Package net.simplace.sim.components.soil.ampsom

Class AMPSom

java.lang.Object

net.simplace.sim.model.FWSimComponent

net.simplace.sim.components.soil.ampsom.AMPSom

All Implemented Interfaces:

net.simplace.sim.util.FWSimFieldContainer

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

A measureable pool soil organic carbon and nitrogen model

The model is described in the paper of Tougma, 2025 - see references.

In order to couple the SimComponent with other SimComponents, the use of AMPSomAuxiliary might be helpful.

Notice regarding numerics: The model is defined by ordinary differential equations but the SimComponent interacts only on daily steps with other SimComponents. Therefore the SimComponent uses internally a time step of 1 and explicit Runge-Kutta method with 4 substeps (rk4).

References

Tougma, I. A. et al, AMPSOM: A measureable pool soil organic carbon and nitrogen model for arable cropping systems, Environmental Modeling & Software, 2025, doi:doi.org/10.1016/j.envsoft.2024.106291

Author:

Gunther Krauss, Inès Tougma

Component Variables

Content Type	Name	Description	Data Type	Unit	Min Value	Max Value	Default Value
constant	cBulkDensity	Each layer bulk density	DOUBLEARRAY	g/cm3	-	-	-
constant	cC12Co2Initial	The 12C amount of the CO2 produiced by microbes	DOUBLEARRAY	g/m2	-	-	-
constant	cC12DomInitial	The 12C amount of the DOM pool	DOUBLEARRAY	g/m2	-	-	-
constant	cC12MaomDomInitial	The 12C amount of the mineral-associated organic matter coming from DOM adsorption	DOUBLEARRAY	g/m2	-	-	-
constant	cC12MaomNecromassInitial	The 12C amount of the mineral-associated organic matter coming from necromass adsorption	DOUBLEARRAY	g/m2	-	-	-
constant	cC12MicrobesInitial	The 12C amount of the microbial pool	DOUBLEARRAY	g/m2	-	-	-
constant	cC12NecromassInitial	The 12C amount of the necromass pool	DOUBLEARRAY	g/m2	-	-	-
constant	cC12PomInitial	The 12C amount of the POM pool	DOUBLEARRAY	g/m2	-	-	-
constant	cC14Co2Initial	The 14C amount of the CO2 produiced by microbes	DOUBLEARRAY	g/m2	-	-	-
constant	cC14DomInitial	The 14C amount of the DOM dool	DOUBLEARRAY	g/m2	-	-	-
constant	cC14MaomDomInitial	The 14C amount of the mineral-associated organic matter coming from DOM adsorption	DOUBLEARRAY	g/m2	-	-	-
constant	cC14MaomNecromassInitial	The 14C amount of the mineral-associated organic matter coming from necromass adsorption	DOUBLEARRAY	g/m2	-	-	-
constant	cC14MicrobesInitial	The 14C amount of the microbial pool	DOUBLEARRAY	g/m2	-	-	-
constant	cC14NecromassInitial	The 14C amount of the necromass pool	DOUBLEARRAY	g/m2	-	-	-
constant	cC14PomInitial	The 14C amount of the POM pool	DOUBLEARRAY	g/m2	-	-	-
constant	cCN12FreeMicrob	-	DOUBLE		-	-	8.0
constant	cClayPercentage	percent of clay in each layer	DOUBLEARRAY	%	-	-	-
constant	cCue	Microbes' carbon use efficiency	DOUBLE		-	-	0.4
constant	cD13CAtmosphere	Ratio of 12C over 13C in athmospheric CO2	DOUBLE		-	-	-8.0
constant	cD13CBgVeg	Ratio of 12C over 13C in below-ground vegetation	DOUBLE		-	-	-26.5
constant	cD13CRhizodeposits	Ratio of 12C over 13C in rhizodeposition	DOUBLE		-	-	-26.5
constant	cDb0	-	DOUBLE		-	-	3.14E-8
constant	cDbEFoldDepth	-	DOUBLE		-	-	0.147
constant	cExudationDist	-	DOUBLE		-	-	2.0
constant	cExudationK	-	DOUBLE		-	-	1.5
constant	cFineRootBeta	-	DOUBLE		-	-	0.8932318
constant	cKAdsDom	Affinity of minerals for DOC	DOUBLE	g/m3	-	-	0.08654371
constant	cKAdsNecro	Affinity of Minerals for necromass C	DOUBLE	g/m3	0.02	20.0	2.0
constant	cKDesDom	Constant parameter for MAOM-DOC desorption	DOUBLE	d-1	1.0E-8	1.0E-5	1.0E-7
