Reference guide #

calculate_aggregated_variables()[source]#: Calculate the integrative variables of the axis recursively.

grains#: the grains

label#: the label of the axis

mstruct#: structural mass of the axis (g)

nitrates#: nitrates in the axis (µmol N)

phloem#: the phloem

phytomers#: the list of phytomers

roots#: the roots

senesced_mstruct#: senesced structural mass of the axis (g)

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

The class Chaff defines the CN exchanges in a chaff.

PARAMETERS = <openalea.cnwheat.parameters.ChaffParameters object>#: the internal parameters of the chaffs

class openalea.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]#

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

PARAMETERS = <openalea.cnwheat.parameters.ChaffElementParameters object>#: the internal parameters of the chaffs elements

class openalea.cnwheat.model.EcophysiologicalConstants[source]#

Bases: object

Ecophysiological constants.

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_MOLAR_MASS_C_RATIO = 0.38#: (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)

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)

C_MOLAR_MASS = 12#: Molar mass of carbon (g mol-1)

HEXOSE_MOLAR_MASS_C_RATIO = 0.42#: Contribution of C in hexose mass

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

NB_C_TRIOSEP = 3#: Number of C in 1 mol of trioseP

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)

PROTEINS_MOLAR_MASS_C_RATIO = 0.38#: As for AA

PROTEINS_MOLAR_MASS_N_RATIO = 0.151#: Mean contribution of N in protein mass (Penning De Vries 1989)

RATIO_C_mstruct = 0.44#: Mean contribution of carbon to structural dry mass (g C g-1 mstruct)

TRIOSESP_MOLAR_MASS_C_RATIO = 0.21#: Contribution of C in triosesP mass

class openalea.cnwheat.model.Grains(label='grains', age_from_flowering=0, starch=0, structure=1, proteins=0)[source]#

Bases: 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)

INIT_COMPARTMENTS = <openalea.cnwheat.parameters.GrainsInitCompartments object>#: the initial values of compartments and state parameters

PARAMETERS = <openalea.cnwheat.parameters.GrainsParameters object>#: the internal parameters of the grains

RGR_Structure#: RGR of grain structure (dimensionless?)

R_grain_growth_starch#: grain starch growth respiration (µmol` C respired)

R_grain_growth_struct#: grain struct respiration (µmol` C respired)

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

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

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

age_from_flowering#: seconds

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:

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:

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:

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:

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

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:

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 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:

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

initialize()[source]#: Initialize the derived attributes of the organ.

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

proteins#: µmol` of N proteins

starch#: µmol` of C starch

structural_dry_mass#: g of MS

structure#: µmol` of C sucrose

class openalea.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: Organ

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

D_Fructan#: fructan degradation (µmol` C g-1 mstruct)

D_Proteins#: protein degradation (µmol` N g-1 mstruct)

INIT_COMPARTMENTS = <openalea.cnwheat.parameters.HiddenZoneInitCompartments object>#: the initial values of compartments and state parameters

Nstruct#: g

PARAMETERS = <openalea.cnwheat.parameters.HiddenZoneParameters object>#: the internal parameters of the hidden zone

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

S_Fructan#: fructan synthesis (µmol` C g-1 mstruct)

S_Proteins#: protein synthesis (µmol` N g-1 mstruct)

Total_Organic_Nitrogen#: current total nitrogen amount (µmol` N)

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

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

amino_acids#: µmol` N

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:

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:

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:

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:

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:

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:

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:

calculate_aggregated_variables()[source]#: Calculate the integrative variables of the organ recursively.

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:

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:

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:

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:

cohorts#

TEMPORARY. Devrait être porté à l’échelle de la plante uniquement mais je ne vois pas comment faire mieux

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

cohorts_replications#: dictionary of number of replications per cohort rank

fructan#: µmol` C

index#: the index of the phytomer TEMPORARY

mstruct#: g

property nb_replications#

proteins#: µmol` N

sucrose#: µmol` C

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

The class Internode defines the CN exchanges in an internode.

PARAMETERS = <openalea.cnwheat.parameters.InternodeParameters object>#: the internal parameters of the internodes

class openalea.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]#

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

PARAMETERS = <openalea.cnwheat.parameters.InternodeElementParameters object>#: the internal parameters of the internodes elements

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

The class Lamina defines the CN exchanges in a lamina.

PARAMETERS = <openalea.cnwheat.parameters.LaminaParameters object>#: the internal parameters of the laminae

class openalea.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]#

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

PARAMETERS = <openalea.cnwheat.parameters.LaminaElementParameters object>#: the internal parameters of the laminae elements

class openalea.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.

calculate_aggregated_variables()[source]#: Calculate the integrative variables of the organ recursively.

initialize()[source]#: Initialize the derived attributes of the organ.

label#: the label of the organ

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

The class Peduncle defines the CN exchanges in a peduncle.

PARAMETERS = <openalea.cnwheat.parameters.PeduncleParameters object>#: the internal parameters of the peduncles

class openalea.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]#

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

PARAMETERS = <openalea.cnwheat.parameters.PeduncleElementParameters object>#: the internal parameters of the peduncles elements

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

Bases: Organ

The class Phloem defines the CN exchanges in a phloem.

INIT_COMPARTMENTS = <openalea.cnwheat.parameters.PhloemInitCompartments object>#: the initial values of compartments and state parameters

PARAMETERS = <openalea.cnwheat.parameters.PhloemParameters object>#: the internal parameters of the phloem

amino_acids#: µmol` N amino acids

static calculate_amino_acids_derivative(contributors)[source]#

delta amino acids

Parameters:: contributors (list [PhotosyntheticOrganElement, Grains, Roots, HiddenZone]) – Organs exchanging N with the phloem
Returns:: delta amino acids (µmol` N amino acids)
Return type:: float

static calculate_sucrose_derivative(contributors)[source]#

delta sucrose

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

sucrose#: µmol` C sucrose

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

Bases: 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 = <openalea.cnwheat.parameters.PhotosyntheticOrganParameters object>#: the internal parameters of the photosynthetic organs

calculate_aggregated_variables()[source]#: Calculate the integrative variables of the organ recursively.

enclosed_element#: the enclosed element

exposed_element#: the exposed element

mstruct#: the structural dry mass

nitrates(µmol N)#: nitrates (µmol N)

senesced_mstruct#: senesced structural dry mass

class openalea.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.

