def main(self,
tair,
par,
vpd,
wind,
pressure,
Ca,
doy,
hod,
lat,
lon,
LAI,
rnet=None):
"""
Parameters:
----------
tair : float
air temperature (deg C)
par : float
Photosynthetically active radiation (umol m-2 s-1)
vpd : float
Vapour pressure deficit (kPa, needs to be in Pa, see conversion
below)
wind : float
wind speed (m s-1)
pressure : float
air pressure (using constant) (Pa)
Ca : float
ambient CO2 concentration
doy : float
day of day
hod : float
hour of day
lat : float
latitude
lon : float
longitude
lai : floar
leaf area index
Returns:
--------
An : float
net leaf assimilation (umol m-2 s-1)
gs : float
stomatal conductance (mol m-2 s-1)
et : float
transpiration (mol H2O m-2 s-1)
"""
F = FarquharC3(theta_J=0.85,
peaked_Jmax=True,
peaked_Vcmax=True,
model_Q10=True,
gs_model=self.gs_model,
gamma=self.gamma,
g0=self.g0,
g1=self.g1,
D0=self.D0,
alpha=self.alpha)
P = PenmanMonteith(self.leaf_width, self.SW_abs)
# set initial values
dleaf = vpd
Cs = Ca
Tleaf = tair
Tleaf_K = Tleaf + c.DEG_2_KELVIN
cos_zenith = calculate_solar_geometry(doy, hod, lat, lon)
zenith_angle = np.rad2deg(np.arccos(cos_zenith))
elevation = 90.0 - zenith_angle
# Is the sun up?
if elevation > 0.0 and par > 50.0:
iter = 0
while True:
(An, gsc) = F.photosynthesis(Cs=Cs,
Tleaf=Tleaf_K,
Par=par,
Jmax25=self.Jmax25,
Vcmax25=self.Vcmax25,
Q10=self.Q10,
Eaj=self.Eaj,
Eav=self.Eav,
deltaSj=self.deltaSj,
deltaSv=self.deltaSv,
Rd25=self.Rd25,
Hdv=self.Hdv,
Hdj=self.Hdj,
vpd=dleaf)
# Calculate new Tleaf, dleaf, Cs
(new_tleaf, et, le_et, gbH,
gw) = self.calc_leaf_temp(P,
Tleaf,
tair,
gsc,
par,
vpd,
pressure,
wind,
rnet=rnet)
gbc = gbH * c.GBH_2_GBC
if gbc > 0.0 and An > 0.0:
Cs = Ca - An / gbc # boundary layer of leaf
else:
Cs = Ca
if np.isclose(et, 0.0) or np.isclose(gw, 0.0):
dleaf = vpd
else:
dleaf = (et * pressure / gw) * c.PA_2_KPA # kPa
# Check for convergence...?
if math.fabs(Tleaf - new_tleaf) < 0.02:
break
if iter > self.iter_max:
#raise Exception('No convergence: %d' % (iter))
An = 0.0
gsc = 0.0
et = 0.0
break
# Update temperature & do another iteration
Tleaf = new_tleaf
Tleaf_K = Tleaf + c.DEG_2_KELVIN
iter += 1
an_canopy = An * LAI
gsw_canopy = gsc * c.GSC_2_GSW * LAI
et_canopy = et * LAI
tcanopy = Tleaf
else:
an_canopy = 0.0
gsw_canopy = 0.0
et_canopy = 0.0
tcanopy = tair
return (an_canopy, gsw_canopy, et_canopy, tcanopy)
def main():
lat = -23.575001
lon = 152.524994
doy = 180.0
#
## Met data ...
#
(par, tair, vpd) = get_met_data(lat, lon, doy)
wind = 2.5
pressure = 101325.0
Ca = 400.0
# more realistic VPD
rh = 40.
esat = calc_esat(tair)
ea = rh / 100. * esat
vpd = (esat - ea) * c.PA_2_KPA
vpd = np.where(vpd < 0.05, 0.05, vpd)
#plt.plot(vpd)
#plt.show()
#sys.exit()
## Parameters
#
g0 = 0.001
g1 = 1.5635 # Puechabon
D0 = 1.5 # kpa
Vcmax25 = 60.0
Jmax25 = Vcmax25 * 1.67
Rd25 = 2.0
Eaj = 30000.0
Eav = 60000.0
deltaSj = 650.0
deltaSv = 650.0
Hdv = 200000.0
Hdj = 200000.0
Q10 = 2.0
gamma = 0.0
leaf_width = 0.02
LAI = 3.
