Reference guide

This manual details, for each module of cnwheat, the functions and objects included in cnwheat, describing what they are and what they do.

cnwheat package

cnwheat.simulation module

exception cnwheat.simulation.SimulationError[source]

Bases: Exception

Abstract class for the management of simulation errors. Do not instance it directly.

exception cnwheat.simulation.SimulationConstructionError[source]

Bases: cnwheat.simulation.SimulationError

Exception raised when a problem occurs in the constructor, in particular when the arguments are not consistent with each other.

exception cnwheat.simulation.SimulationInitializationError[source]

Bases: cnwheat.simulation.SimulationError

Exception raised when a problem occurs at initialization time, in particular when checking the consistency of inputs population and soils (see initialize()).

exception cnwheat.simulation.SimulationRunError[source]

Bases: cnwheat.simulation.SimulationError

Exception raised when running a simulation, for example when a problem occurs during the integration of the system of differential equations.

class cnwheat.simulation.Simulation(respiration_model, delta_t=1, culm_density=None, interpolate_forcings=False, senescence_forcings_delta_t=None, photosynthesis_forcings_delta_t=None)[source]

Bases: object

The Simulation class permits to initialize and run the model.

User should use method initialize() to initialize the model, and method run() to run the model.

Parameters:
  • respiration_model (class) –

    the model of respiration to use. This model must define a class implementing these functions:

    • R_Nnit_upt(U_Nnit, sucrose): Nitrate uptake respiration.
      • Parameters:
        • U_Nnit (float) - uptake of N nitrates (µmol` N)
        • sucrose (float) - amount of C sucrose in organ (µmol` C)
      • Returns: _R_Nnit_upt (µmol` C respired)
      • Returns Type: float
    • R_phloem(sucrose_loading, sucrose, mstruct): Phloem loading respiration
      • Parameters:
        • sucrose_loading (float) - Loading flux from the C substrate pool to phloem (µmol` C g-1 mstruct)
        • sucrose (float) - amount of C sucrose in organ (µmol` C)
        • mstruct (float) - structural dry mass of organ (g)
      • Returns: _R_phloem (µmol` C respired)
      • Returns Type: float
    • R_Nnit_red(s_amino_acids, sucrose, mstruct, root=False): Nitrate reduction-linked respiration Distinction is made between nitrate realised in roots or in shoots where a part of the energy required is derived from ATP and reducing power obtained directly from photosynthesis (rather than C substrate)
      • Parameters:
        • s_amino_acids (float) - consumption of N for the synthesis of amino acids (µmol` N g-1 mstruct) (in the present version, this is used to approximate nitrate reduction needed in the original model of Thornley and Cannell, 2000)
        • sucrose (float) - amount of C sucrose in organ (µmol` C)
        • mstruct (float) - structural dry mass of organ (g)
        • root (bool) - specifies if the nitrate reduction-linked respiration is computed for shoot (False) or root (True) tissues.
      • Returns: _R_Nnit_upt (µmol` C respired)
      • Returns Type: float
    • R_residual(sucrose, mstruct, Ntot, delta_t, Ts): Residual maintenance respiration (cost from protein turn-over, cell ion gradients, futile cycles…)
      • Parameters:
        • sucrose (float) - amount of C sucrose (µmol` C)
        • mstruct (float) - structural dry mass of organ (g)
        • Ntot (float) - total N in organ (µmol` N)
        • delta_t (float) - timestep (s)
        • Ts (float) - organ temperature (°C)
      • Returns: _R_residual (µmol` C respired)
      • Returns Type: float
    • R_grain_growth(mstruct_growth, starch_filling, mstruct): Grain growth respiration
      • Parameters:
        • mstruct_growth (float) - gross growth of grain structure (µmol` C added in grain structure)
        • starch_filling (float) - gross growth of grain starch (µmol` C added in grain starch g-1 mstruct)
        • mstruct (float) - structural dry mass of organ (g)
      • Returns: R_grain_growth (µmol` C respired)
      • Returns Type: float
  • delta_t (int) – the delta t of the simulation (in seconds) ; default is 1.
  • [int, int] culm_density (dict) – culm density (culm m-2).
  • interpolate_forcings (bool) – if True: interpolate senescence and photosynthesis forcings from values of senescence_forcings_delta_t`and `senescence_forcings_delta_t. Default is False (do not interpolate the forcings).
  • senescence_forcings_delta_t (int) –
    the delta t of the senescence forcings (in seconds) ; default is None.
    If the user sets interpolate_forcings to True, then he/she must also set senescence_forcings_delta_t to an integer value greater or equal to delta_t. For example, if interpolate_forcings is True and delta_t==3600, then senescence_forcings_delta_t must be greater or equal to 3600, that is for example 7200.
    param int photosynthesis_forcings_delta_t:
     
    the delta t of the photosynthesis forcings (in seconds) ; default is None.
    If the user sets interpolate_forcings to True, then he/she must also set photosynthesis_forcings_delta_t to an integer value greater or equal to delta_t. For example, if interpolate_forcings is True and delta_t==3600, then photosynthesis_forcings_delta_t must be greater or equal to 3600, that is for example 7200.
    • interpolate_forcings (bool) - if True: interpolate senescence and photosynthesis forcings from values of senescence_forcings_delta_t and senescence_forcings_delta_t. Default is False (do not interpolate the forcings).
    • senescence_forcings_delta_t (int) - the delta t of the senescence forcings (in seconds) ; default is None. If the user sets interpolate_forcings to True, then he/she must also set senescence_forcings_delta_t to an integer value greater or equal to delta_t. For example, if interpolate_forcings is True and delta_t==3600, then senescence_forcings_delta_t must be greater or equal to 3600, that is for example 7200.
    • photosynthesis_forcings_delta_t (int) - the delta t of the photosynthesis forcings (in seconds) ; default is None. If the user sets interpolate_forcings to True, then he/she must also set photosynthesis_forcings_delta_t to an integer value greater or equal to delta_t. For example, if interpolate_forcings is True and delta_t==3600, then photosynthesis_forcings_delta_t must be greater or equal to 3600, that is for example 7200.
MODEL_COMPARTMENTS_NAMES = {<class 'cnwheat.model.Plant'>: [], <class 'cnwheat.model.Axis'>: ['C_exudated', 'sum_respi_shoot', 'sum_respi_roots'], <class 'cnwheat.model.Phytomer'>: [], <class 'cnwheat.model.Organ'>: ['age_from_flowering', 'amino_acids', 'cytokinins', 'nitrates', 'proteins', 'starch', 'structure', 'sucrose'], <class 'cnwheat.model.HiddenZone'>: ['amino_acids', 'fructan', 'proteins', 'sucrose'], <class 'cnwheat.model.PhotosyntheticOrganElement'>: ['amino_acids', 'cytokinins', 'fructan', 'nitrates', 'proteins', 'starch', 'sucrose', 'triosesP'], <class 'cnwheat.model.Soil'>: ['nitrates']}

the name of the compartments attributes in the model, for objects of types model.Plant, model.Axis, model.Phytomer, model.Organ, model.HiddenZone, model.PhotosyntheticOrganElement, and model.Soil.

T_INDEX = ['t']

the time index

PLANTS_INDEXES = ['plant']

the index to locate the plants in the modeled system

PLANTS_T_INDEXES = ['t', 'plant']

concatenation of T_INDEX and PLANTS_INDEXES

PLANTS_STATE_PARAMETERS = ['Tair']

the parameters which define the state of the modeled system at plant scale

PLANTS_STATE = ['Tair']

the variables which define the state of the modeled system at plant scale, formed be the concatenation of PLANTS_STATE_PARAMETERS and the names of the compartments associated to each plant (see MODEL_COMPARTMENTS_NAMES)

PLANTS_INTERMEDIATE_VARIABLES = []

the variables that we need to compute in order to compute fluxes and/or compartments values at plant scale

PLANTS_FLUXES = []

the fluxes exchanged between the compartments at plant scale

PLANTS_INTEGRATIVE_VARIABLES = []

the variables computed by integrating values of plant components parameters/variables recursively

PLANTS_RUN_VARIABLES = ['Tair']

all the variables computed during a run step of the simulation at plant scale

AXES_INDEXES = ['plant', 'axis']

the indexes to locate the axes in the modeled system

AXES_T_INDEXES = ['t', 'plant', 'axis']

concatenation of T_INDEX and AXES_INDEXES

AXES_STATE_PARAMETERS = ['mstruct', 'senesced_mstruct']

the parameters which define the state of the modeled system at axis scale

AXES_STATE = ['mstruct', 'senesced_mstruct', 'C_exudated', 'sum_respi_shoot', 'sum_respi_roots']

the variables which define the state of the modeled system at axis scale, formed be the concatenation of AXES_STATE_PARAMETERS and the names of the compartments associated to each axis (see MODEL_COMPARTMENTS_NAMES)

AXES_INTERMEDIATE_VARIABLES = []

the variables that we need to compute in order to compute fluxes and/or compartments values at axis scale

AXES_FLUXES = []

the fluxes exchanged between the compartments at axis scale

AXES_INTEGRATIVE_VARIABLES = ['Total_Transpiration']

the variables computed by integrating values of axis components parameters/variables recursively

AXES_RUN_VARIABLES = ['mstruct', 'senesced_mstruct', 'C_exudated', 'sum_respi_shoot', 'sum_respi_roots', 'Total_Transpiration']

all the variables computed during a run step of the simulation at axis scale

PHYTOMERS_INDEXES = ['plant', 'axis', 'metamer']

the indexes to locate the phytomers in the modeled system

PHYTOMERS_T_INDEXES = ['t', 'plant', 'axis', 'metamer']

concatenation of T_INDEX and PHYTOMERS_INDEXES

PHYTOMERS_STATE_PARAMETERS = ['mstruct']

the parameters which define the state of the modeled system at phytomer scale

PHYTOMERS_STATE = ['mstruct']

the variables which define the state of the modeled system at phytomer scale, formed be the concatenation of PHYTOMERS_STATE_PARAMETERS and the names of the compartments associated to each phytomer (see MODEL_COMPARTMENTS_NAMES)

PHYTOMERS_INTERMEDIATE_VARIABLES = []

the variables that we need to compute in order to compute fluxes and/or compartments values at phytomer scale

PHYTOMERS_FLUXES = []

the fluxes exchanged between the compartments at phytomer scale

PHYTOMERS_INTEGRATIVE_VARIABLES = []

the variables computed by integrating values of phytomer components parameters/variables recursively

PHYTOMERS_RUN_VARIABLES = ['mstruct']

all the variables computed during a run step of the simulation at phytomer scale

ORGANS_INDEXES = ['plant', 'axis', 'organ']

the indexes to locate the organs in the modeled system

ORGANS_T_INDEXES = ['t', 'plant', 'axis', 'organ']

concatenation of T_INDEX and ORGANS_INDEXES

ORGANS_STATE_PARAMETERS = ['mstruct', 'Nstruct', 'senesced_mstruct']

the parameters which define the state of the modeled system at organ scale

ORGANS_STATE = ['mstruct', 'Nstruct', 'senesced_mstruct', 'age_from_flowering', 'amino_acids', 'cytokinins', 'nitrates', 'proteins', 'starch', 'structure', 'sucrose']

the variables which define the state of the modeled system at organ scale, formed be the concatenation of ORGANS_STATE_PARAMETERS and the names of the compartments associated to each organ (see MODEL_COMPARTMENTS_NAMES)

ORGANS_INTERMEDIATE_VARIABLES = ['C_exudation', 'HATS_LATS', 'N_exudation', 'RGR_Structure', 'R_Nnit_red', 'R_Nnit_upt', 'Respi_growth', 'R_grain_growth_starch', 'R_grain_growth_struct', 'R_residual', 'regul_transpiration', 'sum_respi']

the variables that we need to compute in order to compute fluxes and/or compartments values at organ scale

ORGANS_FLUXES = ['Export_Amino_Acids', 'Export_Nitrates', 'Export_cytokinins', 'S_Amino_Acids', 'S_cytokinins', 'S_grain_starch', 'S_grain_structure', 'S_Proteins', 'Unloading_Amino_Acids', 'Unloading_Sucrose', 'Uptake_Nitrates']

the fluxes exchanged between the compartments at organ scale

ORGANS_INTEGRATIVE_VARIABLES = ['Total_Organic_Nitrogen']

the variables computed by integrating values of organ components parameters/variables recursively

ORGANS_RUN_VARIABLES = ['mstruct', 'Nstruct', 'senesced_mstruct', 'age_from_flowering', 'amino_acids', 'cytokinins', 'nitrates', 'proteins', 'starch', 'structure', 'sucrose', 'C_exudation', 'HATS_LATS', 'N_exudation', 'RGR_Structure', 'R_Nnit_red', 'R_Nnit_upt', 'Respi_growth', 'R_grain_growth_starch', 'R_grain_growth_struct', 'R_residual', 'regul_transpiration', 'sum_respi', 'Export_Amino_Acids', 'Export_Nitrates', 'Export_cytokinins', 'S_Amino_Acids', 'S_cytokinins', 'S_grain_starch', 'S_grain_structure', 'S_Proteins', 'Unloading_Amino_Acids', 'Unloading_Sucrose', 'Uptake_Nitrates', 'Total_Organic_Nitrogen']

all the variables computed during a run step of the simulation at organ scale

HIDDENZONE_INDEXES = ['plant', 'axis', 'metamer']

the indexes to locate the hidden zones in the modeled system

HIDDENZONE_T_INDEXES = ['t', 'plant', 'axis', 'metamer']

concatenation of T_INDEX and HIDDENZONE_INDEXES

HIDDENZONE_STATE_PARAMETERS = ['Nstruct', 'mstruct', 'ratio_DZ']

the parameters which define the state of the modeled system at hidden zone scale

HIDDENZONE_STATE = ['Nstruct', 'mstruct', 'ratio_DZ', 'amino_acids', 'fructan', 'proteins', 'sucrose']

the variables which define the state of the modeled system at hidden zone scale, formed be the concatenation of HIDDENZONE_STATE_PARAMETERS and the names of the compartments associated to each hidden zone (see MODEL_COMPARTMENTS_NAMES)

HIDDENZONE_INTERMEDIATE_VARIABLES = ['nb_replications']

the variables that we need to compute in order to compute fluxes and/or compartments values at hidden zone scale

HIDDENZONE_FLUXES = ['D_Fructan', 'D_Proteins', 'S_Fructan', 'S_Proteins', 'Unloading_Amino_Acids', 'Unloading_Sucrose']

the fluxes exchanged between the compartments at hidden zone scale

HIDDENZONE_INTEGRATIVE_VARIABLES = []

the variables computed by integrating values of hidden zone components parameters/variables recursively