Ag#: Gross assimilation (µmol` m-2 s-1)

Amino_Acids_import#: Total amino acids imported from roots (µmol` N amino acids)

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

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

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

D_cytokinins#: Rate of cytokinins degradation (AU g-1 mstruct)

INIT_COMPARTMENTS = <openalea.cnwheat.parameters.PhotosyntheticOrganElementInitCompartments object>#: the initial values of compartments and state parameters

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

Loading_Sucrose#: Rate of sucrose loading to phloem (µmol` C)

Nitrates_import#: Total nitrates imported from roots (µmol` N nitrates)

Nstruct#: Structural N mass (g)

PARAMETERS = <openalea.cnwheat.parameters.PhotosyntheticOrganElementParameters object>#: the internal parameters of the photosynthetic organs elements

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

R_Nnit_red#: Nitrate reduction-linked respiration (µmol` C respired)

R_phloem_loading#: Phloem loading respiration (µmol` C respired)

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

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

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

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

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

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

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

Total_Organic_Nitrogen#: current total nitrogen amount (µmol` N)

Tr#: Transpiration rate (mmol m-2 s-1)

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

Ts#: Organ temperature (°C)

amino_acids#: µmol` N

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:

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:

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:

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:

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:

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:

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:

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:

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:

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

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:

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:

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:

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:

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:

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:

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:

calculate_aggregated_variables()[source]#: Calculate the integrative variables of the element.

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

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:

cohorts#

TEMPORARY. Devrait être porté à l’échelle de la plante uniquement mais je ne vois pas comment faire mieux

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

cohorts_replications#: dictionary of number of replications per cohort rank

cytokinins#: AU

cytokinins_import#: Import of cytokinins (AU)

fructan#: µmol` C

green_area#: green area (m-2)

index#: the index of the phytomer TEMPORARY

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

label#: the label of the element

mstruct#: Structural dry mass (g)

property nb_replications#

nitrates#: µmol` N

proteins#: µmol` N

senesced_mstruct#: Senesced structural dry mass (g)

starch#: µmol` C

sucrose#: µmol` C

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

triosesP#: µmol` C

class openalea.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:

1 photosynthetic organ: chaff, peduncle,
lamina, internode, or sheath.
or 1 hiddenzone.

PARAMETERS = <openalea.cnwheat.parameters.PhytomerParameters object>#: the internal parameters of the phytomers

calculate_aggregated_variables()[source]#: Calculate the integrative variables of the phytomer recursively.

chaff#: the chaff

cohorts#

TEMPORARY. Devrait être porté à l’échelle de la plante uniquement mais je ne vois pas comment faire mieux

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

cohorts_replications#: dictionary of number of replications per cohort rank

hiddenzone#: the hidden zone

index#: the index of the phytomer

internode#: the internode

lamina#: the lamina

mstruct#: the structural mass of the phytomer (g)

property nb_replications#

nitrates#: nitrates of the phytomer (µmol N)

peduncle#: the peduncle

senesced_mstruct#: senesced structural mass of the phytomer (g)

sheath#: the sheath

class openalea.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 = <openalea.cnwheat.parameters.PlantParameters object>#: the internal parameters of the plants

axes#: the list of axes

calculate_aggregated_variables()[source]#: Calculate the integrative variables of the plant recursively.

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

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

cohorts#

TEMPORARY

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

index#: the index of the plant

class openalea.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 = <openalea.cnwheat.parameters.PopulationParameters object>#: the internal parameters of the population

calculate_aggregated_variables()[source]#: Calculate the integrative variables of the population recursively.

plants#: the list of plants

class openalea.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: Organ

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

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

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

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

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

HATS_LATS#: Nitrate influx (µmol` N)

INIT_COMPARTMENTS = <openalea.cnwheat.parameters.RootsInitCompartments object>#: the initial values of compartments and state parameters

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

Nstruct#: Structural N mass (g)

PARAMETERS = <openalea.cnwheat.parameters.RootsParameters object>#: the internal parameters of the roots

R_Nnit_red#: Nitrate reduction-linked respiration (µmol` C respired)

R_Nnit_upt#: Nitrate uptake respiration (µmol` C respired)

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

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

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

Total_Organic_Nitrogen#: current amount of organic N (µmol` N)

Unloading_Amino_Acids#: current Unloading of amino acids from phloem to roots

Unloading_Sucrose#: current Unloading of sucrose from phloem to roots

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

amino_acids#: µmol` N amino acids

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

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:

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:

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:

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:

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:

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:

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:

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_aggregated_variables()[source]#: Calculate the integrative variables of the organ recursively.

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:

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:

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_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:

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_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:

cytokinins#: AU cytokinins

mstruct#: Structural mass (g)

nitrates#: µmol` N nitrates

regul_transpiration#: Dimensionless regulating factor of metabolite exports from roots by shoot transpiration

senesced_mstruct#: Senesced structural mass (g)

sucrose#: µmol` C sucrose

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

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

The class Sheath defines the CN exchanges in a sheath.

PARAMETERS = <openalea.cnwheat.parameters.SheathParameters object>#: the internal parameters of the sheaths

class openalea.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]#

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

PARAMETERS = <openalea.cnwheat.parameters.SheathElementParameters object>#: the internal parameters of the sheaths elements

class openalea.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.

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

PARAMETERS = <openalea.cnwheat.parameters.SoilParameters object>#: the internal parameters of the soil

Tsoil#: soil temperature (°C)

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)
soil_contributors ((float, int)) – A tuple with (Nitrate uptake per axis (µmol` N nitrates), the plant id)
culm_density (dict [plant_id, culm_density]) – 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:

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

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

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

nitrates#: µmol` N nitrates

volume#: volume of soil explored by roots (m3)

`openalea.cnwheat.parameters` module#

openalea.cnwheat.parameters.AXIS_INIT_COMPARTMENTS = <openalea.cnwheat.parameters.AxisInitCompartments object>#: The instance of class cnwheat.parameters.HiddenZoneInitCompartments for current process

openalea.cnwheat.parameters.AXIS_PARAMETERS = <openalea.cnwheat.parameters.AxisParameters object>#: The instance of class cnwheat.parameters.AxisParameters for current process

class openalea.cnwheat.parameters.AxisInitCompartments[source]#

Bases: object

Initial values for compartments of axis.

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

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

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

class openalea.cnwheat.parameters.AxisParameters[source]#

Bases: object

Internal parameters of axes.

