# -*- coding: latin-1 -*-
from __future__ import division # use "//" to do integer division
from openalea.farquharwheat import model
from openalea.farquharwheat import parameters
"""
farquharwheat.simulation
~~~~~~~~~~~~~~~~~~~~~~~~
The module :mod:`farquharwheat.simulation` is the front-end to run the Farquhar-Wheat :mod:`model <farquharwheat.model>`.
"""
[docs]
class SimulationError(Exception):
pass
[docs]
class Simulation(object):
"""The Simulation class permits to initialize and run a simulation.
"""
def __init__(self, update_parameters=None):
#: The inputs of Farquhar-Wheat.
#:
#: `inputs` is a dictionary of dictionaries:
#: {(plant_index, axis_label, metamer_index, organ_label, element_label): {element_input_name: element_input_value, ...}, ...}
#: See :meth:`Model.run <farquharwheat.model.run>`
#: for more information about the inputs.
self.inputs = {}
#: The outputs of Farquhar-Wheat.
#:
#: `outputs` is a dictionary of dictionaries:
#: {(plant_index, axis_label, metamer_index, organ_label, element_label): {element_output_name: element_output_value, ...}, ...}
#: See :meth:`Model.run <farquharwheat.model.run>`
#: for more information about the outputs.
self.outputs = {}
#: Update parameters if specified
if update_parameters:
parameters.__dict__.update(update_parameters)
[docs]
def initialize(self, inputs):
"""
Initialize :attr:`inputs` from `inputs`.
:param dict inputs: Dictionary of two dictionaries :
- `elements` : The inputs by element.
- `axes` : The inputs by axis.
`inputs` must be a dictionary with the same structure as :attr:`inputs`.
See :meth:`Model.run <farquharwheat.model.run>`
for more information about the inputs.
"""
self.inputs.clear()
self.inputs.update(inputs)
[docs]
def run(self, Ta, ambient_CO2, RH, Ur):
"""
Compute Farquhar variables for each element in :attr:`inputs` and put
the results in :attr:`outputs`.
:param float Ta: air temperature at t (degree Celsius)
:param float ambient_CO2: air CO2 at t (µmol mol-1)
:param float RH: relative humidity at t (decimal fraction)
:param float Ur: wind speed at the top of the canopy at t (m s-1)
"""
self.outputs.update({inputs_type: {} for inputs_type in self.inputs['elements'].keys()})
for (element_id, element_inputs) in self.inputs['elements'].items():
axis_id = element_id[:2]
organ_label = element_id[3]
axe_label = axis_id[1]
if axe_label != 'MS': # Calculation only for the main stem
continue
# In case it is an HiddenElement, we need temperature calculation. Cases of Visible Element without geomtry proprety (because too small) don't have photosynthesis calculation neither.
if element_inputs['height'] is None:
Ag, An, Rd, Tr, gs = 0., 0., 0., 0., 0.
Ts = self.inputs['axes'][axis_id]['SAM_temperature']
else:
PARa = element_inputs['PARa'] #: Amount of absorbed PAR per unit area (µmol m-2 s-1)
height_canopy = self.inputs['axes'][axis_id]['height_canopy']
if parameters.SurfacicProteins:
surfacic_photosynthetic_proteins = model.calculate_surfacic_photosynthetic_proteins(element_inputs['proteins'],
element_inputs['green_area'])
surfacic_nitrogen = model.calculate_surfacic_nonstructural_nitrogen_Farquhar(surfacic_photosynthetic_proteins)
else:
surfacic_nitrogen = model.calculate_surfacic_nitrogen(element_inputs['nitrates'],
element_inputs['amino_acids'],
element_inputs['proteins'],
element_inputs['Nstruct'],
element_inputs['green_area'])
surfacic_NSC = model.calculate_surfacic_WSC(element_inputs['sucrose'], element_inputs['starch'], element_inputs['fructan'], element_inputs['green_area'])
if not parameters.prim_scale:
#: Computation at organ scale
Ag, An, Rd, Tr, Ts, gs = model.run(surfacic_nitrogen,
parameters.NSC_Retroinhibition,
surfacic_NSC,
element_inputs['width'],
element_inputs['height'],
PARa, Ta, ambient_CO2,
RH, Ur, organ_label, height_canopy)
else:
#: Computation at primitive scale
Ag_prim_list = []
for PARa_prim in element_inputs['PARa_prim']: #: Amount of absorbed PAR per unit area (µmol m-2 s-1)
Ag_prim, An, Rd, Tr, Ts, gs = model.run(surfacic_nitrogen,
parameters.NSC_Retroinhibition,
surfacic_NSC,
element_inputs['width'],
element_inputs['height'],
PARa_prim, Ta, ambient_CO2,
RH, Ur, organ_label, height_canopy)
Ag_prim_list.append(Ag_prim)
if not Ag_prim_list:
Ag = 0
else:
Ag = sum([Ag_prim * area_prim for Ag_prim, area_prim in zip(Ag_prim_list, element_inputs['area_prim'])]) / sum(element_inputs['area_prim'])
element_outputs = {'Ag': Ag, 'An': An, 'Rd': Rd,
'Tr': Tr, 'Ts': Ts, 'gs': gs,
'width': element_inputs['width'], 'height': element_inputs['height']}
self.outputs[element_id] = element_outputs