constant	cKDesNecro	Constant parameter for necromass desorption	DOUBLE	d-1	2.0E-8	2.0E-5	2.0E-7
constant	cKDom	Affinity of microbes (enzymes) for dissolved organic carbon (DOC) as a ratio of microbes carbon content over DOC	DOUBLE	g/m3	0.002	0.2	0.02
constant	cKMic	Carrying capacity of microbes as percentage of total C	DOUBLE	%	-	-	0.05
constant	cKMicDom	-	DOUBLE		-	-	0.864
constant	cKNecro	Affinity of microbes for necromass C depolymerisation	DOUBLE	g/m3	0.04	40.0	4.0
constant	cKPom	Affinity of microbes (enzymes) for particulate organic carbon (POC)as a ratio of microbes carbon content over POC	DOUBLE		0.001	0.1	0.01
constant	cKSWC	moisture constant reflecting the impact of water content on soil-adsorbed organic carbon (SOC) desorption	DOUBLEARRAY		-	-	-
constant	cLitterInfluencedDepth	-	DOUBLE	m	-	-	0.4
constant	cNDomInitial	The N amount of the DOM pool	DOUBLEARRAY	g/m2	-	-	-
constant	cNMaomDomInitial	The N amount of the mineral-associated organic matter coming from DOM adsorption	DOUBLEARRAY	g/m2	-	-	-
constant	cNMaomNecromassInitial	The N amount of the mineral-associated organic matter coming from necromass adsorption	DOUBLEARRAY	g/m2	-	-	-
constant	cNMicrobesC	Microbes' C/N ratio	DOUBLE		-	-	8.0
constant	cNMicrobesInitial	The N amount of the microbial pool	DOUBLEARRAY	g/m2	-	-	-
constant	cNMinInitial	The mineral nitrogen	DOUBLEARRAY	g/m2	-	-	-
constant	cNNecromassInitial	The N amount of the necromass pool	DOUBLEARRAY	g/m2	-	-	-
constant	cNPomInitial	The N amount of the POM pool	DOUBLEARRAY	g/m2	-	-	-
constant	cNs	A saturation exponent reflecting the effects of pore connectivity on dissolved organic carbon (DOC) diffusion	DOUBLEARRAY		-	-	-
constant	cNue	Microbes' nitrogen use efficiency	DOUBLE		-	-	0.9
constant	cOptSWC	The optimal Soil Water Content	DOUBLEARRAY	%	-	-	-
constant	cPorosity	The soil porosity	DOUBLEARRAY		-	-	-
constant	cSiltPercentage	percent of silt in each layer	DOUBLEARRAY	%	-	-	-
constant	cSoilLayerDepth	Bottom depth of each soil layer	DOUBLEARRAY	m	-	-	-
constant	cSurfInitial	-	DOUBLEARRAY		-	-	-
constant	cVAdsDom	Maximum fractions of DOC that can be adsorbed per day	DOUBLE	d-1	0.05	0.5	0.1
constant	cVAdsNecro	Maximum fractions of necromass C that can be adsorbed per day	DOUBLE	d-1	0.09	0.6	0.2
constant	cVDom	Maximum fraction of dissolved organic matter (DOC) that can be up taken by microbes per day	DOUBLE	d-1	0.05	0.5	0.1
constant	cVNecro	Maximum fractions of necromass C that can be depolymerized per day	DOUBLE	d-1	0.05	0.5	0.1
constant	cVPom	Maximum fractions of POC that can be depolymerized per day	DOUBLE	d-1	0.05	0.5	0.1
input	iC12DomFlow	Vertical movement of dissolved C12	DOUBLEARRAY	g/(m2 d)	-	-	-
input	iC14DomFlow	Vertical movement of dissolved C14	DOUBLEARRAY	g/(m2 d)	-	-	-
input	iCDomRateFromLitter	C from litter that enters DOM pools in upper layers	DOUBLE	g/(m2 d)	-	-	0.0
input	iCPomRateFromLitter	C from litter that enters POM pools in upper layers	DOUBLE	g/(m2 d)	-	-	0.0
input	iD14Atmosphere	-	DOUBLE		-	-	-
input	iFineRootLength	fine root length	DOUBLE	metre	-	-	5.4
input	iFineRootLengthPerLayer	fine root length per layer	DOUBLEARRAY	metre	-	-	-
input	iInputBelowGroundC	Dead roots C	DOUBLEARRAY	g/m2	-	-	-
input	iInputBelowGroundN	Dead roots N	DOUBLEARRAY	g/m2	-	-	-
input	iInputRhizodepositionC	Rhizodeposits C	DOUBLEARRAY	g/m2	-	-	-
input	iInputRhizodepositionN	Rhizodeposits N	DOUBLEARRAY	g/m2	-	-	-
input	iNDomFlow	Vertical movement of dissolved organic N	DOUBLEARRAY	g/(m2 d)	-	-	-
input	iNDomRateFromLitter	N from litter that enters DOM pools in upper layers	DOUBLE	g/(m2 d)	-	-	0.0
input	iNMinExternalRate	-	DOUBLEARRAY	g/(m2 d)	-	-	-
input	iNPomRateFromLitter	N from litter that enters POM pools in upper layers	DOUBLE	g/(m2 d)	-	-	0.0
input	iSWC	The average daily Soil Water Content (SWC)	DOUBLEARRAY	%	-	-	-
input	iTemp	The average daily soil temperature	DOUBLEARRAY	°C	-	-	-
state	sC12Co2	The 12C amount of the CO2 produiced by microbes	DOUBLEARRAY	g/m2	-	-	-
state	sC12Dom	The 12C amount of the DOM pool	DOUBLEARRAY	g/m2	-	-	-
state	sC12MaomDom	The 12C amount of the mineral-associated organic matter coming from DOM adsorption	DOUBLEARRAY	g/m2	-	-	-
state	sC12MaomNecromass	The 12C amount of the mineral-associated organic matter coming from necromass adsorption	DOUBLEARRAY	g/m2	-	-	-
state	sC12Microbes	The 12C amount of the microbial pool	DOUBLEARRAY	g/m2	-	-	-
state	sC12Necromass	The 12C amount of the necromass pool	DOUBLEARRAY	g/m2	-	-	-
state	sC12Pom	The 12C amount of the POM pool	DOUBLEARRAY	g/m2	-	-	-
state	sC14Co2	The 14C amount of the CO2 produiced by microbes	DOUBLEARRAY	g/m2	-	-	-
state	sC14Dom	The 14C amount of the DOM dool	DOUBLEARRAY	g/m2	-	-	-
state	sC14MaomDom	The 14C amount of the mineral-associated organic matter coming from DOM adsorption	DOUBLEARRAY	g/m2	-	-	-
state	sC14MaomNecromass	The 14C amount of the mineral-associated organic matter coming from necromass adsorption	DOUBLEARRAY	g/m2	-	-	-
state	sC14Microbes	The 14C amount of the microbial pool	DOUBLEARRAY	g/m2	-	-	-
state	sC14Necromass	The 14C amount of the necromass pool	DOUBLEARRAY	g/m2	-	-	-
state	sC14Pom	The 14C amount of the POM pool	DOUBLEARRAY	g/m2	-	-	-
state	sGrossMineralisation	Gross N mineralisation	DOUBLEARRAY	g/m2	-	-	-
state	sImmobilisation	N immobilisation	DOUBLEARRAY	g/m2	-	-	-
state	sNDom	The N amount of the DOM pool	DOUBLEARRAY	g/m2	-	-	-
state	sNMaomDom	The N amount of the mineral-associated organic matter coming from DOM adsorption	DOUBLEARRAY	g/m2	-	-	-
state	sNMaomNecromass	The N amount of the mineral-associated organic matter coming from necromass adsorption	DOUBLEARRAY	g/m2	-	-	-
state	sNMicrobes	The N amount of the microbial pool	DOUBLEARRAY	g/m2	-	-	-
state	sNMin	The mineral nitrogen	DOUBLEARRAY	g/m2	-	-	-
state	sNNecromass	The N amount of the necromass pool	DOUBLEARRAY	g/m2	-	-	-
state	sNPom	The N amount of the POM pool	DOUBLEARRAY	g/m2	-	-	-
state	sNetMineralisation	Net N mineralisation (gross mineralisation - immobilisation)	DOUBLEARRAY	g/m2	-	-	-
state	sSurf	-	DOUBLEARRAY		-	-	-
rate	rC12Co2Rate	The variation per day of the 12C amount of the CO2 produiced by microbes	DOUBLEARRAY	g/(m2 d)	-	-	-
rate	rC12DomRate	The variation per day of the 12C amount of the DOM dool	DOUBLEARRAY	g/(m2 d)	-	-	-
rate	rC12MaomDomRate	The variation per day of the 12C amount of the mineral-associated organic matter coming from DOM adsorption	DOUBLEARRAY	g/(m2 d)	-	-	-
rate	rC12MaomNecromassRate	The variation per day of the 12C amount of the mineral-associated organic matter coming from necromass adsorption	DOUBLEARRAY	g/(m2 d)	-	-	-
rate	rC12MicrobesRate	The variation per day of the 12C amount of the microbial pool	DOUBLEARRAY	g/(m2 d)	-	-	-
rate	rC12NecromassRate	The variation per day of the 12C amount of the necromass pool	DOUBLEARRAY	g/(m2 d)	-	-	-
rate	rC12PomRate	The variation per day of the 12C amount of the POM pool	DOUBLEARRAY	g/(m2 d)	-	-	-
rate	rC14Co2Rate	The variation per day of the 14C amount of the CO2 produiced by microbes	DOUBLEARRAY	g/(m2 d)	-	-	-
rate	rC14DomRate	The variation per day of the 14C amount of the DOM dool	DOUBLEARRAY	g/(m2 d)	-	-	-
