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")
