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CanopyLayers

Structures

Land.CanopyLayers.Canopy4RT — Type
mutable struct Canopy4RT

A canopy struct for the radiation transfer module

Fields

  • nLayer::Int64

: Number of canopy layers

  • LAI::AbstractFloat

: Leaf Area Index

  • Ω::AbstractFloat

: Clumping factor

  • clump_a::AbstractFloat

: Structure factor a

  • clump_b::AbstractFloat

: Structure factor b

  • leaf_width::AbstractFloat

: Leaf width

  • hc::AbstractFloat

: Vegetation height

  • LIDFa::AbstractFloat

: Leaf Inclination

  • LIDFb::AbstractFloat

: Variation in leaf inclination

  • hot::AbstractFloat

: HotSpot parameter (still need to check!)

  • height::AbstractFloat

: Canopy height [m]

  • z0m::AbstractFloat

: Canopy roughness [m]

  • z0h::AbstractFloat

: Tree roughtnes [m]

  • d::AbstractFloat

: Canopy displacement height [m]

  • Cd::AbstractFloat

: m/sqrt(s) turbulent transfer coefficient

  • litab::Vector{FT} where FT<:AbstractFloat

: List of mean inclination angles [°]

  • litab_bnd::Matrix{FT} where FT<:AbstractFloat

: List of inclination angle boundaries [°]

  • lazitab::Vector{FT} where FT<:AbstractFloat

: List of mean azimuth angles [°]

  • cos_ttlo::Vector{FT} where FT<:AbstractFloat

: Cosine of lazitab

  • cos_philo::Vector{FT} where FT<:AbstractFloat

: Cosine of lazitab - raa (relative azimuth angle), update with time

  • cos_ttli::Vector{FT} where FT<:AbstractFloat

: Cosine of litab

  • sin_ttli::Vector{FT} where FT<:AbstractFloat

: Sine of litab

  • vol_scatt::Vector{FT} where FT<:AbstractFloat

: Cache for volome scatter function

  • lidf::Vector{FT} where FT<:AbstractFloat

: Inclination angles weight distribution

  • xl::Vector{FT} where FT<:AbstractFloat

: List of level location (level = layer + 1)

  • dx::AbstractFloat

: 1/nLayer

  • nAzi::Int64

: Number of azimuth angles

  • nIncl::Int64

: Number of inclination angles

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Land.CanopyLayers.CanopyOpticals — Type
mutable struct CanopyOpticals{FT}

A struct for canopy optical properties

Fields

  • nAzi::Int64

: Number of azimuth angles

  • nIncl::Int64

: Number of inclination agles

  • nLayer::Int64

: Number of canopy layers

  • nWL::Int64

: Number of wave lengths

  • sdb::Any

: Solar -> Diffuse backscatter weight

  • sdf::Any

: Solar -> Diffuse forward scatter weight

  • dob::Any

: Diffuse -> Directional backscatter weight

  • dof::Any

: Diffuse -> Directional forward scatter weight

  • ddb::Any

: Diffuse -> Diffuse backscatter weight

  • ddf::Any

: Diffuse -> Diffuse forward scatter weight

  • ks::Any

: Solar beam extinction coefficient weight

  • ko::Any

: Outgoing beam extinction coefficient weight

  • bf::Any

: ?

  • sob::Any

: Weight of specular2directional backscatter coefficient

  • sof::Any

: Weight of specular2directional forward coefficient

  • Ps::Vector

: Probability of directly viewing a leaf in solar direction

  • Po::Vector

: Probability of directly viewing a leaf in viewing direction

  • Pso::Vector

: Bi-directional probability of directly viewing a leaf (solar->canopy->viewing)

  • fs::Matrix

: conversion factor fs to compute irradiance on inclined leaf

  • absfs::Matrix

: abs(fs)

  • absfsfo::Matrix

: abs(fs*fo)

  • fsfo::Matrix

: fs*fo

  • fo::Matrix

: conversion factor fo for angle towards observer (not sun like fs)

  • absfo::Matrix

: abs(fo)

