Reference guide #

phytomers#: the list of phytomers

plant_water_content#: plant water content (g H2O)

water_influx#: water influx in non growing organs (g H2O)

class openalea.cnwgrass.hydraulics.model.HiddenZone(label='hiddenzone', fructan=0, leaf_enclosed_mstruct=1.26e-07, leaf_pseudo_age=-1, hiddenzone_age=0, amino_acids=7.5e-05, proteins=0.0011, sucrose=0.000384, length_hz_En=None, lamina_Lmax=None, mstruct=1.26e-07, osmotic_water_potential=-0.8, water_potential=-0.11900250579120161, leaf_pseudostem_length=4e-05, leaf_L=5e-05, thickness=0.0005, width=0.003, turgor_water_potential=0.6809974942087984, water_content=7.500000000000001e-05, water_influx=0, water_outflow=0, cohorts=None, cohorts_replications=None, leaf_Wmax=None, leaf_is_growing=True, index=None)[source]#

Bases: Organ

The class HiddenZone.

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

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

amino_acids#: \(:math:\)\mu mol N``

calculate_aggregated_variables()[source]#

Returns:

static calculate_delta_organ_dimensions_elastic(delta_turgor_water_potential, organ_dimensions)[source]#

Reversible delta of organ dimensions according to turgor water potential, dimensions and extensibility. Hidden zone geometry is supposed to be a rectangular prism.

Parameters:

delta_turgor_water_potential (float) – delta of turgor water potential integrated over delta t (MPa)
organ_dimensions (dict) – dict of organ dimensions at time t. Keys = [length’, ‘width’, ‘thickness’] (m)

Returns:

Delta of organ specific-dimensions (m). Keys = [‘leaf_L’’, ‘width’, ‘thickness’]

Return type:

static calculate_delta_organ_dimensions_plastic(turgor_water_potential, phi, organ_dimensions)[source]#

Irreversible delta of organ dimensions according to turgor water potential, dimensions and plasticity. Hidden zone geometry is supposed to be a rectangular prism.

Parameters:

turgor_water_potential (float) – MPa
phi (dict) – dict of cell wall extensibility (MPa). Keys = [‘x’, ‘y’, ‘z]
organ_dimensions (dict) – dict of organ dimensions at time t. Keys = [length’, ‘width’, ‘thickness’] (m)

Returns:

Delta of organ specific-dimensions (m). Keys = [‘Leaf_L’’, ‘width’, ‘thickness’]

Return type:

static calculate_delta_turgor_water_potential(phi, turgor_water_potential, organ_volume, delta_water_content)[source]#

Delta of turgor water potential of hidden zone.

Parameters:

phi (dict [str, float]) – float phi: dict of cell wall extensibility (MPa). Keys = [‘x’, ‘y’, ‘z]
turgor_water_potential (float) – MPa
organ_volume (float) – m3
delta_water_content (float) – delta water content integrated over delta t (g)

Returns:

Delta of turgor water potential (MPa)

Return type:

static calculate_delta_water_content(water_influx, water_outflow)[source]#

delta of water flow for the hidden zone.

Parameters:

water_influx (float) – Water influx integrated over delta_t (g H2O)
water_outflow (float) – Water loss through the emerged lamina or sheath if any (g H2O)

Returns:

Delta of water flow into the organ (g)

Return type:

static calculate_extensibility_temperature(age, delta_teq, delta_t)[source]#

Hidden zone extensibility in each dimension in relation to non-reversible dimensional changes. From Coussement et al. (2018) With temperature effect on leaf_pseudo_age and on maximum extensibility.

Parameters:

age (float) – hidden zone age (°Cd)
delta_teq (float) – temperature-compensated time (s)
delta_t (float) – time step of the simulation (s)

Returns:

Extensibility z, y and x (MPa-1): {‘z’: float, ‘y’: float, ‘x’: float}

Return type:

static calculate_hiddenzone_length(leaf_L, leaf_pseudostem_length)[source]#

Length of the hidden zone

Parameters:

leaf_L (float) – Total leaf length (m)
leaf_pseudostem_length (float) – Length of the pseudostem (m)

Returns:

Length of the hidden zone (m)

Return type:

static calculate_initial_volume(mstruct)[source]#

Hidden zone initial volume calculated from mstruct. This calculation is only performed at t = previous leaf emergence

Parameters:

mstruct (float) –

Returns:

volume (m3), water content (g)

Return type:

(float, float)

static calculate_organ_volume(hiddenzone_dimensions)[source]#

HiddenZone volume, assumed to be equal to a box dimensions.

Parameters:: hiddenzone_dimensions (dict) – dict of hidden zone dimensions at time t. Keys = [‘length’, ‘thickness’, ‘width’] (m)
Returns:: volume (m3)
Return type:: float

static calculate_osmotic_water_potential(fructan, sucrose, amino_acids, volume, temperature)[source]#

Osmotic water potential of the organ calculated according to metabolites

Parameters:

fructan (float) – µmol C under the form of fructan
sucrose (float) – µmol C under the form of sucrose
amino_acids (float) – µmol N under the form of amino acids
volume (float) – (g H2O)
temperature (float) – hidden zone temperature, approximated by SAM temperature (°C)

Returns:

Osmotic water potential (MPa)

Return type:

static calculate_resistance(hiddenzone_dimensions)[source]#

Resistance of water flow between the hiddenzone and the xylem. Relations were set proportional to the length and inversely proportional to the area of organ’s cross-section. From Coussement et al. (2018)

Parameters:: hiddenzone_dimensions (dict) – dict of hidden zone dimensions at time t. Keys = [‘length’, ‘thickness’, ‘width’] (m)
Returns:: resistance (MPa s g-1)
Return type:: float

static calculate_time_equivalent_Tref(temperature_hz, time)[source]#

Return the time equivalent to a reference temperature i.e. temperature-compensated time (Parent, 2010).

