# -*- coding: utf-8 -*-
# Copyright (c) 2004-2014 Alterra, Wageningen-UR
# Allard de Wit (allard.dewit@wur.nl), April 2014
from collections import namedtuple
from math import exp
from ..traitlets import Float, Int, Instance, AfgenTrait
from ..decorators import prepare_rates, prepare_states
from ..base_classes import ParamTemplate, StatesTemplate, SimulationObject,\
VariableKiosk
from .. import exceptions as exc
from warnings import warn
# Template for namedtuple containing partitioning factors
class PartioningFactors(namedtuple("partitioning_factors", "FR FL FS FO")):
pass
[docs]class DVS_Partitioning(SimulationObject):
"""Class for assimilate partioning based on development stage (`DVS`).
`DVS_partioning` calculates the partitioning of the assimilates to roots,
stems, leaves and storage organs using fixed partitioning tables as a
function of crop development stage. The available assimilates are first
split into below-ground and abovegrond using the values in FRTB. In a
second stage they are split into leaves (`FLTB`), stems (`FSTB`) and storage
organs (`FOTB`).
Since the partitioning fractions are derived from the state variable `DVS`
they are regarded state variables as well.
**Simulation parameters** (To be provided in cropdata dictionary):
======= ============================================= ======= ============
Name Description Type Unit
======= ============================================= ======= ============
FRTB Partitioning to roots as a function of TCr -
development stage.
FSTB Partitioning to stems as a function of TCr -
development stage.
FLTB Partitioning to leaves as a function of TCr -
development stage.
FOTB Partitioning to storage organs as a function TCr -
of development stage.
======= ============================================= ======= ============
**State variables**
======= ================================================= ==== ============
Name Description Pbl Unit
======= ================================================= ==== ============
FR Fraction partitioned to roots. Y -
FS Fraction partitioned to stems. Y -
FL Fraction partitioned to leaves. Y -
FO Fraction partitioned to storage orgains Y -
======= ================================================= ==== ============
**Rate variables**
None
**Signals send or handled**
None
**External dependencies:**
======= =================================== ================= ============
Name Description Provided by Unit
======= =================================== ================= ============
DVS Crop development stage DVS_Phenology -
======= =================================== ================= ============
*Exceptions raised*
A PartitioningError is raised if the partitioning coefficients to leaves,
stems and storage organs on a given day do not add up to '1'.
"""
[docs] class Parameters(ParamTemplate):
FRTB = AfgenTrait()
FLTB = AfgenTrait()
FSTB = AfgenTrait()
FOTB = AfgenTrait()
[docs] class StateVariables(StatesTemplate):
FR = Float(-99.)
FL = Float(-99.)
FS = Float(-99.)
FO = Float(-99.)
PF = Instance(PartioningFactors)
[docs] def initialize(self, day, kiosk, parvalues):
"""
:param day: start date of the simulation
:param kiosk: variable kiosk of this PCSE instance
:param parvalues: `ParameterProvider` object providing parameters as
key/value pairs
"""
self.params = self.Parameters(parvalues)
self.kiosk = kiosk
# initial partitioning factors (pf)
DVS = self.kiosk["DVS"]
FR = self.params.FRTB(DVS)
FL = self.params.FLTB(DVS)
FS = self.params.FSTB(DVS)
FO = self.params.FOTB(DVS)
# Pack partitioning factors into tuple
PF = PartioningFactors(FR, FL, FS, FO)
# Initial states
self.states = self.StateVariables(kiosk, publish=["FR","FL","FS","FO"],
FR=FR, FL=FL, FS=FS, FO=FO, PF=PF)
self._check_partitioning()
def _check_partitioning(self):
"""Check for partitioning errors."""
FR = self.states.FR
FL = self.states.FL
FS = self.states.FS
FO = self.states.FO
checksum = FR+(FL+FS+FO)*(1.-FR) - 1.
if abs(checksum) >= 0.0001:
msg = ("Error in partitioning!\n")
msg += ("Checksum: %f, FR: %5.3f, FL: %5.3f, FS: %5.3f, FO: %5.3f\n" \
% (checksum, FR, FL, FS, FO))
self.logger.error(msg)
warn(msg)
# raise exc.PartitioningError(msg)
[docs] @prepare_states
def integrate(self, day, delt=1.0):
"""Update partitioning factors based on development stage (DVS)"""
params = self.params
DVS = self.kiosk["DVS"]
self.states.FR = params.FRTB(DVS)
self.states.FL = params.FLTB(DVS)
self.states.FS = params.FSTB(DVS)
self.states.FO = params.FOTB(DVS)
# Pack partitioning factors into tuple
self.states.PF = PartioningFactors(self.states.FR, self.states.FL,
self.states.FS, self.states.FO)
self._check_partitioning()
[docs] def calc_rates(self, day, drv):
""" Return partitioning factors based on current DVS.
"""
# rate calculation does nothing for partioning as it is a derived
# state
return self.states.PF
class DVS_Partitioning_NPK(SimulationObject):
"""Class for assimilate partitioning based on development stage (`DVS`)
with influence of NPK stress.
