Plant utils functions

AUTHORS: Julien Ruffault (julien.ruff@gmail.com), Nicolas Martin-StPaul (nicolas.martin@inrae.fr)

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rs_comp

 rs_comp (pi_ft:float, e_symp:float, p_min:float)

Compute Rs from pmin (resolution from Bartlet et al 2012 EcolLett and email Herve Cochard 19/06/2015)

	Type	Details
pi_ft	float	Osmotic potential at full turgor (MPa)
e_symp	float	Modulus of elastoicoty of the Symplasm (MPa/%)
p_min	float	Unknown parameter definition
Returns	float

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turgor_comp

 turgor_comp (pi_ft:float, e_symp:float, r_stemp:float)

Turgor pressure

	Type	Details
pi_ft	float	Osmotic potential at full turgor (MPa)
e_symp	float	Modulus of elastoicoty of the Symplasm (MPa/%)
r_stemp	float	Unknown parameter definition
Returns	float

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compute_turgor_from_psi

 compute_turgor_from_psi (pi_ft:float, e_symp:float, psi:List)

Computes Turgor pressure from Pressure-Volume curves parameters and water potential

	Type	Details
pi_ft	float	Osmotic potential at full turgor (MPa)
e_symp	float	Modulus of elastoicoty of the Symplasm (MPa/%)
psi	typing.List	List of Water potential of the organ (MPa)
Returns	array

Example: Compute turgor

compute_turgor_from_psi(pi_ft=2, e_symp=3, psi=[1, 2, 3])

array([0., 0., 0.])

Error: Function only return zeros

for each_psi in range(1, 10):
    print(compute_turgor_from_psi(pi_ft=2, e_symp=3, psi=[each_psi]))

[0.]
[0.]
[0.]
[0.]
[0.]
[0.]
[0.]
[0.]
[0.]

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osmo_comp

 osmo_comp (pi_ft:float, r_stemp:float)

Compute osmotic potential

	Type	Details
pi_ft	float	Osmotic potential at full turgor (MPa)
r_stemp	float	Unknown parameter definition
Returns	float

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psi_total_symp_comp

 psi_total_symp_comp (pi_ft:float, e_symp:float, r_stemp:float)

Compute Total potential

	Type	Details
pi_ft	float	Osmotic potential at full turgor (MPa)
e_symp	float	Modulus of elastoicoty of the Symplasm (MPa/%)
r_stemp	float	Unknown parameter definition
Returns	float

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stomatal_regulation_turgor

 stomatal_regulation_turgor (turgor_pressure:float,
                             max_turgor_pressure:float, e_max:float,
                             e_cuti:float)

This function computes stomatal regulation if stomatal closure is limited (linearly) by turgor pressure

	Type	Details
turgor_pressure	float	Turgor pressure
max_turgor_pressure	float	Maximum turgor pressure,
e_max	float	Unknown parameter definition
e_cuti	float	Residual Transpiration
Returns	array

Example: Compute Stomatal Regulation

stomatal_regulation_turgor(
    turgor_pressure=1, max_turgor_pressure=2, e_max=3, e_cuti=4
)

array([1.5, 3. ])

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plc_comp

 plc_comp (p_min:float, slope:float, p50:float)

Compute Percentage loss of conductivity

	Type	Details
p_min	float	Unknown parameter definition
slope	float	Unknown parameter definition
p50	float	Unknown parameter definition
Returns	float

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plc_prime_comp

 plc_prime_comp (plc:float, slope:float)

This function computes PLC Prime from PLC current value

	Type	Details
plc	float	Computed using the plc_comp function
slope	float	Unknown parameter definition
Returns	float

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gs_curve

 gs_curve (x:float, slope_gs:float, p50_gs:float, psi_start_closing:float,
           psi_close:float, pi_ft:float, e_symp:float,
           turgor_pressure_at_gs_max:float, gs_max:float,
           transpiration_model:str=['jarvis', 'granier'],
           stomatal_reg_formulation:str=['sigmoid', 'piecewise_linear',
           'turgor'])

