Leaf params

leaf_phys_params


def leaf_phys_params(
    params:Params, # Waveband indices:
- vis : int
    Waveband index for visible radiation.
- nir : int
    Waveband index for near-infrared radiation.
    physcon:PhysCon, # Physical constants:
- tfrz : float
    Freezing point of water (K).
- rgas : float
    Universal gas constant (J/K/mol).
    leaf:Leaf, # Leaf object with the following input attribute:
- c3psn : int
    Photosynthetic pathway: 1 = C3, 0 = C4 plant.
)->Leaf: # Updated Leaf object with the following attributes:

Photosynthetic parameters at 25°C:
- vcmax25 : float
    Maximum carboxylation rate at 25°C (umol/m2/s).
- jmax25 : float
    Maximum electron transport rate at 25°C (umol/m2/s).
- rd25 : float
    Leaf respiration rate at 25°C (umol CO2/m2/s).
- kc25 : float
    Michaelis-Menten constant for CO2 at 25°C (umol/mol).
- ko25 : float
    Michaelis-Menten constant for O2 at 25°C (mmol/mol).
- cp25 : float
    CO2 compensation point at 25°C (umol/mol).

Activation energies:
- kcha : float
    Activation energy for Kc (J/mol).
- koha : float
    Activation energy for Ko (J/mol).
- cpha : float
    Activation energy for Cp (J/mol).
- vcmaxha : float
    Activation energy for Vcmax (J/mol).
- jmaxha : float
    Activation energy for Jmax (J/mol).
- rdha : float
    Activation energy for Rd (J/mol).

High temperature deactivation:
- vcmaxhd : float
    Deactivation energy for Vcmax (J/mol).
- jmaxhd : float
    Deactivation energy for Jmax (J/mol).
- rdhd : float
    Deactivation energy for Rd (J/mol).
- vcmaxse : float
    Entropy term for Vcmax (J/mol/K).
- jmaxse : float
    Entropy term for Jmax (J/mol/K).
- rdse : float
    Entropy term for Rd (J/mol/K).
- vcmaxc : float
    Vcmax scaling factor for high temperature inhibition (25°C = 1.0).
- jmaxc : float
    Jmax scaling factor for high temperature inhibition (25°C = 1.0).
- rdc : float
    Rd scaling factor for high temperature inhibition (25°C = 1.0).

Electron transport and co-limitation:
- phi_psii : float
    Quantum yield of PS II (-).
- theta_j : float
    Empirical curvature parameter for electron transport rate (-).
- colim_c3 : float
    Empirical curvature parameter for C3 co-limitation (-).
- colim_c4a : float
    Empirical curvature parameter for C4 co-limitation (-).
- colim_c4b : float
    Empirical curvature parameter for C4 co-limitation (-).
- qe_c4 : float
    C4 quantum yield (mol CO2 / mol photons).
- kp25_c4 : float
    C4 initial slope of CO2 response curve at 25°C (mol/m2/s).

Leaf structural properties:
- dleaf : float
    Leaf dimension (m).
- emiss : float
    Leaf emissivity (-).
- rho : list[float]
    Leaf reflectance for visible and near-infrared wavebands (-).
- tau : list[float]
    Leaf transmittance for visible and near-infrared wavebands (-).

Stomatal and hydraulic parameters:
- iota : float
    Stomatal efficiency, An/E (umol CO2 / mol H2O).
- capac : float
    Plant capacitance (mmol H2O/m2 leaf area/MPa).
- minl_wp : float
    Minimum leaf water potential (MPa).
- gplant : float
    Stem (xylem-to-leaf) hydraulic conductance (mmol H2O/m2 leaf area/s/MPa).
- g0 : float  
    Minimum Conductance (mol/m2/s) 
- g1_medlyn : float 
    Medlyn slope parameter (kPa^0.5). Controls stomatal sensitivity to VPD. Higher g1 = less conservative.
- stomatal_model: str
    Stomatal model to use "optimization", "medlyn" or "profit_max"  
- a_psi: float
    Parameter that controls the steepness of this curve in the "profit_max" model

Set leaf physiological parameters.

Parameters:

Params: Waveband indices - vis : int Waveband index for visible radiation. - nir : int Waveband index for near-infrared radiation.
PhysCon: Physical constants
- tfrz: Freezing point of water (K).
- rgas: Universal gas constant (J/K/mol).
Leaf: Leaf object with the following input attribute:
- c3psn: Photosynthetic pathway: 1 = C3, 0 = C4 plant.

