BESS-JPL 1.6.0__py3-none-any.whl

BESS_JPL/SZA/__init__.py

@@ -0,0 +1 @@
+from .SZA import *

BESS_JPL/SZA/daylight_hours.py

@@ -0,0 +1,74 @@
+"""
+This module calculates sunrise hour and daylight hours.
+
+Developed by Gregory Halverson in the Jet Propulsion Laboratory Year-Round Internship Program (Columbus Technologies and Services, ANRE Tech.), in coordination with the ECOSTRESS mission and master's thesis studies at California State University, Northridge.
+"""
+import warnings
+from numpy import tan, cos, sin, pi, arccos, where, radians, degrees
+
+__author__ = 'Gregory Halverson'
+
+
+def day_angle_rad_from_doy(doy):
+    """
+    This function calculates day angle in radians from day of year between 1 and 365.
+    """
+    return (2 * pi * (doy - 1)) / 365
+
+
+def solar_dec_deg_from_day_angle_rad(day_angle_rad):
+    """
+    This function calculates solar declination in degrees from day angle in radians. 
+    """
+    return (0.006918 - 0.399912 * cos(day_angle_rad) + 0.070257 * sin(day_angle_rad) - 0.006758 * cos(
+        2 * day_angle_rad) + 0.000907 * sin(2 * day_angle_rad) - 0.002697 * cos(3 * day_angle_rad) + 0.00148 * sin(
+        3 * day_angle_rad)) * (180 / pi)
+
+
+def sha_deg_from_doy_lat(doy, latitude):
+    """
+    This function calculates sunrise hour angle in degrees from latitude in degrees and day of year between 1 and 365. 
+    """
+    # calculate day angle in radians
+    day_angle_rad = day_angle_rad_from_doy(doy)
+
+    # calculate solar declination in degrees
+    solar_dec_deg = solar_dec_deg_from_day_angle_rad(day_angle_rad)
+
+    # convert latitude to radians
+    latitude_rad = radians(latitude)
+
+    # convert solar declination to radians
+    solar_dec_rad = radians(solar_dec_deg)
+
+    # calculate cosine of sunrise angle at latitude and solar declination
+    # need to keep the cosine for polar correction
+    sunrise_cos = -tan(latitude_rad) * tan(solar_dec_rad)
+
+    # calculate sunrise angle in radians from cosine
+    warnings.filterwarnings('ignore')
+    sunrise_rad = arccos(sunrise_cos)
+    warnings.resetwarnings()
+
+    # convert to degrees
+    sunrise_deg = degrees(sunrise_rad)
+
+    # apply polar correction
+    sunrise_deg = where(sunrise_cos >= 1, 0, sunrise_deg)
+    sunrise_deg = where(sunrise_cos <= -1, 180, sunrise_deg)
+
+    return sunrise_deg
+
+
+def sunrise_from_sha(sha_deg):
+    """
+    This function calculates sunrise hour from sunrise hour angle in degrees. 
+    """
+    return 12.0 - (sha_deg / 15.0)
+
+
+def daylight_from_sha(sha_deg):
+    """
+    This function calculates daylight hours from sunrise hour angle in degrees.
+    """
+    return (2.0 / 15.0) * sha_deg

BESS_JPL/__init__.py

@@ -0,0 +1,10 @@
+from .BESS_JPL import *
+
+from os.path import join, dirname, abspath
+
+with open(join(abspath(dirname(__file__)), "version.txt")) as f:
+    version = f.read()
+
+__version__ = version
+__author__ = "Gregory H. Halverson"
+

BESS_JPL/calculate_VCmax.py

@@ -0,0 +1,54 @@
+from os.path import join, abspath, dirname
+
+import rasters as rt
+import numpy as np
+
+from .constants import *
+
+def calculate_VCmax(
+        LAI: np.ndarray,
+        LAI_minimum: np.ndarray,
+        LAI_maximum: np.ndarray,
+        peakVCmax_C3: np.ndarray,
+        peakVCmax_C4: np.ndarray,
+        SZA: np.ndarray,
+        kn: np.ndarray,
+        A: np.ndarray = A):
+    sf = np.clip(np.clip(LAI - LAI_minimum, 0, None) / np.clip(LAI_maximum - LAI_minimum, 1, None), 0, 1)
+    sf = np.where(np.isreal(sf), sf, 0)
+    sf = np.where(np.isnan(sf), 0, sf)
+
+    # calculate maximum carboxylation rate at 25C for C3 plants
+    VCmax_C3 = A * peakVCmax_C3 + (1 - A) * peakVCmax_C3 * sf
+
+    # calculate maximum carboxylation rate at 25C for C4 plants
+    VCmax_C4 = A * peakVCmax_C4 + (1 - A) * peakVCmax_C4 * sf
+
+    # kb = 0.5 / np.cos(np.radians(SZA))
+    kb = np.where(SZA > 89, 50.0, 0.5 / np.cos(np.radians(SZA)))
+    kn_kb_Lc = kn + kb * LAI
+    exp_neg_kn_kb_Lc = np.exp(-kn_kb_Lc)
+    LAI_VCmax_C3 = LAI * VCmax_C3
+    exp_neg_kn = np.exp(-kn)
+
+    # calculate total maximum carboxylation rate at 25C for C3 plants
+    VCmax_C3_total = LAI_VCmax_C3 * (1 - exp_neg_kn) / kn
+
+    # calculate sunlit maximum carboxylation rate at 25C for C3 plants
+    VCmax_C3_sunlit = LAI_VCmax_C3 * (1 - exp_neg_kn_kb_Lc) / kn_kb_Lc
+
+    # calculate shaded maximum carboxylation rate at 25C for C3 plants
+    VCmax_C3_shaded = VCmax_C3_total - VCmax_C3_sunlit
+
+    LAI_VCmax_C4 = LAI * VCmax_C4
+
+    # calculate total maximum carboxylation rate at 25C for C4 plants
+    VCmax_C4_total = LAI_VCmax_C4 * (1 - exp_neg_kn) / kn
+
+    # calculate sunlit maximum carboxylation rate at 25C for C4 plants
+    VCmax_C4_sunlit = LAI_VCmax_C4 * (1 - exp_neg_kn_kb_Lc) / kn_kb_Lc
+
+    # calculate shaded maximum carboxylation rate at 25C for C4 plants
+    VCmax_C4_shaded = VCmax_C4_total - VCmax_C4_sunlit
+
+    return VCmax_C3_sunlit, VCmax_C4_sunlit, VCmax_C3_shaded, VCmax_C4_shaded

BESS_JPL/canopy_energy_balance.py

@@ -0,0 +1,146 @@
+import numpy as np
+
+def process_paw_and_gao_LE(
+        Rn: np.ndarray,  # net radiation (W m-2)
+        Ta_K: np.ndarray,  # air temperature (K)
+        VPD_Pa: np.ndarray,  # vapor pressure (Pa)
+        Cp: np.ndarray,  # specific heat of air (J kg-1 K-1)
+        rhoa: np.ndarray,  # air density (kg m-3)
+        gamma: np.ndarray,  # psychrometric constant (Pa K-1)
+        Rc: np.ndarray,
+        rs: np.ndarray,
+        desTa: np.ndarray,
+        ddesTa: np.ndarray) -> np.ndarray:
+    """
+    :param Rn:  net radiation (W m-2)
+    :param Ta_K:  air temperature (K)
+    :param VPD_Pa:  vapor pressure (Pa)
+    :param Cp:  specific heat of air (J kg-1 K-1)
+    :param rhoa:  air density (kg m-3)
+    :param gamma:  psychrometric constant (Pa K-1)
+    :param Rc:
+    :param rs:
+    :param desTa:
+    :param ddesTa:
+    :return:  latent heat flux (W m-2)
+    """
+    # To reduce redundant computation
+    rc = rs
+    ddesTa_Rc2 = ddesTa * Rc * Rc
+    gamma_Rc_rc = gamma * (Rc + rc)
+    rhoa_Cp_gamma_Rc_rc = rhoa * Cp * gamma_Rc_rc
+
+    # Solution (Paw and Gao 1988)
+    a = 1.0 / 2.0 * ddesTa_Rc2 / rhoa_Cp_gamma_Rc_rc  # Eq. (10b)
+    b = -1.0 - Rc * desTa / gamma_Rc_rc - ddesTa_Rc2 * Rn / rhoa_Cp_gamma_Rc_rc  # Eq. (10c)
+    c = rhoa * Cp / gamma_Rc_rc * VPD_Pa + desTa * Rc / gamma_Rc_rc * Rn + 1.0 / 2.0 * ddesTa_Rc2 / rhoa_Cp_gamma_Rc_rc * Rn * Rn  # Eq. (10d) in Paw and Gao (1988)
+
+    # calculate latent heat flux
+    LE = (-b + np.sign(b) * np.sqrt(b * b - 4.0 * a * c)) / (2.0 * a)  # Eq. (10a)
+    LE = np.real(LE)
+
+    # Constraints
+    # LE[LE > Rn] = Rn[LE > Rn]
+    LE = np.clip(LE, 0, Rn)
+    # LE[Rn < 0.0] = 0.0
+    # LE[LE < 0.0] = 0.0
+    # LE[Ta < 273.15] = 0.0
+    LE = np.where(Ta_K < 273.15, 0, LE)
+
+    return LE
+
+def canopy_energy_balance(
+        An: np.ndarray,  # net assimulation (An) [umol m-2 s-1],
+        ASW: np.ndarray,  # total absorbed shortwave radiation by sunlit/shade canopy (ASW) [umol m-2 s-1],
+        ALW: np.ndarray,  # total absorbed longwave radiation by sunlit/shade canopy (ALW) [umol m-2 s-1],
+        Tf_K: np.ndarray,  # leaf temperature in Kelvin
+        Ps_Pa: np.ndarray,  # surface pressure in Pascal
+        Ca: np.ndarray,  # ambient CO2 concentration [umol mol-1],
+        Ta_K: np.ndarray,  # air temperature in Kelvin
+        RH: np.ndarray,  # relative humidity as a fraction
+        VPD_Pa: np.ndarray,  # vapor pressure deficit in Pascal
+        desTa: np.ndarray,  # 1st derivative of saturated vapour pressure
+        ddesTa: np.ndarray,  # 2nd derivative of saturated vapour pressure
+        gamma: np.ndarray,  # psychrometric constant [pa K-1],
+        Cp: np.ndarray,  # specific heat of air [J kg-1 K-1],
+        rhoa: np.ndarray,  # air density [kg m-3],
+        Rc: np.ndarray,  # aerodynamic resistance [s m-1],
+        ball_berry_slope: np.ndarray,  # Ball-Berry slope [-],
+        ball_berry_intercept: np.ndarray,  # Ball-Berry intercept [-].
+        C4_photosynthesis: bool):  # flag for C4 photosynthesis
+    """
+    =============================================================================
+
+    Module     : Canopy energy balance
+    Input      : net assimulation (An) [umol m-2 s-1],
+               : total absorbed shortwave radiation by sunlit/shade canopy (ASW) [umol m-2 s-1],
+               : total absorbed longwave radiation by sunlit/shade canopy (ALW) [umol m-2 s-1],
+               : sunlit/shade leaf temperature (Tf) [K],
+               : surface pressure (Ps) [Pa],
+               : ambient CO2 concentration (Ca) [umol mol-1],
+               : air temperature (Ta) [K],
+               : relative humidity (RH) [-],
+               : water vapour deficit (VPD) [Pa],
+               : 1st derivative of saturated vapour pressure (desTa),
+               : 2nd derivative of saturated vapour pressure (ddesTa),
+               : psychrometric constant (gamma) [pa K-1],
+               : air density (rhoa) [kg m-3],
+               : aerodynamic resistance (ra) [s m-1],
+               : Ball-Berry slope (m) [-],
+               : Ball-Berry intercept (b0) [-].
+    Output     : sunlit/shade canopy net radiation (Rn) [W m-2],
+               : sunlit/shade canopy latent heat (LE) [W m-2],
+               : sunlit/shade canopy sensible heat (H) [W m-2],
+               : sunlit/shade leaf temperature (Tl) [K],
+               : stomatal resistance to vapour transfer from cell to leaf surface (rs) [s m-1],
+               : inter-cellular CO2 concentration (Ci) [umol mol-1].
+    References : Paw U, K. T., & Gao, W. (1988). Applications of solutions to non-linear energy budget equations.
+                 Agricultural and Forest Meteorology, 43(2), 121�145. doi:10.1016/0168-1923(88)90087-1
+
+
+    Conversion from MatLab by Robert Freepartner, JPL/Raytheon/JaDa Systems
+    March 2020
+
+    =============================================================================
+    """
+    # Convert factor
+    cf = 0.446 * (273.15 / Tf_K) * (Ps_Pa / 101325.0)
+
+    # Stefan_Boltzmann_constant
+    sigma = 5.670373e-8  # [W m-2 K-4] (Wiki)
+
+    # Ball-Berry stomatal conductance
+    # https://onlinelibrary.wiley.com/doi/full/10.1111/pce.12990
+    gs1 = ball_berry_slope * RH * An / Ca + ball_berry_intercept  # [mol m-2 s-1]
+
+    # intercellular CO2 concentration
+    Ci = Ca - 1.6 * An / gs1  # [umol./mol]
+
+    # constrain intercellular CO2 concentration based on ambient CO2 concentration differently depending on C3 or C4 photosynthesis
+    Ci = np.clip(Ci, 0.2 * Ca, 0.6 * Ca) if C4_photosynthesis else np.clip(Ci, 0.5 * Ca, 0.9 * Ca)
+
+    # Stomatal resistance to vapour transfer from cell to leaf surface
+    rs = 1.0 / (gs1 / cf * 1e-2)  # [s m-1]
+
+    # Stomatal H2O conductance
+    gs2 = 1.0 / rs  # [m s-1]
+
+    # Canopy net radiation
+    Rn = np.clip(ASW + ALW - 4.0 * 0.98 * sigma * (Ta_K ** 3) * (Tf_K - Ta_K), 0, None)
+
+    # TODO explore options for alternate latent heat flux models in the BESS canopy energy balance calculation
+
+    # caluclate latent heat flux using Paw and Gao (1988)
+    # https://www.sciencedirect.com/science/article/abs/pii/0168192388900871
+    LE = process_paw_and_gao_LE(Rn, Ta_K, VPD_Pa, Cp, rhoa, gamma, Rc, rs, desTa, ddesTa)
+
+    # update sensible heat flux
+    H = np.clip(Rn - LE, 0, Rn)
+
+    # update difference between air and canopy temperature
+    dT = np.clip(Rc / (rhoa * Cp) * H, -20, 20)  # Eq. (6)
+
+    # update canopy temperature in Kelvin
+    Tf_K = Ta_K + dT
+
+    return Rn, LE, H, Tf_K, gs2, Ci

BESS_JPL/canopy_longwave_radiation.py

@@ -0,0 +1,92 @@
+import numpy as np
+
+
+def canopy_longwave_radiation(
+        LAI: np.ndarray,
+        SZA: np.ndarray,
+        Ts_K: np.ndarray,
+        Tf_K: np.ndarray,
+        Ta_K: np.ndarray,
+        epsa: np.ndarray,
+        epsf: float,
+        epss: float,
+        ALW_min: float = None,
+        intermediate_min: float = None,
+        intermediate_max: float = None):
+    """
+    =============================================================================
+
+    Module     : Canopy longwave radiation transfer
+    Input      : leaf area index (LAI) [-],
+               : extinction coefficient for longwave radiation (kd) [m-1],
+               : extinction coefficient for beam radiation (kb) [m-1],
+               : air temperature (Ta) [K],
+               : soil temperature (Ts) [K],
+               : foliage temperature (Tf) [K],
+               : clear-sky emissivity (epsa) [-],
+               : soil emissivity (epss) [-],
+               : foliage emissivity (epsf) [-].
+    Output     : total absorbed LW by sunlit leaves (Q_LSun),
+               : total absorbed LW by shade leaves (Q_LSh).
+    References : Wang, Y., Law, R. M., Davies, H. L., McGregor, J. L., & Abramowitz, G. (2006).
+                 The CSIRO Atmosphere Biosphere Land Exchange (CABLE) model for use in climate models and as an offline model.
