class StateVariables(StatesTemplate):
TAGP = Float(-99.)
GASST = Float(-99.)
MREST = Float(-99.)
CTRAT = Float(-99.)
CEVST = Float(-99.)
HI = Float(-99.)
DOF = Instance(datetime.date)
FINISH_TYPE = Unicode(allow_none=True)
class StateVariables(StatesTemplate):
PTa = Float(-99.)
#Soil water balance
TPE = Float(-99.)
TPT = Float(-99.)
TPREC = Float(-99.)
TINTERC = Float(-99.)
TRUNOFF = Float(-99.)
PERC = Float(-99.)
TE = Float(-99.)
Ta = Float(-99.)
WC = Instance(np.ndarray)
WCv = Instance(np.ndarray)
#To chech WB closed
TT = Float(-99.)
WB_close = Float(-99.)
Diff_WC = Float(-99.)
TWC = Float(-99.)
W_Stress = Float(-99.)
class StateVariables(StatesTemplate):
DVS = Float(-99.) # Development stage
TSUM = Float(-99.) # Temperature sum state
TSUME = Float(-99.) # Temperature sum for emergence state
# States which register phenological events
DOS = Instance(date) # Day of sowing
DOE = Instance(date) # Day of emergence
DOR1 = Instance(date) # Day of start of flowering
DOR3 = Instance(date) # Day of pod development
DOR5 = Instance(date) # Day of seed filling
DOR8 = Instance(date) # Day of full ripeness
DOH = Instance(date) # Day of harvest
STAGE = Enum(
[None, "emerging", "vegetative", "reproductive", "mature"])
class TestSimulationObject(SimulationObject):
"""This wraps the SimulationObject for testing to ensure that the computations are not
carried out before crop emergence (e.g. DVS >= 0). The latter does not apply for the
phenology simobject itself which simulates emergence. The phenology simobject is recognized
because the variable DVS is not an external variable.
"""
test_class = None
subsimobject = Instance(SimulationObject)
def initialize(self, day, kiosk, parvalues):
self.subsimobject = self.test_class(day, kiosk, parvalues)
def calc_rates(self, day, drv):
# some simobject do not provide a `calc_rates()` function but are directly callable
# here we check for those cases.
func = self.subsimobject if callable(
self.subsimobject) else self.subsimobject.calc_rates
if not self.kiosk.is_external_state("DVS"):
func(day, drv)
else:
if self.kiosk.DVS >= 0:
func(day, drv)
else:
self.subsimobject.zerofy()
def integrate(self, day, delt=1.0):
# If the simobject is callable, we do not need integration so we use the `nothing()` function.
func = nothing if callable(
self.subsimobject) else self.subsimobject.integrate
if not self.kiosk.is_external_state("DVS"):
func(day, delt)
else:
if self.kiosk.DVS >= 0:
func(day, delt)
else:
self.subsimobject.touch()
class Wofost(SimulationObject):
"""Top level object organizing the different components of the WOFOST crop
simulation.
The CropSimulation object organizes the different processes of the crop
simulation. Moreover, it contains the parameters, rate and state variables
which are relevant at the level of the entire crop. The processes that are
implemented as embedded simulation objects consist of:
1. Phenology (self.pheno)
2. Partitioning (self.part)
3. Assimilation (self.assim)
4. Maintenance respiration (self.mres)
5. Evapotranspiration (self.evtra)
6. Leaf dynamics (self.lv_dynamics)
7. Stem dynamics (self.st_dynamics)
8. Root dynamics (self.ro_dynamics)
9. Storage organ dynamics (self.so_dynamics)
**Simulation parameters:**
======== =============================================== ======= ==========
Name Description Type Unit
======== =============================================== ======= ==========
CVL Conversion factor for assimilates to leaves SCr -
CVO Conversion factor for assimilates to storage SCr -
organs.
CVR Conversion factor for assimilates to roots SCr -
CVS Conversion factor for assimilates to stems SCr -
======== =============================================== ======= ==========
**State variables:**
=========== ================================================= ==== ===============
Name Description Pbl Unit
=========== ================================================= ==== ===============
TAGP Total above-ground Production N |kg ha-1|
GASST Total gross assimilation N |kg CH2O ha-1|
MREST Total gross maintenance respiration N |kg CH2O ha-1|
CTRAT Total crop transpiration accumulated over the
crop cycle N cm
CEVST Total soil evaporation accumulated over the
crop cycle N cm
HI Harvest Index (only calculated during N -
`finalize()`)
DOF Date representing the day of finish of the crop N -
simulation.
FINISH_TYPE String representing the reason for finishing the N -
simulation: maturity, harvest, leave death, etc.
=========== ================================================= ==== ===============
**Rate variables:**
======= ================================================ ==== =============
Name Description Pbl Unit
======= ================================================ ==== =============
GASS Assimilation rate corrected for water stress N |kg CH2O ha-1 d-1|
MRES Actual maintenance respiration rate, taking into
account that MRES <= GASS. N |kg CH2O ha-1 d-1|
ASRC Net available assimilates (GASS - MRES) N |kg CH2O ha-1 d-1|
DMI Total dry matter increase, calculated as ASRC
times a weighted conversion efficiency. Y |kg ha-1 d-1|
ADMI Aboveground dry matter increase Y |kg ha-1 d-1|
======= ================================================ ==== =============
"""
# sub-model components for crop simulation
pheno = Instance(SimulationObject)
part = Instance(SimulationObject)
assim = Instance(SimulationObject)
mres = Instance(SimulationObject)
evtra = Instance(SimulationObject)
lv_dynamics = Instance(SimulationObject)
st_dynamics = Instance(SimulationObject)
ro_dynamics = Instance(SimulationObject)
so_dynamics = Instance(SimulationObject)
# Parameters, rates and states which are relevant at the main crop
# simulation level
class Parameters(ParamTemplate):
CVL = Float(-99.)
