SoilPlantAirContinuum

mutable struct SPACContainer1L{FT}

Struct that contains 1-layer gas exchange information.

Fields

• ag

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

• an

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

• c

  Leaf internal CO₂ partial pressure [Pa]

• e

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

• gh

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

• p

  Xylem end pressure [MPa]

• t

  Leaf temperature [K]

mutable struct SPACContainer2L{FT}

Struct that contains 2-layer gas exchange information.

Fields

• cont_sh

• cont_sl

• frac_sh

  Shaded layer fraction

• frac_sl

  Sunlit layer fraction

• la_sh

  Shaded layer leaf area [m²]

• la_sl

  Sunlit layer leaf area [m²]

• lai_sh

  Shaded layer LAI

• lai_sl

  Sunlit layer LAI

• par_sh

  Shaded layer PAR [μmol m⁻² s⁻¹]

• par_sl

  Sunlit layer PAR [μmol m⁻² s⁻¹]

• rad_sh

  Shaded layer absorbed energy [W m⁻²]

• rad_sl

  Sunlit layer absorbed energy [W m⁻²]

mutable struct SPACMono{FT}

Struct that mono species SoilPlantAirContinuum system.

Fields

• soil_bounds

  Soil layers bounds [m]

• air_bounds

  Air layers bounds [m]

• z_root

  Root depth [m]

• z_canopy

  Canopy maximal height [m]

• plant_hs

  Plant hydraulic system

• n_canopy

  Number of canopy layers

• n_root

  Number of root layers

• plant_ps

  Plant photosynthesis systems

• ba

  Basal area [m²]

• ga

  Ground area [m²]

• la

  Leaf area [m²]

• envirs

  Air layers

• mswc

  Maximal soil water content

• swc

  Current soil water content

• p_soil

  Array of soil matric potential [MPa]

• h_soil

  Maximal soil depth [m]

• latitude

  Latitude [°]

• longitude

  Longitude [°]

• elevation

  Elevation [m]

• photo_set

  Photosynthesis parameter set

• stomata_model

  Stomatal behavior scheme

• angles

  Solar angle container

• canopy_rt

  Canopy4RT container

• wl_set

  Wave length container

• rt_dim

  RT dimensions

• can_rad

  CanopyRads container

• can_opt

  CanopyOpticals container

• leaves_rt

  Array of LeafBios container

• soil_opt

  SoilOpticals container

• in_rad

  Incoming radiation container

• rt_con

  RT container

mutable struct SPACSimple{FT}

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

Fields

• hs

  Hydraulic systems

• ec

  Critical flow rate

• ps

  Photosynthesis system

• vtoj

  Ratio between Vcmax25 and Jmax25

• envir

  Environmental conditions

• container1L

  Container for gas exchange for a layer

• container2L

  Container for gas exchange of sunlit and shaded layers

• containerKS

  Container for default hydraulic conductance

• containerOP

  Container for optimizer

• opt_f_sl

  Container for optimal sunlit layer flow rate

• opt_f_sh

  Container for optimal shaded layer flow rate

• opt_laba

  Container for optimal leaf area per basal area

• opt_vmax

  Container for optimal Vcmax25

• lai

  Leaf area index

• laba

  Leaf area per basal area

• g_max

  Maximal stomatal conductance limit at 25 °C

• gaba

  Ground area per basal area

• width

  Leaf width

• mswc

  Maximal soil water content

• swc

  Current soil water content

• p_soil

  Soil matrical water potential

• h_soil

  Soil depth, 2X mean root depth

• c_cons

  Leaf construction cost per leaf area

• c_vmax

  Leaf nutrient cost per Vcmax25 per leaf area

• latitude

  Latitude [°]

• longitude

  Longitude [°]

• elevation

  Elevation [m]

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

Update soil moisture and soil matrix potential, given

• nodeSPACSimple type struct
• swc Given soil water content

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

Update soil moisture and soil matrix potential, given

• nodeSPACSimple type struct
• p Given soil maxtrix potential

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

Update soil moisture and soil matrix potential, given

• nodeSPACSimple type struct
• p_25 Given soil maxtrix potential at 25 Celcius

soil_moisture!(node::SPACSimple{FT}, flow, dt=1.0) where {FT<:AbstractFloat}

Update soil moisture and soil matrix potential, given

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

atmospheric_pressure(h::FT)

Calculate the atmospheric pressure, given

• h elevation in [m]

atmospheric_pressure(h::FT)

Calculate the atmospheric pressure, given

• h elevation in [m]

ppm_to_Pa(h::FT)

Convert ppm to Pa, given

• h elevation in [m]

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

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

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

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

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

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]

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

Return the radiative conductance of leaf, given

• T leaf temperature

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

Return the energy been radiated out, given

• T leaf temperature

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

Return the boundary layer conductance, given

• wind Wind speed
• width Leaf width

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

• nodeSPACSimple 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

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

Return leaf temperature, given

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

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

Return leaf temperature, given

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

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

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

function create_dataframe(FT, weather::DataFrame)

Create a data frame to storesimulation output, given

• FT Floating number type
• weather Weather profile in a growing season

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

Initialize the RT parameters for a given

• nodeSPACMono type struct

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

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

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