa]

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ClimaCache.Leaves1D — Type

mutable struct Leaves1D{FT<:AbstractFloat} <: ClimaCache.AbstractLeaf{FT<:AbstractFloat}

Structure to save leaf parameters for a single canopy layer. This structure is meant for canopy level research and canopy radiative transfer scheme with sunlit and shaded partitioning.

Fields

CP::AbstractFloat: Specific heat capacity of leaf [J K⁻¹ kg⁻¹]
G_LIMITS::Vector{FT} where FT<:AbstractFloat: Minimal and maximum stomatal conductance for H₂O at 25 °C [mol m⁻² s⁻¹]
WIDTH::AbstractFloat: Leaf width [m]
BIO::ClimaCache.BroadbandLeafBiophysics: BroadbandLeafBiophysics type leaf biophysical parameters
HS::ClimaCache.LeafHydraulics: LeafHydraulics type leaf hydraulic system
HS2::ClimaCache.LeafHydraulics: LeafHydraulics type leaf hydraulic system used for other calculations (say sunlit and shaded leaf partitioning)
PRC::Union{ClimaCache.CytochromeReactionCenter{FT}, ClimaCache.VJPReactionCenter{FT}} where FT<:AbstractFloat: AbstractReactionCenter type photosynthesis reaction center
PSM::Union{ClimaCache.C3CytochromeModel{FT}, ClimaCache.C3VJPModel{FT}, ClimaCache.C4VJPModel{FT}} where FT<:AbstractFloat: AbstractPhotosynthesisModel type photosynthesis model
SM::ClimaCache.AbstractStomataModel: Stomatal model
g_CO₂_b::Vector{FT} where FT<:AbstractFloat: Boundary leaf diffusive conductance to CO₂ [mol m⁻² s⁻¹]
ppar::Vector{FT} where FT<:AbstractFloat: Absorbed photosynthetically active radiation used for photosynthesis [μmol m⁻² s⁻¹]
t::Vector{FT} where FT<:AbstractFloat: Current leaf temperature
e::Vector{FT} where FT<:AbstractFloat: Total stored energy per area [J m⁻²]
g_H₂O_s::Vector{FT} where FT<:AbstractFloat: Stomatal conductance to water vapor [mol m⁻² s⁻¹]
∂e∂t::Vector{FT} where FT<:AbstractFloat: Marginal increase in energy [W m⁻²]
∂g∂t::Vector{FT} where FT<:AbstractFloat: Marginal increase of conductance per time [mol m⁻² s⁻²]
a_gross::Vector{FT} where FT<:AbstractFloat: Gross photosynthetic rate [μmol m⁻² s⁻¹]
a_net::Vector{FT} where FT<:AbstractFloat: Net photosynthetic rate [μmol m⁻² s⁻¹]
_cp::Vector{FT} where FT<:AbstractFloat: Combined specific heat capacity of leaf per area [J K⁻¹ m⁻²]
_g_CO₂::Vector{FT} where FT<:AbstractFloat: Total leaf diffusive conductance to CO₂ [mol m⁻² s⁻¹]
_p_CO₂_i::Vector{FT} where FT<:AbstractFloat: Leaf internal CO₂ partial pressure [Pa]
_p_CO₂_s::Vector{FT} where FT<:AbstractFloat: Leaf surface CO₂ partial pressure [Pa]

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ClimaCache.Leaves2D — Type

mutable struct Leaves2D{FT<:AbstractFloat} <: ClimaCache.AbstractLeaf{FT<:AbstractFloat}

Structure to save leaf parameters for a single canopy layer. This structure is meant for canopy level research and canopy radiative transfer scheme with sunlit and shaded partitioning as well as leaf angular distribution.

Fields

DIM_AZI::Int64: Dimension of azimuth angles
DIM_INCL::Int64: Dimension of inclination angles
APAR_CAR::Bool: Whether APAR absorbed by carotenoid is counted as PPAR
CP::AbstractFloat: Specific heat capacity of leaf [J K⁻¹ kg⁻¹]
G_LIMITS::Vector{FT} where FT<:AbstractFloat: Minimal and maximum stomatal conductance for H₂O at 25 °C [mol m⁻² s⁻¹]
WIDTH::AbstractFloat: Leaf width [m]
BIO::ClimaCache.HyperspectralLeafBiophysics: HyperspectralLeafBiophysics type leaf biophysical parameters
HS::ClimaCache.LeafHydraulics: LeafHydraulics type leaf hydraulic system
PRC::Union{ClimaCache.CytochromeReactionCenter{FT}, ClimaCache.VJPReactionCenter{FT}} where FT<:AbstractFloat: AbstractReactionCenter type photosynthesis reaction center
PSM::Union{ClimaCache.C3CytochromeModel{FT}, ClimaCache.C3VJPModel{FT}, ClimaCache.C4VJPModel{FT}} where FT<:AbstractFloat: AbstractPhotosynthesisModel type photosynthesis model
SM::ClimaCache.AbstractStomataModel: Stomatal model
g_CO₂_b::AbstractFloat: Boundary leaf diffusive conductance to CO₂ [mol m⁻² s⁻¹]
ppar_shaded::AbstractFloat: Absorbed photosynthetically active radiation used for photosynthesis for shaded leaves [μmol m⁻² s⁻¹]
ppar_sunlit::Matrix{FT} where FT<:AbstractFloat: Absorbed photosynthetically active radiation used for photosynthesis for sunlit leaves [μmol m⁻² s⁻¹]
t::AbstractFloat: Current leaf temperature [K]
e::AbstractFloat: Total stored energy per area [J m⁻²]
g_H₂O_s_shaded::AbstractFloat: Stomatal conductance to water vapor for shaded leaves [mol m⁻² s⁻¹]
g_H₂O_s_sunlit::Matrix{FT} where FT<:AbstractFloat: Stomatal conductance to water vapor for sunlit leaves [mol m⁻² s⁻¹]
∂e∂t::AbstractFloat: Marginal increase in energy [W m⁻²]
∂g∂t_shaded::AbstractFloat: Marginal increase of conductance per time for shaded leaves [mol m⁻² s⁻²]
∂g∂t_sunlit::Matrix{FT} where FT<:AbstractFloat: Marginal increase of conductance per timefor sunlit leaves [mol m⁻² s⁻²]
a_gross_shaded::AbstractFloat: Gross photosynthetic rate for shaded leaves [μmol m⁻² s⁻¹]
a_gross_sunlit::Matrix{FT} where FT<:AbstractFloat: Gross photosynthetic rate for sunlit leaves [μmol m⁻² s⁻¹]
a_net_shaded::AbstractFloat: Net photosynthetic rate for shaded leaves [μmol m⁻² s⁻¹]
a_net_sunlit::Matrix{FT} where FT<:AbstractFloat: Net photosynthetic rate for sunlit leaves [μmol m⁻² s⁻¹]
ϕ_f_shaded::AbstractFloat: Fluorescence quantum yield for shaded leaves [-]
ϕ_f_sunlit::Matrix{FT} where FT<:AbstractFloat: Fluorescence quantum yield for sunlit leaves [-]
_cp::AbstractFloat: Combined specific heat capacity of leaf per area [J K⁻¹ m⁻²]
_g_CO₂_shaded::AbstractFloat: Total leaf diffusive conductance to CO₂ for shaded leaves [mol m⁻² s⁻¹]
_g_CO₂_sunlit::Matrix{FT} where FT<:AbstractFloat: Total leaf diffusive conductance to CO₂ for sunlit leaves [mol m⁻² s⁻¹]
_p_CO₂_i_shaded::AbstractFloat: Leaf internal CO₂ partial pressure for shaded leaves [Pa]
_p_CO₂_i_sunlit::Matrix{FT} where FT<:AbstractFloat: Leaf internal CO₂ partial pressure for sunlit leaves [Pa]
_p_CO₂_s_shaded::AbstractFloat: Leaf surface CO₂ partial pressure for shaded leaves [Pa]
_p_CO₂_s_sunlit::Matrix{FT} where FT<:AbstractFloat: Leaf surface CO₂ partial pressure for sunlit leaves [Pa]

