def run_sim(self):
""" Run model simulation! """
project_day = 0
# figure out the number of years for simulation and the number of
# days in each year
years = uniq(self.met_data["year"])
days_in_year = [self.met_data["year"].count(yr) for yr in years]
# =============== #
# YEAR LOOP #
# =============== #
for i, yr in enumerate(years):
self.day_output = [] # empty daily storage list for outputs
daylen = calculate_daylength(days_in_year[i], self.params.latitude)
if self.control.deciduous_model:
self.P.calculate_phenology_flows(daylen, self.met_data,
days_in_year[i], project_day)
self.zero_stuff()
# =============== #
# DAY LOOP #
# =============== #
for doy in xrange(days_in_year[i]):
# litterfall rate: C and N fluxes
(fdecay, rdecay) = self.lf.calculate_litter(doy)
# co2 assimilation, N uptake and loss
self.pg.calc_day_growth(project_day, fdecay, rdecay,
daylen[doy], doy,
float(days_in_year[i]), i)
# soil C & N model fluxes
self.cs.calculate_csoil_flows(project_day)
self.ns.calculate_nsoil_flows()
# calculate C:N ratios and increment annual flux sums
self.day_end_calculations(project_day, days_in_year[i])
#print self.state.shoot, self.state.lai
#print self.fluxes.gpp * 100, self.state.lai
# =============== #
# END OF DAY #
# =============== #
self.save_daily_outputs(yr, doy+1)
project_day += 1
# =============== #
# END OF YEAR #
# =============== #
if self.control.deciduous_model:
self.pg.allocate_stored_c_and_n(init=False)
if self.control.print_options == "DAILY" and self.spin_up == False:
self.print_output_file()
# close output files
if self.control.print_options == "END" and self.spin_up == False:
self.print_output_file()
self.pr.clean_up()
M = MateC4(control, params, state, fluxes, met_data)
# flai = "/Users/mdekauwe/research/NCEAS_face/GDAY_ornl_simulation/experiments/silvias_LAI.txt"
# lai_data = np.loadtxt(flai)
project_day = 0
# figure out the number of years for simulation and the number of
# 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
def run_sim(self):
""" Run model simulation! """
# local variables
years = self.years
days_in_year = self.days_in_year
# =============== #
# YEAR LOOP #
# =============== #
project_day = 0
for i, yr in enumerate(years):
self.day_output = [] # empty daily storage list for outputs
daylen = calculate_daylength(days_in_year[i], self.params.latitude)
if self.control.deciduous_model:
self.P.calculate_phenology_flows(daylen, self.met_data,
days_in_year[i], project_day)
self.zero_stuff()
# =============== #
# DAY LOOP #
# =============== #
for doy in xrange(days_in_year[i]):
#for pft in xrange(4):
# litterfall rate: C and N fluxes
(fdecay, rdecay) = self.lf.calculate_litter(doy)
# co2 assimilation, N uptake and loss
self.pg.calc_day_growth(project_day, fdecay,
rdecay, daylen[doy], doy,
float(days_in_year[i]), i)
# soil C & N model fluxes
self.cs.calculate_csoil_flows(project_day)
self.ns.calculate_nsoil_flows(project_day)
# calculate C:N ratios and increment annual flux sums
self.day_end_calculations(project_day, days_in_year[i])
#print self.state.lai, self.fluxes.gpp*100, self.state.pawater_root, self.state.shootnc
# =============== #
# END OF DAY #
# =============== #
if not self.spin_up:
self.save_daily_outputs(yr, doy + 1)
# check the daily water balance
#self.cb.check_water_balance(project_day)
project_day += 1
# =============== #
# END OF YEAR #
# =============== #
if self.control.deciduous_model:
print "**", self.state.cstore
self.pg.allocate_stored_c_and_n(init=False)
if self.control.print_options == "DAILY" and not self.spin_up:
self.print_output_file()
# close output files
if self.control.print_options == "END" and not self.spin_up:
self.print_output_file()