CVO = Float(-99.)
CVR = Float(-99.)
CVS = Float(-99.)
class StateVariables(StatesTemplate):
TAGP = Float(-99.)
GASST = Float(-99.)
MREST = Float(-99.)
CTRAT = Float(-99.)
CEVST = Float(-99.)
HI = Float(-99.)
DOF = Instance(datetime.date)
FINISH_TYPE = Unicode(allow_none=True)
class RateVariables(RatesTemplate):
GASS = Float(-99.)
MRES = Float(-99.)
ASRC = Float(-99.)
DMI = Float(-99.)
ADMI = Float(-99.)
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.rates = self.RateVariables(kiosk, publish=["DMI", "ADMI"])
self.kiosk = kiosk
# Initialize components of the crop
self.pheno = Phenology(day, kiosk, parvalues)
self.part = Partitioning(day, kiosk, parvalues)
self.assim = Assimilation(day, kiosk, parvalues)
self.mres = MaintenanceRespiration(day, kiosk, parvalues)
self.evtra = Evapotranspiration(day, kiosk, parvalues)
self.ro_dynamics = Root_Dynamics(day, kiosk, parvalues)
self.st_dynamics = Stem_Dynamics(day, kiosk, parvalues)
self.so_dynamics = Storage_Organ_Dynamics(day, kiosk, parvalues)
self.lv_dynamics = Leaf_Dynamics(day, kiosk, parvalues)
# Initial total (living+dead) above-ground biomass of the crop
TAGP = self.kiosk.TWLV + self.kiosk.TWST + self.kiosk.TWSO
self.states = self.StateVariables(
kiosk,
publish=["TAGP", "GASST", "MREST", "HI"],
TAGP=TAGP,
GASST=0.0,
MREST=0.0,
CTRAT=0.0,
CEVST=0.0,
HI=0.0,
DOF=None,
FINISH_TYPE=None)
# Check partitioning of TDWI over plant organs
checksum = parvalues["TDWI"] - self.states.TAGP - self.kiosk["TWRT"]
if abs(checksum) > 0.0001:
msg = "Error in partitioning of initial biomass (TDWI)!"
raise exc.PartitioningError(msg)
# assign handler for CROP_FINISH signal
self._connect_signal(self._on_CROP_FINISH, signal=signals.crop_finish)
@staticmethod
def _check_carbon_balance(day, DMI, GASS, MRES, CVF, pf):
(FR, FL, FS, FO) = pf
checksum = (GASS - MRES -
(FR + (FL + FS + FO) *
(1. - FR)) * DMI / CVF) * 1. / (max(0.0001, GASS))
if abs(checksum) >= 0.0001:
msg = "Carbon flows not balanced on day %s\n" % day
msg += "Checksum: %f, GASS: %f, MRES: %f\n" % (checksum, GASS,
MRES)
msg += "FR,L,S,O: %5.3f,%5.3f,%5.3f,%5.3f, DMI: %f, CVF: %f\n" % \
(FR, FL, FS, FO, DMI, CVF)
raise exc.CarbonBalanceError(msg)
@prepare_rates
def calc_rates(self, day, drv):
p = self.params
r = self.rates
k = self.kiosk
# Phenology
self.pheno.calc_rates(day, drv)
crop_stage = self.pheno.get_variable("STAGE")
# if before emergence there is no need to continue
# because only the phenology is running.
if crop_stage == "emerging":
return
# Potential assimilation
PGASS = self.assim(day, drv)
# (evapo)transpiration rates
self.evtra(day, drv)
# water stress reduction
r.GASS = PGASS * k.RFTRA
# Respiration
PMRES = self.mres(day, drv)
r.MRES = min(r.GASS, PMRES)
# Net available assimilates
r.ASRC = r.GASS - r.MRES
# DM partitioning factors (pf), conversion factor (CVF),
# dry matter increase (DMI) and check on carbon balance
pf = self.part.calc_rates(day, drv)
CVF = 1. / ((pf.FL / p.CVL + pf.FS / p.CVS + pf.FO / p.CVO) *
(1. - pf.FR) + pf.FR / p.CVR)
r.DMI = CVF * r.ASRC
self._check_carbon_balance(day, r.DMI, r.GASS, r.MRES, CVF, pf)
# distribution over plant organ
# Below-ground dry matter increase and root dynamics
self.ro_dynamics.calc_rates(day, drv)
# Aboveground dry matter increase and distribution over stems,
# leaves, organs
r.ADMI = (1. - pf.FR) * r.DMI
self.st_dynamics.calc_rates(day, drv)
self.so_dynamics.calc_rates(day, drv)
self.lv_dynamics.calc_rates(day, drv)
@prepare_states
def integrate(self, day, delt=1.0):
rates = self.rates
states = self.states
# crop stage before integration
crop_stage = self.pheno.get_variable("STAGE")
# Phenology
self.pheno.integrate(day, delt)
# if before emergence there is no need to continue
# because only the phenology is running.
# Just run a touch() to to ensure that all state variables are available
# in the kiosk
if crop_stage == "emerging":
self.touch()
return
# Partitioning
self.part.integrate(day, delt)
# Integrate states on leaves, storage organs, stems and roots
self.ro_dynamics.integrate(day, delt)
self.so_dynamics.integrate(day, delt)
self.st_dynamics.integrate(day, delt)
self.lv_dynamics.integrate(day, delt)
# Integrate total (living+dead) above-ground biomass of the crop
states.TAGP = self.kiosk.TWLV + self.kiosk.TWST + self.kiosk.TWSO
# total gross assimilation and maintenance respiration
states.GASST += rates.GASS
states.MREST += rates.MRES
# total crop transpiration and soil evaporation
states.CTRAT += self.kiosk.TRA
states.CEVST += self.kiosk.EVS
@prepare_states
def finalize(self, day):
# Calculate Harvest Index
if self.states.TAGP > 0:
self.states.HI = self.kiosk.TWSO / self.states.TAGP
else:
msg = "Cannot calculate Harvest Index because TAGP=0"
self.logger.warning(msg)
self.states.HI = -1.
