Commit b1f74030 authored by jouke's avatar jouke
Browse files

Updated the results of default runs using the new code. 

- overall results look good and are rather similar
- code has fewer warnings related to errors,
- code produces more info warnings
- Barley results are quite different related to new weather etc
- Lupin results dart-85 quite different because of fixed stress response
parent 588c5501

OpenSimRoot/InputFiles/environments/CKA/water.xml

+64 −24
Original line number Diff line number Diff line
@@ -57,6 +57,24 @@ Mediumfine 0.010 0.412 0.0082 1.2179 0.1789 0.5000 4.000 
Fine 0.010 	0.481 0.0198 1.0861 0.0793 3.7124 8.500

Very Fine 	0.010 0.538 0.0168 1.0730 0.0680 0.0001 8.235

Organica 		0.010 0.766 0.0130 1.2039 0.1694 0.4000 8.000





Landl 2019 table 2 data for Campus Klein Altendorf

https://acsess.onlinelibrary.wiley.com/doi/full/10.2136/vzj2018.11.0196





horizont	depth(cm)	sand	silt	clay(%)	BD(g/cm3)	thr	ths	alpha	n	ks

Ap			0–30		7	76	17				1.29		0.041	0.4857	0.0103	1.2767	5.08

E/B			31–40		5	75	20				1.32		0.041	0.4778	0.0056	1.299	1.56

Bt1			41–75		5	68	27				1.42		0.041	0.4502	0.0047	1.2691	1.31

Bt2			76–115		4	67	29				1.52		0.041	0.4223	0.0041	1.2468	1.2

Bw			116–160		6	74	20				1.46		0.041	0.4381	0.005	1.2732	1.62













-->

	<SimulaDirective path="environment/soil">

	<SimulaBase name="water">
@@ -72,53 +90,75 @@ Organica 0.010 0.766 0.0130 1.2039 0.1694 0.4000 8.000 
			name_column2="residualWaterContent"

			name_column1="depth"

			unit_column1="cm"

			unit_column2="100%"> 0 0.067 -300 0.067

			unit_column2="100%"> 0 0.041 -300 0.041

		</SimulaTable>

		<SimulaTable

			name_column2="saturatedWaterContent"

			name_column1="depth"

			unit_column1="cm"

			unit_column2="100%"

			TinterpolationMethod="step">

				<!--Luo L, Lin H, Halleck P. 2008. Quantifying Soil Structure and Preferential Flow in Intact Soil Using X-ray Computed Tomography. Soil Sci Soc Am J 72: 1058-1069.-->

			0 0.460 -15 0.450 -25 0.430 -35 0.390 -65 0.390 -300 0.390

			unit_column2="100%">

-0	0.4857

-15	0.4857

-30	0.4857

-35	0.4778

-45	0.4502

-70	0.4502

-80	0.4223

-110	0.4223

-120	0.4381

-300	0.4381

		</SimulaTable>

		<SimulaTable

			name_column2="vanGenuchten:alpha"

			name_column1="depth"

			unit_column1="cm"

			unit_column2="1/cm">

				<!--see hodnet and tomasella 2002 - rocksprings has a hagerstown silt loam-->

			0 0.02 -300 0.02

0	0.0103

-15	0.0103

-30	0.0103

-35	0.0056

-45	0.0047

-70	0.0047

-80	0.0041

-110	0.0041

-120	0.005

-300	0.005



		</SimulaTable>

		<SimulaTable

			name_column2="vanGenuchten:n"

			name_column1="depth"

			unit_column1="cm"

			unit_column2="noUnit"> 

				<!--see hodnet and tomasella 2002 - rocksprings has a hagerstown silt loam-->

			0 1.41 -300 1.41

0	1.2767

-15	1.2767

-30	1.2767

-35	1.299

-45	1.2691

-70	1.2691

-80	1.2468

-110	1.2468

-120	1.2732

-300	1.2732



		</SimulaTable>

		<SimulaTable

			name_column2="saturatedConductivity"

			name_column1="depth"

			unit_column1="cm"

			unit_column2="cm/day"

			TinterpolationMethod="step">

				<!--Luo L, Lin H, Halleck P. 2008. Quantifying Soil Structure and Preferential Flow in Intact Soil Using X-ray Computed Tomography. Soil Sci Soc Am J 72: 1058-1069.