# only close printing file if not in spin up mode as we have yet
# written the daily output...
if self.spin_up:
return (yr, doy + 1)
else:
self.pr.clean_up()
def run_sim(self):
""" Run model simulation! """
# local variable
years = self.years
days_in_year = self.days_in_year
if self.control.disturbance:
# Figure out if any years have a disturbance
self.db.initialise(years)
# ===================== #
# Y E A R L O O P #
# ===================== #
project_day = 0
for i, yr in enumerate(years):
self.day_output = [] # empty daily storage list for outpu
daylen = calculate_daylength(days_in_year[i], self.params.latitude)
if self.control.deciduous_model:
self.P.calculate_phenology_flows(daylen, self.met_data,
days_in_year[i], project_day)
# Change window size to length of growing season
self.pg.sma.window_size = self.P.growing_seas_len
self.zero_stuff()
# =================== #
# D A Y L O O P #
# =================== #
for doy in xrange(days_in_year[i]):
# standard litter calculation
# litterfall rate: C and N fluxe
(fdecay, rdecay) = self.lf.calculate_litter(doy)
# Fire Disturbance?
if (self.control.disturbance != 0 and
self.params.disturbance_doy == doy):
self.db.check_for_fire(yr, self.pg)
# Hurricane?
elif (self.control.hurricane == 1 and
self.params.hurricane_yr == yr and
self.params.hurricane_doy == doy):
self.db.hurricane()
# photosynthesis & growth
fsoilT = self.cs.soil_temp_factor(project_day)
self.pg.calc_day_growth(project_day, fdecay, rdecay,
daylen[doy], doy,
float(days_in_year[i]), i, fsoilT)
# soil C & N calculation
self.cs.calculate_csoil_flows(project_day, doy)
self.ns.calculate_nsoil_flows(project_day, doy)
if self.control.ncycle == False:
# Turn off all N calculations
self.reset_all_n_pools_and_fluxes()
# calculate C:N ratios and increment annual flux sum
self.day_end_calculations(days_in_year[i])
# checking if we died during the timestep
# - added for desert simulation
if (not self.control.deciduous_model and
self.control.disturbance == 0):
self.are_we_dead()
#print self.state.plantc, self.state.soilc
#print yr, doy, self.state.lai, self.fluxes.gpp*100
#print self.fluxes.gpp*100, self.state.prev_sma
# ======================= #
# E N D O F D A Y #
# ======================= #
if not self.spin_up:
self.save_daily_outputs(yr, doy+1)
# check the daily water balance
#self.cb.check_water_balance(project_day)
project_day += 1
# ========================= #
# E N D O F Y E A R #
# ========================= #
# Allocate stored C&N for the following year
if self.control.deciduous_model:
# Using average alloc fracs across growing season instead
#self.pg.calc_carbon_allocation_fracs(0.0) #comment this!!
self.pg.calculate_average_alloc_fractions(self.P.growing_seas_len)
self.pg.allocate_stored_c_and_n(init=False)
# reset the stress buffer at the end of the growing season
self.pg.sma.reset_stream()
#print self.fluxes.alleaf, self.fluxes.alroot, \
# (self.fluxes.albranch+self.fluxes.alstem)
#print
# GDAY died in the previous year, re-establish gday for the next yr
# - added for desert simulation
if (self.dead and not
self.control.deciduous_model and
self.control.disturbance == 0):
self.re_establish_gday()
if self.control.print_options == "DAILY" and not self.spin_up:
self.print_output_file()
# close output file
if self.control.print_options == "END" and not self.spin_up:
self.print_output_file()
