def jmax_and_vcmax_func(self, temp):
""" Maximum rate of electron transport (jmax) and of rubisco activity
Parameters:
-----------
temp : float
air temperature
Returns:
--------
jmax : float
maximum rate of electron transport
vcmax : float
maximum rate of Rubisco activity
"""
if float_gt(temp, 10.0):
jmax = (self.params.jmaxna * (1.0 + (temp - 25.0) *
(0.05 + (temp - 25.0) *
(-1.81 * 1E-3 + (temp - 25.0) *
(-1.37 * 1E-4)))))
vcmax = (self.params.vcmaxna * (1.0 + (temp - 25.0) *
(0.0485 + (temp - 25.0) *
(-6.93 * 1E-4 + (temp - 25.0) *
(-3.9 * 1E-5)))))
elif float_gt(temp, 0.0):
jmax = self.params.jmaxna * 0.0305 * temp
vcmax = self.params.vcmaxna * 0.0238 * temp
else:
jmax = 0.0
vcmax = 0.0
return jmax, vcmax
def jmax_and_vcmax_func(self, temp):
""" Maximum rate of electron transport (jmax) and of rubisco activity
Parameters:
-----------
temp : float
air temperature
Returns:
--------
jmax : float
maximum rate of electron transport
vcmax : float
maximum rate of Rubisco activity
"""
if float_gt(temp, 10.0):
jmax = (self.params.jmaxna * (1.0 + (temp - 25.0) * (0.05 +
(temp - 25.0) * (-1.81 * 1E-3 + (temp - 25.0) *
(-1.37 * 1E-4)))))
vcmax = (self.params.vcmaxna * (1.0 + (temp - 25.0) *
(0.0485 + (temp - 25.0) * (-6.93 * 1E-4 + (temp - 25.0) *
(-3.9 * 1E-5)))))
elif float_gt(temp, 0.0):
jmax = self.params.jmaxna * 0.0305 * temp
vcmax = self.params.vcmaxna * 0.0238 * temp
else:
jmax = 0.0
vcmax = 0.0
return jmax, vcmax
def partition_plant_litter_n(self, nsurf, nsoil):
""" Partition litter N from the plant (surface) and roots into metabolic
and structural pools
Parameters:
-----------
nsurf : float
N input from surface pool
nsoil : float
N input from soil pool
"""
# constant structural input n:c as per century
if not self.control.strfloat:
# dead plant litter -> structural pool
# n flux -> surface structural pool
self.fluxes.n_surf_struct_litter = (self.fluxes.surf_struct_litter /
self.params.structcn)
# n flux -> soil structural pool
self.fluxes.n_soil_struct_litter = (self.fluxes.soil_struct_litter /
self.params.structcn)
# if not enough N for structural, all available N goes to structural
if float_gt( self.fluxes.n_surf_struct_litter, nsurf):
self.fluxes.n_surf_struct_litter = nsurf
if float_gt(self.fluxes.n_soil_struct_litter, nsoil):
self.fluxes.n_soil_struct_litter = nsoil
# structural input n:c is a fraction of metabolic
else:
c_surf_struct_litter = (self.fluxes.surf_struct_litter *
self.params.structrat +
self.fluxes.surf_metab_litter)
if float_eq(c_surf_struct_litter, 0.0):
self.fluxes.n_surf_struct_litter = 0.0
else:
self.fluxes.n_surf_struct_litter = (nsurf *
self.fluxes.surf_struct_litter *
self.params.structrat /
c_surf_struct_litter)
c_soil_struct_litter = (self.fluxes.soil_struct_litter *
self.params.structrat +
self.fluxes.soil_metab_litter)
if float_eq(c_soil_struct_litter, 0.0):
self.fluxes.n_soil_struct_litter = 0.
else:
self.fluxes.n_soil_struct_litter = (nsurf *
self.fluxes.soil_struct_litter *
self.params.structrat /
c_soil_struct_litter)
# remaining N goes to metabolic pools
self.fluxes.n_surf_metab_litter = (nsurf -
self.fluxes.n_surf_struct_litter)
self.fluxes.n_soil_metab_litter = (nsoil -
self.fluxes.n_soil_struct_litter)
def partition_plant_litter_n(self, nsurf, nsoil):
""" Partition litter N from the plant (surface) and roots into metabolic
and structural pools
Parameters:
-----------
nsurf : float
N input from surface pool
nsoil : float
N input from soil pool
"""
# constant structural input n:c as per century
if not self.control.strfloat:
# dead plant litter -> structural pool
# n flux -> surface structural pool
self.fluxes.n_surf_struct_litter = (self.fluxes.surf_struct_litter /
self.params.structcn)
# n flux -> soil structural pool
self.fluxes.n_soil_struct_litter = (self.fluxes.soil_struct_litter /
self.params.structcn)
# if not enough N for structural, all available N goes to structural
if float_gt( self.fluxes.n_surf_struct_litter, nsurf):
self.fluxes.n_surf_struct_litter = nsurf
if float_gt(self.fluxes.n_soil_struct_litter, nsoil):
self.fluxes.n_soil_struct_litter = nsoil
# structural input n:c is a fraction of metabolic
else:
c_surf_struct_litter = (self.fluxes.surf_struct_litter *
self.params.structrat +
self.fluxes.surf_metab_litter)
if float_eq(c_surf_struct_litter, 0.0):
self.fluxes.n_surf_struct_litter = 0.0
else:
self.fluxes.n_surf_struct_litter = (nsurf *
self.fluxes.surf_struct_litter *
self.params.structrat /
c_surf_struct_litter)
c_soil_struct_litter = (self.fluxes.soil_struct_litter *
self.params.structrat +
self.fluxes.soil_metab_litter)
if float_eq(c_soil_struct_litter, 0.0):
self.fluxes.n_soil_struct_litter = 0.
else:
self.fluxes.n_soil_struct_litter = (nsurf *
self.fluxes.soil_struct_litter *
self.params.structrat /
c_soil_struct_litter)
# remaining N goes to metabolic pools
self.fluxes.n_surf_metab_litter = (nsurf -
self.fluxes.n_surf_struct_litter)
self.fluxes.n_soil_metab_litter = (nsoil -
self.fluxes.n_soil_struct_litter)
def soil_temp_factor(self, project_day):
"""Soil-temperature activity factor (A9).
Parameters:
-----------
project_day : int
current simulation day (index)
Returns:
--------
tfac : float
soil temperature factor [degC]
"""
tsoil = self.met_data["tsoil"][project_day]
if float_gt(tsoil, 0.0):
tfac = 0.0326 + 0.00351 * tsoil ** 1.652 - (tsoil / 41.748) ** 7.19
if float_lt(tfac, 0.0):
tfac = 0.0
else:
# negative number cannot be raised to a fractional power
# number would need to be complex
tfac = 0.0
return tfac
def epsilon(self, asat, par, daylen, alpha):
""" Canopy scale LUE using method from Sands 1995, 1996.
Sands derived daily canopy LUE from Asat by modelling the light response
of photosysnthesis as a non-rectangular hyperbola with a curvature
(theta) and a quantum efficiency (alpha).
Assumptions of the approach are:
- horizontally uniform canopy
- PAR varies sinusoidally during daylight hours
- extinction coefficient is constant all day
- Asat and incident radiation decline through the canopy following
Beer's Law.
- leaf transmission is assumed to be zero.
* Numerical integration of "g" is simplified to 6 intervals.
Parameters:
----------
asat : float
Light-saturated photosynthetic rate at the top of the canopy
par : float
photosyntetically active radiation (umol m-2 d-1)
daylen : float
length of day (hrs).
theta : float
curvature of photosynthetic light response curve
alpha : float
quantum yield of photosynthesis (mol mol-1)
Returns:
-------
lue : float
integrated light use efficiency over the canopy (umol C umol-1 PAR)
References:
-----------
See assumptions above...
* Sands, P. J. (1995) Australian Journal of Plant Physiology,
22, 601-14.
"""
delta = 0.16666666667 # subintervals scaler, i.e. 6 intervals
h = daylen * const.SECS_IN_HOUR # number of seconds of daylight
if float_gt(asat, 0.0):
# normalised daily irradiance
q = pi * self.params.kext * alpha * par / (2.0 * h * asat)
integral_g = 0.0
for i in xrange(1, 13, 2):
sinx = sin(pi * i / 24.0)
arg1 = sinx
arg2 = 1.0 + q * sinx
arg3 = sqrt((1.0 + q * sinx) ** 2.0 - 4.0 * self.params.theta * q * sinx)
integral_g += arg1 / (arg2 + arg3) * delta
lue = alpha * integral_g * pi
else:
lue = 0.0
return lue
def calc_soil_evaporation(self, tavg, net_rad, press, daylen, sw_rad):
""" Use Penman eqn to calculate top soil evaporation flux at the
potential rate.
Soil evaporation is dependent upon soil wetness and plant cover. The net
radiation term is scaled for the canopy cover passed to this func and
the impact of soil wetness is accounted for in the wtfac term. As the
soil dries the evaporation component reduces significantly.
Key assumptions from Ritchie...
* When plant provides shade for the soil surface, evaporation will not
be the same as bare soil evaporation. Wind speed, net radiation and VPD
will all belowered in proportion to the canopy density. Following
Ritchie role ofwind, VPD are assumed to be negligible and are therefore
ignored.
These assumptions are based on work with crops and whether this holds
for tree shading where the height from the soil to the base of the
crown is larger is questionable.
units = (mm/day)
References:
-----------
* Ritchie, 1972, Water Resources Research, 8, 1204-1213.
Parameters:
-----------
tavg : float
average daytime temp [degC]
net_rad : float
net radiation [mj m-2 day-1]
press : float
average daytime pressure [kPa]
Returns:
--------
soil_evap : float
soil evaporation [mm d-1]
"""
P = Penman()
soil_evap = P.calc_evaporation(net_rad, tavg, press)
# Surface radiation is reduced by overstory LAI cover. This empirical
# fit comes from Ritchie (1972) and is formed by a fit between the LAI
# of 5 crops types and the fraction of observed net radiation at the
# surface. Whilst the LAI does cover a large range, nominal 0–6, there
# are only 12 measurements and only three from LAI > 3. So this might
# not hold as well for a forest canopy?
# Ritchie 1972, Water Resources Research, 8, 1204-1213.
if float_gt(self.state.lai, 0.0):
soil_evap *= exp(-0.398 * self.state.lai)
# reduce soil evaporation if top soil is dry
soil_evap *= self.state.wtfac_topsoil
tconv = 60.0 * 60.0 * daylen # seconds to day
return soil_evap * tconv
def soil_temp_factor(self, project_day):
"""Soil-temperature activity factor (A9). Fit to Parton's fig 2a
Parameters:
-----------
project_day : int
current simulation day (index)
Returns:
--------
tfac : float
soil temperature factor [degC]
"""
tsoil = self.met_data['tsoil'][project_day]
if float_gt(tsoil, 0.0):
self.fluxes.tfac_soil_decomp = (0.0326 + 0.00351 * tsoil**1.652 -
(tsoil / 41.748)**7.19)
if float_lt(self.fluxes.tfac_soil_decomp, 0.0):
self.fluxes.tfac_soil_decomp = 0.0
else:
# negative number cannot be raised to a fractional power
# number would need to be complex
self.fluxes.tfac_soil_decomp = 0.0
return self.fluxes.tfac_soil_decomp
def calc_transpiration(self):
""" units mm/day """
if float_gt(self.fluxes.wue, 0.0):
self.fluxes.transpiration = self.fluxes.gpp_gCm2 / self.fluxes.wue
else:
self.fluxes.transpiration = 0.0
def calc_soil_evaporation(self, tavg, net_rad, press, daylen, sw_rad):
""" Use Penman eqn to calculate top soil evaporation flux at the
potential rate.
