def adj_for_low_temp(self, param, Tk, lower_bound=0.0, upper_bound=10.0):
"""
Function allowing Jmax/Vcmax to be forced linearly to zero at low T
"""
Tc = Tk - const.DEG_TO_KELVIN
if float_lt(Tc, lower_bound):
param = 0.0
elif float_lt(Tc, upper_bound):
param *= (Tc - lower_bound) / (upper_bound - lower_bound)
return param
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 assim(self, ci, gamma_star, a1, a2):
"""Morning and afternoon calcultion of photosynthesis with the
limitation defined by the variables passed as a1 and a2, i.e. if we
are calculating vcmax or jmax limited.
Parameters:
----------
ci : float
intercellular CO2 concentration.
gamma_star : float
CO2 compensation point in the abscence of mitochondrial respiration
a1 : float
variable depends on whether the calculation is light or rubisco
limited.
a2 : float
variable depends on whether the calculation is light or rubisco
limited.
Returns:
-------
assimilation_rate : float
assimilation rate assuming either light or rubisco limitation.
"""
if float_lt(ci, gamma_star):
return 0.0
else:
return a1 * (ci - gamma_star) / (a2 + ci)
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 adj_params_for_low_temp(self,
param,
Tk,
lower_bound=0.0,
upper_bound=10.0):
"""
Function allowing Jmax/Vcmax to be forced linearly to zero at low T
"""
Tc = Tk - const.DEG_TO_KELVIN
if float_lt(Tc, lower_bound):
param = 0.0
elif float_lt(Tc, upper_bound):
param *= (Tc - lower_bound) / (upper_bound - lower_bound)
return param
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 nc_ratio(carbon_val, nitrogen_val, pool):
"""Calculate nitrogen:carbon ratios
Parameters:
----------
carbon_val : float
C value
nitrogen_val: float
N value#
Returns:
--------
value : float
N:C ratio
"""
if float_lt(carbon_val, 0.0):
# Note, previously the else branch was set to 1E6...presumably this
# was a hack to deal with the scenario for example where
# self.state.metabsurf and self.state.metabsurfn both start at zero.
# This was fine as this ratio isn't used in the code. Since I have
# commented out these diagnostics we shouldn't end up here unless there
# really is an error!!
msg = "Dianostic for %s pool N:C has invalid values C:%s, N:%s" % \
(pool, carbon_val, nitrogen_val)
raise ValueError(msg)
return nitrogen_val / carbon_val
def assim(self, ci, gamma_star, a1, a2):
"""Morning and afternoon calcultion of photosynthesis with the
limitation defined by the variables passed as a1 and a2, i.e. if we
are calculating vcmax or jmax limited.
Parameters:
----------
ci : float
intercellular CO2 concentration.
gamma_star : float
CO2 compensation point in the abscence of mitochondrial respiration
a1 : float
variable depends on whether the calculation is light or rubisco
limited.
a2 : float
variable depends on whether the calculation is light or rubisco
limited.
Returns:
-------
assimilation_rate : float
assimilation rate assuming either light or rubisco limitation.
"""
if float_lt(ci, gamma_star):
return 0.0
else:
return a1 * (ci - gamma_star) / (a2 + ci)
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 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 main():
# sweep the cmd line
options, args = cmdline_parser()
from file_parser import initialise_model_data
# pylint: disable=C0103
# pylint: disable=C0324
# pylint: disable=C0103
fname = "gday"
fdir = "/Users/mdekauwe/src/python/GDAY_model/params"
(adj_control, adj_params,
adj_state, adj_files,
adj_fluxes, met_data) = initialise_model_data(fname, default_dir=fdir)
# figure out photosynthesis
P = PlantProdModel(adj_control, adj_params, adj_state, adj_fluxes, met_data)
adj_state.lai = (adj_params.slainit * const.M2_AS_HA /
const.KG_AS_TONNES / adj_params.cfracts *
adj_state.shoot)
# Specific LAI (m2 onesided/kg DW)
adj_state.sla = adj_params.slainit
adj_control.assim_model = 3
num_days = len(met_data['doy'])
for i in xrange(num_days):
if float_lt(adj_state.lai, adj_params.lai_cover):
gcover = adj_state.lai / adj_params.lai_cover
else:
gcover = 1.0
adj_state.fapar = ((1.0 - exp(-adj_params.kext * adj_state.lai /
gcover)) * gcover)
adj_state.shootnc = adj_state.shootn / adj_state.shoot
P.run_sim(i)
print adj_fluxes.gpp / const.HA_AS_M2 * const.TONNES_AS_G
#print adj_state.lai
# this is done in derive so do here
# Specific LAI (m2 onesided/kg DW)
adj_state.sla = (adj_state.lai / const.M2_AS_HA *
const.KG_AS_TONNES *
adj_params.cfracts / adj_state.shoot)
return
def carbon_production(self, project_day, daylen):
""" Calculate GPP, NPP and plant respiration
Parameters:
-----------
project_day : integer
simulation day
daylen : float
daytime length (hrs)
References:
-----------
* Jackson, J. E. and Palmer, J. W. (1981) Annals of Botany, 47, 561-565.
