SoilPlantAirContinuum

Types

Land.SoilPlantAirContinuum.SPACContainer1L — Type

mutable struct SPACContainer1L{FT}

Struct that contains 1-layer gas exchange information.

Fields

ag::AbstractFloat

: Mean gross photosynthetic rate [μmol m⁻² s⁻¹]

an::AbstractFloat

: Mean net photosynthetic rate [μmol m⁻² s⁻¹]

c::AbstractFloat

: Leaf internal CO₂ partial pressure [Pa]

e::AbstractFloat

: Flow rate per basal area [mol s⁻¹ m⁻²]

gh::AbstractFloat

: Leaf diffusive conductance to H₂O [mol m⁻² s⁻¹]

p::AbstractFloat

: Xylem end pressure [MPa]

t::AbstractFloat

: Leaf temperature [K]

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Land.SoilPlantAirContinuum.SPACContainer2L — Type

mutable struct SPACContainer2L{FT}

Struct that contains 2-layer gas exchange information.

Fields

cont_sh::Land.SoilPlantAirContinuum.SPACContainer1L
cont_sl::Land.SoilPlantAirContinuum.SPACContainer1L
frac_sh::AbstractFloat

: Shaded layer fraction

frac_sl::AbstractFloat

: Sunlit layer fraction

la_sh::AbstractFloat

: Shaded layer leaf area [m²]

la_sl::AbstractFloat

: Sunlit layer leaf area [m²]

lai_sh::AbstractFloat

: Shaded layer LAI

lai_sl::AbstractFloat

: Sunlit layer LAI

par_sh::AbstractFloat

: Shaded layer PAR [μmol m⁻² s⁻¹]

par_sl::AbstractFloat

: Sunlit layer PAR [μmol m⁻² s⁻¹]

rad_sh::AbstractFloat

: Shaded layer absorbed energy [W m⁻²]

rad_sl::AbstractFloat

: Sunlit layer absorbed energy [W m⁻²]

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Land.SoilPlantAirContinuum.SPACMono — Type

mutable struct SPACMono{FT}

Struct that mono species SoilPlantAirContinuum system.

Fields

soil_bounds::Vector{FT} where FT<:AbstractFloat

: Soil layers bounds [m]

air_bounds::Vector{FT} where FT<:AbstractFloat

: Air layers bounds [m]

z_root::AbstractFloat

: Root depth [m]

z_canopy::AbstractFloat

: Canopy maximal height [m]

plant_hs::Union{Land.PlantHydraulics.GrassLikeOrganism{FT}, Land.PlantHydraulics.PalmLikeOrganism{FT}, Land.PlantHydraulics.TreeLikeOrganism{FT}} where FT<:AbstractFloat

: Plant hydraulic system

n_canopy::Int64

: Number of canopy layers

n_root::Int64

: Number of root layers

plant_ps::Array{Land.StomataModels.CanopyLayer{FT}, 1} where FT<:AbstractFloat

: Plant photosynthesis systems

ba::AbstractFloat

: Basal area [m²]

ga::AbstractFloat

: Ground area [m²]

la::AbstractFloat

: Leaf area [m²]

envirs::Array{Land.Photosynthesis.AirLayer{FT}, 1} where FT<:AbstractFloat

: Air layers

wind_z0::AbstractFloat

: Aerodynamic roughness [m]

wind_d::AbstractFloat

: Zero plane displacement [m]

wind_zs::Vector{FT} where FT<:AbstractFloat

: Mean layer height [m]

winds::Vector{FT} where FT<:AbstractFloat

: Wind speed per layer [m s⁻¹]

mswc::Vector{FT} where FT<:AbstractFloat

: Maximal soil water content

swc::Vector{FT} where FT<:AbstractFloat

: Current soil water content

p_soil::Vector{FT} where FT<:AbstractFloat

: Array of soil matric potential [MPa]

h_soil::AbstractFloat

: Maximal soil depth [m]

latitude::AbstractFloat

: Latitude [°]

longitude::AbstractFloat

: Longitude [°]

elevation::AbstractFloat

: Elevation [m]

photo_set::Union{Land.Photosynthesis.C3ParaSet{FT}, Land.Photosynthesis.C4ParaSet{FT}} where FT<:AbstractFloat

