BESS-JPL 1.6.0__py3-none-any.whl

BESS_JPL/carbon_water_fluxes.py

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+from os.path import join, abspath, dirname
+from typing import Union
+
+import numpy as np
+import rasters as rt
+from rasters import Raster, RasterGeometry
+from .C3_photosynthesis import calculate_C3_photosynthesis
+from .C4_photosynthesis import calculate_C4_photosynthesis
+from .canopy_longwave_radiation import canopy_longwave_radiation
+from .canopy_energy_balance import canopy_energy_balance
+from .soil_energy_balance import soil_energy_balance
+
+PASSES = 1
+
+
+def load_ball_berry_intercept_C3(self, geometry: RasterGeometry) -> Raster:
+    filename = join(abspath(dirname(__file__)), "ball_berry_intercept_C3.tif")
+    image = rt.Raster.open(filename, geometry=geometry, resampling=self.resampling)
+
+    return image
+
+def load_ball_berry_slope_C3(self, geometry: RasterGeometry) -> Raster:
+    filename = join(abspath(dirname(__file__)), "ball_berry_slope_C3.tif")
+    image = rt.Raster.open(filename, geometry=geometry, resampling=self.resampling)
+
+    return image
+
+def load_ball_berry_slope_C4(self, geometry: RasterGeometry) -> Raster:
+    filename = join(abspath(dirname(__file__)), "ball_berry_slope_C4.tif")
+    image = rt.Raster.open(filename, geometry=geometry, resampling=self.resampling)
+
+    return image
+
+def carbon_water_fluxes(
+        canopy_temperature_K: np.ndarray,  # canopy temperature in Kelvin
+        soil_temperature_K: np.ndarray,  # soil temperature in Kelvin
+        LAI: np.ndarray,  # leaf area index
+        Ta_K: np.ndarray,  # air temperature in Kelvin
+        APAR_sunlit: np.ndarray,  # sunlit leaf absorptance to photosynthetically active radiation [umol m-2 s-1]
+        APAR_shaded: np.ndarray,  # shaded leaf absorptance to photosynthetically active radiation [umol m-2 s-1]
+        ASW_sunlit: np.ndarray,  # sunlit absorbed shortwave radiation [W m-2]
+        ASW_shaded: np.ndarray,  # shaded absorbed shortwave radiation [W m-2]
+        ASW_soil: np.ndarray,  # absorbed shortwave radiation in soil
+        Vcmax25_sunlit: np.ndarray,  # sunlit maximum carboxylation rate at 25C
+        Vcmax25_shaded: np.ndarray,  # shaded maximum carboxylation rate at 25C
+        ball_berry_slope: np.ndarray,  # Ball-Berry slope
+        ball_berry_intercept: Union[np.ndarray, float],  # Ball-Berry intercept
+        sunlit_fraction: np.ndarray,  # sunlit fraction of canopy
+        G: np.ndarray,  # soil heat flux in W m-2
+        SZA: np.ndarray,  # solar zenith angle in degrees
+        Ca: np.ndarray,  # atmospheric CO2 concentration in umol mol-1
+        Ps_Pa: np.ndarray,  # surface pressure in Pascal
+        gamma: np.ndarray,  # psychrometric constant in Pa K-1
+        Cp: np.ndarray,  # specific heat capacity of air in J kg-1 K-1
+        rhoa: np.ndarray,  # air density in kg m-3
+        VPD_Pa: np.ndarray,  # vapor pressure deficit in Pascal
+        RH: np.ndarray,  # relative humidity as a fraction
+        desTa: np.ndarray,
+        ddesTa: np.ndarray,
+        epsa: np.ndarray,
+        Rc: np.ndarray,
+        Rs: np.ndarray,
+        carbon_uptake_efficiency: np.ndarray,  # intrinsic quantum efficiency of carbon uptake
+        fStress: np.ndarray,
+        C4_photosynthesis: bool,  # C3 or C4 photosynthesis
+        passes: int = PASSES):  # number of iterations
+    # carbon = 4 if C4_photosynthesis else 3
+    GPP_max = 50 if C4_photosynthesis else 40
+
+    # this model originally initialized soil and canopy temperature to air temperature
+    Tf_K_sunlit = canopy_temperature_K
+    Tf_K_shaded = canopy_temperature_K
+    Tf_K = canopy_temperature_K
+    Ts_K = soil_temperature_K
+
+    # initialize intercellular CO2 concentration to atmospheric CO2 concentration depending on C3 or C4 photosynthesis
+    chi = 0.4 if C4_photosynthesis else 0.7
+    Ci_sunlit = Ca * chi
+    Ci_shaded = Ca * chi
+
+    ball_berry_intercept = ball_berry_intercept * fStress
+
+    epsf = 0.98
+    epss = 0.96
+
+    # initialize sunlit partition (overwritten when iterations process)
+
+    # initialize sunlit net assimilation rate to zero
+    An_sunlit = Tf_K_sunlit * 0
+
+    # initialize sunlit net radiation to zero
+    Rn_sunlit = Tf_K_sunlit * 0
+
+    # initialize sunlit latent heat flux to zero
+    LE_sunlit = Tf_K_sunlit * 0
+
+    # initialize sunlit sensible heat flux to zero
+    H_sunlit = Tf_K_sunlit * 0
+
+    # initialize shaded partition (overwritten when iterations process)
+
+    # initialize shaded net assimilation rate to zero
+    An_shaded = Tf_K_shaded * 0
+
+    # initialize shaded net radiation to zero
+    Rn_shaded = Tf_K_shaded * 0
+