ALPHA#: Proportion of the structural mass containing the substrates

openalea.cnwheat.parameters.CHAFF_ELEMENT_PARAMETERS = <openalea.cnwheat.parameters.ChaffElementParameters object>#: The instance of class cnwheat.parameters.ChaffElementParameters for current process

openalea.cnwheat.parameters.CHAFF_PARAMETERS = <openalea.cnwheat.parameters.ChaffParameters object>#: The instance of class cnwheat.parameters.ChaffParameters for current process

class openalea.cnwheat.parameters.ChaffElementParameters[source]#

Internal parameters of chaffs elements.

ALPHA#: Proportion of structural mass containing substrate

class openalea.cnwheat.parameters.ChaffParameters[source]#

Internal parameters of chaffs.

openalea.cnwheat.parameters.GRAINS_INIT_COMPARTMENTS = <openalea.cnwheat.parameters.GrainsInitCompartments object>#: The instance of class cnwheat.parameters.GrainsInitCompartments for current process

openalea.cnwheat.parameters.GRAINS_PARAMETERS = <openalea.cnwheat.parameters.GrainsParameters object>#: The instance of class cnwheat.parameters.GrainsParameters for current process

class openalea.cnwheat.parameters.GrainsInitCompartments[source]#

Bases: object

Initial values for compartments of grains.

age_from_flowering#: initial value of age_from_flowering (s)

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

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

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

class openalea.cnwheat.parameters.GrainsParameters[source]#

Bases: object

Internal parameters of grains.

ALPHA#: Proportion of structural mass containing substrate

Arrhenius_ref#

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

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

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

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

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

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

openalea.cnwheat.parameters.HIDDEN_ZONE_INIT_COMPARTMENTS = <openalea.cnwheat.parameters.HiddenZoneInitCompartments object>#: The instance of class cnwheat.parameters.HiddenZoneInitCompartments for current process

openalea.cnwheat.parameters.HIDDEN_ZONE_PARAMETERS = <openalea.cnwheat.parameters.HiddenZoneParameters object>#: The instance of class cnwheat.parameters.HiddenZoneParameters for current process

class openalea.cnwheat.parameters.HiddenZoneInitCompartments[source]#

Bases: object

Initial values for compartments of hidden zones.

Nstruct#: initial value of Nstruct (g)

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

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

mstruct#: initial value of mstruct (g)

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

ratio_DZ#: initial value of ratio of Division Zone into the HiddenZone

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

class openalea.cnwheat.parameters.HiddenZoneParameters[source]#

Bases: object

Internal parameters of hidden growing zones.

ALPHA#: Proportion of structural mass containing substrate

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

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

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

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

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

N_REGUL_SFRUCTAN#: Parameter of the regulation function of fructan synthesis (dimensionless)

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

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

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

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

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

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

delta_Dproteins#: Relative rate of proteins degradation (s-1)

openalea.cnwheat.parameters.INTERNODE_ELEMENT_PARAMETERS = <openalea.cnwheat.parameters.InternodeElementParameters object>#: The instance of class cnwheat.parameters.InternodeElementParameters for current process

openalea.cnwheat.parameters.INTERNODE_PARAMETERS = <openalea.cnwheat.parameters.InternodeParameters object>#: The instance of class cnwheat.parameters.InternodeParameters for current process

class openalea.cnwheat.parameters.InternodeElementParameters[source]#

Internal parameters of internodes elements.

ALPHA#: Proportion of structural mass containing substrate

class openalea.cnwheat.parameters.InternodeParameters[source]#

Internal parameters of internodes.

openalea.cnwheat.parameters.LAMINA_ELEMENT_PARAMETERS = <openalea.cnwheat.parameters.LaminaElementParameters object>#: The instance of class cnwheat.parameters.LaminaElementParameters for current process

openalea.cnwheat.parameters.LAMINA_PARAMETERS = <openalea.cnwheat.parameters.LaminaParameters object>#: The instance of class cnwheat.parameters.LaminaParameters for current process

class openalea.cnwheat.parameters.LaminaElementParameters[source]#

Internal parameters of laminae elements.

ALPHA#: Proportion of structural mass containing substrate

class openalea.cnwheat.parameters.LaminaParameters[source]#

Internal parameters of laminae.

openalea.cnwheat.parameters.PEDUNCLE_ELEMENT_PARAMETERS = <openalea.cnwheat.parameters.PeduncleElementParameters object>#: The instance of class cnwheat.parameters.PeduncleElementParameters for current process

openalea.cnwheat.parameters.PEDUNCLE_PARAMETERS = <openalea.cnwheat.parameters.PeduncleParameters object>#: The instance of class cnwheat.parameters.PeduncleParameters for current process

openalea.cnwheat.parameters.PHLOEM_INIT_COMPARTMENTS = <openalea.cnwheat.parameters.PhloemInitCompartments object>#: The instance of class cnwheat.parameters.PhloemInitCompartments for current process

openalea.cnwheat.parameters.PHLOEM_PARAMETERS = <openalea.cnwheat.parameters.PhloemParameters object>#: The instance of class cnwheat.parameters.PhloemParameters for current process

openalea.cnwheat.parameters.PHOTOSYNTHETIC_ORGAN_ELEMENT_INIT_COMPARTMENTS = <openalea.cnwheat.parameters.PhotosyntheticOrganElementInitCompartments object>#: The instance of class cnwheat.parameters.PhotosyntheticOrganElementInitCompartments for current process

openalea.cnwheat.parameters.PHOTOSYNTHETIC_ORGAN_ELEMENT_PARAMETERS = <openalea.cnwheat.parameters.PhotosyntheticOrganElementParameters object>#: The instance of class cnwheat.parameters.PhotosyntheticOrganElementParameters for current process

openalea.cnwheat.parameters.PHOTOSYNTHETIC_ORGAN_PARAMETERS = <openalea.cnwheat.parameters.PhotosyntheticOrganParameters object>#: The instance of class cnwheat.parameters.PhotosyntheticOrganParameters for current process

openalea.cnwheat.parameters.PHYTOMER_PARAMETERS = <openalea.cnwheat.parameters.PhytomerParameters object>#: The instance of class cnwheat.parameters.PhytomerParameters for current process

openalea.cnwheat.parameters.PLANT_PARAMETERS = <openalea.cnwheat.parameters.PlantParameters object>#: The instance of class cnwheat.parameters.PlantParameters for current process

openalea.cnwheat.parameters.POPULATION_PARAMETERS = <openalea.cnwheat.parameters.PopulationParameters object>#: The instance of class cnwheat.parameters.PopulationParameters for current process

class openalea.cnwheat.parameters.PeduncleElementParameters[source]#

Internal parameters of peduncles elements.

