SoilPlantAirContinuum

Types

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]

SoilPlantAirContinuum.SPACContainer2L — Type

mutable struct SPACContainer2L{FT}

Struct that contains 2-layer gas exchange information.

Fields

cont_sh::SoilPlantAirContinuum.SPACContainer1L
cont_sl::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]

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::PlantHydraulics.AbstractPlantOrganism
Plant hydraulic system
n_canopy::Int64
Number of canopy layers
n_root::Int64
Number of root layers
plant_ps::Array{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{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::Photosynthesis.AbstractPhotoModelParaSet{FT} where FT<:AbstractFloat
Photosynthesis parameter set
stomata_model::StomataModels.AbstractStomatalModel
Stomatal behavior scheme
angles::CanopyLayers.SolarAngles{FT} where FT<:AbstractFloat
Solar angle container
canopy_rt::CanopyLayers.Canopy4RT
Canopy4RT container
wl_set::CanopyLayers.WaveLengths{FT} where FT<:AbstractFloat
Wave length container
rt_dim::CanopyLayers.RTDimensions
RT dimensions
can_rad::CanopyLayers.CanopyRads{FT} where FT<:AbstractFloat
CanopyRads container
can_opt::CanopyLayers.CanopyOpticals{FT} where FT<:AbstractFloat
CanopyOpticals container
leaves_rt::Array{CanopyLayers.LeafBios{FT}, 1} where FT<:AbstractFloat
Array of LeafBios container
soil_opt::CanopyLayers.SoilOpticals{FT} where FT<:AbstractFloat
SoilOpticals container
in_rad::CanopyLayers.IncomingRadiation{FT} where FT<:AbstractFloat
Incoming radiation container
rt_con::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

SoilPlantAirContinuum.SPACSimple — Type

mutable struct SPACSimple{FT}

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

Fields

hs::PlantHydraulics.TreeSimple{FT} where FT<:AbstractFloat
Hydraulic systems
ec::AbstractFloat
Critical flow rate
ps::Photosynthesis.Leaf
Photosynthesis system
vtoj::AbstractFloat
Ratio between Vcmax25 and Jmax25
envir::Photosynthesis.AirLayer
Environmental conditions
container1L::SoilPlantAirContinuum.SPACContainer1L
Container for gas exchange for a layer
container2L::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]

Soil

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

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

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

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]

Planet

SoilPlantAirContinuum.atmospheric_pressure_ratio — Function

atmospheric_pressure(h::FT)

Calculate the atmospheric pressure, given

h elevation in [m]

SoilPlantAirContinuum.atmospheric_pressure — Function

atmospheric_pressure(h::FT)

Calculate the atmospheric pressure, given

h elevation in [m]

SoilPlantAirContinuum.ppm_to_Pa — Function

ppm_to_Pa(h::FT)

Convert ppm to Pa, given

h elevation in [m]

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

Big-leaf model

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

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

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

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

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]

SoilPlantAirContinuum.radiative_conductance — Function

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

Return the radiative conductance of leaf, given

T leaf temperature

SoilPlantAirContinuum.black_body_emittance — Function

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

Return the energy been radiated out, given

T leaf temperature

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

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

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

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

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

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

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

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

Optimal investment

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

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

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