Soil evaporation is dependent upon soil wetness and plant cover. The net
radiation term is scaled for the canopy cover passed to this func and
the impact of soil wetness is accounted for in the wtfac term. As the
soil dries the evaporation component reduces significantly.
Key assumptions from Ritchie...
* When plant provides shade for the soil surface, evaporation will not
be the same as bare soil evaporation. Wind speed, net radiation and VPD
will all belowered in proportion to the canopy density. Following
Ritchie role ofwind, VPD are assumed to be negligible and are therefore
ignored.
These assumptions are based on work with crops and whether this holds
for tree shading where the height from the soil to the base of the
crown is larger is questionable.
units = (mm/day)
References:
-----------
* Ritchie, 1972, Water Resources Research, 8, 1204-1213.
Parameters:
-----------
tavg : float
average daytime temp [degC]
net_rad : float
net radiation [mj m-2 day-1]
press : float
average daytime pressure [kPa]
Returns:
--------
soil_evap : float
soil evaporation [mm d-1]
"""
P = Penman()
soil_evap = P.calc_evaporation(net_rad, tavg, press)
# Surface radiation is reduced by overstory LAI cover. This empirical
# fit comes from Ritchie (1972) and is formed by a fit between the LAI
# of 5 crops types and the fraction of observed net radiation at the
# surface. Whilst the LAI does cover a large range, nominal 0–6, there
# are only 12 measurements and only three from LAI > 3. So this might
# not hold as well for a forest canopy?
# Ritchie 1972, Water Resources Research, 8, 1204-1213.
if float_gt(self.state.lai, 0.0):
soil_evap *= exp(-0.398 * self.state.lai)
# reduce soil evaporation if top soil is dry
soil_evap *= self.state.wtfac_topsoil
tconv = 60.0 * 60.0 * daylen # seconds to day
return soil_evap * tconv
def epsilon(self, asat, par, daylen, alpha):
""" Canopy scale LUE using method from Sands 1995, 1996.
Sands derived daily canopy LUE from Asat by modelling the light response
of photosysnthesis as a non-rectangular hyperbola with a curvature
(theta) and a quantum efficiency (alpha).
Assumptions of the approach are:
- horizontally uniform canopy
- PAR varies sinusoidally during daylight hours
- extinction coefficient is constant all day
- Asat and incident radiation decline through the canopy following
Beer's Law.
- leaf transmission is assumed to be zero.
* Numerical integration of "g" is simplified to 6 intervals.
Parameters:
----------
asat : float
photosynthetic rate at the top of the canopy
par : float
incident photosyntetically active radiation
daylen : float
length of day (hrs).
theta : float
curvature of photosynthetic light response curve
alpha : float
quantum yield of photosynthesis (mol mol-1)
Returns:
-------
lue : float
integrated light use efficiency over the canopy (mol C mol-1 PAR)
References:
-----------
See assumptions above...
* Sands, P. J. (1995) Australian Journal of Plant Physiology,
22, 601-14.
"""
delta = 0.16666666667 # subintervals scaler, i.e. 6 intervals
h = daylen * const.HRS_TO_SECS
theta = self.params.theta # local var
if float_gt(asat, 0.0):
q = pi * self.params.kext * alpha * par / (2.0 * h * asat)
integral_g = 0.0
for i in xrange(1, 13, 2):
sinx = sin(pi * i / 24.)
arg1 = sinx
arg2 = 1.0 + q * sinx
arg3 = sqrt((1.0 + q * sinx)**2.0 - 4.0 * theta * q * sinx)
integral_g += arg1 / (arg2 + arg3) * delta
lue = alpha * integral_g * pi
else:
lue = 0.0
return lue
def decay_in_dry_soils(self, decay_rate, decay_rate_dry):
"""Decay rates (e.g. leaf litterfall) can increase in dry soil, adjust
decay param
Parameters:
-----------
decay_rate : float
default model parameter decay rate [tonnes C/ha/day]
decay_rate_dry : float
default model parameter dry deacy rate [tonnes C/ha/day]
Returns:
--------
decay_rate : float
adjusted deacy rate if the soil is dry [tonnes C/ha/day]
"""
# turn into fraction...
smc_root = self.state.pawater_root / self.params.wcapac_root
new_decay_rate = (decay_rate_dry - (decay_rate_dry - decay_rate) *
(smc_root - self.params.watdecaydry) /
(self.params.watdecaywet - self.params.watdecaydry))
if float_lt(new_decay_rate, decay_rate):
new_decay_rate = decay_rate
if float_gt(new_decay_rate, decay_rate_dry):
new_decay_rate = decay_rate_dry
return new_decay_rate
def soil_temp_factor(self, project_day):
"""Soil-temperature activity factor (A9). Fit to Parton's fig 2a
Parameters:
-----------
project_day : int
current simulation day (index)
Returns:
--------
tfac : float
soil temperature factor [degC]
"""
tsoil = self.met_data['tsoil'][project_day]
if float_gt(tsoil, 0.0):
self.fluxes.tfac_soil_decomp = (0.0326 + 0.00351 * tsoil**1.652 -
(tsoil / 41.748)**7.19)
if float_lt(self.fluxes.tfac_soil_decomp, 0.0):
self.fluxes.tfac_soil_decomp = 0.0
else:
# negative number cannot be raised to a fractional power
# number would need to be complex
self.fluxes.tfac_soil_decomp = 0.0
return self.fluxes.tfac_soil_decomp
def nc_limit(self, cpool, npool, ncmin, ncmax):
""" Release N to 'Inorgn' pool or fix N from 'Inorgn', in order to keep
the N:C ratio of a litter pool within the range 'ncmin' to 'ncmax'.
Parameters:
-----------
cpool : float
various C pool (state)
npool : float
various N pool (state)
ncmin : float
maximum N:C ratio
ncmax : float
minimum N:C ratio
Returns:
--------
fix/rel : float
amount of N to be added/released from the inorganic pool
"""
nmax = cpool * ncmax
nmin = cpool * ncmin
if float_gt(npool, nmax): #release
rel = npool - nmax
self.fluxes.nlittrelease += rel
return -rel
elif float_lt(npool, nmin): #fix
fix = nmin - npool
self.fluxes.nlittrelease -= fix
return fix
else:
return 0.0
def calc_infiltration(self, rain):
""" Estimate "effective" rain, or infiltration I guess.
Simple assumption that infiltration relates to leaf area
and therefore canopy storage capacity (wetloss). Interception is
likely to be ("more") erroneous if a canopy is subject to frequent daily
rainfall I would suggest.
Parameters:
-------
rain : float
rainfall [mm d-1]
"""
if float_gt(rain, 0.0):
self.fluxes.interception = self.state.lai * self.params.wetloss
self.fluxes.interception = clip(self.fluxes.interception,
min=self.fluxes.interception,
max=rain)
self.fluxes.erain = (rain * self.params.rfmult -
self.fluxes.interception)
else:
self.fluxes.interception = 0.0
self.fluxes.erain = 0.0
def nc_limit(self, cpool, npool, ncmin, ncmax):
""" Release N to 'Inorgn' pool or fix N from 'Inorgn', in order to keep
the N:C ratio of a litter pool within the range 'ncmin' to 'ncmax'.
Parameters:
-----------
cpool : float
various C pool (state)
npool : float
various N pool (state)
ncmin : float
maximum N:C ratio
ncmax : float
minimum N:C ratio
Returns:
--------
fix/rel : float
amount of N to be added/released from the inorganic pool
"""
nmax = cpool * ncmax
nmin = cpool * ncmin
if float_gt(npool, nmax): #release
rel = npool - nmax
self.fluxes.nlittrelease += rel
return -rel
elif float_lt(npool, nmin): #fix
fix = nmin - npool
self.fluxes.nlittrelease -= fix
return fix
else:
return 0.0
def inputs_from_structrual_pool(self, nsurf, nsoil):
"""structural pool input fluxes
Parameters:
-----------
nsurf : float
N input from surface pool
nsoil : float
N input from soil pool
"""
# constant structural input n:c as per century
if not self.control.strfloat:
# dead plant -> structural
# surface
self.fluxes.nresid[0] = self.fluxes.cresid[0] / self.params.structcn
# soil
self.fluxes.nresid[1] = self.fluxes.cresid[1] / self.params.structcn
# if not enough N for structural, all available N goes to structural
if float_gt(self.fluxes.nresid[0], nsurf):
self.fluxes.nresid[0] = nsurf
if float_gt(self.fluxes.nresid[1], nsoil):
self.fluxes.nresid[1] = nsoil
else:
# structural input n:c is a fraction of metabolic
cwgtsu = (self.fluxes.cresid[0] * self.params.structrat +
self.fluxes.cresid[2])
if float_eq(cwgtsu, 0.0):
self.fluxes.nresid[0] = 0.0
else:
self.fluxes.nresid[0] = (nsurf * self.fluxes.cresid[0] *
self.params.structrat / cwgtsu)
cwgtsl = (self.fluxes.cresid[1] * self.params.structrat +
self.fluxes.cresid[3])
if float_eq(cwgtsl, 0.0):
self.fluxes.nresid[1] = 0.
else:
self.fluxes.nresid[1] = (nsurf * self.fluxes.cresid[1] *
self.params.structrat / cwgtsl)
def calculate_top_of_canopy_n(self):
""" Calculate the canopy N at the top of the canopy (g N m-2), N0.
See notes and Chen et al 93, Oecologia, 93,63-69.
"""
if float_gt(self.state.lai, 0.0):
# calculation for canopy N content at the top of the canopy
N0 = self.state.ncontent * self.params.kext / (1.0 - exp(-self.params.kext * self.state.lai))
else:
N0 = 0.0
return N0
def adjust_cproduction(self, option):
""" select model?