Parameters:

temperature_hz (float) – hiddenzone temperature, approximated by SAM temperature (degree Celsius)
time (float) – time duration (s)

Returns:

temperature-compensated time (s)

Return type:

static calculate_volume(water_content)[source]#

Hidden zone volume, assumed to be proportional to water content.

Parameters:: water_content (float) – g H2O
Returns:: volume (m3)
Return type:: float

static calculate_water_flux(organ_water_potential, xylem_water_potential, resistance, delta_t)[source]#

Water flow into the organ according to water potential gradient with the xylem.

Parameters:

organ_water_potential (float) – water potential of the current organ (MPa)
xylem_water_potential (float) – water potential of the xylem (MPa)
resistance (float) – transport resistance between organ and xylem (MPa s g-1)
delta_t (float) – time step of the simulation (s)

Returns:

Water influx into the current organ integrated over delta_t (g)

Return type:

static calculate_water_potential(turgor_water_potential, osmotic_water_potential)[source]#

Total water potential of the organ

Parameters:

turgor_water_potential (float) – MPa
osmotic_water_potential (float) – MPa

Returns:

Total water potential (MPa)

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

extensibility#: MPa-1

fructan#: \(:math:\)\mu mol C``

hiddenzone_age#: °Cd

initial_volume#: m3

lamina_Lmax#: m

leaf_L#: m

leaf_Lmax#: m

leaf_Wmax#: m

leaf_enclosed_mstruct#: g

leaf_is_growing#

leaf_pseudo_age#: °Cd

leaf_pseudostem_length#: m

length#: m

length_hz_En#: m

mstruct#: g

property nb_replications#

osmotic_water_potential#: MPa

proteins#: \(:math:\)\mu mol N``

resistance#: resistance of water flux between two organs (MPa s g-1)

sucrose#: \(:math:\)\mu mol C``

thickness#: m

turgor_water_potential#: MPa

water_content#: g H2O

water_influx#: current flow of water from xylem to hiddenzone integrated over delta t (g H2O)

water_outflow#: current flow of water from hiddenzone to emerged lamina if any integrated over delta t (g H2O)

water_potential#: MPa

width#: m

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

Bases: PhotosyntheticOrgan

The class Internode.

class openalea.cnwgrass.hydraulics.model.InternodeElement(label=None, is_growing=None, temperature=0, age=None, green_area=0.0001, mstruct=0, Ts=12, Tr=0, sucrose=0, amino_acids=0, proteins=0, fructan=0, osmotic_water_potential=-0.8, water_potential=-0.11900250579120161, turgor_water_potential=0.6809974942087984, water_influx=0, Wmax=None, length=4e-05, thickness=0.0005, width=0.003, water_content=6.0000000000000015e-05, cohorts=None, cohorts_replications=None, index=None)[source]#

Bases: PhotosyntheticOrganElement

The class InternodeElement.

INIT_COMPARTMENTS = <openalea.cnwgrass.hydraulics.parameters.InternodeElementInitCompartments object>#: the initial values of compartments and state parameters

PARAMETERS = <openalea.cnwgrass.hydraulics.parameters.InternodeElementParameters object>#: the internal parameters of the internode

class openalea.cnwgrass.hydraulics.model.Lamina(label='lamina', exposed_element=None, enclosed_element=None)[source]#

Bases: PhotosyntheticOrgan

The class Lamina.

class openalea.cnwgrass.hydraulics.model.LaminaElement(label=None, is_growing=None, temperature=0, age=None, green_area=0.0001, mstruct=0, Ts=12, Tr=0, sucrose=0, amino_acids=0, proteins=0, fructan=0, osmotic_water_potential=-0.8, water_potential=-0.11900250579120161, turgor_water_potential=0.6809974942087984, water_influx=0, Wmax=None, length=4e-05, thickness=0.0005, width=0.003, water_content=6.0000000000000015e-05, cohorts=None, cohorts_replications=None, index=None)[source]#

Bases: PhotosyntheticOrganElement

The class LaminaElement.

INIT_COMPARTMENTS = <openalea.cnwgrass.hydraulics.parameters.LaminaElementInitCompartments object>#: the initial values of compartments and state parameters

PARAMETERS = <openalea.cnwgrass.hydraulics.parameters.LaminaElementParameters object>#: the internal parameters of the lamina

class openalea.cnwgrass.hydraulics.model.Organ(label)[source]#

Bases: object

The class Organ.

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

PARAMETERS = <openalea.cnwgrass.hydraulics.parameters.OrganParameters object>#: the internal parameters of the organ

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

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

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

Bases: Organ

The class PhotosyntheticOrgan defines the water flow in a photosynthetic organ.

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

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

Total_Transpiration_turgor#: g H2O

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

green_area#: m2

water_content#: g H2O

water_influx#: g H2O

class openalea.cnwgrass.hydraulics.model.PhotosyntheticOrganElement(label=None, is_growing=None, temperature=0, age=None, green_area=0.0001, mstruct=0, Ts=12, Tr=0, sucrose=0, amino_acids=0, proteins=0, fructan=0, osmotic_water_potential=-0.8, water_potential=-0.11900250579120161, turgor_water_potential=0.6809974942087984, water_influx=0, Wmax=None, length=4e-05, thickness=0.0005, width=0.003, water_content=6.0000000000000015e-05, cohorts=None, cohorts_replications=None, index=None)[source]#

Bases: object

The class PhotosyntheticOrganElement defines the water flow 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).