					  0	74.000

					-15 74.000

					-25 64.800

					-35 50.400

					-65 50.400

					-300 50.400 -->

					<!--These numbers seem high, may rocksprings is more like a sandy clay loam?-->

					<!-- silt loam 0.45*24=10.8 -->

			0 10.8 -300 10.8

			unit_column2="cm/day">

-0	5.08

-15	5.08

-30	5.08

-35	1.56

-45	1.31

-70	1.31

-80	1.2

-110	1.2

-120	1.62

-300	1.62



		</SimulaTable>

		<SimulaConstant

			name="volumetricWaterContentInBarberCushman"

			unit="cm3/cm3">0.3</SimulaConstant>

	</SimulaBase>

	</SimulaDirective>

</SimulationModelIncludeFile>

OpenSimRoot/tests/defaultInputFiles/refOutput/runBarley/tabled_output.tab

+8056 −8137

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OpenSimRoot/tests/defaultInputFiles/refOutput/runBarley/warnings.txt

+21 −53
Original line number Diff line number Diff line 
Simulation took (hours:minutes:seconds): 3:16:58

Simulation took (hours:minutes:seconds): 1:35:31

THE MODEL PUT OUT WARNINGS:

AerodynamicResistance: /plants/canopyHeight not found. Assuming 0.5 m	1x

At 80 days mem usage was 1767 mB.	1x

At 80 days mem usage was 1396 mB.	1x

CarbonCostOfNutrientUptake: cost not simulated for nitrate uptake is not simulated	1x

ConstantRootGrowth: growthRateMultiplier found	4543x

Enabling Probe All Objects for current the model is faster and more accurate if "carbonAllocation2Shoot" and "plantNutrientUptake" is called first. Enable this in parameter section to get rid of this message.	1x

FieldPlanting: adjusting area per plant from 30.000000 to 40.000000	1x

FieldPlanting: setting maxCorner to 5	0	2	1x

FieldPlanting: setting minCorner to -5	-199	-2	1x

GenerateRoot: using root class specific template for hypocotyl	1x

GetValuesFromSWMS::calculate: using a predictor for tables	20603666x

HydraulicConductance: simulating effects of RCS on radial hydraulic conductivity	31482x

HydraulicConductivity:: soilHydraulicConductivityAtTheRootSurface not found. Not considering its influence on radial conductivity	31482x

IntegrationBase:: setting defaultSpatialIntegrationLength to 1.000000.	1x

LeafAreaIndex: using mean leaf area based on box size and the leaf area of all plants.	1x

LightInterception: used conversion factor to get PAR in umol/cm2/day is 1.000000	1x

LightInterception: using /environment/atmosphere/shortwaveRadiation	1x

LocalNutrientResponse: Did not found anything to respond to for'impactOn:branchingFrequency'.	4543x

LocalNutrientResponse: Did not found anything to respond to for'impactOn:gravitropism'.	4540x

LocalNutrientResponse: Did not found anything to respond to for'impactOn:rootPotentialLongitudinalGrowth'.	4518x

MeanLeafAreaIndex: Assuming all plants are planted at t = 0. If this is not the case, add 'plantsPlantedAtDifferentTimes' under 'environment'.	1x

Mesh: creating mesh with dimensions horizontalx,z =11,5, verticaly=200	1x

OpenSimRoot was built on Jul 11 2025 from git version eaba97548f plus uncommitted changes	1x