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Stomatal Models

ClimaCache.AbstractBetaParameter — Type

abstract type AbstractBetaParameter

Hierarchy of AbstractBetaParameter:

BetaParameterG1 PARAM_Y
BetaParameterKleaf PARAM_X
BetaParameterKsoil PARAM_X
BetaParameterPleaf PARAM_X
BetaParameterPsoil PARAM_X
BetaParameterVcmax PARAM_Y
BetaParameterΘ PARAM_X

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ClimaCache.BetaParameterG1 — Type

Empty struct indicating that the function tunes G1 parameter of an empirical model

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ClimaCache.BetaParameterKleaf — Type

Empty struct indicating that the beta function is based on Kleaf

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ClimaCache.BetaParameterKsoil — Type

Empty struct indicating that the beta function is based on Ksoil

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ClimaCache.BetaParameterPleaf — Type

Empty struct indicating that the beta function is based on Pleaf

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ClimaCache.BetaParameterPsoil — Type

Empty struct indicating that the beta function is based on Psoil

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ClimaCache.BetaParameterVcmax — Type

Empty struct indicating that the function tunes Vcmax for an empirical model

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ClimaCache.BetaParameterΘ — Type

Empty struct indicating that the beta function is based on soil water content

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ClimaCache.BetaFunction — Type

mutable struct BetaFunction{FT<:AbstractFloat}

Struct to tune G1 or Vcmax based on leaf hydraulic conductance

Fields

FUNC::Function: Function to turn variables to β tuning factor
PARAM_X::Union{ClimaCache.BetaParameterKleaf, ClimaCache.BetaParameterKsoil, ClimaCache.BetaParameterPleaf, ClimaCache.BetaParameterPsoil, ClimaCache.BetaParameterΘ}: Input parameter to base on
PARAM_Y::Union{ClimaCache.BetaParameterG1, ClimaCache.BetaParameterVcmax}: Target parameter to tune
β₁::AbstractFloat: Tuning factor computed
β₂::AbstractFloat: Tuning factor computed for HS2

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ClimaCache.AbstractStomataModel — Type

abstract type AbstractStomataModel{FT<:AbstractFloat}

Hierarchy of AbstractStomataModel:

AndereggSM
BallBerrySM
EllerSM
GentineSM
LeuningSM
MedlynSM
SperrySM
WangSM
Wang2SM

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ClimaCache.AndereggSM — Type

mutable struct AndereggSM{FT<:AbstractFloat} <: ClimaCache.AbstractStomataModel{FT<:AbstractFloat}

Struct for Anderegg stomatal model. The equation used for Anderegg type model is

\[\dfrac{∂Θ}{∂E} = \dfrac{2aP + b}{K}\]

where K is $\dfrac{∂E}{∂P}$.

Fields

A::AbstractFloat: Quadratic equation parameter [μmol m⁻² s⁻¹ MPa⁻²]
B::AbstractFloat: Quadratic equation parameter [μmol m⁻² s⁻¹ MPa⁻¹]
K::AbstractFloat: Slope constant [mol² m⁻² s⁻¹ μmol⁻¹]

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ClimaCache.BallBerrySM — Type

mutable struct BallBerrySM{FT<:AbstractFloat} <: ClimaCache.AbstractStomataModel{FT<:AbstractFloat}

Struct for Ball Berry stomatal model. The equation used for Ball-Berry type model is

\[gs = g0 + g1 ⋅ RH ⋅ \dfrac{A}{Cs}\]

Fields

G0::AbstractFloat: Minimal stomatal conductance [mol m⁻² s⁻¹]
G1::AbstractFloat: Slope of conductance-photosynthesis correlation [-]
β::ClimaCache.BetaFunction: Beta function to force stomatal response to soil moisture
τ::AbstractFloat: Time constant for the prognostic stomatal conductance [s]

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ClimaCache.EllerSM — Type

mutable struct EllerSM{FT<:AbstractFloat} <: ClimaCache.AbstractStomataModel{FT<:AbstractFloat}

Empty struct for Eller stomatal model. The equation used for Eller type model is

\[\dfrac{∂Θ}{∂E} = -\dfrac{∂K}{∂E} ⋅ \dfrac{A}{K}\]

where K is $\dfrac{∂E}{∂P}$.