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

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

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

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

Total_Transpiration_turgor#: (g H2O)

Tr#: mmol H20 m-2 s-1

Ts#: °C

Wmax#: m

age#: °Cd

amino_acids#: \(:math:\)\mu mol N``

static calculate_Total_Transpiration(Tr, green_area, delta_t)[source]#

Total organ transpiration

Parameters:

Tr (float) – Transpiration rate (mmol H2O m-2 s-1)
green_area (float) – Green area (m2)
delta_t (float) – time step of the simulation (s)

Returns:

Total transpiration (g H2O)

Return type:

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

static calculate_delta_organ_dimensions(delta_turgor_water_potential, organ_dimensions)[source]#

Delta of lamina dimensions according to turgor water potential, dimensions, and elasticity.

Parameters:

delta_turgor_water_potential (float) – delta of turgor water potential integrated over delta t (MPa)
organ_dimensions (dict) – dict of organ dimensions at time t. Keys = [‘length’, ‘thickness’, ‘width’] (m)

Returns:

Delta of organ specific-dimensions (m). Keys = [‘length’, ‘width’, ‘thickness’]

Return type:

static calculate_delta_turgor_water_potential(volume, delta_water_content)[source]#

Delta of turgor water potential according to organ volume and elasticity. Extensibility (phi) is supposed to be 0 as this tissue is mature (growth completed).

Parameters:

volume (float) – organ volume at time t (m3).
delta_water_content (float) – delta water content integrated over delta t (g)

Returns:

Delta of turgor water potential (MPa)

Return type:

static calculate_delta_water_content(water_influx, Total_Transpiration_turgor)[source]#

Delta of water flow for the lamina.

Parameters:

water_influx (float) – Water influx from xylem integrated over delta_t (g)
Total_Transpiration_turgor (float) – Element transpiration (g H2O)

Returns:

Delta of water flow into the organ (g H2O)

Return type:

static calculate_organ_volume(organ_dimensions)[source]#

Photosynthetic element volume, assumed to be equal to a box dimensions. :param dict organ_dimensions: dict of organ dimensions at time t. Keys = [‘length’, ‘thickness’, ‘width’] (m)

Returns:: volume (m3)
Return type:: float

static calculate_osmotic_water_potential(sucrose, amino_acids, volume, temperature, fructan)[source]#

Osmotic water potential of the hiddenzone calculated according to metabolites

Parameters:

sucrose (float) – µmol C under the form of sucrose
amino_acids (float) – µmol N under the form of amino acids
volume (float) – (m3)
temperature (float) – air temperature (°C)
fructan (float) – µmol C under the form of fructan

Returns:

Osmotic water potential (MPa)

Return type:

static calculate_resistance(organ_dimensions)[source]#

Resistance of water flow between the lamina and xylem Relations were set proportional to the length and inversely proportional to the area of organ’s cross section. :param dict organ_dimensions: dict of organ dimensions at time t. Keys = [‘length’, ‘thickness’, ‘width’] (m)

Returns:: resistance (MPa s g-1)
Return type:: float

static calculate_total_water_influx(water_influx)[source]#

Water influx from xylem to organ

Parameters:: water_influx (float) – Water influx (g H2O)
Returns:: Total water influx (g H2O)

static calculate_volume(water_content)[source]#

Photosynthetic element volume, assumed to be proportional to water content.

Parameters:: water_content (float) – (g H2O)
Returns:: volume (m3)
Return type:: float

static calculate_water_flux(water_potential, xylem_water_potential, resistance, delta_t)[source]#

Water flow into the organ according to water potential gradient with the xylem.

Parameters:

water_potential (float) – water potential of the current organ (MPa)
xylem_water_potential (float) – water potential of the xylem (MPa)
resistance (float) – transport resistance between organ and xylem (MPa s g-1)
delta_t (float) – time step of the simulation (s)

Returns:

Water influx into the current organ integrated over delta_t (g H2O)

Return type:

static calculate_water_potential(turgor_water_potential, osmotic_water_potential)[source]#

Total water potential of the organ

Parameters:

turgor_water_potential (float) – MPa
osmotic_water_potential (float) – MPa

Returns:

Total water potential (MPa)

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

delta_t#: the delta t of the simulation (in seconds)

fructan#: \(:math:\)\mu mol C``

green_area#: m2

is_growing#

label#: the label of the element

length#: m

mstruct#: g

property nb_replications#

osmotic_water_potential#: MPa

proteins#: \(:math:\)\mu mol N``

resistance#: resistance of water flux between two organs (MPa s g-1)

sucrose#: \(:math:\)\mu mol C``

temperature#: °C

thickness#: m

turgor_water_potential#: MPa

water_content#: g H2O

water_influx#: current flow of water from xylem to organ integrated over delta t (g H2O)

water_potential#: MPa

width#: m

class openalea.cnwgrass.hydraulics.model.Phytomer(index=None, lamina=None, internode=None, sheath=None, hiddenzone=None, cohorts=None, cohorts_replications=None)[source]#

Bases: object

The class Phytomer.

A phytomer must have at least:

1 photosynthetic organ: lamina, internode,
or sheath.

or 1 hiddenzone.

