Commit a125a62b authored by jouke's avatar jouke
Browse files

combined templates avoiding duplication.

parent 76f43872

OpenSimRoot/InputFiles/templates/plantTemplate.IncludeNitrate3D.xml

+10 −130
Original line number Diff line number Diff line
@@ -19,12 +19,12 @@ You should have received the GNU GENERAL PUBLIC LICENSE v3 with this file in lic 


 -->

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

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

	<SimulaDirective path="/soil">

		<SimulaBase name="nitrate">

			<SimulaConstant

				name="includeThisNutrientInSWMSSimulation"

				type="bool">true</SimulaConstant>

			

			<!--SimulaConstant name="meshRefinementFactor"

				type="integer">2</SimulaConstant -->

			<SimulaTable
@@ -148,24 +148,11 @@ You should have received the GNU GENERAL PUBLIC LICENSE v3 with this file in lic 
				unit="umol" />

		</SimulaBase>

	</SimulaDirective>

	<SimulaDirective path="/plantTemplate">

		<SimulaBase name="nitrate">

			<SimulaDerivative

				name="plantOptimalNutrientContent"

				unit="uMol"

				function="plantTotal" />

			<SimulaDerivative

				name="plantMinimalNutrientContent"

				unit="uMol"

				function="plantTotal" />

	<SimulaDirective path="/plantTemplate/nitrate">

			<SimulaVariable

				name="plantNutrientUptake"

				unit="uMol"

				function="plantTotal" />

			<SimulaVariable

				name="plantNutrientFixation"

				unit="uMol"

				function="bnf.V1" />

			<SimulaVariable

				name="nutrientStressFactor"

				unit="100%"
@@ -177,51 +164,19 @@ You should have received the GNU GENERAL PUBLIC LICENSE v3 with this file in lic 
				name="rootsBelowD90ForNutrient"

				unit="cm"

				function="rootsBelowD95Solute" />

		</SimulaBase>

	</SimulaDirective>

	<SimulaDirective path="/shootTemplate">

		<SimulaBase name="nitrate">

			<SimulaLink

				name="leafOptimalNutrientConcentration"

				unit="uMol/g" />

			<SimulaDerivative

				name="leafOptimalNutrientContent"

				unit="uMol"

				function="leafOptimalNutrientContent" />

			<SimulaLink

				name="leafMinimalNutrientConcentration"

				unit="uMol/g" />

			<SimulaDerivative

				name="leafMinimalNutrientContent"

				unit="uMol"

				function="leafMinimalNutrientContent" />

	<SimulaDirective path="/shootTemplate/nitrate">

			<SimulaConstant

				name="leafNutrientUptake"

				unit="uMol">0

			</SimulaConstant>

			<SimulaLink

				name="stemOptimalNutrientConcentration"

				unit="uMol/g" />

			<SimulaDerivative

				name="stemOptimalNutrientContent"

				unit="uMol"

				function="stemOptimalNutrientContent" />

			<SimulaLink

				name="stemMinimalNutrientConcentration"

				unit="uMol/g" />

			<SimulaDerivative

				name="stemMinimalNutrientContent"

				unit="uMol"

				function="stemMinimalNutrientContent" />

			<SimulaConstant

				name="stemNutrientUptake"

				unit="uMol">0

			</SimulaConstant>

		</SimulaBase>

	</SimulaDirective>

	<SimulaDirective path="/hypocotylTemplate">

		<SimulaDirective path="growthpoint">

			<SimulaBase name="nitrate">

		<SimulaDirective path="growthpoint/nitrate">

				<SimulaConstant

					name="nutrientFluxDensity"

					unit="uMol/cm"> 0
@@ -229,18 +184,6 @@ You should have received the GNU GENERAL PUBLIC LICENSE v3 with this file in lic 
				<SimulaConstant

					name="rootSegmentNutrientUptake"

					unit="uMol"> 0</SimulaConstant>

				<SimulaLink

					name="optimalNutrientConcentration"

					unit="uMol/g" />

				<SimulaLink

					name="minimalNutrientConcentration"

					unit="uMol/g" />

				<SimulaConstant

					name="rootSegmentOptimalNutrientContent"

					unit="uMol">0</SimulaConstant>

				<SimulaConstant

					name="rootSegmentMinimalNutrientContent"

					unit="uMol">0</SimulaConstant>

				<SimulaLink

					name="Cmin"

					unit="uM" />
@@ -256,25 +199,8 @@ You should have received the GNU GENERAL PUBLIC LICENSE v3 with this file in lic 
					unit_column1="day"

					unit_column2="uMol/cm3"