  • cosΘ_l::Matrix

: Cosine of leaf azimuths

  • cos2Θ_l::Matrix

: cos of leaf azimuth sqared

  • sigb::Matrix

: diffuse backscatter scattering coefficient for diffuse incidence

  • sigf::Matrix

: diffuse forward scattering coefficient for diffuse incidence

  • sb::Matrix

: diffuse backscatter scattering coefficient for specular incidence

  • sf::Matrix

: diffuse forward scattering coefficient for specular incidence

  • vb::Matrix

: directional backscatter scattering coefficient for diffuse incidence

  • vf::Matrix

: directional forward scattering coefficient for diffuse incidence

  • w::Matrix

: bidirectional scattering coefficent (directional-directional)

  • a::Matrix

: attenuation

  • Xsd::Matrix

: Effective layer transmittance (direct->diffuse)

  • Xdd::Matrix

: Effective layer transmittance (diffuse->diffuse)

  • R_sd::Matrix

: Effective layer reflectance (direct->diffuse)

  • R_dd::Matrix

: Effective layer reflectance (diffuse->diffuse)

  • Es_::Matrix

: Solar direct radiation per layer)

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Land.CanopyLayers.CanopyRads — Type
mutable struct CanopyRads{FT}

A struct for canopy radiation information

Fields

  • nAzi::Int64

: Number of azimuth angles

  • nIncl::Int64

: Number of inclination agles

  • nLayer::Int64

: Number of canopy layers

  • nLevel::Int64

: Number of canopy levels

  • nWL::Int64

: Number of wave lengths

  • nWLF::Int64

: Number of wave lengths for SIF

  • intEout::Any

: Integrated TOC outgoing flux [W m⁻²]

  • incomingPAR::Any

: Incident spectrally integrated total PAR [mol m⁻² s⁻¹]

  • incomingPAR_direct::Any

: Incident spectrally integrated direct PAR [mol m⁻² s⁻¹]

  • incomingPAR_diffuse::Any

: Incident spectrally integrated diffuse PAR [mol m⁻² s⁻¹]

  • RnSoil_diffuse::Any

: Net radiation of shaded soil [W m⁻²]

  • RnSoil_direct::Any

: Net Short-wave radiation of sunlit soil [W m⁻²]

  • RnSoil::Any

: Net Short-wave radiation of soil (shaded + sunlit) [W m⁻²]

  • RnSoilLW::Any

: Net long-wave radiation of soil (shaded + sunlit) [W m⁻²]

  • absPAR_shade::Vector

: Net PAR of shaded leaves [mol m⁻² s⁻¹]

  • absPAR_shadeCab::Vector

: Net PAR by Cab+Car of shaded leaves [moles m⁻² s⁻¹]

  • intNetSW_sunlit::Vector

: Spectrally integrated net absorbed direct radiation in each layer per leaf area [W m⁻²]

  • intNetSW_shade::Vector

: Spectrally integrated net absorbed diffuse radiation in each layer per leaf area [W m⁻²]

  • intNetLW_sunlit::Vector

: Spectrally integrated net absorbed direct radiation in each layer per leaf area [W m⁻²]

  • intNetLW_shade::Vector

: Spectrally integrated net absorbed diffuse radiation in each layer per leaf area [W m⁻²]

  • T_sun::Vector

: Leaf temperature (sunlit) [K]

  • T_shade::Vector

: Leaf temperature (shaded) [K]

  • ϕ_shade::Vector

: Fluorescence yield for shaded leaves

  • H_shade::Vector

: Sensible Heat flux H of shaded leaves [W m⁻²]

  • LE_shade::Vector

: Latent Heat flux LE of shaded leaves [W m⁻²]

  • NPQ_shade::Vector

: NPQ of shaded leaves

  • GPP_shade::Vector

: GPP of shaded leaves [μmol m⁻² s⁻¹]

  • gs_shade::Vector

: gs of shaded leaves [mol m⁻² s⁻¹]

  • ψl_shade::Vector

: Leaf water potential of shaded leaves [MPa]

  • Cc_shade::Vector

: Cc of shaded leaves [µmol/mol]

  • Pi_shade::Vector

: internal CO₂ concentration of shaded leaves [µmol/mol]

  • Lo::Vector

: Short-wave TOC outgoing radiance in observation direction [mW m⁻² nm⁻¹ sr⁻¹]

  • Eout::Vector

: Short-wave TOC outgoing radiation [mW m⁻² nm⁻¹]