# only close printing file if not in spin up mode as we have ye
# written the daily output...
if self.spin_up:
return (yr, doy+1)
else:
# Need to pass the project day to calculate NROWS for .hdr file
self.pr.clean_up(project_day)
# Specific LAI (m2 onesided/kg DW)
state.sla = params.slainit
project_day = 0
# figure out the number of years for simulation and the number of
# 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 /
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:
def run_sim(self):
""" Run model simulation! """
# class instances
cf = CarbonFlows(self.control, self.params, self.state, self.fluxes,
self.met_data)
nf = NitrogenFlows(self.control, self.params, self.state, self.fluxes)
lf = LitterProduction(self.control, self.params, self.state,
self.fluxes)
pg = PlantGrowth(self.control, self.params, self.state, self.fluxes,
self.met_data)
cpl = CarbonPools(self.control, self.params, self.state, self.fluxes)
npl = NitrogenPools(self.control, self.params, self.state, self.fluxes,
self.met_data)
##################
self.control.deciduous_model = 1
self.control.numyears_sim = 12
self.state.nc_fy = 0.06
self.state.npp_store = 5.2154
##################
if self.control.deciduous_model:
total = self.initialise_deciduous_model()
# In the first year we don't have last years data, so I have
# precalculated the average of all the november-jan chilling values
last_yrs_accumulated_ncd = 17.0
P = Phenology(self.fluxes, self.state, last_yrs_accumulated_ncd)
# calculate initial C:N ratios and zero annual flux sums
self.derive(1, self.date, INIT=True)
self.state.pawater_root = self.params.wcapac_root
self.state.pawater_tsoil = self.state.pawater_tsoil
project_day = 0
for yr in xrange(self.control.startyear,
self.control.startyear+self.control.numyears_sim-1):
yr_days = calc_days_in_year(self.date.year)
daylen = calculate_daylength(self.date, yr_days,
self.params.latitude)
if self.control.deciduous_model:
self.zero_annual_sums()
P.calculate_phenology_flows(daylen, self.date, self.met_data,
yr_days)
for d in xrange(yr_days):
# litterfall rate: C and N fluxes
(fdecay, rdecay) = lf.calculate_litter_flows(d)
# co2 assimilation, N uptake and loss
pg.grow(project_day, self.date, fdecay, rdecay, daylen[d], doy=d)
# soil model fluxes
cf.calculate_cflows(project_day)
nf.calculate_nflows()
self.fluxes.nep = self.calculate_nep()
# soil model - update pools
(cact, cslo, cpas) = cpl.calculate_cpools()
npl.calculate_npools(cact, cslo, cpas, project_day)
# calculate C:N ratios and increment annual flux sums
self.derive(project_day, self.date)
print self.fluxes.gpp * 100, self.state.lai
if self.control.print_options == 0:
self.pr.save_daily_output(project_day + 1, self.date)
self.increment_date(yr_days)
project_day += 1
sys.exit()
# =============== #
# END OF THE YEAR #
# =============== #
if self.control.deciduous_model:
self.allocate_stored_c_and_n(total)
if self.control.print_options == 1:
# need to save initial SLA to current one!
self.params.slainit = (self.state.lai / const.M2_AS_HA *
const.KG_AS_TONNES * self.params.cfracts /
self.state.shoot)
self.correct_rate_constants(output=True)
self.pr.save_state()
# house cleaning, close ouput files
self.pr.tidy_up()
def run_sim(self):
""" Run model simulation! """
# local variable
years = self.years
days_in_year = self.days_in_year
if self.control.disturbance:
# Figure out if any years have a disturbance
self.db.initialise(years)
# ===================== #
# Y E A R L O O P #
# ===================== #
project_day = 0
for i, yr in enumerate(years):
self.day_output = [] # empty daily storage list for outpu
daylen = calculate_daylength(days_in_year[i], self.params.latitude)
if self.control.deciduous_model:
self.P.calculate_phenology_flows(daylen, self.met_data,
days_in_year[i], project_day)
# Change window size to length of growing season
self.pg.sma.window_size = self.P.growing_seas_len
self.zero_stuff()
# =================== #
# D A Y L O O P #
# =================== #
for doy in xrange(days_in_year[i]):
# standard litter calculation
# litterfall rate: C and N fluxe
(fdecay, rdecay) = self.lf.calculate_litter(doy)
# Fire Disturbance?
if (self.control.disturbance != 0
and self.params.disturbance_doy == doy):
self.db.check_for_fire(yr, self.pg)