+
+
+    Conversion from MatLab by Robert Freepartner, JPL/Raytheon/JaDa Systems
+    March 2020
+
+    =============================================================================
+    """
+    # SZA[SZA > 89.0] = 89.0
+    SZA = np.clip(SZA, None, 89)
+    kb = 0.5 / np.cos(SZA * np.pi / 180.0)  # Table A1 in Ryu et al 2011
+    kd = 0.78  # Table A1 in Ryu et al 2011
+
+    # Stefan_Boltzmann_constant
+    sigma = 5.670373e-8  # [W m-2 K-4] (Wiki)
+
+    # Long wave radiation flux densities from air, soil and leaf
+    La = np.clip(epsa * sigma * Ta_K ** 4, 0, None)
+    Ls = np.clip(epss * sigma * Ts_K ** 4, 0, None)
+    Lf = np.clip(epsf * sigma * Tf_K ** 4, 0, None)
+
+    # For simplicity
+    kd_LAI = kd * LAI
+
+    soil_leaf_difference = Ls - Lf
+
+    if intermediate_min is not None:
+        soil_leaf_difference = np.clip(soil_leaf_difference, intermediate_min, None)
+
+    air_leaf_difference = La - Lf
+
+    if intermediate_min is not None:
+        air_leaf_difference = np.clip(air_leaf_difference, intermediate_min, intermediate_max)
+    
+    # Absorbed longwave radiation by sunlit leaves
+    numerator = soil_leaf_difference * kd * (np.exp(-kd_LAI) - np.exp(-kb * LAI)) / (kd - kb) + kd * air_leaf_difference * (1.0 - np.exp(-(kb + kd) * LAI))
+    denominator = kd + kb
+    
+    if ALW_min is not None:
+        numerator = np.clip(numerator, ALW_min, None)
+
+    ALW_sunlit = numerator / denominator  # Eq. (44)
+
+    soil_air_leaf = Ls + La - 2 * Lf
+
+    if intermediate_min is not None or intermediate_max is not None:
+        soil_air_leaf = np.clip(soil_air_leaf, intermediate_min, intermediate_max)
+    
+    # Absorbed longwave radiation by shaded leaves
+    ALW_shaded = (1.0 - np.exp(-kd_LAI)) * soil_air_leaf - ALW_sunlit  # Eq. (45)
+    
+    if ALW_min is not None:
+        ALW_shaded = np.clip(ALW_shaded, ALW_min, None)
+
+    # Absorbed longwave radiation by soil
+    ALW_soil = (1.0 - np.exp(-kd_LAI)) * Lf + np.exp(-kd_LAI) * La  # Eq. (41)
+
+    if ALW_min is not None:
+        ALW_soil = np.clip(ALW_soil, ALW_min, None)
+
+    return ALW_sunlit, ALW_shaded, ALW_soil, Ls, La, Lf

BESS_JPL/canopy_shortwave_radiation.py

@@ -0,0 +1,234 @@
+import numpy as np
+
+from check_distribution import check_distribution
+
+
+def canopy_shortwave_radiation(
+        PARDiff: np.ndarray,
+        PARDir: np.ndarray,
+        NIRDiff: np.ndarray,
+        NIRDir: np.ndarray,
+        UV: np.ndarray,
+        SZA: np.ndarray,
+        LAI: np.ndarray,
+        CI: np.ndarray,
+        albedo_visible: np.ndarray,
+        albedo_NIR: np.ndarray):
+    """
+    =============================================================================
+
+    Module     : Canopy radiative transfer
+    Input      : diffuse PAR radiation (PARDiff) [W m-2],
+               : direct PAR radiation (PARDir) [W m-2],
+               : diffuse NIR radiation (NIRDiff) [W m-2],
+               : direct NIR radiation (NIRDir) [W m-2],
+               : ultroviolet radiation (UV) [W m-2],
+               : solar zenith angle (SZA) [degree],
+               : leaf area index (LAI) [-],
+               : clumping index (CI) [-],
+               : VIS albedo (ALB_VIS) [-],
+               : NIR albedo (ALB_NIR) [-],
+               : leaf maximum carboxylation rate at 25C for C3 plant (Vcmax25_C3Leaf) [umol m-2 s-1],
+               : leaf maximum carboxylation rate at 25C for C4 plant (Vcmax25_C4Leaf) [umol m-2 s-1].