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ClimaCache.GentineSM — Type

mutable struct GentineSM{FT<:AbstractFloat} <: ClimaCache.AbstractStomataModel{FT<:AbstractFloat}

Struct for Gentine stomatal model. The equation used for Gentine type model is

\[gs = g0 + g1 ⋅ \dfrac{k_{leaf}}{k_{max}} ⋅ \dfrac{A}{Ci}.\]

Fields

G0::AbstractFloat: Minimal stomatal conductance [mol m⁻² s⁻¹]
G1::AbstractFloat: Slope of conductance-photosynthesis correlation [-]
β::ClimaCache.BetaFunction: Beta function to force stomatal response to soil moisture
τ::AbstractFloat: Time constant for the prognostic stomatal conductance [s]

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ClimaCache.LeuningSM — Type

mutable struct LeuningSM{FT<:AbstractFloat} <: ClimaCache.AbstractStomataModel{FT<:AbstractFloat}

Struct for Leuning stomatal model. The equation used for Leuning type model is

\[gs = g0 + g1 ⋅ \dfrac{A}{Cs - Γ^{*}} ⋅ \dfrac{1}{1 + \dfrac{VPD}{d0}}\]

Fields

D0::AbstractFloat: Fitting parameter of d/d0 below the fraction, same unit as vpd [Pa]
G0::AbstractFloat: Minimal stomatal conductance [mol m⁻² s⁻¹]
G1::AbstractFloat: Slope of conductance-photosynthesis correlation [-]
β::ClimaCache.BetaFunction: Beta function to force stomatal response to soil moisture
τ::AbstractFloat: Time constant for the prognostic stomatal conductance [s]

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ClimaCache.MedlynSM — Type

mutable struct MedlynSM{FT<:AbstractFloat} <: ClimaCache.AbstractStomataModel{FT<:AbstractFloat}

Struct for Medlyn stomatal model. The equation used for Medlyn type model is

\[gs = g0 + 1.6 ⋅ \left( 1 + \dfrac{g1}{\sqrt{VPD}} \right) ⋅ \dfrac{A}{Ca}\]

Fields

G0::AbstractFloat: Minimal stomatal conductance [mol m⁻² s⁻¹]
G1::AbstractFloat: Slope of conductance-photosynthesis correlation [sqrt(Pa)]
β::ClimaCache.BetaFunction: Beta function to force stomatal response to soil moisture
τ::AbstractFloat: Time constant for the prognostic stomatal conductance [s]

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ClimaCache.SperrySM — Type

mutable struct SperrySM{FT<:AbstractFloat} <: ClimaCache.AbstractStomataModel{FT<:AbstractFloat}

Empty struct for Sperry stomatal model. The equation used for Sperry type model is

\[\dfrac{∂Θ}{∂E} = -\dfrac{∂K}{∂E} ⋅ \dfrac{A_{max}}{K_{max}}\]

where K is $\dfrac{∂E}{∂P}$.

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ClimaCache.WangSM — Type

mutable struct WangSM{FT<:AbstractFloat} <: ClimaCache.AbstractStomataModel{FT<:AbstractFloat}

Empty struct for Wang stomatal model. The equation used for Wang type model is

\[\dfrac{∂Θ}{∂E} = \dfrac{A}{E_{crit} - E}\]

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ClimaCache.Wang2SM — Type

mutable struct Wang2SM{FT<:AbstractFloat} <: ClimaCache.AbstractStomataModel{FT<:AbstractFloat}

Empty struct for a new Wang stomatal model modified from Anderegg model. The equation used for new Wang2SM type model is

\[\dfrac{∂Θ}{∂E} = \dfrac{aAP}{K}\]

where K is $\dfrac{∂E}{∂P}$.

Fields

A::AbstractFloat: Quadratic equation parameter [MPa⁻²]
K::AbstractFloat: Slope constant [mol² m⁻² s⁻¹ μmol⁻¹]

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Radiation

ClimaCache.WaveLengthSet — Type

struct WaveLengthSet{FT<:AbstractFloat}

Immutable structure that stores wave length information.

Fields

DATASET::String: File path to the Netcdf dataset
WL_NIR::Vector{FT} where FT<:AbstractFloat: Wavelength limits for NIR [nm]
WL_PAR::Vector{FT} where FT<:AbstractFloat: Wavelength limits for PAR [nm]
WL_SIF::Vector{FT} where FT<:AbstractFloat: Wavelength limits for SIF emission [nm]
WL_SIFE::Vector{FT} where FT<:AbstractFloat: Wavelength limits for SIF excitation [nm]
Λ::Vector{FT} where FT<:AbstractFloat: Wavelength (bins) [nm]
Λ_LOWER::Vector{FT} where FT<:AbstractFloat: Lower boundary wavelength [nm]
Λ_UPPER::Vector{FT} where FT<:AbstractFloat: Upper boundary wavelength [nm]
IΛ_NIR::Vector{Int64}: Indicies of Λ_NIR in Λ
IΛ_PAR::Vector{Int64}: Indicies of Λ_PAR in Λ
IΛ_SIF::Vector{Int64}: Indicies of Λ_SIF in Λ
IΛ_SIFE::Vector{Int64}: Indicies of Λ_SIFE in Λ
DIM_NIR::Int64: Number of wavelength bins for NIR
DIM_PAR::Int64: Number of wavelength bins for PAR
DIM_SIF::Int64: Number of wavelength bins for SIF
DIM_SIFE::Int64: Number of wavelength bins for SIFE
DIM_WL::Int64: Number of wavelength bins
ΔΛ::Vector{FT} where FT<:AbstractFloat: Differential wavelength [nm]
ΔΛ_PAR::Vector{FT} where FT<:AbstractFloat: Differential wavelength for PAR [nm]
ΔΛ_SIFE::Vector{FT} where FT<:AbstractFloat: Differential wavelength for SIF excitation [nm]
Λ_PAR::Vector{FT} where FT<:AbstractFloat: Wavelength bins for PAR [nm]
Λ_SIF::Vector{FT} where FT<:AbstractFloat: Wavelength bins for SIF [nm]
Λ_SIFE::Vector{FT} where FT<:AbstractFloat: Wavelength bins for SIF excitation [nm]

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ClimaCache.AbstractRadiation — Type

abstract type AbstractRadiation{FT<:AbstractFloat}

Hierarchy of AbstractRadiation:

BroadbandRadiation
HyperspectralRadiation

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ClimaCache.BroadbandRadiation — Type

mutable struct BroadbandRadiation{FT<:AbstractFloat} <: ClimaCache.AbstractRadiation{FT<:AbstractFloat}

Structure that stores broadband radiation information

Fields

e_diffuse_nir::AbstractFloat: Diffuse radiation from NIR region [W m⁻²]
e_diffuse_par::AbstractFloat: Diffuse radiation from PAR region [W m⁻²]
e_direct_nir::AbstractFloat: Direct radiation from NIR region [W m⁻²]
e_direct_par::AbstractFloat: Direct radiation from PAR region [W m⁻²]

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ClimaCache.HyperspectralRadiation — Type

mutable struct HyperspectralRadiation{FT<:AbstractFloat} <: ClimaCache.AbstractRadiation{FT<:AbstractFloat}

Structure that stores hyperspectral radiation information

Fields

e_diffuse::Vector{FT} where FT<:AbstractFloat: Diffuse radiation [mW m⁻² nm⁻¹]
e_direct::Vector{FT} where FT<:AbstractFloat: Direct radiation [mW m⁻² nm⁻¹]

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ClimaCache.HyperspectralAbsorption — Type

struct HyperspectralAbsorption{FT<:AbstractFloat}

Immutable struct that contains leaf biophysical traits used to run leaf reflection and transmittance.

