Gas-Exchange User Guide#

Introduction#

This is the documentation for Gas-Exchange, a model of leaf photosynthesis based on Farquhar’s approach. The models computes C assimilation, stomatal conductance and organ temperature for individual shoot organs. The model also provides an option to calculate the photosynthesis at an infra-leaf scale (scene primitive).

  • Calculation of C assimilation was adapted from the Farquhar model proposed by Müller et al. (2005) and Braune et al. (2009) for wheat. The model was adapted to account for the metabolic contents provided by CN-Metabolism model : (i) the actual surfacic N amount (stimulation of the assimilation rates) and (ii) the actual non-structural carbohydrate content (TPU limitation).

  • Calculation of the stomatal conductance is obtained either from the approach of BWB,Leuning, Tuzet or a combination of the two latter (called hydraulics). The choice of the stomatal model bu users is made in the front end script main.py and should be one of ‘BWB’, ‘Leuning’, ‘Tuzet’ or ‘hydraulics’. The models ‘Tuzet’ and ‘hydraulics’ require to provide the organ water potential.

  • Leaf energy balance is computed from the weather data inputs, C assimilation and stomatal conductance in order to simulate organ temperature.

The 3 processes described above are therefore coupled and iteratively computed until internal CO2 (Ci) and leaf temperature converge at each time step.

Inputs of Gas-Exchange#

  • ambient_CO2: atmospheric CO2 concentration (ppm)

  • RH : relative air humidity (decimal fraction)

  • Ur : wind speed at 2m height above canopy (m s-1)

  • height_canopy (m)

  • height : organ height (m)

  • width : lamina width or sheath diameter (m)

  • PARa : PAR absorbed (µmol m-2 s-1)

  • nitrates : amount of nitrates (µmol N)

  • amino_acids : amount of amino acids (µmol N)

  • proteins : amount of proteins (µmol N)

  • Nstruct : structural N (g)

  • sucrose : amount of sucrose (µmol C)

  • starch : amount of starch (µmol C)

  • fructan : amount of fructan (µmol C)

  • PARa_prim: PAR absorbed by the primitive (µmol m-2 s-1)

  • area_prim: area of the primitive (m²)

  • organ_label

  • water_potential: the water potential of the organ (MPa), depending on the chosen stomatal model

Outputs of Gas-Exchange#

  • Ag: gross C assimilation (µmol m-2 s-1)

  • An : Net C assimilation (µmol m-2 s-1)

  • Rd : respiration (µmol m-2 s-1)

  • Tr : transpiration (mmol m-2 s-1)

  • Ts : organ surface temperature (°C)

  • gs : stomatal conductance for water (mol m-2 s-1)

Package architecture#

Gas-Exchange is a Python package which consists of several Python modules: