Create vegetation parameters

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

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source

create_vegetation_parameters

 create_vegetation_parameters (stand_parameters:Dict,
                               soil_parameters:Dict,
                               file_path:pathlib.Path=None,
                               list_of_parameters:List=None,
                               modeling_options:Dict=None, sep:str=';')

Create a dictionary with the vegetation parameters to run

	Type	Default	Details
stand_parameters	typing.Dict		Dictionary created using the create_stand_parameters function
soil_parameters	typing.Dict		Dictionary created using the create_soil_parameters function
file_path	Path	None	Path to a csv file trait parameters. Check read_vegetation_file for more information i.e path/to/parameter_values.csv
list_of_parameters	typing.List	None	A list containing the necessary input parameters instead of reading them in file. Will only be used if ‘file_path’ arguement is not provided
modeling_options	typing.Dict	None	Dictionary created using the create_modeling_options function
sep	str	;	CSV file separator can be ‘,’ or ‘;’
Returns	typing.Dict		Dictionary containing parameters to run the model

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: Create vegetation parameters dictionary

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="sigmoid",
    transpiration_model="jarvis",
    numerical_scheme="implicit",
    pedo_transfer_formulation="campbell",
)
modeling_options_dict

defaultdict(list,
            {'constant_climate': False,
             'etp_formulation': 'pt',
             'rn_formulation': 'linear',
             'pedo_transfer_formulation': 'campbell',
             'time_step_for_evapo': 2,
             'time': array([ 0,  2,  4,  6,  8, 10, 12, 14, 16, 18, 20, 22]),
             'reset_swc': True,
             'avoid_water_soil_transfer': True,
             'comp_options': defaultdict(list,
                         {'numerical_scheme': 'implicit',
                          'nsmalltimesteps': 12.0,
                          'lsym': 1,
                          'ssym': 1,
                          'clapo': 1,
                          'ctapo': 1,
                          'eord': 1,
                          'lcav': 1,
                          'scav': 1}),
             'stomatal_reg_formulation': 'sigmoid',
             'soil_evapo': True,
             'defoliation': True,
             'threshold_mortality': 51,
             'transpiration_model': 'jarvis',
             'print_prog': True})

stand_params = create_stand_parameters(
    file_path="./sample_data/stand_example.csv",
    lai_max=None,
    latitude=None,
    longitude=None,
    sep=";",
)
stand_params

defaultdict(list, {'lai_max': 4.5, 'latitude': 48.73, 'longitude': 6.23})

soil_params = create_soil_parameters(
    file_path="./sample_data/soil_example.csv",
    modeling_options=modeling_options_dict,
    default_soil=False,
    offset_psoil=1,
    psoil_at_field_capacity=-1,
)
soil_params

There is an offset on Psoil of 1 MPa
Psoil at field capacity = -0.001 MPa
You are using campbell pedotransfer formulation
Available water capacity Wilting: 273.74477742718403 mm
Available water capacity Residual: 307.81195119276424 mm
Can soil_params["v_soil_storage_capacity"] be negative?? Ask

defaultdict(list,
            {'offset_psoil': 1,
             'psoil_at_field_capacity': -0.001,
             'pedo_transfer_formulation': 'campbell',
             'soil_depths': array([0.2, 1. , 4. ]),
             'layer_thickness': array([0.2, 0.8, 3. ]),
             'g_soil_0': 30.0,
             'rock_fragment_content': array([75., 82., 94.]),
             'b_campbell': array([-4., -4., -4.]),
             'psie': array([-0.025, -0.025, -0.025]),
             'ksat_campbell': 1.69,
             'saturation_capacity_campbell': array([0.39, 0.39, 0.39]),
             'wilting_point': array([0.1401286, 0.1401286, 0.1401286]),
             'field_capacity': array([0.87206651, 0.87206651, 0.87206651]),
             'residual_capacity_campbell': array([0.0490399, 0.0490399, 0.0490399]),
             'v_field_capacity': array([ 43.60332556, 125.57757762, 156.97197202]),
             'v_saturation_capacity_campbell': array([19.5 , 56.16, 70.2 ]),
             'v_residual_capacity_campbell': array([2.45199519, 7.06174614, 8.82718268]),
             'v_wilting_point': array([ 7.00643018, 20.17851893, 25.22314866]),
             'v_saturation_capacity': array([19.5 , 56.16, 70.2 ]),
             'v_soil_storage_capacity_wilt_campbell': 273.74477742718403,
             'v_soil_storage_capacity_res_campbell': 307.81195119276424,
             'v_soil_storage_capacity': 273.74477742718403})

create_vegetation_parameters(
    file_path="./sample_data/vegetation_example_wide.csv",
    list_of_parameters=None,
    soil_parameters=soil_params,
    stand_parameters=stand_params,
    modeling_options=modeling_options_dict,
    sep=",",
)

frac_leaf_sym' set to 0.4
Available water capacity @Tlp (Campbell):280.7301527422195 mm
Available water capacity @P50 (Campbell):283.4407203700769 mm

/workspaces/sureau_ecos_py/sureau_ecos_py/plant_utils.py:894: UserWarning: Foliage evergreen has no params
  warnings.warn("Foliage evergreen has no params")
/tmp/ipykernel_26798/1456394742.py:82: UserWarning: Make sure that depth from soil_parameters is in meters
  warnings.warn("Make sure that depth from soil_parameters is in meters")

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,
             'p50_gs': -2.3449999999999998,
             'slope_gs': 181.81818181818173,
             'lai_max': 4.5,
             'root_distribution': array([0.45620566, 0.49624184, 0.04755251]),
             'taw_at_tlp': 280.7301527422195,
             'taw_at_p50': 283.4407203700769,
             'la': array([1633.66617127, 1777.03517271,  170.28487559]),
             'lv': array([32673.32342536, 12340.52203273,   946.02708659]),
             'k_slapo_init': 3.1,
             'k_rsapo_init': array([0.70711877, 0.76917484, 0.07370639]),
             'k_lsym_init': 1.5499999999999998,
             'k_plant_init': 0.62})