Growth#: g H20

INIT_COMPARTMENTS = <openalea.cnwgrass.hydraulics.parameters.PhytomerInitCompartments object>#: the initial values of compartments and state parameters

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

Total_Transpiration_turgor#: g H20

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

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

property nb_replications#

sheath#: the sheath

total_water_influx#: g H20

water_content#: g H2O

water_influx#: g H20

class openalea.cnwgrass.hydraulics.model.Plant(index=None, axes=None)[source]#

Bases: object

The class Plant defines the water flow at plant scale.

A plant must have at least one axis.

PARAMETERS = <openalea.cnwgrass.hydraulics.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.

cohorts#

TEMPORARY

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

class openalea.cnwgrass.hydraulics.model.Population(plants=None)[source]#

Bases: object

The class Population.

A population must have at least one plant.

PARAMETERS = <openalea.cnwgrass.hydraulics.parameters.PopulationParameters object>#: the internal parameters of the population

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

class openalea.cnwgrass.hydraulics.model.Roots(label='roots')[source]#

Bases: Organ

The class Roots.

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

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

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

Bases: PhotosyntheticOrgan

The class Sheath.

class openalea.cnwgrass.hydraulics.model.SheathElement(label=None, is_growing=None, temperature=0, age=None, green_area=0.0001, mstruct=0, Ts=12, Tr=0, sucrose=0, amino_acids=0, proteins=0, fructan=0, osmotic_water_potential=-0.8, water_potential=-0.11900250579120161, turgor_water_potential=0.6809974942087984, water_influx=0, Wmax=None, length=4e-05, thickness=0.0005, width=0.003, water_content=6.0000000000000015e-05, cohorts=None, cohorts_replications=None, index=None)[source]#

Bases: PhotosyntheticOrganElement

The class SheathElement.

INIT_COMPARTMENTS = <openalea.cnwgrass.hydraulics.parameters.SheathElementInitCompartments object>#: the initial values of compartments and state parameters

PARAMETERS = <openalea.cnwgrass.hydraulics.parameters.SheathElementParameters object>#: the internal parameters of the sheath

class openalea.cnwgrass.hydraulics.model.Soil(water_content, constant_water_content=True, hourly_rehydration=0)[source]#

Bases: object

The class Soil defines the soil water potential as function of the soil relative water content.

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

SRWC#: Soil Relative Water Content (%)

static calculate_SRWC(water_content)[source]#

Soil Relative Water Content

Parameters:

water_content (float) – soil water content (g)

Returns:

SRWC (dimensionless)

Return type:

calculate_water_content_derivative(soil_water_outputs, constant_water_content)[source]#

delta soil nitrates.

Parameters:

soil_water_outputs (float) – Sum of water used for plant transpiration of growth over delta_t (g)
constant_water_content (bool) – whether the water content is constant or not

Returns:

delta water_content (g)

Return type:

static calculate_water_potential(SRWC)[source]#

Total water potential of the xylem (Mpa) Equation from Chen et al. (2019), adapted for a deep loam-clay soil (leached soil on loessic silt), typical of Grignon (France).

Parameters:

SRWC (float) –

Returns:

Total water potential (MPa)

Return type:

water_content#: water content of the soil (g)

water_potential#: Water potential of the soil (MPa)

class openalea.cnwgrass.hydraulics.model.Xylem(label='xylem', water_potential=-0.11900250579120161)[source]#

Bases: Organ

The class Xylem defines the water exchanges in a xylem.

INIT_COMPARTMENTS = <openalea.cnwgrass.hydraulics.parameters.XylemInitCompartments object>#: the initial values of compartments and state parameters

PARAMETERS = <openalea.cnwgrass.hydraulics.parameters.XylemParameters object>#: the internal parameters of the xylem

static calculate_xylem_water_potential(soil_water_potential, total_water_influx, Growth, delta_t)[source]#

Total water potential of the xylem

Parameters:

soil_water_potential (float) – MPa
total_water_influx (float) – g H2O
Growth (float) – g H2O
delta_t (float) – time step of the simulation (s)

Returns:

Total water potential (MPa)

Return type:

delta_t#: the delta t of the simulation (in seconds)

water_potential#: MPa

`openalea.cnwgrass.hydraulics.parameters` module#

hydraulics.parameters #

The module hydraulics.parameters defines the parameters of the model.

openalea.cnwgrass.hydraulics.parameters.AMINO_ACIDS_N_RATIO = 1.17#: Mean number of mol of N in 1 mol of the major amino acids of plants (Glu, Gln, Ser, Asp, Ala, Gly)

openalea.cnwgrass.hydraulics.parameters.AXIS_INIT_COMPARTMENTS = <openalea.cnwgrass.hydraulics.parameters.AxisInitCompartments object>#: The instance of class hydraulics.parameters.PhytomerInitCompartments for current process

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

class openalea.cnwgrass.hydraulics.parameters.AxisInitCompartments[source]#

Bases: object

Initial values for compartments of axis.

SAM_temperature#: initial temperature of shoot apical meristem (°C)

class openalea.cnwgrass.hydraulics.parameters.AxisParameters[source]#

Bases: object

Internal parameters of axes.

openalea.cnwgrass.hydraulics.parameters.CELSIUS_2_KELVIN = 273.15#: conversion factor from degree Celsius to Kelvin

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

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

openalea.cnwgrass.hydraulics.parameters.HOUR_TO_SECOND_CONVERSION_FACTOR = 3600.0#: Number of seconds in 1 hour

class openalea.cnwgrass.hydraulics.parameters.HiddenZoneInitCompartments[source]#

Bases: object

Initial values for compartments of hidden zones.