"""
if self.state.lai > 0.0:
# average leaf nitrogen content (g N m-2 leaf)
leafn = (self.state.shootnc * self.params.cfracts /
self.state.sla * const.KG_AS_G)
# total nitrogen content of the canopy
self.state.ncontent = leafn * self.state.lai
else:
self.state.ncontent = 0.0
# fractional ground cover.
if float_lt(self.state.lai, self.params.lai_cover):
frac_gcover = self.state.lai / self.params.lai_cover
else:
frac_gcover = 1.0
# Radiance intercepted by the canopy, accounting for partial closure
# Jackson and Palmer (1981), derived from beer's law
if self.state.lai > 0.0:
self.state.light_interception = ((1.0 - exp(-self.params.kext *
self.state.lai / frac_gcover)) *
frac_gcover)
else:
self.state.light_interception = 0.0
if self.control.water_stress:
# Calculate the soil moisture availability factors [0,1] in the
# topsoil and the entire root zone
(self.state.wtfac_tsoil,
self.state.wtfac_root) = self.sm.calculate_soil_water_fac()
else:
# really this should only be a debugging option!
self.state.wtfac_tsoil = 1.0
self.state.wtfac_root = 1.0
# Estimate photosynthesis
if self.control.assim_model == "BEWDY":
self.bw.calculate_photosynthesis(frac_gcover, project_day, daylen)
elif self.control.assim_model == "MATE":
self.mt.calculate_photosynthesis(project_day, daylen)
else:
raise AttributeError('Unknown assimilation model')
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 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 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 calc_npp(M, control, params, state, fluxes, met_data):
state.lai = (params.slainit * const.M2_AS_HA /
const.KG_AS_TONNES / params.cfracts *
state.shoot)
# Specific LAI (m2 onesided/kg DW)
state.sla = params.slainit
year = str(control.startyear)
month = str(control.startmonth)
day = str(control.startday)
datex = datetime.datetime.strptime((year + month + day), "%Y%m%d")
npp = np.zeros(0)
for project_day in xrange(365):
state.shootnc = state.shootn / state.shoot
state.ncontent = (state.shootnc * params.cfracts /
state.sla * const.KG_AS_G)
daylen = day_length(datex, params.latitude)
state.wtfac_root = 1.0
#state.lai = laidata[project_day]
if float_lt(state.lai, params.lai_cover):
frac_gcover = state.lai / params.lai_cover
else:
frac_gcover = 1.0
state.light_interception = ((1.0 - math.exp(-params.kext *
state.lai / frac_gcover)) *
frac_gcover)
M.calculate_photosynthesis(project_day, daylen)
npp = np.append(npp, fluxes.npp_gCm2)
datex += datetime.timedelta(days=1)
return npp.sum()
def mate_day_length(date, latitude):
""" Calculate number of sunlight hours (units = h d-1)
Routine comes from MATE, though not sure how right this is, are the
hemispheres inverted? Check
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_dec = (23.4 * math.pi / 180.0 * math.cos(2.0 * math.pi /
yr_days * (doy + 10.0)))
if float_lt(latitude, 0.0):
solar_dec *= -1.0
dayl = (math.acos(-math.tan(latitude * conv) * math.tan(solar_dec)) *
24.0 / math.pi)
return dayl
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 update_plant_state(self, fdecay, rdecay):
""" Daily change in C content
Parameters:
-----------
fdecay : float
foliage decay rate
rdecay : float
fine root decay rate
"""
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
self.state.shootn += (self.fluxes.npleaf - fdecay * self.state.shootn -
self.fluxes.neaten)
self.state.rootn += self.fluxes.nproot - rdecay * self.state.rootn
self.state.branchn += (self.fluxes.npbranch - self.params.bdecay *
self.state.branchn)
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
# 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
# if foliage or 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
extrar = 0.