SimulationObject.finalize(self, day)
def _on_CROP_FINISH(self, day, finish_type=None):
"""Handler for setting day of finish (DOF) and reason for
crop finishing (FINISH).
"""
self._for_finalize["DOF"] = day
self._for_finalize["FINISH_TYPE"] = finish_type
class Water_balance(SimulationObject):
'''Parameters**
============ ================================================= ==== ========
Name Description Unit
============ ================================================= ==== ========
FCP Field capacity mH2O m Soil
PWPP Permanent wilting point mH2O m Soi
ADWCP Air dry water content mH2O m Soi
TCK Thickness of soil layer m
RUNOFF1 Parameter 1 for runoff function
RUNOFF2 Parameter 2 for runoff function
RMIN Root resistance J kg-1
PSIPWP Permanent wilting water potential J kg-1
PSIFC Field capacity water potential J kg-1
S Surface storage condition m
RDMAX Maximun root depth m
m
============ ================================================= ==== ========
Rates**
============ ================================================= ==== ========
Name Description Unit
============ ================================================= ==== ========
FC Parameter FCP in m of H2O per layer m
PWP Parameter PWPP in m of H2O per layer m
INTERC Precipitation intercepted by the canopy m
RUNOFF Rate of runoff m
INFIL Water available for infiltration m
RW Rate of recharging water in each layer m
NWC Rate of water in the 1st layer m
EVS Rate of soil evaporation m
RDr Rate of root growth m
B Value for power equation of soil potential
A Value for power equation of soil potential
SPSI Soil potential per layer J kg-1 m-1
FROOT Root fraction per layer
AVESPSI Soil potential weighten by rooting fraction J kg-1 m-1
RBAR Root resistance J kg-1 m-1
PSIX Xilem Potential J kg-1 m-1
LOSS Rate of water loss per layer mH2O m
TL Transpiration per layer m
AT Actual Evapotranspiration per layer m
T Total Evapotranspiration m
============ ================================================= ==== ========
State variables**
Name Description Unit
============ ================================================= ==== ========
TINTERC Total interception by the canopy m
GPREC Ground precipitation m
TRUNOFF Total runoff m
PERC Total deep percolation m
TWC Water content m-3 m-3
TEVS Total soil evaporation m
TRD Root depth m
TFR Root fraction in each layer
============ ================================================= ==== ========
**External dependencies:**
======= =================================== ================= ============
Name Description Provided by 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 -
DVS Development stage
======= =================================== ================= ============
'''
pheno = Instance(SimulationObject)
class Parameters(ParamTemplate):
#Soil water balance
FCP = Float(-99.)
PWPP = Float(-99.)
ADWCP = Float(-99.)
TCK = Float(-99.)
RUNOFF1 = Float(-99.)
RUNOFF2 = Float(-99.)
RMIN = Float(-99.)
PSIPWP = Float(-99.)
PSIFC = Float(-99.)
S = Float(-99.)
RDMAX = Float(-99.)
class RateVariables(RatesTemplate):
PE = Float(-99.)
PT = Float(-99.)
EPT = Float(-99.)
PREC = Float(-99.)
nl = Int
FC = Float(-99.)
PWP = Float(-99.)
ADWC = Float(-99.)
B = Float(-99.)
A = Float(-99.)
INTERC = Float(-99.)
GPREC = Float(-99.)
RUNOFF = Float(-99.)
INFIL = Float(-99.)
RW = Float(-99.)
values_RW = []
RWATER = Instance(np.ndarray)
NWC = Float(-99.)
EVS = Float(-99.)
SPSI = Float(-99.)
values_SPSI = []
SP = Instance(np.ndarray)
#root
FcR = Instance(np.ndarray)
values_FR = []
FROOT = Float(-99.)
AVEPSI = Float(-99.)
RBAR = Float(-99.)
PSIX = Float(-99.)
z = Float(-99.)
LOSS = Instance(np.ndarray)
W = Instance(np.ndarray)
arr_bool = Instance(np.ndarray)
arr_TRUE = Instance(np.ndarray)
TL = Instance(np.ndarray)
net_RW = Instance(np.ndarray)
T = Float(-99.)
arr_subt = Instance(np.ndarray)
arr_mult = Instance(np.ndarray)
AT = Instance(np.ndarray)
check = Float(-99.)
class StateVariables(StatesTemplate):
PTa = Float(-99.)
#Soil water balance
TPE = Float(-99.)
TPT = Float(-99.)
TPREC = Float(-99.)
TINTERC = Float(-99.)
TRUNOFF = Float(-99.)
PERC = Float(-99.)
TE = Float(-99.)
Ta = Float(-99.)
WC = Instance(np.ndarray)
WCv = Instance(np.ndarray)
#To chech WB closed
TT = Float(-99.)
WB_close = Float(-99.)
Diff_WC = Float(-99.)
TWC = Float(-99.)
W_Stress = Float(-99.)
def initialize(self, day, kiosk, parametervalues):
self.params = self.Parameters(parametervalues)
self.rates = self.RateVariables(kiosk, publish=None)
self.kiosk = kiosk
layers = math.floor(self.params.RDMAX / self.params.TCK)
self.states = self.StateVariables(
kiosk,
publish=["Ta", "W_Stress", "PTa"],
PTa=0,
TPE=0.0,
TPT=0.0,
WC=np.full(layers, self.params.FCP * self.params.TCK),
WCv=np.full(layers, self.params.FCP * self.params.TCK),
TT=0.0,
Diff_WC=0.,
W_Stress=0,
TINTERC=0,
TRUNOFF=0,
PERC=0,
TE=0,
Ta=0,
WB_close=0,
TPREC=0.0,
TWC=0.)
@prepare_rates
def calc_rates(self, day, drv):
p = self.params
r = self.rates
s = self.states
k = self.kiosk
if "FI" not in self.kiosk:
k.FI = 0.0
else:
k.FI = self.kiosk["FI"]
if "TRD" not in self.kiosk:
k.TRD = 0.0
else:
k.TRD = self.kiosk["TRD"]
r.PE = convert_cm_to_m(drv.ET0 * (1 - k.FI))
r.PT = convert_cm_to_m(drv.ET0 * k.FI)
r.ETP = convert_cm_to_m(drv.ET0) * 100 * 10
# Convert fc and pwp to m of H2O
r.nl = math.floor(p.RDMAX / p.TCK)
r.FC = p.FCP * p.TCK
r.PWP = p.PWPP * p.TCK
r.ADWC = p.ADWCP * p.TCK
# Parameters for eq os SPSI
r.B = math.log(p.PSIPWP / p.PSIFC) / math.log(p.FCP / p.PWPP)
r.A = math.exp((math.log(-p.PSIFC)) +
r.B * math.log(max(p.FCP, sys.float_info.min)))
# Interception
r.PREC = drv.RAIN / 100
if drv.RAIN != 0.:
r.INTERC = min(drv.RAIN / 100, 0.001 * k.FI)
r.GPREC = ((drv.RAIN / 100) - r.INTERC)
# Runoff calculation
if r.GPREC <= 0.2 * p.S:
r.RUNOFF = 0
else:
r.RUNOFF = (
(r.GPREC - p.RUNOFF1 * p.S)**2) / (r.GPREC + p.RUNOFF2 * p.S)
r.INFIL = ((drv.RAIN / 100) - r.INTERC - r.RUNOFF)
# Recharge water per layer
r.values_RW = []
r.values_FR = []
r.values_SPSI = []
for j in range(s.WC.shape[0]):
if r.INFIL > 0:
if r.INFIL <= (r.FC - s.WC[j]):
r.RW = r.INFIL
r.INFIL = 0.
else:
r.RW = r.FC - s.WC[j]
r.INFIL = r.INFIL - (r.FC - s.WC[j])
else:
r.RW = 0
r.values_RW.append(r.RW)
r.RWATER = np.array(r.values_RW)
# Evaporation calculation
if j < 1:
# if s.WC[0]>r.PWP:
# r.EVS=r.PE
if s.WC[0] < r.PWP:
r.PE = r.PE * (((s.WC[0] / p.TCK) - p.ADWCP) /
(p.PWPP - p.ADWCP))**2.
r.NWC = s.WC[0] - r.PE
r.EVS = r.PE
if r.NWC < r.ADWC:
r.NWC = r.ADWC
r.EVS = r.EVS - r.NWC
# Fraction root per layer
if j >= 1:
r.z += p.TCK
if r.z <= k.TRD:
r.FROOT = p.TCK * (2. *
(k.TRD - r.z) + p.TCK) / (k.TRD * k.TRD)
elif r.z > k.TRD and (r.z - p.TCK) < k.TRD:
r.FROOT = ((k.TRD - r.z + p.TCK) / k.TRD)**2.
else:
r.FROOT = 0.
r.SPSI = -r.A * mp.exp(
-r.B * math.log(max(
(s.WC[j] / p.TCK), sys.float_info.min)))
r.AVEPSI += (r.FROOT * r.SPSI)
r.values_FR.append(r.FROOT)
r.FcR = np.array(r.values_FR)
r.values_SPSI.append(r.SPSI)
r.SP = np.array(r.values_SPSI)
r.RBAR = p.RMIN / max(k.FI, 1e-70)
r.PSIX = r.AVEPSI - (r.RBAR * r.PT)
if r.PSIX < p.PSIPWP: r.PSIX = p.PSIPWP
# Transpiration calculation
r.arr_subt = np.subtract(r.SP, r.PSIX)
r.arr_mult = np.multiply(r.FcR, r.arr_subt)
r.LOSS = np.true_divide(r.arr_mult, (r.RBAR * p.TCK))
# check loss under water deficit
r.W = np.true_divide(s.WC[1::], p.TCK)
r.arr_bool = (np.subtract(r.W, r.LOSS)) < p.PWPP
r.arr_TRUE = np.subtract(r.W, p.PWPP)
# Actual evapotranspiration
r.TL = np.multiply(np.where(r.arr_bool, r.arr_TRUE, r.LOSS), p.TCK)
r.AT = np.append(r.EVS, r.TL)
r.T = np.sum(r.TL)
r.net_RW = np.subtract(r.RWATER, r.AT)
@prepare_states
def integrate(self, day, delt):
p = self.params
r = self.rates
s = self.states
k = self.kiosk
s.PTa = r.PT
# Soil water balance
s.TPE += r.PE
s.TPT = r.PT
s.TPREC = r.PREC
s.TINTERC += r.GPREC
s.TRUNOFF += r.RUNOFF
s.PERC += r.INFIL
s.TE += r.EVS
s.Ta = r.T
s.WC = np.add(s.WC, r.net_RW)
s.WCv = (s.WC / p.TCK)
# check WB closed
s.TT += r.T
s.Diff_WC = np.sum(np.subtract(np.full(r.nl, r.FC), s.WC))
s.WB_close = s.TINTERC - s.TRUNOFF - s.PERC - s.TT - s.TE + s.Diff_WC
s.TWC = (np.sum(np.subtract(s.WC, r.PWP))) * 1000
s.W_Stress = r.T / max(r.PT, 1e-70)
class RateVariables(RatesTemplate):
PE = Float(-99.)