# Cambell & Norman, 11.5, pg 178
# The solar absorptivities of leaves (-0.5) from Table 11.4 (Gates, 1980)
# with canopies (~0.8) from Table 11.2 reveals a surprising difference.
# The higher absorptivityof canopies arises because of multiple reflections
# among leaves in a canopy and depends on the architecture of the canopy.
SW_abs = 0.8 # use canopy absorptance of solar radiation
##
### Run Big-leaf
##
B = BigLeaf(g0,
g1,
D0,
gamma,
Vcmax25,
Jmax25,
Rd25,
Eaj,
Eav,
deltaSj,
deltaSv,
Hdv,
Hdj,
Q10,
leaf_width,
SW_abs,
gs_model="medlyn")
An_bl = np.zeros(48)
gsw_bl = np.zeros(48)
et_bl = np.zeros(48)
tcan_bl = np.zeros(48)
hod = 0
for i in range(len(par)):
(An_bl[i], gsw_bl[i], et_bl[i],
tcan_bl[i]) = B.main(tair[i], par[i], vpd[i], wind, pressure, Ca, doy,
hod, lat, lon, LAI)
hod += 1
##
### Run 2-leaf
##
T = TwoLeaf(g0,
g1,
D0,
gamma,
Vcmax25,
Jmax25,
Rd25,
Eaj,
Eav,
deltaSj,
deltaSv,
Hdv,
Hdj,
Q10,
leaf_width,
SW_abs,
gs_model="medlyn")
An_tl = np.zeros(48)
gsw_tl = np.zeros(48)
et_tl = np.zeros(48)
tcan_tl = np.zeros(48)
hod = 0
for i in range(len(par)):
(An_tl[i], gsw_tl[i], et_tl[i],
tcan_tl[i]) = T.main(tair[i], par[i], vpd[i], wind, pressure, Ca, doy,
hod, lat, lon, LAI)
hod += 1
##
### Run 2-leaf opt
##
T = TwoLeafOpt(g0,
g1,
D0,
gamma,
Vcmax25,
Jmax25,
Rd25,
Eaj,
Eav,
deltaSj,
deltaSv,
Hdv,
Hdj,
Q10,
leaf_width,
SW_abs,
gs_model="medlyn")
An_tlo = np.zeros(48)
gsw_tlo = np.zeros(48)
et_tlo = np.zeros(48)
tcan_tlo = np.zeros(48)
hod = 0
for i in range(len(par)):
(An_tlo[i], gsw_tlo[i], et_tlo[i],
tcan_tlo[i]) = T.main(tair[i], par[i], vpd[i], wind, pressure, Ca,
doy, hod, lat, lon, LAI)
hod += 1
##
### Run 2-leaf Manon
##
Ao = np.zeros(48)
gso = np.zeros(48)
Eo = np.zeros(48)
Aob = np.zeros(48)
gsob = np.zeros(48)
Eob = np.zeros(48)
hod = 0
for i in range(len(par)):
cos_zenith = calculate_solar_geometry(doy, hod, lat, lon)
zenith_angle = np.rad2deg(np.arccos(cos_zenith))
elevation = 90.0 - zenith_angle
if elevation > 0.0 and par[i] > 50.0:
p = declared_params()
p.PPFD = par[i]
p.sw_rad_day = par[i] * c.PAR_2_SW
p.LAI = LAI
p.coszen = cos_zenith
p.VPD = vpd[i]
p.precip = 0
p.Tair = tair[i]
p.Vmax25 = Vcmax25
p.g1 = g1
p.CO2 = Ca / 1000 * 101.325
p.JV = 1.67
p.Rlref = Rd25
p.Ej = Eaj
p.Ev = Eav
p.deltaSv = deltaSv
p.deltaSj = deltaSj
p.max_leaf_width = leaf_width
p.gamstar25 = 4.33 # 42.75 / 101.25 umol m-2 s-1
p.Kc25 = 41.0264925 # 404.9 umol m-2 s-1
p.Ko25 = 28208.88 # 278.4 mmol mol-1
p.O2 = 21.27825 # 210 *1000. / 101.25 210 mmol mol-1
p.alpha = 0.3
p.albedo = 0.2
p.Egamstar = 37830.0
p.Ec = 79430.0
p.Eo = 36380.0
p.P50 = 2.02 # Puechabon
p.P88 = 4.17
p.kmax = 0.862457122856143
_, _, fscale2can = absorbed_radiation_2_leaves(p)
p = p.append(pd.Series([np.nansum(fscale2can)], index=['fscale']))
Eo[i], gso[i], Ao[i], __, __ = solve_std(p, p.fc, photo='Farquhar')
#"""
try:
fstom_opt_psi, Eo[i], gso[i], Ao[i], _, _ = profit_psi(
p, photo='Farquhar', res='med', case=2)
p = p.append(
pd.Series([fstom_opt_psi], index=['fstom_opt_psi']))
except (ValueError, AttributeError):
(Eo[i], gso[i], Ao[i]) = (0., 0., 0.)