SRWC#: %

Tr#: mmol H20 m-2 s-1

amino_acids#: \(:math:\)\mu mol N``

delta_teq#

time equivalent to a reference temperature i.e. temperature-compensated time (Parent, 2010)

Type:: s #

fructan#: \(:math:\)\mu mol C``

green_area#: m2

hiddenzone_age#: °Cd

lamina_Lmax#: m

leaf_L#: m

leaf_Wmax#: m

leaf_enclosed_mstruct#: g

leaf_is_growing#

leaf_pseudo_age#: °Cd

leaf_pseudostem_length#: m

length_hz_En#: m

mstruct#: g

osmotic_water_potential#: Mpa

proteins#: \(:math:\)\mu mol N``

sucrose#: \(:math:\)\mu mol C``

temperature#: °C

thickness#: m

turgor_water_potential#: MPa

water_influx#: g H2O

water_outflow#: g H2O

water_potential#: MPa

width#: m

class openalea.cnwgrass.hydraulics.parameters.HiddenZoneParameters[source]#

Internal parameters of hidden growing zones.

GAMMA#

0.3 Mpa for soybean.

Type:: Critical value for the pressure component which must be exceeded for irreversible volume changes (MPa). Found from Coussement et al., 2018

OFFSET_LEAF#: Offset used for the final fitting of the beta function (m)

OFFSET_MASS_VOLUME#: Offset of the relation between leaf dry mass and its volume at the time of the previous leaf emergence (m3). Found from Williams 1960, Fig 11.

RATIO_MSTRUCT_DM#: Ratio mstruct/dry matter (dimensionless). From growth model.

SLOPE_MASS_VOLUME#: Slope of the relation between leaf dry mass and its volume at the time of the previous leaf emergence (m3 g-1). Found from Williams 1960, Fig 11.

Sa#: (mol m-3) Parameter of a sigmoidal function of equivalent solutes concentration used in osmotic water potential

Sb#: (-) Parameter of a sigmoidal function of equivalent solutes concentration used in osmotic water potential

Sc#: (-) Parameter of a sigmoidal function of equivalent solutes concentration used in osmotic water potential

Sd#: (mol m-3) Parameter of a sigmoidal function of equivalent solutes concentration used in osmotic water potential

TL_ratio#

WL_ratio#

epsilon#

thickness, z: length.

Type:: Dimension-specific elasticity in relation to reversible dimensional changes (MPa). x
Type:: width, y

leaf_Lmax_MAX#: Maximum leaf_Lmax (m) (Gauthier et al., 2021)

leaf_Wmax_Marion#: m

phi_initial#: Initial dimension-specific cell wall extensibility in relation to non-reversible dimensional changes (MPa-1 s-1)

tbase#: beginning of leaf elongation in automate growth (s at 12°c); fitted from adapted data from Fournier 2005

tend#: end of leaf elongation in automate growth (s at 12°c); fitted from adapted data from Fournier 2005

tmax#: time at which leaf elongation rate is maximal in automate growth (s at 12°c); fitted from adapted data from Fournier 2005

openalea.cnwgrass.hydraulics.parameters.INTERNODE_ELEMENT_INIT_COMPARTMENTS = <openalea.cnwgrass.hydraulics.parameters.InternodeElementInitCompartments object>#: The instance of class hydraulics.parameters.InternodeElementInitCompartments for current process

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

class openalea.cnwgrass.hydraulics.parameters.InternodeElementInitCompartments[source]#

Bases: object

Initial values for compartments of internode elements.

thickness#: m

width#: m

class openalea.cnwgrass.hydraulics.parameters.InternodeElementParameters[source]#

Internal parameters of internodes.

epsilon#

thickness, z: length.

Type:: Dimension-specific elasticity in relation to reversible dimensional changes (MPa). x
Type:: width, y

openalea.cnwgrass.hydraulics.parameters.LAMINA_ELEMENT_INIT_COMPARTMENTS = <openalea.cnwgrass.hydraulics.parameters.LaminaElementInitCompartments object>#: The instance of class hydraulics.parameters.LaminaElementInitCompartments for current process

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

class openalea.cnwgrass.hydraulics.parameters.LaminaElementInitCompartments[source]#

Bases: object

Initial values for compartments of lamina elements.

thickness#: m

width#: m

class openalea.cnwgrass.hydraulics.parameters.LaminaElementParameters[source]#

Internal parameters of lamina.

epsilon#

thickness, z: length.

Type:: Dimension-specific elasticity in relation to reversible dimensional changes (MPa). x
Type:: width, y

openalea.cnwgrass.hydraulics.parameters.NB_C_SUCROSE = 12#: Number of C in 1 mol of sucrose

openalea.cnwgrass.hydraulics.parameters.OFFSET_MASS_VOLUME = 1.82312e-13#: Offset of the relation between leaf dry mass and its volume at the time of the previous leaf emergence (m3). Found from Williams 1960, Fig 11.

openalea.cnwgrass.hydraulics.parameters.ORGAN_PARAMETERS = <openalea.cnwgrass.hydraulics.parameters.OrganParameters object>#: The instance of class hydraulics.parameters.PhytomerParameters for current process

class openalea.cnwgrass.hydraulics.parameters.OrganParameters[source]#

Bases: object

Internal parameters of organs.

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

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

openalea.cnwgrass.hydraulics.parameters.PHYTOMER_INIT_COMPARTMENTS = <openalea.cnwgrass.hydraulics.parameters.PhytomerInitCompartments object>#: The instance of class hydraulics.parameters.PhytomerInitCompartments for current process

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

openalea.cnwgrass.hydraulics.parameters.PI = 3.141592653#: Pi (?)

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

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

class openalea.cnwgrass.hydraulics.parameters.PhotosyntheticOrganElementInitCompartments[source]#

Bases: object

Initial values for compartments of photosynthetic organ elements.