ALPHA#: Proportion of structural mass containing substrate

class openalea.cnwheat.parameters.PeduncleParameters[source]#

Internal parameters of peduncles.

class openalea.cnwheat.parameters.PhloemInitCompartments[source]#

Bases: object

Initial values for compartments of phloem.

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

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

class openalea.cnwheat.parameters.PhloemParameters[source]#

Bases: object

Internal parameters of phloems.

ALPHA#: Proportion of structural mass containing substrate

class openalea.cnwheat.parameters.PhotosyntheticOrganElementInitCompartments[source]#

Bases: object

Initial values for compartments of photosynthetic organ elements.

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

Nstruct#: initial value of Nstruct (g)

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

Ts#: initial value of Ts (Organ temperature)

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

cytokinins#: initial value of cytokinins (AU)

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

green_area#: initial value of green_area (m2)

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

mstruct#: initial value of mstruct (g)

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

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

senesced_mstruct#: initial value of senesced_mstruct (g)

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

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

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

class openalea.cnwheat.parameters.PhotosyntheticOrganElementParameters[source]#

Bases: object

Internal parameters of photosynthetic organs elements.

class openalea.cnwheat.parameters.PhotosyntheticOrganParameters[source]#

Bases: object

Internal parameters of photosynthetic organs.

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

DELTA_DSTARCH#: Relative rate of starch degradation (s-1)

DELTA_D_CYTOKININS#: Relative rate of cytokinins degradation (s-1)

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

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

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

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

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

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

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

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

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

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

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

N_REGUL_SFRUCTAN#: Parameter of the regulation function of fructan synthesis (dimensionless)

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

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

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

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

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

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

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

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

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

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

class openalea.cnwheat.parameters.PhytomerParameters[source]#

Bases: object

Internal parameters of phytomers.

class openalea.cnwheat.parameters.PlantParameters[source]#

Bases: object

Internal parameters of plants.

class openalea.cnwheat.parameters.PopulationParameters[source]#

Bases: object

Internal parameters of populations.

openalea.cnwheat.parameters.ROOTS_INIT_COMPARTMENTS = <openalea.cnwheat.parameters.RootsInitCompartments object>#: The instance of class cnwheat.parameters.RootsInitCompartments for current process

openalea.cnwheat.parameters.ROOTS_PARAMETERS = <openalea.cnwheat.parameters.RootsParameters object>#: The instance of class cnwheat.parameters.RootsParameters for current process

class openalea.cnwheat.parameters.RootsInitCompartments[source]#

Bases: object

Initial values for compartments of roots.

Nstruct#: initial value of Nstruct (g)

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

cytokinins#: initial value of cytokinins (AU)

mstruct#: initial value of mstruct (g)

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

senesced_mstruct#: initial value of senesced_mstruct (g)

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

class openalea.cnwheat.parameters.RootsParameters[source]#

Bases: object

Internal parameters of roots.

ALPHA#: Proportion of structural mass containing substrate

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

NET_INFLUX_UPTAKE_RATIO#

nitrate influx)

Type:: ratio (net uptake

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

N_NIT_CYTOKININS#: A parameter for cytokinins synthesis (dimensionless)

N_SUC_CYTOKININS#: A parameter for cytokinins synthesis (dimensionless)

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

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

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

openalea.cnwheat.parameters.SHEATH_ELEMENT_PARAMETERS = <openalea.cnwheat.parameters.SheathElementParameters object>#: The instance of class cnwheat.parameters.SheathElementParameters for current process

openalea.cnwheat.parameters.SHEATH_PARAMETERS = <openalea.cnwheat.parameters.SheathParameters object>#: The instance of class cnwheat.parameters.SheathParameters for current process

openalea.cnwheat.parameters.SOIL_PARAMETERS = <openalea.cnwheat.parameters.SoilParameters object>#: The instance of class cnwheat.parameters.SoilParameters for current process

class openalea.cnwheat.parameters.SheathElementParameters[source]#

Internal parameters of sheaths elements.

ALPHA#: Proportion of structural mass containing substrate

class openalea.cnwheat.parameters.SheathParameters[source]#

Internal parameters of sheaths.

class openalea.cnwheat.parameters.SoilParameters[source]#

Bases: object

Internal parameters of soil.

openalea.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.

openalea.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

`openalea.cnwheat.tools` module#

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

Bases: UserWarning

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

openalea.cnwheat.tools.OUTPUTS_INDEXES = ['t', 'plant', 'axis', 'metamer', 'organ', 'element']#: All the possible indexes of CN-Wheat outputs

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

Bases: object

Display a console progress bar.

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

block_character#: the character to represent a block

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

last_upper_t#: the last upper t displayed by the progress bar

progress_mapping#: a mapping to optimize the refresh rate

set_t_max(t_max)[source]#: “Set t_max and update other attributes accordingly.

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

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

uncomplete_character#: the character to represent the uncompleted part of the progress bar

update(t)[source]#: Update the progress bar if needed.

exception openalea.cnwheat.tools.ProgressBarError[source]#: Bases: Exception

openalea.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.

openalea.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 ‘’.
y_label (str or unicode) – 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})

openalea.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.

`openalea.cnwheat.converter` module#

openalea.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

openalea.cnwheat.converter.CNWHEAT_CLASSES_TO_DATAFRAME_ORGANS_MAPPING = {<class 'openalea.cnwheat.model.Chaff'>: 'ear', <class 'openalea.cnwheat.model.Grains'>: 'grains', <class 'openalea.cnwheat.model.HiddenZone'>: 'hiddenzone', <class 'openalea.cnwheat.model.Internode'>: 'internode', <class 'openalea.cnwheat.model.Lamina'>: 'blade', <class 'openalea.cnwheat.model.Peduncle'>: 'peduncle', <class 'openalea.cnwheat.model.Phloem'>: 'phloem', <class 'openalea.cnwheat.model.Roots'>: 'roots', <class 'openalea.cnwheat.model.Sheath'>: 'sheath'}#: the mapping of the CN-Wheat organ classes to organ names in MTG

openalea.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

openalea.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

openalea.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

openalea.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

openalea.cnwheat.converter.PHYTOMERS_VARIABLES = ['plant', 'axis', 'metamer', 'mstruct']#: the columns of the outputs dataframe at PHYTOMER scale

openalea.cnwheat.converter.PLANTS_VARIABLES = ['plant', 'Tair']#: the columns of the outputs dataframe at PLANT scale

openalea.cnwheat.converter.SOILS_VARIABLES = ['plant', 'axis', 'Tsoil', 'volume', 'nitrates', 'Conc_Nitrates_Soil', 'mineralisation']#: the columns of the outputs dataframe at SOIL scale

openalea.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

openalea.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)

