OpenSimRoot XML Input Parameters Reference

opensimroot-parameters.md

OpenSimRoot XML Input Parameters

A comprehensive listing of all input parameters that can be specified in OpenSimRoot XML configuration files, organized by functional category.

Parameters are specified in .xml files under InputFiles/plantParameters/[Species]/[Variety]/ for plant traits, InputFiles/environments/ for soil/atmosphere, and InputFiles/templates/ for reusable module templates. All are defined using <SimulaBase>, <SimulaTable>, and <SimulaConstant> XML elements.

Total: ~196 unique parameter names across ~20 functional modules.

---

Simulation Control

Parameter	Unit	Description
startTime	day	Simulation start time
endTime	day	Simulation end time
timeInterval	day	Output time interval
SimulaStochastic::numberOfSamples	—	Number of stochastic samples
randomNumberGeneratorSeed	—	RNG seed
defaultSpatialIntegrationLength	cm	Spatial integration step
maxTimeBetweenRootNodes	cm	Max time step for root nodes

Planting & Plant Position

Parameter	Unit	Description
plantType	string	Species/variety identifier
plantingTime	day	Day plant is placed
plantingDepth	cm	Depth of plant placement
plantPosition	coordinate	3D coordinates of plant
numberOfRows	—	Number of rows
numberOfPlantsInTheRow	—	Plants per row
rowSpacing	cm	Between-row spacing
inTheRowSpacing	cm	Within-row spacing
rowDirection	—	Row orientation

Environment Geometry

Parameter	Unit	Description
minCorner	coordinate	Min corner of simulation box
maxCorner	coordinate	Max corner of simulation box
resolution	coordinate	Grid resolution
roundPot	bool	Cylindrical pot?
rotateBox	bool	Rotate simulation box?
rotationAxis	—	Axis of rotation
rotationAngle	degrees	Rotation angle
rotationCenter	coordinate	Rotation center

Soil & Water

Parameter	Unit	Description
bulkDensity	g/cm³	Soil bulk density
profileDepth	cm	Soil profile depth
initialHydraulicHead	cm	Initial water potential
depthOfWaterTable	cm	Groundwater depth (time-dependent)
residualWaterContent	fraction	Wilting point water content
saturatedWaterContent	fraction	Saturation water content
vanGenuchten:alpha	1/cm	VG curve parameter
vanGenuchten:n	—	VG curve parameter
saturatedConductivity	cm/day	Saturated hydraulic conductivity
volumetricWaterContentInBarberCushman	cm³/cm³	Water content for nutrient uptake
volumetricWaterContentAtTheRootSurface	cm³/cm³	Water content near roots
waterPotentialAtTheCollar	cm	Plant water potential at collar
diffusionCoefficient	cm²/day	Nutrient diffusion in soil
longitudinalDispersivity	cm	Longitudinal mixing length
transverseDispersivity	cm	Transverse mixing length
saturatedDiffusionCoefficient	cm²/day	Diffusion at saturation
adsorptionCoefficient	—	Nutrient sorption to soil

Root Hydraulics

Parameter	Unit	Description
axialHydraulicConductivity	cm/day	Along-root water conductance
radialHydraulicConductivity	cm/day	Radial water conductance
xylemWaterPotential	cm	Xylem water potential (time-dependent)
rootSegmentWaterUptake	cm³/day	Water uptake per segment
rootSegmentPotentialWaterUptake	cm³/day	Potential water uptake
rootWaterOutflowRate	cm³/day	Root water release
relativeWaterContentInTopLayer	—	Water availability scaling

Atmosphere & Weather

Parameter	Unit	Description
irradiation	µMol/cm²/day	PAR
PAR/RDD	fraction	PAR-to-total radiation ratio
shortwaveRadiation	MJ/m²/day	Short-wave radiation
netRadiation	MJ/m²/day	Net radiation at crop
netRadiationSoil	MJ/m²/day	Net radiation at soil
atmosphericTransmissionCoefficient	—	Clearness index
albedoCrop	—	Crop reflectance
albedoSoil	—	Soil reflectance
spectralQuality	—	Light wavelength composition
extinctionCoefficient	—	Light extinction in canopy
precipitation	cm/day	Rainfall (time-dependent)
evaporation	cm/day	Evaporation rate (time-dependent)
relativeHumidity	fraction	Air humidity
averageDailyTemperature	°C	Air temperature
windSpeed	m/s	Wind speed
CO2Concentration	ppm	Atmospheric CO₂
O2Concentration	ppm	Atmospheric O₂
latitude	degrees	Geographic latitude
altitude	m	Elevation
startYear	—	Calendar start year
startMonth	—	Calendar start month
startDay	—	Calendar start day
solarRadiationAt1AU	MJ/m²/day	Solar constant
timeOffset	hours	Time zone offset