SRWC#: %

Tr#: mmol H20 m-2 s-1

Ts#: °C

Wmax#: °Cd

age#: °Cd

amino_acids#: \(:math:\)\mu mol N``

fructan#: \(:math:\)\mu mol C``

green_area#: initial value of green_area (m2)

is_growing#

length#: m init

mstruct#: g

osmotic_water_potential#: MPa

proteins#: \(:math:\)\mu mol N``

sucrose#: \(:math:\)\mu mol C``

temperature#: °C

thickness#: m init

turgor_water_potential#: MPa

water_influx#: g H2O

water_outflow#: g H2O

water_potential#: MPa

width#: m init

class openalea.cnwgrass.hydraulics.parameters.PhotosyntheticOrganElementParameters[source]#

Bases: object

Internal parameters of Photosynthetic Organ Element.

Sa#: (mol m-3) Parameter of a sigmoidal function of equivalent solutes concentration used in osmotic water potential

Sb#: (-) Parameter of a sigmoidal function of equivalent solutes concentration used in osmotic water potential

Sc#: (-) Parameter of a sigmoidal function of equivalent solutes concentration used in osmotic water potential

Sd#: (mol m-3) Parameter of a sigmoidal function of equivalent solutes concentration used in osmotic water potential

epsilon#

thickness, z: length.

Type:: Dimension-specific elasticity in relation to reversible dimensional changes (MPa). x
Type:: width, y

class openalea.cnwgrass.hydraulics.parameters.PhytomerInitCompartments[source]#

Bases: object

Initial values for compartments of hidden zones.

Tr#: mmol H20 m-2 s-1

green_area#: m2

class openalea.cnwgrass.hydraulics.parameters.PhytomerParameters[source]#

Bases: object

Internal parameters of phytomers.

class openalea.cnwgrass.hydraulics.parameters.PlantParameters[source]#

Bases: object

Internal parameters of plants.

class openalea.cnwgrass.hydraulics.parameters.PopulationParameters[source]#

Bases: object

Internal parameters of populations.

openalea.cnwgrass.hydraulics.parameters.R = 8.31#: Perfect gas constant (J mol-1 K-1)

openalea.cnwgrass.hydraulics.parameters.RATIO_MSTRUCT_DM = 0.8#: Ratio mstruct/dry matter (dimensionless). From growth model.

openalea.cnwgrass.hydraulics.parameters.RHO_WATER = 1000000.0#: Water density (g m-3)

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

openalea.cnwgrass.hydraulics.parameters.ROOTS_PARAMETERS = <openalea.cnwgrass.hydraulics.parameters.RootsParameters object>#: The instance of class cnmetabolism.parameters.XylemParameters for current process

class openalea.cnwgrass.hydraulics.parameters.RootsInitCompartments[source]#

Bases: object

Initial values for compartments of roots

class openalea.cnwgrass.hydraulics.parameters.RootsParameters[source]#

Bases: object

Internal parameters of roots.

openalea.cnwgrass.hydraulics.parameters.SHEATH_ELEMENT_INIT_COMPARTMENTS = <openalea.cnwgrass.hydraulics.parameters.SheathElementInitCompartments object>#: The instance of class hydraulics.parameters.SheathElementInitCompartments for current process

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

openalea.cnwgrass.hydraulics.parameters.SLOPE_MASS_VOLUME = 3.23337e-06#: Slope of the relation between leaf dry mass and its volume at the time of the previous leaf emergence (m3 g-1). Found from Williams 1960, Fig 11.

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

openalea.cnwgrass.hydraulics.parameters.SUCROSE_MOLAR_MASS = 342#: g mol-1

class openalea.cnwgrass.hydraulics.parameters.SheathElementInitCompartments[source]#

Bases: object

Initial values for compartments of sheath elements.

thickness#: m

width#: m

class openalea.cnwgrass.hydraulics.parameters.SheathElementParameters[source]#

Internal parameters of sheaths.

epsilon#

thickness, z: length.

Type:: Dimension-specific elasticity in relation to reversible dimensional changes (MPa). x
Type:: width, y

class openalea.cnwgrass.hydraulics.parameters.SoilParameters[source]#

Bases: object

Internal parameters of soil.

Soil_a#: Mpa - Parameter for soil water function (adapté pour sol limono-argileux profond, Grignon)

Soil_b#: % - Parameter for soil water function (adapté pour sol limono-argileux profond, Grignon)

openalea.cnwgrass.hydraulics.parameters.VANT_HOFF_AMINO_ACIDS = 1.25#: Van’t Hoff coefficient estimated for amino acids (dimensionless)

openalea.cnwgrass.hydraulics.parameters.VANT_HOFF_SUCROSE = 1#: Van’t Hoff coefficient of sucrose (dimensionless)

openalea.cnwgrass.hydraulics.parameters.VSTORAGE = 0.8#: Storage portion of the volume of the organ (-)

openalea.cnwgrass.hydraulics.parameters.WATER_MOLAR_MASS = 18#: g mol-1

openalea.cnwgrass.hydraulics.parameters.XYLEM_INIT_COMPARTMENTS = <openalea.cnwgrass.hydraulics.parameters.XylemInitCompartments object>#: The instance of class cnmetabolism.parameters.XylemInitCompartments for current process

openalea.cnwgrass.hydraulics.parameters.XYLEM_PARAMETERS = <openalea.cnwgrass.hydraulics.parameters.XylemParameters object>#: The instance of class cnmetabolism.parameters.XylemParameters for current process

class openalea.cnwgrass.hydraulics.parameters.XylemInitCompartments[source]#

Bases: object

Initial values for compartments of xylem.