`openalea.cnwheat.postprocessing` module#

openalea.cnwheat.postprocessing.AXES_INDEXES = ['plant', 'axis']#: the indexes to locate the axes in the modeled system

openalea.cnwheat.postprocessing.AXES_POSTPROCESSING_VARIABLES = ['C_N_ratio', 'C_N_ratio_shoot', 'N_content', 'N_content_shoot', 'N_content_roots', 'N_content_mstruct', 'N_content_mstruct_shoot', 'N_content_total_DM_shoot', 'N_content_mstruct_roots', 'sum_N_g', 'sum_N_g_shoot', 'sum_dry_mass', 'sum_dry_mass_shoot', 'sum_dry_mass_laminae', 'sum_dry_mass_stem', 'sum_dry_mass_roots', 'dry_mass_phloem', 'shoot_roots_ratio', 'shoot_roots_mstruct_ratio', 'Total_Photosynthesis', 'Tillers_Photosynthesis', 'Tillers_Photosynthesis_An', 'NNI', 'NS', 'NS_shoot', 'NS_stem', 'NS_laminae', 'NS_roots', 'mstruct_shoot', 'mstruct_laminae', 'mstruct_stem', 'C_respired_shoot', 'C_respired_roots', 'Cont_WSC_DM', 'Cont_WSC_DM_shoot', 'Cont_WSC_DM_roots', 'Cont_WSC_DM_laminae', 'Cont_WSC_DM_stem', 'sum_C_g', 'sum_NSC_g']#: axes post-processing variables

openalea.cnwheat.postprocessing.AXES_RUN_POSTPROCESSING_VARIABLES = {'C_N_ratio', 'C_N_ratio_shoot', 'C_exudated', 'C_respired_roots', 'C_respired_shoot', 'Cont_WSC_DM', 'Cont_WSC_DM_laminae', 'Cont_WSC_DM_roots', 'Cont_WSC_DM_shoot', 'Cont_WSC_DM_stem', 'NNI', 'NS', 'NS_laminae', 'NS_roots', 'NS_shoot', 'NS_stem', 'N_content', 'N_content_mstruct', 'N_content_mstruct_roots', 'N_content_mstruct_shoot', 'N_content_roots', 'N_content_shoot', 'N_content_total_DM_shoot', 'Tillers_Photosynthesis', 'Tillers_Photosynthesis_An', 'Total_Photosynthesis', 'Total_Transpiration', 'axis', 'dry_mass_phloem', 'mstruct', 'mstruct_laminae', 'mstruct_shoot', 'mstruct_stem', 'plant', 'senesced_mstruct', 'shoot_roots_mstruct_ratio', 'shoot_roots_ratio', 'sum_C_g', 'sum_NSC_g', 'sum_N_g', 'sum_N_g_shoot', 'sum_dry_mass', 'sum_dry_mass_laminae', 'sum_dry_mass_roots', 'sum_dry_mass_shoot', 'sum_dry_mass_stem', 'sum_respi_roots', 'sum_respi_shoot', 't'}#: concatenation of AXES_T_INDEXES, AXES_RUN_VARIABLES and AXES_POSTPROCESSING_VARIABLES

openalea.cnwheat.postprocessing.AXES_T_INDEXES = ['t', 'plant', 'axis']#: concatenation of T_INDEX and AXES_INDEXES

openalea.cnwheat.postprocessing.ELEMENTS_INDEXES = ['plant', 'axis', 'metamer', 'organ', 'element']#: the indexes to locate the elements in the modeled system

openalea.cnwheat.postprocessing.ELEMENTS_POSTPROCESSING_VARIABLES = ['Conc_Amino_Acids', 'Conc_Fructan', 'Conc_Nitrates', 'Conc_Proteins', 'Conc_Starch', 'Conc_Sucrose', 'Conc_TriosesP', 'Cont_Fructan_DM', 'Conc_cytokinins', 'Surfacic_NS', 'NS', 'N_content', 'N_content_total_DM', 'N_tot', 'nb_replications', 'SLA', 'SLN', 'SLN_nonstruct', 'sum_dry_mass', 'Photosynthetic_efficiency', 'Cont_WSC_DM']#: elements post-processing variables

openalea.cnwheat.postprocessing.ELEMENTS_RUN_POSTPROCESSING_VARIABLES = {'Ag', 'Amino_Acids_import', 'Conc_Amino_Acids', 'Conc_Fructan', 'Conc_Nitrates', 'Conc_Proteins', 'Conc_Starch', 'Conc_Sucrose', 'Conc_TriosesP', 'Conc_cytokinins', 'Cont_Fructan_DM', 'Cont_WSC_DM', 'D_Fructan', 'D_Proteins', 'D_Starch', 'D_cytokinins', 'Loading_Amino_Acids', 'Loading_Sucrose', 'NS', 'N_content', 'N_content_total_DM', 'N_tot', 'Nitrates_import', 'Nstruct', 'PARa', 'Photosynthesis', 'Photosynthetic_efficiency', 'R_Nnit_red', 'R_phloem_loading', 'R_residual', 'Regul_S_Fructan', 'SLA', 'SLN', 'SLN_nonstruct', 'S_Amino_Acids', 'S_Fructan', 'S_Proteins', 'S_Starch', 'S_Sucrose', 'Surfacic_NS', 'Total_Organic_Nitrogen', 'Tr', 'Transpiration', 'Ts', 'amino_acids', 'axis', 'cytokinins', 'cytokinins_import', 'element', 'fructan', 'green_area', 'is_growing', 'length', 'metamer', 'mstruct', 'nb_replications', 'nitrates', 'organ', 'plant', 'proteins', 'senesced_mstruct', 'starch', 'sucrose', 'sum_dry_mass', 'sum_respi', 't', 'triosesP'}#: concatenation of ELEMENTS_T_INDEXES, ELEMENTS_RUN_VARIABLES and ELEMENTS_POSTPROCESSING_VARIABLES

openalea.cnwheat.postprocessing.ELEMENTS_T_INDEXES = ['t', 'plant', 'axis', 'metamer', 'organ', 'element']#: concatenation of T_INDEX and ELEMENTS_INDEXES

class openalea.cnwheat.postprocessing.Element[source]#

Bases: object

Post-processing to apply on Element outputs.

static calculate_C_g(triosesP, sucrose, starch, fructan, amino_acids, proteins, mstruct)[source]#

Mass of carbon metabolites

Parameters:

triosesP (float) – Amount of triose phosphates (µmol` C)
sucrose (float) – Amount of sucrose (µmol` C)
starch (float) – Amount of starch (µmol` C)
fructan (float) – Amount of fructan (µmol` C)
amino_acids (float) – Amount of amino acids (µmol` N)
proteins (float) – Amount of proteins (µmol` N)
mstruct (float) – strcural mass (g)

Returns:

Dry mass (g)

Return type:

static calculate_Conc_Amino_Acids(amino_acids, mstruct)[source]#

Amino_acid concentration.

