Commit 27852edb authored by jouke's avatar jouke
Browse files

Updates input files to get a better straightRoot example with closer 

agreement between the three potassiumuptake models, and to get soil
impedance to work with drought
parent 3e3c8ecf

OpenSimRoot/InputFiles/environments/pots/atmosphere.xml

+0 −3
Original line number Diff line number Diff line
@@ -5,9 +5,6 @@ 
			<SimulaConstant name="irradiation"  unit="uMol/cm2/day"> 

					2944

			</SimulaConstant>

			<SimulaConstant name="PAR/RDD"  unit="100%" >

					1. 

			</SimulaConstant>

			<SimulaTable name_column2="precipitation" name_column1="time" unit_column1="day" unit_column2="cm/day"> 

				0 0. 80 0.

			</SimulaTable>

OpenSimRoot/InputFiles/plantParameters/straightRoot/plantTemplate.IncludePotassiumBC.xml

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

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

<!--

Copyright © 2016, The Pennsylvania State University

All rights reserved.



Copyright © 2016 Forschungszentrum Jülich GmbH

All rights reserved.



Redistribution and use in source and binary forms, with or without modification, are permitted under the GNU General Public License v3 and provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.



Disclaimer

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.



You should have received the GNU GENERAL PUBLIC LICENSE v3 with this file in license.txt but can also be found at http://www.gnu.org/licenses/gpl-3.0.en.html



 -->

<SimulationModelIncludeFile

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

	 xsi:noNamespaceSchemaLocation="https://rootmodels.gitlab.io/opensimroot/XML/SimulaXMLSchema.xsd">
@@ -117,7 +98,7 @@ You should have received the GNU GENERAL PUBLIC LICENSE v3 with this file in lic 
				name="rootSegmentNutrientUptakeBCExp"

				unit="uMol"

				integrationFunction="BarberCushmanSolver"

				function="barber_cushman_1981_nutrient_uptake_explicit" />

				function="dummyClass" />

		</SimulaDirective>

	</SimulaDirective>

</SimulationModelIncludeFile>
 
 No newline at end of file

OpenSimRoot/InputFiles/plantParameters/straightRoot/simulationControlParameters.xml

+2 −2
Original line number Diff line number Diff line
@@ -36,10 +36,10 @@ You should have received the GNU GENERAL PUBLIC LICENSE v3 with this file in lic 
		<!--TODO current timestepping module for simulapoint does not control errors correctly - rootlength is not what is should be-->

			<SimulaConstant

				name="defaultSpatialIntegrationLength"

				unit="cm">0.1</SimulaConstant>

				unit="cm">0.05</SimulaConstant>

			<SimulaConstant

				name="maxTimeBetweenRootNodes"

				unit="cm">0.2</SimulaConstant>

				unit="cm">0.1</SimulaConstant>

		</SimulaBase>

		<SimulaBase name="outputParameters">

			<SimulaBase name="defaults">

OpenSimRoot/InputFiles/plantParameters/straightRoot/straightRoot.xml

+15 −32
Original line number Diff line number Diff line 
<?xml version="1.0" encoding="UTF-8"?>

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

<!--

Copyright © 2016, The Pennsylvania State University

All rights reserved.



Copyright © 2016 Forschungszentrum Jülich GmbH

All rights reserved.



Redistribution and use in source and binary forms, with or without modification, are permitted under the GNU General Public License v3 and provided that the following conditions are met:

1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

2. Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

3. Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.



Disclaimer

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.