+    # initialize shaded latent heat flux to zero
+    LE_shaded = Tf_K_shaded * 0
+
+    # initialize shaded sensible heat flux to zero
+    H_shaded = Tf_K_shaded * 0
+
+    # initialize soil partition (overwritten when iterations process)
+
+    # initialize soil net radiation to zero
+    Rn_soil = Ts_K * 0
+
+    # initialize soil latent heat flux to zero
+    LE_soil = Ts_K * 0
+
+    # Iteration
+    for iter in range(1, passes + 1):
+
+        # Longwave radiation
+        # CLR:[ALW_Sun, ALW_shaded, ALW_Soil, Ls, La]
+        ALW_sunlit, ALW_shaded, ALW_soil, Ls, La, Lf = canopy_longwave_radiation(
+            LAI=LAI,  # leaf area index (LAI) [-]
+            SZA=SZA,  # solar zenith angle (degrees)
+            Ts_K=Ts_K,  # soil temperature (Ts) [K]
+            Tf_K=Tf_K,  # foliage temperature (Tf) [K]
+            Ta_K=Ta_K,  # air temperature (Ta) [K]
+            epsa=epsa,  # clear-sky emissivity (epsa) [-]
+            epsf=epsf,  # foliage emissivity (epsf) [-]
+            epss=epss  # soil emissivity (epss) [-],
+        )
+
+        # calculate sunlit photosynthesis
+        if C4_photosynthesis:
+            # calculate sunlit photosynthesis for C4 plants
+            An_sunlit = calculate_C4_photosynthesis(
+                Tf_K=Tf_K_sunlit,  # sunlit leaf temperature (Tf) [K]
+                Ci=Ci_sunlit,  # sunlit intercellular CO2 concentration (Ci) [umol mol-1]
+                APAR=APAR_sunlit,  # sunlit leaf absorptance to photosynthetically active radiation [umol m-2 s-1]
+                Vcmax25=Vcmax25_sunlit  # sunlit maximum carboxylation rate at 25C (Vcmax25) [umol m-2 s-1]
+            )
+        else:
+            # calculate sunlit photosynthesis for C3 plants
+            An_sunlit = calculate_C3_photosynthesis(
+                Tf_K=Tf_K_sunlit,  # sunlit leaf temperature (Tf) [K]
+                Ci=Ci_sunlit,  # sunlit intercellular CO2 concentration (Ci) [umol mol-1]
+                APAR=APAR_sunlit,  # sunlit leaf absorptance to photosynthetically active radiation [umol m-2 s-1]
+                Vcmax25=Vcmax25_sunlit,  # sunlit maximum carboxylation rate at 25C (Vcmax25) [umol m-2 s-1]
+                Ps_Pa=Ps_Pa,  # surface pressure (Ps) [Pa]
+                carbon_uptake_efficiency=carbon_uptake_efficiency  # intrinsic quantum efficiency for carbon uptake
+            )
+
+        # calculate sunlit energy balance
+        Rn_sunlit_new, LE_sunlit_new, H_sunlit_new, Tf_K_sunlit_new, gs2_sunlit_new, Ci_sunlit_new = canopy_energy_balance(
+            An=An_sunlit,  # net assimulation (An) [umol m-2 s-1]
+            ASW=ASW_sunlit,  # total absorbed shortwave radiation by sunlit canopy (ASW) [umol m-2 s-1]
+            ALW=ALW_sunlit,  # total absorbed longwave radiation by sunlit canopy (ALW) [umol m-2 s-1]
+            Tf_K=Tf_K_sunlit,  # sunlit leaf temperature (Tf) [K]
+            Ps_Pa=Ps_Pa,  # surface pressure (Ps) [Pa]
+            Ca=Ca,  # ambient CO2 concentration (Ca) [umol mol-1]
+            Ta_K=Ta_K,  # air temperature (Ta) [K]
+            RH=RH,  # relative humidity (RH) [-]
+            VPD_Pa=VPD_Pa,  # water vapour deficit (VPD) [Pa]
+            desTa=desTa,  # 1st derivative of saturated vapour pressure (desTa)
+            ddesTa=ddesTa,  # 2nd derivative of saturated vapour pressure (ddesTa)
+            gamma=gamma,  # psychrometric constant (gamma) [pa K-1]
+            Cp=Cp,  # specific heat of air at constant pressure (Cp) [J kg-1 K-1]
+            rhoa=rhoa,  # air density (rhoa) [kg m-3]
+            Rc=Rc,  # TODO is this Ra or Rc in Ball-Berry?
+            ball_berry_slope=ball_berry_slope,  # Ball-Berry slope (m) [-]
+            ball_berry_intercept=ball_berry_intercept,  # Ball-Berry intercept (b0) [-]
+            C4_photosynthesis=C4_photosynthesis  # process for C4 plants instead of C3
+        )
+
+        # filter in sunlit energy balance estimates
+        Rn_sunlit = np.where(np.isnan(Rn_sunlit_new), Rn_sunlit, Rn_sunlit_new)
+        LE_sunlit = np.where(np.isnan(LE_sunlit_new), LE_sunlit, LE_sunlit_new)
+        H_sunlit = np.where(np.isnan(H_sunlit_new), H_sunlit, H_sunlit_new)
+        Tf_K_sunlit = np.where(np.isnan(Tf_K_sunlit_new), Tf_K_sunlit, Tf_K_sunlit_new)
+        Ci_sunlit = np.where(np.isnan(Ci_sunlit_new), Ci_sunlit, Ci_sunlit_new)
+
+        # Photosynthesis (shade)
+        if C4_photosynthesis:
+            An_shaded = calculate_C4_photosynthesis(
+                Tf_K=Tf_K_shaded,  # shaded leaf temperature (Tf) [K]
+                Ci=Ci_shaded,  # shaded intercellular CO2 concentration (Ci) [umol mol-1]
+                APAR=APAR_shaded,  # shaded absorbed photosynthetically active radiation (APAR) [umol m-2 s-1]