Parameters:

amino_acids (float) – Amount of amino acids (µmol` N)
mstruct (float) – Structural mass

Returns:

Amino_acid concentration (µmol` amino acids g-1 mstruct)

Return type:

static calculate_Conc_Nitrates(nitrates, mstruct)[source]#

Nitrate concentration.

Parameters:

nitrates (float) – Amount of nitrates (µmol` N)
mstruct (float) – Structural mass

Returns:

Nitrate concentration (µmol` nitrates g-1 mstruct)

Return type:

static calculate_N_g(nitrates, amino_acids, proteins, Nstruct)[source]#

Mass of N metabolites

Parameters:

nitrates (float) – Amount of nitrates (µmol` N)
amino_acids (float) – Amount of amino acids (µmol` N)
proteins (float) – Amount of proteins (µmol` N)
Nstruct (float) – N structural mass(g)

Returns:

Dry mass (g)

Return type:

static calculate_SLA(dry_mass, green_area)[source]#

Specific Leaf Area (SLA, m2.kg-1)

Parameters:

dry_mass (float) – Dry mass (g)
green_area (float) – Green area (m-2)

Returns:

Specific Leaf Area (SLA, m2 kg-1)

Return type:

static calculate_SLN(nitrates, amino_acids, proteins, Nstruct, green_area)[source]#

Surfacic Leaf Nitrogen (SLN, g.m-2)

Parameters:

nitrates (float) – Amount of nitrates (µmol` N)
amino_acids (float) – Amount of amino_acids (µmol` N)
proteins (float) – Amount of proteins (µmol` N)
Nstruct (float) – Structural N (g)
green_area (float) – Green area (m-2)

Returns:

Surfacic Leaf Nitrogen (SLN, g.m-2)

Return type:

static calculate_SLN_nonstruct(nitrates, amino_acids, proteins, green_area)[source]#

Surfacic Leaf Nitrogen (SLN, g.m-2)

Parameters:

nitrates (float) – Amount of nitrates (µmol` N)
amino_acids (float) – Amount of amino_acids (µmol` N)
proteins (float) – Amount of proteins (µmol` N)
green_area (float) – Green area (m-2)

Returns:

Surfacic Leaf Nitrogen (SLN, g.m-2)

Return type:

static calculate_WSC_g(triosesP, sucrose, starch, fructan)[source]#

Mass of Water Soluble Carbohydrates

Parameters:

triosesP – Amount of triose phosphates (µmol` C)
sucrose (float) – Amount of sucrose (µmol` C)
starch (float) – Amount of sucrose (µmol` C)
fructan (float) – Amount of sucrose (µmol` C)

Returns:

Water Soluble Carbohydrates (g)

Return type:

static calculate_conc_cytokinins(cytokinins, mstruct)[source]#

Cytokinin concentration.

Parameters:

cytokinins (float) – Amount of cytokinins (AU)
mstruct (float) – Structural mass

Returns:

Cytokinin concentration (AU g-1 mstruct)

Return type:

static calculate_conc_fructan(fructan, mstruct)[source]#

Fructan concentration.

Parameters:

fructan (float) – Amount of fructan (µmol` C)
mstruct (float) – Structural mass

Returns:

Fructan concentration (µmol` fructan g-1 mstruct, eq. glucose).

Return type:

static calculate_conc_proteins(proteins, mstruct)[source]#

Protein concentration.

Parameters:

proteins (float) – Amount of proteins (µmol` N)
mstruct (float) – Structural mass

Returns:

Protein concentration (g proteins g-1 mstruct)

Return type:

static calculate_conc_starch(starch, mstruct)[source]#

Starch concentration.

Parameters:

starch (float) – Amount of sucrose (µmol` C)
mstruct (float) – Structural mass

Returns:

Starch concentration (µmol` starch g-1 mstruct)

Return type:

static calculate_conc_sucrose(sucrose, mstruct)[source]#

Sucrose concentration.

Parameters:

sucrose (float) – Amount of sucrose (µmol` C)
mstruct (float) – Structural mass

Returns:

Sucrose concentration (µmol` sucrose g-1 mstruct)

Return type:

static calculate_conc_triosesP(triosesP, mstruct)[source]#

Triose Phosphates concentration.

Parameters:

triosesP (float) – Amount of triose phosphates (µmol` C)
mstruct (float) – Structural mass

Returns:

Triose phosphates concentration (µmol` triosesP g-1 mstruct)

Return type:

static calculate_dry_mass(triosesP, sucrose, starch, fructan, nitrates, amino_acids, proteins, mstruct)[source]#

Dry mass

Parameters:

triosesP – Amount of triose phosphates (µmol` C)
sucrose (float) – Amount of sucrose (µmol` C)
starch (float) – Amount of sucrose (µmol` C)
fructan (float) – Amount of sucrose (µmol` C)
nitrates (float) – Amount of nitrates (µmol` N)
amino_acids (float) – Amount of sucrose (µmol` N)
proteins (float) – Amount of sucrose (µmol` N)
mstruct (float) – strcural mass (g)

Returns:

Dry mass (g)

Return type:

static calculate_fructan_g(fructan)[source]#

Mass of fructans

Parameters:: fructan (float) – Amount of fructans (µmol` C)
Returns:: Dry mass (g)
Return type:: float

static calculate_ratio_non_structural(dry_mass, mstruct)[source]#

Surfacic content of nitrogen

Parameters:

dry_mass (float) – Dry mass (g)
mstruct (float) – Structural mass (g)

Returns:

Surfacic non structural mass (g m-2)

Return type:

static calculate_surfacic_non_structural(dry_mass, mstruct, green_area)[source]#

Surfacic content of non structural mass

Parameters:

dry_mass (float) – Dry mass (g)
mstruct (float) – Structural mass (g)
green_area (float) – Green area (m-2)

Returns:

Surfacic non structural mass (g m-2)

Return type:

class openalea.cnwheat.postprocessing.Grains[source]#

Bases: object

Post-processing to apply on Grains outputs.

static calculate_WSC_g(sucrose, starch)[source]#

Mass of Water Soluble Carbohydrates

Parameters:

sucrose (float) – Amount of sucrose (µmol` C)
starch (float) – Amount of sucrose (µmol` C)

Returns:

Water Soluble Carbohydrates (g)

Return type:

static calculate_dry_mass(structure, starch, proteins)[source]#

Grain total dry mass.

