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
# timing...
import sys
import time
start_time = time.time()
from file_parser import initialise_model_data
import datetime
from utilities import float_eq, float_lt, float_gt, calculate_daylength, uniq
met_header = 4
# fname = "/Users/mdekauwe/research/NCEAS_face/GDAY_ornl_simulation/params/NCEAS_or_youngforest.cfg"
fname = "/Users/mdekauwe/research/FACE/GDAY_simulations/KSCO/experiment/params/NCEAS_KSCO_model_indust.cfg"
(control, params, state, files, fluxes, met_data, print_opts) = initialise_model_data(fname, met_header, DUMP=False)
control.ps_pathway = "C4"
if control.ps_pathway == "C3":
M = MateC3(control, params, state, fluxes, met_data)
else:
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"])
def __init__(self, fname=None, DUMP=False, spin_up=False, met_header=4):
""" Set up model
* Read meterological forcing file
* Read user config file and adjust the model parameters, control or
initial state attributes that are used within the code.
* Setup all class instances...perhaps this isn't the tidyest place for
this?
* Initialise things, zero stores etc.
Parameters:
----------
fname : string
filename of model parameters, including path
chk_cmd_line : logical
parse the cmd line?
DUMP : logical
dump a the default parameters to a file
met_header : in
row number of met file header with variable name
Returns:
-------
Nothing
Controlling class of the model, runs things.
"""
self.day_output = [] # store daily output
# initialise model structures and read met data
(self.control, self.params,
self.state, self.files,
self.fluxes, self.met_data,
self.print_opts) = initialise_model_data(fname, met_header, DUMP=DUMP)
# params are defined in per year, needs to be per day
# Important this is done here as rate constants elsewhere in the code
# are assumed to be in units of days not years!
self.correct_rate_constants(output=False)
# class instance
self.cs = CarbonSoilFlows(self.control, self.params, self.state,
self.fluxes, self.met_data)
self.ns = NitrogenSoilFlows(self.control, self.params, self.state,
self.fluxes, self.met_data)
self.lf = Litter(self.control, self.params, self.state, self.fluxes)
self.pg = PlantGrowth(self.control, self.params, self.state,
self.fluxes, self.met_data)
self.cb = CheckBalance(self.control, self.params, self.state,
self.fluxes, self.met_data)
self.db = Disturbance(self.control, self.params, self.state,
self.fluxes, self.met_data)
if self.control.deciduous_model:
if self.state.max_lai is None:
self.state.max_lai = 0.01 # initialise to something really low
self.state.max_shoot = 0.01 # initialise to something really low
# Are we reading in last years average growing season?
if (float_eq(self.state.avg_alleaf, 0.0) and
float_eq(self.state.avg_alstem, 0.0) and
float_eq(self.state.avg_albranch, 0.0) and
float_eq(self.state.avg_alleaf, 0.0) and
float_eq(self.state.avg_alroot, 0.0) and
float_eq(self.state.avg_alcroot, 0.0)):
self.pg.calc_carbon_allocation_fracs(0.0) #comment this!!
else:
self.fluxes.alleaf = self.state.avg_alleaf
self.fluxes.alstem = self.state.avg_alstem
self.fluxes.albranch = self.state.avg_albranch
self.fluxes.alroot = self.state.avg_alroot
self.fluxes.alcroot = self.state.avg_alcroot
self.pg.allocate_stored_c_and_n(init=True)
#self.pg.enforce_sensible_nstore()
self.P = Phenology(self.fluxes, self.state, self.control,
self.params.previous_ncd,
store_transfer_len=self.params.store_transfer_len)
self.pr = PrintOutput(self.params, self.state, self.fluxes,
self.control, self.files, self.print_opts)
# build list of variables to prin
(self.print_state, self.print_fluxes) = self.pr.get_vars_to_print()
# print model defaul
if DUMP == True:
self.pr.save_default_parameters()
sys.exit(0)
self.dead = False # johnny 5 is alive
# calculate initial stuff, e.g. C:N ratios and zero annual flux sum
self.day_end_calculations(INIT=True)
self.state.pawater_root = self.params.wcapac_root
self.state.pawater_topsoil = self.params.wcapac_topsoil
self.spin_up = spin_up
self.state.lai = max(0.01, (self.params.sla * const.M2_AS_HA /
const.KG_AS_TONNES / self.params.cfracts *
self.state.shoot))
# figure out the number of years for simulation and the number of
# days in each year
self.years = uniq(self.met_data["year"])
self.days_in_year = [self.met_data["year"].count(yr)
for yr in self.years]
if self.control.water_stress == False:
sys.stderr.write("**** You have turned off the drought stress")
sys.stderr.write(", I assume you're debugging??!\n")
