def calculate_photosynthesis(self, tair, par, vpd, ca, daylen, sw):
Tair_K = [tair + const.DEG_TO_KELVIN, \
tair + const.DEG_TO_KELVIN]
vpd = [vpd, vpd]
state.wtfac_root = calc_sw_modifier(sw, self.params.ctheta_root,
self.params.ntheta_root)
# calculate mate params & account for temperature dependencies
gamma_star = self.calculate_co2_compensation_point(Tair_K)
Km = self.calculate_michaelis_menten_parameter(Tair_K)
N0 = self.calculate_top_of_canopy_n()
(jmax, vcmax) = self.calculate_jmax_and_vcmax(Tair_K, N0)
ci = [self.calculate_ci(vpd[k], ca) for k in self.am, self.pm]
# quantum efficiency calculated for C3 plants
alpha = self.calculate_quantum_efficiency(ci, gamma_star)
# Rubisco carboxylation limited rate of photosynthesis
ac = [self.assim(ci[k], gamma_star[k], a1=vcmax[k], a2=Km[k]) \
for k in self.am, self.pm]
# Light-limited rate of photosynthesis allowed by RuBP regeneration
aj = [self.assim(ci[k], gamma_star[k], a1=jmax[k]/4.0, \
a2=2.0*gamma_star[k]) for k in self.am, self.pm]
# light-saturated photosynthesis rate at the top of the canopy (gross)
asat = [min(aj[k], ac[k]) for k in self.am, self.pm]
# LUE (umol C umol-1 PAR)
lue = [self.epsilon(asat[k], par, daylen, alpha[k]) \
for k in self.am, self.pm]
lue_avg = sum(lue) / 2.0 # use average to simulate canopy photosynthesis
if float_eq(self.state.lai, 0.0):
self.fluxes.apar = 0.0
else:
# absorbed photosynthetically active radiation (umol m-2 s-1)
self.fluxes.apar = par * self.state.fipar
# gC m-2 d-1
self.fluxes.gpp_gCm2 = (self.fluxes.apar * lue_avg * const.UMOL_TO_MOL *
const.MOL_C_TO_GRAMS_C)
self.fluxes.gpp_am_pm[self.am] = ((self.fluxes.apar / 2.0) *
lue[self.am] * const.UMOL_TO_MOL *
const.MOL_C_TO_GRAMS_C)
self.fluxes.gpp_am_pm[self.pm] = ((self.fluxes.apar / 2.0) *
lue[self.pm] * const.UMOL_TO_MOL *
const.MOL_C_TO_GRAMS_C)
# photosynthesis -> umol m-2 s-1
A = self.fluxes.apar * lue_avg / (daylen * 3600.)
return A
def calculate_photosynthesis(self, tair, par, vpd, ca, daylen, sw):
Tk_am = tair + const.DEG_TO_KELVIN
Tk_pm = tair + const.DEG_TO_KELVIN
vpd_am = vpd
vpd_pm = vpd
state.wtfac_root = calc_sw_modifier(sw, self.params.ctheta_root,
self.params.ntheta_root)
# calculate mate params & account for temperature dependencies
N0 = self.calculate_top_of_canopy_n()
gamma_star_am = self.calculate_co2_compensation_point(Tk_am)
gamma_star_pm = self.calculate_co2_compensation_point(Tk_pm)
Km_am = self.calculate_michaelis_menten_parameter(Tk_am)
Km_pm = self.calculate_michaelis_menten_parameter(Tk_pm)
(jmax_am, vcmax_am) = self.calculate_jmax_and_vcmax(Tk_am, N0)
(jmax_pm, vcmax_pm) = self.calculate_jmax_and_vcmax(Tk_pm, N0)
ci_am = self.calculate_ci(vpd_am, ca)
ci_pm = self.calculate_ci(vpd_pm, ca)
# quantum efficiency calculated for C3 plants
alpha_am = self.calculate_quantum_efficiency(ci_am, gamma_star_am)
alpha_pm = self.calculate_quantum_efficiency(ci_pm, gamma_star_pm)
