Merge pull request #1 from mngauthier/develop_MG

Develop mg

example/elements_inputs.csv

@@ -1,13 +1,13 @@
-plant,axis,metamer,organ,element,width,height,PARa,nitrates,amino_acids,proteins,Nstruct,green_area
-1,MS,10,blade,LeafElement1,0.018,0.6,0.004,0,16,380,0.00102,0.00346
-1,MS,10,internode,HiddenElement,0.00257,0.3,0,0,17,66,0.00064,0.00113
-1,MS,10,sheath,StemElement,0.0011,0.5,0,0,12,128,0.00068,0.0006
-1,MS,11,blade,LeafElement1,0.014,0.38,0.012,0,10,210,0.00083,0.0034
-1,MS,11,internode,HiddenElement,0.00099,0.18,0,0,21,20,0.00033,0.0004
-1,MS,11,sheath,StemElement,0.00091,0.3,0.002,0,8,47,0.00021,0.0005
-1,MS,12,blade,LeafElement1,0.0125,0.24,0.052,0,6,85,0.00053,0.00228
-1,MS,12,internode,HiddenElement,0.00093,0.08,0,0,18,20,0.00014,0.00025
-1,MS,12,sheath,StemElement,0.00051,0.18,0.014,0,5,13,0.00011,0.0004
-1,MS,13,peduncle,HiddenElement,0.00349,0.65,0.002,0,20,120,0.00086,0.00159
-1,MS,13,peduncle,StemElement,0.00349,0.5,0.026,0,10,61,0.00044,0.00081
-1,MS,14,ear,StemElement,0.00265,0.7,0.06,0,25,260,0.00107,0.00075
+plant,axis,metamer,organ,element,width,height,PARa,nitrates,amino_acids,proteins,Nstruct,green_area,sucrose,starch,fructan
+1,MS,10,blade,LeafElement1,0.018,0.6,100,0,16,580,0.00102,0.00346,10,0,2000
+1,MS,10,internode,HiddenElement,0.00257,0.3,0,0,17,66,0.00064,0.00113,0,0,0
+1,MS,10,sheath,StemElement,0.0011,0.5,0,0,12,128,0.00068,0.0006,0,0,0
+1,MS,11,blade,LeafElement1,0.014,0.38,100,0,10,210,0.00083,0.0034,0,0,0
+1,MS,11,internode,HiddenElement,0.00099,0.18,0,0,21,20,0.00033,0.0004,0,0,0
+1,MS,11,sheath,StemElement,0.00091,0.3,100,0,8,47,0.00021,0.0005,0,0,0
+1,MS,12,blade,LeafElement1,0.0125,0.24,100,0,6,85,0.00053,0.00228,0,0,0
+1,MS,12,internode,HiddenElement,0.00093,0.08,0,0,18,20,0.00014,0.00025,0,0,0
+1,MS,12,sheath,StemElement,0.00051,0.18,100,0,5,13,0.00011,0.0004,0,0,0
+1,MS,13,peduncle,HiddenElement,0.00349,0.65,100,0,20,120,0.00086,0.00159,0,0,0
+1,MS,13,peduncle,StemElement,0.00349,0.5,100,0,10,61,0.00044,0.00081,0,0,0
+1,MS,14,ear,StemElement,0.00265,0.7,100,0,25,260,0.00107,0.00075,0,0,0

farquharwheat/__init__.py

@@ -10,4 +10,4 @@
     
 """
 
-__version__ = '1.0'
+__version__ = '2.0'

farquharwheat/converter.py

@@ -16,7 +16,8 @@
 """
 
 #: the inputs needed by FarquharWheat at element scale
-FARQUHARWHEAT_ELEMENTS_INPUTS = ['width', 'height', 'PARa', 'nitrates', 'amino_acids', 'proteins', 'Nstruct', 'green_area']
+FARQUHARWHEAT_ELEMENTS_INPUTS = ['width', 'height', 'PARa', 'nitrates', 'amino_acids', 'proteins', 'Nstruct', 'green_area',
+                                 'sucrose', 'starch', 'fructan']
 #: the inputs needed by FarquharWheat at axis scale
 FARQUHARWHEAT_AXES_INPUTS = ['SAM_temperature', 'height_canopy']
 
@@ -78,7 +79,7 @@ def to_dataframe(data_dict):
     data_df = pd.DataFrame(data_dict.values())
     df = pd.concat([ids_df, data_df], axis=1)
     df.sort_values(by=ELEMENT_TOPOLOGY_COLUMNS, inplace=True)
-    columns_sorted = ELEMENT_TOPOLOGY_COLUMNS + [column_name for column_name in FARQUHARWHEAT_ELEMENTS_INPUTS_OUTPUTS if column_name in df.columns]
+    columns_sorted = ELEMENT_TOPOLOGY_COLUMNS + [column_name for column_name in sorted(FARQUHARWHEAT_ELEMENTS_INPUTS_OUTPUTS) if column_name in df.columns]
     df = df.reindex(columns_sorted, axis=1, copy=False)
     df.reset_index(drop=True, inplace=True)
     return df

farquharwheat/parameters.py

@@ -0,0 +1,151 @@
+# -*- coding: latin-1 -*-
+
+"""
+    farquharwheat.paramters
+    ~~~~~~~~~~~~~~~~~~~
+
+    The module :mod:`farquharwheat.parameters` defines the constant parameters.
+
+    :copyright: Copyright 2014-2015 INRA-ECOSYS, see AUTHORS.
+    :license: see LICENSE for details.
+
+"""
+# -- Version of the photosynthesis sub model
+MODEL_VERSION = ['Barillot2016', 'SurfacicProteins', 'SurfacicProteins_Retroinhibition'][2]
+
+if MODEL_VERSION == 'Barillot2016':
+    # Dependence to surfacic_nitrogen including structural nitrogen
+
+    # -- Nitrogen dependance of photosynthetic parameters (derived from Braune et al. (2009) and Evers et al. (2010):
+    #     * S_surfacic_nitrogen: slope of the relation between surfacic_nitrogen and the parameter
+    #         * alpha: mol e- m2 mol-1 photon g-1 N
+    #         * Vc_max25: µmol CO2 g-1 N s-1
+    #         * Jmax25: µmol e- g-1 N s-1
+    #         * TPU25: µmol CO2 g-1 N s-1
+    #         * Rdark25: µmol CO2 g-1 N s-1
+    #     * surfacic_nitrogen_min: minimum amount of nitrogen below which photosynthesis rate is zero (g (N) m-2)
+    #     * beta: intercept parameter of the relation between alpha and surfacic_nitrogen (mol e- mol-1 photons)
+    #     * delta1 and delta2: parameters of m (scaling factor of gs) dependance to surfacic_nitrogen (m2 g-1 and dimensionless, respectively)
+    PARAM_N = {'S_surfacic_nitrogen': {'Vc_max25': 84.965, 'Jmax25': 117.6, 'alpha': 0.0413, 'TPU25': 9.25, 'Rdark25': 0.493},
+               'surfacic_nitrogen_min': {'Vc_max25': 0.17, 'Jmax25': 0.17, 'TPU25': 0.229, 'Rdark25': 0.118}, 'beta': 0.2101, 'delta1': 14.7, 'delta2': -0.548}
+    NA_0 = 2  # Initial value of surfacic_nitrogen (g m-2), used if no surfacic_nitrogen is provided by user
+    Psurf_to_SLNnonstruct = 1.06  #: Conversion factor from surfacic protein content to non structural SLN (estimation from NEMA and Ljutovac simulations)
+
+if MODEL_VERSION in ['SurfacicProteins', 'SurfacicProteins_Retroinhibition']:
+    # Dependence to surfacic_nitrogen without structural nitrogen
+
+    # -- Nitrogen dependance of photosynthetic parameters (derived from Braune et al. (2009) and Evers et al. (2010):
+    #     * S_surfacic_nitrogen: slope of the relation between surfacic_nitrogen and the parameter
+    #         * alpha: mol e- m2 mol-1 photon g-1 N
+    #         * Vc_max25: µmol CO2 g-1 N s-1
+    #         * Jmax25: µmol e- g-1 N s-1
+    #         * TPU25: µmol CO2 g-1 N s-1
+    #         * Rdark25: µmol CO2 g-1 N s-1
+    #     * surfacic_nitrogen_min: minimum amount of nitrogen below which photosynthesis rate is zero (g (N) m-2)
+    #     * beta: intercept parameter of the relation between alpha and surfacic_nitrogen (mol e- mol-1 photons)