extras = 0.
if float_gt(self.state.shootn, (self.state.shoot * ncmaxf)):
extras = self.state.shootn - self.state.shoot * ncmaxf
#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
ncmaxr = ncmaxf * self.params.ncrfac # max root n:c
if float_gt(self.state.rootn, (self.state.root * ncmaxr)):
extrar = self.state.rootn - self.state.root * ncmaxr
#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
for i, yr in enumerate(years):
daylen = calculate_daylength(days_in_year[i], params.latitude)
for doy in xrange(days_in_year[i]):
state.wtfac_root = 1.0
#state.lai = lai_data[project_day]
state.lai = 2.0
if state.lai > 0.0:
state.shootnc = 0.03 #state.shootn / state.shoot
state.ncontent = (state.shootnc * params.cfracts /
state.sla * const.KG_AS_G)
else:
state.ncontent = 0.0
if float_lt(state.lai, params.lai_cover):
frac_gcover = state.lai / params.lai_cover
else:
frac_gcover = 1.0
state.fipar = ((1.0 - exp(-params.kext *
state.lai / frac_gcover)) *
frac_gcover)
M.calculate_photosynthesis(project_day, daylen[doy])
print fluxes.gpp_gCm2#, state.lai
project_day += 1
def update_plant_state(self, fdecay, rdecay, project_day):
""" Daily change in C content
Parameters:
-----------
fdecay : float
foliage decay rate
rdecay : float
fine root decay rate
"""
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
if self.control.deciduous_model:
self.state.shootn += (self.fluxes.npleaf -
(self.fluxes.deadleafn - self.fluxes.neaten))
else:
self.state.shootn += (self.fluxes.npleaf -
fdecay * self.state.shootn -
self.fluxes.neaten)
self.state.shootn = max(0.0, self.state.shootn)
self.state.rootn += self.fluxes.nproot - rdecay * self.state.rootn
self.state.branchn += (self.fluxes.npbranch - self.params.bdecay *
self.state.branchn)
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
self.state.exu_pool += self.fluxes.cprootexudate
self.fluxes.microbial_resp = self.calc_microbial_resp(project_day)
self.state.exu_pool -= self.fluxes.microbial_resp
#print self.fluxes.microbial_resp, self.fluxes.cprootexudate
self.calculate_cn_store()
if not self.control.deciduous_model:
# 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
# if foliage or 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
extrar = 0.
extras = 0.
if float_gt(self.state.shootn, (self.state.shoot * ncmaxf)):
extras = self.state.shootn - self.state.shoot * ncmaxf
#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
ncmaxr = ncmaxf * self.params.ncrfac # max root n:c
if float_gt(self.state.rootn, (self.state.root * ncmaxr)):
extrar = self.state.rootn - self.state.root * ncmaxr
#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 update_plant_state(self, fdecay, rdecay):
""" Daily change in C content
Parameters:
-----------
fdecay : float
foliage decay rate
rdecay : float
fine root decay rate
"""
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
if self.control.deciduous_model:
self.state.shootn += (self.fluxes.npleaf -
(self.fluxes.deadleafn - self.fluxes.neaten))
else:
self.state.shootn += (self.fluxes.npleaf -
fdecay * self.state.shootn -
self.fluxes.neaten)
self.state.shootn = max(0.0, self.state.shootn)
self.state.rootn += self.fluxes.nproot - rdecay * self.state.rootn
self.state.branchn += (self.fluxes.npbranch - self.params.bdecay *
self.state.branchn)
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
# 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
# if foliage or 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
extrar = 0.
extras = 0.