					function="getValuesFromSWMS" />

			</SimulaBase>

		</SimulaDirective>

		<SimulaBase name="nitrate">

			<SimulaDerivative

				name="rootOptimalNutrientContent"

				unit="uMol"

				function="rootTotal.v2" />

			<SimulaDerivative

				name="rootSystemOptimalNutrientContent"

				unit="uMol"

				function="rootSystemTotal" />

			<SimulaDerivative

				name="rootMinimalNutrientContent"

				unit="uMol"

				function="rootTotal.v2" />

			<SimulaDerivative

				name="rootSystemMinimalNutrientContent"

				unit="uMol"

				function="rootSystemTotal" />

		<SimulaDirective path="nitrate">

			<SimulaVariable

				name="rootNutrientUptake"

				unit="uMol"
@@ -283,11 +209,10 @@ You should have received the GNU GENERAL PUBLIC LICENSE v3 with this file in lic 
				name="rootSystemNutrientUptake"

				unit="uMol"

				function="rootSystemTotal" />

		</SimulaBase>

		</SimulaDirective>

	</SimulaDirective>

	<SimulaDirective path="/siblingRootTemplate">

		<SimulaDirective path="growthpoint">

			<SimulaBase name="nitrate">

		<SimulaDirective path="growthpoint/nitrate">

				<SimulaConstant

					name="nutrientFluxDensity"

					unit="uMol/cm"> 0
@@ -295,18 +220,6 @@ You should have received the GNU GENERAL PUBLIC LICENSE v3 with this file in lic 
				<SimulaConstant

					name="rootSegmentNutrientUptake"

					unit="uMol"> 0</SimulaConstant>

				<SimulaLink

					name="optimalNutrientConcentration"

					unit="uMol/g" />

				<SimulaConstant

					name="rootSegmentOptimalNutrientContent"

					unit="uMol">0</SimulaConstant>

				<SimulaLink

					name="minimalNutrientConcentration"

					unit="uMol/g" />

				<SimulaConstant

					name="rootSegmentMinimalNutrientContent"

					unit="uMol">0</SimulaConstant>

				<SimulaLink

					name="Cmin"

					unit="uM" />
@@ -322,25 +235,8 @@ You should have received the GNU GENERAL PUBLIC LICENSE v3 with this file in lic 
					unit_column1="day"

					unit_column2="uMol/cm3"

					function="getValuesFromSWMS" />

			</SimulaBase>

		</SimulaDirective>

		<SimulaBase name="nitrate">

			<SimulaDerivative

				name="rootOptimalNutrientContent"

				unit="uMol"

				function="rootTotal.v2" />

			<SimulaDerivative

				name="rootSystemOptimalNutrientContent"

				unit="uMol"

				function="rootSystemTotal" />

			<SimulaDerivative

				name="rootMinimalNutrientContent"

				unit="uMol"

				function="rootTotal.v2" />

			<SimulaDerivative

				name="rootSystemMinimalNutrientContent"

				unit="uMol"

				function="rootSystemTotal" />

		<SimulaDirective path="nitrate">

			<SimulaVariable

				name="rootNutrientUptake"

				unit="uMol"
@@ -349,10 +245,9 @@ You should have received the GNU GENERAL PUBLIC LICENSE v3 with this file in lic 
				name="rootSystemNutrientUptake"

				unit="uMol"

				function="rootSystemTotal" />

		</SimulaBase>

		</SimulaDirective>

	<SimulaDirective path="/dataPointTemplate">

		<SimulaBase name="nitrate">

	</SimulaDirective>

	<SimulaDirective path="/dataPointTemplate/nitrate">

			<SimulaVariable

				name="rootSegmentNutrientUptake"

				unit="uMol"
@@ -369,20 +264,6 @@ You should have received the GNU GENERAL PUBLIC LICENSE v3 with this file in lic 
			<SimulaLink

				name="Cmin"

				unit="uM" />

			<SimulaLink

				name="optimalNutrientConcentration"

				unit="uMol/g" />

			<SimulaLink

				name="minimalNutrientConcentration"

				unit="uMol/g" />

			<SimulaDerivative

				name="rootSegmentOptimalNutrientContent"

				unit="uMol"

				function="rootSegmentOptimalNutrientContent" />

			<SimulaDerivative

				name="rootSegmentMinimalNutrientContent"

				unit="uMol"

				function="rootSegmentMinimalNutrientContent" />

			<SimulaTable

				name_column1="time"

				name_column2="nutrientConcentrationAtTheRootSurface"
@@ -390,6 +271,5 @@ You should have received the GNU GENERAL PUBLIC LICENSE v3 with this file in lic 
				unit_column2="uMol/cm3"

				function="getValuesFromSWMS" />

			<!-- 0 1 50 1 </SimulaTable -->

		</SimulaBase>

	</SimulaDirective>

</SimulationModelIncludeFile>

OpenSimRoot/InputFiles/templates/plantTemplate.IncludeNitrateBasic.xml

+0 −63
Original line number Diff line number Diff line
@@ -37,66 +37,33 @@ You should have received the GNU GENERAL PUBLIC LICENSE v3 with this file in lic 
	</SimulaDirective>

	<SimulaDirective path="/shootTemplate">

		<SimulaBase name="nitrate">

			<SimulaLink

				name="leafOptimalNutrientConcentration"

				unit="uMol/g" />

			<SimulaDerivative

				name="leafOptimalNutrientContent"

				unit="uMol"

				function="leafOptimalNutrientContent" />

			<SimulaLink

				name="leafMinimalNutrientConcentration"

				unit="uMol/g" />

			<SimulaDerivative

				name="leafMinimalNutrientContent"

				unit="uMol"

				function="leafMinimalNutrientContent" />

			<SimulaConstant

				name="leafNutrientUptake"

				unit="uMol">0</SimulaConstant>

			<SimulaLink

				name="stemOptimalNutrientConcentration"

				unit="uMol/g" />

			<SimulaDerivative

				name="stemOptimalNutrientContent"

				unit="uMol"

				function="stemOptimalNutrientContent" />

			<SimulaLink

				name="stemMinimalNutrientConcentration"

				unit="uMol/g" />

			<SimulaDerivative

				name="stemMinimalNutrientContent"

				unit="uMol"

				function="stemMinimalNutrientContent" />

			<SimulaConstant

				name="stemNutrientUptake"

				unit="uMol">0</SimulaConstant>

		</SimulaBase>

	</SimulaDirective>

	<SimulaDirective path="/hypocotylTemplate">

		<SimulaDirective path="growthpoint">

			<SimulaBase name="nitrate">

				<SimulaLink

					name="optimalNutrientConcentration"

					unit="uMol/g" />

				<SimulaLink

					name="minimalNutrientConcentration"

					unit="uMol/g" />

				<SimulaConstant

					name="rootSegmentOptimalNutrientContent"

					unit="uMol">0</SimulaConstant>

				<SimulaConstant

					name="rootSegmentMinimalNutrientContent"

					unit="uMol">0</SimulaConstant>

				<SimulaLink

					name="Cmin"

					unit="uM" />

				<SimulaLink

					name="Imax"

					unit="uMol/cm2/day" />

				<SimulaLink

					name="Km"

					unit="uM" />

			</SimulaBase>

		</SimulaDirective>

		<SimulaBase name="nitrate">
@@ -121,27 +88,12 @@ You should have received the GNU GENERAL PUBLIC LICENSE v3 with this file in lic 
	<SimulaDirective path="/siblingRootTemplate">

		<SimulaDirective path="growthpoint">

			<SimulaBase name="nitrate">

				<SimulaLink

					name="optimalNutrientConcentration"

					unit="uMol/g" />

				<SimulaConstant

					name="rootSegmentOptimalNutrientContent"

					unit="uMol">0</SimulaConstant>

				<SimulaLink

					name="minimalNutrientConcentration"

					unit="uMol/g" />

				<SimulaConstant

					name="rootSegmentMinimalNutrientContent"

					unit="uMol">0</SimulaConstant>

				<SimulaLink

					name="Cmin"

					unit="uM" />

				<SimulaLink

					name="Imax"

					unit="uMol/cm2/day" />

				<SimulaLink

					name="Km"

					unit="uM" />

			</SimulaBase>

		</SimulaDirective>

		<SimulaBase name="nitrate">
@@ -165,21 +117,6 @@ You should have received the GNU GENERAL PUBLIC LICENSE v3 with this file in lic 
	</SimulaDirective>

	<SimulaDirective path="/dataPointTemplate">

		<SimulaBase name="nitrate">

			<SimulaLink

				name="Imax"

				unit="uMol/cm2/day" />

			<SimulaLink

				name="Km"

				unit="uM" />

			<SimulaLink

				name="Cmin"

				unit="uM" />

			<SimulaLink

				name="optimalNutrientConcentration"

				unit="uMol/g" />

			<SimulaLink

				name="minimalNutrientConcentration"

				unit="uMol/g" />

			<SimulaDerivative

				name="rootSegmentOptimalNutrientContent"

				unit="uMol"