  • alb_obs::Vector

: Short-wave Albedo in viewing direction

  • alb_direct::Vector

: Short-wave Albedo for direct incoming radiation

  • alb_diffuse::Vector

: Short-wave Albedo for diffuse incoming radiation

  • E_up::Matrix

: Upwelling diffuse short-wave radiation within canopy [mW m⁻² nm⁻¹]

  • E_down::Matrix

: Downwelling diffuse short-wave radiation within canopy [mW m⁻² nm⁻¹]

  • netSW_sunlit::Matrix

: Net absorbed direct radiation in each layer [mW m⁻² nm⁻¹]

  • netSW_shade::Matrix

: net absorbed diffuse radiation in each layer [mW m⁻² nm⁻¹]

  • absPAR_sun::Array{FT, 3} where FT

: net PAR of sunlit leaves [mol m⁻² s⁻¹]

  • absPAR_sunCab::Array{FT, 3} where FT

: net PAR by Cab+Car of sunlit leaves [mol m⁻² s⁻¹]

  • T_sun3D::Array{FT, 3} where FT

: Leaf temperature (sunlit) [K]

  • ϕ_sun::Array{FT, 3} where FT

: Fluorescence yield for sunlit leaves

  • H_sun::Array{FT, 3} where FT

: Sensible Heat flux H of sunlit leaves [W m⁻²]

  • LE_sun::Array{FT, 3} where FT

: Latent Heat flux LE of sunlit leaves [W m⁻²]

  • NPQ_sun::Array{FT, 3} where FT

: NPQ of sunlit leaves

  • GPP_sun::Array{FT, 3} where FT

: GPP of sunlit leaves [μmol m⁻² s⁻¹]

  • gs_sun::Array{FT, 3} where FT

: gs of sunlit leaves [mol m⁻² s⁻¹]

  • ψl_sun::Array{FT, 3} where FT

: Leaf water potential of sunlit leaves [MPa]

  • Cc_sun::Array{FT, 3} where FT

: Cc of sunlit leaves [µmol/mol]

  • Pi_sun::Array{FT, 3} where FT

: Internal CO₂ concentration of sunlit leaves [µmol/mol]

  • SIF_hemi::Vector

: Hemispheric total outgoing SIF flux [mW m⁻² nm⁻¹])

  • SIF_obs::Vector

: Observer-direction outgoing SIF radiance (mW m⁻² nm⁻¹ sr⁻¹))

  • SIF_obs_sunlit::Vector

: Observer-direction outgoing SIF radiance, sunlit leaves (mW m⁻² nm⁻¹ sr⁻¹)

  • SIF_obs_shaded::Vector

: Observer-direction outgoing SIF radiance, shaded leaves (mW m⁻² nm⁻¹ sr⁻¹)

  • SIF_obs_scattered::Vector

: Observer-direction outgoing SIF radiance, scattered (mW m⁻² nm⁻¹ sr⁻¹)

  • SIF_obs_soil::Vector

: Observer-direction outgoing SIF radiance, soil-reflected (mW m⁻² nm⁻¹ sr⁻¹)

  • SIF_sum::Vector

: Total SIF sum of layer sources [mW m⁻² nm⁻¹])

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Land.CanopyLayers.IncomingRadiation — Type
mutable struct IncomingRadiation{FT}

Incoming radiation information

Fields

  • E_direct::Vector

: Direct incoming radiation [mW m⁻² nm⁻¹]

  • E_diffuse::Vector

: Diffuse incoming radiation [mW m⁻² nm⁻¹]

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Land.CanopyLayers.LeafBios — Type
mutable struct LeafBios{FT}

A struct of leaf biological parameters

Fields

  • nWL::Int64

: Number of wave length

  • nWLE::Int64

: Number of wave length for excitation

  • nWLF::Int64

: Number of wave length for SIF

  • N::Any

: Leaf structure parameter

  • Cab::Any

: Chlorophyll a+b content [µg cm⁻²]

  • Car::Any

: Carotenoid content [µg cm⁻²]

  • Ant::Any

: Anthocynanin content [µg cm⁻²]

  • Cs::Any

: Senescent material fraction

  • Cw::Any

: Equivalent water thickness [cm]

  • Cm::Any

: Dry matter content (dry leaf mass per unit area) [g cm⁻²]

  • Cx::Any

: Fractionation between Zeaxanthin and Violaxanthin in Car (1=all Zeaxanthin) (-)

