net.simplace.sim.components.models.gecros.Gecros

Simulates crop biomass by calculating photosynthesis.

Consult reference for description of algorithms.

This module calculates the crop and soil water part. There is also a version, where crop and soil water part are splitted into two different modules.

Changes

By default, the component calculates DTR by the corrected formula: $$ DTR = DDTR \cdot SINB(1.+0.4 SINB)/DSINBE $$

In the original code, DTR was calculated by $$ DTR = DDTR (SINB \cdot SC/1367.)/DSINBE $$ By setting cLegacyMode to true, one can switch to this formula.

Reference:

(Y) Yin, X. and van Laar, H.H. (2005): Crop Systems Dynamics. An ecophysiological simulation model for genotype-by-environment interactions. Wageningen Academic Publishers, Wageningen, The Netherlands.

Component Variables

Content TypeNameDescriptionData TypeUnitMin ValueMax ValueDefault Value
constantcAnthesisDSDevelopment stage of anthesisDOUBLE1--1.0
constantcBHCInitial value for microbial biomass in the soil and humified organic matter in the soil (BIO + HUM)DOUBLEg/m2--3500.0
constantcBIORDecomposition rate constant for microbial biomass in the soil (BIO)DOUBLEa-1--0.66
constantcBLDLeaf angle (from horizontal)DOUBLE°--50.0
constantcC3C4Crop type (true for C3, false for C4 crops)BOOLEAN1--false
constantcCBFactor for initial N concentration of seed fillDOUBLE1--0.75
constantcCCFIXC cost of symbiotic N fixationDOUBLEg/g--6.0
constantcCDMHTStem dry weight per unit of plant heightDOUBLEgram_per_square_metre_reciprocal_metre--345.0
constantcCFVC fraction in the vegetative organsDOUBLEg/g--0.473
constantcCLAYPercentage of clay in the soilDOUBLE%--23.4
constantcCO2AAmbient CO2 concentrationDOUBLEmicromole_per_mole--350.0
constantcCOEFRFactor for change in radiationDOUBLE1--1.0
constantcCOEFTIncrement of temperatureDOUBLE°C--0.0
constantcCOEFVFactor for change in vapour pressureDOUBLE1--1.0
constantcCOSLDAmplitude of sine of solar heightDOUBLE1--0.0
constantcCXFactor for final N concentration of seed fillDOUBLE1--1.0
constantcDAYLAstronomic daylengthDOUBLEh--0.0
constantcDDLPPhotoperiodic daylengthDOUBLEh--0.0
constantcDETERCrop type (true determinate crops, false for indeterminate crops)BOOLEAN1--false
constantcDPMIInitial value of decomposable plant material (DPM)DOUBLEg/m2--0.0
constantcDPMR0Standard value for decomposition rate constant (DPMR) for decomposable plant material (DPM)DOUBLEa-1--10.0
constantcDRPMRatio decomposable plant material/resistant plant material (DPM/RPM) of added plant materialDOUBLE1--1.44
constantcDSINBEDaily total of effective solar heightDOUBLEs/d--0.0
constantcEAJMAXEnergy of activation for maximum rate of electron transport through photosystem II (JMAX)DOUBLEJ/mol--48041.88
constantcEGEfficiency of germinationDOUBLEg/g--0.35
constantcEPSPdevelopment stage for end of photoperiod-sensitive phaseDOUBLE1--0.7
constantcESDIdevelopment stage for end of seed-number determining period for indeterminate cropsDOUBLE1--1.35
constantcFBIOCFraction of initial value for for micobial biomass in the soil (BIOI) in initial total soil organic carbon (TOC)DOUBLE1--0.03
constantcFCRSHInitial fraction of C in the shootDOUBLEg/g--0.5
constantcFFATFraction of fat in the storage organsDOUBLEg/g--0.02
constantcFLIGFraction of lignin in the storage organsDOUBLEg/g--0.06
constantcFMINFraction of minerals in the storage organsDOUBLEg/g--0.03