: Photosynthesis parameter set

stomata_model::Union{Land.StomataModels.EmpiricalStomatalModel{FT}, Land.StomataModels.OptimizationStomatalModel{FT}} where FT<:AbstractFloat

: Stomatal behavior scheme

angles::Land.CanopyLayers.SolarAngles{FT} where FT<:AbstractFloat

: Solar angle container

canopy_rt::Land.CanopyLayers.Canopy4RT

: Canopy4RT container

wl_set::Land.CanopyLayers.WaveLengths{FT} where FT<:AbstractFloat

: Wave length container

rt_dim::Land.CanopyLayers.RTDimensions

: RT dimensions

can_rad::Land.CanopyLayers.CanopyRads{FT} where FT<:AbstractFloat

: CanopyRads container

can_opt::Land.CanopyLayers.CanopyOpticals{FT} where FT<:AbstractFloat

: CanopyOpticals container

leaves_rt::Array{Land.CanopyLayers.LeafBios{FT}, 1} where FT<:AbstractFloat

: Array of LeafBios container

soil_opt::Land.CanopyLayers.SoilOpticals{FT} where FT<:AbstractFloat

: SoilOpticals container

in_rad::Land.CanopyLayers.IncomingRadiation{FT} where FT<:AbstractFloat

: Incoming radiation container

rt_con::Land.CanopyLayers.RTCache{FT} where FT<:AbstractFloat

: RT container

f_SL::Vector{FT} where FT<:AbstractFloat

: Container for sunlit leaf area fraction in each layer

f_gpp::AbstractFloat

: Canopy GPP per ground area

f_npp::AbstractFloat

: Canopy GPP per ground area

f_H₂O::AbstractFloat

: Canopy water flux per ground area

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Land.SoilPlantAirContinuum.SPACSimple — Type

mutable struct SPACSimple{FT}

Struct that simplest mono species SoilPlantAirContinuum system, with 1 root, stem, and leaf.

Fields

hs::Land.PlantHydraulics.TreeSimple{FT} where FT<:AbstractFloat

: Hydraulic systems

ec::AbstractFloat

: Critical flow rate

ps::Land.Photosynthesis.Leaf

: Photosynthesis system

vtoj::AbstractFloat

: Ratio between Vcmax25 and Jmax25

envir::Land.Photosynthesis.AirLayer

: Environmental conditions

container1L::Land.SoilPlantAirContinuum.SPACContainer1L

: Container for gas exchange for a layer

container2L::Land.SoilPlantAirContinuum.SPACContainer2L

: Container for gas exchange of sunlit and shaded layers

containerKS::Vector{FT} where FT<:AbstractFloat

: Container for default hydraulic conductance

containerOP::AbstractFloat

: Container for optimizer

opt_f_sl::AbstractFloat

: Container for optimal sunlit layer flow rate

opt_f_sh::AbstractFloat

: Container for optimal shaded layer flow rate

opt_laba::AbstractFloat

: Container for optimal leaf area per basal area

opt_vmax::AbstractFloat

: Container for optimal Vcmax25

lai::AbstractFloat

: Leaf area index

laba::AbstractFloat

: Leaf area per basal area

g_max::AbstractFloat

: Maximal stomatal conductance limit at 25 °C

gaba::AbstractFloat

: Ground area per basal area

width::AbstractFloat

: Leaf width

mswc::AbstractFloat

: Maximal soil water content

swc::AbstractFloat

: Current soil water content

p_soil::AbstractFloat

: Soil matrical water potential

h_soil::AbstractFloat

: Soil depth, 2X mean root depth

c_cons::AbstractFloat

: Leaf construction cost per leaf area

c_vmax::AbstractFloat

: Leaf nutrient cost per Vcmax25 per leaf area

latitude::AbstractFloat

: Latitude [°]

longitude::AbstractFloat

: Longitude [°]

elevation::AbstractFloat

: Elevation [m]