+    #     * delta1 and delta2: parameters of m (scaling factor of gs) dependance to surfacic_nitrogen (m2 g-1 and dimensionless, respectively)
+    PARAM_N = {'S_surfacic_nitrogen': {'Vc_max25': 84.965, 'Jmax25': 117.6, 'alpha': 0.0413, 'TPU25': 9.25, 'Rdark25': 0.493},
+               'surfacic_nitrogen_min': {'Vc_max25': 0., 'Jmax25': 0., 'TPU25': 0., 'Rdark25': 0.}, 'beta': 0.2101 + 0.0083, 'delta1': 14.7, 'delta2': -0.548}
+    NA_0 = 2  # Initial value of surfacic_nitrogen (g m-2), used if no surfacic_nitrogen is provided by user
+    Psurf_to_SLNnonstruct = 1.06  #: Conversion factor from surfacic protein content to non structural SLN (estimation from NEMA and Ljutovac simulations)
+
+# -- Molecular weights
+MM_WATER = 18  # Molar mass of water (g mol-1)
+N_MOLAR_MASS = 14  # Molar mass of nitrogen (g mol-1)
+
+# -- Physical parameter
+A = 2.5  # Attenuation coefficient of wind within a wheat canopy. From Campbell and Norman (1998), 2nd edition. Can also be estimated by: A = sqrt((0.2*LAI*h)/sqrt((4*width*h)/(pi*LAI))
+GAMMA = 66E-3  # Psychrometric constant (KPa K-1). Mean value
+I0 = 1370  # Extraterrestrial solar radiation (W m-2)
+K = 0.40  # Von Kármán's constant (dimensionless)
+LAMBDA = 2260E3  # Latent heat for vaporisation of water (J kg-1)
+RHOCP = 1256  # Volumetric heat capacity of air (J m-3 K-1)
+SIGMA = 5.6704E-8  # Stefan-Bolzmann constant (W-2 K-4)
+ZR = 2  # Height above canopy at which reference wind (Ur) is measured (m)
+
+s_A = 239  # Factor in the calculation of the Saturation vapour pressure
+s_B = 17.4  # Factor in the calculation of the Saturation vapour pressure
+s_C = 0.611  # Factor in the calculation of the Saturation vapour pressure
+s_expo = 2  # exponent in the calculation of the Saturation vapour pressure
+
+R = 8.3144  # Gas constant (J mol-1 K-1)
+KELVIN_DEGREE = 273.15  #: Conversion factor from degree C to Kelvin
+PATM = 1.01325E5  # Atmospheric pressure (Pa)
+
+Ur_min = 0.1  # Minimum wind speed (m s-1) TODO: Temporary patch to avoid div 0 error
+Zh_d = 0.7  # estimation factor canopy heigh into Zero plane displacement height
+Zh_Zo = 0.1  # estimation factor canopy heigh into roughness length
+rhb_blade_A = 154  # factor in Boundary layer resistance to heat calculation for blade
+rhb_other_A = 1.2E-5  # factor A in Boundary layer resistance to heat calculation for other organs than blades
+rhb_other_B = 1.5E-5  # factor B in Boundary layer resistance to heat calculation for other organs than blades
+rhb_other_C = 0.47  # factor C in Boundary layer resistance to heat calculation for other organs than blades
+ra_expo = 2  # exponent in calculation of Turbulence resistance to heat
+
+PARa_to_RGa = 1.53  # Used to convert PAR absorbed into RG absorbed (see details in notice entitiled "Notes sur le calcul du rayonnement net à partir du PAR absorbé")
+Watt_to_PPFD = 4.55  # It is assumed that 1 W m-2 of PAR is equivalent to 4.55 µmol m-2 s-1 of PAR (Goudriaan and Laar, 1994)
+rbh_rbw = 0.96  # estimation factor Boundary layer resistance for water from Boundary layer resistance to heat
+
+# -- Photosynthetic parameter
+O = 21000  # Intercellular O2 concentration, µmol mol(air)-1 or Pa, from Bernacchi et al. (2001)
+KC25 = 404  # Affinity constant of RuBisCO for C, µmol mol-1 or Pa, from Bernacchi et al. (2001) (estimation in Braune et al. (2009) not enough accurate)