Root Growth & Morphology

Parameter	Unit	Description
rootType	string	Root type identifier
diameter	cm	Root diameter
density	g/cm³	Root dry matter density
lengthRootTip	cm	Root apical meristem length
lengthRootTipWithoutXylemVessels	cm	Meristem without xylem
numberOfXylemPoles	integer	Xylem poles
growthRate	cm/day	Root growth rate (time-dependent)
secondaryGrowthRate	cm/day	Diameter growth rate (time-dependent)
secondaryGrowthScalingFactor	—	Diameter growth scaling
branchingAngle	degrees	Lateral branching angle
branchingFrequency	roots/cm	Lateral root density
branchingSpatialOffset	cm	Branch initiation spacing
branchEmergenceDelay	day	Time before lateral emerges
gravitropism	—	Gravitropism strength
gravitropism.v2	coordinate	Stochastic gravitropism vector
soilImpedence	—	Impedance response
soilImpedence.v2	coordinate	Stochastic impedance vector
cannotgrowup	bool	Prevent upward growth
regularTopology	integer	Regular lateral spacing

Root Hairs

Parameter	Unit	Description
rootHairLength	cm	Hair length (time-dependent)
rootHairDiameter	cm	Hair diameter
rootHairDensity	#/cm²	Hair density (time-dependent)

Impedance & Stress Response

Parameter	Unit	Description
soilImpedanceFor50PercentGrowthSlowdown	kPa	Impedance at 50% reduction
scalingExponentForRootDiameterIncreaseFromImpedance	—	Diameter response to impedance
soilWaterContentForImpedance	cm³/cm³	Water content affecting impedance
allowBranchesToFormAboveGround	bool	Allow aerial roots
impactBy:phosphorus	table	P stress on growth
impactBy:nitrate	table	N stress on growth
impactBy:potassium	table	K stress on growth
impactBy:water	table	Water stress on growth
impactBy:bulkDensity	table	Impedance stress

Shoot & Leaf Development

Parameter	Unit	Description
leafAreaExpansionRate	cm²/day	Leaf area growth (time-dependent)
specificLeafArea	cm²/g	Leaf area per unit weight
leafWidth	cm	Leaf width
crownDiameter	cm	Crown diameter (time-dependent)
speedOfAging	—	Leaf senescence rate
reduceRespiration	bool	Reduce respiration in senescence
remobilizeNutrients	bool	Nutrient remobilization

Tillers (Grasses)

Parameter	Unit	Description
firstTillerTime	day	First tiller appearance
numberOfTillers	integer	Number of tillers
maxTillerOrder	integer	Max branching order
timeDelayBetweenTillerOrders	day	Time between tiller generations
relativeTillerPositions	—	Spatial arrangement
tillerRootType1 / tillerRootType2 / tillerRootType3	—	Root types per tiller generation
leafAreaExpansionRatePerTiller	cm²/day	Leaf growth per tiller

Photosynthesis

Parameter	Unit	Description
lightUseEfficiency	g/µMol	Carbon gain per photon
maxCarboxylationEfficiencyAt25C	µmol/m²/s	Rubisco Vmax
maxPEPCarboxylationAt25C	µmol/m²/s	PEP carboxylase Vmax
RubiscoCO2MichaelisConstantAt25C	µM	Rubisco Km for CO₂
RubiscoO2MichaelisConstantAt25C	µM	Rubisco Km for O₂
rubiscoSpecificityAt25C	—	CO₂/O₂ specificity
MichaelisPEPAt25C	µM	PEP carboxylase Km
CO2CompensationPointWithoutDayRespirationAt25C	ppm	CO₂ compensation point
maximumElectronTransportRateAt25C	—	Electron transport capacity
bundleSheathConductanceAt25C	—	Bundle sheath conductance
C4Photosynthesis	bool	Use C4 pathway
irradianceCurvatureFactor	—	Light response curvature
BBSlope	—	Ball-Berry stomatal slope

Photosynthesis Temperature Kinetics

Each enzyme parameter above has associated temperature response parameters:

Suffix	Unit	Description
*ActivationEnergy	J/mol	Arrhenius activation energy
*DeactivationEnergy	J/mol	High-temperature deactivation
*EntropyTerm	J/mol/K	Entropy term for temperature response

These apply to: carboxylation, RubiscoCO2Michaelis, RubiscoO2Michaelis, rubiscoSpecificity, maximumElectronTransportRate, PEPCarboxylation, MichaelisPEP, bundleSheathConductance, CO2CompensationPoint, dayRespiration.