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Soil

Land.SoilPlantAirContinuum.soil_moisture_swc! — Function

soil_moisture_swc!(node::SPACSimple{FT}, swc::FT) where {FT<:AbstractFloat}

Update soil moisture and soil matrix potential, given

node SPACSimple type struct
swc Given soil water content

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Land.SoilPlantAirContinuum.soil_moisture_p! — Function

soil_moisture_p!(node::SPACSimple{FT}, p::FT) where {FT<:AbstractFloat}

Update soil moisture and soil matrix potential, given

node SPACSimple type struct
p Given soil maxtrix potential

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Land.SoilPlantAirContinuum.soil_moisture_p25! — Function

soil_moisture_p25!(
            node::SPACSimple{FT},
            p_25::FT
) where {FT<:AbstractFloat}

Update soil moisture and soil matrix potential, given

node SPACSimple type struct
p_25 Given soil maxtrix potential at 25 Celcius

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Land.SoilPlantAirContinuum.soil_moisture! — Function

soil_moisture!(
            node::SPACSimple{FT},
            flow::FT,
            Δt::FT = FT(1)
) where {FT<:AbstractFloat}

Update soil moisture and soil matrix potential, given

node SPACSimple type struct
flow Mean outlet flow rate in [Kg h⁻¹]
Δt Time period in [h]

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Planet

Land.SoilPlantAirContinuum.atmospheric_pressure_ratio — Function

atmospheric_pressure(h::FT)

Calculate the atmospheric pressure, given

h elevation in [m]

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Land.SoilPlantAirContinuum.atmospheric_pressure — Function

atmospheric_pressure(h::FT)

Calculate the atmospheric pressure, given

h elevation in [m]

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Land.SoilPlantAirContinuum.ppm_to_Pa — Function

ppm_to_Pa(h::FT)

Convert ppm to Pa, given

h elevation in [m]

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Land.SoilPlantAirContinuum.zenith_angle — Function

zenith_angle(
            latd::FT,
            decd::FT,
            lhad::FT
) where {FT<:AbstractFloat}
zenith_angle(
            latd::FT,
            day::FT,
            hour::FT,
            minute::FT
) where {FT<:AbstractFloat}

Calculate the zenith angle, given

latd Latitude in degree
decd Declination of the Sun in degree
lhad Local hour angle in degree
day Day of year
hour Hour of day
minute Minute of hour

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Big-leaf model

Land.SoilPlantAirContinuum.gain_risk_map — Function

gain_risk_map(
            node::SPACSimple{FT},
            photo_set::AbstractPhotoModelParaSet{FT}
) where {FT<:AbstractFloat}

Return the matrix of optimizers at different sunlit and shaded layer flow rates, given

node [SPACSimple] type struct
photo_set [AbstractPhotoModelParaSet] type photosynthesis parameter set

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Land.SoilPlantAirContinuum.leaf_gas_exchange_nonopt! — Function

leaf_gas_exchange_nonopt!(
            node::SPACSimple{FT},
            photo_set::AbstractPhotoModelParaSet{FT},
            flow::FT,
            par::FT,
            rad::FT,
            la::FT,
            container::SPACContainer1L{FT}
) where {FT<:AbstractFloat}
leaf_gas_exchange_nonopt!(
            node::SPACSimple{FT},
            photo_set::AbstractPhotoModelParaSet{FT},
            flow::FT
) where {FT<:AbstractFloat}
leaf_gas_exchange_nonopt!(
            node::SPACSimple{FT},
            photo_set::AbstractPhotoModelParaSet{FT},
            f_sl::FT,
            f_sh::FT
) where {FT<:AbstractFloat}