constantcFNRSHInitial fraction of N in the shootDOUBLEg/g--0.63
constantcFOACFraction of organic acids in the storage organsDOUBLEg/g--0.04
constantcHTMXMaximum plant heightDOUBLEm--0.7054
constantcHUMRDecomposition rate constant for humified organic matter in the soil (HUM)DOUBLEa-1--0.02
constantcLEGUMECrop type (true for leguminous crops, false for non-leguminous crops)BOOLEAN1--false
constantcLNCIInitial N concentration in living leaves (LNC) (or actual N concentration in living shoot (HNC))DOUBLEg/g--0.055
constantcLODGELodging (true for cases with lodging, false for cases without lodging)BOOLEAN1--false
constantcLWIDTHLeaf widthDOUBLEm--0.025
constantcLegacyModeIf true, it calculates DTR with the formula published in (Y). If false (default) it uses the correct formulaBOOLEAN--false
constantcMTDRMinimum thermal days for reproductive (seed fill) phaseDOUBLEd--23.0889
constantcMTDVMinimum thermal days for vegetative growth phaseDOUBLEd--34.7627
constantcMULTFMultiplication factor for initial soil water statusDOUBLE1--1.0
constantcMaturityDSDevelopment stage of maturityDOUBLE1--2.0
constantcMilkripenessDSDevelopment stage of milk ripenessDOUBLE1--1.3
constantcNAIInitial ammonium-N in the soilDOUBLEg/m2--0.0
constantcNNIInitial nitrate-N in the soilDOUBLEg/m2--0.0
constantcNPLPlant density per m2DOUBLE1--60.0
constantcNSWISwitch variable for N supply for crop: false=user defined (NINPA, NINPN); true=simulatedBOOLEAN1--false
constantcNUPTXmaximum crop N uptakeDOUBLEg/(m2 d)--0.65
constantcPMEHfraction of sigmoid curve inflexion in entire plant height growth periodDOUBLE1--0.8
constantcPMESfraction of sigmoid curve inflexion in entire seed growth periodDOUBLE1--0.5
constantcPNLSFraction of dead leaf N incorporated into soil litter NDOUBLE1--1.0
constantcPNPREProportion of seed N that comes from non-structural N in vegetative organs accumulated before end of seed-number detemrining periodDOUBLE1--0.7
constantcPSENPhotoperiod sensitivity of phenological developmentDOUBLEh-1--0.0
constantcRAResidual ammonium-N in the soilDOUBLEg/m2--1.0
constantcRDMXMaximum rooting depthDOUBLEcm--100.0
constantcRNResidual nitrate-N in the soilDOUBLEg/m2--1.0
constantcRNCMINMinimum N concentration in the rootsDOUBLEg/g--0.005
constantcRPMR0Standard value for decompostion rate constant (RPMR) for resistant plant material (RPM)DOUBLEa-1--0.3
constantcRSSSoil resistance for water vapour transfer, equivalent to leaf stomatal resistanceDOUBLEsecond-time_per_metre--100.0
constantcSCSolar constantDOUBLEJ/(m2 s)--0.0
constantcSD1Thickness of upper evaporative soil layerDOUBLEcm--5.0
constantcSEEDNCStandard seed (storage organ) N concentrationDOUBLEg/g--0.04625
constantcSEEDWSingle seed weightDOUBLEg--0.2148
constantcSINLDSeasonal offset of sine of solar heightDOUBLE1--0.0
constantcSLA0Specific leaf area constantDOUBLEm2/g--0.0333
constantcSLNMINMinimum or base specific leaf N concentration (SLN) for photosynthesisDOUBLEg/m2--0.5
constantcSLPCrop type (true for short-day crops, false for long-day crops)BOOLEAN1--false
constantcSPSPdevelopment stage for start of photoperiod-sensitive phaseDOUBLE1--0.2
constantcSTEMNCNitrogen concentration in the stemDOUBLEg/g--0.015
constantcTBDBase temperature for phenologyDOUBLE°C--0.0
constantcTCDCeiling temperature for phenologyDOUBLE°C--36.0
constantcTCPTime ConstantDOUBLEd--1.0
constantcTCTTime constant for soil temperature dynamicsDOUBLEd--4.0