It seems hybrid is the same as biomass, so check this and remove. I
have set it up so that a call to hybrid just calls biomass
Parameters:
-----------
option : integer
model option
"""
if option == 1 or option == 3:
self.monteith_rescap_model()
elif option == 2 and float_gt(self.params.fwpmax, self.params.fwpmin):
self.biomass_model()
elif option == 3 and float_gt(self.params.fwpmax, self.params.fwpmin):
self.hybrid_model() # same as calling biomass model!
else:
err_msg = "Unknown water bal model (try 1-3): %s\n" % option
raise RuntimeError, err_msg
def clip(value, min=None, max=None):
""" clip value btw defined range """
if float_lt(value, min):
value = min
elif float_gt(value, max):
value = max
return value
def calculate_top_of_canopy_n(self):
""" Calculate the canopy N at the top of the canopy (g N m-2), N0.
See notes and Chen et al 93, Oecologia, 93,63-69.
"""
if float_gt(self.state.lai, 0.0):
# calculation for canopy N content at the top of the canopy
N0 = (self.state.ncontent * self.params.kext /
(1.0 - exp(-self.params.kext * self.state.lai)))
else:
N0 = 0.0
return N0
def calc_evaporation(self, vpd, wind, gs, net_rad, tavg, press, canht=None,
ga=None):
"""
Parameters:
-----------
vpd : float
vapour pressure def [kPa]
wind : float
average daytime wind speed [m s-1]
gs : float
stomatal conductance [m s-1]
net_rad : float
net radiation [mj m-2 s-1]
tavg : float
daytime average temperature [degC]
press : float
average daytime pressure [kPa]
Returns:
--------
et : float
evapotranspiration [mm d-1]
"""
# if not read from met file calculate atmospheric pressure from sea lev
if press == None:
press = self.calc_atmos_pressure()
lambdax = self.calc_latent_heat_of_vapourisation(tavg)
gamma = self.calc_pyschrometric_constant(lambdax, press)
slope = self.calc_slope_of_saturation_vapour_pressure_curve(tavg)
rho = self.calc_density_of_air(tavg)
if ga is None:
ga = self.canopy_boundary_layer_conductance(wind, canht)
if float_gt(gs, 0.0):
# decoupling coefficent, Jarvis and McNaughton, 1986
# when omega is close to zero, it is said to be well coupled and
# gs is the dominant controller of water loss (gs<ga).
e = slope / gamma # chg of latent heat relative to sensible heat of air
omega = (e + 1.0) / (e + 1.0 + (ga / gs))
arg1 = ((slope * net_rad ) + (rho * self.cp * vpd * ga))
arg2 = slope + gamma * (1.0 + (ga / gs))
et = (arg1 / arg2) / lambdax
else:
et = 0.0
omega = 0.0
return et, omega
def calc_evaporation(self, vpd, wind, gs, net_rad, tavg, press, canht=None,
ga=None):
"""
Parameters:
-----------
vpd : float
vapour pressure def [kPa]
wind : float
average daytime wind speed [m s-1]
gs : float
stomatal conductance [m s-1]
net_rad : float
net radiation [mj m-2 s-1]
tavg : float
daytime average temperature [degC]
press : float
average daytime pressure [kPa]
Returns:
--------
et : float
evapotranspiration [mm d-1]
"""
# if not read from met file calculate atmospheric pressure from sea lev
if press == None:
press = self.calc_atmos_pressure()
lambdax = self.calc_latent_heat_of_vapourisation(tavg)
gamma = self.calc_pyschrometric_constant(lambdax, press)
slope = self.calc_slope_of_saturation_vapour_pressure_curve(tavg)
rho = self.calc_density_of_air(tavg)
if ga is None:
ga = self.canopy_boundary_layer_conductance(wind, canht)
if float_gt(gs, 0.0):
# decoupling coefficent, Jarvis and McNaughton, 1986
# when omega is close to zero, it is said to be well coupled and
# gs is the dominant controller of water loss (gs<ga).
e = slope / gamma # chg of latent heat relative to sensible heat of air
omega = (e + 1.0) / (e + 1.0 + (ga / gs))
arg1 = ((slope * net_rad ) + (rho * self.cp * vpd * ga))
arg2 = slope + gamma * (1.0 + (ga / gs))
et = (arg1 / arg2) / lambdax
else:
et = 0.0
omega = 0.0
return et, omega
def calc_evaporation(self, vpd, wind, gs, net_rad, tavg, press):
"""
Parameters:
-----------
vpd : float
vapour pressure def [kPa]
wind : float
average daytime wind speed [m s-1]
gs : float
stomatal conductance [m s-1]
net_rad : float
net radiation [mj m-2 s-1]
tavg : float
daytime average temperature [degC]
press : float
average daytime pressure [kPa]
Returns:
--------
et : float
evapotranspiration [mm d-1]
"""
# if not read from met file calculate atmospheric pressure from sea lev
if press == None:
press = self.calc_atmos_pressure()
lambdax = self.calc_latent_heat_of_vapourisation(tavg)
gamma = self.calc_pyschrometric_constant(lambdax, press)
slope = self.calc_slope_of_saturation_vapour_pressure_curve(tavg)
rho = self.calc_density_of_air(tavg)
ga = self.calc_atmos_boundary_layer_conductance(wind)
# our model is a big leaf, so canopy conductance, gc = gs
gc = gs
if float_gt(gc, 0.0):
# decoupling coefficent, Jarvis and McNaughton, 1986
e = slope / gamma # chg of latent heat relative to sensible heat of air
omega = (e + 1.0) / (e + 1.0 + (ga / gc))
arg1 = ((slope * net_rad ) + (rho * self.cp * vpd * ga))
arg2 = slope + gamma * (1.0 + ga / gc)
et = (arg1 / arg2) / lambdax
else:
et = 0.0
omega = 0.0
return et
def epsilon(self, amax, par, daylen, alpha):
""" Canopy scale LUE using method from Sands 1995, 1996.
Numerical integration of g is simplified to 6 intervals. Leaf
transmission is assumed to be zero.
Parameters:
----------
amax : float
photosynthetic rate at the top of the canopy
par : float
incident photosyntetically active radiation
daylen : float
length of day in hours.
theta : float
curvature of photosynthetic light response curve
alpha : float
quantum yield of photosynthesis (mol mol-1)
Returns:
-------
lue : float
integrated light use efficiency over the canopy
References:
-----------
See assumptions above...
* Sands, P. J. (1995) Australian Journal of Plant Physiology,
22, 601-14.
* LUE stuff comes from Sands 1996
"""
delta = 0.16666666667 # subintervals scaler, i.e. 6 intervals
h = daylen * const.HRS_TO_SECS
theta = self.params.theta # local var
if float_gt(amax, 0.0):
q = pi * self.params.kext * alpha * par / (2.0 * h * amax)
integral = 0.0
for i in xrange(1, 13, 2):
sinx = sin(pi * i / 24.)
arg1 = sinx
arg2 = 1.0 + q * sinx
arg3 = sqrt((1.0 + q * sinx)**2.0 - 4.0 * theta * q * sinx)
integral += arg1 / (arg2 + arg3) * delta
lue = alpha * integral * pi
else:
lue = 0.0
return lue
def calc_wue(self, vpd, ca, amb_co2):
"""water use efficiency
Not sure of units conversions here, have to ask BM
Parameters:
-----------
vpd : float
average daily vpd [kPa]
ca : float
atmospheric co2, depending on flag set in param file this will be
ambient or elevated. [umol mol-1]
"""
if self.control.wue_model == 0:
# Gday original implementation
# (gC / kg H20)
if float_gt(vpd, 0.0):
# WUE Power law dependence on co2, Pepper et al 2005.
co2_ratio = (ca / amb_co2)
co2_adjustment = co2_ratio**self.params.co2_effect_on_wue
# wue inversely proportional to daily mean vpd
self.fluxes.wue = self.params.wue0 * co2_adjustment / vpd
else:
self.fluxes.wue = 0.0
elif self.control.wue_model == 1 and self.control.assim_model == 7:
conv = const.MOL_C_TO_GRAMS_C / const.MOL_WATER_TO_GRAMS_WATER
self.fluxes.wue = (conv * 1000.0 * (ca * const.UMOL_TO_MOL *
(1.0 - self.fluxes.cica_avg) /
(1.6 * vpd / 101.0)))
#if self.fluxes.wue > 20.0: self.fluxes.wue = 20.0 # FIX THIS!!!
# what is this? ask BM
elif self.control.wue_model == 2:
self.fluxes.wue = (self.params.wue0 * 0.27273 / vpd *
ca / amb_co2)
elif self.control.wue_model == 3 :
if float_eq(self.fluxes.transpiration, 0.0):
self.fluxes.wue = 0.0
else:
self.fluxes.wue = (self.fluxes.gpp_gCm2 /
self.fluxes.transpiration)
else:
raise AttributeError('Unknown WUE calculation option')
def epsilon(self, amax, par, daylen, alpha):
""" Canopy scale LUE using method from Sands 1995, 1996.
Parameters:
----------
amax : float
photosynthetic rate at the top of the canopy
par : float
incident photosyntetically active radiation
daylen : float
length of day in hours.
theta : float
curvature of photosynthetic light response curve
alpha : float
quantum yield of photosynthesis (mol mol-1)
Returns:
-------
lue : float
integrated light use efficiency over the canopy
References:
-----------
See assumptions above...
* Sands, P. J. (1995) Australian Journal of Plant Physiology, 22, 601-14.
"""
if float_gt(amax, 0.0):
q = (math.pi * self.params.kext * alpha * par /
(2.0 * daylen * const.HRS_TO_SECS * amax))
# check sands but shouldn't it be 2 * q * sin x on the top?
f = (lambda x: x / (1.0 + q * x + math.sqrt((1.0 + q * x)**2.0 -
4.0 * self.params.theta * q * x)))
g = [f(math.sin(math.pi * i / 24.)) for i in xrange(1, 13, 2)]
#Trapezoidal rule - seems more accurate
gg = 0.16666666667 * sum(g)
lue = alpha * gg * math.pi
else:
lue = 0.0
return lue
def day_length(date, latitude):
""" Figure out number of sunlight hours, (hours day-1)
Routine from sdgvm. date is a python object, see datetime library for
more info
Parameters:
-----------
date : date format string
date object, yr/month/day
latitude : float
latitude [degrees]
Returns:
--------
dayl : float
daylength [hrs]
"""
conv = math.pi / 180.0
# day of year 1-365/366
doy = int(date.strftime('%j'))
# Total number of days in year
if calendar.isleap(date.year):
yr_days = 366.
else:
yr_days = 365.
solar_declin = -23.4 * math.cos(conv * yr_days * (doy + 10.0) / yr_days)
temx = -math.tan(latitude * conv) * math.tan(solar_declin * conv)
if float_lt(math.fabs(temx), 1.0):
has = math.acos(temx) / conv
dayl = 2.0 * has / 15.0
elif float_gt(temx, 0.0):
dayl = 0.0
else:
dayl = 24.0
return dayl
def calculate_mineralisation(self):
"""Mineralisation calculations.
Plant N uptake, soil N loss, N gross mineralisation, N immobilisation
"""
# gross n mineralisation (t/ha/yr)
self.fluxes.ngross = (sum(self.fluxes.nstruct) +
sum(self.fluxes.nmetab) +
sum(self.fluxes.nactive) +
sum(self.fluxes.nslow) + self.fluxes.npassive)
# N:C new SOM - slope is an object containing active, slow and passive
slope = self.calc_new_nc_slope_params()
# Mineral N pool
(numer1, numer2, denom) = self.calc_mineral_npool(slope)
# evaluate n immobilisation in new SOM
self.fluxes.nimmob = numer1 + denom * self.state.inorgn
if float_gt(self.fluxes.nimmob, numer2):
self.fluxes.nimmob = numer2
def grazer_inputs(self):
""" Grazer inputs from faeces and urine, flux detd by faeces c:n """
if self.control.grazing:
self.params.faecesn = self.fluxes.faecesc / self.params.faecescn
else:
self.params.faecesn = 0.0
# make sure faecesn <= total n input to soil from grazing
arg = self.fluxes.neaten * self.params.fractosoil
if float_gt(self.params.faecesn, arg):
self.params.faecesn = self.fluxes.neaten * self.params.fractosoil
# urine=total-faeces
if self.control.grazing:
self.fluxes.nurine = self.fluxes.neaten * self.params.fractosoil - self.params.faecesn
else:
self.fluxes.nurine = 0.0
if float_lt(self.fluxes.nurine, 0.0):
self.fluxes.nurine = 0.0
def grazer_inputs(self):
""" Grazer inputs from faeces and urine, flux detd by faeces c:n """
if self.control.grazing:
self.params.faecesn = self.fluxes.faecesc / self.params.faecescn
else:
self.params.faecesn = 0.0
# make sure faecesn <= total n input to soil from grazing
arg = self.fluxes.neaten * self.params.fractosoil
if float_gt(self.params.faecesn, arg):
self.params.faecesn = self.fluxes.neaten * self.params.fractosoil
# urine=total-faeces
if self.control.grazing:
self.fluxes.nurine = (self.fluxes.neaten * self.params.fractosoil -
self.params.faecesn)
else:
self.fluxes.nurine = 0.0
if float_lt(self.fluxes.nurine, 0.0):
self.fluxes.nurine = 0.0
def model_one(self, day):
""" old g'day n:c and temperature factors
References:
-----------
* mcmurtrie et al 1992 aust j bot
Parameters:
-----------
day : integer
simulation day
Returns:
--------
npp : float
net primary productivity
"""
(sw_rad, ca, temp) = self.get_met_data(day)
if float_eq(sw_rad, 0.0):
sw_rad = 0.000001
rco2 = 1.632 * (ca - 60.9) / (ca + 121.8)
gpp_max = ((self.params.cfracts * sw_rad / const.M2_AS_HA *
self.params.epsilon * const.G_AS_TONNES) * rco2)
# leaf n:c effect on photosynthetic efficiency (theta = 1).
if float_gt(self.state.shootnc, self.params.n_crit):
lue = 1.0
else:
rat = self.state.shootnc / self.params.n_crit
if float_eq(self.params.ncpower, 1.0):
lue = rat
else:
lue = pow(rat, self.params.ncpower)
return lue * gpp_max * self.state.light_interception
def decay_in_dry_soils(self, decay_rate, decay_rate_dry):
"""Decay rates (e.g. leaf litterfall) can increase in dry soil, adjust
decay param. This is based on field measurements by F. J. Hingston
(unpublished) cited in Corbeels.
Parameters:
-----------
decay_rate : float
default model parameter decay rate [tonnes C/ha/day]
decay_rate_dry : float
default model parameter dry deacy rate [tonnes C/ha/day]
Returns:
--------
decay_rate : float
adjusted deacy rate if the soil is dry [tonnes C/ha/day]
Reference:
----------
Corbeels et al. (2005) Ecological Modelling, 187, 449-474.
"""
# turn into fraction...
smc_root = self.state.pawater_root / self.params.wcapac_root
new_decay_rate = decay_rate_dry - (decay_rate_dry - decay_rate) * (smc_root - self.params.watdecaydry) / (
self.params.watdecaywet - self.params.watdecaydry
)
if float_lt(new_decay_rate, decay_rate):
new_decay_rate = decay_rate
if float_gt(new_decay_rate, decay_rate_dry):
new_decay_rate = decay_rate_dry
return new_decay_rate
def decay_in_dry_soils(self, decay_rate, decay_rate_dry):
"""Decay rates (e.g. leaf litterfall) can increase in dry soil, adjust
decay param. This is based on field measurements by F. J. Hingston
(unpublished) cited in Corbeels.
Parameters:
-----------
decay_rate : float
default model parameter decay rate [tonnes C/ha/day]
decay_rate_dry : float
default model parameter dry deacy rate [tonnes C/ha/day]
Returns:
--------
decay_rate : float
adjusted deacy rate if the soil is dry [tonnes C/ha/day]
Reference:
----------
Corbeels et al. (2005) Ecological Modelling, 187, 449-474.
"""
# turn into fraction...
smc_root = self.state.pawater_root / self.params.wcapac_root
new_decay_rate = (decay_rate_dry - (decay_rate_dry - decay_rate) *
(smc_root - self.params.watdecaydry) /
(self.params.watdecaywet - self.params.watdecaydry))
if float_lt(new_decay_rate, decay_rate):
new_decay_rate = decay_rate
if float_gt(new_decay_rate, decay_rate_dry):
new_decay_rate = decay_rate_dry
return new_decay_rate
def calculate_nimmobilisation(self):
""" Calculated N immobilised in new soil organic matter
General equation for new soil N:C ratio vs Nmin, expressed as linear
equation passing through point Nmin0, actncmin (etc). Values can be
Nmin0=0, Actnc0=Actncmin
if Nmin < Nmincrit:
New soil N:C = soil N:C (when Nmin=0) + slope * Nmin
if Nmin > Nmincrit
New soil N:C = max soil N:C
NB N:C ratio of new passive SOM can change even if assume Passiveconst
Returns:
--------
nimob : float
N immobilsed
"""
# N:C new SOM - active, slow and passive
self.state.actncslope = self.calculate_nc_slope(self.params.actncmax,
self.params.actncmin)
self.state.slowncslope = self.calculate_nc_slope(self.params.slowncmax,
self.params.slowncmin)
self.state.passncslope = self.calculate_nc_slope(self.params.passncmax,
self.params.passncmin)
nmin = self.params.nmin0 * const.G_M2_2_TONNES_HA
arg1 = ((self.fluxes.cactive[1] + self.fluxes.cslow[1]) *
(self.params.passncmin - self.state.passncslope * nmin))
arg2 = ((self.fluxes.cstruct[0] + self.fluxes.cstruct[2] +
self.fluxes.cactive[0]) *
(self.params.slowncmin - self.state.slowncslope * nmin))
arg3 = ((self.fluxes.cstruct[1] + self.fluxes.cstruct[3] +
sum(self.fluxes.cmetab) + self.fluxes.cslow[0] +
self.fluxes.passive) * (self.params.actncmin -
self.state.actncslope * nmin))
numer1 = arg1 + arg2 + arg3
arg1 = ((self.fluxes.cactive[1] + self.fluxes.cslow[1]) *
self.params.passncmax)
arg2 = ((self.fluxes.cstruct[0] + self.fluxes.cstruct[2] +
self.fluxes.cactive[0]) * self.params.slowncmax)
arg3 = ((self.fluxes.cstruct[1] + self.fluxes.cstruct[3] +
sum(self.fluxes.cmetab) + self.fluxes.cslow[0] +
self.fluxes.passive) * self.params.actncmax)
numer2 = arg1 + arg2 + arg3
arg1 = ((self.fluxes.cactive[1] + self.fluxes.cslow[1]) *
self.state.passncslope)
arg2 = ((self.fluxes.cstruct[0] + self.fluxes.cstruct[2] +
self.fluxes.cactive[0]) * self.state.slowncslope)
arg3 = ((self.fluxes.cstruct[1] + self.fluxes.cstruct[3] +
sum(self.fluxes.cmetab) + self.fluxes.cslow[0] +
self.fluxes.passive) * self.state.actncslope)
denom = arg1 + arg2 + arg3
# evaluate N immobilisation in new SOM
nimmob = numer1 + denom * self.state.inorgn
if float_gt(nimmob, numer2):
nimmob = numer2
return nimmob
def calculate_n_immobilisation(self):
""" N immobilised in new soil organic matter, the reverse of
mineralisation. Micro-organisms in the soil compete with plants for N.
Immobilisation is the process by which nitrate and ammonium are taken up
by the soil organisms and thus become unavailable to the plant
(->organic N).
When C:N ratio is high the microorganisms need more nitrogen from
the soil to decompose the carbon in organic materials. This N will be
immobilised until these microorganisms die and the nitrogen is
released.