SRWC#: %

soil_water_potential#: MPa

water_potential#: MPa

class openalea.cnwgrass.hydraulics.parameters.XylemParameters[source]#

Bases: object

Internal parameters of xylem.

R_soil#

1E-05

Type:: Flow resistance between soil and xylem (Mpa s g-1 m)

R_xylem_hz#

Type:: Flow resistance between xylem and shoot organs (Mpa s g-1 m)

R_xylem_organ#

0.25

Type:: Flow resistance between xylem and shoot organs (Mpa s g-1 m)

`openalea.cnwgrass.hydraulics.tools` module#

hydraulics.tools #

This module provides tools to help for the validation of the outputs:

set up of loggers,

openalea.cnwgrass.hydraulics.tools.OUTPUTS_INDEXES = ['t', 'plant', 'axis', 'metamer', 'organ', 'element']#: All the possible indexes of Turgor_Growth outputs

openalea.cnwgrass.hydraulics.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 hydraulics.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 old logs. False otherwise.

`openalea.cnwgrass.hydraulics.converter` module#

hydraulics.converter #

The module hydraulics.converter defines functions to convert dataframes to/from Hydraulics inputs or outputs format.

openalea.cnwgrass.hydraulics.converter.AXES_VARIABLES = ['plant', 'axis', 'SAM_temperature', 'Total_Transpiration_turgor', 'Growth', 'water_influx', 'plant_water_content']#: the columns of the outputs dataframe at AXIS scale

openalea.cnwgrass.hydraulics.converter.DATAFRAME_TO_hydraulics_ELEMENTS_NAMES_MAPPING = {'HiddenElement': 'enclosed_element', 'LeafElement1': 'exposed_element', 'StemElement': 'exposed_element'}#: the mapping of the name of each element, from Dataframe to Hydraulics

openalea.cnwgrass.hydraulics.converter.ELEMENTS_VARIABLES = ['plant', 'axis', 'metamer', 'organ', 'element', 'amino_acids', 'green_area', 'mstruct', 'proteins', 'sucrose', 'fructan', 'Ts', 'Tr', 'age', 'is_growing', 'Wmax', 'length', 'turgor_water_potential', 'water_content', 'width', 'thickness', 'osmotic_water_potential', 'resistance', 'water_potential', 'volume', 'epsilon_volume', 'organ_volume', 'WC_mstruct', 'water_influx', 'Total_Transpiration_turgor', 'total_water_influx']#: the columns of the outputs dataframe at ELEMENTS scale

openalea.cnwgrass.hydraulics.converter.HIDDENZONE_VARIABLES = ['plant', 'axis', 'metamer', 'leaf_pseudo_age', 'leaf_pseudostem_length', 'fructan', 'amino_acids', 'proteins', 'sucrose', 'mstruct', 'hiddenzone_age', 'leaf_enclosed_mstruct', 'leaf_Wmax', 'length_hz_En', 'lamina_Lmax', 'leaf_L', 'turgor_water_potential', 'water_content', 'width', 'thickness', 'osmotic_water_potential', 'resistance', 'water_potential', 'volume', 'length', 'phi_width', 'phi_thickness', 'phi_length', 'phi_volume', 'epsilon_volume', 'organ_volume', 'WC_mstruct', 'omega', 'leaf_Lmax', 'delta_hiddenzone_dimensions_plastic', 'delta_weq', 'delta_leaf_L', 'water_influx', 'water_outflow', 'Growth']#: the columns of the outputs dataframe at HIDDENZONE scale

openalea.cnwgrass.hydraulics.converter.ORGANS_VARIABLES = ['plant', 'axis', 'organ', 'age', 'amino_acids', 'proteins', 'sucrose', 'mstruct', 'Tr', 'green_area', 'SRWC', 'Tsoil', 'water_potential']#: the columns of the outputs dataframe at ORGANS scale

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

openalea.cnwgrass.hydraulics.converter.PLANTS_VARIABLES = ['plant']#: the columns of the outputs dataframe at PLANT scale

openalea.cnwgrass.hydraulics.converter.SOILS_VARIABLES = ['plant', 'axis', 'water_content', 'SRWC', 'water_potential']#: the columns of the outputs dataframe at SOIL scale

openalea.cnwgrass.hydraulics.converter.from_dataframes(axes_inputs=None, hiddenzones_inputs=None, elements_inputs=None, organs_inputs=None, soils_inputs=None)[source]#

If elements_inputs and hiddenzones_inputs are not None, converts elements_inputs and hiddenzones_inputs to a population.

Parameters:

hiddenzones_inputs (pandas.DataFrame) – Hidden zone inputs, with one line per hidden zone.
elements_inputs (pandas.DataFrame) – Element inputs, with one line per element.
organs_inputs (pandas.DataFrame) – Organs (xylem and roots) inputs, with one line per organ.
soils_inputs (pandas.DataFrame) – Soils inputs, with one line by soil.