Fields

DATASET::String: File path to the Netcdf dataset
K_ANT::Vector{FT} where FT<:AbstractFloat: Specific absorption coefficients of anthocynanin [-]
K_BROWN::Vector{FT} where FT<:AbstractFloat: Specific absorption coefficients of senescent material (brown pigments) [-]
K_CAB::Vector{FT} where FT<:AbstractFloat: Specific absorption coefficients of chlorophyll a and b [-]
K_CAR_V::Vector{FT} where FT<:AbstractFloat: Specific absorption coefficients of violaxanthin carotenoid [-]
K_CAR_Z::Vector{FT} where FT<:AbstractFloat: Specific absorption coefficients of zeaxanthin carotenoid [-]
K_CBC::Vector{FT} where FT<:AbstractFloat: Specific absorption coefficients of carbon-based constituents [-]
K_H₂O::Vector{FT} where FT<:AbstractFloat: Specific absorption coefficients of water [-]
K_LMA::Vector{FT} where FT<:AbstractFloat: Specific absorption coefficients of dry matter [-]
K_PRO::Vector{FT} where FT<:AbstractFloat: Specific absorption coefficients of protein [-]
K_PS::Vector{FT} where FT<:AbstractFloat: Specific absorption coefficients of PS I and II [-]
NR::Vector{FT} where FT<:AbstractFloat: Refractive index [-]

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ClimaCache.SunSensorGeometry — Type

mutable struct SunSensorGeometry{FT<:AbstractFloat}

Structure that stores sun sensor geometry information.

Fields

HAA::AbstractFloat: Hill facing azimuth angle [°], 0 for North, 180 for south
HSA::AbstractFloat: Hill slope angle [°]
saa::AbstractFloat: Solar azimuth angle [°], a function of time
sza::AbstractFloat: Solar zenith angle [°], a function of lat and time
vaa::AbstractFloat: Viewing azimuth angle [°]
vza::AbstractFloat: Viewing zenith angle [°]

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ClimaCache.HyperspectralMLCanopyOpticalProperty — Type

mutable struct HyperspectralMLCanopyOpticalProperty{FT<:AbstractFloat}

Structure for Verhoef LIDF algorithm

Fields

DIM_AZI::Int64: Dimension of azimuth angles
DIM_INCL::Int64: Dimension of inclination angles
DIM_LAYER::Int64: Dimension of canopy layers
DIM_SIF::Int64: Dimension of SIF wave length bins
DIM_SIFE::Int64: Dimension of SIF excitation wave length bins
DIM_WL::Int64: Dimension of short wave length bins
ddb::AbstractFloat: Backward diffuse->diffuse scatter weight
ddf::AbstractFloat: Forward diffuse->diffuse scatter weight
dob::AbstractFloat: Backward diffuse->observer scatter weight
dof::AbstractFloat: Forward diffuse->observer scatter weight
fo::Matrix{FT} where FT<:AbstractFloat: Conversion factor fo for angle towards observer at different inclination and azimuth angles
fs::Matrix{FT} where FT<:AbstractFloat: Conversion factor fs for angles from solar at different inclination and azimuth angles
ko::AbstractFloat: Observer direction beam extinction coefficient weight (diffuse)
ks::AbstractFloat: Solar direction beam extinction coefficient weight (direct)
p_sunlit::Vector{FT} where FT<:AbstractFloat: Probability of directly viewing a leaf in solar direction at different layers
po::Vector{FT} where FT<:AbstractFloat: Probability of directly viewing a leaf in observer direction at different layer boundaries
ps::Vector{FT} where FT<:AbstractFloat: Probability of directly viewing a leaf in solar direction at different layer boundaries
pso::Vector{FT} where FT<:AbstractFloat: Bi-directional probability of directly viewing a leaf at different layer boundaries (solar->canopy->observer)
sdb::AbstractFloat: Directional->diffuse backscatter weight
sdf::AbstractFloat: Directional->diffuse forward scatter weight
sob::AbstractFloat: Solar directional->observer weight of specular2directional backscatter coefficient
sof::AbstractFloat: Solar directional->observer weight of specular2directional forward coefficient
ϵ::Vector{FT} where FT<:AbstractFloat: Effective emissivity for different layers
ρ_dd::Matrix{FT} where FT<:AbstractFloat: Effective reflectance for diffuse->diffuse
ρ_lw::Vector{FT} where FT<:AbstractFloat: Effective reflectance for longwave radiation
ρ_sd::Matrix{FT} where FT<:AbstractFloat: Effective reflectance for directional->diffuse
σ_ddb::Matrix{FT} where FT<:AbstractFloat: Backward scattering coefficient for diffuse->diffuse at different layers and wavelength bins
σ_ddf::Matrix{FT} where FT<:AbstractFloat: Forward scattering coefficient for diffuse->diffuse at different layers and wavelength bins
σ_dob::Matrix{FT} where FT<:AbstractFloat: Backward scattering coefficient for diffuse->observer at different layers and wavelength bins
σ_dof::Matrix{FT} where FT<:AbstractFloat: Forward scattering coefficient for diffuse->observer at different layers and wavelength bins
σ_sdb::Matrix{FT} where FT<:AbstractFloat: Backward scattering coefficient for solar directional->diffuse at different layers and wavelength bins
σ_sdf::Matrix{FT} where FT<:AbstractFloat: Forward scattering coefficient for solar directional->diffuse at different layers and wavelength bins
σ_so::Matrix{FT} where FT<:AbstractFloat: Bidirectional from solar to observer scattering coefficient at different layers and wavelength bins
τ_dd::Matrix{FT} where FT<:AbstractFloat: Effective tranmittance for diffuse->diffuse
τ_lw::Vector{FT} where FT<:AbstractFloat: Effective tranmittance for longwave radiation
τ_sd::Matrix{FT} where FT<:AbstractFloat: Effective tranmittance for solar directional->diffuse
_Co::Vector{FT} where FT<:AbstractFloat: cos(inclination) * cos(vza) at different inclination angles
_Cs::Vector{FT} where FT<:AbstractFloat: cos(inclination) * cos(sza) at different inclination angles
_So::Vector{FT} where FT<:AbstractFloat: sin(inclination) * sin(vza) at different inclination angles
_Ss::Vector{FT} where FT<:AbstractFloat: sin(inclination) * sin(sza) at different inclination angles
_abs_fo::Matrix{FT} where FT<:AbstractFloat: abs of fo
_abs_fs::Matrix{FT} where FT<:AbstractFloat: abs of fs
_abs_fs_fo::Matrix{FT} where FT<:AbstractFloat: abs of fs * fo
_bf::AbstractFloat: Weighted sum of cos²(inclination)
_cos_θ_azi_raa::Vector{FT} where FT<:AbstractFloat: Cosine of Θ_AZI - raa
_fo_cos_θ_incl::Matrix{FT} where FT<:AbstractFloat: fo * cos Θ_INCL
_fs_cos_θ_incl::Matrix{FT} where FT<:AbstractFloat: fs * cos Θ_INCL
_fs_fo::Matrix{FT} where FT<:AbstractFloat: fs * fo
_ko::Vector{FT} where FT<:AbstractFloat: Outgoing beam extinction coefficient weights at different inclination angles
_ks::Vector{FT} where FT<:AbstractFloat: Solar beam extinction coefficient weights at different inclination angles
_mat⁺::Matrix{FT} where FT<:AbstractFloat: Upwelling matrix for SIF excitation
_mat⁻::Matrix{FT} where FT<:AbstractFloat: Downwelling matrix for SIF excitation
_sb::Vector{FT} where FT<:AbstractFloat: Backward scattering coefficients at different inclination angles
_sf::Vector{FT} where FT<:AbstractFloat: Forward scattering coefficients at different inclination angles
_tmp_mat_incl_azi_1::Matrix{FT} where FT<:AbstractFloat: Temporary cache used for matrix adding up purpose (DIMINCL * DIMAZI)
_tmp_mat_incl_azi_2::Matrix{FT} where FT<:AbstractFloat: Temporary cache used for matrix adding up purpose (DIMINCL * DIMAZI)
_tmp_vec_azi::Vector{FT} where FT<:AbstractFloat: Temporary cache used for vector operations (DIM_AZI)
_tmp_vec_layer::Vector{FT} where FT<:AbstractFloat: Temporary cache used for vector operations (DIM_LAYER)
_tmp_vec_sif_1::Vector{FT} where FT<:AbstractFloat: Cache variable to store the SIF information
_tmp_vec_sif_2::Vector{FT} where FT<:AbstractFloat: Cache variable to store the SIF information
_tmp_vec_sif_3::Vector{FT} where FT<:AbstractFloat: Cache variable to store the SIF information
_tmp_vec_sif_4::Vector{FT} where FT<:AbstractFloat: Cache variable to store the SIF information
_tmp_vec_sif_5::Vector{FT} where FT<:AbstractFloat: Cache variable to store the SIF information
_tmp_vec_sif_6::Vector{FT} where FT<:AbstractFloat: Cache variable to store the SIF information
_tmp_vec_sife_1::Vector{FT} where FT<:AbstractFloat: Cache variable to store the SIF excitation information
_tmp_vec_sife_2::Vector{FT} where FT<:AbstractFloat: Cache variable to store the SIF excitation information
_tmp_vec_sife_3::Vector{FT} where FT<:AbstractFloat: Cache variable to store the SIF excitation information
_tmp_vec_λ::Vector{FT} where FT<:AbstractFloat: Temporary cache used for vector operations (DIM_WL)
_ρ_dd::Matrix{FT} where FT<:AbstractFloat: Reflectance for diffuse->diffuse at each canopy layer
_ρ_lw::Vector{FT} where FT<:AbstractFloat: Reflectance for longwave radiation at each canopy layer
_ρ_sd::Matrix{FT} where FT<:AbstractFloat: Reflectance for solar directional->diffuse at each canopy layer
_τ_dd::Matrix{FT} where FT<:AbstractFloat: Tranmittance for diffuse->diffuse at each canopy layer
_τ_lw::Vector{FT} where FT<:AbstractFloat: Tranmittance for longwave radiation at each canopy layer
_τ_sd::Matrix{FT} where FT<:AbstractFloat: Tranmittance for solar directional->diffuse at each canopy layer
_τ_ss::AbstractFloat: Tranmittance for solar directional->directional at each canopy layer