  • fqe::Any

: Leaf fluorescence efficiency (Fo standard)

  • ρ_LW::Any

: Broadband thermal reflectance (-)

  • τ_LW::Any

: Broadband thermal transmission (-)

  • ρ_SW::Vector

: Shortwave leaf reflectance

  • τ_SW::Vector

: Shortwave leaf transmission

  • α_SW::Vector

: Shortwave absorption

  • kChlrel::Vector

: Relative absorbtion by Chlorophyll+Car

  • kChlrel_old::Vector

: Relative absorbtion by Chlorophyll

  • Mb::Matrix

: Fluorescence excitation matrix backwards

  • Mf::Matrix

: Fluorescence excitation matrix forwards

  • ndub::Int64

: Doubling adding layers

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Land.CanopyLayers.LeafOpticals — Type
mutable struct LeafOpticals{FT}

Struct for leaf optical properties

Fields

  • nr::Vector

  • Km::Vector

  • Kab::Vector

  • Kant::Vector

  • Kcar::Vector

  • Kw::Vector

  • KBrown::Vector

  • phi::Vector

  • KcaV::Vector

  • KcaZ::Vector

  • lambda::Vector

: Wave length [nm], same as WL in WaveLengths`

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Land.CanopyLayers.RTDimensions — Type
mutable struct RTDimensions

Struct that stores matrix dimension information

Fields

  • nAzi::Int64

: Number of azimuth angles

  • nIncl::Int64

: Number of inclination agles

  • nLayer::Int64

: Number of canopy layers

  • nLevel::Int64

: Number of canopy layer boundaries nLayer+1

  • nPAR::Int64

: Number of PAR wave lengths

  • nWL::Int64

: Number of wave lengths

  • nWLE::Int64

: Number of wave length for excitation

  • nWLF::Int64

: Number of wave lengths for SIF

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Land.CanopyLayers.SoilOpticals — Type
mutable struct SoilOpticals{FT}

A struct of soil optical parameters

Fields

  • T::Any

: Soil surface temperature

  • color::Int64

: Soil color class

  • ρ_NIR::Any

: Shortwave albedo for NIR

  • ρ_PAR::Any

: Shortwave albedo for PAR

  • ρ_SW::Vector

: Shortwave albedo that matches WL from WaveLengths

  • ρ_SW_SIF::Vector

: Shortwave albedo that matches WLF from WaveLengths

  • ε_SW::Vector

: Shortwave absorption that equals 1 - ρ_SW

  • SW_mat_raw_4::Matrix

: Shortwave albedo matrix from 4 bands, wavelengths are 400:10:2500 nm

  • SW_mat_raw_2::Matrix

: Shortwave albedo matrix from 2 bands, wavelengths are 400:10:2500 nm

  • SW_mat_4::Matrix

: Shortwave albedo matrix from 4 bands with WL from WaveLengths

  • SW_mat_2::Matrix

: Shortwave albedo matrix from 2 bands with WL from WaveLengths

  • SW_vec_4::Vector

: Shortwave albedo weight from 4 bands

  • SW_vec_2::Vector

: Shortwave albedo weight from 2 bands

  • ρ_SW_raw::Vector

: Shortwave albedo, wavelengths are 400:10:2500 nm

  • ρ_LW::Vector

: Longtwave albedo

  • dry_NIR::Any

: Mean value for day band 1 in NIR region

  • dry_PAR::Any

: Mean value for day band 1 in PAR region

  • wet_NIR::Any

: Mean value for day band 1 in NIR region

  • wet_PAR::Any

: Mean value for day band 1 in PAR region

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Land.CanopyLayers.SolarAngles — Type
struct SolarAngles{FT}

Struct for observation and solar angles

Fields

  • hza::Any

: Hill zenith angle [°], hill slope angle

  • haa::Any

: Hill azimuth angle [°], 0 for North, 180 for south

  • saa::Any

: Solar azimuth angle [°], a function of time

  • sza::Any

: Solar zenith angle [°], a function of lat and time

  • vaa::Any

: Viewing azimuth angle [°]

  • vza::Any

: Viewing zenith angle [°]

  • raa::Any

: Relative azimuth angle [°], difference between saa and vaa

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Land.CanopyLayers.WaveLengths — Type
mutable struct WaveLengths{FT}