Simulate leaf level gas exchange and fill it into the container for 1-layer or 2-layer canopy, given

node [SPACSimple] type struct
photo_set [AbstractPhotoModelParaSet] type struct
flow Flow rate per basal area into the leaves (e.g., for sunlit leaves)
f_sl Flow rate per basal area into the sunlit leaves
f_sh Flow rate per basal area into the shaded leaves
par Leaf-level photosynthetic active radiation
rad Leaf-level absorbed radiative energy
la Leaf area of the leaves (total or each layer)
container [SPACContainer1L] type container

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Land.SoilPlantAirContinuum.leaf_gas_exchange! — Function

leaf_gas_exchange!(
            node::SPACSimple{FT},
            photo_set::AbstractPhotoModelParaSet{FT},
            flow::FT,
            par::FT,
            rad::FT,
            la::FT,
            container::SPACContainer1L{FT}
) where {FT<:AbstractFloat}
leaf_gas_exchange!(
            node::SPACSimple{FT},
            photo_set::AbstractPhotoModelParaSet{FT},
            flow::FT
) where {FT<:AbstractFloat}
leaf_gas_exchange!(
            node::SPACSimple{FT},
            photo_set::AbstractPhotoModelParaSet{FT},
            f_sl::FT,
            f_sh::FT
) where {FT<:AbstractFloat}

Simulate leaf level gas exchange and fill it into the container for 1-layer or 2-layer canopy, given

node [SPACSimple] type struct
photo_set [AbstractPhotoModelParaSet] type struct
flow Flow rate per basal area into the leaves (e.g., for sunlit leaves)
f_sl Flow rate per basal area into the sunlit leaves
f_sh Flow rate per basal area into the shaded leaves
par Leaf-level photosynthetic active radiation
rad Leaf-level absorbed radiative energy
la Leaf area of the leaves (total or each layer)
container [SPACContainer1L] type container

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Land.SoilPlantAirContinuum.optimize_flows! — Function

optimize_flows!(
            node::SPACSimple{FT},
            photo_set::AbstractPhotoModelParaSet{FT}
) where {FT<:AbstractFloat}

Optimize the flow rates in sunlit and shaded layers, given

node [SPACSimple] type struct
photo_set [AbstractPhotoModelParaSet] type struct

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Land.SoilPlantAirContinuum.big_leaf_partition! — Function

big_leaf_partition!(
            node::SPACSimple{FT},
            zenith::FT,
            r_all::FT
) where {FT <:AbstractFloat}

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

partition Container for partition
zenith Zenith angle in degree
r_all Total radiation in [W m⁻²]

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Land.SoilPlantAirContinuum.radiative_conductance — Function

radiative_conductance(T::FT) where {FT<:AbstractFloat}

Return the radiative conductance of leaf, given

T leaf temperature

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Land.SoilPlantAirContinuum.black_body_emittance — Function

black_body_emittance(T::FT) where {FT<:AbstractFloat}

Return the energy been radiated out, given

T leaf temperature

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Land.SoilPlantAirContinuum.boundary_layer_conductance — Function

boundary_layer_conductance(wind::FT, width::FT) where {FT<:AbstractFloat}

Return the boundary layer conductance, given

wind Wind speed
width Leaf width

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Land.SoilPlantAirContinuum.leaf_temperature — Function

leaf_temperature(
            node::SPACSimple{FT},
            rad::FT,
            e_rad::FT,
            epla::FT
) where {FT<:AbstractFloat}
leaf_temperature(
            node::SPACSimple{FT},
            rad::FT,
            flow::FT
) where {FT<:AbstractFloat}

Return leaf temperature, given

node SPACSimple type struct
rad Absorbed solar radiation per leaf area
e_rad Emitted absorbed radiation per leaf area
epla Flow rate per leaf area
flow Total flow rate per basal area