rate	rC14MaomDomRate	The variation per day of the 14C amount of the mineral-associated organic matter coming from DOM adsorption	DOUBLEARRAY	g/(m2 d)	-	-	-
rate	rC14MaomNecromassRate	The variation per day of the 14C amount of the mineral-associated organic matter coming from necromass adsorption	DOUBLEARRAY	g/(m2 d)	-	-	-
rate	rC14MicrobesRate	The variation per day of the 14C amount of the microbial pool	DOUBLEARRAY	g/(m2 d)	-	-	-
rate	rC14NecromassRate	The variation per day of the 14C amount of the necromass pool	DOUBLEARRAY	g/(m2 d)	-	-	-
rate	rC14PomRate	The variation per day of the 14C amount of the POM pool	DOUBLEARRAY	g/(m2 d)	-	-	-
rate	rGrossMineralisationRate	Gross N mineralisation per day	DOUBLEARRAY	g/(m2 d)	-	-	-
rate	rImmobilisationRate	N immobilisation per day	DOUBLEARRAY	g/(m2 d)	-	-	-
rate	rNDomRate	The variation per day of the N amount of the DOM dool	DOUBLEARRAY	g/(m2 d)	-	-	-
rate	rNMaomDomRate	The variation per day of the N amount of the mineral-associated organic matter coming from DOM adsorption	DOUBLEARRAY	g/(m2 d)	-	-	-
rate	rNMaomNecromassRate	The variation per day of the N amount of the mineral-associated organic matter coming from necromass adsorption	DOUBLEARRAY	g/(m2 d)	-	-	-
rate	rNMicrobesRate	The variation per day of the N amount of the microbial pool	DOUBLEARRAY	g/(m2 d)	-	-	-
rate	rNMinRate	The mineral nitrogen change per day	DOUBLEARRAY	g/(m2 d)	-	-	-
rate	rNNecromassRate	The variation per day of the N amount of the Necromass pool	DOUBLEARRAY	g/(m2 d)	-	-	-
rate	rNPomRate	The variation per day of the N amount of the POM pool	DOUBLEARRAY	g/(m2 d)	-	-	-
rate	rNetMineralisationRate	Net N mineralisation per day (gross mineralisation - immobilisation)	DOUBLEARRAY	g/(m2 d)	-	-	-
rate	rSurfRate	-	DOUBLEARRAY		-	-	-
out	DomCN	The C/N ratio of the DOM pool	DOUBLEARRAY	1	-	-	-
out	MaomDomCN	The C/N ratio of the mineral-associated organic matter coming from DOM adsorption	DOUBLEARRAY	1	-	-	-
out	MaomNecromassCN	The C/N ratio of the mineral-associated organic matter coming from necromass adsorption	DOUBLEARRAY	1	-	-	-
out	MicrobesCN	The C/N ratio of the microbial pool	DOUBLEARRAY	1	-	-	-
out	NecromassCN	The C/N ratio of the necromass pool	DOUBLEARRAY	1	-	-	-
out	PomCN	The C/N ratio of the POM pool	DOUBLEARRAY	1	-	-	-
out	RhizosphereVolumeFraction	The fraction of soil influenced by the rhizosphere, Calculted following Finzi et al. (2018)	DOUBLEARRAY	1	-	-	-
out	SoilMassArray	The mass of soil in every layer, it is calculated in the model	DOUBLEARRAY	kg	-	-	-

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
AMPSom()	Empty constructor used by class.forName()
AMPSom(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)	Constructor

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()
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()
protected void	process()

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

AMPSom

public AMPSom(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)

Constructor

Parameters:

aName -

aFieldMap -

aInputMap -

aSimComponentElement -

aVarMap -

aOrderNumber -

AMPSom

public AMPSom()

Empty constructor used by class.forName()

Method Details

createVariables

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

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()

Specified by:

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

See Also:

• FWSimComponent.init()

process

protected void process()

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

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)