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ClimaCache.AbstractCanopyRadiationProfile — Type

abstract type AbstractCanopyRadiationProfile{FT<:AbstractFloat}

Hierarchy of AbstractCanopy:

BroadbandSLCanopyRadiationProfile
HyperspectralMLCanopyRadiationProfile

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ClimaCache.BroadbandSLCanopyRadiationProfile — Type

mutable struct BroadbandSLCanopyRadiationProfile{FT<:AbstractFloat} <: ClimaCache.AbstractCanopyRadiationProfile{FT<:AbstractFloat}

Structure to store canopy radiation profiles

Fields

DIM_INCL::Int64: Dimension of inclination angles
apar_shaded::AbstractFloat: Mean shaded leaf APAR (per leaf area) in μmol m⁻² s⁻¹
apar_sunlit::AbstractFloat: Mean sunlit leaf APAR (per leaf area) in μmol m⁻² s⁻¹
k_diffuse::AbstractFloat: Weighted extinction coefficient for diffuse radiation (ratio between projected area to true leaf area)
k_direct::AbstractFloat: Weighted extinction coefficient for direct radiation (ratio between projected area to true leaf area)
lai_shaded::AbstractFloat: Total shaded leaf area index
lai_sunlit::AbstractFloat: Total sunlit leaf area index
par_shaded::AbstractFloat: Mean shaded leaf PAR (per leaf area) in μmol m⁻² s⁻¹
par_sunlit::AbstractFloat: Mean sunlit leaf PAR (per leaf area) in μmol m⁻² s⁻¹
r_net_shaded::AbstractFloat: Net absorbed radiation for shaded leaves [W m⁻²]
r_net_sunlit::AbstractFloat: Net absorbed radiation for sunlit leaves [W m⁻²]
_k_diffuse::Vector{FT} where FT<:AbstractFloat: Extinction coefficient for diffuse radiation at different leaf inclination angles
_k_direct::Vector{FT} where FT<:AbstractFloat: Extinction coefficient for direct radiation at different leaf inclination angles

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ClimaCache.HyperspectralMLCanopyRadiationProfile — Type

mutable struct HyperspectralMLCanopyRadiationProfile{FT<:AbstractFloat} <: ClimaCache.AbstractCanopyRadiationProfile{FT<:AbstractFloat}