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Land.SoilPlantAirContinuum.leaf_temperature_sunlit — Function

leaf_temperature_sunlit(
            node::SPACSimple{FT},
            rad::FT,
            f_sl::FT
) where {FT<:AbstractFloat}

Return leaf temperature, given

node SPACSimple type struct
rad Absorbed solar radiation per leaf area
f_sl Total flow rate per basal area into sunlit leaves

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Land.SoilPlantAirContinuum.leaf_temperature_shaded — Function

leaf_temperature_shaded(
            node::SPACSimple{FT},
            rad::FT,
            f_sh::FT
) where {FT<:AbstractFloat}

Return leaf temperature, given

node SPACSimple type struct
rad Absorbed solar radiation per leaf area
f_sh Total flow rate per basal area into shaded leaves

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Land.SoilPlantAirContinuum.annual_profit — Function

annual_profit(
            node::SPACSimple{FT},
            photo_set::AbstractPhotoModelParaSet{FT},
            weather::Array{FT,2}
) where {FT<:AbstractFloat}

Calculate the profit in the growing season so as to optimize leaf investment, given

node [SPACSimple] type struct
photo_set [AbstractPhotoModelParaSet] type struct
weather Weather profile in a growing season

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Land.SoilPlantAirContinuum.annual_simulation! — Function

annual_simulation!(
            node::SPACSimple{FT},
            photo_set::AbstractPhotoModelParaSet{FT},
            weather::DataFrame,
            output::DataFrame
) where {FT<:AbstractFloat}

Run annual simulation for a growing season, given

node [SPACSimple] type struct
photo_set [AbstractPhotoModelParaSet] type struct
weather Weather profile in a growing season
output The predefined output result

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Land.SoilPlantAirContinuum.create_dataframe — Function

function create_dataframe(FT, weather::DataFrame)

Create a data frame to store simulation output, given

FT Floating number type
weather Weather profile in a growing season

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Land.SoilPlantAirContinuum.initialize_spac_canopy! — Function

initialize_spac_canopy!(node::SPACMono{FT}) where {FT<:AbstractFloat}

Initialize the RT parameters for a given

node SPACMono type struct

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Optimal investment

Land.SoilPlantAirContinuum.leaf_allocation! — Function

leaf_allocation!(
            node::SPACSimple{FT},
            laba::FT
) where {FT<:AbstractFloat}
leaf_allocation!(
            node::SPACSimple{FT},
            photo_set::AbstractPhotoModelParaSet{FT},
            vmax::FT
) where {FT<:AbstractFloat}
leaf_allocation!(
            node::SPACSimple{FT},
            photo_set::AbstractPhotoModelParaSet{FT},
            laba::FT,
            vmax::FT
) where {FT<:AbstractFloat}

Update leaf area and maximal carboxylation rate, given

node [SPACSimple] type struct
photo_set [AbstractPhotoModelParaSet] type struct
laba Given leaf area per basal area
vmax Given Vcmax25

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Land.SoilPlantAirContinuum.optimize_leaf! — Function

optimize_leaf!(
            node::SPACSimple{FT},
            photo_set::AbstractPhotoModelParaSet{FT},
            weather::Array{FT,2},
            printing::Bool
) where {FT<:AbstractFloat}

Optimize leaf area (LAI within 0-20) and photosynthetic capacity (within 5-200), given

node [SPACSimple] type struct
photo_set [AbstractPhotoModelParaSet] type struct
weather Weather profile in a growing season
printing Optional. If true, printing progress

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Land.SoilPlantAirContinuum.optimize_hs! — Function

optimize_hs!(
            node::SPACSimple{FT},
            photo_set::AbstractPhotoModelParaSet{FT},
            weather::Array{FT,2}
) where {FT<:AbstractFloat}

Optimize hydraulic conductance and leaf investment, given

node [SPACSimple] type struct
photo_set [AbstractPhotoModelParaSet] type struct
weather Weather profile in a growing season

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