General equation for new soil N:C ratio vs Nmin, expressed as linear
equation passing through point Nmin0, actncmin (etc). Values can be
Nmin0=0, Actnc0=Actncmin
if Nmin < Nmincrit:
New soil N:C = soil N:C (when Nmin=0) + slope * Nmin
if Nmin > Nmincrit
New soil N:C = max soil N:C
NB N:C ratio of new passive SOM can change even if assume Passiveconst
Returns:
--------
nimob : float
N immobilsed
"""
# N:C new SOM - active, slow and passive
active_nc_slope = self.calculate_nc_slope(self.params.actncmax,
self.params.actncmin)
slow_nc_slope = self.calculate_nc_slope(self.params.slowncmax,
self.params.slowncmin)
passive_nc_slope = self.calculate_nc_slope(self.params.passncmax,
self.params.passncmin)
# C flux entering SOM pools - use short names
active_influxes = self.fluxes.c_into_active
slow_influxes = self.fluxes.c_into_slow
passive_influxes = self.fluxes.c_into_passive
# convert units
nmin = self.params.nmin0 / const.M2_AS_HA * const.G_AS_TONNES
arg1 = ((self.params.passncmin - passive_nc_slope * nmin) *
passive_influxes)
arg2 = (self.params.slowncmin - slow_nc_slope * nmin) * slow_influxes
arg3 = active_influxes * (self.params.actncmin - active_nc_slope * nmin)
numer1 = arg1 + arg2 + arg3
arg1 = passive_influxes * self.params.passncmax
arg2 = slow_influxes * self.params.slowncmax
arg3 = active_influxes * self.params.actncmax
numer2 = arg1 + arg2 + arg3
arg1 = passive_influxes * passive_nc_slope
arg2 = slow_influxes * slow_nc_slope
arg3 = active_influxes * active_nc_slope
denom = arg1 + arg2 + arg3
# evaluate N immobilisation in new SOM
nimmob = numer1 + denom * self.state.inorgn
if float_gt(nimmob, numer2):
nimmob = numer2
return (nimmob, active_nc_slope, slow_nc_slope, passive_nc_slope)
def calculate_npools(self, active_nc_slope, slow_nc_slope,
passive_nc_slope):
"""
Update N pools in the soil
Parameters
----------
active_nc_slope : float
active NC slope
slow_nc_slope: float
slow NC slope
passive_nc_slope : float
passive NC slope
"""
# net N release implied by separation of litter into structural
# & metabolic. The following pools only fix or release N at their
# limiting n:c values.
# N released or fixed from the N inorganic pool is incremented with
# each call to nc_limit and stored in self.fluxes.nlittrelease
self.fluxes.nlittrelease = 0.0
self.state.structsurfn += (self.fluxes.n_surf_struct_litter -
(self.fluxes.n_surf_struct_to_slow +
self.fluxes.n_surf_struct_to_active))
if not self.control.strfloat:
self.state.structsurfn += self.nc_limit(self.state.structsurf,
self.state.structsurfn,
1.0/self.params.structcn,
1.0/self.params.structcn)
self.state.structsoiln += (self.fluxes.n_soil_struct_litter -
(self.fluxes.n_soil_struct_to_slow +
self.fluxes.n_soil_struct_to_active))
if not self.control.strfloat:
self.state.structsoiln += self.nc_limit(self.state.structsoil,
self.state.structsoiln,
1.0/self.params.structcn,
1.0/self.params.structcn)
self.state.metabsurfn += (self.fluxes.n_surf_metab_litter -
self.fluxes.n_surf_metab_to_active)
self.state.metabsurfn += self.nc_limit(self.state.metabsurf,
self.state.metabsurfn,
1.0/25.0, 1.0/10.0)
self.state.metabsoiln += (self.fluxes.n_soil_metab_litter -
self.fluxes.n_soil_metab_to_active)
self.state.metabsoiln += self.nc_limit(self.state.metabsoil,
self.state.metabsoiln,
1.0/25.0, 1.0/10.0)
# When nothing is being added to the metabolic pools, there is the
# potential scenario with the way the model works for tiny bits to be
# removed with each timestep. Effectively with time this value which is
# zero can end up becoming zero but to a silly decimal place
self.precision_control()
# Update SOM pools
n_into_active = (self.fluxes.n_surf_struct_to_active +
self.fluxes.n_soil_struct_to_active +
self.fluxes.n_surf_metab_to_active +
self.fluxes.n_soil_metab_to_active +
self.fluxes.n_slow_to_active +
self.fluxes.n_passive_to_active)
n_out_of_active = (self.fluxes.n_active_to_slow +
self.fluxes.n_active_to_passive)
n_into_slow = (self.fluxes.n_surf_struct_to_slow +
self.fluxes.n_soil_struct_to_slow +
self.fluxes.n_active_to_slow)
n_out_of_slow = (self.fluxes.n_slow_to_active +
self.fluxes.n_slow_to_passive)
n_into_passive = (self.fluxes.n_active_to_passive +
self.fluxes.n_slow_to_passive)
n_out_of_passive = self.fluxes.n_passive_to_active
# N:C of the SOM pools increases linearly btw prescribed min and max
# values as the Nconc of the soil increases.
arg = (self.state.inorgn - self.params.nmin0 / const.M2_AS_HA *
const.G_AS_TONNES)
# active
active_nc = self.params.actncmin + active_nc_slope * arg
if float_gt(active_nc, self.params.actncmax):
active_nc = self.params.actncmax
# release N to Inorganic pool or fix N from the Inorganic pool in order
# to normalise the N:C ratio of a net flux
fixn = self.nc_flux(self.fluxes.c_into_active, n_into_active, active_nc)
self.state.activesoiln += n_into_active + fixn - n_out_of_active
# slow
slow_nc = self.params.slowncmin + slow_nc_slope * arg
if float_gt(slow_nc, self.params.slowncmax):
slow_nc = self.params.slowncmax
# release N to Inorganic pool or fix N from the Inorganic pool in order
# to normalise the N:C ratio of a net flux
fixn = self.nc_flux(self.fluxes.c_into_slow, n_into_slow, slow_nc)
self.state.slowsoiln += n_into_slow + fixn - n_out_of_slow
# passive, update passive pool only if passiveconst=0
pass_nc = self.params.passncmin + passive_nc_slope * arg
if float_gt(pass_nc, self.params.passncmax):
pass_nc = self.params.passncmax
# release N to Inorganic pool or fix N from the Inorganic pool in order
# to normalise the N:C ratio of a net flux
fixn = self.nc_flux(self.fluxes.c_into_passive, n_into_passive, pass_nc)
self.state.passivesoiln += n_into_passive + fixn - n_out_of_passive
# Daily increment of soil inorganic N pool, diff btw in and effluxes
# (grazer urine n goes directly into inorganic pool) nb inorgn may be
# unstable if rateuptake is large
self.state.inorgn += ((self.fluxes.ngross + self.fluxes.ninflow +
self.fluxes.nurine - self.fluxes.nimmob -
self.fluxes.nloss - self.fluxes.nuptake) +
self.fluxes.nlittrelease)
def update_plant_state(self, fdecay, rdecay, project_day, doy):
""" Daily change in C content
Parameters:
-----------
fdecay : float
foliage decay rate
rdecay : float
fine root decay rate
"""
#
# Carbon pools
#
self.state.shoot += (self.fluxes.cpleaf - self.fluxes.deadleaves -
self.fluxes.ceaten)
self.state.root += self.fluxes.cproot - self.fluxes.deadroots
self.state.croot += self.fluxes.cpcroot - self.fluxes.deadcroots
self.state.branch += self.fluxes.cpbranch - self.fluxes.deadbranch
self.state.stem += self.fluxes.cpstem - self.fluxes.deadstems
# annoying but can't see an easier way with the code as it is.
# If we are modelling grases, i.e. no stem them without this
# the sapwood will end up being reduced to a silly number as
# deadsapwood will keep being removed from the pool, even though there
# is no wood.
if self.state.stem <= 0.01:
self.state.sapwood = 0.01
else:
self.state.sapwood += self.fluxes.cpstem - self.fluxes.deadsapwood
#
# Nitrogen pools
#
if self.control.deciduous_model:
self.state.shootn += (self.fluxes.npleaf -
(self.fluxes.lnrate *
self.state.remaining_days[doy]) -
self.fluxes.neaten)
else:
self.state.shootn += (self.fluxes.npleaf -
fdecay * self.state.shootn -
self.fluxes.neaten)
self.state.branchn += (self.fluxes.npbranch - self.params.bdecay *
self.state.branchn)
self.state.rootn += self.fluxes.nproot - rdecay * self.state.rootn
self.state.crootn += self.fluxes.npcroot - self.params.crdecay * self.state.crootn
self.state.stemnimm += (self.fluxes.npstemimm - self.params.wdecay *
self.state.stemnimm)
self.state.stemnmob += (self.fluxes.npstemmob - self.params.wdecay *
self.state.stemnmob -
self.params.retransmob * self.state.stemnmob)
self.state.stemn = self.state.stemnimm + self.state.stemnmob
if self.control.deciduous_model:
self.calculate_cn_store()
#============================
# Enforce maximum N:C ratios.
# ===========================
# This doesn't make sense for the deciduous model because of the ramp
# function. The way the deciduous logic works we now before we start
# how much N we have to allocate so it is impossible (well) to allocate in
# excess. Therefore this is only relevant for evergreen model.
if not self.control.deciduous_model:
# If foliage or root N/C exceeds its max, then N uptake is cut back
# maximum leaf n:c ratio is function of stand age
# - switch off age effect by setting ncmaxfyoung = ncmaxfold
age_effect = ((self.state.age - self.params.ageyoung) /
(self.params.ageold - self.params.ageyoung))
ncmaxf = (self.params.ncmaxfyoung -
(self.params.ncmaxfyoung - self.params.ncmaxfold) *
age_effect)
if float_lt(ncmaxf, self.params.ncmaxfold):
ncmaxf = self.params.ncmaxfold
if float_gt(ncmaxf, self.params.ncmaxfyoung):
ncmaxf = self.params.ncmaxfyoung
extras = 0.0
if self.state.lai > 0.0:
if float_gt(self.state.shootn, (self.state.shoot * ncmaxf)):
extras = self.state.shootn - self.state.shoot * ncmaxf
# Ensure N uptake cannot be reduced below zero.
if float_gt(extras, self.fluxes.nuptake):
extras = self.fluxes.nuptake
self.state.shootn -= extras
self.fluxes.nuptake -= extras
# if root N:C ratio exceeds its max, then nitrogen uptake is cut
# back. n.b. new ring n/c max is already set because it is related
# to leaf n:c
ncmaxr = ncmaxf * self.params.ncrfac # max root n:c
extrar = 0.0
if float_gt(self.state.rootn, (self.state.root * ncmaxr)):
extrar = self.state.rootn - self.state.root * ncmaxr
# Ensure N uptake cannot be reduced below zero.
if float_gt((extras + extrar), self.fluxes.nuptake):
extrar = self.fluxes.nuptake - extras
self.state.rootn -= extrar
self.fluxes.nuptake -= extrar
def calculate_n_immobilisation(self):
""" N immobilised in new soil organic matter, the reverse of
mineralisation. Micro-organisms in the soil compete with plants for N.
Immobilisation is the process by which nitrate and ammonium are taken up
by the soil organisms and thus become unavailable to the plant
(->organic N).
When C:N ratio is high the microorganisms need more nitrogen from
the soil to decompose the carbon in organic materials. This N will be
immobilised until these microorganisms die and the nitrogen is
released.
General equation for new soil N:C ratio vs Nmin, expressed as linear
equation passing through point Nmin0, actncmin (etc). Values can be
Nmin0=0, Actnc0=Actncmin
if Nmin < Nmincrit:
New soil N:C = soil N:C (when Nmin=0) + slope * Nmin
if Nmin > Nmincrit
New soil N:C = max soil N:C
NB N:C ratio of new passive SOM can change even if assume Passiveconst
Returns:
--------
nimob : float
N immobilsed
"""
# N:C new SOM - active, slow and passive
active_nc_slope = self.calculate_nc_slope(self.params.actncmax,
self.params.actncmin)
slow_nc_slope = self.calculate_nc_slope(self.params.slowncmax,
self.params.slowncmin)
passive_nc_slope = self.calculate_nc_slope(self.params.passncmax,
self.params.passncmin)
# C flux entering SOM pools - use short names
active_influxes = self.fluxes.c_into_active
slow_influxes = self.fluxes.c_into_slow
passive_influxes = self.fluxes.c_into_passive
# convert units
nmin = self.params.nmin0 / const.M2_AS_HA * const.G_AS_TONNES
arg1 = ((self.params.passncmin - passive_nc_slope * nmin) *
passive_influxes)
arg2 = (self.params.slowncmin - slow_nc_slope * nmin) * slow_influxes
arg3 = active_influxes * (self.params.actncmin -
active_nc_slope * nmin)
numer1 = arg1 + arg2 + arg3
arg1 = passive_influxes * self.params.passncmax
arg2 = slow_influxes * self.params.slowncmax
arg3 = active_influxes * self.params.actncmax
numer2 = arg1 + arg2 + arg3
arg1 = passive_influxes * passive_nc_slope
arg2 = slow_influxes * slow_nc_slope
arg3 = active_influxes * active_nc_slope
denom = arg1 + arg2 + arg3
# evaluate N immobilisation in new SOM
nimmob = numer1 + denom * self.state.inorgn
if float_gt(nimmob, numer2):
nimmob = numer2
return (nimmob, active_nc_slope, slow_nc_slope, passive_nc_slope)
def calc_carbon_allocation_fracs(self, nitfac, yr_index, project_day):
"""Carbon allocation fractions to move photosynthate through the plant.
Parameters:
-----------
nitfac : float
leaf N:C as a fraction of 'Ncmaxfyoung' (max 1.0)
Returns:
--------
alleaf : float
allocation fraction for shoot
alroot : float
allocation fraction for fine roots
albranch : float
allocation fraction for branches
alstem : float
allocation fraction for stem
References:
-----------
Corbeels, M. et al (2005) Ecological Modelling, 187, 449-474.
McMurtrie, R. E. et al (2000) Plant and Soil, 224, 135-152.
"""
if self.control.alloc_model == "FIXED":
self.state.alleaf = (
self.params.c_alloc_fmax + nitfac *
(self.params.c_alloc_fmax - self.params.c_alloc_fmin))
self.state.alroot = (
self.params.c_alloc_rmax + nitfac *
(self.params.c_alloc_rmax - self.params.c_alloc_rmin))
self.state.albranch = (
self.params.c_alloc_bmax + nitfac *
(self.params.c_alloc_bmax - self.params.c_alloc_bmin))
# allocate remainder to stem
self.state.alstem = (1.0 - self.state.alleaf - self.state.alroot -
self.state.albranch)
#print self.state.alleaf, self.state.alstem, self.state.albranch, self.state.alroot
elif self.control.alloc_model == "GRASSES":
# calculate the N limitation based on available canopy N
# this logic appears counter intuitive, but it works out when
# applied with the perhaps backwards logic below
nf = self.state.shootnc
# case - completely limited by N availability
if nf < self.params.nf_min:
nlim = 0.0
elif nf < self.params.nf_crit:
nlim = ((nf - self.params.nf_min) /
(self.params.nf_crit - self.params.nf_min))
# case - no N limitation
else:
nlim = 1.0
# no constraint on water uptake via root mass, so makes no sense
#limitation = self.sma(min(nlim, self.state.wtfac_root))
# to increase allocation if water stressed.
# dependent on lifespan of the roots...
limitation = self.sma(nlim)
self.state.prev_sma = limitation
# figure out root allocation given available water & nutrients
# hyperbola shape to allocation
self.state.alroot = (
self.params.c_alloc_rmax * self.params.c_alloc_rmin /
(self.params.c_alloc_rmin +
(self.params.c_alloc_rmax - self.params.c_alloc_rmin) *
limitation))
self.state.alstem = 0.0
self.state.albranch = 0.0
self.state.alleaf = (1.0 - self.state.alroot)
#print nlim, limitation, self.state.alleaf, self.state.alroot
elif self.control.alloc_model == "ALLOMETRIC":
# calculate the N limitation based on available canopy N
# this logic appears counter intuitive, but it works out when
# applied with the perhaps backwards logic below
nf = self.state.shootnc
# case - completely limited by N availability
if nf < self.params.nf_min:
nlim = 0.0
elif nf < self.params.nf_crit:
nlim = ((nf - self.params.nf_min) /
(self.params.nf_crit - self.params.nf_min))
# case - no N limitation
else:
nlim = 1.0
# no constraint on water uptake via root mass, so makes no sense
#limitation = self.sma(min(nlim, self.state.wtfac_root))
# to increase allocation if water stressed.
# dependent on lifespan of the roots...
limitation = self.sma(nlim)
self.state.prev_sma = limitation
# figure out root allocation given available water & nutrients
# hyperbola shape to allocation
self.state.alroot = (
self.params.c_alloc_rmax * self.params.c_alloc_rmin /
(self.params.c_alloc_rmin +
(self.params.c_alloc_rmax - self.params.c_alloc_rmin) *
limitation))
#self.state.alroot = (self.params.c_alloc_rmin +
# (self.params.c_alloc_rmax -
# self.params.c_alloc_rmin) * limitation)
# Calculate tree height: allometric reln using the power function
# (Causton, 1985)
self.state.canht = (self.params.heighto *
self.state.stem**self.params.htpower)
# LAI to stem sapwood cross-sectional area (As m-2 m-2)
# (dimensionless)
# Assume it varies between LS0 and LS1 as a linear function of tree
# height (m)
sap_cross_sec_area = (
((self.state.sapwood * const.TONNES_AS_KG * const.M2_AS_HA) /
self.params.cfracts) / self.state.canht / self.params.density)
leaf2sap = self.state.lai / sap_cross_sec_area
# Allocation to leaves dependant on height. Modification of pipe
# theory, leaf-to-sapwood ratio is not constant above a certain
# height, due to hydraulic constraints (Magnani et al 2000; Deckmyn
# et al. 2006).
if self.params.leafsap0 < self.params.leafsap1:
min_target = self.params.leafsap0
else:
min_target = self.params.leafsap1
if self.params.leafsap0 > self.params.leafsap1:
max_target = self.params.leafsap0
else:
max_target = self.params.leafsap1
leaf2sa_target = (self.params.leafsap0 +
(self.params.leafsap1 - self.params.leafsap0) *
(self.state.canht - self.params.height0) /
(self.params.height1 - self.params.height0))
leaf2sa_target = clip(leaf2sa_target,
min=min_target,
max=max_target)
self.state.alleaf = self.alloc_goal_seek(leaf2sap, leaf2sa_target,
self.params.c_alloc_fmax,
self.params.targ_sens)
# Allocation to branch dependent on relationship between the stem
# and branch
target_branch = (self.params.branch0 *
self.state.stem**self.params.branch1)
self.state.albranch = self.alloc_goal_seek(
self.state.branch, target_branch, self.params.c_alloc_bmax,
self.params.targ_sens)
#target_coarse_roots = 0.34 * self.state.stem**0.84
#self.state.alcroot = self.alloc_goal_seek(self.state.croot,
# target_coarse_roots,
# self.params.c_alloc_crmax,
# self.params.targ_sens)
# allocation to stem is the residual
self.state.alstem = (1.0 - self.state.alroot -
self.state.albranch - self.state.alleaf)
#print self.state.alleaf, self.state.albranch, self.state.alstem, self.state.alroot
else:
raise AttributeError('Unknown C allocation model')
# Total allocation should be one, if not print warning:
total_alloc = (self.state.alroot + self.state.alleaf +
self.state.albranch + self.state.alstem)
if float_gt(total_alloc, 1.0):
raise RuntimeError, "Allocation fracs > 1"
def nitrogen_allocation(self, ncbnew, ncwimm, ncwnew, fdecay, rdecay, doy,
days_in_yr, project_day):
""" Nitrogen distribution - allocate available N through system.
N is first allocated to the woody component, surplus N is then allocated
to the shoot and roots with flexible ratios.
References:
-----------
McMurtrie, R. E. et al (2000) Plant and Soil, 224, 135-152.
Parameters:
-----------
ncbnew : float
N:C ratio of branch
ncwimm : float
N:C ratio of immobile stem
ncwnew : float
N:C ratio of mobile stem
fdecay : float
foliage decay rate
rdecay : float
fine root decay rate
"""
# N retranslocated proportion from dying plant tissue and stored within
# the plant
self.fluxes.retrans = self.nitrogen_retrans(fdecay, rdecay, doy)
self.fluxes.nuptake = self.calculate_nuptake(project_day)
# Ross's Root Model.
if self.control.model_optroot == True:
# convert t ha-1 day-1 to gN m-2 year-1
nsupply = (self.calculate_nuptake() * const.TONNES_HA_2_G_M2 *
const.DAYS_IN_YRS)
# covnert t ha-1 to kg DM m-2
rtot = (self.state.root * const.TONNES_HA_2_KG_M2 /
self.params.cfracts)
self.fluxes.nuptake_old = self.fluxes.nuptake
(self.state.root_depth, self.fluxes.nuptake,
self.fluxes.rabove) = self.rm.main(rtot, nsupply, depth_guess=1.0)
#umax = self.rm.calc_umax(self.fluxes.nuptake)
#print umax
# covert nuptake from gN m-2 year-1 to t ha-1 day-1
self.fluxes.nuptake = (self.fluxes.nuptake *
const.G_M2_2_TONNES_HA * const.YRS_IN_DAYS)
# covert from kg DM N m-2 to t ha-1
self.fluxes.deadroots = (self.params.rdecay * self.fluxes.rabove *
self.params.cfracts *
const.KG_M2_2_TONNES_HA)
self.fluxes.deadrootn = (self.state.rootnc *
(1.0 - self.params.rretrans) *
self.fluxes.deadroots)
# Mineralised nitrogen lost from the system by volatilisation/leaching
self.fluxes.nloss = self.params.rateloss * self.state.inorgn
# total nitrogen to allocate
ntot = self.fluxes.nuptake + self.fluxes.retrans
if self.control.deciduous_model:
# allocate N to pools with fixed N:C ratios
# N flux into new ring (immobile component -> structrual components)
self.fluxes.npstemimm = (self.fluxes.wnimrate *
self.state.growing_days[doy])
# N flux into new ring (mobile component -> can be retrans for new
# woody tissue)
self.fluxes.npstemmob = (self.fluxes.wnmobrate *
self.state.growing_days[doy])
self.fluxes.nproot = self.state.n_to_alloc_root / days_in_yr
self.fluxes.npleaf = (self.fluxes.lnrate *
self.state.growing_days[doy])
self.fluxes.npbranch = (self.fluxes.bnrate *
self.state.growing_days[doy])
else:
# allocate N to pools with fixed N:C ratios
# N flux into new ring (immobile component -> structural components)
self.fluxes.npstemimm = self.fluxes.npp * self.state.alstem * ncwimm
# N flux into new ring (mobile component -> can be retrans for new
# woody tissue)
self.fluxes.npstemmob = (self.fluxes.npp * self.state.alstem *
(ncwnew - ncwimm))
self.fluxes.npbranch = (self.fluxes.npp * self.state.albranch *
ncbnew)
# If we have allocated more N than we have available
# - cut back N prodn
arg = (self.fluxes.npstemimm + self.fluxes.npstemmob +
self.fluxes.npbranch)
if float_gt(arg, ntot) and self.control.fixleafnc == False:
self.fluxes.npp *= (
ntot / (self.fluxes.npstemimm + self.fluxes.npstemmob +
self.fluxes.npbranch))
# need to adjust growth values accordingly as well
self.fluxes.cpleaf = self.fluxes.npp * self.state.alleaf
self.fluxes.cproot = self.fluxes.npp * self.state.alroot
self.fluxes.cpbranch = self.fluxes.npp * self.state.albranch
self.fluxes.cpstem = self.fluxes.npp * self.state.alstem
self.fluxes.npbranch = (self.fluxes.npp * self.state.albranch *
ncbnew)
self.fluxes.npstemimm = (self.fluxes.npp * self.state.alstem *
ncwimm)
self.fluxes.npstemmob = (self.fluxes.npp * self.state.alstem *
(ncwnew - ncwimm))
ntot -= (self.fluxes.npbranch + self.fluxes.npstemimm +
self.fluxes.npstemmob)
# allocate remaining N to flexible-ratio pools
self.fluxes.npleaf = (
ntot * self.state.alleaf /
(self.state.alleaf + self.state.alroot * self.params.ncrfac))
self.fluxes.nproot = ntot - self.fluxes.npleaf
def update_plant_state(self, fdecay, rdecay, project_day, doy):
""" Daily change in C content
Parameters:
-----------
fdecay : float
foliage decay rate
rdecay : float
fine root decay rate
"""
#
# Carbon pools
#
self.state.shoot += (self.fluxes.cpleaf - self.fluxes.deadleaves -
self.fluxes.ceaten)
self.state.root += self.fluxes.cproot - self.fluxes.deadroots
self.state.branch += self.fluxes.cpbranch - self.fluxes.deadbranch
self.state.stem += self.fluxes.cpstem - self.fluxes.deadstems
# annoying but can't see an easier way with the code as it is.
# If we are modelling grases, i.e. no stem them without this
# the sapwood will end up being reduced to a silly number as
# deadsapwood will keep being removed from the pool, even though there
# is no wood.
if self.state.stem <= 0.01:
self.state.sapwood = 0.01
else:
self.state.sapwood += self.fluxes.cpstem - self.fluxes.deadsapwood
#
# Nitrogen pools
#
if self.control.deciduous_model:
self.state.shootn += (
self.fluxes.npleaf -
(self.fluxes.lnrate * self.state.remaining_days[doy]) -
self.fluxes.neaten)
else:
self.state.shootn += (self.fluxes.npleaf -
fdecay * self.state.shootn -
self.fluxes.neaten)
self.state.branchn += (self.fluxes.npbranch -
self.params.bdecay * self.state.branchn)
self.state.rootn += self.fluxes.nproot - rdecay * self.state.rootn
self.state.stemnimm += (self.fluxes.npstemimm -
self.params.wdecay * self.state.stemnimm)
self.state.stemnmob += (self.fluxes.npstemmob -
self.params.wdecay * self.state.stemnmob -
self.params.retransmob * self.state.stemnmob)
#print self.state.stemnmob, self.fluxes.npstemmob - self.params.wdecay * self.state.stemnmob, self.fluxes.npstemmob, self.params.wdecay * self.state.stemnmob
self.state.stemn = self.state.stemnimm + self.state.stemnmob
if self.control.deciduous_model:
self.calculate_cn_store()
#============================
# Enforce maximum N:C ratios.
# ===========================
# This doesn't make sense for the deciduous model because of the ramp
# function. The way the deciduous logic works we now before we start
# how much N we have to allocate so it is impossible to allocate in
# excess. Therefore this is only relevant for evergreen model.
if not self.control.deciduous_model:
# If foliage or root N/C exceeds its max, then N uptake is cut back
# maximum leaf n:c ratio is function of stand age
# - switch off age effect by setting ncmaxfyoung = ncmaxfold
age_effect = ((self.state.age - self.params.ageyoung) /
(self.params.ageold - self.params.ageyoung))
ncmaxf = (
self.params.ncmaxfyoung -
(self.params.ncmaxfyoung - self.params.ncmaxfold) * age_effect)
if float_lt(ncmaxf, self.params.ncmaxfold):
ncmaxf = self.params.ncmaxfold
if float_gt(ncmaxf, self.params.ncmaxfyoung):
ncmaxf = self.params.ncmaxfyoung
extras = 0.0
if self.state.lai > 0.0:
if float_gt(self.state.shootn, (self.state.shoot * ncmaxf)):
extras = self.state.shootn - self.state.shoot * ncmaxf
# Ensure N uptake cannot be reduced below zero.
if float_gt(extras, self.fluxes.nuptake):
extras = self.fluxes.nuptake
self.state.shootn -= extras
self.fluxes.nuptake -= extras
# if root N:C ratio exceeds its max, then nitrogen uptake is cut
# back. n.b. new ring n/c max is already set because it is related
# to leaf n:c
ncmaxr = ncmaxf * self.params.ncrfac # max root n:c
extrar = 0.0
if float_gt(self.state.rootn, (self.state.root * ncmaxr)):
extrar = self.state.rootn - self.state.root * ncmaxr
# Ensure N uptake cannot be reduced below zero.
if float_gt((extras + extrar), self.fluxes.nuptake):
extrar = self.fluxes.nuptake - extras
self.state.rootn -= extrar
self.fluxes.nuptake -= extrar
def calc_transpiration(self):
""" units mm/day """
if float_gt(self.fluxes.wue, 0.0):
self.fluxes.transpiration = self.fluxes.gpp_gCm2 / self.fluxes.wue
else:
self.fluxes.transpiration = 0.0
def nitrogen_allocation(self, ncbnew, nccnew, ncwimm, ncwnew, fdecay, rdecay, doy,
days_in_yr, project_day):
""" Nitrogen distribution - allocate available N through system.
N is first allocated to the woody component, surplus N is then allocated
to the shoot and roots with flexible ratios.
References:
-----------
McMurtrie, R. E. et al (2000) Plant and Soil, 224, 135-152.
Parameters:
-----------
ncbnew : float
N:C ratio of branch
ncwimm : float
N:C ratio of immobile stem
ncwnew : float
N:C ratio of mobile stem
fdecay : float
foliage decay rate
rdecay : float
fine root decay rate
"""
# default is we don't need to recalculate the water balance,
# however if we cut back on NPP due to available N below then we do
# need to do this
recalc_wb = False
# N retranslocated proportion from dying plant tissue and stored within
# the plant
self.fluxes.retrans = self.nitrogen_retrans(fdecay, rdecay, doy)
self.fluxes.nuptake = self.calculate_nuptake(project_day)
# Ross's Root Model.
if self.control.model_optroot == True:
# convert t ha-1 day-1 to gN m-2 year-1
nsupply = (self.calculate_nuptake() * const.TONNES_HA_2_G_M2 *
const.DAYS_IN_YRS)
# covnert t ha-1 to kg DM m-2
rtot = (self.state.root * const.TONNES_HA_2_KG_M2 /
self.params.cfracts)
self.fluxes.nuptake_old = self.fluxes.nuptake
(self.state.root_depth,
self.fluxes.nuptake,
self.fluxes.rabove) = self.rm.main(rtot, nsupply, depth_guess=1.0)
#umax = self.rm.calc_umax(self.fluxes.nuptake)
#print umax
# covert nuptake from gN m-2 year-1 to t ha-1 day-1
self.fluxes.nuptake = (self.fluxes.nuptake *
const.G_M2_2_TONNES_HA * const.YRS_IN_DAYS)
# covert from kg DM N m-2 to t ha-1
self.fluxes.deadroots = (self.params.rdecay * self.fluxes.rabove *
self.params.cfracts *
const.KG_M2_2_TONNES_HA)
self.fluxes.deadrootn = (self.state.rootnc *
(1.0 - self.params.rretrans) *
self.fluxes.deadroots)
# Mineralised nitrogen lost from the system by volatilisation/leaching
self.fluxes.nloss = self.params.rateloss * self.state.inorgn
# total nitrogen to allocate
ntot = max(0.0, self.fluxes.nuptake + self.fluxes.retrans)
if self.control.deciduous_model:
# allocate N to pools with fixed N:C ratios
# N flux into new ring (immobile component -> structrual components)
self.fluxes.npstemimm = (self.fluxes.wnimrate *
self.state.growing_days[doy])
# N flux into new ring (mobile component -> can be retrans for new
# woody tissue)
self.fluxes.npstemmob = (self.fluxes.wnmobrate *
self.state.growing_days[doy])
self.fluxes.nproot = self.state.n_to_alloc_root / days_in_yr
self.fluxes.npcroot = (self.fluxes.cnrate *
self.state.growing_days[doy])
self.fluxes.npleaf = (self.fluxes.lnrate *
self.state.growing_days[doy])
self.fluxes.npbranch = (self.fluxes.bnrate *
self.state.growing_days[doy])
else:
# allocate N to pools with fixed N:C ratios
# N flux into new ring (immobile component -> structural components)
self.fluxes.npstemimm = self.fluxes.npp * self.fluxes.alstem * ncwimm
# N flux into new ring (mobile component -> can be retrans for new
# woody tissue)
self.fluxes.npstemmob = (self.fluxes.npp * self.fluxes.alstem *
(ncwnew - ncwimm))
self.fluxes.npbranch = (self.fluxes.npp * self.fluxes.albranch *
ncbnew)
self.fluxes.npcroot = (self.fluxes.npp * self.fluxes.alcroot *
nccnew)
# If we have allocated more N than we have available
# - cut back N prodn
arg = (self.fluxes.npstemimm + self.fluxes.npstemmob +
self.fluxes.npbranch + self.fluxes.npcroot)
if float_gt(arg, ntot) and self.control.fixleafnc == False:
self.fluxes.npp *= (ntot / (self.fluxes.npstemimm +
self.fluxes.npstemmob +
self.fluxes.npbranch ))
# need to adjust growth values accordingly as well
self.fluxes.cpleaf = self.fluxes.npp * self.fluxes.alleaf
self.fluxes.cproot = self.fluxes.npp * self.fluxes.alroot
self.fluxes.cpcroot = self.fluxes.npp * self.fluxes.alcroot
self.fluxes.cpbranch = self.fluxes.npp * self.fluxes.albranch
self.fluxes.cpstem = self.fluxes.npp * self.fluxes.alstem
self.fluxes.npbranch = (self.fluxes.npp * self.fluxes.albranch *
ncbnew)
self.fluxes.npstemimm = (self.fluxes.npp * self.fluxes.alstem *
ncwimm)
self.fluxes.npstemmob = (self.fluxes.npp * self.fluxes.alstem *
(ncwnew - ncwimm))
self.fluxes.npcroot = (self.fluxes.npp * self.fluxes.alcroot *
nccnew)
# Also need to recalculate GPP and thus Ra and return a flag
# so that we know to recalculate the water balance.
self.fluxes.gpp = self.fluxes.npp / self.params.cue
conv = const.G_AS_TONNES / const.M2_AS_HA
self.fluxes.gpp_gCm2 = self.fluxes.gpp / conv
self.fluxes.gpp_am_pm[0] = self.fluxes.gpp_gCm2 / 2.0
self.fluxes.gpp_am_pm[1] = self.fluxes.gpp_gCm2 / 2.0
# New respiration flux
self.fluxes.auto_resp = self.fluxes.gpp - self.fluxes.npp
recalc_wb = True
ntot -= (self.fluxes.npbranch + self.fluxes.npstemimm +
self.fluxes.npstemmob + self.fluxes.npcroot)
ntot = max(0.0, ntot)
# allocate remaining N to flexible-ratio pools
self.fluxes.npleaf = (ntot * self.fluxes.alleaf /
(self.fluxes.alleaf + self.fluxes.alroot *
self.params.ncrfac))
self.fluxes.nproot = ntot - self.fluxes.npleaf
return recalc_wb
def calculate_npools(self):
""" Calculate new soil N pools. """
# net source fluxes.
nstsu = self.fluxes.nresid[0] # s surf
nstsl = self.fluxes.nresid[1] # s soil
nmtsu = self.fluxes.nresid[2] # m surf
nmtsl = self.fluxes.nresid[3] # m soil
nact = (self.fluxes.nstruct[1] + self.fluxes.nstruct[3] +
self.fluxes.nmetab[0] + self.fluxes.nmetab[1] +
self.fluxes.nslow[0] + self.fluxes.npassive)
nslo = (self.fluxes.nstruct[0] + self.fluxes.nstruct[2] +
self.fluxes.nactive[0])
npas = self.fluxes.nactive[1] + self.fluxes.nslow[1]
# net effluxes.
lstsu = (self.fluxes.nstruct[0] + self.fluxes.nstruct[1]) # s surf
lstsl = (self.fluxes.nstruct[2] + self.fluxes.nstruct[3]) # s soil
lmtsu = self.fluxes.nmetab[0] # m surf
lmtsl = self.fluxes.nmetab[1] # m soil
lact = (self.fluxes.nactive[0] + self.fluxes.nactive[1])
lslo = (self.fluxes.nslow[0] + self.fluxes.nslow[1])
lpas = self.fluxes.npassive
# net N release implied by separation of litter into structural
# & metabolic. The following pools only fix or release N at their
# limiting n:c values.
# N released or fixed from the N inorganic pool is incremented with
# each call to nclimit and stored in self.fluxes.nlittrelease
self.fluxes.nlittrelease = 0.0
self.state.structsurfn += nstsu - lstsu
if not self.control.strfloat:
self.state.structsurfn += self.nclimit(self.state.structsurf,
self.state.structsurfn,
1.0/self.params.structcn,
1.0/self.params.structcn)
self.state.structsoiln += nstsl - lstsl
if not self.control.strfloat:
self.state.structsoiln += self.nclimit(self.state.structsoil,
self.state.structsoiln,
1.0/self.params.structcn,
1.0/self.params.structcn)
self.state.metabsurfn += nmtsu - lmtsu
self.state.metabsurfn += self.nclimit(self.state.metabsurf,
self.state.metabsurfn,
1.0/25.0, 1.0/10.0)
self.state.metabsoiln += nmtsl - lmtsl
self.state.metabsoiln += self.nclimit(self.state.metabsoil,
self.state.metabsoiln,
1.0/25.0, 1.0/10.0)
# When nothing is being added to the metabolic pools, there is the
# potential scenario with the way the model works for tiny bits to be
# removed with each timestep. Effectively with time this value which is
# zero can end up becoming zero but to a silly decimal place
self.precision_control()
# N:C of the SOM pools increases linearly btw prescribed min and max
# values as the Nconc of the soil increases.
arg = (self.state.inorgn - self.params.nmin0 / const.M2_AS_HA *
const.G_AS_TONNES)
# active
actnc = self.params.actncmin + self.state.actncslope * arg
if float_gt(actnc, self.params.actncmax):
actnc = self.params.actncmax
fixn = ncflux(self.fluxes.cact, nact, actnc)
self.state.activesoiln += nact + fixn - lact
# slow
slownc = self.params.slowncmin + self.state.slowncslope * arg
if float_gt(slownc, self.params.slowncmax):
slownc = self.params.slowncmax
fixn = ncflux(self.fluxes.cslo, nslo, slownc)
self.state.slowsoiln += nslo + fixn - lslo
# passive
passnc = self.params.passncmin + self.state.passncslope * arg
if float_gt(passnc, self.params.passncmax):
passnc = self.params.passncmax
fixn = ncflux(self.fluxes.cpas, npas, passnc)
# update passive pool only if passiveconst=0
self.state.passivesoiln += npas + fixn - lpas
# Daily increment of soil inorganic N pool, diff btw in and effluxes
# (grazer urine n goes directly into inorganic pool) nb inorgn may be
# unstable if rateuptake is large
self.state.inorgn += ((self.fluxes.ngross + self.fluxes.ninflow +
self.fluxes.nurine - self.fluxes.nimmob -
self.fluxes.nloss - self.fluxes.nuptake) +
self.fluxes.nlittrelease)
def calculate_npools(self, active_nc_slope, slow_nc_slope,
passive_nc_slope):
"""
Update N pools in the soil
Parameters
----------
active_nc_slope : float
active NC slope
slow_nc_slope: float
slow NC slope
passive_nc_slope : float
passive NC slope
"""
# net N release implied by separation of litter into structural
# & metabolic. The following pools only fix or release N at their
# limiting n:c values.
# N released or fixed from the N inorganic pool is incremented with
# each call to nc_limit and stored in self.fluxes.nlittrelease
self.fluxes.nlittrelease = 0.0
self.state.structsurfn += (self.fluxes.n_surf_struct_litter -
(self.fluxes.n_surf_struct_to_slow +
self.fluxes.n_surf_struct_to_active))
if not self.control.strfloat:
self.state.structsurfn += self.nc_limit(self.state.structsurf,
self.state.structsurfn,
1.0 / self.params.structcn,
1.0 / self.params.structcn)
self.state.structsoiln += (self.fluxes.n_soil_struct_litter -
(self.fluxes.n_soil_struct_to_slow +
self.fluxes.n_soil_struct_to_active))
if not self.control.strfloat:
self.state.structsoiln += self.nc_limit(self.state.structsoil,
self.state.structsoiln,
1.0 / self.params.structcn,
1.0 / self.params.structcn)
self.state.metabsurfn += (self.fluxes.n_surf_metab_litter -
self.fluxes.n_surf_metab_to_active)
self.state.metabsurfn += self.nc_limit(self.state.metabsurf,
self.state.metabsurfn,
1.0 / 25.0, 1.0 / 10.0)
self.state.metabsoiln += (self.fluxes.n_soil_metab_litter -
self.fluxes.n_soil_metab_to_active)
self.state.metabsoiln += self.nc_limit(self.state.metabsoil,
self.state.metabsoiln,
1.0 / 25.0, 1.0 / 10.0)
# When nothing is being added to the metabolic pools, there is the
# potential scenario with the way the model works for tiny bits to be
# removed with each timestep. Effectively with time this value which is
# zero can end up becoming zero but to a silly decimal place
self.precision_control()
# Update SOM pools
n_into_active = (self.fluxes.n_surf_struct_to_active +
self.fluxes.n_soil_struct_to_active +
self.fluxes.n_surf_metab_to_active +
self.fluxes.n_soil_metab_to_active +
self.fluxes.n_slow_to_active +
self.fluxes.n_passive_to_active)
n_out_of_active = (self.fluxes.n_active_to_slow +
self.fluxes.n_active_to_passive)
n_into_slow = (self.fluxes.n_surf_struct_to_slow +
self.fluxes.n_soil_struct_to_slow +
self.fluxes.n_active_to_slow)
n_out_of_slow = (self.fluxes.n_slow_to_active +
self.fluxes.n_slow_to_passive)
n_into_passive = (self.fluxes.n_active_to_passive +
self.fluxes.n_slow_to_passive)
n_out_of_passive = self.fluxes.n_passive_to_active
# N:C of the SOM pools increases linearly btw prescribed min and max
# values as the Nconc of the soil increases.
arg = (self.state.inorgn -
self.params.nmin0 / const.M2_AS_HA * const.G_AS_TONNES)
# active
active_nc = self.params.actncmin + active_nc_slope * arg
if float_gt(active_nc, self.params.actncmax):
active_nc = self.params.actncmax
# release N to Inorganic pool or fix N from the Inorganic pool in order
# to normalise the N:C ratio of a net flux
fixn = self.nc_flux(self.fluxes.c_into_active, n_into_active,
active_nc)
self.state.activesoiln += n_into_active + fixn - n_out_of_active
# slow
slow_nc = self.params.slowncmin + slow_nc_slope * arg
if float_gt(slow_nc, self.params.slowncmax):
slow_nc = self.params.slowncmax
# release N to Inorganic pool or fix N from the Inorganic pool in order
# to normalise the N:C ratio of a net flux
fixn = self.nc_flux(self.fluxes.c_into_slow, n_into_slow, slow_nc)
self.state.slowsoiln += n_into_slow + fixn - n_out_of_slow
# passive, update passive pool only if passiveconst=0
pass_nc = self.params.passncmin + passive_nc_slope * arg
if float_gt(pass_nc, self.params.passncmax):
pass_nc = self.params.passncmax
# release N to Inorganic pool or fix N from the Inorganic pool in order
# to normalise the N:C ratio of a net flux
fixn = self.nc_flux(self.fluxes.c_into_passive, n_into_passive,
pass_nc)
self.state.passivesoiln += n_into_passive + fixn - n_out_of_passive
# Daily increment of soil inorganic N pool, diff btw in and effluxes
# (grazer urine n goes directly into inorganic pool) nb inorgn may be
# unstable if rateuptake is large
self.state.inorgn += (
(self.fluxes.ngross + self.fluxes.ninflow + self.fluxes.nurine -
self.fluxes.nimmob - self.fluxes.nloss - self.fluxes.nuptake) +
self.fluxes.nlittrelease)