Returns:

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

Return type:

(model.Population, dict)

openalea.cnwgrass.hydraulics.converter.hydraulics_CLASSES_TO_DATAFRAME_ORGANS_MAPPING = {<class 'openalea.cnwgrass.hydraulics.model.HiddenZone'>: 'hiddenzone', <class 'openalea.cnwgrass.hydraulics.model.Internode'>: 'internode', <class 'openalea.cnwgrass.hydraulics.model.Lamina'>: 'blade', <class 'openalea.cnwgrass.hydraulics.model.Organ'>: 'organs', <class 'openalea.cnwgrass.hydraulics.model.Roots'>: 'roots', <class 'openalea.cnwgrass.hydraulics.model.Sheath'>: 'sheath', <class 'openalea.cnwgrass.hydraulics.model.Xylem'>: 'xylem'}#: the mapping of the Hydraulics organs classes to organs names in MTG

openalea.cnwgrass.hydraulics.converter.to_dataframes(population=None, soils=None)[source]#

Convert a Hydraulics population to Pandas dataframes 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 Hydraulics 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:

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) * element scale: plant index, axis id, phytomer index, organs type, element type, state parameters, state variables, intermediate variables, fluxes and integrative variables of each element (see ELEMENTS_VARIABLES) * xylem scale: xylem index, state parameters, state variables, intermediate variables, fluxes and integrative variables of xylem (see XYLEM_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, pandas.DataFrame)

`openalea.cnwgrass.hydraulics.postprocessing` module#

hydraulics.postprocessing #

The module hydraulics.postprocessing defines post-processing to apply on Turgor-Wheat outputs, and provides a front-end to automatize the generation of graphs for validation of the outputs.

Please use front-ends postprocessing() and generate_graphs().

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

openalea.cnwgrass.hydraulics.postprocessing.AXES_POSTPROCESSING_VARIABLES = []#: axes post-processing variables

openalea.cnwgrass.hydraulics.postprocessing.AXES_RUN_POSTPROCESSING_VARIABLES = {'Growth', 'SAM_temperature', 'Total_Transpiration_turgor', 'axis', 'plant', 'plant_water_content', 't', 'water_influx'}#: concatenation of AXES_T_INDEXES, AXES_RUN_VARIABLES and AXES_POSTPROCESSING_VARIABLES

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

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

openalea.cnwgrass.hydraulics.postprocessing.ELEMENTS_POSTPROCESSING_VARIABLES = []#: elements post-processing variables

openalea.cnwgrass.hydraulics.postprocessing.ELEMENTS_RUN_POSTPROCESSING_VARIABLES = ['t', 'plant', 'axis', 'metamer', 'organ', 'element', 'amino_acids', 'green_area', 'mstruct', 'proteins', 'sucrose', 'fructan', 'Ts', 'Tr', 'age', 'is_growing', 'Wmax', 'length', 'turgor_water_potential', 'water_content', 'width', 'thickness', 'osmotic_water_potential', 'resistance', 'water_potential', 'volume', 'epsilon_volume', 'organ_volume', 'WC_mstruct', 'water_influx', 'Total_Transpiration_turgor', 'total_water_influx']#: concatenation of ELEMENTS_T_INDEXES, ELEMENTS_RUN_VARIABLES and ELEMENTS_POSTPROCESSING_VARIABLES

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

class openalea.cnwgrass.hydraulics.postprocessing.Element[source]#

Bases: object

Post-processing to apply on Element outputs.

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

openalea.cnwgrass.hydraulics.postprocessing.HIDDENZONE_POSTPROCESSING_VARIABLES = ['conc_solutes_vol', 'conc_solutes_mass', 'LER']#: hidden zones post-processing variables

openalea.cnwgrass.hydraulics.postprocessing.HIDDENZONE_RUN_POSTPROCESSING_VARIABLES = ['t', 'plant', 'axis', 'metamer', 'leaf_pseudo_age', 'leaf_pseudostem_length', 'fructan', 'amino_acids', 'proteins', 'sucrose', 'mstruct', 'hiddenzone_age', 'leaf_enclosed_mstruct', 'leaf_Wmax', 'length_hz_En', 'lamina_Lmax', 'leaf_L', 'turgor_water_potential', 'water_content', 'width', 'thickness', 'osmotic_water_potential', 'resistance', 'water_potential', 'volume', 'length', 'phi_width', 'phi_thickness', 'phi_length', 'phi_volume', 'epsilon_volume', 'organ_volume', 'WC_mstruct', 'omega', 'leaf_Lmax', 'delta_hiddenzone_dimensions_plastic', 'delta_weq', 'delta_leaf_L', 'water_influx', 'water_outflow', 'Growth', 'conc_solutes_vol', 'conc_solutes_mass', 'LER']#: concatenation of HIDDENZONE_T_INDEXES, HIDDENZONE_RUN_VARIABLES and HIDDENZONE_POSTPROCESSING_VARIABLES

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

class openalea.cnwgrass.hydraulics.postprocessing.HiddenZone[source]#

Bases: object

Post-processing to apply on HiddenZone outputs.

static calculate_LER(leaf_L, init_leaf_L, delta_t)[source]#

Calculates Leaf elongation rate in phase II

Parameters:

leaf_L (float) – Leaf length at time t (m)
init_leaf_L (float) – Leaf length at time t-1 (m)
delta_t (float) – Delta time (h)

Returns:

Leaf elongation rate (mm h-1)

Return type:

static calculate_conc_solutes_mass(fructan, sucrose, amino_acids, mstruct)[source]#

Massic concentration of solutes used for osmotic water potential calculation

Parameters:

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

Returns:

Solutes massic concentration (mol m-3)

Return type:

static calculate_conc_solutes_vol(sucrose, fructan, amino_acids, volume)[source]#

Volumic concentration of solutes used for osmotic water potential calculation

Parameters:

sucrose (float) – Amount of sucrose (µmol` C)
amino_acids (float) – Amount of amino acids (µmol` N)
fructan (float) – Amount of fructan (µmol` C)
volume (float) – Volume (m3)

Returns:

Solutes volumic concentration (mol m-3)

Return type: