Commit 86cdd920 authored by jouke's avatar jouke
Browse files

Removing some warnings from the default bean runs.

parent 38da4143

OpenSimRoot/InputFiles/plantParameters/Bean/Carioca/carioca.xml

+1 −2
Original line number Diff line number Diff line
@@ -730,8 +730,7 @@ costs 3–5 kg[C] kg [N] 1 fixed (7–12 mol CO 2 mol N 2 1 ) 
		<SimulaIncludeFile fileName="plantParameters/Bean/Carioca/aerenchyma.xml" />

	<!--SimulaIncludeFile fileName="plantParameters/Bean/Carioca/etiolation.xml"/-->

		<SimulaIncludeFile fileName="plantParameters/Bean/Carioca/respiration.xml" />

		<!-- The exudation parameters for this species lead to a very high fraction of carbon produced being spent on exudation. Because of this, exudation has been disabled by default until new measurements of the parameters are available. Take care when enabling this again. -->

		<!--SimulaIncludeFile fileName="plantParameters/Bean/Carioca/exudates.xml" /-->

		<SimulaIncludeFile fileName="plantParameters/Bean/Carioca/exudates.xml" />

		<SimulaIncludeFile fileName="plantParameters/Bean/Carioca/rootHairs.xml" />

		<SimulaIncludeFile fileName="plantParameters/Bean/Carioca/angles.xml" />

		<SimulaIncludeFile

OpenSimRoot/InputFiles/plantParameters/Bean/Carioca/exudates.xml

+16 −27
Original line number Diff line number Diff line
@@ -22,12 +22,12 @@ You should have received the GNU GENERAL PUBLIC LICENSE v3 with this file in lic 
	<!-- Root Exudation parameters for bean	-->

	

<!-- Nielsen et al 1994 page 164 text & figure 3: 

distance 				nmole C/mm/hour		g/cm/day

distance 				nmole C/mm/hour		g/cm/day	g/cm2/day  

from roottip

tip (mm)				6.65			0.00001915

13-23 					5.25			0.00001511

26-36 					5.9				0.00001699

39-49 					4.73			0.00001362

tip (mm)				6.65			0.00001915      1,71E-06

13-23 					5.25			0.00001511		1,35E-06

26-36 					5.9				0.00001699		1,51E-06

39-49 					4.73			0.00001362		1,21E-06



this results in ~ 0.12 g C/g root/day in the model

this results in a little less than respiration (2/3),
@@ -65,87 +65,76 @@ walker et al 2003: effect of root architecture on root exudates virtually unexpl 
			name_column1="time since creation"

			unit_column1="day"

			name_column2="relativeCarbonCostOfExudation"

			unit_column2="g/cm/day"> 0 0.00001915 1.8 0.00001511 3.1 0.00001699

			4.4 0.00001362 100 0.00001362</SimulaTable>

			unit_column2="g/cm2/day"> 0 1.7e-6 10 1.2e-6 20 0.0 100 0 </SimulaTable>

	</SimulaDirective>

	<SimulaDirective path="basalWhorl1">

		<SimulaTable

			name_column1="time since creation"

			unit_column1="day"

			name_column2="relativeCarbonCostOfExudation"

			unit_column2="g/cm/day"> 0 0.00001915 1.8 0.00001511 3.1 0.00001699

			4.4 0.00001362 100 0.00001362</SimulaTable>

			unit_column2="g/cm2/day">  0 1.7e-6 10 1.2e-6 20 0.0 100 0 </SimulaTable>

	</SimulaDirective>

	<SimulaDirective path="basalWhorl2">

		<SimulaTable

			name_column1="time since creation"

			unit_column1="day"

			name_column2="relativeCarbonCostOfExudation"

			unit_column2="g/cm/day"> 0 0.00001915 1.8 0.00001511 3.1 0.00001699

			4.4 0.00001362 100 0.00001362</SimulaTable>

			unit_column2="g/cm2/day">  0 1.7e-6 10 1.2e-6 20 0.0 100 0 </SimulaTable>

	</SimulaDirective>

	<SimulaDirective path="basalWhorl3">

		<SimulaTable

			name_column1="time since creation"

			unit_column1="day"

			name_column2="relativeCarbonCostOfExudation"

			unit_column2="g/cm/day"> 0 0.00001915 1.8 0.00001511 3.1 0.00001699

			4.4 0.00001362 100 0.00001362</SimulaTable>

			unit_column2="g/cm2/day">  0 1.7e-6 10 1.2e-6 20 0.0 100 0 </SimulaTable>

	</SimulaDirective>

	<SimulaDirective path="hypocotylBornRoots">

		<SimulaTable

			name_column1="time since creation"

			unit_column1="day"

			name_column2="relativeCarbonCostOfExudation"

			unit_column2="g/cm/day"> 0 0.00001915 1.8 0.00001511 3.1 0.00001699

			4.4 0.00001362 100 0.00001362</SimulaTable>

			unit_column2="g/cm2/day">  0 1.7e-6 10 1.2e-6 20 0.0 100 0 </SimulaTable>

	</SimulaDirective>

	<SimulaDirective path="lateralPrimaryRoot">

		<SimulaTable

			name_column1="time since creation"