constantcTHETAconvexity for light response of electron transport (J2) in photosynthesisDOUBLE1--0.7
constantcTMDevelopment stage when transition from CB to CX is fastestDOUBLE1--1.5
constantcTOCTotal organic C in the soilDOUBLEg/m2--7193.0
constantcTODOptimum temperature for phenologyDOUBLE°C--27.6
constantcTSENcurvature for temperature responseDOUBLE1--0.409
constantcTSOILIInitial soil temperatureDOUBLE°C--0.0
constantcWCFCSoil water content in field capacityDOUBLEm3/m3--0.25
constantcWCMAXSoil water content at maximum water holding capacityDOUBLEm3/m3--0.35
constantcWCMINMinimum soil water contentDOUBLEm3/m3--0.05
constantcWRBcritical root weight densityDOUBLEgram_per_square_metre_reciprocal_centimetre--0.25
constantcWSWISwitch variable for water supply for crop: false=user defined (WINPUT); true=simulatedBOOLEAN1--false
constantcXJNslope of linear relationship between maximum rate of electron transport through photosystem II (JMAX) and leaf NDOUBLEmicromole_per_second-time_gram--124.0
constantcXVNslope of linear relationship between maximum rate of Rubisco-limited carboxylation (VCMX) and leaf NDOUBLEmicromole_per_second-time_gram--62.0
constantcYGVGrowth efficiency for vegetative organs (i.e roots, stems, leaves)DOUBLEg/g--0.8
inputiDoHarvestTrigger for harvestingBOOLEAN1--false
inputiDoSowTrigger for sowingBOOLEAN1--false
inputiFERNAAmmonium-N application rateDOUBLEg/(m2 d)--0.0
inputiFERNNNitrate-N application rateDOUBLEg/(m2 d)--0.0
inputiIRRIRate of water added by irrigationDOUBLEmm/d--0.0
inputiNINPAUser-defined ammonium-N supply to cropDOUBLEg/(m2 d)--0.0
inputiNINPNUser-defined nitrate-N supply to cropDOUBLEg/(m2 d)--0.0
inputiRAINPrecipitationDOUBLEmm--0.0
inputiRDDDaily global radiationDOUBLEJ/(m2 d)--0.0
inputiTMMNDaily minimum temperatureDOUBLE°C--0.0
inputiTMMXDaily maximum temperature DOUBLE°C--0.0
inputiVPAir vapour pressureDOUBLEkPa--0.0
inputiWINPUTUser-defined water supply to cropDOUBLEmm/d--0.0
inputiWNWind speedDOUBLEm/s--0.0
statesBIOMicrobial biomass in the soilDOUBLEg/m2--0.0
statesCLVAmount of C in the living leavesDOUBLEg/m2--0.0
statesCLVDAmount of C in dead leavesDOUBLEg/m2--0.0
statesCLVDSAmount of C in dead leaves that have become litter in the soilDOUBLEg/m2--0.0
statesCRTDAmount of C in dead rootsDOUBLEg/m2--0.0
statesCRVRAmount of C in root reservesDOUBLEg/m2--0.0
statesCRVSAmount of C in stem reservesDOUBLEg/m2--0.0
statesCSOAmount of carbon in storage organsDOUBLEg/m2--0.0
statesCSRTAmount of carbon in structural rootsDOUBLEg/m2--0.0
statesCSSTAmount of carbon in structural stemsDOUBLEg/m2--0.0
statesCTDUCumulative thermal-day unitDOUBLEd--0.0
statesCumulativeActualTranspirationCumulative canopy transpiration (TTCAN)DOUBLEmm--0.0
statesDCDSRShortfall of C demand for seed fill in previous time stepsDOUBLEg/m2--0.0
statesDCDTPC demand for structural stem growth at the previous time stepDOUBLEg/(m2 d)--0.0
statesDCDTRShortfall of C demand for structural stems in previous time stepsDOUBLEg/m2--0.0
statesDPMDecomposable plant materialDOUBLEg/m2--0.0
statesDPNOrganic N in DPMDOUBLEg/m2--0.0
statesDSDevelopment stageDOUBLE1--0.0
statesHTPlant heightDOUBLEm--0.0
statesHUMHumified organic matter in soilDOUBLEg/m2--0.0
statesLAICCarbon-determined LAIDOUBLEm2/m2--0.0
statesLITNTTotal litter N entering the soil (LITN) during crop growthDOUBLEg/m2--0.0
statesNALLAmmonium-N in the lower soil layerDOUBLEg/m2--0.0