# timing...
import sys
import time
start_time = time.time()
from file_parser import initialise_model_data
import datetime
from utilities import float_eq, float_lt, float_gt, calculate_daylength, uniq
met_header=4
#fname = "/Users/mdekauwe/research/NCEAS_face/GDAY_ornl_simulation/params/NCEAS_or_youngforest.cfg"
fname = "/Users/mdekauwe/research/FACE/GDAY_simulations/KSCO/experiment/params/NCEAS_KSCO_model_indust.cfg"
(control, params, state, files,
fluxes, met_data,
print_opts) = initialise_model_data(fname, met_header, DUMP=False)
control.ps_pathway = "C4"
if control.ps_pathway == "C3":
M = MateC3(control, params, state, fluxes, met_data)
else:
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)
# Specific LAI (m2 onesided/kg DW)
state.sla = params.slainit
if __name__ == "__main__":
from file_parser import initialise_model_data
from utilities import float_lt, day_length
import datetime
fname = "/Users/mdekauwe/src/python/pygday/params/duke_testing.cfg"
(control, params, state, files,
fluxes, met_data,
print_opts) = initialise_model_data(fname, DUMP=False)
B = Bewdy(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)
def __init__(self, fname=None, chk_cmd_line=True, DUMP=False):
""" Set up model
Read meterological forcing file and user config file and adjust the
model parameters, control or initial state attributes that are used
within the code.
Parameters:
----------
fname : string
filename of model parameters, including path
chk_cmd_line : logical
parse the cmd line?
DUMP : logical
dump a the default parameters to a file
Returns:
-------
Nothing
Controlling class of the model, runs things.
"""
# sweep the cmd line
if chk_cmd_line == True:
options, args = cmdline_parser()
DUMP=options.DUMP
(self.control, self.params,
self.state, self.files,
self.fluxes, self.met_data,
print_opts) = initialise_model_data(fname, DUMP=DUMP)
# printing stuff
self.pr = PrintOutput(self.params, self.state, self.fluxes,
self.control, self.files, print_opts)
# print model defaults
if DUMP == True:
self.pr.save_default_parameters()
sys.exit(0)
if self.control.print_options > 1:
raise ValueError("Unknown output print option: %s (try 0 or 1)" %
self.control.print_options)
# set initial lai -> m2/m2
self.state.lai = (self.params.slainit * const.M2_AS_HA /
const.KG_AS_TONNES / self.params.cfracts *
self.state.shoot)
# Specific leaf area (m2 onesided/kg DW)
self.state.sla = self.params.slainit
# start date of simulation
self.date = self.simulation_start_date()
self.time_constants = ['rateuptake', 'rateloss', 'retransmob',
'fdecay', 'fdecaydry', 'rdecay', 'rdecaydry',
'bdecay', 'wdecay', 'kdec1', 'kdec2', 'kdec3',
'kdec4', 'kdec5', 'kdec6', 'kdec7', 'nuptakez']
self.correct_rate_constants(output=False)
def __init__(self, fname=None, DUMP=False, spin_up=False):
""" Set up model
Read meterological forcing file and user config file and adjust the
model parameters, control or initial state attributes that are used
within the code.
Parameters:
----------
fname : string
filename of model parameters, including path
chk_cmd_line : logical
parse the cmd line?
DUMP : logical
dump a the default parameters to a file
Returns:
-------
Nothing
Controlling class of the model, runs things.
"""
self.day_output = [] # store daily outputs
(self.control, self.params,
self.state, self.files,
self.fluxes, self.met_data,
self.print_opts) = initialise_model_data(fname, DUMP=DUMP)
if self.control.water_stress == False:
sys.stderr.write("**** You have turned off the drought stress")
sys.stderr.write(", I assume you're debugging??!\n")
# printing stuff
self.pr = PrintOutput(self.params, self.state, self.fluxes,
self.control, self.files, self.print_opts)
# build list of variables to print
(self.print_state, self.print_fluxes) = self.pr.get_vars_to_print()
# print model defaults
if DUMP == True:
self.pr.save_default_parameters()
sys.exit(0)
self.correct_rate_constants(output=False)
# class instances
self.cs = CarbonSoilFlows(self.control, self.params, self.state,
self.fluxes, self.met_data)
self.ns = NitrogenSoilFlows(self.control, self.params, self.state,
self.fluxes, self.met_data)
self.lf = Litter(self.control, self.params, self.state, self.fluxes)
self.pg = PlantGrowth(self.control, self.params, self.state,
self.fluxes, self.met_data)
if self.control.deciduous_model:
self.pg.calc_carbon_allocation_fracs(0.0)
self.pg.allocate_stored_c_and_n(init=True)
self.P = Phenology(self.fluxes, self.state, self.control,
self.params.previous_ncd,
store_transfer_len=self.params.store_transfer_len)
# calculate initial C:N ratios and zero annual flux sums
self.day_end_calculations(0, INIT=True)
self.state.pawater_root = self.params.wcapac_root
self.state.pawater_tsoil = self.params.wcapac_topsoil
self.spin_up = spin_up
self.state.sla = self.params.slainit # Specific leaf area (m2/kg DW)
self.state.lai = (self.params.slainit * const.M2_AS_HA /
const.KG_AS_TONNES / self.params.cfracts *
self.state.shoot)
def __init__(self, fname=None, DUMP=False, spin_up=False, met_header=4):
""" Set up model
* Read meterological forcing file
* Read user config file and adjust the model parameters, control or
initial state attributes that are used within the code.