To obtain plots of the gs regulation curve

	Type	Default	Details
x	float		Unknown parameter definition
slope_gs	float		Unknown parameter definition
p50_gs	float		Unknown parameter definition
psi_start_closing	float		Unknown parameter definition
psi_close	float		Unknown parameter definition
pi_ft	float		Osmotic potential at full turgor (MPa)
e_symp	float		Modulus of elastoicoty of the Symplasm (MPa/%)
turgor_pressure_at_gs_max	float		Unknown parameter definition
gs_max	float		Unknown parameter definition
transpiration_model	str	[‘jarvis’, ‘granier’]	Transpiration model type
stomatal_reg_formulation	str	[‘sigmoid’, ‘piecewise_linear’, ‘turgor’]
Returns	float		type of regulation to be used for stomatal response to leaf symplasmic water potential, either sigmoid or piecewise_linear

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compute_gmin

 compute_gmin (leaf_temp:float, gmin_20:float, t_phase:float, q10_1:float,
               q10_2:float, gmin_temp_off=False)

Calculate minimum conductance (gmin) following Cochard et al. (2019)

	Type	Default	Details
leaf_temp	float		Temperature of the leaf (degC)
gmin_20	float		leaf conductance at 20 degC
t_phase	float		Temperature for phase transition of gmin
q10_1	float		Q10 values for g_min= f(T) below T_phase
q10_2	float		Q10 values for g_cuti = f(T) above T_phase
gmin_temp_off	bool	False	Unknown parameter definition
Returns	float

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compute_emin

 compute_emin (gmin:float, vpd:float, g_bl:float, g_crown:float,
               air_pressure:float=101.3)

Calculate minimum transpiration (emin)

	Type	Default	Details
gmin	float		minimum conductance
vpd	float		Vapor Pressure Deficit (kPa)
g_bl	float		Unknown parameter definition
g_crown	float		Unknown parameter definition. Use compute_g_crown
air_pressure	float	101.3	Surface air pressure (kPa)
Returns	float

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compute_dfmc

 compute_dfmc (vpd:float, fm0=5.43, fm1=52.91, m=0.64)

Compute dead fuel moisture content from VPD following De Dios et al. (2015)

	Type	Default	Details
vpd	float		Vapor pressure deficit (kPA)
fm0	float	5.43	Minimum fuel moisture content (% dry weight)
fm1	float	52.91	Maximum fuel moisture content (% dry weight)
m	float	0.64	Rate of decay
Returns	float		Fuel moisture content (% dry weight)

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distribute_conductances

 distribute_conductances (k_plant_init:float, ri:float,
                          frac_leaf_sym:float=0.4)

Calcultate hydraulic conductances in the different portions of the plant (trunk, leaf and root) according to predetermined rules

	Type	Default	Details
k_plant_init	float		Conductance of the plant from root to leaf
ri	float		Root distribution within the soil layers.
frac_leaf_sym	float	0.4	Proportion of k_plant_init assigned to the leaf (apoplasm to symplasm pathway)
Returns	typing.Dict

Example: Distribute conductances

distribute_conductances(k_plant_init=1, ri=2, frac_leaf_sym=0.4)

defaultdict(list,
            {'k_slapo_init': 5.0,
             'k_lsym_init': 2.5,
             'k_rsapo_init': 5.0,
             'k_plant_init': 1})

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compute_g_crown

 compute_g_crown (g_crown0:float, wind_speed:float)

Calcultate g_crown

	Type	Details
g_crown0	float	Unknown parameter definition
wind_speed	float	Unknown parameter definition
Returns	float

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convert_flux_from_mmolm2s_to_mm

 convert_flux_from_mmolm2s_to_mm (x:float, time_step:float, lai:float)

Convert an instantaneous flux in mmol.m-2Leaf.s-1 to a amount in mm (L.m2soil) over a defined time period

	Type	Details
x	float	The amount of water in mm (L.m-2soil)
time_step	float	Time step (in hours)
lai	float	Leaf area index of the stand (m2leaf.m-2soil)
Returns	float