+                Vcmax25=Vcmax25_shaded  # shaded maximum carboxylation rate at 25C (Vcmax25) [umol m-2 s-1]
+            )
+        else:
+            An_shaded = calculate_C3_photosynthesis(
+                Tf_K=Tf_K_shaded,  # shaded leaf temperature (Tf) [K]
+                Ci=Ci_shaded,  # shaed intercellular CO2 concentration (Ci) [umol mol-1]
+                APAR=APAR_shaded,  # shaded absorbed photosynthetically active radiation (APAR) [umol m-2 s-1]
+                Vcmax25=Vcmax25_shaded,  # shaded maximum carboxylation rate at 25C (Vcmax25) [umol m-2 s-1]
+                Ps_Pa=Ps_Pa,  # surface pressure (Ps) [Pa]
+                carbon_uptake_efficiency=carbon_uptake_efficiency  # intrinsic quantum efficiency for carbon uptake
+            )
+
+        # calculated shaded energy balance
+        Rn_shaded_new, LE_shaded_new, H_shaded_new, Tf_K_shaded_new, gs2_shaded_new, Ci_shaded_new = canopy_energy_balance(
+            An=An_shaded,  # net assimulation (An) [umol m-2 s-1]
+            ASW=ASW_shaded,  # total absorbed shortwave radiation by shaded canopy (ASW) [umol m-2 s-1]
+            ALW=ALW_shaded,  # total absorbed longwave radiation by shaded canopy (ALW) [umol m-2 s-1]
+            Tf_K=Tf_K_shaded,  # shaded leaf temperature (Tf) [K]
+            Ps_Pa=Ps_Pa,  # surface pressure (Ps) [Pa]
+            Ca=Ca,  # ambient CO2 concentration (Ca) [umol mol-1]
+            Ta_K=Ta_K,  # air temperature (Ta) [K]
+            RH=RH,  # relative humidity as a fraction
+            VPD_Pa=VPD_Pa,  # water vapour deficit (VPD) [Pa]
+            desTa=desTa,  # 1st derivative of saturated vapour pressure (desTa)
+            ddesTa=ddesTa,  # 2nd derivative of saturated vapour pressure (ddesTa)
+            gamma=gamma,  # psychrometric constant (gamma) [pa K-1]
+            Cp=Cp,  # specific heat of air (Cp) [J kg-1 K-1]
+            rhoa=rhoa,  # air density (rhoa) [kg m-3]
+            Rc=Rc,
+            ball_berry_slope=ball_berry_slope,  # Ball-Berry slope (m) [-]
+            ball_berry_intercept=ball_berry_intercept,  # Ball-Berry intercept (b0) [-]
+            C4_photosynthesis=C4_photosynthesis  # process for C4 plants instead of C3
+        )
+
+        # filter in shaded energy balance estimates
+        Rn_shaded = np.where(np.isnan(Rn_shaded_new), Rn_shaded, Rn_shaded_new)
+        LE_shaded = np.where(np.isnan(LE_shaded_new), LE_shaded, LE_shaded_new)
+        H_shaded = np.where(np.isnan(H_shaded_new), H_shaded, H_shaded_new)
+        Tf_K_shaded = np.where(np.isnan(Tf_K_shaded_new), Tf_K_shaded, Tf_K_shaded_new)
+        Ci_shaded = np.where(np.isnan(Ci_shaded_new), Ci_shaded, Ci_shaded_new)
+
+        # calculate soil energy balance
+        Rn_soil_new, LE_soil_new, Ts_K_soil_new = soil_energy_balance(
+            Ts_K=Ts_K,  # soil temperature in Kelvin
+            Ta_K=Ta_K,  # air temperature in Kelvin
+            G=G,  # soil heat flux (G) [W m-2]
+            VPD=VPD_Pa,  # water vapour deficit in Pascal
+            RH=RH,  # relative humidity as a fraction
+            gamma=gamma,  # psychrometric constant (gamma) [pa K-1]
+            Cp=Cp,  # specific heat of air (Cp) [J kg-1 K-1]
+            rhoa=rhoa,  # air density (rhoa) [kg m-3]
+            desTa=desTa,
+            Rs=Rs,
+            ASW_soil=ASW_soil,  # total absorbed shortwave radiation by soil (ASW) [umol m-2 s-1]
+            ALW_soil=ALW_soil,  # total absorbed longwave radiation by soil (ALW) [umol m-2 s-1]
+            Ls=Ls,
+            epsa=epsa
+        )
+
+        # filter in soil energy balance estimates
+        # where new estimates are missing, retain the prior estimates
+        Rn_soil = np.where(np.isnan(Rn_soil_new), Rn_soil, Rn_soil_new)
+        LE_soil = np.where(np.isnan(LE_soil_new), LE_soil, LE_soil_new)
+        Ts_K = np.where(np.isnan(Ts_K_soil_new), Ts_K, Ts_K_soil_new)
+
+        # combine sunlit and shaded foliage temperatures
+        Tf_K_new = (((Tf_K_sunlit ** 4) * sunlit_fraction + (Tf_K_shaded ** 4) * (1 - sunlit_fraction)) ** 0.25)
+        Tf_K = np.where(np.isnan(Tf_K_new), Tf_K, Tf_K_new)
+
+    # calculate canopy latent heat flux
+    LE_canopy = np.clip(LE_sunlit + LE_shaded, 0, 1000)
+
+    # calculate latent heat flux
+    LE = np.clip(LE_sunlit + LE_shaded + LE_soil, 0, 1000)  # [W m-2]
+
+    # calculate gross primary productivity
+    GPP = np.clip(An_sunlit + An_shaded, 0, GPP_max)  # [umol m-2 s-1]
+
+    # calculate canopy net radiation
+    Rn_canopy = np.clip(Rn_sunlit + Rn_shaded, 0, None)
+
+    # calculate net radiation
+    Rn = np.clip(Rn_sunlit + Rn_shaded + Rn_soil, 0, 1000)  # [W m-2]
+
+    return GPP, LE, LE_soil, LE_canopy, Rn, Rn_soil, Rn_canopy