Structure to store canopy radiation profiles

Fields

DIM_AZI::Int64: Dimension of azimuth angles
DIM_INCL::Int64: Dimension of inclination angles
DIM_LAYER::Int64: Dimension of canopy layers
DIM_PAR::Int64: Dimension of PAR wave length bins
DIM_SIF::Int64: Dimension of SIF wave length bins
DIM_WL::Int64: Dimension of short wave length bins
albedo::Vector{FT} where FT<:AbstractFloat: Albedo towards the viewing direction
apar_shaded::Vector{FT} where FT<:AbstractFloat: Mean APAR for shaded leaves [μmol m⁻² s⁻¹]
apar_sunlit::Array{FT, 3} where FT<:AbstractFloat: APAR for sunlit leaves [μmol m⁻² s⁻¹]
e_diffuse_down::Matrix{FT} where FT<:AbstractFloat: Downwelling diffuse short-wave radiation at each canopy layer boundary [mW m⁻² nm⁻¹]
e_diffuse_up::Matrix{FT} where FT<:AbstractFloat: Upwelling diffuse short-wave radiation at each canopy layer boundary [mW m⁻² nm⁻¹]
e_direct::Matrix{FT} where FT<:AbstractFloat: Solar directly radiation at each canopy layer boundary [mW m⁻² nm⁻¹]
e_net_diffuse::Matrix{FT} where FT<:AbstractFloat: Net diffuse radiation at each canopy layer for APAR [mW m⁻² nm⁻¹]
e_net_direct::Matrix{FT} where FT<:AbstractFloat: Net direct radiation at each canopy layer for APAR [mW m⁻² nm⁻¹]
e_o::Vector{FT} where FT<:AbstractFloat: Total radiation towards the viewing direction [mW m⁻² nm⁻¹]
e_sum_diffuse::Matrix{FT} where FT<:AbstractFloat: Sum diffuse radiation at each canopy layer for PAR [mW m⁻² nm⁻¹]
e_sum_direct::Matrix{FT} where FT<:AbstractFloat: Sum direct radiation at each canopy layer for PAR [mW m⁻² nm⁻¹]
e_v::Matrix{FT} where FT<:AbstractFloat: Radiation towards the viewing direction per layer (including soil) [mW m⁻² nm⁻¹]
par_in::AbstractFloat: Total incoming radiation PAR [μmol m⁻² s⁻¹]
par_in_diffuse::AbstractFloat: Diffuse incoming radiation PAR [μmol m⁻² s⁻¹]
par_in_direct::AbstractFloat: Direct incoming radiation PAR [μmol m⁻² s⁻¹]
par_shaded::Vector{FT} where FT<:AbstractFloat: Mean PAR for shaded leaves (before absorption) [μmol m⁻² s⁻¹]
par_sunlit::Array{FT, 3} where FT<:AbstractFloat: PAR for sunlit leaves (before absorption) [μmol m⁻² s⁻¹]
r_lw::Vector{FT} where FT<:AbstractFloat: Longwave energy flux from leaves per leaf area (one side) [W m⁻²]
r_lw_down::Vector{FT} where FT<:AbstractFloat: Downwelling longwave energy flux [W m⁻²]
r_lw_up::Vector{FT} where FT<:AbstractFloat: Upwelling longwave energy flux [W m⁻²]
r_net_lw::Vector{FT} where FT<:AbstractFloat: Net longwave energy absorption for all leaves [W m⁻²]
r_net_sw::Vector{FT} where FT<:AbstractFloat: Net shortwave energy absorption for all leaves [W m⁻²]
r_net_sw_shaded::Vector{FT} where FT<:AbstractFloat: Net shortwave energy absorption for shaded leaves [W m⁻²]
r_net_sw_sunlit::Vector{FT} where FT<:AbstractFloat: Net shortwave energy absorption for sunlit leaves [W m⁻²]
s_layer_down::Matrix{FT} where FT<:AbstractFloat: Downwelling SIF for sunlit leaves at each wavelength for a layer
s_layer_up::Matrix{FT} where FT<:AbstractFloat: Upwelling SIF for sunlit leaves at each wavelength for a layer
sif_down::Matrix{FT} where FT<:AbstractFloat: Downwelling SIF
sif_obs::Vector{FT} where FT<:AbstractFloat: SIF at observer direction
sif_obs_shaded::Vector{FT} where FT<:AbstractFloat: SIF at observer direction from shaded APAR
sif_obs_scatter::Vector{FT} where FT<:AbstractFloat: SIF at observer direction from scattering
sif_obs_soil::Vector{FT} where FT<:AbstractFloat: SIF at observer direction from soil reflection
sif_obs_sunlit::Vector{FT} where FT<:AbstractFloat: SIF at observer direction from sunlit APAR
sif_up::Matrix{FT} where FT<:AbstractFloat: Upwelling SIF
_apar_shaded::Vector{FT} where FT<:AbstractFloat: Mean APAR for shaded leaves per wavelength [μmol m⁻² s⁻¹ nm⁻¹]
_apar_sunlit::Vector{FT} where FT<:AbstractFloat: APAR for sunlit leaves per wavelength [μmol m⁻² s⁻¹ nm⁻¹]
_par_shaded::Vector{FT} where FT<:AbstractFloat: Mean PAR for shaded leaves per wavelength (before absorption) [μmol m⁻² s⁻¹ nm⁻¹]
_par_sunlit::Vector{FT} where FT<:AbstractFloat: PAR for sunlit leaves per wavelength (before absorption) [μmol m⁻² s⁻¹ nm⁻¹]
_ppar_shaded::Vector{FT} where FT<:AbstractFloat: Mean APAR for shaded leaves for photosynthesis per wavelength [μmol m⁻² s⁻¹ nm⁻¹]
_ppar_sunlit::Vector{FT} where FT<:AbstractFloat: APAR for sunlit leaves for photosynthesis per wavelength [μmol m⁻² s⁻¹ nm⁻¹]
_r_emit_down::Vector{FT} where FT<:AbstractFloat: Downwelling longwave energy flux cache [W m⁻²]
_r_emit_up::Vector{FT} where FT<:AbstractFloat: Upwelling longwave energy flux cache [W m⁻²]
_s_emit_down::Matrix{FT} where FT<:AbstractFloat: Downwelling SIF for sunlit leaves at each wavelength
_s_emit_up::Matrix{FT} where FT<:AbstractFloat: Upwelling SIF for sunlit leaves at each wavelength
_s_shaded_down::Vector{FT} where FT<:AbstractFloat: Downwelling SIF for shaded leaves at each wavelength
_s_shaded_up::Vector{FT} where FT<:AbstractFloat: Upwelling SIF for shaded leaves at each wavelength
_s_sunlit_down::Vector{FT} where FT<:AbstractFloat: Downwelling SIF for sunlit leaves at each wavelength
_s_sunlit_up::Vector{FT} where FT<:AbstractFloat: Upwelling SIF for sunlit leaves at each wavelength
_sif_obs_shaded::Matrix{FT} where FT<:AbstractFloat: Cache to compute SIF at observer direction from shaded APAR
_sif_obs_scatter::Matrix{FT} where FT<:AbstractFloat: Cache to compute SIF at observer direction from scattering
_sif_obs_sunlit::Matrix{FT} where FT<:AbstractFloat: Cache to compute SIF at observer direction from sunlit APAR