* Setup all class instances...perhaps this isn't the tidyest place for
this?
* Initialise things, zero stores etc.
Parameters:
----------
fname : string
filename of model parameters, including path
chk_cmd_line : logical
parse the cmd line?
DUMP : logical
dump a the default parameters to a file
met_header : int
row number of met file header with variable names
Returns:
-------
Nothing
Controlling class of the model, runs things.
"""
self.day_output = [] # store daily outputs
# initialise model structures and read met data
(self.control, self.params, self.state, self.files, self.fluxes,
self.met_data, self.print_opts) = initialise_model_data(fname,
met_header,
DUMP=DUMP)
# params are defined in per year, needs to be per day
# Important this is done here as rate constants elsewhere in the code
# are assumed to be in units of days not years!
self.correct_rate_constants(output=False)
# class instances
self.cs = CarbonSoilFlows(self.control, self.params, self.state,
self.fluxes, self.met_data)
self.ns = NitrogenSoilFlows(self.control, self.params, self.state,
self.fluxes, self.met_data)
self.lf = Litter(self.control, self.params, self.state, self.fluxes)
self.pg = PlantGrowth(self.control, self.params, self.state,
self.fluxes, self.met_data)
self.cb = CheckBalance(self.control, self.params, self.state,
self.fluxes, self.met_data)
if self.control.deciduous_model:
self.pg.calc_carbon_allocation_fracs(0.0, 0, 0) #comment this!!
self.pg.allocate_stored_c_and_n(init=True)
self.P = Phenology(
self.fluxes,
self.state,
self.control,
self.params.previous_ncd,
store_transfer_len=self.params.store_transfer_len)
self.pr = PrintOutput(self.params, self.state, self.fluxes,
self.control, self.files, self.print_opts)
# build list of variables to print
(self.print_state, self.print_fluxes) = self.pr.get_vars_to_print()
# print model defaults
if DUMP == True:
self.pr.save_default_parameters()
sys.exit(0)
# calculate initial stuff, e.g. C:N ratios and zero annual flux sums
self.day_end_calculations(0, INIT=True)
self.state.pawater_root = self.params.wcapac_root
self.state.pawater_topsoil = self.params.wcapac_topsoil
self.spin_up = spin_up
self.state.sla = self.params.slainit # Specific leaf area (m2/kg DW)
self.state.lai = (self.params.slainit * const.M2_AS_HA /
const.KG_AS_TONNES / self.params.cfracts *
self.state.shoot)
# figure out the number of years for simulation and the number of
# days in each year
self.years = uniq(self.met_data["year"])
self.days_in_year = [self.met_data["year"].count(yr) \
for yr in self.years]
if self.control.water_stress == False:
sys.stderr.write("**** You have turned off the drought stress")
sys.stderr.write(", I assume you're debugging??!\n")
arg1 = self.params.alpha_j / 4.0
arg2 = ((ci - gamma_star) / (ci + 2. * gamma_star))
return arg1 * arg2 * const.MOL_C_TO_GRAMS_C
if __name__ == "__main__":
from file_parser import initialise_model_data
from utilities import float_lt, day_length
import datetime
fname = "/Users/mdekauwe/src/python/pygday/params/duke_testing.cfg"
(control, params, state, files, fluxes, met_data,
print_opts) = initialise_model_data(fname, DUMP=False)
B = Bewdy(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")
#laifname = "/Users/mdekauwe/research/NCEAS_face/GDAY_duke_simulation/experiments/lai"
import numpy as np
# timing...
import sys
import time
start_time = time.time()
from file_parser import initialise_model_data
import datetime
from utilities import float_eq, float_lt, float_gt, calculate_daylength, uniq
met_header = 4
#fname = "/Users/mdekauwe/research/NCEAS_face/GDAY_ornl_simulation/params/NCEAS_or_youngforest.cfg"
fname = "/Users/mdekauwe/research/FACE/GDAY_simulations/KSCO/experiment/params/NCEAS_KSCO_model_indust.cfg"
(control, params, state, files, fluxes, met_data,
print_opts) = initialise_model_data(fname, met_header, DUMP=False)
control.ps_pathway = "C4"
if control.ps_pathway == "C3":
M = MateC3(control, params, state, fluxes, met_data)
else:
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)
# Specific LAI (m2 onesided/kg DW)
state.sla = params.slainit
project_day = 0