			unit_column1="day"

			name_column2="relativeCarbonCostOfExudation"

			unit_column2="g/cm/day"> 0 0.00001915 1.8 0.00001511 3.1 0.00001699

			4.4 0.00001362 100 0.00001362</SimulaTable>

			unit_column2="g/cm2/day">  0 1.7e-6 10 1.2e-6 20 0.0 100 0 </SimulaTable>

	</SimulaDirective>

	<SimulaDirective path="lateralPrimaryRootFastGrowing">

		<SimulaTable

			name_column1="time since creation"

			unit_column1="day"

			name_column2="relativeCarbonCostOfExudation"

			unit_column2="g/cm/day"> 0 0.00001915 1.8 0.00001511 3.1 0.00001699

			4.4 0.00001362 100 0.00001362</SimulaTable>

			unit_column2="g/cm2/day">  0 1.7e-6 10 1.2e-6 20 0.0 100 0 </SimulaTable>

	</SimulaDirective>

	<SimulaDirective path="lateralBasalRoots">

		<SimulaTable

			name_column1="time since creation"

			unit_column1="day"

			name_column2="relativeCarbonCostOfExudation"

			unit_column2="g/cm/day"> 0 0.00001915 1.8 0.00001511 3.1 0.00001699

			4.4 0.00001362 100 0.00001362</SimulaTable>

			unit_column2="g/cm2/day">  0 1.7e-6 10 1.2e-6 20 0.0 100 0 </SimulaTable>

	</SimulaDirective>

	<SimulaDirective path="lateralHypocotylBornRoots">

		<SimulaTable

			name_column1="time since creation"

			unit_column1="day"

			name_column2="relativeCarbonCostOfExudation"

			unit_column2="g/cm/day"> 0 0.00001915 1.8 0.00001511 3.1 0.00001699

			4.4 0.00001362 100 0.00001362</SimulaTable>

			unit_column2="g/cm2/day">  0 1.7e-6 10 1.2e-6 20 0.0 100 0 </SimulaTable>

	</SimulaDirective>

	<SimulaDirective path="finelateral">

		<SimulaTable

			name_column1="time since creation"

			unit_column1="day"

			name_column2="relativeCarbonCostOfExudation"

			unit_column2="g/cm/day"> 0 0.00001915 1.8 0.00001511 3.1 0.00001699

			4.4 0.00001362 100 0.00001362</SimulaTable>

			unit_column2="g/cm2/day">  0 1.7e-6 10 1.2e-6 20 0.0 100 0 </SimulaTable>

	</SimulaDirective>

	<SimulaDirective path="finelateralFastGrowing">

		<SimulaTable

			name_column1="time since creation"

			unit_column1="day"

			name_column2="relativeCarbonCostOfExudation"

			unit_column2="g/cm/day"> 0 0.00001915 1.8 0.00001511 3.1 0.00001699

			4.4 0.00001362 100 0.00001362</SimulaTable>

			unit_column2="g/cm2/day">  0 1.7e-6 10 1.2e-6 20 0.0 100 0 </SimulaTable>

	</SimulaDirective>

</SimulationModelIncludeFile>

OpenSimRoot/InputFiles/runBean.xml

+1 −20
Original line number Diff line number Diff line 
<?xml version="1.0" encoding="UTF-8"?>

<!--

	Simulation file for SimRoot version 5. This development version, build July 2007

	Author: Jouke Postma

	Note: 

	

	PLEASE KEEP THIS HEADER UP TO DATE! LIST BELOW WHO YOU ARE, WHEN AND WHAT CHANGES YOU MADE AND WHY. LIST YOUR SOURCE AS MUCH AS POSSIBLE!



	change log: 

	11-july-07 added support for include files. 

	

	

-->

<!--STYLE SHEET SECTION: feel free to attach any stylesheet of your choosing-->

<!--?xml-stylesheet type="text/xsl" href="tree-view2.xsl"?-->





<!--SIMULATION MODEL-->

<SimulationModel

	xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"

	 xsi:noNamespaceSchemaLocation="https://rootmodels.gitlab.io/opensimroot/XML/SimulaXMLSchema.xsd">
@@ -49,9 +32,7 @@ 
	<!--

	If leaving out water and nitrate, enable this to have a rough estimate of carbon cost of nitrate fixation and uptake

	-->

	<!-- 

	SimulaIncludeFile fileName="templates/plantTemplate.IncludeNitrateBasic.xml" /

	-->

	<SimulaIncludeFile fileName="templates/plantTemplate.IncludeNitrateBasic.xml" />

    <!--SimulaIncludeFile fileName="templates/plantTemplate.IncludeWaterModule.xml" />

	<SimulaIncludeFile fileName="templates/plantTemplate.IncludeNitrate3D.xml" />

	<SimulaIncludeFile fileName="templates/plantTemplate.IncludePotassium3D.xml" /-->