HIDDENZONE_RUN_VARIABLES = ['Nstruct', 'mstruct', 'ratio_DZ', 'amino_acids', 'fructan', 'proteins', 'sucrose', 'nb_replications', 'D_Fructan', 'D_Proteins', 'S_Fructan', 'S_Proteins', 'Unloading_Amino_Acids', 'Unloading_Sucrose']

all the variables computed during a run step of the simulation at plnat scale

ELEMENTS_INDEXES = ['plant', 'axis', 'metamer', 'organ', 'element']

the indexes to locate the elements in the modeled system

ELEMENTS_T_INDEXES = ['t', 'plant', 'axis', 'metamer', 'organ', 'element']

concatenation of T_INDEX and ELEMENTS_INDEXES

ELEMENTS_STATE_PARAMETERS = ['Ag', 'Nstruct', 'Tr', 'Ts', 'green_area', 'is_growing', 'mstruct', 'senesced_mstruct']

the parameters which define the state of the modeled system at element scale

ELEMENTS_STATE = ['Ag', 'Nstruct', 'Tr', 'Ts', 'green_area', 'is_growing', 'mstruct', 'senesced_mstruct', 'amino_acids', 'cytokinins', 'fructan', 'nitrates', 'proteins', 'starch', 'sucrose', 'triosesP']

the variables which define the state of the modeled system at element scale, formed be the concatenation of ELEMENTS_STATE_PARAMETERS and the names of the compartments associated to each element (see MODEL_COMPARTMENTS_NAMES)

ELEMENTS_INTERMEDIATE_VARIABLES = ['Photosynthesis', 'R_Nnit_red', 'R_phloem_loading', 'R_residual', 'Transpiration', 'sum_respi', 'nb_replications']

the variables that we need to compute in order to compute fluxes and/or compartments values at element scale

ELEMENTS_FLUXES = ['Amino_Acids_import', 'D_Fructan', 'D_Proteins', 'D_Starch', 'D_cytokinins', 'Loading_Amino_Acids', 'Loading_Sucrose', 'Nitrates_import', 'Regul_S_Fructan', 'S_Fructan', 'S_Starch', 'S_Sucrose', 'S_Amino_Acids', 'S_Proteins', 'cytokinins_import']

the fluxes exchanged between the compartments at element scale

ELEMENTS_INTEGRATIVE_VARIABLES = ['Total_Organic_Nitrogen']

the variables computed by integrating values of element components parameters/variables recursively

ELEMENTS_RUN_VARIABLES = ['Ag', 'Nstruct', 'Tr', 'Ts', 'green_area', 'is_growing', 'mstruct', 'senesced_mstruct', 'amino_acids', 'cytokinins', 'fructan', 'nitrates', 'proteins', 'starch', 'sucrose', 'triosesP', 'Photosynthesis', 'R_Nnit_red', 'R_phloem_loading', 'R_residual', 'Transpiration', 'sum_respi', 'nb_replications', 'Amino_Acids_import', 'D_Fructan', 'D_Proteins', 'D_Starch', 'D_cytokinins', 'Loading_Amino_Acids', 'Loading_Sucrose', 'Nitrates_import', 'Regul_S_Fructan', 'S_Fructan', 'S_Starch', 'S_Sucrose', 'S_Amino_Acids', 'S_Proteins', 'cytokinins_import', 'Total_Organic_Nitrogen']

all the variables computed during a run step of the simulation at element scale

SOILS_INDEXES = ['plant', 'axis']

the indexes to locate the soils in the modeled system

SOILS_T_INDEXES = ['t', 'plant', 'axis']

concatenation of T_INDEX and SOILS_INDEXES

SOILS_STATE_PARAMETERS = ['Tsoil', 'volume']

the parameters which define the state of the modeled system at soil scale

SOILS_STATE = ['Tsoil', 'volume', 'nitrates']

the variables which define the state of the modeled system at soil scale, formed be the concatenation of SOILS_STATE_PARAMETERS and the names of the compartments associated to each soil (see MODEL_COMPARTMENTS_NAMES)

SOILS_INTERMEDIATE_VARIABLES = ['Conc_Nitrates_Soil', 'mineralisation']

the variables that we need to compute in order to compute fluxes and/or compartments values at soil scale

SOILS_FLUXES = []

the fluxes exchanged between the compartments at soil scale

SOILS_INTEGRATIVE_VARIABLES = []

the variables computed by integrating values of soil components parameters/variables recursively

SOILS_RUN_VARIABLES = ['Tsoil', 'volume', 'nitrates', 'Conc_Nitrates_Soil', 'mineralisation']

all the variables computed during a run step of the simulation at soil scale

ALL_STATE_PARAMETERS = {<class 'cnwheat.model.Plant'>: ['Tair'], <class 'cnwheat.model.Axis'>: ['mstruct', 'senesced_mstruct'], <class 'cnwheat.model.Phytomer'>: ['mstruct'], <class 'cnwheat.model.Organ'>: ['mstruct', 'Nstruct', 'senesced_mstruct'], <class 'cnwheat.model.HiddenZone'>: ['Nstruct', 'mstruct', 'ratio_DZ'], <class 'cnwheat.model.PhotosyntheticOrganElement'>: ['Ag', 'Nstruct', 'Tr', 'Ts', 'green_area', 'is_growing', 'mstruct', 'senesced_mstruct'], <class 'cnwheat.model.Soil'>: ['Tsoil', 'volume']}

a dictionary of all the variables which define the state of the modeled system, for each scale

ROOTS_FORCINGS = ('Nstruct', 'mstruct')

the names of the roots (scenescence) forcings

ELEMENTS_PHOTOSYNTHESIS_FORCINGS = ('Ag', 'Tr', 'Ts')

the names of the elements photosynthesis forcings

ELEMENTS_SENESCENCE_FORCINGS = ('Nstruct', 'green_area', 'mstruct')

the names of the elements scenescence forcings

ELEMENTS_FORCINGS = ('Ag', 'Tr', 'Ts', 'Nstruct', 'green_area', 'mstruct')

the names of the elements photosynthesis and scenescence forcings

LOGGERS_NAMES = {'compartments': {<class 'cnwheat.model.Plant'>: 'cnwheat.compartments.plants', <class 'cnwheat.model.Axis'>: 'cnwheat.compartments.axes', <class 'cnwheat.model.Phytomer'>: 'cnwheat.compartments.phytomers', <class 'cnwheat.model.Organ'>: 'cnwheat.compartments.organs', <class 'cnwheat.model.HiddenZone'>: 'cnwheat.compartments.hiddenzones', <class 'cnwheat.model.PhotosyntheticOrganElement'>: 'cnwheat.compartments.elements', <class 'cnwheat.model.Soil'>: 'cnwheat.compartments.soils'}, 'derivatives': {<class 'cnwheat.model.Plant'>: 'cnwheat.derivatives.plants', <class 'cnwheat.model.Axis'>: 'cnwheat.derivatives.axes', <class 'cnwheat.model.Phytomer'>: 'cnwheat.derivatives.phytomers', <class 'cnwheat.model.Organ'>: 'cnwheat.derivatives.organs', <class 'cnwheat.model.HiddenZone'>: 'cnwheat.derivatives.hiddenzones', <class 'cnwheat.model.PhotosyntheticOrganElement'>: 'cnwheat.derivatives.elements', <class 'cnwheat.model.Soil'>: 'cnwheat.derivatives.soils'}}

the name of the loggers for compartments and derivatives

respiration_model = None

the model of respiration to use

population = None

the population to simulate on

soils = None

The inputs of the soils.

soils is a dictionary of objects of type model.Soil:
{(plant_index, axis_label): soil_object, …}
initial_conditions = None

the initial conditions of the compartments in the population and soils

initial_conditions_mapping = None

dictionary to map the compartments to their indexes in initial_conditions

progressbar = None

progress bar to show the progress of the solver

show_progressbar = None

True: show the progress bar ; False: DO NOT show the progress bar

delta_t = None

the delta t of the simulation (in seconds)

time_step = None

time step of the simulation (in hours)

time_grid = None

the time grid of the simulation (in hours)

culm_density = None

culm density (culm m-2)

interpolate_forcings = None

a boolean flag which indicates if we want to interpolate or not the forcings (True: interpolate, False: do not interpolate)

t_offset = None

the absolute time offset elapsed from the beginning of the simulation

senescence_forcings_delta_t_ratio = None

the ratio between the delta t of the senescence forcings and the delta t of the simulation

photosynthesis_forcings_delta_t_ratio = None

the ratio between the delta t of the photosynthesis forcings and the delta t of the simulation

previous_forcings_values = None

previous values of the forcings

new_forcings_values = None

new values of the forcings

interpolation_functions = None

functions to interpolate the forcings

nfev_total = None

cumulative number of RHS function evaluations

initialize(population, soils, Tair=12, Tsoil=12)[source]
Initialize:

from population and soils.

Parameters:
  • population (model.Population) – a population of plants.
  • soils (dict) – the soil associated to each axis. soils must be a dictionary with the same structure as soils
  • Tair (float) – air temperature (°C)
  • Tsoil (float) – soil temperature (°C)
run(show_progressbar=False)[source]

Compute CN exchanges which occurred in population and soils over delta_t.

Parameters:show_progressbar (bool) – True: show the progress bar of the solver ; False: do not show the progress bar (default).

cnwheat.model module

class cnwheat.model.EcophysiologicalConstants[source]

Bases: object

Ecophysiological constants.

C_MOLAR_MASS = 12

Molar mass of carbon (g mol-1)

NB_C_TRIOSEP = 3

Number of C in 1 mol of trioseP

NB_C_HEXOSES = 6

Number of C in 1 mol of hexoses (glucose, fructose)

NB_C_SUCROSE = 12

Number of C in 1 mol of sucrose

HEXOSE_MOLAR_MASS_C_RATIO = 0.42

Contribution of C in hexose mass

TRIOSESP_MOLAR_MASS_C_RATIO = 0.21

Contribution of C in triosesP mass

RATIO_C_mstruct = 0.44

Mean contribution of carbon to structural dry mass (g C g-1 mstruct)

AMINO_ACIDS_C_RATIO = 4.15

Mean number of mol of C in 1 mol of the major amino acids of plants (Glu, Gln, Ser, Asp, Ala, Gly)

AMINO_ACIDS_N_RATIO = 1.25

Mean number of mol of N in 1 mol of the major amino acids of plants (Glu, Gln, Ser, Asp, Ala, Gly)

PROTEINS_MOLAR_MASS_N_RATIO = 0.151

Mean contribution of N in protein mass (Penning De Vries 1989)

AMINO_ACIDS_MOLAR_MASS_N_RATIO = 0.135

Mean contribution of N in amino acids mass of the major amino acids of plants (Glu, Gln, Ser, Asp, Ala, Gly)

NITRATES_MOLAR_MASS_N_RATIO = 0.23

Contribution of N in amino acids mass

N_MOLAR_MASS = 14

Molar mass of nitrogen (g mol-1)

AMINO_ACIDS_MOLAR_MASS_C_RATIO = 0.38

(Penning De Vries 1989)

PROTEINS_MOLAR_MASS_C_RATIO = 0.38

As for AA

class cnwheat.model.Population(plants=None)[source]

Bases: object

The class Population defines the CN exchanges at population scale.

A population must have at least one plant.

PARAMETERS = <cnwheat.parameters.PopulationParameters object>

the internal parameters of the population

plants = None

the list of plants

calculate_aggregated_variables()[source]

Calculate the integrative variables of the population recursively.

class cnwheat.model.Plant(index=None, axes=None)[source]

Bases: object

The class Plant defines the CN exchanges at plant scale.

A plant must have at least one axis.

PARAMETERS = <cnwheat.parameters.PlantParameters object>

the internal parameters of the plants

index = None

the index of the plant

axes = None

the list of axes

cohorts = None

list of cohort values - Hack to treat tillering cases : TEMPORARY

calculate_aggregated_variables()[source]

Calculate the integrative variables of the plant recursively.

static calculate_temperature_effect_on_conductivity(Tair)[source]

Effect of the temperature on phloeme translocation conductivity (Farrar 1988) Should multiply the rate at 20°C

Parameters:Tair (float) – Air temperature (°C)
Returns:Correction to apply to conductivity coefficients.
Return type:float
static calculate_temperature_effect_on_Vmax(Tair)[source]

Effect of the temperature on maximal enzyme activity Should multiply the rate at 20°C

Parameters:Tair (float) – Air temperature (°C)
Returns:Correction to apply to enzyme activity
Return type:float
class cnwheat.model.Axis(label=None, roots=None, phloem=None, grains=None, phytomers=None, C_exudated=0, sum_respi_shoot=0, sum_respi_roots=0.001)[source]

Bases: object

The class Axis defines the CN exchanges at axis scale.

An axis must have:
PARAMETERS = <cnwheat.parameters.AxisParameters object>

the internal parameters of the axes

INIT_COMPARTMENTS = <cnwheat.parameters.AxisInitCompartments object>

the initial values of compartments and state parameters

label = None

the label of the axis

roots = None

the roots

phloem = None

the phloem

grains = None

the grains

phytomers = None

the list of phytomers

Total_Transpiration = None

the total transpiration (mmol s-1)

mstruct = None

structural mass of the axis (g)

senesced_mstruct = None

senesced structural mass of the axis (g)

nitrates = None

nitrates in the axis (µmol N)

calculate_aggregated_variables()[source]

Calculate the integrative variables of the axis recursively.

static calculate_C_exudated(C_exudation, N_exudation, roots_mstruct)[source]

delta sucrose

Parameters:
  • C_exudation (float) – Rates of sucrose exudated (µmol` C g-1 mstruct h-1)
  • N_exudation (float) – Rate of amino acids exudated (µmol` N g-1 mstruct h-1)
  • roots_mstruct (float) – RStructural mass of the roots (g)
Returns:

delta C loss by exudation (µmol` C)
Return type:

float
class cnwheat.model.Phytomer(index=None, chaff=None, peduncle=None, lamina=None, internode=None, sheath=None, hiddenzone=None, cohorts=None, cohorts_replications=None)[source]

Bases: object

The class Phytomer defines the CN exchanges at phytomer scale.