`DVS_Partitioning_NPK` calculates the partitioning of the assimilates to roots,
stems, leaves and storage organs using fixed partitioning tables as a
function of crop development stage. The only different with the normal
partitioning class is the effect of nitrogen stress on partitioning to
leaves (parameter NPART). The available assimilates are first
split into below-ground and aboveground using the values in FRTB. In a
second stage they are split into leaves (`FLTB`), stems (`FSTB`) and storage
organs (`FOTB`).
Since the partitioning fractions are derived from the state variable `DVS`
they are regarded state variables as well.
**Simulation parameters** (To be provided in cropdata dictionary):
======= ============================================= ======= ============
Name Description Type Unit
======= ============================================= ======= ============
FRTB Partitioning to roots as a function of TCr -
development stage.
FSTB Partitioning to stems as a function of TCr -
development stage.
FLTB Partitioning to leaves as a function of TCr -
development stage.
FOTB Partitioning to starge organs as a function TCr -
of development stage.
NPART Coefficient for the effect of N stress on SCR -
leaf biomass allocation
======= ============================================= ======= ============
**State variables**
======= ================================================= ==== ============
Name Description Pbl Unit
======= ================================================= ==== ============
FR Fraction partitioned to roots. Y -
FS Fraction partitioned to stems. Y -
FL Fraction partitioned to leaves. Y -
FO Fraction partitioned to storage orgains Y -
======= ================================================= ==== ============
**Rate variables**
None
**Signals send or handled**
None
**External dependencies:**
======= =================================== ================= ============
Name Description Provided by Unit
======= =================================== ================= ============
DVS Crop development stage DVS_Phenology -
TRA Actual transpiration Simple_Evapotranspiration mm d-1
TRAMX Maximum transpiration Simple_Evapotranspiration mm d-1
NNI Nitrogen nutrition index npk_dynamics -
======= =================================== ================= ============
*Exceptions raised*
A PartitioningError is raised if the partitioning coefficients to leaves,
stems and storage organs on a given day do not add up to '1'.
"""
class Parameters(ParamTemplate):
FRTB = AfgenTrait()
FLTB = AfgenTrait()
FSTB = AfgenTrait()
FOTB = AfgenTrait()
NPART = Float(-99.) # coefficient for the effect of N stress on leaf allocation
class StateVariables(StatesTemplate):
FR = Float(-99.)
FL = Float(-99.)
FS = Float(-99.)
FO = Float(-99.)
PF = Instance(PartioningFactors)
def initialize(self, day, kiosk, parameters):
"""
:param day: start date of the simulation
:param kiosk: variable kiosk of this PCSE instance
:param parameters: dictionary with WOFOST cropdata key/value pairs
"""
self.params = self.Parameters(parameters)
# initial partioning factors (pf)
k = self.kiosk
FR = self.params.FRTB(k.DVS)
FL = self.params.FLTB(k.DVS)
FS = self.params.FSTB(k.DVS)
FO = self.params.FOTB(k.DVS)
# Pack partitioning factors into tuple
PF = PartioningFactors(FR, FL, FS, FO)
# Initial states
self.states = self.StateVariables(kiosk, publish=["FR","FL","FS","FO"],
FR=FR, FL=FL, FS=FS, FO=FO, PF=PF)
self._check_partitioning()
def _check_partitioning(self):
"""Check for partitioning errors."""
FR = self.states.FR
FL = self.states.FL
FS = self.states.FS
FO = self.states.FO
checksum = FR+(FL+FS+FO)*(1.-FR) - 1.
if abs(checksum) >= 0.0001:
msg = ("Error in partitioning!\n")
msg += ("Checksum: %f, FR: %5.3f, FL: %5.3f, FS: %5.3f, FO: %5.3f\n" \
% (checksum, FR, FL, FS, FO))
self.logger.error(msg)
raise exc.PartitioningError(msg)
@prepare_states
def integrate(self, day, delt=1.0):
"""
Update partitioning factors based on development stage (DVS)
and the Nitrogen nutrition Index (NNI)
"""
p = self.params
s = self.states
k = self.kiosk
if k.RFTRA < k.NNI:
# Water stress is more severe than nitrogen stress and the
# partitioning follows the original LINTUL2 assumptions
# Note: we use specifically nitrogen stress not nutrient stress!!!
FRTMOD = max(1., 1./(k.RFTRA + 0.5))
s.FR = min(0.6, p.FRTB(k.DVS) * FRTMOD)
s.FL = p.FLTB(k.DVS)
s.FS = p.FSTB(k.DVS)
s.FO = p.FOTB(k.DVS)
else:
# Nitrogen stress is more severe than water stress resulting in
# less partitioning to leaves and more to stems
FLVMOD = exp(-p.NPART * (1.0 - k.NNI))
s.FL = p.FLTB(k.DVS) * FLVMOD
s.FS = p.FSTB(k.DVS) + p.FLTB(k.DVS) - s.FL
s.FR = p.FRTB(k.DVS)
s.FO = p.FOTB(k.DVS)
# Pack partitioning factors into tuple
s.PF = PartioningFactors(s.FR, s.FL, s.FS, s.FO)
self._check_partitioning()
def calc_rates(self, day, drv):
""" Return partitioning factors based on current DVS.
"""
# rate calculation does nothing for partitioning as it is a derived state
return self.states.PF