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convert_flux_from_mm_to_mmolm2s

 convert_flux_from_mm_to_mmolm2s (x:float, time_step:float, lai:float)

Convert flux in L.m-2soil to an instantaneous flux in mmol/m-2leaf.s-1 over a defined time period

	Type	Details
x	float	The amount of water in mm (L.m-2soil)
time_step	float	Time step (in hours)
lai	float	Leaf area index of the stand (m2leaf.m-2soil)
Returns	float

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calculate_ebound_mm_granier

 calculate_ebound_mm_granier (etp:float, lai:float, a:float=-0.006,
                              b:float=0.134, c:float=0)

No description found in R source code

	Type	Default	Details
etp	float		Unknown parameter definition
lai	float		Leaf area index of the stand (m2leaf.m-2soil)
a	float	-0.006	Unknown parameter definition
b	float	0.134	Unknown parameter definition
c	float	0	Unknown parameter definition
Returns	float

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calculate_ebound_granier

 calculate_ebound_granier (etp:float, lai:float, time_step:float)

No description found in R source code

	Type	Details
etp	float	Unknown parameter definition
lai	float	Leaf area index of the stand (m2leaf.m-2soil)
time_step	float	Time step (in hours)
Returns	float

Example: Calculate ebound

calculate_ebound_granier(etp=1, lai=2, time_step=3)

0.6275720164609054

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convert_f_cm3_to_v_mm

 convert_f_cm3_to_v_mm (x:float, rock_fragment_content:float,
                        layer_thickness:float)

Convert soil parameter from from cm3.cm-3 to mm according to thickness and rock fragment content

	Type	Details
x	float	Soil value to be converted (in m3.m-3)
rock_fragment_content	float	Rock fragment content of the soil layer (%)
layer_thickness	float	Thickness of the soil layer (in m)
Returns	float	y soil parameter in mm

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compute_tleaf

 compute_tleaf (t_air:float, par:float, potential_par:float,
                wind_speed:float, relative_humidity:int, gs:float,
                g_cuti:float, e_inst:float, psi_leaf:float,
                leaf_size:float=50, leaf_angle:int=45,
                turn_off_eb:bool=False, transpiration_model:str=['jarvis',
                'granier'])

Compute leaf temperature and Vapour Pressure deficit

	Type	Default	Details
t_air	float		Air temperature (degC)
par	float		Unknown parameter definition
potential_par	float		Unknown parameter definition. Calculated using potential_par function?
wind_speed	float		Unknown parameter definition (m/s)
relative_humidity	int		Air relative_humidity(%)
gs	float		Stomatal conductance
g_cuti	float		leaf conductance
e_inst	float		Unknown parameter definition
psi_leaf	float		Unknown parameter definition
leaf_size	float	50	Characteristic dimension from vegetation params in mm i.e. 1 (pine needle) to 3000 (banana leaf)
leaf_angle	int	45	Leaf angle (depuis le plan horizontal : 0-90 deg)
turn_off_eb	bool	False	Unknown parameter definition. Tleaf Energy balance?
transpiration_model	str	[‘jarvis’, ‘granier’]	Transpiration model type
Returns	typing.Dict		Dictionary with parameters

Example: Compute tleaf

compute_tleaf(
    t_air=60,
    par=100,
    potential_par=1,
    wind_speed=3,
    relative_humidity=60,
    gs=1,
    g_cuti=2,
    e_inst=3,
    psi_leaf=4,
    leaf_size=50,
    leaf_angle=45,
    turn_off_eb=False,
    transpiration_model="jarvis",
)

defaultdict(list,
            {'t_leaf': 60.394042704329365,
             'g_bl': 3076.697970227172,
             'vpd_leaf': 8.880103411681098,
             'vpd_air': 7.978058190496631,
             'delta_t': 0.39404270432936683})

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read_vegetation_file

 read_vegetation_file (file_path:pathlib.Path, modeling_options:Dict,
                       sep:str=';')

Function for reading a data frame containing information about vegetation characteristics

	Type	Default	Details
file_path	Path		Path to a csv file containing parameter values i.e path/to/file_name.csv
modeling_options	typing.Dict		Dictionary created using the create_modeling_options function
sep	str	;	CSV file separator can be ‘,’ or ‘;’
Returns	typing.Dict

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VegetationFile

 VegetationFile (*args, **kwargs)

Schema for validating the input CSV spreadsheet with trait parameters.