Struct for pre-set wave length parameters

Fields

  • minwlPAR::Any

: Minimal WL for PAR [nm]

  • maxwlPAR::Any

: Maximal WL for PAR [nm]

  • minwlNIR::Any

: Minimal WL for NIR [nm]

  • maxwlNIR::Any

: Maximal WL for NIR [nm]

  • minwle::Any

: Minimal WL for SIF excitation [nm]

  • maxwle::Any

: Maximal WL for SIF excitation [nm]

  • minwlf::Any

: Minimal WL for SIF emission/fluorescence [nm]

  • maxwlf::Any

: Maximal WL for SIF emission/fluorescence [nm]

  • sWL::Vector

: Standard wave length [nm]

  • dWL::Vector

: Differential wavelength

  • optis::Land.CanopyLayers.LeafOpticals

: Leaf optical parameter set

  • WL::Vector

: Wave length [nm]

  • iWLE::Vector{Int64}

: Index of WLE in WL

  • iWLF::Vector{Int64}

: Index of WLF in WL

  • iPAR::Vector{Int64}

: index of wlPAR in WL

  • iNIR::Vector{Int64}

: index of wlNIR in WL

  • WLE::Vector

: excitation wave length [nm]

  • WLF::Vector

: Fluorescence wave length [nm]

  • WL_iPAR::Vector

: Wave length for PAR

  • dWL_iPAR::Vector

: Differential wave length for PAR

  • dWL_iWLE::Vector

: Differential wave length for iWLE

  • nPAR::Int64

: Length of WL_iPAR

  • nWL::Int64

: Length of WL

  • nWLE::Int64

: length of WLE

  • nWLF::Int64

: length of WLF

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Caches

Land.CanopyLayers.CFCache — Type
mutable struct CFCache{FT}

Cache to speed canopy_fluxes! by pre-allocating arrays

Fields

  • abs_wave::Vector

: absorbed energy from wave lengths

  • absfs_lidf::Vector

: absfs' * lidf [nAzi]

  • E_all::Vector

: wave length energy [same as dWL]

  • E_iPAR::Vector

: wave length energy [same as iPAR]

  • lPs::Vector

: lPs [nLayer]

  • kChlrel::Vector

: kChlrel [same as iPAR]

  • PAR_diff::Vector

: diffusive PAR [same as iPAR]

  • PAR_diffCab::Vector

: diffusive PAR for photosynthesis [same as iPAR]

  • PAR_dir::Vector

: direct PAR [same as iPAR]

  • PAR_dirCab::Vector

: diffusive PAR for photosynthesis [same as iPAR]

source
Land.CanopyLayers.CGCache — Type
mutable struct CGCache{FT}

Cache to speed canopy_geometry! by pre-allocating arrays

Fields

  • _Co::Vector

: cos_ttli .* cos(vza) dim: nIncl

  • _Cs::Vector

: cos_ttli .* cos(sza) dim: nIncl

  • _So::Vector

: sin_ttli .* sin(vza) dim: nIncl

  • _Ss::Vector

: sin_ttli .* sin(sza) dim: nIncl

  • _1s::Matrix

: maxtrix filled with 1 dim: (1, nAzi)

  • _2d::Matrix

: 2D array to speed up _cds and _cdo dim: (nIncl, nAzi)

  • _cdo::Matrix

: Co * _1s .+ _So * cosphilo' dim: (nIncl, nAzi)

  • _cds::Matrix

: Cs * _1s .+ _Ss * costtlo' dim: (nIncl, nAzi)

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Land.CanopyLayers.SFCache — Type
mutable struct SFCache{FT}

Cache to speed SIF_fluxes! by pre-allocating arrays

Fields

  • M⁻_sun::Vector

  • M⁺_sun::Vector

  • wfEs::Vector

  • sfEs::Vector

  • sbEs::Vector

  • M⁺⁻::Vector

  • M⁺⁺::Vector

  • M⁻⁺::Vector

  • M⁻⁻::Vector

  • sun_dwl_iWlE::Vector

  • tmp_dwl_iWlE::Vector

  • ϕ_cosΘ_lidf::Vector

  • vfEplu_shade::Vector

  • vbEmin_shade::Vector

  • vfEplu_sun::Vector

  • vbEmin_sun::Vector

  • sigfEmin_shade::Vector

  • sigbEmin_shade::Vector

  • sigfEmin_sun::Vector

  • sigbEmin_sun::Vector

  • sigfEplu_shade::Vector

  • sigbEplu_shade::Vector

  • sigfEplu_sun::Vector

  • sigbEplu_sun::Vector

  • zeroB::Vector

  • tmp_1d_nWlF::Vector

  • tmp_1d_nLayer::Vector

  • dnorm::Vector

  • τ_dd::Matrix

: transmission of diffusive light?