BESS_JPL/constants.py

@@ -0,0 +1,8 @@
+A = 0.3
+KPAR = 0.5
+MIN_FIPAR = 0.0
+MAX_FIPAR = 1.0
+MIN_LAI = 0.0
+MAX_LAI = 10.0
+BALL_BERRY_INTERCEPT_C4 = 0.04
+RESAMPLING = "cubic"

BESS_JPL/interpolate_C3_C4.py

@@ -0,0 +1,12 @@
+import numpy as np
+
+
+def interpolate_C3_C4(C3: np.ndarray, C4: np.ndarray, C4_fraction: np.ndarray) -> np.ndarray:
+    """
+    Interpolate between C3 and C4 plants based on C4 fraction
+    :param C3: value for C3 plants
+    :param C4: value for C4 plants
+    :param C4_fraction: fraction of C4 plants
+    :return: interpolated value
+    """
+    return C3 * (1 - C4_fraction) + C4 * C4_fraction

BESS_JPL/load_C4_fraction.py

@@ -0,0 +1,10 @@
+from os.path import join, abspath, dirname
+
+import rasters as rt
+from rasters import Raster, RasterGeometry
+
+def load_C4_fraction(geometry: RasterGeometry = None, resampling: str = "nearest") -> Raster:
+    filename = join(abspath(dirname(__file__)), "C4_fraction.tif")
+    image = Raster.open(filename, geometry=geometry, resampling=resampling)
+
+    return image

BESS_JPL/load_NDVI_maximum.py

@@ -0,0 +1,10 @@
+from os.path import join, abspath, dirname
+
+import rasters as rt
+from rasters import Raster, RasterGeometry
+
+def load_NDVI_maximum(geometry: RasterGeometry = None, resampling: str = "nearest") -> Raster:
+    filename = join(abspath(dirname(__file__)), "NDVI_maximum.tif")
+    image = Raster.open(filename, geometry=geometry, resampling=resampling)
+
+    return image

BESS_JPL/load_NDVI_minimum.py

@@ -0,0 +1,10 @@
+from os.path import join, abspath, dirname
+
+import rasters as rt
+from rasters import Raster, RasterGeometry
+
+def load_NDVI_minimum(geometry: RasterGeometry = None, resampling: str = "nearest") -> Raster:
+    filename = join(abspath(dirname(__file__)), "NDVI_minimum.tif")
+    image = Raster.open(filename, geometry=geometry, resampling=resampling)
+
+    return image

BESS_JPL/load_ball_berry_intercept_C3.py

@@ -0,0 +1,10 @@
+from os.path import join, abspath, dirname
+
+import rasters as rt
+from rasters import Raster, RasterGeometry
+
+def load_ball_berry_intercept_C3(geometry: RasterGeometry = None, resampling: str = "nearest") -> Raster:
+    filename = join(abspath(dirname(__file__)), "ball_berry_intercept_C3.tif")
+    image = Raster.open(filename, geometry=geometry, resampling=resampling)
+
+    return image

BESS_JPL/load_ball_berry_slope_C3.py

@@ -0,0 +1,10 @@
+from os.path import join, abspath, dirname
+
+import rasters as rt
+from rasters import Raster, RasterGeometry
+
+def load_ball_berry_slope_C3(geometry: RasterGeometry = None, resampling: str = "nearest") -> Raster:
+    filename = join(abspath(dirname(__file__)), "ball_berry_slope_C3.tif")
+    image = Raster.open(filename, geometry=geometry, resampling="nearest")
+
+    return image

BESS_JPL/load_ball_berry_slope_C4.py

@@ -0,0 +1,10 @@
+from os.path import join, abspath, dirname
+
+import rasters as rt
+from rasters import Raster, RasterGeometry
+
+def load_ball_berry_slope_C4(geometry: RasterGeometry = None, resampling: str = "nearest") -> Raster:
+    filename = join(abspath(dirname(__file__)), "ball_berry_slope_C4.tif")
+    image = Raster.open(filename, geometry=geometry, resampling="nearest")
+
+    return image

BESS_JPL/load_carbon_uptake_efficiency.py

@@ -0,0 +1,10 @@
+from os.path import join, abspath, dirname
+
+import rasters as rt
+from rasters import Raster, RasterGeometry
+
+def load_carbon_uptake_efficiency(geometry: RasterGeometry = None, resampling: str = "nearest") -> Raster:
+    filename = join(abspath(dirname(__file__)), "carbon_uptake_efficiency.tif")
+    image = Raster.open(filename, geometry=geometry, resampling=resampling)
+
+    return image