List of traits required:

term_in_code	term_in_paper	Definition	Units
P50_VC_Leaf	ψ50,L	Water potential causing 50% Cavitation in the vulnerability curve	MPa
slope_VC_Leaf	slopeL	Slope of rate of leaf embolism spread at ψ50,L	%/MPa
epsilonSym_Leaf	εL	Modulus of elasticity of the leaf symplasm	MPa
PiFullTurgor_Leaf	π0L	Osmotic potential at full turgor of the leaf symplasm	MPa
apoFrac_Leaf	αLApo	Apoplasmic Fraction in leaves/Leaf apoplasmic fraction	Unitless
LDMC	LDMC	Leaf dry matter content (dry mass over saturated mass)	mgMS/g??
LMA	LMA	Leaf mass per area	g/m2leaf
K	k	Light extinction coefficient of the vegetation layer	unitless
k_PlantInit	not found	Hydaulic conductance of the plant from soil to leaves	mmol/MPa/s/m2leaf?
gmin20	gcuti20	Minimum conductance (gmin) at the reference temperature.	mmol/m2leaf/s-1
TPhase_gmin	TPhase	Temperature for phase transition of minimum conductance/Temperature for transition phase of gcuti	degC
Q10_1_gmin	Q10a	Q10 value for gmin = f(T) <= Tphase_gmin/ Temperature dependance of gcuti when T ≤ TPhase	unitless
Q10_2_gmin	Q10b	Q10 value for gmin = f(T) > Tphase_gmin/ Temperature dependance of gcuti when T > TPhase	unitless
gmin_S	not found	conductance (gmin) of the stem	Unitless??
canopyStorageParam	cws	Depth of water that can be retained by leaves and trunks per unit of leaf area index (used to compute the canopy water storage capacity as a function of LAI	l/m2leaf
rootRadius	dR	radius of roots	meters
fRootToLeaf	RaLa	Root-to-leaf area ratio	unitless
betaRootProfile	β	parameter for the distribution of roots in the soil	unitless
PiFullTurgor_Stem	π0S	Osmotic potential at full turgor of the stem symplasm	MPa
epsilonSym_Stem	εS	Modulus of elasticity of the stem symplasm	MPa
apoFrac_Stem	αSApo	Stem apoplasmic fraction of the wood water volume	Unitless
symFrac_Stem	αSSym	Stem symplasmic fraction of the wood water volume	Unitless
vol_Stem	VS	Volume of tissue of the stem (includes the root, trunk and branches)	L m−2 soil
fTRBToLeaf	not found	Definition not found
C_LApoInit	CLApo	Capacitance of the leaf apoplasm	mmol m−2 leaf MPa−1
C_SApoInit	CSApo	Capacitance of the stem apoplasm	mmol m−2 leaf MPa−1
P50_VC_Stem	ψ50,S	Water potential causing 50 % loss of stem hydraulic conductance	MPa
slope_VC_Stem	slopeS	Slope of rate of stem embolism spread at ψ50,S	% MPa−1
k_SSymInit	not found	Definition not found	not found
foliage	not found	Definition not found	Not applicable
not found	t0	Initial date of the forcing period for leaf phenology	DOY
not found	TD	Minimum temperature to start cumulating temperature for budburst	◦C
not found	F∗	Amount of forcing temperature to reach budburst	◦C
RAI	RLAI	LAI growth rate per day	LAI d−1
k_RSApoInit	KR-SApo,max	Maximum conductance from the root surface to the stem apoplasm	mmol m−2 leaf s −1 MPa−1
k_SLApoInit	KSApo−LApo,max	Maximum conductance from trunk apoplasm to the leaf apoplasm	mmol m−2 leaf s −1 MPa−1
not found	KSSym	Conductance from the stem apoplasm to stem symplasm	mmol m−2 leaf s −1 MPa−1
k_LSymInit	KLSym	Conductance from the leaf apoplasm to leaf symplasm	mmol m−2 leaf s −1 MPa−1
not found	Succulence	Leaf succulence (water content per unit of leaf area)	g m−2 leaf
P50_gs	ψgs50	Water potential causing 50 % stomatal closure	MPa
not found	slopegs	Rate of decrease in stomatal conductance at ψgs,50	% MPa−1
not found	gstom_min	Minimum stomatal conductance	mmol m−2 leaf s −1
not found	gstom_max	Maximum stomatal conductance	mmol m−2 leaf s −1
not found	δ	Response of gstom to light	unitless
not found	Toptim	Temperature at maximal stomatal conductance	◦C
not found	Tsens	Stomatal sensitivity to temperature	◦C
not found	θs	Soil water content at saturation	unitless
not found	θr	Residual soil water content	unitless
not found	α	Inverse of the air entry potential	1/MPa
not found	n	Pore size distribution index	unitless
not found	I	Shape parameter for the Van Genuchten equation	unitless
not found	ksat	Soil hydraulic conductivity at saturation	mmol m−1 soil s −1 MPa−1
not found	gsoil0	Reference soil conductance to water vapor	mmol m−2 soil s −1