You should have received the GNU GENERAL PUBLIC LICENSE v3 with this file in license.txt but can also be found at http://www.gnu.org/licenses/gpl-3.0.en.html



 -->

<SimulationModelIncludeFile xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="../../../scripts/XML/SimulaXMLSchema.xsd">

<SimulationModelIncludeFile

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

	xsi:noNamespaceSchemaLocation="https://rootmodels.gitlab.io/opensimroot/XML/SimulaXMLSchema.xsd">

	<SimulaBase name="straightRoot">

		<SimulaBase name="resources"></SimulaBase>

		<SimulaBase name="shoot">
@@ -33,7 +16,7 @@ You should have received the GNU GENERAL PUBLIC LICENSE v3 with this file in lic 
			</SimulaConstant>

			<SimulaTable

				name_column1="time"

				name_column2="specificLeafArea"

				name_column2="leafAreaRatio"

				unit_column1="day"

				unit_column2="g/cm2"

				> 0 0.0015 24 0.0025 40 0.0030 60 0.0030
@@ -98,19 +81,19 @@ You should have received the GNU GENERAL PUBLIC LICENSE v3 with this file in lic 
				unit="cm"

				type="coordinate"

				distribution="uniform"

				minimum="-0.00005"

				maximum="0.00005" />

				minimum="-0.000005"

				maximum="0.000005" />

			<SimulaStochastic

				name="gravitropism.v2"

				unit="cm"

				type="coordinate"

				distribution="uniform"

				minimum="+0.4"

				maximum="+0.5" />

				minimum="+0.8"

				maximum="+0.9" />

			<SimulaBase name="potassium">

				<SimulaConstant

					name="Imax"

					unit="uMol/cm2/day">2.592</SimulaConstant>

					unit="uMol/cm2/day">0.5</SimulaConstant>

				<SimulaConstant

					name="Km"

					unit="uMol/ml"> 14e-3</SimulaConstant>
@@ -183,19 +166,19 @@ You should have received the GNU GENERAL PUBLIC LICENSE v3 with this file in lic 
				unit="cm"

				type="coordinate"

				distribution="uniform"

				minimum="-0.005"

				maximum="0.005" />

				minimum="-0.00005"

				maximum="0.00005" />

			<SimulaStochastic

				name="gravitropism.v2"

				unit="cm"

				type="coordinate"

				distribution="uniform"

				minimum="-0.15"

				maximum="-0.05" />

				minimum="-0.9"

				maximum="-0.8" />

			<SimulaBase name="potassium">

				<SimulaConstant

					name="Imax"

					unit="uMol/cm2/day">2.592</SimulaConstant>

					unit="uMol/cm2/day">0.1</SimulaConstant>

				<SimulaConstant

					name="Km"

					unit="uMol/ml"> 14e-3</SimulaConstant>
@@ -261,7 +244,7 @@ You should have received the GNU GENERAL PUBLIC LICENSE v3 with this file in lic 
			<SimulaBase name="potassium">

				<SimulaConstant

					name="Imax"

					unit="uMol/cm2/day">2.592</SimulaConstant>

					unit="uMol/cm2/day">0.1</SimulaConstant>

				<SimulaConstant

					name="Km"

					unit="uMol/ml"> 14e-3</SimulaConstant>

OpenSimRoot/InputFiles/runStraightRoot.xml

+7 −3
Original line number Diff line number Diff line 
<?xml version="1.0" encoding="UTF-8"?>

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

	xsi:noNamespaceSchemaLocation="https://rootmodels.gitlab.io/opensimroot/XML/SimulaXMLSchema.xsd"

    defaultStartingTimeStep="0.2"

	synchronizationTimeStep="0.2" 

	defaultMaximumTimeStep="0.2"

    defaultStartingTimeStep="0.01"

	synchronizationTimeStep="0.05" 

	defaultMaximumTimeStep="0.05"

	defaultMinimumTimeStep="0.0001"

>
@@ -48,6 +48,10 @@ 
	<!--SimulaIncludeFile fileName="environments/Rocksprings/Rocksprings-bean.xml" 

		/ -->

	<SimulaIncludeFile fileName="environments/pots/pot.xml" />

	<!--  point sink here is sensitive to resolution -->

    <SimulaDirective path="/environment/dimensions">

      <SimulaConstant name="resolution" type="coordinate" replacesPreviousDeclaration="true"> 0.1 0.1 0.1 </SimulaConstant>

    </SimulaDirective>



	<SimulaBase name="rootTypeParameters">

		<SimulaIncludeFile fileName="plantParameters/straightRoot/straightRoot.xml" />