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ClimaCache.AbstractLIDFAlgorithm — Type

abstract type AbstractLIDFAlgorithm{FT<:AbstractFloat}

Hierarchy of AbstractLIDFAlgorithm:

VerhoefLIDF

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ClimaCache.VerhoefLIDF — Type

mutable struct VerhoefLIDF{FT<:AbstractFloat} <: ClimaCache.AbstractLIDFAlgorithm{FT<:AbstractFloat}

Structure for Verhoef LIDF algorithm

Fields

A::AbstractFloat: Leaf inclination angle distribution function parameter a
B::AbstractFloat: Leaf inclination angle distribution function parameter b

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ClimaCache.AbstractCanopy — Type

abstract type AbstractCanopy{FT<:AbstractFloat}

Hierarchy of AbstractCanopy:

BroadbandSLCanopy
HyperspectralMLCanopy

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ClimaCache.BroadbandSLCanopy — Type

mutable struct BroadbandSLCanopy{FT<:AbstractFloat} <: ClimaCache.AbstractCanopy{FT<:AbstractFloat}

Structure to save single layer broadband canopy parameters

Fields

DIM_INCL::Int64: Dimension of inclination angles
LIDF::ClimaCache.VerhoefLIDF: Leaf inclination angle distribution function algorithm
RADIATION::ClimaCache.BroadbandSLCanopyRadiationProfile: Canopy radiation profiles
P_INCL::Vector{FT} where FT<:AbstractFloat: Inclination angle distribution
Θ_INCL_BNDS::Matrix{FT} where FT<:AbstractFloat: Bounds of inclination angles [°]
Θ_INCL::Vector{FT} where FT<:AbstractFloat: Mean inclination angles [°]
ci::AbstractFloat: Clumping index
lai::AbstractFloat: Leaf area index

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ClimaCache.HyperspectralMLCanopy — Type

mutable struct HyperspectralMLCanopy{FT<:AbstractFloat} <: ClimaCache.AbstractCanopy{FT<:AbstractFloat}

Structure to save multiple layer hyperspectral canopy parameters

Fields

DIM_AZI::Int64: Dimension of azimuth angles
DIM_INCL::Int64: Dimension of inclination angles
DIM_LAYER::Int64: Dimension of canopy layers
HOT_SPOT::AbstractFloat: Hot spot parameter
LHA::ClimaCache.HyperspectralAbsorption: Hyperspectral absorption features of different leaf components
LIDF::ClimaCache.VerhoefLIDF: Leaf inclination angle distribution function algorithm
WLSET::ClimaCache.WaveLengthSet: Wave length set used to paramertize other variables
OPTICS::ClimaCache.HyperspectralMLCanopyOpticalProperty: Canopy optical properties
RADIATION::ClimaCache.HyperspectralMLCanopyRadiationProfile: Canopy radiation profiles
P_INCL::Vector{FT} where FT<:AbstractFloat: Inclination angle distribution
Θ_AZI::Vector{FT} where FT<:AbstractFloat: Mean azimuth angles [°]
Θ_INCL_BNDS::Matrix{FT} where FT<:AbstractFloat: Bounds of inclination angles [°]
Θ_INCL::Vector{FT} where FT<:AbstractFloat: Mean inclination angles [°]
Ω_A::AbstractFloat: Clumping structure a
Ω_B::AbstractFloat: Clumping structure b
ci::AbstractFloat: Clumping index
lai::AbstractFloat: Leaf area index
_1_AZI::Vector{FT} where FT<:AbstractFloat: Ones with the length of Θ_AZI
_COS_Θ_AZI::Vector{FT} where FT<:AbstractFloat: Cosine of Θ_AZI
_COS²_Θ_INCL::Vector{FT} where FT<:AbstractFloat: Square of cosine of Θ_INCL
_COS²_Θ_INCL_AZI::Matrix{FT} where FT<:AbstractFloat: Square of cosine of Θ_INCL at different azimuth angles
_x_bnds::Vector{FT} where FT<:AbstractFloat: Cache for level boundary locations

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SPAC

ClimaCache.Root — Type

mutable struct Root{FT<:AbstractFloat}

Structure to save root parameters

Fields

HS::ClimaCache.RootHydraulics: RootHydraulics type root hydraulic system
t::AbstractFloat: Current temperature [K]
e::AbstractFloat: Total stored energy in water [J]
∂e∂t::AbstractFloat: Marginal increase in energy [W]

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ClimaCache.Stem — Type

mutable struct Stem{FT<:AbstractFloat}

Structure to save stem parameters

Fields

HS::ClimaCache.StemHydraulics: StemHydraulics type stem hydraulic system
t::AbstractFloat: Current temperature
e::AbstractFloat: Total stored energy in water [J]
∂e∂t::AbstractFloat: Marginal increase in energy [W]

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ClimaCache.AbstractSPACSystem — Type

abstract type AbstractSPACSystem{FT<:AbstractFloat}

Hierarchy of AbstractSPACSystem:

MonoElementSPAC
MonoMLGrassSPAC
MonoMLPalmSPAC
MonoMLTreeSPAC

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ClimaCache.MonoElementSPAC — Type

mutable struct MonoElementSPAC{FT<:AbstractFloat} <: ClimaCache.AbstractSPACSystem{FT<:AbstractFloat}

Struct for simplest SPAC system

Fields

AIR::ClimaCache.AirLayer: Air conditions
LEAF::ClimaCache.Leaf: Leaf system
METEO::ClimaCache.Meteorology: Meteorology information
ROOT::ClimaCache.Root: Root system
SOIL::ClimaCache.Soil: Soil component
STEM::ClimaCache.Stem: Stem system
_krs::Vector{FT} where FT<:AbstractFloat: Relative hydraulic conductance

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ClimaCache.MonoMLGrassSPAC — Type

mutable struct MonoMLGrassSPAC{FT<:AbstractFloat} <: ClimaCache.AbstractSPACSystem{FT<:AbstractFloat}