PotentialLeafArea::leafArea is sum of tillers	1x

ReadXMLfile: Setting default maximum time step to 0.1	1x

ReadXMLfile: Setting default minimum time step to 0.1	1x

ReadXMLfile: Setting default starting time step to 0.1	1x

ReadXMLfile: Setting default synchronization time step to 0.1	1x

HydraulicConductance: simulating effects of RCS on radial hydraulic conductivity	34987x

LocalNutrientResponse: Did not found anything to respond to for'impactOn:gravitropism'.	5692x

LocalNutrientResponse: Did not found anything to respond to for'impactOn:interBranchingDistance'.	5700x

LocalNutrientResponse: Did not found anything to respond to for'impactOn:rootPotentialLongitudinalGrowth'.	5666x

OpenSimRoot was built on Jun  1 2026 from git version 84009e7773 plus uncommitted changes	1x

ReadXMLfile: Setting default maximum time step to 0.2	1x

ReadXMLfile: Setting default minimum time step to 0.2	1x

ReadXMLfile: Setting default starting time step to 0.2	1x

ReadXMLfile: Setting default synchronization time step to 0.2	1x

ReadXMLfile: Setting explicitCoupling to true	1x

ReservesSinkBased: Expiring seed reserves at 28.000000 d.a.g. with 82.483242% of the initial 0.020500g left.	1x

RootBrances: fixing TimeShift error for seminalSteep - check your branching rules. This may also happen if the growth rate of the parent root is increasing over time.	1x

RootBranches:: using branchingFrequencyModifier of the parent growth point.	4174x

RootDiameter: using length - diameter relation. e.g. longer laterals are thicker	4543x

RootGrowthDirection: timeScalingFactor not found. Defaulting to 5.	1x

ReservesSinkBased: Expiring seed reserves at 28.000000 d.a.g. with 15.276595% of the initial 0.020500g left.	1x

RootGrowthDirection:setInitialDirection: not rotating, as the root is not attached	15x

RootRespiration: respiration affected by RCS	62964x

Seeding random number generator with  1575732916.	1x

StomatalResistance: dailyBulkStomatalResistance as sibling of /origin/plants/stomatalResistancenot found, using default value of 100 m/s	1x

RootRespiration: respiration affected by RCS	69974x

SimulaBase::getPath: Found deprecated pathspecificWeight Consider  updating to specificWeightCortex	69974x

SimulaBase::getPath: Found deprecated pathspecificWeight Consider  updating to specificWeigtSteel	34987x

StomatalResistance: dailyBulkStomatalResistance as sibling of /origin/plants/stomatalResistancenot found, using default value of 100 s/m. Consider defining meanStomatalConductance in mol/m2/s.	1x

StressFactor: impactOn:nodalRootBranchingDelay not found in stressImpactFactors for plant type barleyScarlett	1x

StressFactor: impactOn:nodalRootBranchingFrequency not found in stressImpactFactors for plant type barleyScarlett	1x

StressFactor: no impact found for water and stressFactor:impactOn:nodalRootBranchingDelayusing raw impact factor.	1x

StressFactor: no impact found for water and stressFactor:impactOn:nodalRootBranchingFrequencyusing raw impact factor.	1x

StressFactor: impactOn:nodalRootinterBranchingDistance not found in stressImpactFactors for plant type barleyScarlett	1x

TillerFormation: No vertical offset found, placing tiller location at ground surface	2x

TillerFormation: Tiller root type 1 not defined, defaulting to nodalRootsOfTillers or nodalrootsOfTillers.	2x

TillerFormation: Time between tiller orders not set. Defaulting to 5 days.	2x

TillerFormation: number of tillers per order not specified, defaulting to 12	2x

TillerFormation: potentialTimeDelayBetweenTillers not found, using timeDelayBetweenTillers	2x

TimeConversion:: startYear not given. Using 2015	1x

WatFlow: Reducing timestep to limit rate changes in h per dt	28x

WatFlow: Smaller dt suggested as boundary flux and sink > theta	3x

WaterStressFactor: waterStressResponseCurve not found in the shoot parameters, inserting default response.	1x