A phytomer must have at least:
PARAMETERS = <cnwheat.parameters.PhytomerParameters object>

the internal parameters of the phytomers

index = None

the index of the phytomer

chaff = None

the chaff

peduncle = None

the peduncle

lamina = None

the lamina

internode = None

the internode

sheath = None

the sheath

hiddenzone = None

the hidden zone

mstruct = None

the structural mass of the phytomer (g)

senesced_mstruct = None

senesced structural mass of the phytomer (g)

nitrates = None

nitrates of the phytomer (µmol N)

cohorts = None

list of cohort values - Hack to treat tillering cases : TEMPORARY. Devrait être porté à l’échelle de la plante uniquement mais je ne vois pas comment faire mieux

cohorts_replications = None

dictionary of number of replications per cohort rank

calculate_aggregated_variables()[source]

Calculate the integrative variables of the phytomer recursively.

nb_replications
class cnwheat.model.Organ(label)[source]

Bases: object

The class Organ defines the CN exchanges at organ scale.

Organ is the base class of all organs. DO NOT INSTANTIATE IT.

label = None

the label of the organ

initialize()[source]

Initialize the derived attributes of the organ.

calculate_aggregated_variables()[source]

Calculate the integrative variables of the organ recursively.

class cnwheat.model.HiddenZone(label='hiddenzone', mstruct=6.39e-08, Nstruct=2.06e-09, sucrose=0.001, fructan=0, amino_acids=0.001, proteins=0, ratio_DZ=1, cohorts=None, cohorts_replications=None, index=None)[source]

Bases: cnwheat.model.Organ

The class HiddenZone defines the CN exchanges in an hidden zone.

PARAMETERS = <cnwheat.parameters.HiddenZoneParameters object>

the internal parameters of the hidden zone

INIT_COMPARTMENTS = <cnwheat.parameters.HiddenZoneInitCompartments object>

the initial values of compartments and state parameters

cohorts = None

list of cohort values - Hack to treat tillering cases : TEMPORARY. Devrait être porté à l’échelle de la plante uniquement mais je ne vois pas comment faire mieux

cohorts_replications = None

dictionary of number of replications per cohort rank

index = None

the index of the phytomer TEMPORARY

mstruct = None

g

Nstruct = None

g

sucrose = None

µmol` C

fructan = None

µmol` C

amino_acids = None

µmol` N

proteins = None

µmol` N

Unloading_Sucrose = None

current Unloading of sucrose from phloem to hiddenzone integrated over delta t (µmol` C)

Unloading_Amino_Acids = None

current Unloading of amino acids from phloem to hiddenzone integrated over delta t (µmol` N)

S_Proteins = None

protein synthesis (µmol` N g-1 mstruct)

S_Fructan = None

fructan synthesis (µmol` C g-1 mstruct)

D_Fructan = None

fructan degradation (µmol` C g-1 mstruct)

D_Proteins = None

protein degradation (µmol` N g-1 mstruct)

R_residual = None

Residual maintenance respiration (cost from protein turn-over, cell ion gradients, futile cycles…) (µmol` C respired)

Total_Organic_Nitrogen = None

current total nitrogen amount (µmol` N)

nb_replications
calculate_aggregated_variables()[source]

Calculate the integrative variables of the organ recursively.

static calculate_Total_Organic_Nitrogen(amino_acids, proteins, Nstruct)[source]

Total amount of organic N (amino acids + proteins + Nstruct). Used to calculate residual respiration.

Parameters:
  • amino_acids (float) – Amount of amino acids (µmol` N)
  • proteins (float) – Amount of proteins (µmol` N)
  • Nstruct (float) – Structural N mass (g)
Returns:

Total amount of organic N (µmol` N)
Return type:

float
calculate_Unloading_Sucrose(sucrose, sucrose_phloem, mstruct_axis, T_effect_conductivity)[source]

Rate of sucrose Unloading from phloem to the hidden zone (µmol` C sucrose unloaded h-1). Transport-resistance equation

Parameters:
  • sucrose (float) – Sucrose amount in the hidden zone (µmol` C)
  • sucrose_phloem (float) – Sucrose amount in phloem (µmol` C)
  • mstruct_axis (float) – The structural dry mass of the axis (g)
  • T_effect_conductivity (float) – Effect of the temperature on the conductivity rate at 20°C (AU)
Returns:

Rate of Sucrose Unloading (µmol` C h-1)
Return type:

float
calculate_Unloading_Amino_Acids(amino_acids, amino_acids_phloem, mstruct_axis, T_effect_conductivity)[source]

Rate of amino acids Unloading from phloem to the hidden zone (µmol` N amino acids unloaded h-1). Transport-resistance equation

Parameters:
  • amino_acids (float) – Amino_acids amount in the hidden zone (µmol` N)
  • amino_acids_phloem (float) – Amino_acids amount in phloem (µmol` N)
  • mstruct_axis (float) – The structural dry mass of the axis (g)
  • T_effect_conductivity (float) – Effect of the temperature on the conductivity rate at 20°C (AU)
Returns:

Rate of Amino_acids Unloading (µmol` N h-1)
Return type:

float
calculate_S_proteins(amino_acids, T_effect_Vmax)[source]

Rate of protein synthesis (µmol` N proteins h-1 g-1 MS). Michaelis-Menten function of amino acids.

Parameters:
  • amino_acids (float) – Amino acid amount in the hidden zone (µmol` N)
  • T_effect_Vmax (float) – Correction to apply to enzyme activity
Returns:

Rate of Protein synthesis (µmol` N g-1 mstruct h-1)
Return type:

float
calculate_D_Proteins(proteins, T_effect_Vmax)[source]

Rate of protein degradation (µmol` N proteins h-1 g-1 MS). First order kinetic

Parameters:
  • proteins (float) – Protein amount in the hidden zone (µmol` N)
  • T_effect_Vmax (float) – Correction to apply to enzyme activity
Returns:

Rate of Protein degradation (µmol` N g-1 mstruct h-1)
Return type:

float
calculate_Regul_S_Fructan(Unloading_Sucrose)[source]

Regulating function for fructan maximal rate of synthesis. Negative regulation by the loading of sucrose from the phloem (“swith-off” sigmoïdal kinetic).

Parameters:Unloading_Sucrose (float) – Sucrose unloading (µmol` C)
Returns:Maximal rate of fructan synthesis (µmol` C g-1 mstruct)
Return type:float
calculate_S_Fructan(sucrose, Regul_S_Fructan, T_effect_Vmax)[source]

Rate of fructan synthesis (µmol` C fructan g-1 mstruct h-1). Sigmoïdal function of sucrose.

Parameters:
  • sucrose (float) – Amount of sucrose (µmol` C)
  • Regul_S_Fructan (float) – Maximal rate of fructan synthesis regulated by sucrose loading (µmol` C g-1 mstruct)
  • T_effect_Vmax (float) – Correction to apply to enzyme activity
Returns:

Rate of Fructan synthesis (µmol` C g-1 mstruct)
Return type:

float
calculate_D_Fructan(sucrose, fructan, T_effect_Vmax)[source]

Rate of fructan degradation (µmol` C fructan g-1 mstruct h-1). Inhibition function by the end product i.e. sucrose (Bancal et al., 2012).

Parameters:
  • sucrose (float) – Amount of sucrose (µmol` C)
  • fructan (float) – Amount of fructan (µmol` C)
  • T_effect_Vmax (float) – Correction to apply to enzyme activity
Returns:

Rate of Fructan degradation (µmol` C g-1 mstruct)
Return type:

float
calculate_sucrose_derivative(Unloading_Sucrose, S_Fructan, D_Fructan, hiddenzone_Loading_Sucrose_contribution, R_residual)[source]

delta sucrose of hidden zone.

Parameters:
  • Unloading_Sucrose (float) – Sucrose unloaded (µmol` C)
  • S_Fructan (float) – Fructan synthesis (µmol` C g-1 mstruct)
  • D_Fructan (float) – Fructan degradation (µmol` C g-1 mstruct)
  • hiddenzone_Loading_Sucrose_contribution (float) – Sucrose imported from the emerged tissues (µmol` C)
  • R_residual (float) – Residual respiration (µmol` C)
Returns:

delta sucrose (µmol` C sucrose)
Return type:

float
calculate_amino_acids_derivative(Unloading_Amino_Acids, S_Proteins, D_Proteins, hiddenzone_Loading_Amino_Acids_contribution)[source]

delta amino acids of hidden zone.

Parameters:
  • Unloading_Amino_Acids (float) – Amino acids unloaded (µmol` N)
  • S_Proteins (float) – Protein synthesis (µmol` N g-1 mstruct)
  • D_Proteins (float) – Protein degradation (µmol` N g-1 mstruct)
  • hiddenzone_Loading_Amino_Acids_contribution (float) – Amino acids imported from the emerged tissues (µmol` N)
Returns:

delta amino acids (µmol` N amino acids)
Return type:

float
calculate_fructan_derivative(S_Fructan, D_Fructan)[source]

delta fructans of hidden zone.

Parameters:
  • S_Fructan (float) – Fructans synthesis (µmol` C g-1 mstruct)
  • D_Fructan (float) – Fructans degradation (µmol` C g-1 mstruct)
Returns:

delta fructans (µmol` C fructans)
Return type:

float
calculate_proteins_derivative(S_Proteins, D_Proteins)[source]

delta proteins of hidden zone.

Parameters:
  • S_Proteins (float) – Protein synthesis (µmol` N g-1 mstruct)
  • D_Proteins (float) – Protein degradation (µmol` N g-1 mstruct)
Returns:

delta proteins (µmol` N proteins)
Return type:

float
class cnwheat.model.Phloem(label='phloem', sucrose=500, amino_acids=100)[source]

Bases: cnwheat.model.Organ

The class Phloem defines the CN exchanges in a phloem.

PARAMETERS = <cnwheat.parameters.PhloemParameters object>

the internal parameters of the phloem

INIT_COMPARTMENTS = <cnwheat.parameters.PhloemInitCompartments object>

the initial values of compartments and state parameters

sucrose = None

µmol` C sucrose

amino_acids = None

µmol` N amino acids

static calculate_sucrose_derivative(contributors)[source]

delta sucrose

Parameters:[PhotosyntheticOrganElement, Grains, Roots, HiddenZone] contributors (list) – Organs exchanging C with the phloem
Returns:delta sucrose (µmol` C sucrose)
Return type:float
static calculate_amino_acids_derivative(contributors)[source]

delta amino acids

Parameters:[PhotosyntheticOrganElement, Grains, Roots, HiddenZone] contributors (list) – Organs exchanging N with the phloem
Returns:delta amino acids (µmol` N amino acids)
Return type:float
class cnwheat.model.Grains(label='grains', age_from_flowering=0, starch=0, structure=1, proteins=0)[source]

Bases: cnwheat.model.Organ

The class Grains defines the CN exchanges in a set of grains.

AMINO_ACIDS_MOLAR_MASS_N_RATIO = 0.136

Mean contribution of N in amino acids mass contained in gluten (Glu, Gln and Pro)

PARAMETERS = <cnwheat.parameters.GrainsParameters object>

the internal parameters of the grains

INIT_COMPARTMENTS = <cnwheat.parameters.GrainsInitCompartments object>

the initial values of compartments and state parameters

age_from_flowering = None

seconds

starch = None

µmol` of C starch

structure = None

µmol` of C sucrose

proteins = None

µmol` of N proteins

structural_dry_mass = None

g of MS

S_grain_structure = None

current synthesis of grain structure integrated over a delta t (µmol` C)

S_grain_starch = None

current synthesis of grain starch integrated over a delta t (µmol` C g-1 mstruct)

S_Proteins = None

current synthesis of grain proteins integrated over a delta t (µmol` N)

RGR_Structure = None

RGR of grain structure (dimensionless?)

R_grain_growth_struct = None

grain struct respiration (µmol` C respired)

R_grain_growth_starch = None

grain starch growth respiration (µmol` C respired)

initialize()[source]

Initialize the derived attributes of the organ.

static calculate_structural_dry_mass(structure)[source]

Grain structural dry mass.

Parameters:structure (float) – Grain structural C mass (µmol` C)
Returns:Grain structural dry mass (g)
Return type:float
static modified_Arrhenius_equation(temperature)[source]

Return value of equation from Johnson and Lewin (1946) for temperature. The equation is modified to return zero below zero degree.

Parameters:temperature (float) – organ temperature (degree Celsius)
Returns:Return value of Eyring equation from Johnson and Lewin (1946) for temperature (dimensionless). The equation is modified to return zero below zero degree.
Return type:float
calculate_temperature_effect_on_growth(Tair)[source]

Effect of the temperature on elongation. Return value of equation from Johnson and Lewin (1946) for temperature. The equation is modified to return zero below zero degree. Identical to modified_Arrhenius_equation in ElongWheat. Should multiply the rate at 20°C

Parameters:Tair (float) – Air temperature(°C)
Returns:Correction to apply to RGR Structure of the grains (dimensionless)
Return type:float
static calculate_RGR_Structure(sucrose_phloem, mstruct_axis, T_effect_growth)[source]

Relative Growth Rate of grain structure, regulated by sucrose concentration in phloem.

Parameters:
  • sucrose_phloem (float) – Sucrose amount in phloem (µmol` C)
  • mstruct_axis (float) – The structural dry mass of the axis (g)
  • T_effect_growth (float) – Effect of the temperature on the growth rate at 20°C (AU)
Returns:

RGR of grain structure at 20°C (s-1)
Return type:

float
calculate_S_grain_structure(prec_structure, RGR_Structure)[source]

Rate of grain structure synthesis (µmol` C structure h-1). Exponential function, RGR regulated by sucrose concentration in the phloem.

Parameters:
  • prec_structure (float) – Grain structure at t-1 (µmol` C)
  • RGR_Structure (float) – Relative Growth Rate of grain structure (dimensionless?)
Returns:

Rate of Synthesis of grain structure (µmol` C h-1)
Return type:

float
calculate_S_grain_starch(sucrose_phloem, mstruct_axis, T_effect_Vmax)[source]

Rate of starch synthesis in grains (i.e. grain filling) (µmol` C starch g-1 mstruct h-1). Michaelis-Menten function of sucrose concentration in the phloem.

Parameters:
  • sucrose_phloem (float) – Sucrose concentration in phloem (µmol` C g-1 mstruct)
  • mstruct_axis (float) – The structural dry mass of the axis (g)
  • T_effect_Vmax (float) – Correction to apply to enzyme activity
Returns:

Rate of Synthesis of grain starch (µmol` C g-1 mstruct h-1)
Return type:

float
static calculate_S_proteins(S_grain_structure, S_grain_starch, amino_acids_phloem, sucrose_phloem, structural_dry_mass)[source]

Protein synthesis in grains. N is assumed to be co-transported along with the unloaded sucrose from phloem (using the ratio amino acids:sucrose of phloem).