Example: Read vegetation CSV file

modeling_options_dict = create_modeling_options(
    time_step_for_evapo=2,
    reset_swc=True,
    avoid_water_soil_transfer=True,
    constant_climate=False,
    defoliation=True,
    soil_evapo=True,
    threshold_mortality=51,
    etp_formulation="pt",
    rn_formulation="linear",
    comp_options_for_evapo="custom",
    stomatal_reg_formulation="turgor",
    transpiration_model="jarvis",
    numerical_scheme="implicit",
    pedo_transfer_formulation="vg",
)

read_vegetation_file(
    file_path="./sample_data/vegetation_example_wide.csv",
    modeling_options=modeling_options_dict,
    sep=",",
)

frac_leaf_sym' set to 0.4

/tmp/ipykernel_37992/2639462457.py:235: UserWarning: Foliage evergreen has no params
  warnings.warn("Foliage evergreen has no params")

defaultdict(list,
            {'c_lapoinit': 1e-05,
             'c_sapoinit': 2e-05,
             'fcrit': 450,
             'foliage': 'evergreen',
             'jarvis_par': 0.006,
             'k': 0.5,
             'k_plantinit': 0.62,
             'k_ssyminit': 0.26,
             'ldmc': 570,
             'lma': 106,
             'p12_gs': -2.07,
             'p50_vc_leaf': -3.4,
             'p50_vc_stem': -3.4,
             'p88_gs': -2.62,
             'pt_coeff': 1.14,
             'pifullturgor_leaf': -2.1,
             'pifullturgor_stem': -2.1,
             'psi_close': -2,
             'psi_start_closing': -0.5,
             'q10_1_gmin': 1.2,
             'q10_2_gmin': 4.8,
             'tphase_gmin': 37.5,
             'tbase': 3,
             'tgs_optim': 25,
             'tgs_sens': 17,
             'apofrac_leaf': 0.4,
             'apofrac_stem': 0.4,
             'betarootprofile': 0.97,
             'canopystorageparam': 1.5,
             'daystart': 55,
             'epsilonsym_leaf': 10,
             'epsilonsym_stem': 10,
             'froottoleaf': 1,
             'ftrbtoleaf': 0.8,
             'g_crown0': 45,
             'gmin20': 4,
             'gmin_s': 3,
             'gs_max': 200,
             'gs_night': 20,
             'nbdaylai': 21,
             'rootradius': 0.0002,
             'slope_vc_leaf': 60,
             'slope_vc_stem': 60,
             'symfrac_stem': 0.2,
             'turgor_pressure_at_gs_max': 2,
             'vol_stem': 40,
             'frac_leaf_sym': 0.4})