PT = Float(-99.)
EPT = Float(-99.)
PREC = Float(-99.)
nl = Int
FC = Float(-99.)
PWP = Float(-99.)
ADWC = Float(-99.)
B = Float(-99.)
A = Float(-99.)
INTERC = Float(-99.)
GPREC = Float(-99.)
RUNOFF = Float(-99.)
INFIL = Float(-99.)
RW = Float(-99.)
values_RW = []
RWATER = Instance(np.ndarray)
NWC = Float(-99.)
EVS = Float(-99.)
SPSI = Float(-99.)
values_SPSI = []
SP = Instance(np.ndarray)
#root
FcR = Instance(np.ndarray)
values_FR = []
FROOT = Float(-99.)
AVEPSI = Float(-99.)
RBAR = Float(-99.)
PSIX = Float(-99.)
z = Float(-99.)
LOSS = Instance(np.ndarray)
W = Instance(np.ndarray)
arr_bool = Instance(np.ndarray)
arr_TRUE = Instance(np.ndarray)
TL = Instance(np.ndarray)
net_RW = Instance(np.ndarray)
T = Float(-99.)
arr_subt = Instance(np.ndarray)
arr_mult = Instance(np.ndarray)
AT = Instance(np.ndarray)
check = Float(-99.)
class Campbell(SimulationObject):
"""Parameters**
============ ================================================= ==== ========
Name Description Unit
============ ================================================= ==== ========
DVV1 Paramter 1 for vapor deficit equation
DVV2 Paramter 2 for vapor deficit equation
DVV3 Paramter 3 for vapor deficit equation
NTR Nitrogen content in grain g.g-1
LNTR Nitrogen content in leaves g.g-1
FNTR Fraction of N translocated from leaves to seeds
HD Factor to standardize humidity content at 13%
K Light extinction coefficient (Kukal and Irmak, 2020)
Ppar Proportion of PAR in the total radiation
WUE Dry matter water ratio Pa
DSLA Specific leaf area for dead leaves m-2 kg-1
RUE Radiation use efficiency (Kukal and Irmak, 2020) g Mj m2
GCC Conversion coefficient (CHO to soyeban seed)
LAIC Critic leaf area index m-2 m-2
FTRANSL Fraction of TDM to be translocated
RDRSHM Maximum relative death rate of leaves due to shading (LINTUL2) d-1
============ ================================================= ==== ========
Rates**
============ ================================================= ==== ========
Name Description Unit
============ ================================================= ==== ========
FI Fractional interception
PE Potential evaporation m
PT Potential transpiration m
VDD Correction by vapor deficit water KPa
PARi Intercepted PAR Mj m-2
DM Rate of growth kg m-2
ROOT Growth rate root kg m-2
STEMS Growth rate stems kg m-2
LEAF Growth rate leaf kg m-2
SEED Growth rate storage organs kg m-2
TN Translocated nitrogen from leaves to grains kg m-2
DLEAF Senescence rate of leaf kg m-2
RDRSH Relative death rate of leaves due to shading (LINTUL2) d-1
RDRT Table of RDR as a function of temperature
============ ================================================= ==== ========
State variables**
Name Description Unit
============ ================================================= ==== ========
TPE Total potential evaporation m
TPT Total potential transpiration m
TDM Total above-ground biomass kg m-2
TROOT Total weight of roots kg m-2
TSTEMS Total weight of stems kg m-2
TLEAF Total weight of leaves m-2 m-2
TSEED Total weight of storage organs kg m-2
LAI Leaf area index m-2 m-2
TDLEAF Total of dead leaves m-2 m-2
GLEAF Total of green leaves m-2 m-2
SLA Specific leaf area m-2 kg-1
============ ================================================= ==== ========
**External dependencies:**
======= =================================== ================= ============
Name Description Provided by 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 -
DVS Development stage
======= =================================== ================= ============
"""
# sub-model components for crop simulation
pheno = Instance(SimulationObject)
part = Instance(SimulationObject)
soil = Instance(SimulationObject)
class Parameters(ParamTemplate):
RDRT = AfgenTrait()
RDRSHM = Float(-99.)
LAIC = Float(-99.)
DVV1 = Float(-99.)
DVV2 = Float(-99.)
DVV3 = Float(-99.)
initLAI = Float(-99.)
K = Float(-99.)
Ppar = Float(-99.)
WUE = Float(-99.)
DSLA = Float(-99.)
NTR = Float(-99.)
LNTR = Float(-99.)
FNTR = Float(-99.)
HD = Float(-99.)
GCC = Float(-99.)
FTRANSL = Float(-99.)
SLATB = AfgenTrait()
RUE = Float(-99.)