#"""
hod += 1
fig = plt.figure(figsize=(16, 4))
fig.subplots_adjust(hspace=0.1)
fig.subplots_adjust(wspace=0.2)
plt.rcParams['text.usetex'] = False
plt.rcParams['font.family'] = "sans-serif"
plt.rcParams['font.sans-serif'] = "Helvetica"
plt.rcParams['axes.labelsize'] = 14
plt.rcParams['font.size'] = 14
plt.rcParams['legend.fontsize'] = 10
plt.rcParams['xtick.labelsize'] = 14
plt.rcParams['ytick.labelsize'] = 14
almost_black = '#262626'
# change the tick colors also to the almost black
plt.rcParams['ytick.color'] = almost_black
plt.rcParams['xtick.color'] = almost_black
# change the text colors also to the almost black
plt.rcParams['text.color'] = almost_black
# Change the default axis colors from black to a slightly lighter black,
# and a little thinner (0.5 instead of 1)
plt.rcParams['axes.edgecolor'] = almost_black
plt.rcParams['axes.labelcolor'] = almost_black
ax1 = fig.add_subplot(131)
ax2 = fig.add_subplot(132)
ax3 = fig.add_subplot(133)
#ax1.plot(np.arange(48)/2., An_bl, label="Big leaf")
ax1.plot(np.arange(48) / 2., An_tl, label="Two leaf")
ax1.plot(np.arange(48) / 2., An_tlo, label="Two leaf Opt")
ax1.plot(np.arange(48) / 2., Ao, label="Two leaf Manon")
ax1.legend(numpoints=1, loc="best")
ax1.set_ylabel("$A_{\mathrm{n}}$ ($\mathrm{\mu}$mol m$^{-2}$ s$^{-1}$)")
#ax2.plot(np.arange(48)/2., et_bl * c.MOL_TO_MMOL, label="Big leaf")
ax2.plot(np.arange(48) / 2., et_tl * c.MOL_TO_MMOL, label="Two leaf")
ax2.plot(np.arange(48) / 2., et_tlo * c.MOL_TO_MMOL, label="Two leaf opt")
ax2.plot(np.arange(48) / 2., Eo, label="Two leaf Manon")
ax2.set_ylabel("E (mmol m$^{-2}$ s$^{-1}$)")
ax2.set_xlabel("Hour of day")
#ax3.plot(np.arange(48)/2., tcan_bl, label="Tcanopy$_{1leaf}$")
ax3.plot(np.arange(48) / 2., tcan_tl, label="Tcanopy$_{2leaf}$")
ax3.plot(np.arange(48) / 2., tair, label="Tair")
ax3.set_ylabel("Temperature (deg C)")
ax3.legend(numpoints=1, loc="best")
ax1.locator_params(nbins=6, axis="y")
ax2.locator_params(nbins=6, axis="y")
plt.show()
fig.savefig("/Users/%s/Desktop/A_E_Tcan.pdf" % (os.getlogin()),
bbox_inches='tight',
pad_inches=0.1)
def main(self,
tair,
par,
vpd,
wind,
pressure,
Ca,
doy,
hod,
lat,
lon,
lai,
rnet=None):
"""
Parameters:
----------
tair : float
air temperature (deg C)
par : float
Photosynthetically active radiation (umol m-2 s-1)
vpd : float
Vapour pressure deficit (kPa, needs to be in Pa, see conversion
below)
wind : float
wind speed (m s-1)
pressure : float
air pressure (using constant) (Pa)
Ca : float
ambient CO2 concentration
doy : float
day of day
hod : float
hour of day
lat : float
latitude
lon : float
longitude
lai : floar
leaf area index
Returns:
--------
An : float
net leaf assimilation (umol m-2 s-1)
gs : float
stomatal conductance (mol m-2 s-1)
et : float
transpiration (mol H2O m-2 s-1)
"""
F = FarquharC3(theta_J=0.85,
peaked_Jmax=True,
peaked_Vcmax=True,
model_Q10=True,
gs_model=self.gs_model,
gamma=self.gamma,
g0=self.g0,
g1=self.g1,
D0=self.D0,
alpha=self.alpha)
P = PenmanMonteith(self.leaf_width, self.SW_abs)
An = np.zeros(2) # sunlit, shaded
gsc = np.zeros(2) # sunlit, shaded
et = np.zeros(2) # sunlit, shaded
Tcan = np.zeros(2) # sunlit, shaded
cos_zenith = calculate_solar_geometry(doy, hod, lat, lon)
zenith_angle = np.rad2deg(np.arccos(cos_zenith))
elevation = 90.0 - zenith_angle
sw_rad = par * c.PAR_2_SW # W m-2
# get diffuse/beam frac
(diffuse_frac, direct_frac) = spitters(doy, sw_rad, cos_zenith)