+    Output     : total absorbed PAR by sunlit leaves (APAR_Sun) [umol m-2 s-1],
+               : total absorbed PAR by shade leaves (APAR_Sh) [umol m-2 s-1],
+               : total absorbed SW by sunlit leaves (ASW_Sun) [W m-2],
+               : total absorbed SW by shade leaves (ASW_Sh) [W m-2],
+               : sunlit canopy maximum carboxylation rate at 25C for C3 plant (Vcmax25_C3Sun) [umol m-2 s-1],
+               : shade canopy maximum carboxylation rate at 25C for C3 plant (Vcmax25_C3Sh) [umol m-2 s-1],
+               : sunlit canopy maximum carboxylation rate at 25C for C4 plant (Vcmax25_C4Sun) [umol m-2 s-1],
+               : shade canopy maximum carboxylation rate at 25C for C4 plant (Vcmax25_C4Sh) [umol m-2 s-1],
+               : fraction of sunlit canopy (fSun) [-],
+               : ground heat storage (G) [W m-2],
+               : total absorbed SW by soil (ASW_Soil) [W m-2].
+    References : Ryu, Y., Baldocchi, D. D., Kobayashi, H., Van Ingen, C., Li, J., Black, T. A., Beringer, J.,
+                 Van Gorsel, E., Knohl, A., Law, B. E., & Roupsard, O. (2011).
+
+                 Integration of MODIS land and atmosphere products with a coupled-process model i
+                 to estimate gross primary productivity and evapotranspiration from 1 km to global scales.
+                 Global Biogeochemical Cycles, 25(GB4017), 1-24. doi:10.1029/2011GB004053.1.
+
+
+    Conversion from MatLab by Robert Freepartner, JPL/Raytheon/JaDa Systems
+    March 2020
+
+    =============================================================================
+    """
+    # Leaf scattering coefficients and soil reflectance (Sellers 1985)
+    SIGMA_P = 0.175
+    RHO_PSOIL = 0.15
+    SIGMA_N = 0.825
+    RHO_NSOIL = 0.30
+
+    # Extinction coefficient for diffuse and scattered diffuse PAR
+    kk_Pd = 0.72  # Table A1
+
+    # Check for None parameters
+    parameters = {
+        "PARDiff": PARDiff,
+        "PARDir": PARDir,
+        "NIRDiff": NIRDiff,
+        "NIRDir": NIRDir,
+        "UV": UV,
+        "SZA": SZA,
+        "LAI": LAI,
+        "CI": CI,
+        "albedo_visible": albedo_visible,
+        "albedo_NIR": albedo_NIR
+    }
+
+    for param_name, param_value in parameters.items():
+        check_distribution(param_value, param_name)
+        if param_value is None:
+            raise ValueError(f"The parameter '{param_name}' cannot be None.")
+
+    # Beam radiation extinction coefficient of canopy
+    kb = np.where(SZA > 89, 50.0, 0.5 / np.cos(np.radians(SZA)))  # Table A1
+    check_distribution(kb, "kb")
+
+    # Extinction coefficient for beam and scattered beam PAR
+    kk_Pb = np.where(SZA > 89, 50.0, 0.46 / np.cos(np.radians(SZA)))  # Table A1
+    check_distribution(kk_Pb, "kk_Pb")
+
+    # Extinction coefficient for beam and scattered beam NIR
+    kk_Nb = kb * np.sqrt(1.0 - SIGMA_N)  # Table A1
+    check_distribution(kk_Nb, "kk_Nb")
+
+    # Extinction coefficient for diffuse and scattered diffuse NIR
+    kk_Nd = 0.35 * np.sqrt(1.0 - SIGMA_N)  # Table A1
+    check_distribution(kk_Nd, "kk_Nd")
+
+    # Sunlit fraction
+    fSun = np.clip(1.0 / kb * (1.0 - np.exp(-kb * LAI * CI)) / LAI, 0, 1)  # Integration of Eq. (1)
+    fSun = np.where(LAI == 0, 0, fSun)  # Eq. (1)
+    check_distribution(fSun, "fSun")
+
+    # For simplicity
+    L_CI = LAI * CI
+    check_distribution(L_CI, "L_CI")
+    exp_kk_Pd_L_CI = np.exp(-kk_Pd * L_CI)
+    check_distribution(exp_kk_Pd_L_CI, "exp_kk_Pd_L_CI")
+    exp_kk_Nd_L_CI = np.exp(-kk_Nd * L_CI)
+    check_distribution(exp_kk_Nd_L_CI, "exp_kk_Nd_L_CI")
+
+    # Total absorbed incoming PAR
+    Q_PDn = (1.0 - albedo_visible) * PARDir * (1.0 - np.exp(-kk_Pb * L_CI)) + (1.0 - albedo_visible) * PARDiff * (
+            1.0 - exp_kk_Pd_L_CI)  # Eq. (2)
+    check_distribution(Q_PDn, "Q_PDn")
+
+    # Absorbed incoming beam PAR by sunlit leaves
+    Q_PbSunDn = PARDir * (1.0 - SIGMA_P) * (1.0 - np.exp(-kb * L_CI))  # Eq. (3)
+    check_distribution(Q_PbSunDn, "Q_PbSunDn")
+
+    # Absorbed incoming diffuse PAR by sunlit leaves
+    Q_PdSunDn = PARDiff * (1.0 - albedo_visible) * (1.0 - np.exp(-(kk_Pd + kb) * L_CI)) * kk_Pd / (
+            kk_Pd + kb)  # Eq. (4)
+    check_distribution(Q_PdSunDn, "Q_PdSunDn")
+
+    # Absorbed incoming scattered PAR by sunlit leaves
+    Q_PsSunDn = PARDir * (
+            (1.0 - albedo_visible) * (1.0 - np.exp(-(kk_Pb + kb) * L_CI)) * kk_Pb / (kk_Pb + kb) - (1.0 - SIGMA_P) * (
+            1.0 - np.exp(-2.0 * kb * L_CI)) / 2.0)  # Eq. (5)
+    Q_PsSunDn = np.clip(Q_PsSunDn, 0, None)
+    check_distribution(Q_PsSunDn, "Q_PsSunDn")
+
+    # Absorbed incoming PAR by sunlit leaves
+    Q_PSunDn = Q_PbSunDn + Q_PdSunDn + Q_PsSunDn  # Eq. (6)
+    check_distribution(Q_PSunDn, "Q_PSunDn")
+
+    # Absorbed incoming PAR by shade leaves
+    Q_PShDn = np.clip(Q_PDn - Q_PSunDn, 0, None)  # Eq. (7)
+    check_distribution(Q_PShDn, "Q_PShDn")
+
+    # Incoming PAR at soil surface
+    I_PSoil = np.clip((1.0 - albedo_visible) * PARDir + (1 - albedo_visible) * PARDiff - (Q_PSunDn + Q_PShDn), 0, None)
+    check_distribution(I_PSoil, "I_PSoil")
+
+    # Absorbed PAR by soil
+    APAR_Soil = np.clip((1.0 - RHO_PSOIL) * I_PSoil, 0, None)
+    check_distribution(APAR_Soil, "APAR_Soil")
+
+    # Absorbed outgoing PAR by sunlit leaves
+    Q_PSunUp = np.clip(I_PSoil * RHO_PSOIL * exp_kk_Pd_L_CI, 0, None)  # Eq. (8)
+    check_distribution(Q_PSunUp, "Q_PSunUp")
+
+    # Absorbed outgoing PAR by shade leaves
+    Q_PShUp = np.clip(I_PSoil * RHO_PSOIL * (1 - exp_kk_Pd_L_CI), 0, None)  # Eq. (9)
+    check_distribution(Q_PShUp, "Q_PShUp")
+
+    # Total absorbed PAR by sunlit leaves
+    APAR_Sun = Q_PSunDn + Q_PSunUp  # Eq. (10)
+    check_distribution(APAR_Sun, "APAR_Sun")
+
+    # Total absorbed PAR by shade leaves
+    APAR_Sh = Q_PShDn + Q_PShUp  # Eq. (11)
+    check_distribution(APAR_Sh, "APAR_Sh")
+
+    # Absorbed incoming NIR by sunlit leaves
+    Q_NSunDn = NIRDir * (1.0 - SIGMA_N) * (1.0 - np.exp(-kb * L_CI)) + NIRDiff * (1 - albedo_NIR) * (
+            1.0 - np.exp(-(kk_Nd + kb) * L_CI)) * kk_Nd / (kk_Nd + kb) + NIRDir * (
+                       (1.0 - albedo_NIR) * (1.0 - np.exp(-(kk_Nb + kb) * L_CI)) * kk_Nb / (kk_Nb + kb) - (
+                       1.0 - SIGMA_N) * (1.0 - np.exp(-2.0 * kb * L_CI)) / 2.0)  # Eq. (14)
+    Q_NSunDn = np.clip(Q_NSunDn, 0, None)
+    check_distribution(Q_NSunDn, "Q_NSunDn")
+
+    # Absorbed incoming NIR by shade leaves
+    Q_NShDn = (1.0 - albedo_NIR) * NIRDir * (1.0 - np.exp(-kk_Nb * L_CI)) + (1.0 - albedo_NIR) * NIRDiff * (
+            1.0 - exp_kk_Nd_L_CI) - Q_NSunDn  # Eq. (15)
+    Q_NShDn = np.clip(Q_NShDn, 0, None)
+    check_distribution(Q_NShDn, "Q_NShDn")
+
+    # Incoming NIR at soil surface
+    I_NSoil = (1.0 - albedo_NIR) * NIRDir + (1.0 - albedo_NIR) * NIRDiff - (Q_NSunDn + Q_NShDn)
+    I_NSoil = np.clip(I_NSoil, 0, None)
+    check_distribution(I_NSoil, "I_NSoil")
+
+    # Absorbed NIR by soil
+    ANIR_Soil = (1.0 - RHO_NSOIL) * I_NSoil
+    ANIR_Soil = np.clip(ANIR_Soil, 0, None)
+    check_distribution(ANIR_Soil, "ANIR_Soil")
+
+    # Absorbed outgoing NIR by sunlit leaves
+    Q_NSunUp = I_NSoil * RHO_NSOIL * exp_kk_Nd_L_CI  # Eq. (16)
+    Q_NSunUp = np.clip(Q_NSunUp, 0, None)
+    check_distribution(Q_NSunUp, "Q_NSunUp")
+
+    # Absorbed outgoing NIR by shade leaves
+    Q_NShUp = I_NSoil * RHO_NSOIL * (1.0 - exp_kk_Nd_L_CI)  # Eq. (17)
+    Q_NShUp = np.clip(Q_NShUp, 0, None)
+    check_distribution(Q_NShUp, "Q_NShUp")
+
+    # Total absorbed NIR by sunlit leaves
+    ANIR_Sun = Q_NSunDn + Q_NSunUp  # Eq. (18)
+    check_distribution(ANIR_Sun, "ANIR_Sun")
+
+    # Total absorbed NIR by shade leaves
+    ANIR_Sh = Q_NShDn + Q_NShUp  # Eq. (19)
+    check_distribution(ANIR_Sh, "ANIR_Sh")
+
+    # UV
+    UVDir = UV * PARDir / (PARDir + PARDiff + 1e-5)
+    UVDiff = UV - UVDir
+    Q_U = (1.0 - 0.05) * UVDiff * (1.0 - np.exp(-kk_Pb * L_CI)) + (1.0 - 0.05) * UVDiff * (1.0 - exp_kk_Pd_L_CI)
+    AUV_Sun = Q_U * fSun
+    AUV_Sh = Q_U * (1 - fSun)
+    AUV_Soil = (1.0 - 0.05) * UV - Q_U
+
+    # Ground heat storage
+    G = APAR_Soil * 0.28
+    check_distribution(G, "G")
+
+    # Summary
+    ASW_Sun = APAR_Sun + ANIR_Sun + AUV_Sun
+    ASW_Sun = np.where(LAI == 0, 0, ASW_Sun)
+    ASW_Sh = APAR_Sh + ANIR_Sh + AUV_Sh
+    ASW_Sh = np.where(LAI == 0, 0, ASW_Sh)
+    ASW_Soil = APAR_Soil + ANIR_Soil + AUV_Soil
+    APAR_Sun = np.where(LAI == 0, 0, APAR_Sun)
+    APAR_Sun = APAR_Sun * 4.56
+    APAR_Sh = np.where(LAI == 0, 0, APAR_Sh)
+    APAR_Sh = APAR_Sh * 4.56
+
+    # TODO not sure about these variables: Vcmax25_C3Sun, Vcmax25_C3Sh, Vcmax25_C4Sun, Vcmax25_C4Sh
+
+    return fSun, APAR_Sun, APAR_Sh, ASW_Sun, ASW_Sh, ASW_Soil, G