RDMAX = Float(-99.)
class RateVariables(RatesTemplate):
RDRDV = Float(-99.)
RDRSH = Float(-99.)
RDR = Float(-99.)
DLAI = Float(-99.)
DM_W = Float(-99.)
DM_R = Float(-99.)
DM = Float(-99.)
PDM = Float(-99.)
VDD = Float(-99.)
FI = Float(-99.)
ROOT = Float(-99.)
STEMS = Float(-99.)
LEAF = Float(-99.)
WLEAF = Float(-99.)
SEED = Float(-99.)
PSEED = Float(-99.)
TN = Float(-99.)
WDLEAF = Float(-99.)
DLEAF = Float(-99.)
GLEAF = Float(-99.)
TRANSL = Float(-99.)
#root
RD = Float(-99.)
WD = Float(-99.)
class StateVariables(StatesTemplate):
TDM = Float(-99.)
TDMv = Float(-99.)
TSTEM = Float(-99.)
TLEAF = Float(-99.)
TSEED = Float(-99.)
YIELD = Float(-99.)
LAI = Float(-99.)
LAIFlowering = Float(-99.)
TDLEAF = Float(-99.)
SLA = Float(-99.)
TDMFlowering = Float(-99.)
TDMTRANSL = Float(-99.)
POOLTRSL = Float(-99.)
#root
TRD = Float(-99.)
da = Int
CWDv = Float(-99.)
CWDr = Float(-99.)
def initialize(self, day, kiosk, parametervalues):
self.params = self.Parameters(parametervalues)
self.rates = self.RateVariables(kiosk, publish=["FI"])
self.kiosk = kiosk
# Initialize components of the crop
self.pheno = Phenology(day, kiosk, parametervalues)
self.part = Partitioning(day, kiosk, parametervalues)
DVS = self.kiosk["DVS"]
SLA = self.params.SLATB(DVS)
# =============================================================================
# # Initial total (living+dead) above-ground biomass of the crop
# FR = self.kiosk["FR"]
# FS = self.kiosk["FS"]
# FL = self.kiosk["FL"]
# FO = self.kiosk["FO"]
# =============================================================================
self.states = self.StateVariables(kiosk,
publish=["TRD"],
TDM=0.00,
TDMv=0,
GLEAF=0.0,
TSTEM=0.0,
TLEAF=0.0,
TSEED=0.0,
YIELD=0.0,
LAI=self.params.initLAI,
TDLEAF=0,
SLA=SLA,
TRD=0.0,
da=0,
TDMFlowering=None,
LAIFlowering=None,
TDMTRANSL=0,
POOLTRSL=0,
CWDv=0.,
CWDr=0.)
@prepare_rates
def calc_rates(self, day, drv):
p = self.params
r = self.rates
s = self.states
k = self.kiosk
self.pheno.calc_rates(day, drv)
crop_stage = self.pheno.get_variable("STAGE")
# if before emergence there is no need to continue
# because only the phenology is running.
if crop_stage == "emerging":
return
self.part.calc_rates(day, drv)
r.VDD = convert_hPa_to_KPa(drv.TMAX - drv.TMIN) * (
(p.DVV1 * drv.TEMP + p.DVV2) * drv.TEMP + p.DVV3)
print("VDD=", r.VDD)
r.FI = 1. - mp.exp(-p.K * s.LAI)
r.PARi = convert_j_Mj(drv.IRRAD) * p.Ppar * r.FI
if k.DVS < 2:
if "Ta" not in self.kiosk:
k.Ta = 0.001
else:
k.Ta = self.kiosk["Ta"]
if "W_Stress" not in self.kiosk:
k.W_Stress = 0.0
else:
k.W_Stress = self.kiosk["W_Stress"]
if "PTa" not in self.kiosk:
k.PTa = 0.0
else:
k.PTa = self.kiosk["PTa"]
r.DM_W = k.Ta * (p.WUE / r.VDD)
print("Ta=", k.Ta)
print("DM=", r.DM_W)
r.DM_R = convert_g_kg(r.PARi * p.RUE)
r.DM = min(r.DM_W, r.DM_R)
r.PDM = k.PTa * (p.WUE / r.VDD)
r.STEMS = r.DM * k.FS
r.WLEAF = r.DM * k.FL
r.LEAF = r.DM * k.FL * convert_ha_m2(s.SLA)
r.PSEED = r.PDM * k.FO
# Biomass reallocated from vegetative to seed
if s.TDMTRANSL > 0:
r.TRANSL = r.PSEED - (r.DM * k.FO)
r.SEED = (r.DM * k.FO) + r.TRANSL
else:
r.SEED = r.DM * k.FO
# Senescence from N translocation
r.TN = ((r.SEED * p.NTR) / p.FNTR)
#senescence rate from LINTUL
if k.DVS > 1.5:
r.RDRDV = p.RDRT(drv.TEMP)
r.RDRSH = p.RDRSHM * ((s.LAI - p.LAIC) / p.LAIC)
if r.RDRSH > 0 or r.RDRSH < 0.03:
r.RDRSH = r.RDRSH
if r.RDRSH < 0:
r.RDRSH = 0
if r.RDRSH > 0.03:
r.RDRSH = 0.03
else:
r.RDRDV = 0
r.RDR = max(r.RDRDV, r.RDRSH)
r.DLAI = s.LAI * r.RDR
r.WDLEAF = r.TN / p.LNTR
r.DLEAF = r.WDLEAF * p.DSLA
r.GLEAF = r.LEAF - max(r.DLAI, r.DLEAF)
#Rooting growth
r.RD = p.RDMAX * (1. / (1 + 44.2 * math.exp(-15 * (s.da) / (140))))
r.WD = k.PTa - k.Ta
@prepare_states
def integrate(self, day, delt):
p = self.params
r = self.rates
s = self.states
k = self.kiosk
# crop stage before integration
crop_stage = self.pheno.get_variable("STAGE")
self.pheno.integrate(day, delt=1.0)