WaterUptakeDoussanModel: Ignoring node with name growthpoint	4541x

WaterUptakeDoussanModel::build: using same matrix	3242x

Watflow: Using Free drainage bottom boundary.	1x

Watflow:: using potentialEvaporation from/origin/atmosphere/potentialEvaporation	1x

Watflow::Surface area water mesh is 40	1x

Watflow::set_atmosphere: Using interception from atmosphere section	700x

Watflow::updateLists: soilHydraulicConductivityAtTheRootSurface not found	34591x

localNutrientResponse: NOT including response to hydraulicHeadAtRootSurface as impactBy:water wasn't found in impactOn:branchingFrequency	4543x

localNutrientResponse: NOT including response to hydraulicHeadAtRootSurface as impactBy:water wasn't found in impactOn:gravitropism	4540x

localNutrientResponse: NOT including response to hydraulicHeadAtRootSurface as impactBy:water wasn't found in impactOn:rootPotentialLongitudinalGrowth	4518x

localNutrientResponse: including response to hydraulicHeadAtRootSurface	24x

tag2Object: Double declaration found, using last read for /origin/dataPointTemplate/rootDiameter	1x

tag2Object: Double declaration found, using last read for /origin/shootTemplate/leafArea	1x

tag2Object: Double declaration found, using last read for /origin/shootTemplate/potentialLeafArea	1x
 
Watflow: Precipitation exceeds infiltration rate, assuming runoff.	197x

localNutrientResponse: NOT including response to hydraulicHeadAtRootSurface as impactBy:water wasn't found in impactOn:gravitropism	5692x

localNutrientResponse: NOT including response to hydraulicHeadAtRootSurface as impactBy:water wasn't found in impactOn:interBranchingDistance	5700x

localNutrientResponse: NOT including response to hydraulicHeadAtRootSurface as impactBy:water wasn't found in impactOn:rootPotentialLongitudinalGrowth	5666x

OpenSimRoot/tests/defaultInputFiles/refOutput/runBean/tabled_output.tab

+2109 −1986

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OpenSimRoot/tests/defaultInputFiles/refOutput/runBean/warnings.txt

+25 −35
Original line number Diff line number Diff line 
Simulation took (hours:minutes:seconds): 1:1:41

Simulation took (hours:minutes:seconds): 1:4:7

THE MODEL PUT OUT WARNINGS:

At 40 days mem usage was 1680 mB.	1x

BarberCushman: volumetricWaterContentAtTheRootSurface not found, using reference theta	58727x

BarberCushmanExplicit: Peclet criteria not fulfilled. Upwind used in compartment.	46635x

BarberCushmanExplicit: competition effective. (edge depletion == r1)	259664x

BarberCushmanExplicit: retrying with a smaller timestep	11138x

BarberCushmanExplicit: severe competition: k<4, you may want to use smaller delta r for phosphorus	8x

CarbonCostOfBiologicalNitrogenFixation: cost not simulated for nitrogen fixation is not simulated	1x

CarbonCostOfExudates: parameter relativeCarbonCostOfExudation missing in /origin/rootTypeParameters/Bean-Carioca-SimRoot4/basalWhorl1. No exudates simulated.	548x

CarbonCostOfExudates: parameter relativeCarbonCostOfExudation missing in /origin/rootTypeParameters/Bean-Carioca-SimRoot4/basalWhorl2. No exudates simulated.	524x

CarbonCostOfExudates: parameter relativeCarbonCostOfExudation missing in /origin/rootTypeParameters/Bean-Carioca-SimRoot4/finelateral. No exudates simulated.	9585x

CarbonCostOfExudates: parameter relativeCarbonCostOfExudation missing in /origin/rootTypeParameters/Bean-Carioca-SimRoot4/finelateralFastGrowing. No exudates simulated.	2429x