+KO25 = 278.4E3  # Affinity constant of RuBisCO for O, µmol mol-1 or Pa, from Bernacchi et al. (2001) (estimation in Braune et al. (2009) not enough accurate)
+GAMMA25 = 39  # CO2 compensation point, µmol(CO2) mol-1 (air), from Braune et al. (2009)
+THETA = 0.72  # curvature parameter of J, dimensionless
+EFFICENCY_STEM = 0.78
+J_expo = 2  # exponent in calculation of the Electron transport rate (Muller et al. (2005), Evers et al. (2010))
+J_A = 4  # factor A in calculation of the Electron transport rate (Muller et al. (2005), Evers et al. (2010))
+J_B = 2  # factor B in calculation of the Electron transport rate (Muller et al. (2005), Evers et al. (2010))
+Aj_A = 4  # parameter in the calculation of the Rate of assimilation under RuBP regeneration limitation
+Aj_B = 8  # parameter in the calculation of the Rate of assimilation under RuBP regeneration limitation
+Vomax_A = 0.5  # parameter in the calculation of the Maximum rate of Vo
+Ap_A = 3  # parameter in the calculation of the Rate of assimilation under TPU limitation
+Rd_A = 0.33  # parameter A in the calculation of the Rd
+Rd_B = 0.5  # parameter B in the calculation of the Rd
+Rd_C = 15  # parameter C in the calculation of the Rd
+Ci_init_ratio = 0.7
+
+# -- Stomatal conductance parameter
+GSMIN = 0.05  # Minimum gsw, measured in the dark (mol m-2 s-1). Braune et al. (2009).
+GB = 3.5  # Boundary layer conductance to water vapour (mol m-2 s-1). Muller et al., (2005)
+K_Cs = 1.37  # factor in CO2 concentration at organ surface. From Prieto et al. (2012).
+gsw_gs_CO2 = 1.6  # conversion factor from gsw into gs_CO2
+Ci_A = 1.37  # factor in Ci calculation. Comes from (1.6)^(2/3)
+
+# -- Temperature dependance of photosynthetic parameters (parameter values derived from Braune et al. (2009) except for Kc, Ko, and Rdark (Bernacchi et al., 2001))
+#     * deltaHa, deltaHd: enthalpie of activation and deactivation respectively (kJ mol-1)
+#     * deltaS: entropy term (kJ mol-1 K-1)
+#     * Tref: reference temperature (K)
+
+PARAM_TEMP = {'deltaHa': {'Vc_max': 89.7, 'Jmax': 48.9, 'TPU': 47., 'Kc': 79.43, 'Ko': 36.38, 'Gamma': 35., 'Rdark': 46.39},
+              'deltaHd': {'Vc_max': 149.3, 'Jmax': 152.3, 'TPU': 152.3},
+              'deltaS': {'Vc_max': 0.486, 'Jmax': 0.495, 'TPU': 0.495}, 'Tref': 298.15}
+
+DELTA_CONVERGENCE = 0.01  #: The relative delta for Ci and Ts convergence.
+
+# -- Inhibition of the photosynthesis by carbohydrates (from Azcon-Bieto 1983)
+WSC_min = 100000  # Surfacic WSC content above which inhibition of the photosynthesis by WSC occures (µmol C m-2)
+Inhibition_max = 1  # Maximum inhibition ratio
+K_Inhibition = 938000  # 'Affinity' coefficient for the inhibition of the photosynthesis by WSC (µmol C m-2)
+
+
+class ElementDefaultProperties(object):
+    """
+    Properties by default for the elements. Used in FarquharWheat facade.
+    """
+    def __init__(self):
+        self.PARa = 0
+        self.nitrates = 0
+        self.proteins = 0
+        self.Nstruct = 0
+        self.sucrose = 0
+        self.fructan = 0
+        self.starch = 0
+        self.green_area = 0
+
+
+class AxisDefaultProperties(object):
+    """
+    Properties by default for the axis. Used in FarquharWheat facade.
+    """
+    def __init__(self):
+        self.height_canopy = 0.78