# if before emergence there is no need to continue
# because only the phenology is running.
# Just run a touch() to to ensure that all state variables are available
# in the kiosk
if crop_stage == "emerging":
self.touch()
return
self.part.integrate(day, delt=1.0)
DVS = self.kiosk["DVS"]
s.SLA = p.SLATB(DVS)
s.TDM += r.DM
print("TDM", s.TDM)
s.TDMv += r.STEMS + r.WLEAF
if s.TDMFlowering is None and k.DVS >= 1.:
s.TDMFlowering = s.TDMv
s.TDMTRANSL = s.TDMFlowering * p.FTRANSL
s.TDMTRANSL -= r.TRANSL
s.TSEED += r.SEED
s.YIELD = s.TSEED * p.GCC * p.HD
s.TSTEM += r.STEMS
s.TLEAF += r.DM * k.FL
s.LAI += r.GLEAF
if s.LAIFlowering is None and k.DVS >= 1.3:
s.LAIFlowering = s.LAI
s.da += 1
s.TRD = r.RD
if k.DVS < 1:
s.CWDv += r.WD
else:
s.CWDr += r.WD
class SoybeanPhenology(SimulationObject):
"""Implements the algorithms for phenologic development in WOFOST specifically for soybean.
Phenologic development in WOFOST is expresses using a unitless scale which
takes the values 0 at emergence, 1 at Anthesis (flowering) and 2 at
maturity. This type of phenological development is mainly representative
for cereal crops. All other crops that are simulated with WOFOST are
forced into this scheme as well, although this may not be appropriate for
all crops. For example, for potatoes development stage 1 represents the
start of tuber formation rather than flowering.
**Simulation parameters**
======= ============================================= ======= ============
Name Description Type Unit
======= ============================================= ======= ============
TSUMEM Temperature sum from sowing to emergence SCr |C| day
TBASEM Base temperature for emergence SCr |C|
TEFFMX Maximum effective temperature for emergence SCr |C|
DVRMAX1 Maximum development rate emergence to anthesis SCr |C| day
DVRMAX2 Maximum develpment rate anthesis to maturity SCr |C| day
DVSI Initial development stage at emergence. SCr -
Usually this is zero, but it can be higher
for crops that are transplanted (e.g. paddy
rice)
DVSEND Final development stage SCr -
MG Maturity group rating for daylength sensivity SCr -
Topt Optimum temperature for phenological dev. SCr |C|
Tmin Temperature below which development is zero. SCr |C|
Tmax Temperature above which development is zero. SCr |C|
======= ============================================= ======= ============
**State variables**
======= ================================================= ==== ============
Name Description Pbl Unit
======= ================================================= ==== ============
DVS Development stage Y -
TSUM Temperature sum N |C| day
TSUME Temperature sum for emergence N |C| day
DOS Day of sowing N -
DOE Day of emergence N -
DOR1 Day of R1 stage (beginning of flowering) N -
DOR3 Day of R3 stage (pod development) N -
DOR5 Day of R5 stage (seed development) N -
DOR8 Day of R8 stage (fully ripe N -
STAGE Current phenological stage, can take the N -
folowing values:
`emerging|vegetative|reproductive|mature`
======= ================================================= ==== ============
**Rate variables**
======= ================================================= ==== ============
Name Description Pbl Unit
======= ================================================= ==== ============
DTSUME Increase in temperature sum for emergence N |C|
DTSUM Increase in temperature sum for anthesis or N |C|
maturity
DVR Development rate Y |day-1|
======= ================================================= ==== ============
**External dependencies:**
None
**Signals sent or handled**
`SoybeanPhenology` sends the `crop_finish` signal when maturity is
reached and the `end_type` is 'maturity' or 'earliest'.