CarbonCostOfExudates: parameter relativeCarbonCostOfExudation missing in /origin/rootTypeParameters/Bean-Carioca-SimRoot4/hypocotyl. No exudates simulated.	13x

CarbonCostOfExudates: parameter relativeCarbonCostOfExudation missing in /origin/rootTypeParameters/Bean-Carioca-SimRoot4/hypocotylBornRoots. No exudates simulated.	315x

CarbonCostOfExudates: parameter relativeCarbonCostOfExudation missing in /origin/rootTypeParameters/Bean-Carioca-SimRoot4/lateralBasalRoots. No exudates simulated.	35281x

CarbonCostOfExudates: parameter relativeCarbonCostOfExudation missing in /origin/rootTypeParameters/Bean-Carioca-SimRoot4/lateralHypocotylBornRoots. No exudates simulated.	2620x

CarbonCostOfExudates: parameter relativeCarbonCostOfExudation missing in /origin/rootTypeParameters/Bean-Carioca-SimRoot4/lateralPrimaryRoot. No exudates simulated.	6838x

CarbonCostOfExudates: parameter relativeCarbonCostOfExudation missing in /origin/rootTypeParameters/Bean-Carioca-SimRoot4/lateralPrimaryRootFastGrowing. No exudates simulated.	598x

CarbonCostOfExudates: parameter relativeCarbonCostOfExudation missing in /origin/rootTypeParameters/Bean-Carioca-SimRoot4/primaryRoot. No exudates simulated.	141x

CarbonCostOfNutrientUptake: cost not simulated for nitrate uptake is not simulated	1x

ConstantRootGrowth: growthRateMultiplier found	9420x

At 40 days mem usage was 1603 mB.	1x

BarberCushman: volumetricWaterContentAtTheRootSurface not found, using reference theta	58557x

BarberCushmanExplicit: Peclet criteria not fulfilled. Upwind used in compartment.	76726x

BarberCushmanExplicit: competition effective. (edge depletion == r1)	300282x

BarberCushmanExplicit: retrying with a smaller timestep	11104x

BarberCushmanExplicit: severe competition: k<4, you may want to use smaller delta r for phosphorus	7x

ConstantRootGrowth: growthRateMultiplier found	9398x

Enabling Probe All Objects for current the model is faster and more accurate if "carbonAllocation2Shoot" and "plantNutrientUptake" is called first. Enable this in parameter section to get rid of this message.	1x

GenerateRoot: using root class specific template for hypocotyl	1x

Input files specify deprecated potentialLeafGrowthRate. Using 'leafArea' instead	1x

Input files specify deprecated stressAdjustedPotentialLeafGrowthRate. Using 'leafArea' instead	1x

IntegrationBase:: setting defaultSpatialIntegrationLength to 1.000000.	1x

LeafArea: using /origin/plants/bean/stressFactor:impactOn:leafAreaExpansionRate as stress factor for /origin/plants/bean/plantPosition/shoot/stressAdjustedPotentialLeafArea	1x

LeafArea: using carbon allocation to compute leafArea	1x

LeafArea: using leafAreaExpansionRate from parameter section to compute leafArea	1x

LeafArea: using leafAreaExpansionRate from parameter section to compute potentialLeafArea	1x

LeafAreaIndex: using mean leaf area based on areaPerPlant.	1x

LeafAreaReductionCoefficient: Scaling leaf area expansion rate because the actual leaf area is smaller than the potential	9640682x

LeafAreaReductionCoefficient: Scaling leaf area expansion rate because the actual leaf area is smaller than the potential	4381935x

LightInterception: used conversion factor to get PAR in umol/cm2/day is 100.000000	1x

LightInterception: using /environment/atmosphere/shortwaveRadiation	1x

OpenSimRoot was built on Jul 11 2025 from git version eaba97548f plus uncommitted changes	1x

PlantCarbonBalance: balance error at +11.00 days: error (%) tot=-0.4652 root=-0.5179 alloc=+0.0563 for bean	1x