# Is the sun up?
if elevation > 0.0 and par > 50.0:
(apar, lai_leaf, kb) = calculate_absorbed_radiation_big_leaf(
par, cos_zenith, lai, direct_frac, diffuse_frac)
# Calculate scaling term to go from a single leaf to canopy,
# see Wang & Leuning 1998 appendix C
scalex = calc_leaf_to_canopy_scalar(lai, kb)
# initialise values of Tleaf, Cs, dleaf at the leaf surface
dleaf = vpd
Cs = Ca
Tleaf = tair
Tleaf_K = Tleaf + c.DEG_2_KELVIN
iter = 0
while True:
(An, gsc) = F.photosynthesis(Cs=Cs,
Tleaf=Tleaf_K,
Par=apar,
Jmax25=self.Jmax25,
Vcmax25=self.Vcmax25,
Q10=self.Q10,
Eaj=self.Eaj,
Eav=self.Eav,
deltaSj=self.deltaSj,
deltaSv=self.deltaSv,
Rd25=self.Rd25,
Hdv=self.Hdv,
Hdj=self.Hdj,
vpd=dleaf,
scalex=scalex)
# Calculate new Tleaf, dleaf, Cs
(new_tleaf, et, le_et, gbH,
gw) = self.calc_leaf_temp(P,
Tleaf,
tair,
gsc,
apar,
vpd,
pressure,
wind,
rnet=rnet,
lai=lai)
gbc = gbH * c.GBH_2_GBC
if gbc > 0.0 and An > 0.0:
Cs = Ca - An / gbc # boundary layer of leaf
else:
Cs = Ca
if math.isclose(et, 0.0) or math.isclose(gw, 0.0):
dleaf = vpd
else:
dleaf = (et * pressure / gw) * c.PA_2_KPA # kPa
# Check for convergence...?
if math.fabs(Tleaf - new_tleaf) < 0.02:
break
if iter > self.iter_max:
raise Exception('No convergence: %d' % (iter))
# Update temperature & do another iteration
Tleaf = new_tleaf
Tleaf_K = Tleaf + c.DEG_2_KELVIN
Tcan = Tleaf
iter += 1
# scale to canopy: sum contributions from beam and diffuse leaves
an_canopy = An
gsw_canopy = gsc * c.GSC_2_GSW
et_canopy = et
tcanopy = Tleaf
else:
an_canopy = 0.0
gsw_canopy = 0.0
et_canopy = 0.0
tcanopy = tair
return (an_canopy, gsw_canopy, et_canopy, tcanopy)
### Run Big-leaf
##
C = CoupledModel(g0, g1, D0, gamma, Vcmax25, Jmax25, Rd25, Eaj, Eav,
deltaSj, deltaSv, Hdv, Hdj, Q10, leaf_width, SW_abs,
gs_model="medlyn")
An_bl = np.zeros(48)
gsw_bl = np.zeros(48)
et_bl = np.zeros(48)
tcan_bl = np.zeros(48)
hod = 0
for i in range(len(par)):
cos_zenith = calculate_solar_geometry(doy, hod, lat, lon)
zenith_angle = np.rad2deg(np.arccos(cos_zenith))
elevation = 90.0 - zenith_angle
if elevation > 0.0 and par[i] > 50.0:
(An_bl[i], gsw_bl[i],
et_bl[i], tcan_bl[i]) = C.main(tair[i], par[i], vpd[i],
wind, pressure, Ca, doy, hod,
lat, lon, LAI)
hod += 1
Ao = np.zeros(48)
gso = np.zeros(48)
Eo = np.zeros(48)