  • ρ_dd::Matrix

: extinction of diffuse light?

  • Xdd::Matrix

  • Rdd::Matrix

  • Y::Matrix

  • U::Matrix

  • S⁻::Matrix

  • S⁺::Matrix

  • piLs::Matrix

  • piLd::Matrix

  • Fsmin::Matrix

  • Fsplu::Matrix

  • Fdmin::Matrix

  • Fdplu::Matrix

  • Femo::Matrix

  • M⁺::Matrix

  • M⁻::Matrix

  • ϕ_cosΘ::Matrix

  • F⁻::Matrix

  • F⁺::Matrix

  • net_diffuse::Matrix

  • tmp_2d_nWlF_nLayer::Matrix

  • tmp_2d_nWlF_nLayer_2::Matrix

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Land.CanopyLayers.SWCache — Type
mutable struct SWCache{FT}

Cache to speed short_wave! by pre-allocating arrays

Fields

  • dnorm::Vector

: dnorm?

  • piLo::Vector

: pi * Lo

  • piLoc::Vector

: pi * Lo from canopy

  • piLos::Vector

: pi * Lo from soil

  • piLoc2::Matrix

: pi * Lo from canopy 2D matrix

  • ρ_dd::Matrix

: extinction of diffuse light?

  • ρ_sd::Matrix

: extinction of direct light?

  • τ_dd::Matrix

: transmission of diffusive light?

  • τ_sd::Matrix

: transmission of direct light?

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Land.CanopyLayers.RTCache — Type
mutable struct RTCache{FT}

Collection of caches to speed up RT module

Fields

  • cf_con::Land.CanopyLayers.CFCache

: CFCache type cache

  • cg_con::Land.CanopyLayers.CGCache

: CGCache type cache

  • sf_con::Land.CanopyLayers.SFCache

: SFCache type cache

  • sw_con::Land.CanopyLayers.SWCache

: SWCache type cache

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Initialization of Structures

Land.CanopyLayers.create_leaf_opticals — Function
create_leaf_opticals(
            sWL::Array{FT,1},
            file::String = OPTI_2021
) where {FT<:AbstractFloat}

Create an AbstractLeafOptiPara struct, given

  • sWL Standard wave length
  • opfn File that saves optical parameters
source
Land.CanopyLayers.create_wave_length — Function
create_wave_length(FT, sWLs = [collect(400.0:10.0: 650.1); collect(655.0: 5.0: 770.1); collect(780.0:25.0:2400.1)];
                   max_NIR::Number = 2500, max_PAR::Number = 700, min_NIR::Number = 700, min_PAR::Number = 400, opti_file::String = OPTI_2021)

Create WaveLengths type struct, given

  • FT Floating number type
  • sWLs Shortwave wavelength bins
  • max_NIR Maximal NIR wavelength
  • max_PAR Maximal PAR wavelength
  • min_NIR Minimal NIR wavelength
  • min_PAR Minimal PAR wavelength
  • opti_file Input reference optical file path
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Big Leaf Model

Land.CanopyLayers.big_leaf_partition — Function
big_leaf_partition(
            lai::FT,
            zenith::FT,
            r_all::FT,
            r_dir::FT = FT(0.8)
) where {FT<:AbstractFloat}

Partition the big-leaf canopy into sunlit and shaded layers, given

  • lai Leaf area index
  • zenith Zenith angle in degree
  • r_all Total radiation in [W m⁻²]
  • r_dir Direct radiation partition in r_all

The function returns

  • ratio ratio of sunlit leaves out of all leaves
  • q_slm Mean sunlit layer PAR
  • q_shm Mean shaded layer PAR
  • e_sl Mean sunlit layer absorbed total energy
  • e_sh Mean shaded layer absorbed total energy
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SCOPE Model

