Package net.simplace.sim.components.experimental.lintul5.translocation

Class Biomass

java.lang.Object

net.simplace.sim.model.FWSimComponent

net.simplace.sim.components.experimental.lintul5.translocation.Biomass

All Implemented Interfaces:

net.simplace.sim.util.FWSimFieldContainer

public class Biomass
extends net.simplace.sim.model.FWSimComponent

Lintul5 - Simple generic model for simulation of crop growth - Biomass part

This sim component calculates the biomass part from Lintul5. It does not calculate any NPK related part, but takes the NPK stress factor iNPKI as an input.

References

• (L5) Joost Wolf, User guide for LINTUL5, Wageningen UR, Wageningen, 2012

Author:

G. Krauss

See Also:

• Lintul5
• NPK

Component Variables

Content Type	Name	Description	Data Type	Unit	Min Value	Max Value	Default Value
constant	cDVSDLT	development stage above which death of leaves starts in dependence of mean daily temperature	DOUBLE	1	0.0	-	1.0
constant	cDVSDR	development stage above which death of roots and stems starts	DOUBLE	1	0.0	-	1.0
constant	cDVSI	initial development stage of crop (from 0 to 2)	DOUBLE	1	0.0	-	0.0
constant	cEarsPartitioningTableDVS	DVS for fraction of above-ground dry matter to ears	DOUBLEARRAY		-	-	-
constant	cEarsPartitioningTableFraction	Fraction of above-ground dry matter to ears as function of DVS	DOUBLEARRAY		-	-	-
constant	cFLTB	Deprecated: please use cLeavesPartitioningTableFraction/DVS. Fraction table of abovre-gr. biomass to leaves as function of DVS	DOUBLEARRAY	1	-	-	-
constant	cFOTB	Deprecated: please use cStorageOrgansPartitioningTableFraction/DVS. Fraction table of abovre-gr. biomass to storage organs as function of DVS	DOUBLEARRAY	1	-	-	-
constant	cFRTB	Deprecated: please use cRootsPartitioningTableFraction/DVS. Fraction table of total biomass to roots as function of DVS	DOUBLEARRAY	1	-	-	-
constant	cFSTB	Deprecated: please use cStemsPartitioningTableFraction/DVS. Fraction table of abovre-gr. biomass to stems as function of DVS	DOUBLEARRAY	1	-	-	-
constant	cFruitingEfficiency	Number of grains per storage organs mass	DOUBLE	g^-1	0.0	-	-
constant	cKDIFTB	table of light extinction factor as function of DVS	DOUBLEARRAY	1	0.0	1.0	-
constant	cKDIFTableDVS	DVS for extiction coefficient for diffuse visible light (c.f. KDIFTB)	DOUBLEARRAY	1	-	-	0.0 2.0
constant	cKDIFTableK	Extinction cofficient for diffuse visible light as function of DVS (c.f. KDIFTB)	DOUBLEARRAY	1	-	-	0.6 0.6
constant	cLAICR	Critical leaf area index for overshadowing	DOUBLE	m2/m2	0.0	10.0	4.0
constant	cLeavesPartitioningTableDVS	DVS for fraction of above-ground dry matter to leaves (c.f. FLTB)	DOUBLEARRAY	1	-	-	0.0 0.1 0.25 0.5 0.646 0.95 2.0
constant	cLeavesPartitioningTableFraction	Fraction of above-ground dry matter to leaves as function of DVS (c.f. FLTB)	DOUBLEARRAY	1	0.0	1.0	0.65 0.65 0.7 0.5 0.3 0.0 0.0