PlantCarbonBalance: balance error at +12.00 days: error (%) tot=-0.5104 root=-0.5666 alloc=+0.0595 for bean	1x

PlantCarbonBalance: balance error at +13.00 days: error (%) tot=-0.4876 root=-0.5429 alloc=+0.0583 for bean	1x

PlantCarbonBalance: balance error at +14.00 days: error (%) tot=-0.4626 root=-0.5151 alloc=+0.0555 for bean	1x

OpenSimRoot was built on May  5 2026 from git version 5a7509574f plus uncommitted changes	1x

PlantTotal: Using initial value for plantNutrientUptake from parameter section	1x

ReservesSinkBased: Expiring seed reserves at 25.000000 d.a.g. with 36.441916% of the initial 0.090000g left.	1x

ReservesSinkBased: Expiring seed reserves at 25.000000 d.a.g. with 27.794260% of the initial 0.090000g left.	1x

RootDiameter: no lengthMultiplier2DiameterMultiplier specified for basalWhorl1s of Bean-Carioca-SimRoot4	8x

RootDiameter: no lengthMultiplier2DiameterMultiplier specified for basalWhorl2s of Bean-Carioca-SimRoot4	8x

RootDiameter: no lengthMultiplier2DiameterMultiplier specified for finelateralFastGrowings of Bean-Carioca-SimRoot4	1302x

RootDiameter: no lengthMultiplier2DiameterMultiplier specified for finelaterals of Bean-Carioca-SimRoot4	5124x

RootDiameter: no lengthMultiplier2DiameterMultiplier specified for finelateralFastGrowings of Bean-Carioca-SimRoot4	1276x

RootDiameter: no lengthMultiplier2DiameterMultiplier specified for finelaterals of Bean-Carioca-SimRoot4	5136x

RootDiameter: no lengthMultiplier2DiameterMultiplier specified for hypocotylBornRootss of Bean-Carioca-SimRoot4	20x

RootDiameter: no lengthMultiplier2DiameterMultiplier specified for hypocotyls of Bean-Carioca-SimRoot4	2x

RootDiameter: no lengthMultiplier2DiameterMultiplier specified for lateralBasalRootss of Bean-Carioca-SimRoot4	9848x

RootDiameter: no lengthMultiplier2DiameterMultiplier specified for lateralHypocotylBornRootss of Bean-Carioca-SimRoot4	784x

RootDiameter: no lengthMultiplier2DiameterMultiplier specified for lateralPrimaryRootFastGrowings of Bean-Carioca-SimRoot4	58x

RootDiameter: no lengthMultiplier2DiameterMultiplier specified for lateralHypocotylBornRootss of Bean-Carioca-SimRoot4	758x

RootDiameter: no lengthMultiplier2DiameterMultiplier specified for lateralPrimaryRootFastGrowings of Bean-Carioca-SimRoot4	54x

RootDiameter: no lengthMultiplier2DiameterMultiplier specified for lateralPrimaryRoots of Bean-Carioca-SimRoot4	1684x

RootDiameter: no lengthMultiplier2DiameterMultiplier specified for primaryRoots of Bean-Carioca-SimRoot4	2x

RootDiameter: using length - diameter relation. e.g. longer laterals are thicker	18840x

RootDiameter: using length - diameter relation. e.g. longer laterals are thicker	18796x

RootGrowthDirection: timeScalingFactor not found. Defaulting to 5.	1x

Seeding random number generator with  2145288628.	1x

SimulaTimeDriven, deleting more than two steps	18003x

Seeding random number generator with  -719231600.	1x

SimulaTimeDriven, deleting more than two steps	183x

VTU: root segments with 0 diameter replaced with small diameter	2x

WriteGraph: Can not write graph as the exe is compiled without graph writing capabilities. Please recompile using -DWRITEGRAPH on the g++ commandline.	3x

tag2Object: Double declaration found, using last read for /origin/shootTemplate/leafArea	1x