Land.CanopyLayers.canopy_fluxes! — Function
canopy_fluxes!(
            can::Canopy4RT{FT},
            can_opt::CanopyOpticals{FT},
            can_rad::CanopyRads{FT},
            in_rad::IncomingRadiation{FT},
            soil::SoilOpticals{FT},
            leaves::Array{LeafBios{FT},1},
            wls::WaveLengths{FT},
            rt_con::RTCache{FT}
) where {FT<:AbstractFloat}

Computes a variety of integrated fluxes from the spectrally resolved computations in the short-wave Canopy RT (e.g. absorbed soil radiation, absorbed direct and diffuse PAR by layer (and angles for direct), net direct and diffuse energy balance per layer), given

source
Land.CanopyLayers.canopy_geometry! — Function
canopy_geometry!(
            can::Canopy4RT{FT},
            angles::SolarAngles{FT},
            can_opt::CanopyOpticals{FT},
            rt_con::RTCache{FT}
) where {FT<:AbstractFloat}

Computes canopy optical properties (extinction coefficients for direct and diffuse light) based on the SAIL model. Most important input parameters are leaf inclination and azimuth distribution functions and sun-sensor geometry. Canopy clumping Ω is implemented as in Pinty et al (2015), given

source
Land.CanopyLayers.canopy_matrices! — Function
canopy_matrices!(
            leaves::Array{LeafBios{FT},1},
            can_opt::CanopyOpticals{FT}
) where {FT<:AbstractFloat}

Compute scattering coefficient matrices for direct and diffuse light given geometry dependent overall extinction coefficients and pigment dependent leaf reflectance and transmission (computed via fluspect). This function has to be called before short_wave! can be used.

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Land.CanopyLayers.diffusive_S — Function
diffusive_S(τ_dd::Array{FT},
            ρ_dd::Array{FT},
            S⁻::Array{FT},
            S⁺::Array{FT},
            boundary_top::Array{FT},
            boundary_bottom::Array{FT},
            rsoil::Array{FT}
) where {FT<:AbstractFloat}

Computes 2-stream diffusive radiation transport (used for thermal and SIF) given:

  • τ_dd A 2D Array with layer reflectances
  • ρ_dd A 2D Array with layer transmissions
  • S⁻ A 2D Array with layer source terms in the downwelling direction
  • S⁺ A 2D Array with layer source terms in the upwelling direction
  • boundary_top A 1D array with downwelling radiation at the top (top of canopy)
  • boundary_bottom A 1D array with upwnwelling radiation at the bottom (soil)
  • rsoil A 1D array with soil reflectance
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Land.CanopyLayers.fluspect! — Function
fluspect!(leaf::LeafBios{FT},
          wls::WaveLengths{FT};
          APAR_car::Bool = true
) where {FT<:AbstractFloat}

Computes leaf optical properties (reflectance and transittance) based on pigment concentrations. Also computes Fluorescence excitation matrices. Mostly based on PROSPECT-D for leaf reflectance/transmission and FluSpec for fluorescence.

  • leaf LeafBios type struct
  • wls WaveLengths type struct
  • APAR_car If true, include Car absorption in APAR for photosynthesis
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Land.CanopyLayers.SIF_fluxes! — Function
SIF_fluxes!(leaves::Array{LeafBios{FT},1},
            can_opt::CanopyOpticals{FT},
            can_rad::CanopyRads{FT},
            can::Canopy4RT{FT},
            soil::SoilOpticals{FT},
            wls::WaveLengths{FT},
            rt_con::RTCache{FT},
            rt_dim::RTDimensions;
            photon::Bool = true
) where {FT<:AbstractFloat}

Computes 2-stream diffusive radiation transport for SIF radiation (calls [diffusive_S!] internally). Layer reflectance and transmission is computed from SW optical properties, layer sources from absorbed light and SIF efficiencies. Boundary conditions are zero SIF incoming from atmosphere or soil.