constant	cNLAI	coefficient for the reduction due to nutrient (N-P-K) stress of the LAI increase (during juvenile phase)	DOUBLE	1	-	-	1.0
constant	cNLUE	coefficient for the reduction of RUE due to nutrient (N-P-K) stress	DOUBLE	1	-	-	1.1
constant	cNPART	coefficient for N stress-effect on leaf biomass reduction	DOUBLE	1	-	-	1.0
constant	cNSLA	coefficient for the effect of nutrient (N-P-K) stress on SLA reduction	DOUBLE	1	-	-	0.5
constant	cRDI	Initial rooting depth	DOUBLE	m	0.0	10.0	0.1
constant	cRDRL	max. rel. death rate of leaves due to water stress	DOUBLE	d-1	0.0	1.0	0.05
constant	cRDRLTB	table with relative death rate of leaves vs. TMPA	DOUBLEARRAY	d-1	0.0	1.0	-
constant	cRDRLeavesTableMeanTemp	Daily mean temperature for relative death rate of leaves (c.f. RDRLTB)	DOUBLEARRAY	°C	-	-	-10.0 10.0 15.0 30.0 50.0
constant	cRDRLeavesTableRelativeRate	Relative death rate of leaves as a function of daily mean temperature (c.f. RDRLTB)	DOUBLEARRAY	d-1	-	-	0.0 0.02 0.03 0.05 0.09
constant	cRDRNS	max. relative death rate of leaves due to nutrient (N-P-K) stress	DOUBLE	d-1	0.0	1.0	0.05
constant	cRDRRTB	table with relative death rate of roots vs. DVS	DOUBLEARRAY	d-1	0.0	1.0	-
constant	cRDRRootsTableDVS	DVS for relative death rate of stems (c.f. RDRRTB)	DOUBLEARRAY	1	-	-	0.0 1.5 1.5001 2.0
constant	cRDRRootsTableRelativeRate	Relative death rate of stems as a function of DVS (c.f. RDRRTB)	DOUBLEARRAY	d-1	-	-	0.0 0.0 0.02 0.02
constant	cRDRSHM	rel. death rate of leaves due to shading (above LAICR)	DOUBLE	d-1	0.0	1.0	0.03
constant	cRDRSTB	table with relative death rate of stems vs. DVS	DOUBLEARRAY	d-1	-	-	-
constant	cRDRStemsTableDVS	DVS for relative death rate of roots (c.f. RDRSTB)	DOUBLEARRAY	1	-	-	0.0 1.5 1.5001 2.0
constant	cRDRStemsTableRelativeRate	Relative death rate of roots as a function of DVS (c.f. RDRSTB)	DOUBLEARRAY	d-1	-	-	0.0 0.0 0.02 0.02
constant	cRGRLAI	maximal relative increase in LAI	DOUBLE	d-1	0.0	-	0.00817
constant	cRRI	Maximum daily increase in rooting depth	DOUBLE	m/d	0.0	0.15	0.012
constant	cRWRTI	initial change in living root biomass	DOUBLE	g/(m2 d)	-	-	0.0
constant	cRootsPartitioningTableDVS	DVS for fraction of total dry matter to roots (c.f. FRTB)	DOUBLEARRAY	1	-	-	0.0 0.1 0.2 0.35 0.4 0.5 0.7 0.9 1.2 2.0
constant	cRootsPartitioningTableFraction	Fraction of total dry matter to roots as function of DVS (c.f. FRTB)	DOUBLEARRAY	1	0.0	1.0	0.5 0.5 0.4 0.22 0.17 0.13 0.07 0.03 0.0 0.0
constant	cSLATB	table of specific leaf area as dependent on DVS	DOUBLEARRAY	g/m2	-	-	-
constant	cSLATableDVS	DVS for specific leaf area (c.f. SLATB)	DOUBLEARRAY	1	-	-	0.0 2.0
constant	cSLATableSLA	Specific leaf area as function of DVS (c.f. SLATB)	DOUBLEARRAY	m2/g	-	-	0.0212 0.0212
constant	cScaleFactorKDIF	Scales the y-values of KDIFTB (for sensitivity analysis / calibration)	DOUBLE	1	-	-	1.0
constant	cScaleFactorRDRLeaves	Scales the y-values of RDRLeaves (for sensitivity analysis / calibration)	DOUBLE	1	-	-	1.0
constant	cScaleFactorRDRRoots	Scales the y-values of RDRRoots (for sensitivity analysis / calibration)	DOUBLE	1	-	-	1.0
constant	cScaleFactorRDRStems	Scales the y-values of RDRStems (for sensitivity analysis / calibration)	DOUBLE	1	-	-	1.0
constant	cScaleFactorSLA	Scales the y-values of SLATB (for sensitivity analysis / calibration)	DOUBLE	1	-	-	1.0
constant	cStemsPartitioningTableDVS	DVS for fraction of above-ground dry matter to stems (c.f. FSTB)	DOUBLEARRAY	1	-	-	0.0 0.1 0.25 0.5 0.646 0.95 1.0 2.0
constant	cStemsPartitioningTableFraction	Fraction of above-ground dry matter to stems as function of DVS (c.f. FSTB)	DOUBLEARRAY	1	0.0	1.0	0.35 0.35 0.3 0.5 0.7 1.0 0.0 0.0
constant	cStorageOrgansPartitioningTableDVS	DVS for fraction of above-ground dry matter to storage organs (c.f. FOTB)	DOUBLEARRAY	1	-	-	0.0 0.95 1.0 2.0
constant	cStorageOrgansPartitioningTableFraction	Fraction of above-ground dry matter to storage organs as function of DVS (c.f. FOTB)	DOUBLEARRAY	1	0.0	1.0	0.0 0.0 1.0 1.0
constant	cTBASE	lower threshold temperature for LAI increase	DOUBLE	°C	-	-	0.0
constant	cTDWI	Initial total crop dry weight	DOUBLE	g/m2	0.0	2000.0	21.0
constant	cTranslocationFraction	Fraction of stems and leaves biomass that is reserved for translocation at anthesis	DOUBLE		0.0	1.0	0.2
input	iAVRAD	Daily total irradiation	DOUBLE	J/(m2 d)	-	-	0.0
input	iDVS	development stage of crop (from 0 to 2)	DOUBLE	1	-	-	0.0
input	iDoHarvest	harvesting	BOOLEAN	1	-	-	false
input	iDoSow	sowing	BOOLEAN	1	-	-	false
input	iEMERG	has emerged	BOOLEAN	1	-	-	false
input	iEarPartitioningReductionFactor	Reduces the fraction of above-ground dry matter to ears (e. g. due to stress)	DOUBLE		0.0	1.0	1.0
input	iIDEMERG	Day of emergence	INT	1	0	366	0
input	iLeaveSenescenceHeatStressFactor	Factor that increases leaf senescence due to heat stress	DOUBLE	1	0.0	-	1.0
input	iNNI	-	DOUBLE	1	-	-	1.0
input	iNPKI	-	DOUBLE	1	-	-	1.0
input	iRDM	maximal rooting depth	DOUBLE	m	0.0	10.0	1.25
input	iRTMCO	overall correction factor for RUE in dependence of both CO2 concentration and non-optimal daytime and minimal temperatures	DOUBLE	1	-	-	0.0
input	iRUE	radiation use efficiency	DOUBLE	g/MJ	-	-	0.0
input	iTMAX	maximal air temperature during day (output of routine WEATHR)	DOUBLE	°C	-	-	0.0
input	iTMIN	minimal air temperature during day (output of routine WEATHR)	DOUBLE	°C	-	-	0.0
input	iTRANRF	water stress reduction factor	DOUBLE	1	0.0	1.0	1.0
state	sGTSUM	total biomass of the crop	DOUBLE	g/m2	0.0	-	0.0
state	sGrainNumber	Number of grains	DOUBLE		0.0	-	0.0
state	sLAI	leaf area index (leaf area per soil surface)	DOUBLE	m2/m2	-	-	0.0
state	sRD	actual rooting depth	DOUBLE	m	-	-	0.0
state	sStorageOrgansDemand	Total demand of storage organs biomass	DOUBLE	g m^-2	0.0	-	0.0
state	sTAGB	total above-ground biomass	DOUBLE	g/m2	-	-	0.0
state	sTAGBG	total above-ground living biomass	DOUBLE	g/m2	-	-	0.0
state	sTPAR	total photosynthetically active radiation	DOUBLE	MJ/m2	-	-	0.0
state	sTPARINT	total intercepted radiation (PAR)	DOUBLE	MJ/m2	-	-	0.0
state	sTranslocation	Sum of translocated biomass from stems and leaves to storage organs	DOUBLE	g m^-2	0.0	-	0.0
state	sTranslocationFromLeaves	Sum of translocated biomass from leaves to storage organs	DOUBLE	g m^-2	0.0	-	0.0
state	sTranslocationFromStems	Sum of translocated biomass from stems to storage organs	DOUBLE	g m^-2	0.0	-	0.0
state	sTranslocationPoolMax	Biomass from stems and leaves that is reserved for translocation	DOUBLE	g m^-2	0.0	-	0.0
state	sWEA	Weight of ears	DOUBLE	g m^-2	0.0	-	0.0
state	sWLV	weight of leaves	DOUBLE	g/m2	-	-	0.0
state	sWLVD	weight of dead leaves	DOUBLE	g/m2	-	-	0.0
state	sWLVG	weight of living leaves	DOUBLE	g/m2	-	-	0.0
state	sWRT	weight of roots	DOUBLE	g/m2	-	-	0.0
state	sWRTD	weight of deat roots	DOUBLE	g/m2	-	-	0.0
state	sWSO	weight of storage organs	DOUBLE	g/m2	-	-	0.0
state	sWSOExcess	Total storage organs excess due to sink limitation	DOUBLE	g m^-2	0.0	-	0.0
state	sWST	weight of stems	DOUBLE	g/m2	-	-	0.0
state	sWSTD	weight of dead stems	DOUBLE	g/m2	-	-	0.0
rate	rDLV	decrease in leaf mass by senescence	DOUBLE	g/(m2 d)	-	-	0.0
rate	rDRRT	dead root rate	DOUBLE	g/(m2 d)	-	-	0.0
rate	rDRST	dead stem rate	DOUBLE	g/(m2 d)	-	-	0.0
rate	rGRT	daily increase in total biomass of the crop	DOUBLE	g/(m2 d)	-	-	0.0
rate	rPAR	daily amount of photosynthetically active radiation	DOUBLE	MJ/(m2 d)	-	-	0.0
rate	rPARINT	(or PARAB) daily amount of PAR as intercepted by the crop canopy	DOUBLE	MJ/(m2 d)	-	-	0.0
rate	rRLAI	change in leaf area index	DOUBLE	d-1	-	-	0.0
rate	rRR	root growth rate	DOUBLE	m/d	-	-	0.0
rate	rRWEA	Change rate of ears	DOUBLE	g m^-2 d^-1	-	-	0.0
rate	rRWLVG	change in living leaf biomass	DOUBLE	g/(m2 d)	-	-	0.0
rate	rRWRT	change in living root biomass	DOUBLE	g/(m2 d)	-	-	0.0
rate	rRWSO	change in storage organ biomass	DOUBLE	g/(m2 d)	-	-	0.0
rate	rRWSOExcess	Daily storage organs excess due to sink limitation	DOUBLE	g m^-2 d^-1	0.0	-	0.0
rate	rRWST	change in living stem biomass	DOUBLE	g/(m2 d)	-	-	0.0
rate	rStorageOrgansDemandRate	Daily demand of storage organs biomass	DOUBLE	g m^-2 d^-1	0.0	-	0.0
rate	rTranslocationFromLeavesRate	Daily translocation from leaves to storage organs	DOUBLE	g m^-2 d^-1	0.0	-	0.0
rate	rTranslocationFromStemsRate	Daily translocation from stems to storage organs	DOUBLE	g m^-2 d^-1	0.0	-	0.0
rate	rTranslocationRate	Daily translocation from stems and leaves to storage organs	DOUBLE	g m^-2 d^-1	0.0	-	0.0
out	FINT	fractional light interception	DOUBLE	1	-	-	0.0
out	K	light extinction coefficient as function of actual devstage	DOUBLE	m2/m2	-	-	0.0
out	LAII	-	DOUBLE	m2/m2	0.0	10.0	0.0
out	WithCrop	crop is present	BOOLEAN	1	-	-	false

Nested Class Summary

Nested classes/interfaces inherited from class net.simplace.sim.model.FWSimComponent

net.simplace.sim.model.FWSimComponent.TEST_STATE

Field Summary

Fields inherited from class net.simplace.sim.model.FWSimComponent

iFieldMap, iFrequence, iInputMap, iJexlRule, iMasterComponentGroup, iName, iOrderNumber, isComponentGroup, iSimComponentElement, iSimModel, iVarMap

Constructor Summary

Constructors

Constructor	Description
Biomass()	Empty constructor used by class.forName()
Biomass(String aName, HashMap<String,net.simplace.sim.util.FWSimVariable<?>> aFieldMap, HashMap<String,String> aInputMap, org.jdom2.Element aSimComponentElement, net.simplace.sim.util.FWSimVarMap aVarMap, int aOrderNumber)

Method Summary

Modifier and Type	Method	Description
protected net.simplace.sim.model.FWSimComponent	clone(net.simplace.sim.util.FWSimVarMap aVarMap)	creates a clone from this SimComponent for use in other threads
HashMap<String,net.simplace.sim.util.FWSimVariable<?>>	createVariables()	Create the FWSimVariables as interface for this SimComponent
HashMap<String,net.simplace.sim.util.FWSimVariable<?>>	fillTestVariables(int aParamIndex, net.simplace.sim.model.FWSimComponent.TEST_STATE aDefineOrCheck)	called for single component test to check the components algorithm.
protected void	init()	initializes the fields by getting input and output FWSimVariables from VarMap
protected void	initValues()
protected void	process()	process the algorithm and write the results back to VarMap
protected void	resetValues()

Methods inherited from class net.simplace.sim.model.FWSimComponent

addVariable, bind, checkCondition, createSimComponent, createSimComponent, createSimComponent, createSimComponent, doProcess, getConstantVariables, getContentType, getCreateFormXML, getDescription, getEditFormXML, getFieldMap, getFrequence, getFrequenceRuleScript, getInputs, getInputVariables, getMasterComponentGroup, getName, getOrderNumber, getOutputVariables, getVariable, getVariableField, getVarMap, initialize, isConditionCheck, isVariableAvailable, performLinks, performLinks, readInputs, removeVariable, reset, runComponentTest, setVariablesDefault, toComponentLinkingXML, toDocXML, toGroupXML, toOutputDefinitionXML, toResourcesDataXML, toResourcesDefinitionXML, toString, toXML, writeVarInfos

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Constructor Details

Biomass

public Biomass(String aName,
 HashMap<String,net.simplace.sim.util.FWSimVariable<?>> aFieldMap,
 HashMap<String,String> aInputMap,
 org.jdom2.Element aSimComponentElement,
 net.simplace.sim.util.FWSimVarMap aVarMap,
 int aOrderNumber)

Parameters:

aName -

aFieldMap -

aInputMap -

aSimComponentElement -

aVarMap -

aOrderNumber -

Biomass

public Biomass()

Empty constructor used by class.forName()

Method Details

createVariables

public HashMap<String,net.simplace.sim.util.FWSimVariable<?>> createVariables()

Create the FWSimVariables as interface for this SimComponent

Specified by:

createVariables in interface net.simplace.sim.util.FWSimFieldContainer

Specified by:

createVariables in class net.simplace.sim.model.FWSimComponent

See Also:

• FWSimComponent.createVariables()

init

protected void init()

initializes the fields by getting input and output FWSimVariables from VarMap

Specified by:

init in class net.simplace.sim.model.FWSimComponent

See Also:

• FWSimComponent.init()

initValues

protected void initValues()

resetValues

protected void resetValues()

process

protected void process()

process the algorithm and write the results back to VarMap

Specified by:

process in class net.simplace.sim.model.FWSimComponent

See Also:

• FWSimComponent.process()

fillTestVariables

public HashMap<String,net.simplace.sim.util.FWSimVariable<?>> fillTestVariables(int aParamIndex,
 net.simplace.sim.model.FWSimComponent.TEST_STATE aDefineOrCheck)

called for single component test to check the components algorithm.

Specified by:

fillTestVariables in class net.simplace.sim.model.FWSimComponent

See Also:

• net.simplace.sim.util.FWSimFieldContainer#fillTestVariables(int aParamIndex, TEST_STATE aDefineOrCheck)

clone

protected net.simplace.sim.model.FWSimComponent clone(net.simplace.sim.util.FWSimVarMap aVarMap)

creates a clone from this SimComponent for use in other threads

Specified by:

clone in class net.simplace.sim.model.FWSimComponent

See Also:

• FWSimComponent.clone(net.simplace.sim.util.FWSimVarMap)