# Reducing assimilation if we encounter frost. Frost is assumed to
# impact on the maximum photosynthetic capacity and alpha_j
# So there is only an indirect effect on LAI, this could be changed...
if self.control.frost:
Tmax = self.met_data['tmax'][day]
Tmin = self.met_data['tmin'][day]
Thard = self.calc_frost_hardiness(daylen, Tmin, Tmax)
(total_alpha_limf,
total_amax_limf) = self.calc_frost_impact_factors(
Thard, Tmin, Tmax)
alpha_am *= total_alpha_limf
alpha_pm *= total_alpha_limf
# Rubisco carboxylation limited rate of photosynthesis
ac_am = self.assim(ci_am, gamma_star_am, a1=vcmax_am, a2=Km_am)
ac_pm = self.assim(ci_pm, gamma_star_pm, a1=vcmax_pm, a2=Km_pm)
# Light-limited rate of photosynthesis allowed by RuBP regeneration
aj_am = self.assim(ci_am,
gamma_star_am,
a1=jmax_am / 4.0,
a2=2.0 * gamma_star_am)
aj_pm = self.assim(ci_pm,
gamma_star_pm,
a1=jmax_pm / 4.0,
a2=2.0 * gamma_star_pm)
# light-saturated photosynthesis rate at the top of the canopy (gross)
asat_am = min(aj_am, ac_am)
asat_pm = min(aj_pm, ac_pm)
if self.control.frost:
asat_am *= total_amax_limf
asat_pm *= total_amax_limf
# LUE (umol C umol-1 PAR)
lue_am = self.epsilon(asat_am, par, daylen, alpha_am)
lue_pm = self.epsilon(asat_pm, par, daylen, alpha_pm)
# use average to simulate canopy photosynthesis
lue_avg = (lue_am + lue_pm) / 2.0
if float_eq(self.state.lai, 0.0):
self.fluxes.apar = 0.0
else:
# absorbed photosynthetically active radiation (umol m-2 s-1)
self.fluxes.apar = par * self.state.fipar
apar_half_day = self.fluxes.apar / 2.0
# convert umol m-2 d-1 -> gC m-2 d-1
self.fluxes.gpp_gCm2 = self.fluxes.apar * lue_avg * const.UMOL_2_GRAMS_C
self.fluxes.gpp_am = apar_half_day * lue_am * const.UMOL_2_GRAMS_C
self.fluxes.gpp_pm = apar_half_day * lue_pm * const.UMOL_2_GRAMS_C
# g C m-2 to tonnes hectare-1 day-1
self.fluxes.gpp = self.fluxes.gpp_gCm2 * const.GRAM_C_2_TONNES_HA
# photosynthesis -> umol m-2 s-1
A = self.fluxes.apar * lue_avg / (daylen * 3600.)
return A
def calculate_photosynthesis(self, tair, par, vpd, ca, daylen, sw):
Tk_am = tair + const.DEG_TO_KELVIN
Tk_pm = tair + const.DEG_TO_KELVIN
vpd_am = vpd
vpd_pm = vpd
state.wtfac_root = calc_sw_modifier(sw, self.params.ctheta_root,
self.params.ntheta_root)
# calculate mate params & account for temperature dependencies
N0 = self.calculate_top_of_canopy_n()
gamma_star_am = self.calculate_co2_compensation_point(Tk_am)
gamma_star_pm = self.calculate_co2_compensation_point(Tk_pm)
Km_am = self.calculate_michaelis_menten_parameter(Tk_am)
Km_pm = self.calculate_michaelis_menten_parameter(Tk_pm)
(jmax_am, vcmax_am) = self.calculate_jmax_and_vcmax(Tk_am, N0)
(jmax_pm, vcmax_pm) = self.calculate_jmax_and_vcmax(Tk_pm, N0)
ci_am = self.calculate_ci(vpd_am, ca)
ci_pm = self.calculate_ci(vpd_pm, ca)
# quantum efficiency calculated for C3 plants
alpha_am = self.calculate_quantum_efficiency(ci_am, gamma_star_am)
alpha_pm = self.calculate_quantum_efficiency(ci_pm, gamma_star_pm)
# Reducing assimilation if we encounter frost. Frost is assumed to
# impact on the maximum photosynthetic capacity and alpha_j
# So there is only an indirect effect on LAI, this could be changed...
if self.control.frost:
Tmax = self.met_data['tmax'][day]
Tmin = self.met_data['tmin'][day]
Thard = self.calc_frost_hardiness(daylen, Tmin, Tmax)
(total_alpha_limf,
total_amax_limf) = self.calc_frost_impact_factors(Thard, Tmin, Tmax)
alpha_am *= total_alpha_limf
alpha_pm *= total_alpha_limf
# Rubisco carboxylation limited rate of photosynthesis
ac_am = self.assim(ci_am, gamma_star_am, a1=vcmax_am, a2=Km_am)
ac_pm = self.assim(ci_pm, gamma_star_pm, a1=vcmax_pm, a2=Km_pm)
# Light-limited rate of photosynthesis allowed by RuBP regeneration
aj_am = self.assim(ci_am, gamma_star_am, a1=jmax_am/4.0,
a2=2.0*gamma_star_am)
aj_pm = self.assim(ci_pm, gamma_star_pm, a1=jmax_pm/4.0,
a2=2.0*gamma_star_pm)
# light-saturated photosynthesis rate at the top of the canopy (gross)
asat_am = min(aj_am, ac_am)
asat_pm = min(aj_pm, ac_pm)
if self.control.frost:
asat_am *= total_amax_limf
asat_pm *= total_amax_limf
# LUE (umol C umol-1 PAR)
lue_am = self.epsilon(asat_am, par, daylen, alpha_am)
lue_pm = self.epsilon(asat_pm, par, daylen, alpha_pm)
# use average to simulate canopy photosynthesis
lue_avg = (lue_am + lue_pm) / 2.0
if float_eq(self.state.lai, 0.0):
self.fluxes.apar = 0.0
else:
# absorbed photosynthetically active radiation (umol m-2 s-1)
self.fluxes.apar = par * self.state.fipar
apar_half_day = self.fluxes.apar / 2.0
# convert umol m-2 d-1 -> gC m-2 d-1
self.fluxes.gpp_gCm2 = self.fluxes.apar * lue_avg * const.UMOL_2_GRAMS_C
self.fluxes.gpp_am = apar_half_day * lue_am * const.UMOL_2_GRAMS_C
self.fluxes.gpp_pm = apar_half_day * lue_pm * const.UMOL_2_GRAMS_C
# g C m-2 to tonnes hectare-1 day-1
self.fluxes.gpp = self.fluxes.gpp_gCm2 * const.GRAM_C_2_TONNES_HA
# photosynthesis -> umol m-2 s-1
A = self.fluxes.apar * lue_avg / (daylen * 3600.)
return A