Parameters:

structure (float) – Grain structural C mass (µmol` C)
starch (float) – Grain starch content (µmol` C)
proteins (float) – Grain protein content (µmol` N)

Returns:

Grain total dry mass (g)

Return type:

static calculate_protein_N_mass(proteins)[source]#

Grain total protein mass.

Parameters:: proteins (float) – Grain protein content (µmol` N)
Returns:: Grain total protein mass (g)
Return type:: float

openalea.cnwheat.postprocessing.HIDDENZONE_INDEXES = ['plant', 'axis', 'metamer']#: the indexes to locate the hidden zones in the modeled system

openalea.cnwheat.postprocessing.HIDDENZONE_POSTPROCESSING_VARIABLES = ['Conc_Amino_Acids', 'Conc_Fructan', 'Conc_Proteins', 'Conc_Sucrose', 'RER', 'nb_replications', 'Cont_Fructan_DM', 'Cont_Proteins_DM', 'sum_dry_mass', 'N_content', 'Cont_WSC_DM']#: hidden zones post-processing variables

openalea.cnwheat.postprocessing.HIDDENZONE_RUN_POSTPROCESSING_VARIABLES = {'AA_consumption_mstruct', 'Conc_Amino_Acids', 'Conc_Fructan', 'Conc_Proteins', 'Conc_Sucrose', 'Cont_Fructan_DM', 'Cont_Proteins_DM', 'Cont_WSC_DM', 'D_Fructan', 'D_Proteins', 'N_content', 'Nstruct', 'RER', 'Respi_growth', 'S_Fructan', 'S_Proteins', 'Unloading_Amino_Acids', 'Unloading_Sucrose', 'amino_acids', 'axis', 'delta_leaf_L', 'fructan', 'internode_L', 'leaf_L', 'leaf_is_emerged', 'leaf_pseudostem_length', 'metamer', 'mstruct', 'nb_replications', 'plant', 'proteins', 'ratio_DZ', 'sucrose', 'sucrose_consumption_mstruct', 'sum_dry_mass', 't'}#: concatenation of HIDDENZONE_T_INDEXES, HIDDENZONE_RUN_VARIABLES and HIDDENZONE_POSTPROCESSING_VARIABLES

openalea.cnwheat.postprocessing.HIDDENZONE_T_INDEXES = ['t', 'plant', 'axis', 'metamer']#: concatenation of T_INDEX and HIDDENZONE_INDEXES

class openalea.cnwheat.postprocessing.HiddenZone[source]#

Bases: object

Post-processing to apply on HiddenZone outputs.

static calculate_C_g(sucrose, starch, fructan, amino_acids, proteins, mstruct)[source]#

Mass of carbon metabolites

Parameters:

sucrose (float) – Amount of sucrose (µmol` C)
starch (float) – Amount of starch (µmol` C)
fructan (float) – Amount of fructan (µmol` C)
amino_acids (float) – Amount of amino acids (µmol` N)
proteins (float) – Amount of proteins (µmol` N)
mstruct (float) – strcural mass (g)

Returns:

Dry mass (g)

Return type:

static calculate_Conc_Amino_Acids(amino_acids, mstruct)[source]#

Amino acid concentration.

Parameters:

amino_acids (float) – N amino acids (µmol` N)
mstruct (float) – Structural mass

Returns:

Amino_acid concentration (µmol` amino acids g-1 mstruct)

Return type:

static calculate_N_g(amino_acids, proteins, Nstruct)[source]#

Mass of N metabolites

Parameters:

amino_acids (float) – Amount of amino acids (µmol` N)
proteins (float) – Amount of proteins (µmol` N)
Nstruct (float) – N structural mass(g)

Returns:

Dry mass (g)

Return type:

static calculate_RER(delta_leaf_L, leaf_L, delta_t)[source]#

Relative Extension Rate.

Parameters:

delta_leaf_L (float) – delta of leaf length between t and t-1 (m)
leaf_L (float) – leaf length (m)
delta_t (float) – delta_t (s)

Returns:

Relative Extension Rate (s-1)

Return type:

static calculate_WSC_g(sucrose, fructan)[source]#

Mass of Water Soluble Carbohydrates

Parameters:

sucrose (float) – Amount of sucrose (µmol` C)
fructan (float) – Amount of fructan (µmol` C)

Returns:

Water Soluble Carbohydrates (g)

Return type:

static calculate_conc_fructan(fructan, mstruct)[source]#

Fructan concentration.

Parameters:

fructan (float) – C fructan (µmol` C)
mstruct (float) – Structural mass

Returns:

Fructan concentration (µmol` fructan g-1 mstruct, eq. glucose).

Return type:

static calculate_conc_protein(proteins, mstruct)[source]#

Proteins concentration.

Parameters:

proteins (float) – N proteins (µmol` N)
mstruct (float) – Structural mass

Returns:

Protein concentration (g proteins g-1 mstruct)

Return type:

static calculate_conc_sucrose(sucrose, mstruct)[source]#

Sucrose concentration.

Parameters:

sucrose (float) – C sucrose (µmol` C)
mstruct (float) – Structural mass

Returns:

Sucrose concentration (µmol` sucrose g-1 mstruct)

Return type:

static calculate_dry_mass(sucrose, starch, fructan, amino_acids, proteins, mstruct)[source]#

Dry mass

Parameters:

sucrose (float) – Amount of sucrose (µmol` C)
starch (float) – Amount of starch (µmol` C)
fructan (float) – Amount of fructan (µmol` C)
amino_acids (float) – Amount of amino acids (µmol` N)
proteins (float) – Amount of proteins (µmol` N)
mstruct (float) – strcural mass (g)

Returns:

Dry mass (g)