BESS_JPL/load_kn.py

@@ -0,0 +1,10 @@
+from os.path import join, abspath, dirname
+
+import rasters as rt
+from rasters import Raster, RasterGeometry
+
+def load_kn(geometry: RasterGeometry = None, resampling: str = "nearest") -> Raster:
+    filename = join(abspath(dirname(__file__)), "kn.tif")
+    image = Raster.open(filename, geometry=geometry, resampling="nearest")
+
+    return image

BESS_JPL/load_peakVCmax_C3.py

@@ -0,0 +1,10 @@
+from os.path import join, abspath, dirname
+
+import rasters as rt
+from rasters import Raster, RasterGeometry
+
+def load_peakVCmax_C3(geometry: RasterGeometry = None, resampling: str = "nearest") -> Raster:
+    filename = join(abspath(dirname(__file__)), "peakVCmax_C3.tif")
+    image = Raster.open(filename, geometry=geometry, resampling="nearest")
+
+    return image

BESS_JPL/load_peakVCmax_C4.py

@@ -0,0 +1,10 @@
+from os.path import join, abspath, dirname
+
+import rasters as rt
+from rasters import Raster, RasterGeometry
+
+def load_peakVCmax_C4(geometry: RasterGeometry = None, resampling: str = "nearest") -> Raster:
+    filename = join(abspath(dirname(__file__)), "peakVCmax_C4.tif")
+    image = Raster.open(filename, geometry=geometry, resampling="nearest")
+
+    return image

BESS_JPL/meteorology.py

@@ -0,0 +1,204 @@
+from typing import Tuple
+import numpy as np
+
+
+def SVP_kPa_from_Ta_C(Ta_C: np.ndarray) -> np.ndarray:
+    """
+    saturation vapor pressure in kPa from air temperature in celsius
+    :param Ta_C: air temperature in celsius
+    :return: saturation vapor pressure in kiloPascal
+    """
+    return 0.611 * np.exp((Ta_C * 17.27) / (Ta_C + 237.7))
+
+
+def SVP_Pa_from_Ta_K(Ta_K: np.ndarray) -> np.ndarray:
+    """
+    saturation vapor pressure in kPa from air temperature in celsius
+    :param Ta_K: air temperature in Kelvin
+    :return: saturation vapor pressure in kiloPascal
+    """
+    Ta_C = Ta_K - 273.15
+    SVP_kPa = SVP_kPa_from_Ta_C(Ta_C)
+    SVP_Pa = SVP_kPa * 1000
+
+    return SVP_Pa
+
+
+def meteorology(
+        day_of_year: np.ndarray,  # day of year
+        hour_of_day: np.ndarray,  # hour of day
+        latitude: np.ndarray,  # latitude
+        elevation_m: np.ndarray,  # elevation in meters
+        SZA: np.ndarray,  # solar zenith angle in degrees
+        Ta_K: np.ndarray,  # air temperature in Kelvin
+        Ea_Pa: np.ndarray,  # vapor pressure in Pascal
+        Rg: np.ndarray,  # shortwave radiation in W/m2
+        wind_speed_mps: np.ndarray,  # wind speed in meters per second
+        canopy_height_meters: np.ndarray):  # canopy height in meters
+    """
+    Meteorological calculations for Breathing Earth System Simulator
+    Adapted from Youngryel Ryu's MATLAB code by Gregory Halverson and Robert Freepartner
+    :param day_of_year: day of year
+    :param hour_of_day: hour of day
+    :param latitude: latitude
+    :param elevation_m: elevation in meters
+    :param SZA: solar zenith angle in degrees
+    :param Ta_K: air temperature in Kelvin
+    :param Ea_Pa: vapor pressure in Pascal
+    :param Rg: shortwave radiation in W/m2
+    :param wind_speed_mps: wind speed in meters per second
+    :param canopy_height_meters: canopy height in meters
+    :return: 
+    Ps_Pa surface pressure in Pascal
+    VPD_Pa water vapor deficit in Pascal
+    RH relative humidity as a fraction
+    desTa 1st derivative of saturated vapor pressure
+    ddesTa 2nd derivative of saturated vapor pressure
+    gamma psychrometric constant in Pa K-1
+    Cp specific heat of air in J kg-1 K-1
+    rhoa air density in kg m-3
+    epsa all-sky emissivity
+    R
+    Rc
+    Rs
+    SFd
+    SFd2
+    DL
+    Ra
+    fStress
+    """""
+    # Allen et al., 1998 (FAO)
+
+    # surface pressure
+    Ps_Pa = 101325.0 * (1.0 - 0.0065 * elevation_m / Ta_K) ** (9.807 / (0.0065 * 287.0))  # [Pa]
+
+    # air temperature in Celsius
+    Ta_C = Ta_K - 273.16  # [Celsius]
+
+    # dewpoint temperature in Celsius
+    # Td_C = Td_K - 273.16  # [Celsius]
+
+    # ambient vapour pressure
+    # Ea_Pa = 0.6108 * np.exp((17.27 * Td_C) / (Td_C + 237.3)) * 1000  # [Pa]
+
+    # saturated vapour pressure
+    SVP_Pa = 0.6108 * np.exp((17.27 * Ta_C) / (Ta_C + 237.3)) * 1000  # [Pa]
+
+    # water vapour deficit
+    VPD_Pa = np.clip(SVP_Pa - Ea_Pa, 0, None)  # [Pa]
+
+    # relative humidity
+    RH = np.clip(Ea_Pa / SVP_Pa, 0, 1)  # [-]
+
+    # 1st derivative of saturated vapour pressure
+    desTa = SVP_Pa * 4098.0 * pow((Ta_C + 237.3), (-2))  # [Pa K-1]
+
+    # 2nd derivative of saturated vapour pressure
+    ddesTa = 4098.0 * (desTa * pow((Ta_C + 237.3), (-2)) + (-2) * SVP_Pa * pow((Ta_C + 237.3), (-3)))  # [Pa K-2]
+
+    # latent Heat of Vaporization
+    latent_heat = 2.501 - (2.361e-3 * Ta_C)  # [J kg-1]
+
+    # psychrometric constant
+    gamma = 0.00163 * Ps_Pa / latent_heat  # [Pa K-1]
+
+    # specific heat