Parameters:
  • S_grain_structure (float) – Synthesis of grain structure (µmol` C)
  • S_grain_starch (float) – Synthesis of grain starch (µmol` C g-1 mstruct)
  • amino_acids_phloem (float) – Amino acids concentration in phloem (µmol` N g-1 mstruct)
  • sucrose_phloem (float) – Sucrose concentration in phloem (µmol` C g-1 mstruct)
  • structural_dry_mass (float) – Grain structural dry mass (g)
Returns:

Synthesis of grain proteins (µmol` N)
Return type:

float
static calculate_structure_derivative(S_grain_structure, R_growth)[source]

delta grain structure.

Parameters:
  • S_grain_structure (float) – Synthesis of grain structure (µmol` C)
  • R_growth (float) – Grain growth respiration (µmol` C respired)
Returns:

delta grain structure (µmol` C structure)
Return type:

float
static calculate_starch_derivative(S_grain_starch, structural_dry_mass, R_growth)[source]

delta grain starch.

Parameters:
  • S_grain_starch (float) – Synthesis of grain starch (µmol` C g-1 mstruct)
  • structural_dry_mass (float) – Grain structural dry mass (g)
  • R_growth (float) – Grain growth respiration (µmol` C respired)
Returns:

delta grain starch (µmol` C starch)
Return type:

float
static calculate_proteins_derivative(S_Proteins)[source]

delta grain proteins.

Parameters:S_Proteins (float) – Synthesis of grain proteins (µmol` N)
Returns:delta grain proteins (µmol` N proteins)
Return type:float
class cnwheat.model.Roots(label='roots', mstruct=0.15, senesced_mstruct=0, Nstruct=0.0045, sucrose=0, nitrates=0, amino_acids=0, cytokinins=0)[source]

Bases: cnwheat.model.Organ

The class Roots defines the CN exchanges in a set of roots.

PARAMETERS = <cnwheat.parameters.RootsParameters object>

the internal parameters of the roots

INIT_COMPARTMENTS = <cnwheat.parameters.RootsInitCompartments object>

the initial values of compartments and state parameters

mstruct = None

Structural mass (g)

senesced_mstruct = None

Senesced structural mass (g)

Nstruct = None

Structural N mass (g)

sucrose = None

µmol` C sucrose

nitrates = None

µmol` N nitrates

amino_acids = None

µmol` N amino acids

cytokinins = None

AU cytokinins

Unloading_Sucrose = None

current Unloading of sucrose from phloem to roots

Unloading_Amino_Acids = None

current Unloading of amino acids from phloem to roots

Export_Nitrates = None

Total export of nitrates from roots to shoot organs integrated over a delta t (µmol` N)

Export_Amino_Acids = None

Total export of amino acids from roots to shoot organs integrated over a delta t (µmol` N)

S_Amino_Acids = None

Rate of amino acid synthesis in roots integrated over a delta t (µmol` N g-1 mstruct)

Uptake_Nitrates = None

Rate of nitrate uptake by roots integrated over a delta t (µmol` N nitrates)

S_cytokinins = None

Rate of cytokinin synthesis integrated over a delta t (AU g-1 mstruct)

Export_cytokinins = None

Total export of cytokinin from roots to shoot organs integrated over a delta t (AU)

Total_Organic_Nitrogen = None

current amount of organic N (µmol` N)

R_Nnit_upt = None

Nitrate uptake respiration (µmol` C respired)

R_Nnit_red = None

Nitrate reduction-linked respiration (µmol` C respired)

R_residual = None

Residual maintenance respiration (cost from protein turn-over, cell ion gradients, futile cycles…) (µmol` C respired)

C_exudation = None

C sucrose lost by root exudation integrated over a delta t (µmol` C g-1 mstruct)

N_exudation = None

N amino acids lost by root exudation integrated over a delta t (µmol` N g-1 mstruct)

regul_transpiration = None

Dimensionless regulating factor of metabolite exports from roots by shoot transpiration

HATS_LATS = None

Nitrate influx (µmol` N)

sum_respi = None

Sum of respirations for roots i.e. related to N uptake, amino acids synthesis and residual (µmol` C)

calculate_aggregated_variables()[source]

Calculate the integrative variables of the organ recursively.

static calculate_Total_Organic_Nitrogen(amino_acids, Nstruct)[source]

Total amount of organic N (amino acids + Nstruct). Used to calculate residual respiration.

Parameters:
  • amino_acids (float) – Amount of amino acids (µmol` N)
  • Nstruct (float) – Structural N mass (g)
Returns:

Total amount of organic N (µmol` N)
Return type:

float
static calculate_regul_transpiration(total_transpiration)[source]

A function to regulate metabolite exports from roots by shoot transpiration

Parameters:total_transpiration (float) – Total transpiration (mmol s-1)
Returns:Dimensionless regulating factor
Return type:float
calculate_Unloading_Sucrose(sucrose_roots, sucrose_phloem, mstruct_axis, T_effect_conductivity)[source]

Rate of sucrose Unloading from phloem to roots (µmol` C sucrose unloaded g-1 mstruct h-1).

Parameters:
  • sucrose_roots (float) – Amount of sucrose in roots (µmol` C)
  • sucrose_phloem (float) – Sucrose concentration in phloem (µmol` C g-1 mstruct)
  • mstruct_axis (float) – The structural dry mass of the axis (g)
  • T_effect_conductivity (float) – Effect of the temperature on the conductivity rate at 20°C (AU)
Returns:

Rate of Sucrose Unloading (µmol` C g-1 mstruct h-1)
Return type:

float
static calculate_Unloading_Amino_Acids(Unloading_Sucrose, sucrose_phloem, amino_acids_phloem)[source]

Unloading of amino_acids from phloem to roots. Amino acids are assumed to be co-transported along with the unloaded sucrose from phloem (using the ratio amino acids:sucrose of phloem).

Parameters:
  • Unloading_Sucrose (float) – Sucrose Unloading (µmol` C g-1 mstruct)
  • sucrose_phloem (float) – Sucrose concentration in phloem (µmol` C g-1 mstruct)
  • amino_acids_phloem (float) – Amino acids concentration in phloem (µmol` N g-1 mstruct)
Returns:

Amino acids Unloading (µmol` N g-1 mstruct)
Return type:

float
calculate_Uptake_Nitrates(Conc_Nitrates_Soil, nitrates_roots, sucrose_roots, T_effect_Vmax)[source]
Rate of nitrate uptake by roots
  • Nitrate uptake is calculated as the sum of the 2 transport systems: HATS and LATS
  • HATS and LATS parameters are calculated as a function of root nitrate concentration (negative regulation)
  • Nitrate uptake is finally regulated by the total culm transpiration and sucrose concentration (positive regulation)
Parameters:
  • Conc_Nitrates_Soil (float) – Soil nitrate concentration Unloading (µmol` N m-3 soil)
  • nitrates_roots (float) – Amount of nitrates in roots (µmol` N)
  • sucrose_roots (float) – Amount of sucrose in roots (µmol` C)
  • T_effect_Vmax (float) – Correction to apply to enzyme activity
Returns:

Nitrate uptake (µmol` N nitrates) and nitrate influxes HATS and LATS (µmol` N h-1)
Return type:

(float, float)
calculate_S_amino_acids(nitrates, sucrose, T_effect_Vmax)[source]

Rate of amino acid synthesis in roots (µmol` N amino acids g-1 mstruct h-1). Bi-substrate Michaelis-Menten function of nitrates and sucrose.

Parameters:
  • nitrates (float) – Amount of nitrates in roots (µmol` N)
  • sucrose (float) – Amount of sucrose in roots (µmol` C)
  • T_effect_Vmax (float) – Correction to apply to enzyme activity
Returns:

Amino acids synthesis (µmol` N g-1 mstruct h-1)
Return type:

float
calculate_Export_Nitrates(nitrates, regul_transpiration)[source]

Total export of nitrates from roots to shoot organs Export is calculated as a function on nitrate concentration and culm transpiration.

Parameters:
  • nitrates (float) – Amount of nitrates in roots (µmol` N)
  • regul_transpiration (float) – Regulating factor by transpiration (mmol H2O m-2 s-1)
Returns:

Rate of Export of nitrates (µmol` N h-1)
Return type:

float
calculate_Export_Amino_Acids(amino_acids, regul_transpiration)[source]

Total export of amino acids from roots to shoot organs Amino acids export is calculated as a function of nitrate export using the ratio amino acids:nitrates in roots.

Parameters:
  • amino_acids (float) – Amount of amino acids in roots (µmol` N)
  • regul_transpiration (float) – Regulating factor by transpiration (mmol H2O m-2 s-1)
Returns:

Rate of Export of amino acids (µmol` N h-1)
Returns Type:

float
static calculate_exudation(Unloading_Sucrose, sucrose_roots, amino_acids_roots, amino_acids_phloem)[source]
C sucrose and N amino acids lost by root exudation (µmol` C or N g-1 mstruct).
  • C exudation is calculated as a fraction of C Unloading from phloem
  • N exudation is calculated from C exudation using the ratio amino acids:sucrose of the phloem
Parameters:
  • Unloading_Sucrose (float) – Sucrose Unloading (µmol` C g-1 mstruct h-1)
  • sucrose_roots (float) – Amount of sucrose in roots (µmol` C)
  • amino_acids_roots (float) – Amount of amino acids in roots (µmol` N)
  • amino_acids_phloem (float) – Amount of amino acids in phloem (µmol` N)
Returns:

Rates of C exudated (µmol` C g-1 mstruct h-1) and N_exudation (µmol` N g-1 mstruct h-1)
Return type:

(float, float)
calculate_S_cytokinins(sucrose_roots, nitrates_roots, T_effect_Vmax)[source]

Rate of cytokinin synthesis (AU cytokinins g-1 mstruct h-1). Cytokinin synthesis regulated by both root sucrose and nitrates. As a signal molecule, cytokinins are assumed have a neglected effect on sucrose. Thus, no cost in C is applied to the sucrose pool.

Parameters:
  • sucrose_roots (float) – Amount of sucrose in roots (µmol` C)
  • nitrates_roots (float) – Amount of nitrates in roots (µmol` N)
  • T_effect_Vmax (float) – Correction to apply to enzyme activity
Returns:

Rate of Cytokinin synthesis (AU g-1 mstruct h-1)
Return type:

float
calculate_Export_cytokinins(cytokinins, regul_transpiration)[source]

Total export of cytokinin from roots to shoot organs Cytokinin export is calculated as a function of cytokinin concentration and culm transpiration.

Parameters:
  • cytokinins (float) – Amount of cytokinins in roots (AU)
  • regul_transpiration (float) – Regulating factor by transpiration (mmol H2O m-2 s-1)
Returns:

Rate of Cytokinin export (AU h-1)
Return type:

float
calculate_sucrose_derivative(Unloading_Sucrose, S_Amino_Acids, C_exudation, sum_respi)[source]

delta root sucrose.

Parameters:
  • Unloading_Sucrose (float) – Sucrose Unloading (µmol` C g-1 mstruct)
  • S_Amino_Acids (float) – Amino acids synthesis (µmol` N g-1 mstruct)
  • C_exudation (float) – C exudation (µmol` C g-1 mstruct)
  • sum_respi (float) – Sum of respirations for roots i.e. related to N uptake, amino acids synthesis and residual (µmol` C)
Returns:

delta root sucrose (µmol` C sucrose)
Return type:

float
calculate_nitrates_derivative(Uptake_Nitrates, Export_Nitrates, S_Amino_Acids)[source]

delta root nitrates.

Parameters:
  • Uptake_Nitrates (float) – Nitrate uptake (µmol` N nitrates)
  • Export_Nitrates (float) – Export of nitrates (µmol` N)
  • S_Amino_Acids (float) – Amino acids synthesis (µmol` N g-1 mstruct)
Returns:

delta root nitrates (µmol` N nitrates)
Return type:

float
calculate_amino_acids_derivative(Unloading_Amino_Acids, S_Amino_Acids, Export_Amino_Acids, N_exudation)[source]

delta root amino acids.

Parameters:
  • Unloading_Amino_Acids (float) – Amino acids Unloading (µmol` N g-1 mstruct)
  • S_Amino_Acids (float) – Amino acids synthesis (µmol` N g-1 mstruct)
  • Export_Amino_Acids (float) – Export of amino acids (µmol` N)
  • N_exudation (float) – N exudated (µmol` g-1 mstruct)
Returns:

delta root amino acids (µmol` N amino acids)
Return type:

float
calculate_cytokinins_derivative(S_cytokinins, Export_cytokinins)[source]

delta root cytokinins.

Parameters:
  • S_cytokinins (float) – Cytokinin synthesis (AU g-1 mstruct)
  • Export_cytokinins (float) – Cytokinin export (AU)
Returns:

delta root cytokinins (AU cytokinins)
Return type:

float
class cnwheat.model.PhotosyntheticOrgan(label, exposed_element, enclosed_element)[source]

Bases: cnwheat.model.Organ

The class PhotosyntheticOrgan defines the CN exchanges in a photosynthetic organ.

A photosynthetic organ must have at least 1 photosynthetic organ element: chaff element, lamina element, internode element, peduncle element, or sheath element.

PhotosyntheticOrgan is the base class of all photosynthetic organs. DO NOT INSTANTIATE IT.

PARAMETERS = <cnwheat.parameters.PhotosyntheticOrganParameters object>

the internal parameters of the photosynthetic organs

exposed_element = None

the exposed element

enclosed_element = None

the enclosed element

mstruct = None

the structural dry mass

senesced_mstruct = None

senesced structural dry mass

nitrates = None

nitrates (µmol N)

calculate_aggregated_variables()[source]

Calculate the integrative variables of the organ recursively.

class cnwheat.model.Chaff(label=None, exposed_element=None, enclosed_element=None)[source]

Bases: cnwheat.model.PhotosyntheticOrgan

The class Chaff defines the CN exchanges in a chaff.

PARAMETERS = <cnwheat.parameters.ChaffParameters object>

the internal parameters of the chaffs

class cnwheat.model.Lamina(label=None, exposed_element=None, enclosed_element=None)[source]

Bases: cnwheat.model.PhotosyntheticOrgan

The class Lamina defines the CN exchanges in a lamina.

PARAMETERS = <cnwheat.parameters.LaminaParameters object>

the internal parameters of the laminae

class cnwheat.model.Internode(label=None, exposed_element=None, enclosed_element=None)[source]

Bases: cnwheat.model.PhotosyntheticOrgan

The class Internode defines the CN exchanges in an internode.

PARAMETERS = <cnwheat.parameters.InternodeParameters object>

the internal parameters of the internodes

class cnwheat.model.Peduncle(label=None, exposed_element=None, enclosed_element=None)[source]

Bases: cnwheat.model.PhotosyntheticOrgan

The class Peduncle defines the CN exchanges in a peduncle.

PARAMETERS = <cnwheat.parameters.PeduncleParameters object>

the internal parameters of the peduncles

class cnwheat.model.Sheath(label=None, exposed_element=None, enclosed_element=None)[source]

Bases: cnwheat.model.PhotosyntheticOrgan

The class Sheath defines the CN exchanges in a sheath.

PARAMETERS = <cnwheat.parameters.SheathParameters object>

the internal parameters of the sheaths

class cnwheat.model.PhotosyntheticOrganElement(label=None, green_area=0.0001, mstruct=0.005, senesced_mstruct=0, Nstruct=0.001, triosesP=0, starch=0, sucrose=0, fructan=0, nitrates=0, amino_acids=0, proteins=0, cytokinins=0, Tr=0, Ag=0, Ts=12, is_growing=False, cohorts=None, cohorts_replications=None, index=None)[source]

Bases: object

The class PhotosyntheticOrganElement defines the CN exchanges in a photosynthetic organ element.

An element must belong to an organ of the same type (e.g. a class:LaminaElement must belong to a class:Lamina).

PhotosyntheticOrganElement is the base class of all photosynthetic organs elements. DO NOT INSTANTIATE IT.

PARAMETERS = <cnwheat.parameters.PhotosyntheticOrganElementParameters object>

the internal parameters of the photosynthetic organs elements

INIT_COMPARTMENTS = <cnwheat.parameters.PhotosyntheticOrganElementInitCompartments object>

the initial values of compartments and state parameters

label = None

the label of the element

cohorts = None

list of cohort values - Hack to treat tillering cases : TEMPORARY. Devrait être porté à l’échelle de la plante uniquement mais je ne vois pas comment faire mieux

cohorts_replications = None

dictionary of number of replications per cohort rank

index = None

the index of the phytomer TEMPORARY

mstruct = None

Structural dry mass (g)

senesced_mstruct = None

Senesced structural dry mass (g)

Nstruct = None

Structural N mass (g)

is_growing = None

Flag indicating if the element is growing or not (bool)

green_area = None

green area (m-2)

Tr = None

Transpiration rate (mmol m-2 s-1)

Ag = None

Gross assimilation (µmol` m-2 s-1)

Ts = None

Organ temperature (°C)

triosesP = None

µmol` C

starch = None

µmol` C

sucrose = None

µmol` C

fructan = None

µmol` C

nitrates = None

µmol` N

amino_acids = None

µmol` N

proteins = None

µmol` N

cytokinins = None

AU

Loading_Sucrose = None

Rate of sucrose loading to phloem (µmol` C)

Loading_Amino_Acids = None

Rate of amino acids loading to phloem (µmol` N)

S_Proteins = None

Rate of protein synthesis (µmol` N g-1 mstruct)

S_Amino_Acids = None

Rate of amino acids synthesis (µmol` N g-1 mstruct)

Regul_S_Fructan = None

Maximal rate of fructan synthesis (µmol` C g-1 mstruct)

S_Starch = None

Rate of starch synthesis (µmol` C g-1 mstruct)

D_Starch = None

Rate of starch degradation (µmol` C g-1 mstruct)

S_Sucrose = None

Rate of sucrose synthesis (µmol` C g-1 mstruct)

S_Fructan = None

Rate of fructan synthesis (µmol` C g-1 mstruct)

D_Fructan = None

Rate of fructan degradation ((µmol` C g-1 mstruct)

Nitrates_import = None

Total nitrates imported from roots (µmol` N nitrates)

Amino_Acids_import = None

Total amino acids imported from roots (µmol` N amino acids)

D_Proteins = None

Rate of protein degradation (µmol` N g-1 mstruct)

cytokinins_import = None

Import of cytokinins (AU)

D_cytokinins = None

Rate of cytokinins degradation (AU g-1 mstruct)

Total_Organic_Nitrogen = None

current total nitrogen amount (µmol` N)

R_Nnit_red = None

Nitrate reduction-linked respiration (µmol` C respired)

R_residual = None

Residual maintenance respiration (cost from protein turn-over, cell ion gradients, futile cycles…) (µmol` C respired)

Transpiration = None

Surfacic transpiration rate of an element (mmol H2O s-1)

R_phloem_loading = None

Phloem loading respiration (µmol` C respired)

Photosynthesis = None

Total Photosynthesis of an element integrated over a delta t (µmol` C)

sum_respi = None

Sum of respirations for the element i.e. related to C loading to phloem, amino acids synthesis and residual (µmol` C)

nb_replications
calculate_aggregated_variables()[source]

Calculate the integrative variables of the element.

static calculate_total_Photosynthesis(Ag, green_area)[source]

Total Photosynthesis of an element (µmol` C m-2 h-1 * m2).

Parameters:
  • Ag (float) – Gross Photosynthesis rate (µmol` C m-2 s-1)
  • green_area (float) – Green area (m2)
Returns:

Rate of Total Photosynthesis (µmol` C h-1)
Return type:

float
static calculate_Total_Transpiration(Tr, green_area)[source]

Surfacic transpiration rate of an element

Parameters:
  • Tr (float) – Transpiration rate (mmol H2O m-2 s-1)
  • green_area (float) – Green area (m2)
Returns:

Total transpiration (mmol H2O s-1)
Return type:

float
calculate_Regul_S_Fructan(Loading_Sucrose)[source]

Regulating function for fructan maximal rate of synthesis. Negative regulation by the loading of sucrose from the phloem (“swith-off” sigmoïdal kinetic).

Parameters:Loading_Sucrose (float) – Sucrose loading (µmol` C)
Returns:Maximal rate of fructan synthesis (µmol` C g-1 mstruct h-1)
Return type:float
static calculate_Total_Organic_Nitrogen(amino_acids, proteins, Nstruct)[source]

Total amount of organic N (amino acids + proteins + Nstruct). Used to calculate residual respiration.

Parameters:
  • amino_acids (float) – Amount of amino acids (µmol` N)
  • proteins (float) – Amount of proteins (µmol` N)
  • Nstruct (float) – Structural N mass (g)
Returns:

Total amount of organic N (µmol` N)
Return type:

float
calculate_S_Starch(triosesP, T_effect_Vmax)[source]

Rate of starch synthesis (µmol` C starch g-1 mstruct h-1). Michaelis-Menten function of triose phosphates.

Parameters:
  • triosesP (float) – Amount of triose phosphates (µmol` C)
  • T_effect_Vmax (float) – Correction to apply to enzyme activity
Returns:

Rate of Starch synthesis (µmol` C g-1 mstruct h-1)
Return type:

float
calculate_D_Starch(starch, T_effect_Vmax)[source]

Rate of starch degradation (µmol` C starch g-1 mstruct h-1). First order kinetic.

Parameters:
  • starch (float) – Amount of starch (µmol` C)
  • T_effect_Vmax (float) – Correction to apply to enzyme activity
Returns:

Starch degradation (µmol` C g-1 mstruct h-1)
Return type:

float
calculate_S_Sucrose(triosesP, T_effect_Vmax)[source]

Rate of sucrose synthesis (µmol` C sucrose g-1 mstruct h-1). Michaelis-Menten function of triose phosphates.

Parameters:
  • triosesP (float) – Amount of triose phosphates (µmol` C)
  • T_effect_Vmax (float) – Correction to apply to enzyme activity
Returns:

Rate of Sucrose synthesis (µmol` C g-1 mstruct h-1)
Return type:

float
calculate_Loading_Sucrose(sucrose, sucrose_phloem, mstruct_axis, T_effect_conductivity)[source]

Rate of sucrose loading to phloem (µmol` C sucrose h-1). Transport-resistance model.

Parameters:
  • sucrose (float) – Amount of sucrose in the element (µmol` C)
  • sucrose_phloem (float) – Amount of sucrose in the phloem (µmol` C)
  • mstruct_axis (float) – Structural dry mass of the axis (g)
  • T_effect_conductivity (float) – Effect of the temperature on the conductivity rate at 20°C (AU)
Returns:

Rate of Sucrose loading (µmol` C h-1)
Return type:

float
calculate_export_sucrose(sucrose, sucrose_hiddenzone, mstruct_hiddenzone, T_effect_conductivity)[source]

Rate of sucrose exportation to hidden zone (µmol` C sucrose h-1). Transport-resistance model.

Parameters:
  • sucrose (float) – Amount of sucrose in the element (µmol` C)
  • sucrose_hiddenzone (float) – Sucrose amount in the hidden zone (µmol` C)
  • mstruct_hiddenzone (float) – mstruct of the hidden zone (g)
  • T_effect_conductivity (float) – Effect of the temperature on the conductivity rate at 20°C (AU)
Returns:

Rate of Sucrose export (µmol` C h-1)
Return type:

float
calculate_S_Fructan(sucrose, Regul_S_Fructan, T_effect_Vmax)[source]

Rate of fructan synthesis (µmol` C fructan g-1 mstruct h-1). Sigmoïdal function of sucrose.

Parameters:
  • sucrose (float) – Amount of sucrose (µmol` C)
  • Regul_S_Fructan (float) – Maximal rate of fructan synthesis regulated by sucrose loading (µmol` C g-1 mstruct)
  • T_effect_Vmax (float) – Correction to apply to enzyme activity
Returns:

Rate of Fructan synthesis (µmol` C g-1 mstruct h-1)
Return type:

float
calculate_D_Fructan(sucrose, fructan, T_effect_Vmax)[source]

Rate of fructan degradation (µmol` C fructan g-1 mstruct h-1). Inhibition function by the end product i.e. sucrose (Bancal et al., 2012).

Parameters:
  • sucrose (float) – Amount of sucrose (µmol` C)
  • fructan (float) – Amount of fructan (µmol` C)
  • T_effect_Vmax (float) – Correction to apply to enzyme activity
Returns:

Rate of Fructan degradation (µmol` C g-1 mstruct h-1)
Return type:

float
static calculate_Nitrates_import(Export_Nitrates, element_transpiration, Total_Transpiration)[source]

Total nitrates imported from roots (µmol` N nitrates). Nitrates coming from roots (fraction of uptake + direct export) are distributed according to the contribution of the element to culm transpiration.

Parameters:
  • Export_Nitrates (float) – Exported nitrates by roots (µmol` N)
  • element_transpiration (float) – Element transpiration (mmol H2O s-1)
  • Total_Transpiration (float) – Culm transpiration (mmol H2O s-1)
Returns:

Total nitrates import (µmol` N nitrates)
Return type:

float
static calculate_Amino_Acids_import(roots_exported_amino_acids, element_transpiration, Total_Transpiration)[source]

Total amino acids imported from roots (µmol` N amino acids). Amino acids exported by roots are distributed according to the contribution of the element to culm transpiration.

Parameters:
  • roots_exported_amino_acids (float) – Exported amino acids by roots (µmol` N)
  • element_transpiration (float) – Element transpiration (mmol H2O s-1)
  • Total_Transpiration (float) – Culm transpiration (mmol H2O s-1)
Returns:

Total amino acids import (µmol` N amino acids)
Return type:

float
calculate_S_amino_acids(nitrates, triosesP, T_effect_Vmax)[source]

Rate of amino acids synthesis (µmol` N amino acids h-1 g-1 MS). Bi-substrate Michaelis-Menten function of nitrates and triose phosphates.

Parameters:
  • nitrates (float) – Amount of nitrates (µmol` N)
  • triosesP (float) – Amount of triosesP (µmol` C)
  • T_effect_Vmax (float) – Correction to apply to enzyme activity
Returns:

Rate of Amino acids synthesis (µmol` N h-1 g-1 mstruct)
Return type:

float
calculate_S_proteins(amino_acids, T_effect_Vmax)[source]

Rate of protein synthesis (µmol` N proteins h-1 g-1 MS). Michaelis-Menten function of amino acids.

Parameters:
  • amino_acids (float) – Amount of amino acids (µmol` N)
  • T_effect_Vmax (float) – Correction to apply to enzyme activity
Returns:

Protein synthesis (µmol` N h-1 g-1 mstruct)
Return type:

float
calculate_D_Proteins(proteins, cytokinins, T_effect_Vmax)[source]

Rate of protein degradation (µmol` N proteins s-1 g-1 MS h-1). First order kinetic regulated by cytokinins concentration.

Parameters:
  • proteins (float) – Amount of proteins (µmol` N)
  • cytokinins (float) – Amount of cytokinins (AU)
  • T_effect_Vmax (float) – Correction to apply to enzyme activity
Returns:

Rate of protein degradation (µmol` N g-1 mstruct)
Return type:

float
calculate_Loading_Amino_Acids(amino_acids, amino_acids_phloem, mstruct_axis, T_effect_conductivity)[source]

Rate of amino acids loading to phloem (µmol` N amino acids h-1). Transport-resistance model.

Parameters:
  • amino_acids (float) – Amount of amino acids in the element (µmol` N)
  • amino_acids_phloem (float) – Amount of amino acids in the phloem (µmol` N)
  • mstruct_axis (float) – Structural dry mass of the axis (g)
  • T_effect_conductivity (float) – Effect of the temperature on the conductivity rate at 20°C (AU)
Returns:

Amino acids loading (µmol` N h-1)
Return type:

float
calculate_Export_Amino_Acids(amino_acids, amino_acids_hiddenzone, mstruct_hiddenzone, T_effect_conductivity)[source]

Rate of amino acids exportation to hidden zone (µmol` N amino acids h-1). Transport-resistance model.

Parameters:
  • amino_acids (float) – Amount of amino acids in the element (µmol` N)
  • amino_acids_hiddenzone (float) – Amino acids amount in the hidden zone (µmol` N)
  • mstruct_hiddenzone (float) – mstruct of the hidden zone (g)
  • T_effect_conductivity (float) – Effect of the temperature on the conductivity rate at 20°C (AU)
Returns:

Rate of Amino acids export (µmol` N h-1)
Return type:

float
static calculate_cytokinins_import(roots_exporteD_cytokinins, element_transpiration, Total_Transpiration)[source]

Import of cytokinins (AU). Cytokinin exported by roots are distributed according to the contribution of the element to culm transpiration.

Parameters:
  • roots_exporteD_cytokinins (float) – Exported cytokinins from roots (AU)
  • element_transpiration (float) – Element transpiration (mmol H2O s-1)
  • Total_Transpiration (float) – Culm transpiration (mmol H2O s-1)
Returns:

Cytokinin import (AU)
Return type:

float
calculate_D_cytokinins(cytokinins, T_effect_Vmax)[source]

Rate of cytokinins degradation (AU g-1 mstruct h-1). First order kinetic. Vary with organ temperature.

Parameters:
  • cytokinins (float) – Amount of cytokinins (AU)
  • T_effect_Vmax (float) – Correction to apply to enzyme activity
Returns:

Rate of Cytokinin degradation (AU g-1 mstruct h-1)
Return type:

float
calculate_triosesP_derivative(Photosynthesis, S_Sucrose, S_Starch, S_Amino_Acids)[source]

delta triose phosphates of element.

Parameters:
  • Photosynthesis (float) – Total gross Photosynthesis (µmol` C)
  • S_Sucrose (float) – Sucrose synthesis (µmol` C g-1 mstruct)
  • S_Starch (float) – Starch synthesis (µmol` C g-1 mstruct)
  • S_Amino_Acids (float) – Amino acids synthesis (µmol` N g-1 mstruct)
Returns:

delta triose phosphates (µmol` C triose phosphates)
Return type:

float
calculate_starch_derivative(S_Starch, D_Starch)[source]

delta starch of element.

Parameters:
  • S_Starch (float) – Starch synthesis (µmol` C g-1 mstruct)
  • D_Starch (float) – Starch degradation (µmol` C g-1 mstruct)
Returns:

delta starch (µmol` C starch)
Return type:

float
calculate_sucrose_derivative(S_Sucrose, D_Starch, Loading_Sucrose, S_Fructan, D_Fructan, sum_respi)[source]

delta sucrose of element.

Parameters:
  • S_Sucrose (float) – Sucrose synthesis (µmol` C g-1 mstruct)
  • D_Starch (float) – Starch degradation (µmol` C g-1 mstruct)
  • Loading_Sucrose (float) – Sucrose loading (µmol` C)
  • S_Fructan (float) – Fructan synthesis (µmol` C g-1 mstruct)
  • D_Fructan (float) – Fructan degradation (µmol` C g-1 mstruct)
  • sum_respi (float) – Sum of respirations for the element i.e. related to C loading to phloem, amino acids synthesis and residual (µmol` C)
Returns:

delta sucrose (µmol` C sucrose)
Return type:

float
calculate_fructan_derivative(S_Fructan, D_Fructan)[source]

delta fructan of element.

Parameters:
  • S_Fructan (float) – Fructan synthesis (µmol` C g-1 mstruct)
  • D_Fructan (float) – Fructan degradation (µmol` C g-1 mstruct)
Returns:

delta fructan (µmol` C fructan)
Return type:

float
calculate_nitrates_derivative(Nitrates_import, S_Amino_Acids)[source]

delta nitrates of element.

Parameters:
  • Nitrates_import (float) – Nitrate import from roots (µmol` N)
  • S_Amino_Acids (float) – Amino acids synthesis (µmol` N g-1 mstruct)
Returns:

delta nitrates (µmol` N nitrates)
Return type:

float
calculate_amino_acids_derivative(Amino_Acids_import, S_Amino_Acids, S_Proteins, D_Proteins, Loading_Amino_Acids)[source]

delta amino acids of element.

Parameters:
  • Amino_Acids_import (float) – Amino acids import from roots (µmol` N)
  • S_Amino_Acids (float) – Amino acids synthesis (µmol` N g-1 mstruct)
  • S_Proteins (float) – Protein synthesis (µmol` N g-1 mstruct)
  • D_Proteins (float) – Protein degradation (µmol` N g-1 mstruct)
  • Loading_Amino_Acids (float) – Amino acids loading (µmol` N)
Returns:

delta amino acids (µmol` N amino acids)
Return type:

float
calculate_proteins_derivative(S_Proteins, D_Proteins)[source]

delta proteins of element.

Parameters:
  • S_Proteins (float) – Protein synthesis (µmol` N g-1 mstruct)
  • D_Proteins (float) – Protein degradation (µmol` N g-1 mstruct)
Returns:

delta proteins (µmol` N proteins)
Return type:

float
calculate_cytokinins_derivative(import_cytokinins, D_cytokinins)[source]

delta cytokinins of element.

Parameters:
  • import_cytokinins (float) – Cytokinin import (AU)
  • D_cytokinins (float) – Cytokinin degradation (AU g-1 mstruct)
Returns:

delta cytokinins (AU cytokinins)
Return type:

float
class cnwheat.model.ChaffElement(label=None, green_area=0.0001, mstruct=0.005, senesced_mstruct=0, Nstruct=0.001, triosesP=0, starch=0, sucrose=0, fructan=0, nitrates=0, amino_acids=0, proteins=0, cytokinins=0, Tr=0, Ag=0, Ts=12, is_growing=False, cohorts=None, cohorts_replications=None, index=None)[source]

Bases: cnwheat.model.PhotosyntheticOrganElement

The class ChaffElement defines the CN exchanges in a chaff element.

PARAMETERS = <cnwheat.parameters.ChaffElementParameters object>

the internal parameters of the chaffs elements

class cnwheat.model.LaminaElement(label=None, green_area=0.0001, mstruct=0.005, senesced_mstruct=0, Nstruct=0.001, triosesP=0, starch=0, sucrose=0, fructan=0, nitrates=0, amino_acids=0, proteins=0, cytokinins=0, Tr=0, Ag=0, Ts=12, is_growing=False, cohorts=None, cohorts_replications=None, index=None)[source]

Bases: cnwheat.model.PhotosyntheticOrganElement

The class LaminaElement defines the CN exchanges in a lamina element.

PARAMETERS = <cnwheat.parameters.LaminaElementParameters object>

the internal parameters of the laminae elements

class cnwheat.model.InternodeElement(label=None, green_area=0.0001, mstruct=0.005, senesced_mstruct=0, Nstruct=0.001, triosesP=0, starch=0, sucrose=0, fructan=0, nitrates=0, amino_acids=0, proteins=0, cytokinins=0, Tr=0, Ag=0, Ts=12, is_growing=False, cohorts=None, cohorts_replications=None, index=None)[source]

Bases: cnwheat.model.PhotosyntheticOrganElement

The class InternodeElement defines the CN exchanges in an internode element.

PARAMETERS = <cnwheat.parameters.InternodeElementParameters object>

the internal parameters of the internodes elements

class cnwheat.model.PeduncleElement(label=None, green_area=0.0001, mstruct=0.005, senesced_mstruct=0, Nstruct=0.001, triosesP=0, starch=0, sucrose=0, fructan=0, nitrates=0, amino_acids=0, proteins=0, cytokinins=0, Tr=0, Ag=0, Ts=12, is_growing=False, cohorts=None, cohorts_replications=None, index=None)[source]

Bases: cnwheat.model.PhotosyntheticOrganElement

The class PeduncleElement defines the CN exchanges in a peduncle element.

PARAMETERS = <cnwheat.parameters.PeduncleElementParameters object>

the internal parameters of the peduncles elements

class cnwheat.model.SheathElement(label=None, green_area=0.0001, mstruct=0.005, senesced_mstruct=0, Nstruct=0.001, triosesP=0, starch=0, sucrose=0, fructan=0, nitrates=0, amino_acids=0, proteins=0, cytokinins=0, Tr=0, Ag=0, Ts=12, is_growing=False, cohorts=None, cohorts_replications=None, index=None)[source]

Bases: cnwheat.model.PhotosyntheticOrganElement

The class SheathElement defines the CN exchanges in a sheath element.

PARAMETERS = <cnwheat.parameters.SheathElementParameters object>

the internal parameters of the sheaths elements

class cnwheat.model.Soil(volume=None, nitrates=None, Tsoil=None)[source]

Bases: object

The class Soil defines the amount of nitrogen in the volume of soil explored by roots.

PARAMETERS = <cnwheat.parameters.SoilParameters object>

the internal parameters of the soil

volume = None

volume of soil explored by roots (m3)

Tsoil = None

soil temperature (°C)

constant_Conc_Nitrates = None

If True, the model run with a constant soil nitrate concentration (bool)

nitrates = None

µmol` N nitrates

Conc_Nitrates_Soil = None

soil nitrate concentration Unloading (µmol` N m-3 soil)

mineralisation = None

mineralisation on organic N into nitrates in soil (µmol`)

static calculate_temperature_effect_on_Vmax(Tsoil)[source]

Effect of the temperature on maximal enzyme activity Should multiply the rate at 20°C

Parameters:Tsoil (float) – Soil temperature (°C)
Returns:Correction to apply to enzyme activity
Return type:float
static calculate_temperature_effect_on_conductivity(Tsoil)[source]

Effect of the temperature on phloeme translocation conductivity (Farrar 1988) Should multiply the rate at 20°C

Parameters:Tsoil (float) – Soil temperature (°C)
Returns:Correction to apply to conductivity coefficients.
Return type:float
calculate_Conc_Nitrates(nitrates)[source]

Nitrate concentration in soil.

Parameters:nitrates (float) – Amount of nitrates (µmol` N)
Returns:Nitrate concentration (µmol` nitrates m-3)
Return type:float
static calculate_mineralisation(T_effect_Vmax)[source]

Mineralisation on organic N into nitrates in soil.

Parameters:T_effect_Vmax (float) – Correction to apply to enzyme activity
Returns:Rate of Nitrate mineralisation (µmol` h-1)
Return type:float
static calculate_nitrates_derivative(mineralisation, soil_contributors, culm_density, constant_Conc_Nitrates)[source]

delta soil nitrates.

Parameters:
  • mineralisation (float) – N mineralisation in soil (µmol` m-2 N nitrates)
  • int) soil_contributors ((float,) – A tuple with (Nitrate uptake per axis (µmol` N nitrates), the plant id)
  • [plant_id, culm_density] culm_density (dict) – A dictionary of culm density (culm_density = {plant_id: culm_density, …})
  • constant_Conc_Nitrates (bool) – If True, the model run with a constant soil nitrate concentration.
Returns:

delta nitrates (µmol` N nitrates)
Return type:

float

cnwheat.parameters module

cnwheat.parameters.from_dataframe(object_, dataframe_)[source]

Set attributes of object_ from data in dataframe_.

Parameters:

  • object_ (object) - The object to set.

  • dataframe_ (pandas.DataFrame) - The dataframe used to set the attribute(s) of object_. dataframe_ must have only 2 rows:

    • one row is for the header and contains the name of each attribute,
    • and one row contains the value of each attribute.
cnwheat.parameters.to_dataframe(object_)[source]

Create and return a dataframe from attributes of object_.

Parameters:
  • object_ (object) - The object used to create the dataframe.
Returns:

A dataframe which contains the attributes of object_, with only 2 rows:

  • one row is for the header and contains the name of each attribute,
  • and one row contains the value of each attribute.
Returns Type:

pandas.DataFrame
class cnwheat.parameters.PopulationParameters[source]

Bases: object

Internal parameters of populations.

cnwheat.parameters.POPULATION_PARAMETERS = <cnwheat.parameters.PopulationParameters object>

The instance of class cnwheat.parameters.PopulationParameters for current process

class cnwheat.parameters.PlantParameters[source]

Bases: object

Internal parameters of plants.

cnwheat.parameters.PLANT_PARAMETERS = <cnwheat.parameters.PlantParameters object>

The instance of class cnwheat.parameters.PlantParameters for current process

class cnwheat.parameters.AxisParameters[source]

Bases: object

Internal parameters of axes.

ALPHA = None

Proportion of the structural mass containing the substrates

cnwheat.parameters.AXIS_PARAMETERS = <cnwheat.parameters.AxisParameters object>

The instance of class cnwheat.parameters.AxisParameters for current process

class cnwheat.parameters.AxisInitCompartments[source]

Bases: object

Initial values for compartments of axis.

C_exudated = None

initial value of C exudated by the roots (\(\mu\) mol C)

sum_respi_shoot = None

initial value of C respired by the shoot (exept leaf and internode growth respiration) (\(\mu\) mol C)

sum_respi_roots = None

initial value of C respired by the roots (exept root growth respiration) (\(\mu\) mol C)

cnwheat.parameters.AXIS_INIT_COMPARTMENTS = <cnwheat.parameters.AxisInitCompartments object>

The instance of class cnwheat.parameters.HiddenZoneInitCompartments for current process

class cnwheat.parameters.PhytomerParameters[source]

Bases: object

Internal parameters of phytomers.

cnwheat.parameters.PHYTOMER_PARAMETERS = <cnwheat.parameters.PhytomerParameters object>

The instance of class cnwheat.parameters.PhytomerParameters for current process

class cnwheat.parameters.HiddenZoneParameters[source]

Bases: object

Internal parameters of hidden growing zones.

ALPHA = None

Proportion of structural mass containing substrate

BETA = None

Kind of volumetric mass density at power -2/3 ((g m-3)**(-2/3))

SIGMA = None

Coefficient of surface diffusion. Used in Fick’s law (g m-2 s-1).

VMAX_SFRUCTAN_POT = None

Potential maximal rate of fructan synthesis (\(\mu\) mol C s-1 g-1 MS)

VMAX_SFRUCTAN_RELATIVE = None

Maximal rate of fructan synthesis in the division zone relative to the rate in mature tissus (\(\mu\) mol C s-1 g-1 MS)

K_SFRUCTAN = None

Affinity coefficient of fructan synthesis (\(\mu\) mol C g-1 MS)

K_REGUL_SFRUCTAN = None

Affinity coefficient of the regulation function of fructan synthesis (\(\mu\) mol g-1 MS)

N_REGUL_SFRUCTAN = None

Parameter of the regulation function of fructan synthesis (dimensionless)

VMAX_DFRUCTAN = None

Maximal rate of fructan degradation (\(\mu\) mol C s-1 g-1 MS)

K_DFRUCTAN = None

Affinity coefficient of fructan degradation (\(\mu\) mol C g-1 MS)

delta_Dproteins = None

Relative rate of proteins degradation (s-1)

VMAX_SPROTEINS_DZ = None

Maximal rate of protein synthesis in the division zone (\(\mu\) mol N s-1 g-1 MS)

VMAX_SPROTEINS_EMZ = None

Maximal rate of protein synthesis in the elongation and mature zones (\(\mu\) mol N s-1 g-1 MS)

K_SPROTEINS = None

Affinity coefficient of protein synthesis (\(\mu\) mol N g-1 MS)

cnwheat.parameters.HIDDEN_ZONE_PARAMETERS = <cnwheat.parameters.HiddenZoneParameters object>

The instance of class cnwheat.parameters.HiddenZoneParameters for current process

class cnwheat.parameters.HiddenZoneInitCompartments[source]

Bases: object

Initial values for compartments of hidden zones.

sucrose = None

initial value of sucrose (\(\mu\) mol C)

fructan = None

initial value of fructan (\(\mu\) mol C)

amino_acids = None

initial value of amino_acids (\(\mu\) mol N)

proteins = None

initial value of proteins (\(\mu\) mol N)

mstruct = None

initial value of mstruct (g)

Nstruct = None

initial value of Nstruct (g)

ratio_DZ = None

initial value of ratio of Division Zone into the HiddenZone

cnwheat.parameters.HIDDEN_ZONE_INIT_COMPARTMENTS = <cnwheat.parameters.HiddenZoneInitCompartments object>

The instance of class cnwheat.parameters.HiddenZoneInitCompartments for current process

class cnwheat.parameters.PhloemParameters[source]

Bases: object

Internal parameters of phloems.

ALPHA = None

Proportion of structural mass containing substrate

cnwheat.parameters.PHLOEM_PARAMETERS = <cnwheat.parameters.PhloemParameters object>

The instance of class cnwheat.parameters.PhloemParameters for current process

class cnwheat.parameters.PhloemInitCompartments[source]

Bases: object

Initial values for compartments of phloem.

sucrose = None

initial value of sucrose (\(\mu\) mol C)

amino_acids = None

initial value of amino_acids (\(\mu\) mol N)

cnwheat.parameters.PHLOEM_INIT_COMPARTMENTS = <cnwheat.parameters.PhloemInitCompartments object>

The instance of class cnwheat.parameters.PhloemInitCompartments for current process

class cnwheat.parameters.GrainsParameters[source]

Bases: object

Internal parameters of grains.

ALPHA = None

Proportion of structural mass containing substrate

VMAX_RGR = None

Maximal value of the Relative Growth Rate of grain structure (s-1 at 20°C)

K_RGR = None

Affinity coefficient of the Relative Growth Rate of grain structure (\(\mu\) mol C)

Arrhenius_ref = None
VMAX_STARCH = None

Maximal rate of grain filling of starch (\(\mu\) mol C s-1 at 20°C g-1 MS)

K_STARCH = None

Affinity coefficient of grain filling of starch (\(\mu\) mol C g-1 MS)

FILLING_INIT = None

Time (s at 20°C) at which phloem loading switch from grain structure to accumulation of starch

FILLING_END = None

Time (s at 20°C) at which grains filling stops. (Bertheloot et al., 2011)

cnwheat.parameters.GRAINS_PARAMETERS = <cnwheat.parameters.GrainsParameters object>

The instance of class cnwheat.parameters.GrainsParameters for current process

class cnwheat.parameters.GrainsInitCompartments[source]

Bases: object

Initial values for compartments of grains.

age_from_flowering = None

initial value of age_from_flowering (s)

starch = None

initial value of starch (\(\mu\) mol C)

structure = None

initial value of structure (\(\mu\) mol C)

proteins = None

initial value of proteins (\(\mu\) mol N)

cnwheat.parameters.GRAINS_INIT_COMPARTMENTS = <cnwheat.parameters.GrainsInitCompartments object>

The instance of class cnwheat.parameters.GrainsInitCompartments for current process

class cnwheat.parameters.RootsParameters[source]

Bases: object

Internal parameters of roots.

ALPHA = None

Proportion of structural mass containing substrate

SIGMA_SUCROSE = None

Conductivity of the roots-phloem pathway (g2 \(\mu\) mol-1 m-2 s-1) ; used to compute the sucrose loaded to the phloem

BETA = None

Kind of volumetric mass density at power -2/3 ((g m-3)**(-2/3))

K_C = None

Affinity coefficient for the regulation function by root C (\(\mu\) mol C sucrose g-1 MS)

NET_INFLUX_UPTAKE_RATIO = None

ratio (net uptake : nitrate influx)

MIN_INFLUX_FOR_UPTAKE = None

Minimum influx rate below wich no net absorption happens (\(\mu\) mol C sucrose g-1 mstruct s-1)

A_VMAX_HATS = None

Parameter for estimating the maximal rate of nitrates uptake at saturating soil N concentration;HATS (\(\mu\) mol g-1 s-1)

B_VMAX_HATS = None

Parameter for estimating the maximal rate of nitrates uptake at saturating soil N concentration;HATS (g \(\mu\) mol-1)

A_K_HATS = None

Parameter for estimating the affinity coefficient of nitrates uptake at saturating soil N concentration;HATS (\(\mu\) mol m-3)

B_K_HATS = None

Parameter for estimating the affinity coefficient of nitrates uptake at saturating soil N concentration;HATS (g \(\mu\) mol-1)

A_LATS = None

Parameter for estimating the rate of nitrates uptake at low soil N concentration; LATS (m3 g-1 s-1)

B_LATS = None

Parameter for estimating the rate of nitrates uptake at low soil N concentration; LATS (g \(\mu\) mol-1)

K_NITRATE_EXPORT = None

Relative rate of nitrate export from roots (s-1)

VMAX_AMINO_ACIDS = None

Maximal rate of amino acid synthesis (\(\mu\) mol N s-1 g-1 MS)

K_AMINO_ACIDS_NITRATES = None

Affinity coefficient of amino acid synthesis from nitrates (\(\mu\) mol N g-1 MS)

K_AMINO_ACIDS_SUCROSE = None

Affinity coefficient of amino acid synthesis from sucrose (\(\mu\) mol C g-1 MS)

K_AMINO_ACIDS_EXPORT = None

Relative rate of amino acids export from roots (s-1)

C_EXUDATION = None

Proportion of C exudated from C sucrose unloaded to roots (Keith et al., 1986)

N_EXUDATION_MAX = None

Parameter used to limit the rate of N exudation (dimensionless)

VMAX_S_CYTOKININS = None

Maximal rate of cytokinins synthesis (UA g-1 mstruct s-1)

K_NITRATES_CYTOKININS = None

Affinity coefficient of cytokinins synthesis for nitrates (\(\mu\) mol N nitrates g-1 mstruct)

K_SUCROSE_CYTOKININS = None

Affinity coefficient of cytokinins synthesis for sucrose (\(\mu\) mol C sucrose g-1 mstruct)

N_SUC_CYTOKININS = None

A parameter for cytokinins synthesis (dimensionless)

N_NIT_CYTOKININS = None

A parameter for cytokinins synthesis (dimensionless)

K_CYTOKININS_EXPORT = None

Relative rate of cytokinins export from roots (s-1)

cnwheat.parameters.ROOTS_PARAMETERS = <cnwheat.parameters.RootsParameters object>

The instance of class cnwheat.parameters.RootsParameters for current process

class cnwheat.parameters.RootsInitCompartments[source]

Bases: object

Initial values for compartments of roots.

sucrose = None

initial value of sucrose (\(\mu\) mol C)

nitrates = None

initial value of nitrates (\(\mu\) mol C)

amino_acids = None

initial value of amino_acids (\(\mu\) mol N)

cytokinins = None

initial value of cytokinins (AU)

mstruct = None

initial value of mstruct (g)

senesced_mstruct = None

initial value of senesced_mstruct (g)

Nstruct = None

initial value of Nstruct (g)

cnwheat.parameters.ROOTS_INIT_COMPARTMENTS = <cnwheat.parameters.RootsInitCompartments object>

The instance of class cnwheat.parameters.RootsInitCompartments for current process

class cnwheat.parameters.PhotosyntheticOrganParameters[source]

Bases: object

Internal parameters of photosynthetic organs.

VMAX_SUCROSE = None

Maximal rate of sucrose synthesis (\(\mu\) mol C s-1 g-1 MS)

K_SUCROSE = None

Affinity coefficient of sucrose synthesis (\(\mu\) mol C g-1 MS)

VMAX_STARCH = None

Maximal rate of starch synthesis (\(\mu\) mol C s-1 g-1 MS)

K_STARCH = None

Affinity coefficient of starch synthesis (\(\mu\) mol C g-1 MS)

DELTA_DSTARCH = None

Relative rate of starch degradation (s-1)

VMAX_SFRUCTAN_POT = None

Potential maximal rate of fructan synthesis (\(\mu\) mol C s-1 g-1 MS)

K_SFRUCTAN = None

Affinity coefficient of fructan synthesis (\(\mu\) mol C g-1 MS)

K_REGUL_SFRUCTAN = None

Affinity coefficient of the regulation function of fructan synthesis (\(\mu\) mol g-1 MS)

N_REGUL_SFRUCTAN = None

Parameter of the regulation function of fructan synthesis (dimensionless)

VMAX_DFRUCTAN = None

Maximal rate of fructan degradation (\(\mu\) mol C s-1 g-1 MS)

K_DFRUCTAN = None

Affinity coefficient of fructan degradation (\(\mu\) mol C g-1 MS)

SIGMA_SUCROSE = None

Conductivity of an organ-phloem pathway (g2 \(\mu\) mol-1 m-2 s-1) ; used to compute the sucrose loaded to the phloem

SIGMA_AMINO_ACIDS = None

Conductivity of an organ-phloem pathway (g2 \(\mu\) mol-1 m-2 s-1) ; used to compute the amino acids loaded to the phloem

BETA = None

Kind of volumetric mass density at power -2/3 ((g m-3)**(-2/3))

VMAX_AMINO_ACIDS = None

Maximal rate of amino acid synthesis (\(\mu\) mol N s-1 g-1 MS)

K_AMINO_ACIDS_NITRATES = None

Affinity coefficient of amino acid synthesis from nitrates (\(\mu\) mol N g-1 MS)

K_AMINO_ACIDS_TRIOSESP = None

Affinity coefficient of amino acid synthesis from triosesP (\(\mu\) mol C g-1 MS)

VMAX_SPROTEINS = None

Maximal rate of protein synthesis (\(\mu\) mol N s-1 g-1 MS)

K_SPROTEINS = None

Affinity coefficient of protein synthesis (\(\mu\) mol N g-1 MS)

VMAX_DPROTEINS_CYTOK = None

Maximal regulation of protein degradation by cytokinins (\(\mu\) mol g-1 mstruct s-1)

K_DPROTEINS_CYTOK = None

Affinity coefficient with cytokinins for protein degradation (UA g-1 mstruct)

N_DPROTEINS = None

A coefficient for the regulation of protein degradation by cytokines (dimensionless)

VMAX_DPROTEINS = None

Maximal rate of protein degradation (\(\mu\) mol g-1 mstruct s-1)

K_DPROTEINS = None

Affinity coefficient for protein degradation (\(\mu\) g-1 mstruct)

DELTA_D_CYTOKININS = None

Relative rate of cytokinins degradation (s-1)

cnwheat.parameters.PHOTOSYNTHETIC_ORGAN_PARAMETERS = <cnwheat.parameters.PhotosyntheticOrganParameters object>

The instance of class cnwheat.parameters.PhotosyntheticOrganParameters for current process

class cnwheat.parameters.ChaffParameters[source]

Bases: cnwheat.parameters.PhotosyntheticOrganParameters

Internal parameters of chaffs.

cnwheat.parameters.CHAFF_PARAMETERS = <cnwheat.parameters.ChaffParameters object>

The instance of class cnwheat.parameters.ChaffParameters for current process

class cnwheat.parameters.LaminaParameters[source]

Bases: cnwheat.parameters.PhotosyntheticOrganParameters

Internal parameters of laminae.

cnwheat.parameters.LAMINA_PARAMETERS = <cnwheat.parameters.LaminaParameters object>

The instance of class cnwheat.parameters.LaminaParameters for current process

class cnwheat.parameters.InternodeParameters[source]

Bases: cnwheat.parameters.PhotosyntheticOrganParameters

Internal parameters of internodes.

cnwheat.parameters.INTERNODE_PARAMETERS = <cnwheat.parameters.InternodeParameters object>

The instance of class cnwheat.parameters.InternodeParameters for current process

class cnwheat.parameters.PeduncleParameters[source]

Bases: cnwheat.parameters.PhotosyntheticOrganParameters

Internal parameters of peduncles.

cnwheat.parameters.PEDUNCLE_PARAMETERS = <cnwheat.parameters.PeduncleParameters object>

The instance of class cnwheat.parameters.PeduncleParameters for current process

class cnwheat.parameters.SheathParameters[source]

Bases: cnwheat.parameters.PhotosyntheticOrganParameters

Internal parameters of sheaths.

cnwheat.parameters.SHEATH_PARAMETERS = <cnwheat.parameters.SheathParameters object>

The instance of class cnwheat.parameters.SheathParameters for current process

class cnwheat.parameters.PhotosyntheticOrganElementParameters[source]

Bases: object

Internal parameters of photosynthetic organs elements.

cnwheat.parameters.PHOTOSYNTHETIC_ORGAN_ELEMENT_PARAMETERS = <cnwheat.parameters.PhotosyntheticOrganElementParameters object>

The instance of class cnwheat.parameters.PhotosyntheticOrganElementParameters for current process

class cnwheat.parameters.PhotosyntheticOrganElementInitCompartments[source]

Bases: object

Initial values for compartments of photosynthetic organ elements.

green_area = None

initial value of green_area (m2)

mstruct = None

initial value of mstruct (g)

senesced_mstruct = None

initial value of senesced_mstruct (g)

Nstruct = None

initial value of Nstruct (g)

triosesP = None

initial value of triosesP (\(\mu\) mol C)

starch = None

initial value of starch (\(\mu\) mol C)

sucrose = None

initial value of sucrose (\(\mu\) mol C)

fructan = None

initial value of fructan (\(\mu\) mol C)

nitrates = None

initial value of nitrates (\(\mu\) mol N)

amino_acids = None

initial value of amino_acids (\(\mu\) mol N)

proteins = None

initial value of proteins (\(\mu\) mol N)

cytokinins = None

initial value of cytokinins (AU)

is_growing = None

initial value of is_growing (Flag indicating if the element is growing or not (bool)

Tr = None

initial value of Tr (Transpiration rate (mmol m-2 s-1)

Ts = None

initial value of Ts (Organ temperature)

Ag = None

initial value of Ag (Gross assimilation (\(\mu\) mol m-2 s-1)

cnwheat.parameters.PHOTOSYNTHETIC_ORGAN_ELEMENT_INIT_COMPARTMENTS = <cnwheat.parameters.PhotosyntheticOrganElementInitCompartments object>

The instance of class cnwheat.parameters.PhotosyntheticOrganElementInitCompartments for current process

class cnwheat.parameters.ChaffElementParameters[source]

Bases: cnwheat.parameters.PhotosyntheticOrganElementParameters

Internal parameters of chaffs elements.

ALPHA = None

Proportion of structural mass containing substrate

cnwheat.parameters.CHAFF_ELEMENT_PARAMETERS = <cnwheat.parameters.ChaffElementParameters object>

The instance of class cnwheat.parameters.ChaffElementParameters for current process

class cnwheat.parameters.LaminaElementParameters[source]

Bases: cnwheat.parameters.PhotosyntheticOrganElementParameters

Internal parameters of laminae elements.

ALPHA = None

Proportion of structural mass containing substrate

cnwheat.parameters.LAMINA_ELEMENT_PARAMETERS = <cnwheat.parameters.LaminaElementParameters object>

The instance of class cnwheat.parameters.LaminaElementParameters for current process

class cnwheat.parameters.InternodeElementParameters[source]

Bases: cnwheat.parameters.PhotosyntheticOrganElementParameters

Internal parameters of internodes elements.

ALPHA = None

Proportion of structural mass containing substrate

cnwheat.parameters.INTERNODE_ELEMENT_PARAMETERS = <cnwheat.parameters.InternodeElementParameters object>

The instance of class cnwheat.parameters.InternodeElementParameters for current process

class cnwheat.parameters.PeduncleElementParameters[source]

Bases: cnwheat.parameters.PhotosyntheticOrganElementParameters

Internal parameters of peduncles elements.

ALPHA = None

Proportion of structural mass containing substrate

cnwheat.parameters.PEDUNCLE_ELEMENT_PARAMETERS = <cnwheat.parameters.PeduncleElementParameters object>

The instance of class cnwheat.parameters.PeduncleElementParameters for current process

class cnwheat.parameters.SheathElementParameters[source]

Bases: cnwheat.parameters.PhotosyntheticOrganElementParameters

Internal parameters of sheaths elements.

ALPHA = None

Proportion of structural mass containing substrate

cnwheat.parameters.SHEATH_ELEMENT_PARAMETERS = <cnwheat.parameters.SheathElementParameters object>

The instance of class cnwheat.parameters.SheathElementParameters for current process

class cnwheat.parameters.SoilParameters[source]

Bases: object

Internal parameters of soil.

cnwheat.parameters.SOIL_PARAMETERS = <cnwheat.parameters.SoilParameters object>

The instance of class cnwheat.parameters.SoilParameters for current process

cnwheat.tools module

cnwheat.tools.OUTPUTS_INDEXES = ['t', 'plant', 'axis', 'metamer', 'organ', 'element']

All the possible indexes of CN-Wheat outputs

exception cnwheat.tools.DataWarning(variable, keys)[source]

Bases: UserWarning

Raised when there is no data to plot for a variable.

cnwheat.tools.plot_cnwheat_ouputs(outputs, x_name, y_name, x_label='', y_label='', x_lim=None, title=None, filters={}, plot_filepath=None, colors=[], linestyles=[], explicit_label=True, kwargs={})[source]

Plot outputs, with x=`x_name` and y=`y_name`.

The general algorithm is:

  • find the scale of outputs and keep only the needed columns,
  • apply filters to outputs and make groups according to the scale,
  • plot each group as a new line,
  • save or display the plot.
Parameters:
  • outputs (pandas.DataFrame) – The outputs of CN-Wheat.
  • x_name (str) – x axis of the plot.
  • y_name (str) – y axis of the plot.
  • x_label (str) – The x label of the plot. Default is ‘’.
  • or unicode y_label (str) – The y label of the plot. Default is ‘’.
  • x_lim (float) – the x-axis limit.
  • title (str) – the title of the plot. If None (default), create a title which is the concatenation of y_name and each scales which cardinality is one.
  • filters (dict) – A dictionary whose keys are the columns of outputs for which we want to apply a specific filter. These columns can be one or more element of OUTPUTS_INDEXES. The value associated to each key is a criteria that the rows of outputs must satisfy to be plotted. The values can be either one value or a list of values. If no value is given for any column, then all rows are plotted (default).
  • colors (list) – The colors for lines. If empty, let matplotlib default line colors.
  • linestyles (list) – The styles for lines. If empty, let matplotlib default line styles.
  • plot_filepath (str) – The file path to save the plot. If None, do not save the plot but display it.
  • explicit_label (bool) – True: makes the line label from concatenation of each scale id (default). - False: makes the line label from concatenation of scales containing several distinct elements.
  • kwargs (dict) – key arguments to be passed to matplolib
Examples: 
>>> import pandas as pd
>>> cnwheat_output_df = pd.read_csv('cnwheat_output.csv') # in this example, 'cnwheat_output.csv' must contain at least the columns 't' and 'Conc_Sucrose'.
>>> plot(cnwheat_output_df, x_name = 't', y_name = 'Conc_Sucrose', x_label='Time (Hour)', y_label=u'[Sucrose] (µmol g$^{-1}$ mstruct)', title='{} = f({})'.format('Conc_Sucrose', 't'), filters={'plant': 1, 'axis': 'MS', 'organ': 'Lamina', 'element': 1})
cnwheat.tools.setup_logging(config_filepath='logging.json', level=20, log_model=False, log_compartments=False, log_derivatives=False, remove_old_logs=False)[source]

Setup logging configuration.

Parameters:
  • config_filepath (str) – The file path of the logging configuration.
  • level (int) – The global level of the logging. Use either logging.DEBUG, logging.INFO, logging.WARNING, logging.ERROR or logging.CRITICAL.
  • log_model (bool) – if True, log the messages from cnwheat.model. False otherwise.
  • log_compartments (bool) – if True, log the values of the compartments. False otherwise.
  • log_derivatives (bool) – if True, log the values of the derivatives. False otherwise.
  • remove_old_logs (bool) – if True, remove all files in the logs directory documented in config_filepath.
cnwheat.tools.compare_actual_to_desired(data_dirpath, actual_data_df, desired_data_filename, actual_data_filename=None, precision=4, overwrite_desired_data=False)[source]

Compare

difference = actual_data_df - desired_data_df

to

tolerance = 10**-precision * (1 + abs(desired_data_df))

where

desired_data_df = pd.read_csv(os.path.join(data_dirpath, desired_data_filename))

If difference > tolerance, then raise an AssertionError.

Parameters:
  • data_dirpath (str) – The path of the directory where to find the data to compare.
  • actual_data_df (pandas.DataFrame) – The computed data.
  • desired_data_filename (str) – The file name of the expected data.
  • actual_data_filename (str) – If not None, save the computed data to actual_data_filename, in directory data_dirpath. Default is None.
  • precision (int) – The precision to use for the comparison. Default is 4.
  • overwrite_desired_data (bool) – If True the comparison between actual and desired data is not run. Instead, the desired data will be overwritten using actual data. To be used with caution.
exception cnwheat.tools.ProgressBarError[source]

Bases: Exception

class cnwheat.tools.ProgressBar(bar_length=20, title='', block_character='#', uncomplete_character='-')[source]

Bases: object

Display a console progress bar.

bar_length = None

the number of blocks in the progress bar. MUST BE GREATER THAN ZERO !

t_max = None

the maximum t that the progress bar can display. MUST BE GREATER THAN ZERO !

block_interval = None

the time interval of each block. MUST BE GREATER THAN ZERO !

last_upper_t = None

the last upper t displayed by the progress bar

progress_mapping = None

a mapping to optimize the refresh rate

title = None

the title to write on the left side of the progress bar

block_character = None

the character to represent a block

uncomplete_character = None

the character to represent the uncompleted part of the progress bar

set_t_max(t_max)[source]

“Set t_max and update other attributes accordingly.

update(t)[source]

Update the progress bar if needed.

cnwheat.converter module

cnwheat.converter.PLANTS_VARIABLES = ['plant', 'Tair']

the columns of the outputs dataframe at PLANT scale

cnwheat.converter.AXES_VARIABLES = ['plant', 'axis', 'mstruct', 'senesced_mstruct', 'C_exudated', 'sum_respi_shoot', 'sum_respi_roots', 'Total_Transpiration']

the columns of the outputs dataframe at AXIS scale

cnwheat.converter.PHYTOMERS_VARIABLES = ['plant', 'axis', 'metamer', 'mstruct']

the columns of the outputs dataframe at PHYTOMER scale

cnwheat.converter.ORGANS_VARIABLES = ['plant', 'axis', 'organ', 'mstruct', 'Nstruct', 'senesced_mstruct', 'age_from_flowering', 'amino_acids', 'cytokinins', 'nitrates', 'proteins', 'starch', 'structure', 'sucrose', 'C_exudation', 'HATS_LATS', 'N_exudation', 'RGR_Structure', 'R_Nnit_red', 'R_Nnit_upt', 'Respi_growth', 'R_grain_growth_starch', 'R_grain_growth_struct', 'R_residual', 'regul_transpiration', 'sum_respi', 'Export_Amino_Acids', 'Export_Nitrates', 'Export_cytokinins', 'S_Amino_Acids', 'S_cytokinins', 'S_grain_starch', 'S_grain_structure', 'S_Proteins', 'Unloading_Amino_Acids', 'Unloading_Sucrose', 'Uptake_Nitrates', 'Total_Organic_Nitrogen']

the columns of the outputs dataframe at ORGAN scale

cnwheat.converter.HIDDENZONE_VARIABLES = ['plant', 'axis', 'metamer', 'Nstruct', 'mstruct', 'ratio_DZ', 'amino_acids', 'fructan', 'proteins', 'sucrose', 'nb_replications', 'D_Fructan', 'D_Proteins', 'S_Fructan', 'S_Proteins', 'Unloading_Amino_Acids', 'Unloading_Sucrose']

the columns of the outputs dataframe at HIDDEN ZONE scale

cnwheat.converter.ELEMENTS_VARIABLES = ['plant', 'axis', 'metamer', 'organ', 'element', 'Ag', 'Nstruct', 'Tr', 'Ts', 'green_area', 'is_growing', 'mstruct', 'senesced_mstruct', 'amino_acids', 'cytokinins', 'fructan', 'nitrates', 'proteins', 'starch', 'sucrose', 'triosesP', 'Photosynthesis', 'R_Nnit_red', 'R_phloem_loading', 'R_residual', 'Transpiration', 'sum_respi', 'nb_replications', 'Amino_Acids_import', 'D_Fructan', 'D_Proteins', 'D_Starch', 'D_cytokinins', 'Loading_Amino_Acids', 'Loading_Sucrose', 'Nitrates_import', 'Regul_S_Fructan', 'S_Fructan', 'S_Starch', 'S_Sucrose', 'S_Amino_Acids', 'S_Proteins', 'cytokinins_import', 'Total_Organic_Nitrogen']

the columns of the outputs dataframe at ELEMENT scale

cnwheat.converter.SOILS_VARIABLES = ['plant', 'axis', 'Tsoil', 'volume', 'nitrates', 'Conc_Nitrates_Soil', 'mineralisation']

the columns of the outputs dataframe at SOIL scale

cnwheat.converter.CNWHEAT_CLASSES_TO_DATAFRAME_ORGANS_MAPPING = {<class 'cnwheat.model.Internode'>: 'internode', <class 'cnwheat.model.Lamina'>: 'blade', <class 'cnwheat.model.Sheath'>: 'sheath', <class 'cnwheat.model.Peduncle'>: 'peduncle', <class 'cnwheat.model.Chaff'>: 'ear', <class 'cnwheat.model.Roots'>: 'roots', <class 'cnwheat.model.Grains'>: 'grains', <class 'cnwheat.model.Phloem'>: 'phloem', <class 'cnwheat.model.HiddenZone'>: 'hiddenzone'}

the mapping of the CN-Wheat organ classes to organ names in MTG

cnwheat.converter.DATAFRAME_TO_CNWHEAT_ELEMENTS_NAMES_MAPPING = {'HiddenElement': 'enclosed_element', 'LeafElement1': 'exposed_element', 'StemElement': 'exposed_element'}

the mapping of the name of each element, from Dataframe to CN-Wheat

cnwheat.converter.from_dataframes(organs_inputs=None, hiddenzones_inputs=None, elements_inputs=None, soils_inputs=None, update_parameters=None)[source]

If organs_inputs, hiddenzones_inputs and elements_inputs are not None, convert organs_inputs, hiddenzones_inputs and elements_inputs to a population. If soils_inputs is not None, convert soils_inputs to a dictionary of soils.

Parameters:
  • organs_inputs (pandas.DataFrame) – Organs inputs, with one line by organ.
  • hiddenzones_inputs (pandas.DataFrame) – Hidden zones inputs, with one line by hidden zone.
  • elements_inputs (pandas.DataFrame) – Elements inputs, with one line by element.
  • soils_inputs (pandas.DataFrame) – Soils inputs, with one line by soil.
  • update_parameters (dict) – A dictionary with the parameters to update, should have the form {‘Organ_label1’: {‘param1’: value1, ‘param2’: value2}, …}.
Returns:

If organs_inputs, hiddenzones_inputs and elements_inputs are not None, return a population, and/or if soils_inputs is not None, return a dict of soils.
Return type:

(pandas.DataFrame, dict) or dict
cnwheat.converter.to_dataframes(population=None, soils=None)[source]

Convert a CN-Wheat population and/or a dictionary of soils to Pandas dataframes.

If population is not None, convert population to Pandas dataframes. If soils is not None, convert soils to Pandas dataframe.

Parameters:
  • population (model.Population) – The CN-Wheat population to convert.
  • soils (dict) – The soils to convert.
Returns:

If population is not None, return dataframes describing the internal state and compartments of the population at each scale:

  • plant scale: plant index, state parameters, state variables, intermediate variables, fluxes and integrative variables of each plant (see PLANTS_VARIABLES)
  • axis scale: plant index, axis id, state parameters, state variables, intermediate variables, fluxes and integrative variables of each axis (see AXES_VARIABLES)
  • phytomer scale: plant index, axis id, phytomer index, state parameters, state variables, intermediate variables, fluxes and integrative variables of

each phytomer (see PHYTOMERS_VARIABLES) * organ scale:

  • hidden zones: plant index, axis id, phytomer index, state parameters, state variables, intermediate variables, fluxes and integrative variables of

each hidden zone (see HIDDENZONE_VARIABLES) * roots, phloem and grains: plant index, axis id, organ type, state parameters, state variables, intermediate variables, fluxes and integrative variables of each organ (see ORGANS_VARIABLES)

  • and element scale: plant index, axis id, phytomer index, organ type, element type, state parameters, state variables, intermediate variables, fluxes and integrative variables of

each element (see ELEMENTS_VARIABLES)

and/or

if soils is not None, return a dataframe describing internal state and compartments of the soils, with one line per soil:

  • plant index, axis id, state parameters, state variables, intermediate variables, fluxes and integrative variables of each soil (see SOILS_RUN_VARIABLES)
Return type:

(pandas.DataFrame)