statesNAULAmmonium-N in the upper soil layerDOUBLEg/m2--0.0
statesNDEMPCrop N demand (NDEM) of the previous time stepDOUBLEg/(m2 d)--0.0
statesNFIXRReserve pool of symbiotically fixed nitrogenDOUBLEg/m2--0.0
statesNFIXTTotal symbiotically fixed nitrogen during growthDOUBLEg/m2--0.0
statesNLVNitrogen in living leavesDOUBLEg/m2--0.0
statesNLVDNitrogen in dead leavesDOUBLEg/m2--0.0
statesNNLLNitrate-N in the lower soil layerDOUBLEg/m2--0.0
statesNNULNitrate-N in the upper soil layerDOUBLEg/m2--0.0
statesNREOEEstimated vegetative-organ N remobilizable for seed growth (NRES) accumulated till the end of seed-number determining periodDOUBLEg/m2--0.0
statesNREOFEstimated vegetative-organ N remobilizable for seed growth (NRES) accumulated till the moment at which seed fill startsDOUBLEg/m2--0.0
statesNRTNitrogen in living rootsDOUBLEg/m2--0.0
statesNRTDNitrogen in dead rootsDOUBLEg/m2--0.0
statesNSONitrogen in storage organsDOUBLEg/m2--0.0
statesNSTNitrogen content in stems (including structural stem and reserves)DOUBLEg/m2--0.0
statesNSUPPN supply to crop (NSUP) for the previous time stepDOUBLEg/(m2 d)--0.0
statesRDRooting depth to the soilDOUBLEcm--0.0
statesRMULTotal of respiratory costs of nitrate-N uptake (RMUN) + respiratory costs of ammonium-N uptake (RMUA) + respiratory costs of ash (minerals) uptake (RMUS) + respiration due to phloem loading of C assimilates to roots (RMLD)DOUBLEg/(m2 d)--0.0
statesRPMResistant plant material (difficult to decompose)DOUBLEg/m2--0.0
statesRPNOrganic N in resistant plant material (RPM)DOUBLEg/m2--0.0
statesSFERNANH4-N fertilizer susceptible to volatilizationDOUBLEg/m2--0.0
statesSLNBspecific leaf N constant (SLN) in bottom leaves of canopyDOUBLEg/m2--0.0
statesTDAPARTotal PAR absorbed by the canopy during growthDOUBLEJ/m2--0.0
statesTNLEATotal nitrate-N leached to groundwaterDOUBLEg/m2--0.0
statesTNLVTotal leaf N (including N in senesced leaves)DOUBLEg/m2--0.0
statesTNUPTTotal crop N uptake during growthDOUBLEg/m2--0.0
statesTPCANCumulative canopy photosynthesis over growth periodDOUBLEg/m2--0.0
statesTRESPTotal crop respiratory cost during growthDOUBLEg/m2--0.0
statesTSOILSoil temperatureDOUBLE°C--0.0
statesWLLWater content in the lower soil layerDOUBLEmm--0.0
statesWULWater content of the upper soil layerDOUBLEmm--0.0
raterDeadLeavesRate of dead leavesDOUBLEg/(m2 d)-200.0200.00.0
raterDeadStemsRate of dead stemsDOUBLEg/(m2 d)-200.0200.00.0
outAPCANActual gross canopy photosynthesisDOUBLEg/(m2 d)--0.0
outAPCANNActual standing canopy CO2 assimilation (APCANS) with small plant-N incrementDOUBLEg/(m2 d)--0.0
outAPCANSActual standing-canopy CO2 assimilationDOUBLEg/(m2 d)--0.0
outAboveGroundBiomassAbove ground biomassDOUBLEg/m2--0.0
outActualSoilEvaporationActual soil evaporation (AESOIL)DOUBLEmm/d--0.0
outActualTranspirationActual canopy transpiration (ATCAN)DOUBLEmm/d--0.0
outAnthesisDOYDOY of AnthesisINT11366-
outAnthesisDateDate of AnthesisDATE1---
outCCHKDifference between C added to the crop since initialization and net total of integrated C fluxes, relative to C in the crop accumulated since start of simulation (CCHKIN)DOUBLE%--0.0
outCropCycleCountCounter that is incremented on harvest - can be used for crop rotationINT1--0
outDAPARDaily photosynthetically active radiation (PAR) absorbed by crop canopyDOUBLEJ/(m2 d)--0.0
outDIFSDaytime average soil-air temperature differenceDOUBLE°C--0.0
outDIFSHDaytime average shaded leaf-air temperature differenceDOUBLE°C--0.0