+    # this formula for specific heat was generating extreme negative values that threw off the energy balance calculation
+    # Cp = 0.24 * 4185.5 * (1.0 + 0.8 * (0.622 * Ea_Pa / (Ps_Pa - Ea_Pa)))  # [J kg-1 K-1]
+
+    # ratio molecular weight of water vapour dry air
+    mv_ma = 0.622  # [-] (Wiki)
+
+    # specific humidity
+    q = (mv_ma * Ea_Pa) / (Ps_Pa - 0.378 * Ea_Pa)  # 3 [-] (Garratt, 1994)
+
+    # specific heat of dry air
+    Cpd = 1005 + (Ta_K - 250) ** 2 / 3364  # [J kg-1 K-1] (Garratt, 1994)
+
+    # specific heat of air
+    Cp = Cpd * (1 + 0.84 * q)  # [J kg-1 K-1] (Garratt, 1994)
+
+    # virtual temperature
+    # Tv_K = Ta_K * 1.0 / (1 - 0.378 * Ea_Pa / Ps_Pa)  # [K]
+
+    # air density
+    # rhoa = Ps_Pa / (287.0 * Tv_K)  # [kg m-3]
+
+    # air density
+    rhoa = Ps_Pa / (287.05 * Ta_K)  # [kg m-3] (Garratt, 1994)
+
+    # inverse relative distance Earth-Sun
+    dr = 1.0 + 0.033 * np.cos(2 * np.pi / 365.0 * day_of_year)  # [-]
+
+    # solar declination
+    delta = 0.409 * np.sin(2 * np.pi / 365.0 * day_of_year - 1.39)  # [rad]
+
+    # sunset hour angle
+    # Note: the value for arccos may be invalid (< -1.0 or > 1.0).
+    # This will result in NaN values in omegaS.
+    omegaS = np.arccos(-np.tan(latitude * np.pi / 180.0) * np.tan(delta))  # [rad]
+
+    # omegaS[np.logical_or(np.isnan(omegaS), np.isinf(omegaS))] = 0.0
+    omegaS = np.where(np.isnan(omegaS) | np.isinf(omegaS), 0, omegaS)
+    omegaS = np.real(omegaS)
+
+    # Day length
+    DL = 24.0 / np.pi * omegaS
+
+    # snapshot radiation
+    Ra = 1333.6 * dr * np.cos(SZA * np.pi / 180.0)
+
+    # Daily mean radiation
+    RaDaily = 1333.6 / np.pi * dr * (omegaS * np.sin(latitude * np.pi / 180.0) * np.sin(delta)
+                                     + np.cos(latitude * np.pi / 180.0) * np.cos(delta) * np.sin(omegaS))
+    # clear-sky solar radiation
+    Rgo = (0.75 + 2e-5 * elevation_m) * Ra  # [W m-2]
+
+    # Choi et al., 2008: The Crawford and Duchon’s cloudiness factor with Brunt equation is recommended.
+
+    # cloudy index
+    cloudy = 1.0 - Rg / Rgo  # [-]
+    # cloudy[cloudy < 0] = 0
+    # cloudy[cloudy > 1] = 1
+    cloudy = np.clip(cloudy, 0, 1)
+
+    # clear-sky emissivity
+    epsa0 = 0.605 + 0.048 * (Ea_Pa / 100) ** 0.5  # [-]
+
+    # all-sky emissivity
+    epsa = epsa0 * (1 - cloudy) + cloudy  # [-]
+
+    # Ryu et al. 2008 2012
+
+    # Upscaling factor
+    # non0msk = RaDaily != 0
+    # SFd = np.empty(np.shape(RaDaily))
+    # SFd[non0msk] = 1800.0 * Ra[non0msk] / (RaDaily[non0msk] * 3600 * 24)
+    # SFd[np.logical_not(non0msk)] = 1.0
+    SFd = np.where(RaDaily != 0, 1800.0 * Ra / (RaDaily * 3600 * 24), 1)
+    # SFd[SZA > 89.0] = 1.0
+    SFd = np.where(SZA > 89.0, 1, SFd)
+    # SFd[SFd > 1.0] = 1.0
+    SFd = np.clip(SFd, None, 1)
+
+    # bulk aerodynamic resistance
+    k = 0.4  # von Karman constant
+    z0 = np.clip(canopy_height_meters * 0.05, 0.05, None)
+    ustar = wind_speed_mps * k / (np.log(10.0 / z0))  # Stability item ignored
+    R = wind_speed_mps / (ustar * ustar) + 2.0 / (k * ustar)  # Eq. (2-4) in Ryu et al 2008
+    R = np.clip(R, None, 1000)
+    Rs = 0.5 * R
+    Rc = R  # was: Rc = 0.5 * R * 2
+
+    # Bisht et al., 2005
+    DL = DL - 1.5
+
+    # Time difference between overpass and midday
+    dT = np.abs(hour_of_day - 12.0)
+
+    # Upscaling factor for net radiation
+    SFd2 = 1.5 / (np.pi * np.sin((DL - 2.0 * dT) / (2.0 * DL) * np.pi)) * DL / 24.0
+
+    fStress = RH ** (VPD_Pa / 1000.0)
+
+    return Ps_Pa, VPD_Pa, RH, desTa, ddesTa, gamma, Cp, rhoa, epsa, R, Rc, Rs, SFd, SFd2, DL, Ra, fStress

BESS_JPL/soil_energy_balance.py

@@ -0,0 +1,35 @@
+import numpy as np
+
+
+def soil_energy_balance(
+        Ts_K: np.ndarray,
+        Ta_K: np.ndarray,
+        G: np.ndarray,
+        VPD: np.ndarray,
+        RH: np.ndarray,
+        gamma: np.ndarray,
+        Cp: np.ndarray,
+        rhoa: np.ndarray,
+        desTa: np.ndarray,
+        Rs: np.ndarray,
+        ASW_soil: np.ndarray,
+        ALW_soil: np.ndarray,
+        Ls: np.ndarray,
+        epsa: np.ndarray):
+    # Net radiation
+    # Rn = Rnet - Rn_Sun - Rn_Sh
+    sigma = 5.670373e-8  # [W m-2 K-4] (Wiki)
+    Rn = np.clip(ASW_soil + ALW_soil - Ls - 4.0 * epsa * sigma * (Ta_K ** 3) * (Ts_K - Ta_K), 0, None)
+    # G = Rn * 0.35
+
+    # Latent heat
+    LE = desTa / (desTa + gamma) * (Rn - G) * (RH ** (VPD / 1000.0))  # (Ryu et al., 2011)
+    LE = np.clip(LE, 0, Rn)
+    # Sensible heat
+    H = np.clip(Rn - G - LE, 0, Rn)
+
+    # Update temperature
+    dT = np.clip(Rs / (rhoa * Cp) * H, -20, 20)
+    Ts_K = Ta_K + dT
+
+    return Rn, LE, Ts_K

BESS_JPL/vegetation_conversion/__init__.py

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