if float_gt(self.state.shootn, (self.state.shoot * ncmaxf)):
extras = self.state.shootn - self.state.shoot * ncmaxf
#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
ncmaxr = ncmaxf * self.params.ncrfac # max root n:c
if float_gt(self.state.rootn, (self.state.root * ncmaxr)):
extrar = self.state.rootn - self.state.root * ncmaxr
#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
if self.control.deciduous_model:
# update annual fluxes - store for next year
self.state.clabile_store += self.fluxes.npp
self.state.aroot_uptake += self.fluxes.nuptake
self.state.aretrans += self.fluxes.retrans
self.state.anloss += self.fluxes.nloss
# update N:C of plant pools
if float_eq(self.state.shoot, 0.0):
self.state.shootnc = 0.0
else:
self.state.shootnc = max(self.state.shootn / self.state.shoot,
self.params.ncfmin)
# N:C of stuctural wood as function of N:C of foliage
# (kgN kg-1C)(Medlyn et al 2000)
self.state.nc_ws = (self.params.nc_wsa + self.params.nc_wsb *
self.state.shootnc)
# N:C of new wood as function of N:C of foliage
self.state.nc_wnew = (self.params.nc_wnewa + self.params.nc_wnewb *
self.state.shootnc)
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
# days in each year
years = uniq(met_data["year"])
# years = years[:-1] # dump last year as missing "site" LAI
days_in_year = [met_data["year"].count(yr) for yr in years]
for i, yr in enumerate(years):
daylen = calculate_daylength(days_in_year[i], params.latitude)
for doy in xrange(days_in_year[i]):
state.wtfac_root = 1.0
# state.lai = lai_data[project_day]
state.lai = 2.0
if state.lai > 0.0:
state.shootnc = 0.03 # state.shootn / state.shoot
state.ncontent = state.shootnc * params.cfracts / params.sla * const.KG_AS_G
else:
state.ncontent = 0.0
if float_lt(state.lai, params.lai_cover):
frac_gcover = state.lai / params.lai_cover
else:
frac_gcover = 1.0
state.fipar = (1.0 - exp(-params.kext * state.lai / frac_gcover)) * frac_gcover
M.calculate_photosynthesis(project_day, daylen[doy])
print fluxes.gpp_gCm2 # , state.lai
project_day += 1
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 carbon_production(self, date, day, daylen):
""" Calculate GPP, NPP and plant respiration
Parameters:
-----------
day : intefer
simulation day
date : date string object
date object string (yr/mth/day)
daylen : float
daytime length (hrs)
References:
-----------
* Jackson, J. E. and Palmer, J. W. (1981) Annals of Botany, 47, 561-565.
"""
# leaf nitrogen content
self.state.ncontent = (self.state.shootnc * self.params.cfracts /
self.state.sla * const.KG_AS_G)
# fractional ground cover.
if float_lt(self.state.lai, self.params.lai_cover):
frac_gcover = self.state.lai / self.params.lai_cover
else:
frac_gcover = 1.0
# Radiance intercepted by the canopy, accounting for partial closure
# Jackson and Palmer (1981), derived from beer's law
self.state.light_interception = ((1.0 - math.exp(-self.params.kext *
self.state.lai / frac_gcover)) *
frac_gcover)
sys.path.append("/Users/mdekauwe/src/fortran/maestra")
import physiol
import utils
import maestcom as m
RDFIPT = 7.29966089E-02
TUIPT = 0.71114331
TDIPT = 0.16205148
RNET = 17.933075
WIND = 8.20037797E-02
PAR = 17.746254
TAIR = -0.55100000
RH = 0.73264003
VPD = 157.64043
VMFD = 1.5811477
PRESS = 99700.000
SOILMOIST = 0.0000000
IECO = 1
TVJUP = -100.00000
TVJDN = -100.00000
THETA = 0.94999999
AJQ = 0.30000001
RD0 = 0.50000006
Q10F = 0.10260000
RTEMP = 28.000000
DAYRESP = 0.60000002
TBELOW = -100.00000
MODELGS = 4
GSREF = 0.0000000
I0 = 0.0000000
D0 = 2.66481364E-21
VK1 = 0.0000000
VK2 = 0.0000000
VPD1 = 0.0000000
VPD2 = 0.0000000
VMFD0 = 0.0000000
GSJA = 0.0000000
GSJB = 0.0000000
T0 = 0.0000000
TREF = 0.0000000
TMAX = 0.0000000
SMD1 = 0.0000000
SMD2 = 0.0000000
SOILDATA = 0
SWPEXP = 0.0000000
G0 = 0.0000000
D0L = 2.66246708E-44
GAMMA = 0.0000000
G1 = 3.0573249
GK = 0.0000000