# Hurricane?
elif (self.control.hurricane == 1
and self.params.hurricane_yr == yr
and self.params.hurricane_doy == doy):
self.db.hurricane()
# photosynthesis & growth
fsoilT = self.cs.soil_temp_factor(project_day)
self.pg.calc_day_growth(project_day, fdecay,
rdecay, daylen[doy], doy,
float(days_in_year[i]), i, fsoilT)
# soil C & N calculation
self.cs.calculate_csoil_flows(project_day, doy)
self.ns.calculate_nsoil_flows(project_day, doy)
if self.control.ncycle == False:
# Turn off all N calculations
self.reset_all_n_pools_and_fluxes()
# calculate C:N ratios and increment annual flux sum
self.day_end_calculations(days_in_year[i])
# checking if we died during the timestep
# - added for desert simulation
if (not self.control.deciduous_model
and self.control.disturbance == 0):
self.are_we_dead()
#print self.state.plantc, self.state.soilc
#print yr, doy, self.state.lai, self.fluxes.gpp*100
#print self.fluxes.gpp*100, self.state.prev_sma
# ======================= #
# E N D O F D A Y #
# ======================= #
if not self.spin_up:
self.save_daily_outputs(yr, doy + 1)
# check the daily water balance
#self.cb.check_water_balance(project_day)
project_day += 1
# ========================= #
# E N D O F Y E A R #
# ========================= #
# Allocate stored C&N for the following year
if self.control.deciduous_model:
# Using average alloc fracs across growing season instead
#self.pg.calc_carbon_allocation_fracs(0.0) #comment this!!
self.pg.calculate_average_alloc_fractions(
self.P.growing_seas_len)
self.pg.allocate_stored_c_and_n(init=False)
# reset the stress buffer at the end of the growing season
self.pg.sma.reset_stream()
#print self.fluxes.alleaf, self.fluxes.alroot, \
# (self.fluxes.albranch+self.fluxes.alstem)
#print
# GDAY died in the previous year, re-establish gday for the next yr
# - added for desert simulation
if (self.dead and not self.control.deciduous_model
and self.control.disturbance == 0):
self.re_establish_gday()
if self.control.print_options == "DAILY" and not self.spin_up:
self.print_output_file()
# close output file
if self.control.print_options == "END" and not self.spin_up:
self.print_output_file()
# only close printing file if not in spin up mode as we have ye
# written the daily output...
if self.spin_up:
return (yr, doy + 1)
else:
# Need to pass the project day to calculate NROWS for .hdr file
self.pr.clean_up(project_day)
def run_sim(self):
""" Run model simulation! """
# local variables
years = self.years
days_in_year = self.days_in_year
# =============== #
# YEAR LOOP #
# =============== #
project_day = 0
for i, yr in enumerate(years):
self.day_output = [] # empty daily storage list for outputs
daylen = calculate_daylength(days_in_year[i], self.params.latitude)
if self.control.deciduous_model:
self.P.calculate_phenology_flows(daylen, self.met_data, days_in_year[i], project_day)
self.zero_stuff()
# =============== #
# DAY LOOP #
# =============== #
for doy in xrange(days_in_year[i]):
# for pft in xrange(4):
# litterfall rate: C and N fluxes
(fdecay, rdecay) = self.lf.calculate_litter(doy)
# co2 assimilation, N uptake and loss
self.pg.calc_day_growth(project_day, fdecay, rdecay, daylen[doy], doy, float(days_in_year[i]), i)
# soil C & N model fluxes
self.cs.calculate_csoil_flows(project_day)
self.ns.calculate_nsoil_flows(project_day)
# calculate C:N ratios and increment annual flux sums
self.day_end_calculations(project_day, days_in_year[i])
print self.state.lai, self.fluxes.gpp * 100, self.state.pawater_root, self.state.shootnc
# =============== #
# END OF DAY #
# =============== #
if not self.spin_up:
self.save_daily_outputs(yr, doy + 1)
# check the daily water balance
# self.cb.check_water_balance(project_day)
project_day += 1
# =============== #
# END OF YEAR #
# =============== #
if self.control.deciduous_model:
print "**", self.state.cstore
self.pg.allocate_stored_c_and_n(init=False)
if self.control.print_options == "DAILY" and not self.spin_up:
self.print_output_file()
# close output files
if self.control.print_options == "END" and not self.spin_up:
self.print_output_file()
# only close printing file if not in spin up mode as we have yet
# written the daily output...
if self.spin_up:
return (yr, doy + 1)
else:
self.pr.clean_up()