outDIFSUDaytime average sunlit leaf-air temperature differenceDOUBLE°C--0.0
outEmergenceDOYDOY of EmergenceINT11366-
outEmergenceDateDate of EmergenceDATE1---
outHIHarvest indexDOUBLEg/g--0.0
outIsAnthesistrue if Anthesis occursBOOLEAN1--false
outIsEmergencetrue if Emergence occursBOOLEAN1--false
outIsMaturitytrue if maturity occursBOOLEAN1--false
outIsMilkripenesstrue if milkripeness occursBOOLEAN1--false
outIsPhenologyEventtrue if sowing/emergence/anthesis/maturity occursBOOLEAN1--false
outIsSowingtrue if Sowing occursBOOLEAN1--false
outLAILeaf area indexDOUBLEm2/m2--0.0
outLAINN-Leaf area indexDOUBLEm2/m2--0.0
outMaturityDOYDOY of MaturityINT11366-
outMaturityDateDate of MaturityDATE1---
outMilkripenessDOYDOY of MaturityINT11366-
outMilkripenessDateDate of Milk ripenessDATE1---
outNCHKDifference between N added to the crop since initialization and total of integrated N fluxes, relative to total crop N uptake during growth (TNUPT)DOUBLE%--0.0
outNDEMCrop N demand (NDEM) of the previous time stepDOUBLEg/(m2 d)--0.0
outNMINERmineral N in the soilDOUBLEg/m2--0.0
outPPCANPotential canopy CO2 assimilationDOUBLEg/(m2 d)--0.0
outPSOProtein content in storage organsDOUBLEg/m2--0.0
outPotentialEvapotranspirationPotential evapotranspirationDOUBLEmm/d--0.0
outPotentialSoilEvaporationPotential soil evaporation (PESOIL)DOUBLEmm/s--0.0
outPotentialTranspirationPotential daily canopy transpiration (PTCAN)DOUBLEmm/d--0.0
outRWRTrate of change in dry weight of living rootsDOUBLEg/(m2 d)--0.0
outSLASpecific leaf areaDOUBLEm2/g--0.0
outSLNN-Leaf area indexDOUBLEm2/m2--0.0
outSLNTN-Leaf area indexDOUBLEm2/m2--0.0
outSowingDOYDOY of SowingINT11366-
outSowingDateDate of SowingDATE1---
outWLVDry weight of living leavesDOUBLEg/m2--0.0
outWLVDDry weight of dead leavesDOUBLEg/m2--0.0
outWRTDry weight of living rootsDOUBLEg/m2--0.0
outWRTDDry weight of dead rootsDOUBLEg/m2--0.0
outWSHDry weight of living shoot (above-ground) organsDOUBLEg/m2--0.0
outWSHHDry weight of shoot organs (excluding shedded leaves)DOUBLEg/m2--0.0
outWSODry weight of storage organsDOUBLEg/m2--0.0
outWSTDry weight of stemsDOUBLEg/m2--0.0
outWTOTDry weight of total living organsDOUBLEg/m2--0.0
outWithCropcrop is presentBOOLEAN1--false


See also: GecrosFunctions, net.simplace.sim.components.models.gecros.modular.GecrosCrop, net.simplace.sim.components.models.gecros.modular.GecrosSoilWater




public class Gecros extends net.simplace.sim.model.FWSimComponent {
// Public Constructors
public Gecros();


// Public Instance Methods
public HashMap createVariables(); // Defines
net.simplace.sim.model.FWSimComponent


Create the FWSimVariables as interface for this SimComponent

// Protected Instance Methods
protected void init(); // Defines net.simplace.sim.model.FWSimComponent

Initializes the fields by getting input and output FWSimVariables from VarMap Initial values are calculated and states are set to these initial Values.
protected void initializeModel();

protected void process(); // Defines net.simplace.sim.model.FWSimComponent

Process the algorithm and write the results back to VarMap
protected FWSimComponent clone(FWSimVarMap aVarMap);
// Defines net.simplace.sim.model.FWSimComponent


creates a clone from this SimComponent for use in other threads


}



Hierarchy: java.lang.Object - net.simplace.sim.model.FWSimComponent (net.simplace.sim.util.FWSimFieldContainer) - Gecros