GSC = 3.10860965E-02
RD = 2.08401568E-02
print
VPD = 157.64043
gsmin = 0.0
jmax25 = self.params.jmaxn * self.state.ncontent
vcmax25 = self.params.vcmaxn * self.state.ncontent
itermax = 0
nsides = 1
aleaf = 0.0
eavj = 43790.000
edvj = 200000.00
eavc = 51560.0
edvc = 0.0
delsc = 0.0
et = 0.0
fheat = 0.0
tleaf = 0.0
gbh = 0.0
decoup = 0.0
delsj = 644.43378
wleaf = 2.00000009E-03
if self.control.co2_conc == 0:
ca = self.met_data['amb_co2'][day]
elif self.control.co2_conc == 1:
ca = self.met_data['ele_co2'][day]
(aleaf, et, gbh, decoup, tleaf) = physiol.pstransp(RDFIPT,TUIPT,TDIPT,RNET,WIND,PAR,TAIR, ca, RH,VPD,
VMFD,PRESS,SOILMOIST,jmax25, IECO, eavj, edvj, delsj,
vcmax25,eavc, edvc, delsc,TVJUP,TVJDN,THETA,AJQ,RD0,
Q10F,RTEMP,DAYRESP,TBELOW,MODELGS,GSREF, gsmin,I0,
D0,VK1,VK2,VPD1,VPD2,VMFD0,GSJA,GSJB,T0,TREF,TMAX,
SMD1,SMD2,SOILDATA,SWPEXP,G0,D0L,GAMMA,G1,GK, wleaf,
nsides, itermax, GSC, aleaf, RD, et, fheat, tleaf, gbh, decoup)
print et, aleaf, gbh, decoup, tleaf
sys.exit()
sys.exit()
# Calculate the soil moisture availability factors [0,1] in the topsoil
# and the entire root zone
(self.state.wtfac_tsoil,
self.state.wtfac_root) = self.wb.calculate_soil_water_fac()
# Estimate photosynthesis using an empirical model
if self.control.assim_model >=0 and self.control.assim_model <= 4:
self.pp.calculate_photosynthesis(day)
# Estimate photosynthesis using the mechanistic BEWDY model
elif self.control.assim_model >=5 and self.control.assim_model <= 6:
# calculate plant C uptake using bewdy
self.bw.calculate_photosynthesis(frac_gcover, date, day, daylen)
# Estimate photosynthesis using the mechanistic MATE model. Also need to
# calculate a water availability scalar to determine Ci:Ca reln.
elif self.control.assim_model ==7:
self.mt.calculate_photosynthesis(day, daylen)
else:
raise AttributeError('Unknown assimilation model')
def carbon_production(self, project_day, daylen):
""" Calculate GPP, NPP and plant respiration
Parameters:
-----------
project_day : integer
simulation day
daylen : float
daytime length (hrs)
References:
-----------
* Jackson, J. E. and Palmer, J. W. (1981) Annals of Botany, 47, 561-565.
"""
# leaf nitrogen content
if self.state.lai > 0.0:
# Leaf N content (g m-2)
self.state.ncontent = (self.state.shootnc * self.params.cfracts /
self.state.sla * const.KG_AS_G)
else:
self.state.ncontent = 0.0
# fractional ground cover.
if float_lt(self.state.lai, self.params.lai_cover):
frac_gcover = self.state.lai / self.params.lai_cover
else:
frac_gcover = 1.0
# Radiance intercepted by the canopy, accounting for partial closure
# Jackson and Palmer (1981), derived from beer's law
if self.state.lai > 0.0:
self.state.light_interception = ((1.0 - exp(-self.params.kext *
self.state.lai / frac_gcover)) *
frac_gcover)
else:
self.state.light_interception = 0.0
if self.control.water_stress:
# Calculate the soil moisture availability factors [0,1] in the
# topsoil and the entire root zone
(self.state.wtfac_tsoil,
self.state.wtfac_root) = self.sm.calculate_soil_water_fac()
else:
# really this should only be a debugging option!
self.state.wtfac_tsoil = 1.0
self.state.wtfac_root = 1.0
# Estimate photosynthesis using an empirical model
if self.control.assim_model >=0 and self.control.assim_model <= 4:
self.pp.calculate_photosynthesis(project_day)
# Estimate photosynthesis using the mechanistic BEWDY model
elif self.control.assim_model >=5 and self.control.assim_model <= 6:
# calculate plant C uptake using bewdy
self.bw.calculate_photosynthesis(frac_gcover, project_day, daylen)
# Estimate photosynthesis using the mechanistic MATE model. Also need to
# calculate a water availability scalar to determine Ci:Ca reln.
elif self.control.assim_model ==7:
self.mt.calculate_photosynthesis(project_day, daylen)
else:
raise AttributeError('Unknown assimilation model')