Returns:

Leaf: Updated Leaf object with the following attributes:
- Photosynthetic parameters at 25°C:
  - vcmax25: Maximum carboxylation rate at 25°C (umol/m2/s).
  - jmax25: Maximum electron transport rate at 25°C (umol/m2/s).
  - rd25: Leaf respiration rate at 25°C (umol CO2/m2/s).
  - kc25: Michaelis-Menten constant for CO2 at 25°C (umol/mol).
  - ko25: Michaelis-Menten constant for O2 at 25°C (mmol/mol).
  - cp25: CO2 compensation point at 25°C (umol/mol).
- Activation energies:
  - kcha: Activation energy for Kc (J/mol).
  - koha: Activation energy for Ko (J/mol).
  - cpha: Activation energy for Cp (J/mol).
  - vcmaxha: Activation energy for Vcmax (J/mol).
  - jmaxha: Activation energy for Jmax (J/mol).
  - rdha: Activation energy for Rd (J/mol).
- High temperature deactivation:
  - vcmaxhd: Deactivation energy for Vcmax (J/mol).
  - jmaxhd: Deactivation energy for Jmax (J/mol).
  - rdhd: Deactivation energy for Rd (J/mol).
  - vcmaxse: Entropy term for Vcmax (J/mol/K).
  - jmaxse: Entropy term for Jmax (J/mol/K).
  - rdse: Entropy term for Rd (J/mol/K).
  - vcmaxc: Vcmax scaling factor for high temperature inhibition (25°C = 1.0).
  - jmaxc: Jmax scaling factor for high temperature inhibition (25°C = 1.0).
  - rdc: Rd scaling factor for high temperature inhibition (25°C = 1.0).
- Electron transport and co-limitation:
  - phi_psii: Quantum yield of PS II (-).
  - theta_j: Empirical curvature parameter for electron transport rate (-).
  - colim_c3: Empirical curvature parameter for C3 co-limitation (-).
  - colim_c4a: Empirical curvature parameter for C4 co-limitation (-).
  - colim_c4b: Empirical curvature parameter for C4 co-limitation (-).
  - qe_c4: C4 quantum yield (mol CO2 / mol photons).
  - kp25_c4: C4 initial slope of CO2 response curve at 25°C (mol/m2/s).
- Leaf structural properties:
  - dleaf: Leaf dimension (m).
  - emiss: Leaf emissivity (-).
  - rho: Leaf reflectance for visible and near-infrared wavebands (-).
  - tau: Leaf transmittance for visible and near-infrared wavebands (-).
- Stomatal and hydraulic parameters:
  - iota: Stomatal efficiency, An/E (umol CO2 / mol H2O).
  - capac: Plant capacitance (mmol H2O/m2 leaf area/MPa).
  - minl_wp: Minimum leaf water potential (MPa).
  - gplant: Stem (xylem-to-leaf) hydraulic conductance (mmol H2O/m2 leaf area/s/MPa).
  - g0: Minimum Conductance (mol/m2/s)
  - g1_medlyn: Medlyn slope parameter (kPa^0.5). Controls stomatal sensitivity to VPD. Higher g1 = less conservative.
  - stomatal_model: Stomatal model to use : - “optimization” = original WUE optimization from Bonan Ch. 13 (uses brent_root + stomata_efficiency) - `“medlyn” = Medlyn et al. (2011) empirical model (uses iterative gs-An coupling + hard hydraulic cap) - “profit_max” = Medlyn + Sperry profit-maximisation framework (uses gs sweep + gain-cost optimisation)]
  - a_psi: Parameter that controls the steepness of this curve in the “profit_max” model

Example leaf_physiology_params()

params = Params()
physcon = PhysCon()
leaf = Leaf()

(vars(leaf_phys_params(leaf=leaf, params=params, physcon=physcon)))

{'c3psn': 1,
 'colim': 1,
 'vcmax25': 60.0,
 'jmax25': 100.19999999999999,
 'rd25': 0.8999999999999999,
 'kc25': 404.9,
 'ko25': 278.4,
 'cp25': 42.75,
 'kcha': 79430.0,
 'koha': 36380.0,
 'cpha': 37830.0,
 'vcmaxha': 65330.0,
 'jmaxha': 43540.0,
 'rdha': 46390.0,
 'vcmaxhd': 150000.0,
 'jmaxhd': 150000.0,
 'rdhd': 150000.0,
 'vcmaxse': 490.0,
 'jmaxse': 490.0,
 'rdse': 490.0,
 'vcmaxc': np.float64(1.2068286010531608),
 'jmaxc': np.float64(1.2068286010531608),
 'rdc': np.float64(1.2068286010531608),
 'phi_psii': 0.85,
 'theta_j': 0.9,
 'colim_c3': 0.98,
 'colim_c4a': 0.8,
 'colim_c4b': 0.95,
 'qe_c4': 0.05,
 'kp25_c4': 0.0,
 'dleaf': 0.05,
 'emiss': 0.98,
 'rho': [0.1, 0.4],
 'tau': [0.1, 0.4],
 'iota': 750.0,
 'capac': 2500.0,
 'minlwp': -2.0,
 'gplant': 4.0}