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SIF_fluxes!(leaf::LeafBios{FT},
            in_rad::IncomingRadiation{FT},
            wls::WaveLengths{FT},
            rt_con::RTCache{FT},
            fqe::FT = FT(0.01);
            photon::Bool = true
) where {FT<:AbstractFloat}

Leaf level SIF, given

  • leaf LeafBios type struct
  • in_rad IncomingRadiation type struct
  • wls WaveLengths type struct
  • rt_con RTCache type cache
  • fqe Fluorescence quantum yield (default at 1%)
  • photon If true, use photon unit in the matrix conversion

Note that in_rad assumes direct light with zenith angle of 0, and a zenith angle correction needs to be made before passing it to this function. The up- and down-ward SIF are stored in sf_con as M⁻_sun and M⁺_sun.

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Land.CanopyLayers.thermal_fluxes! — Function
thermal_fluxes!(
            leaves::Array{LeafBios{FT},1},
            can_opt::CanopyOpticals{FT},
            can_rad::CanopyRads{FT},
            can::Canopy4RT{FT},
            soil::SoilOpticals{FT},
            incLW::Array{FT},
            wls::WaveLengths{FT}
) where {FT<:AbstractFloat}

Computes 2-stream diffusive radiation transport for thermal radiation (calls [diffusive_S] internally). Layer reflectance and transmission is computed from LW optical properties, layer sources from temperature and Planck law, boundary conditions from the atmosphere and soil emissivity and temperature. Currently only uses Stefan Boltzmann law to compute spectrally integrated LW but can be easily adjusted to be spectrally resolved.

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Indicies

Land.CanopyLayers.REF_WL — Function
REF_WL(wls::WaveLengths{FT},
       can_rad::CanopyRads{FT}
       wls::WaveLengths{FT},
       twl::FT
) where {FT<:AbstractFloat}

Return the Reflectance, given

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Land.CanopyLayers.SIF_757 — Function
SIF_757(can_rad::CanopyRads{FT},
        wls::WaveLengths{FT};
        oco::Int = 2
) where {FT<:AbstractFloat}

Return the SIF @ 758.68 (OCO2) or 758.77 (OCO3) nm, given

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Land.CanopyLayers.SIF_771 — Function
SIF_771(can_rad::CanopyRads{FT},
        wls::WaveLengths{FT};
        oco::Int = 2
) where {FT<:AbstractFloat}

Return the SIF @ 769.94 (OCO2) or 770.005 (OCO3) nm, given

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Land.CanopyLayers.SIF_WL — Function
SIF_WL(wls::WaveLengths{FT},
       can_rad::CanopyRads{FT}
       wls::WaveLengths{FT},
       twl::FT
) where {FT<:AbstractFloat}

Return the SIF, given

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Utils

Land.CanopyLayers.calctav — Function
calctav(α::FT, nr::FT) where {FT<:AbstractFloat}

Computes transmission of isotropic radiation across an interface between two dielectrics (Stern F., 1964; Allen W.A., 1973)). From calctav.m in PROSPECT-D

  • α angle of incidence
  • nr Index of refraction
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Land.CanopyLayers.e2phot — Function
e2phot(λ::Array{FT}, E::Array{FT}) where {FT<:AbstractFloat}

Calculates the number of moles of photons, given

  • λ An array of wave length in [nm], converted to [m] by _FAC
  • E Joules of energy
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Land.CanopyLayers.e2phot! — Function
e2phot!(
            λ::Array{FT,1},
            E::Array{FT,1},
            cache::Array{FT,1}
) where {FT<:AbstractFloat}

Calculates the number of moles of photons, given

  • λ An array of wave length in [nm], converted to [m] by _FAC
  • E Joules of energy
  • cache Cache to avoid memory allocations
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Land.CanopyLayers.psofunction — Function
psofunction(K::FT,
            k::FT,
            Ω::FT,
            LAI::FT,
            q::FT,
            dso::FT,
            xl::FT
) where {FT<:AbstractFloat}

TODO explain the variables

Return the probability of observing a sunlit leaf at depth xl (pso, see eq 31 in vdT 2009), given

  • xl Leaf depth in the canopy
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Land.CanopyLayers.volscatt! — Function
volscatt!(cache::Array{FT,1},
          sza::FT,
          vza::FT,
          raa::FT,
          ttl::FT
) where {FT<:AbstractFloat}

Calculate interception parameters (chi_s and chi_s) and leaf reflectance multiplier (frho) and transmittance multiplier (ftau), given

  • cache Array cache for results
  • sza Solar zenith angle
  • vza Viewing zenith angle
  • raa Relative azimuth angle
  • ttl Leaf inclination angle
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