Struct for monospecies grass SPAC system

Fields

DIM_AIR::Int64: Dimension of air layers
DIM_LAYER::Int64: Dimension of canopy layers
DIM_ROOT::Int64: Dimension of root layers
Φ_PHOTON::Bool: Whether to convert energy to photons when computing fluorescence
ELEVATION::AbstractFloat: Elevation
LATITUDE::AbstractFloat: Latitude
LONGITUDE::AbstractFloat: Longitude
LEAVES_INDEX::Vector{Int64}: Corresponding air layer per canopy layer
ROOTS_INDEX::Vector{Int64}: Corresponding soil layer per root layer
Z::Vector{FT} where FT<:AbstractFloat: Depth and height information [m]
Z_AIR::Vector{FT} where FT<:AbstractFloat: Air boundaries [m]
AIR::Array{ClimaCache.AirLayer{FT}, 1} where FT<:AbstractFloat: Air for each layer (may be more than canopy layer)
ANGLES::ClimaCache.SunSensorGeometry: Sun sensor geometry
CANOPY::ClimaCache.HyperspectralMLCanopy: Canopy used for radiation calculations
LEAVES::Array{ClimaCache.Leaves2D{FT}, 1} where FT<:AbstractFloat: Leaf per layer
METEO::ClimaCache.Meteorology: Meteorology information
RAD_LW::AbstractFloat: Downwelling longwave radiation [W m⁻²]
RAD_SW::ClimaCache.HyperspectralRadiation: Downwelling shortwave radiation
ROOTS::Array{ClimaCache.Root{FT}, 1} where FT<:AbstractFloat: Root hydraulic system
SOIL::ClimaCache.Soil: Soil component
_fs::Vector{FT} where FT<:AbstractFloat: Flow rate per root layer
_ks::Vector{FT} where FT<:AbstractFloat: Conductances for each root layer at given flow
_ps::Vector{FT} where FT<:AbstractFloat: Pressure for each root layer at given flow

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ClimaCache.MonoMLPalmSPAC — Type

mutable struct MonoMLPalmSPAC{FT<:AbstractFloat} <: ClimaCache.AbstractSPACSystem{FT<:AbstractFloat}

Struct for monospecies palm SPAC system (with trunk)

Fields

DIM_AIR::Int64: Dimension of air layers
DIM_LAYER::Int64: Dimension of canopy layers
DIM_ROOT::Int64: Dimension of root layers
Φ_PHOTON::Bool: Whether to convert energy to photons when computing fluorescence
ELEVATION::AbstractFloat: Elevation
LATITUDE::AbstractFloat: Latitude
LONGITUDE::AbstractFloat: Longitude
LEAVES_INDEX::Vector{Int64}: Corresponding air layer per canopy layer
ROOTS_INDEX::Vector{Int64}: Corresponding soil layer per root layer
Z::Vector{FT} where FT<:AbstractFloat: Depth and height information [m]
Z_AIR::Vector{FT} where FT<:AbstractFloat: Air boundaries [m]
AIR::Array{ClimaCache.AirLayer{FT}, 1} where FT<:AbstractFloat: Air for each layer (more than canopy layer)
ANGLES::ClimaCache.SunSensorGeometry: Sun sensor geometry
CANOPY::ClimaCache.HyperspectralMLCanopy: Canopy used for radiation calculations
LEAVES::Array{ClimaCache.Leaves2D{FT}, 1} where FT<:AbstractFloat: Leaf per layer
METEO::ClimaCache.Meteorology: Meteorology information
RAD_LW::AbstractFloat: Downwelling longwave radiation [W m⁻²]
RAD_SW::ClimaCache.HyperspectralRadiation: Downwelling shortwave radiation
ROOTS::Array{ClimaCache.Root{FT}, 1} where FT<:AbstractFloat: Root hydraulic system
SOIL::ClimaCache.Soil: Soil component
TRUNK::ClimaCache.Stem: Trunk hydraulic system
_fs::Vector{FT} where FT<:AbstractFloat: Flow rate per root layer
_ks::Vector{FT} where FT<:AbstractFloat: Conductances for each root layer at given flow
_ps::Vector{FT} where FT<:AbstractFloat: Pressure for each root layer at given flow

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ClimaCache.MonoMLTreeSPAC — Type

mutable struct MonoMLTreeSPAC{FT<:AbstractFloat} <: ClimaCache.AbstractSPACSystem{FT<:AbstractFloat}

Struct for monospecies tree SPAC system (with trunk and branches)

Fields

DIM_AIR::Int64: Dimension of air layers
DIM_LAYER::Int64: Dimension of canopy layers
DIM_ROOT::Int64: Dimension of root layers
Φ_PHOTON::Bool: Whether to convert energy to photons when computing fluorescence
LEAVES_INDEX::Vector{Int64}: Corresponding air layer per canopy layer
ROOTS_INDEX::Vector{Int64}: Corresponding soil layer per root layer
Z::Vector{FT} where FT<:AbstractFloat: Depth and height information [m]
Z_AIR::Vector{FT} where FT<:AbstractFloat: Air boundaries [m]
ELEVATION::AbstractFloat: Elevation
LATITUDE::AbstractFloat: Latitude
LONGITUDE::AbstractFloat: Longitude
AIR::Array{ClimaCache.AirLayer{FT}, 1} where FT<:AbstractFloat: Air for each layer (more than canopy layer)
ANGLES::ClimaCache.SunSensorGeometry: Sun sensor geometry
BRANCHES::Array{ClimaCache.Stem{FT}, 1} where FT<:AbstractFloat: Branch hydraulic system
CANOPY::ClimaCache.HyperspectralMLCanopy: Canopy used for radiation calculations
LEAVES::Array{ClimaCache.Leaves2D{FT}, 1} where FT<:AbstractFloat: Leaf per layer
METEO::ClimaCache.Meteorology: Meteorology information
RAD_LW::AbstractFloat: Downwelling longwave radiation [W m⁻²]
RAD_SW::ClimaCache.HyperspectralRadiation: Downwelling shortwave radiation
ROOTS::Array{ClimaCache.Root{FT}, 1} where FT<:AbstractFloat: Root hydraulic system
SOIL::ClimaCache.Soil: Soil component
TRUNK::ClimaCache.Stem: Trunk hydraulic system
_fs::Vector{FT} where FT<:AbstractFloat: Flow rate per root layer
_ks::Vector{FT} where FT<:AbstractFloat: Conductances for each root layer at given flow
_ps::Vector{FT} where FT<:AbstractFloat: Pressure for each root layer at given flow

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Utils

Colimitation Methods

ClimaCache.AbstractColimit — Type

abstract type AbstractColimit{FT<:AbstractFloat}

Hierarchy of AbstractColimit

MinimumColimit
QuadraticColimit
SerialColimit

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ClimaCache.MinimumColimit — Type

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

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ClimaCache.QuadraticColimit — Type

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

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ClimaCache.SerialColimit — Type

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

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ClimaCache.SquareColimit — Type

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

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ClimaCache

Environmental Conditions

Plant

Hydraulics

Leaf Level

Stomatal Models

Radiation

SPAC

Utils

Colimitation Methods