"""
photoperiod_reduction_factor = Instance(PhotoperiodReductionFactor)
temperature_reduction_factor = Instance(TemperatureReductionFactor)
class Parameters(ParamTemplate):
TSUMEM = Float(-99.) # Temp. sum for emergence
TBASEM = Float(-99.) # Base temp. for emergence
TEFFMX = Float(-99.) # Max eff temperature for emergence
DVRMAX1 = Float(-99.) # Max development rate towards anthesis
DVRMAX2 = Float(-99.) # Max development rate towards maturity
DVSI = Float(-99.) # Initial development stage
DVSEND = Float(-99.) # Final development stage
CROP_START_TYPE = Enum(["sowing", "emergence"])
CROP_END_TYPE = Enum(["maturity", "harvest", "earliest"])
#-------------------------------------------------------------------------------
class RateVariables(RatesTemplate):
DTSUME = Float(-99.) # increase in temperature sum for emergence
DVR = Float(-99.) # development rate
DAYL = Float(-99)
PHOTORF = Float(-99)
TEMPRF = Float(-99)
#-------------------------------------------------------------------------------
class StateVariables(StatesTemplate):
DVS = Float(-99.) # Development stage
TSUM = Float(-99.) # Temperature sum state
TSUME = Float(-99.) # Temperature sum for emergence state
# States which register phenological events
DOS = Instance(date) # Day of sowing
DOE = Instance(date) # Day of emergence
DOR1 = Instance(date) # Day of start of flowering
DOR3 = Instance(date) # Day of pod development
DOR5 = Instance(date) # Day of seed filling
DOR8 = Instance(date) # Day of full ripeness
DOH = Instance(date) # Day of harvest
STAGE = Enum(
[None, "emerging", "vegetative", "reproductive", "mature"])
#---------------------------------------------------------------------------
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.photoperiod_reduction_factor = PhotoperiodReductionFactor(
day, kiosk, parvalues)
self.temperature_reduction_factor = TemperatureReductionFactor(
day, kiosk, parvalues)
self.params = self.Parameters(parvalues)
self.rates = self.RateVariables(kiosk)
self.kiosk = kiosk
self._connect_signal(self._on_CROP_FINISH, signal=signals.crop_finish)
# Define initial states
DVS = self.params.DVSI
DOS, DOE, STAGE = self._get_initial_stage(day)
self.states = self.StateVariables(kiosk,
publish="DVS",
TSUM=0.,
TSUME=0.,
DVS=DVS,
DOS=DOS,
DOE=DOE,
DOR1=None,
DOR3=None,
DOR5=None,
DOR8=None,
DOH=None,
STAGE=STAGE)
def _get_initial_stage(self, day):
""""""
p = self.params
# Define initial stage type (emergence/sowing) and fill the
# respective day of sowing/emergence (DOS/DOE)
if p.CROP_START_TYPE == "emergence":
STAGE = "vegetative"
DOE = day
DOS = None
# send signal to indicate crop emergence
self._send_signal(signals.crop_emerged)
elif p.CROP_START_TYPE == "sowing":
STAGE = "emerging"
DOS = day
DOE = None
else:
msg = "Unknown start type: %s" % p.CROP_START_TYPE
raise exc.PCSEError(msg)
return DOS, DOE, STAGE
@prepare_rates
def calc_rates(self, day, drv):
"""Calculates the rates for phenological development
"""
p = self.params
r = self.rates
s = self.states
# Day length
r.DAYL = daylength(day, drv.LAT, angle=-0.83)
# temperature reduction factor
r.TEMPRF = self.temperature_reduction_factor(drv.TEMP)
# photoperiod
r.PHOTORF = 1.0
if s.STAGE == "emerging":
r.DTSUME = limit(0., (p.TEFFMX - p.TBASEM), (drv.TEMP - p.TBASEM))
elif s.STAGE == 'vegetative':
r.DVR = p.DVRMAX1 * r.TEMPRF
elif s.STAGE in ['reproductive', 'mature']:
# photoperiod reduction factor
r.PHOTORF = self.photoperiod_reduction_factor(r.DAYL)
r.DVR = p.DVRMAX2 * r.PHOTORF * r.TEMPRF
else: # Problem: no stage defined
msg = "No STAGE defined in phenology submodule"
raise exc.PCSEError(msg)
msg = "Finished rate calculation for %s"
self.logger.debug(msg % day)
#---------------------------------------------------------------------------
@prepare_states
def integrate(self, day, delt):
"""Updates the state variable and checks for phenologic stages
"""
p = self.params
r = self.rates
s = self.states
if s.STAGE == "emerging":
s.TSUME += r.DTSUME
if s.TSUME >= p.TSUMEM:
self._next_stage(day)
elif s.STAGE == 'vegetative':
s.DVS += r.DVR
if s.DVS >= 1.0:
self._next_stage(day)
s.DVS = 1.0
elif s.STAGE == 'reproductive':
s.DVS += r.DVR
# Check of R5 stage is reached at DVS=1.15.
if s.DVS >= 1.15 and s.DOR5 is None:
s.DOR5 = day
# Check if maturity is reached
if s.DVS >= p.DVSEND:
self._next_stage(day)
elif s.STAGE == 'mature':
s.DVS += r.DVR
else: # Problem no stage defined
msg = "No STAGE defined in phenology submodule"
raise exc.PCSEError(msg)
msg = "Finished state integration for %s"
self.logger.debug(msg % day)
#---------------------------------------------------------------------------
def _next_stage(self, day):
"""Moves states.STAGE to the next phenological stage"""
s = self.states
p = self.params
current_STAGE = s.STAGE
if s.STAGE == "emerging":
s.STAGE = "vegetative"
s.DOE = day
# send signal to indicate crop emergence
self._send_signal(signals.crop_emerged)
elif s.STAGE == "vegetative":
s.STAGE = "reproductive"
s.DOR1 = day
elif s.STAGE == "reproductive":
s.STAGE = "mature"
s.DOR8 = day
if p.CROP_END_TYPE in ["maturity", "earliest"]:
self._send_signal(signal=signals.crop_finish,
day=day,
finish_type="maturity")
elif s.STAGE == "mature":
msg = "Cannot move to next phenology stage: maturity already reached!"
raise exc.PCSEError(msg)
else: # Problem no stage defined
msg = "No STAGE defined in phenology submodule."
raise exc.PCSEError(msg)
msg = "Changed phenological stage '%s' to '%s' on %s"
self.logger.info(msg % (current_STAGE, s.STAGE, day))
#---------------------------------------------------------------------------
def _on_CROP_FINISH(self, day, finish_type=None):
"""Handler for setting day of harvest (DOH). Although DOH is not
strictly related to phenology (but to management) this is the most
logical place to put it.
"""
if finish_type == 'harvest':
self._for_finalize["DOH"] = day
class StateVariables(StatesTemplate):
FR = Float(-99.)
FL = Float(-99.)
FS = Float(-99.)
FO = Float(-99.)
PF = Instance(PartioningFactors)