Additional photosynthesis parameters:

• fractionOfPSIIActivityInBundleSheath
• electronTransportPartitioningFactor
• dayRespirationMesophyllFraction
• PEPRegeneration

Respiration

Parameter	Unit	Description
relativeRespirationRateLeafs	g/g/day	Leaf respiration
relativeRespirationRateStems	g/g/day	Stem respiration
dayRespirationAt25C	µmol/m²/s	Day respiration reference
rootSegmentRespiration	g/day	Root respiration per segment
relativeRespiration	g/g/day	Mass-based root respiration
relativeRespirationCortex	g/g/day	Cortex respiration
relativeRespirationSteel	g/g/day	Stele respiration

Transpiration

Parameter	Unit	Description
relativePotentialTranspiration	cm³/cm²/day	Potential transpiration
leafInfraredAbsorptance	—	Leaf thermal absorptance
leafAbsorptance	—	Leaf visible absorptance
referenceVapourPressureDeficit	kPa	Reference VPD
residualConductance	mol/m²/s	Non-stomatal conductance

Carbon & Dry Matter

Parameter	Unit	Description
carbonToDryWeightRatio	fraction	C content (~0.41–0.45)
carbonAllocation2RootsFactor	fraction	Allocation to roots (time-dependent)
carbonAllocation2LeafsFactor	fraction	Allocation to leaves (time-dependent)
maxCarbonAllocation2Shoot	fraction	Max shoot allocation
maxCarbonAllocation2SecondaryGrowth	fraction	Max diameter growth allocation
seedMass	g	Initial seed weight
seedReserveDuration	day	Duration of seed reliance
reserveAllocationRate	g/day	Reserve mobilization (time-dependent)
rootGrowthScalingFactor	—	Carbon limitation on root growth
rootSegmentDryWeight	g	Dry weight per root segment
increaseInRGRDuringRecovery	—	Recovery growth multiplier

Nutrient Uptake (Nitrate / Phosphorus / Potassium)

Parameter	Unit	Description
Imax	µMol/cm²/day	Maximum nutrient influx
Km	µM	Michaelis-Menten constant
Cmin	µM	Minimum concentration for uptake
Efflux	µMol/cm²/day	Nutrient efflux rate
initialNutrientUptake	µMol	Initial nutrient in seed
carbonCostOfNitrateUptake	g/µMol	Respiration cost of uptake
relativeRelianceOnBNF	—	Biological N₂ fixation reliance
leafOptimalNutrientConcentration	µMol/g	Target leaf concentration
leafMinimalNutrientConcentration	µMol/g	Critical leaf concentration
stemOptimalNutrientConcentration	µMol/g	Target stem concentration
stemMinimalNutrientConcentration	µMol/g	Critical stem concentration
rootSegmentOptimalNutrientContent	µMol	Target root segment content
rootSegmentMinimalNutrientContent	µMol	Critical root segment content
radiusDepletionZone	cm	Nutrient depletion zone radius
nutrientFluxDensity	µMol/cm²/day	Flux per root surface area

Exudates & Microbes

Parameter	Unit	Description
relativeCarbonCostOfExudation	—	Exudate C cost fraction
CNRatioMicrobes	—	Microbial C:N ratio
assimilationEfficiencyMicrobes	—	Microbial growth efficiency
initialRelativeMineralisationRate	—	Initial C mineralization

Output & Export Control

Parameter	Unit	Description
run	bool	Enable output module
includeShoots	bool	Include shoots in VTU
includeRoots	bool	Include roots in VTU
includeVTUForDepletionZones	bool	Depletion zone output
includePointData	bool	Point-wise data
voxelsize	cm	Voxel size for rasterization
rootDiameterScalingFactor	fraction	Diameter scaling in images
includeBinaryRawImage	bool	Binary image format
includeVTKImage	bool	VTK image format
overlapFunction	string	"additive" or "maximum"
searchingDepth	integer	Data tree search depth
skipTheseVariables	string	Variables to skip in output
lackTime	day	Garbage collection age threshold