Return type:

static calculate_fructan_g(fructan)[source]#

Mass of fructans

Parameters:: fructan (float) – Amount of fructans (µmol` C)
Returns:: Dry mass (g)
Return type:: float

static calculate_proteins_g(proteins)[source]#

Mass of proteins

Parameters:: proteins (float) – Amount of proteins (µmol` N)
Returns:: Dry mass (g)
Return type:: float

openalea.cnwheat.postprocessing.ORGANS_INDEXES = ['plant', 'axis', 'organ']#: the indexes to locate the organs in the modeled system

openalea.cnwheat.postprocessing.ORGANS_POSTPROCESSING_VARIABLES = ['Conc_Amino_Acids', 'Conc_Nitrates', 'Conc_Sucrose', 'Conc_cytokinins', 'Dry_Mass', 'Proteins_N_Mass', 'N_tot', 'WSC_g']#: organs post-processing variables

openalea.cnwheat.postprocessing.ORGANS_RUN_POSTPROCESSING_VARIABLES = {'AA_consumption_mstruct', 'C_exudation', 'Conc_Amino_Acids', 'Conc_Nitrates', 'Conc_Sucrose', 'Conc_cytokinins', 'Dry_Mass', 'Export_Amino_Acids', 'Export_Nitrates', 'Export_cytokinins', 'HATS_LATS', 'N_exudation', 'N_tot', 'Nstruct', 'Proteins_N_Mass', 'RGR_Structure', 'R_Nnit_red', 'R_Nnit_upt', 'R_grain_growth_starch', 'R_grain_growth_struct', 'R_residual', 'Respi_growth', 'S_Amino_Acids', 'S_Proteins', 'S_cytokinins', 'S_grain_starch', 'S_grain_structure', 'Total_Organic_Nitrogen', 'Unloading_Amino_Acids', 'Unloading_Sucrose', 'Uptake_Nitrates', 'WSC_g', 'age_from_flowering', 'amino_acids', 'axis', 'cytokinins', 'mstruct', 'nitrates', 'organ', 'plant', 'proteins', 'regul_transpiration', 'senesced_mstruct', 'starch', 'structure', 'sucrose', 'sucrose_consumption_mstruct', 'sum_respi', 'synthetized_mstruct', 't'}#: concatenation of ORGANS_T_INDEXES, ORGANS_RUN_VARIABLES and ORGANS_POSTPROCESSING_VARIABLES

openalea.cnwheat.postprocessing.ORGANS_T_INDEXES = ['t', 'plant', 'axis', 'organ']#: concatenation of T_INDEX and ORGANS_INDEXES

openalea.cnwheat.postprocessing.PHYTOMERS_INDEXES = ['plant', 'axis', 'metamer']#: the indexes to locate the phytomers in the modeled system

openalea.cnwheat.postprocessing.PHYTOMERS_POSTPROCESSING_VARIABLES = []#: phytomers post-processing variables

openalea.cnwheat.postprocessing.PHYTOMERS_RUN_POSTPROCESSING_VARIABLES = {'axis', 'metamer', 'mstruct', 'plant', 't'}#: concatenation of PHYTOMERS_T_INDEXES, PHYTOMERS_RUN_VARIABLES and PHYTOMERS_POSTPROCESSING_VARIABLES

openalea.cnwheat.postprocessing.PHYTOMERS_T_INDEXES = ['t', 'plant', 'axis', 'metamer']#: concatenation of T_INDEX and PHYTOMERS_INDEXES

openalea.cnwheat.postprocessing.PLANTS_INDEXES = ['plant']#: the index to locate the plants in the modeled system

openalea.cnwheat.postprocessing.PLANTS_POSTPROCESSING_VARIABLES = []#: plants post-processing variables

openalea.cnwheat.postprocessing.PLANTS_RUN_POSTPROCESSING_VARIABLES = {'Tair', 'plant', 't'}#: concatenation of PLANTS_T_INDEXES, PLANTS_RUN_VARIABLES and PLANTS_POSTPROCESSING_VARIABLES

openalea.cnwheat.postprocessing.PLANTS_T_INDEXES = ['t', 'plant']#: concatenation of T_INDEX and PLANTS_INDEXES

class openalea.cnwheat.postprocessing.Phloem[source]#

Bases: object

Post-processing to apply on Phloem outputs.

static calculate_WSC_g(sucrose)[source]#

Mass of Water Soluble Carbohydrates

Parameters:: sucrose (float) – Amount of sucrose (µmol` C)
Returns:: Water Soluble Carbohydrates (g)
Return type:: float

static calculate_conc_amino_acids(amino_acids, mstruct_axis)[source]#

Amino_acids concentration. Related to the structural dry mass of the culm.

Parameters:

amino_acids (float) – Amount of amino_acids in phloem (µmol` N)
mstruct_axis (float) – The structural dry mass of the axis (g)

Returns:

Amino_acids concentration (µmol` amino_acids g-1 mstruct)

Return type:

static calculate_conc_sucrose(sucrose, mstruct_axis)[source]#

Sucrose concentration. Related to the structural dry mass of the culm

Parameters:

sucrose (float) – Amount of sucrose in phloem (µmol` C)
mstruct_axis (float) – The structural dry mass of the axis (g)

Returns:

Sucrose concentration (µmol` sucrose g-1 mstruct)

Return type:

class openalea.cnwheat.postprocessing.Roots[source]#

Bases: object

Post-processing to apply on Roots outputs.

static calculate_Conc_Amino_Acids(amino_acids, mstruct)[source]#

Amino_acid concentration.

Parameters:

amino_acids (float) – Amount of amino acids (µmol` N)
mstruct (float) – Structural mass (g)

Returns:

Amino_acid concentration (µmol` amino_acids g-1 mstruct)

Return type:

static calculate_Conc_Nitrates(nitrates, mstruct)[source]#

Nitrate concentration.

Parameters:

nitrates (float) – Amount of nitrates (µmol` N)
mstruct (float) – Structural mass (g)

Returns:

Nitrate concentration (µmol` nitrates g-1 mstruct)

Return type:

static calculate_WSC_g(sucrose)[source]#

Mass of Water Soluble Carbohydrates

Parameters:: sucrose (float) – Amount of sucrose (µmol` C)
Returns:: Water Soluble Carbohydrates (g)
Return type:: float

static calculate_conc_cytokinins(cytokinins, mstruct)[source]#

Cytokinin concentration.

Parameters:

cytokinins (float) – Amount of cytokinins (AU)
mstruct (float) – Structural mass (g)

Returns:

cytokinins concentration (AU cytokinins g-1 mstruct)

Return type:

static calculate_conc_sucrose(sucrose, mstruct)[source]#

Sucrose concentration.

Parameters:

sucrose (float) – Amount of sucrose (µmol` C)
mstruct (float) – Structural mass (g)

Returns:

Sucrose concentration (µmol` sucrose g-1 mstruct)

Return type: