Commit 17e17299 authored by jouke's avatar jouke
Browse files

Merge branch 'fixesForManual' of 

git@gitlab.com:rootmodels/OpenSimRoot.git into FixesForFarquhar
parents 51471f70 84009e77

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/Barley/Barke/barley.xml

+10 −10
Original line number Diff line number Diff line
@@ -116,14 +116,14 @@ Scarlett 13.2 14.4 7 
						unit="#">

						13 <!--original value: 6-->

					</SimulaConstant>					

					<!--SimulaConstant name="branchingFrequency" unit="cm">0.0003</SimulaConstant-->

					<!--SimulaConstant name="interBranchingDistance" unit="cm">0.0003</SimulaConstant-->

					<SimulaStochastic

						name="branchingFrequency"

						name="interBranchingDistance"

						unit="cm"

						distribution="uniform"

						minimum="0.001"

						maximum="0.003" />

					<!--SimulaStochastic name="branchingFrequency" unit="cm" distribution="lognormal" mean="0.62" stdev="0.15" minimum="0.1" maximum="2.0" /-->

					<!--SimulaStochastic name="interBranchingDistance" unit="cm" distribution="lognormal" mean="0.62" stdev="0.15" minimum="0.1" maximum="2.0" /-->

					<SimulaConstant

						type="time"

						name="branchingTimeOffset"
@@ -259,9 +259,9 @@ Scarlett 13.2 14.4 7 
				note="for visualization output only">99</SimulaConstant>

			<SimulaBase name="branchList">

				<SimulaBase name="lateral">

					<!--SimulaConstant name="branchingFrequency" unit="cm">0.3</SimulaConstant -->

					<!--SimulaConstant name="interBranchingDistance" unit="cm">0.3</SimulaConstant -->

					<SimulaStochastic

						name="branchingFrequency"

						name="interBranchingDistance"

						unit="cm"

						distribution="lognormal"

						mean="0.62"
@@ -295,9 +295,9 @@ Scarlett 13.2 14.4 7 
				note="for visualization output only">99</SimulaConstant>

			<SimulaBase name="branchList">

				<SimulaBase name="lateral">

					<!--SimulaConstant name="branchingFrequency" unit="cm">0.3</SimulaConstant -->

					<!--SimulaConstant name="interBranchingDistance" unit="cm">0.3</SimulaConstant -->

					<SimulaStochastic

						name="branchingFrequency"

						name="interBranchingDistance"

						unit="cm"

						distribution="lognormal"

						mean="0.62"
@@ -333,7 +333,7 @@ Scarlett 13.2 14.4 7 
				<!-- v.hecht: CKA2013 field experiment (coring data, 48-56 DAS) branching frequency at nodal roots ranged between 2-4 laterals per cm root

				v.hecht: CKA2013 shovelomics, branching frequency ranged between 4.4 - 7.4 laterals per cm (nodal?) root (average 6) or 0.15 - 0.27 cm (average 0.2) between laterals (75 DAS)-->

					<SimulaStochastic

						name="branchingFrequency"

						name="interBranchingDistance"

						unit="cm"

						distribution="lognormal"

						mean="0.62"
@@ -367,7 +367,7 @@ Scarlett 13.2 14.4 7 
			<SimulaBase name="branchList">

				<SimulaBase name="lateral">

					<SimulaStochastic

						name="branchingFrequency"

						name="interBranchingDistance"

						unit="cm"

						distribution="lognormal"

						mean="0.62"
@@ -398,7 +398,7 @@ Scarlett 13.2 14.4 7 
			<SimulaBase name="branchList">

				<SimulaBase name="finelateral">

					<SimulaStochastic

						name="branchingFrequency"

						name="interBranchingDistance"

						unit="cm"

						distribution="lognormal"

						mean="0.5"

OpenSimRoot/InputFiles/plantParameters/Barley/Barke/localNutrientResponses.xml

+3 −3
Original line number Diff line number Diff line
@@ -56,7 +56,7 @@ You should have received the GNU GENERAL PUBLIC LICENSE v3 with this file in lic 
					name_column2="impactBy:nitrate"

					name_column1="localConcentration"> 0 1 2000 1</SimulaTable>

			</SimulaBase>

			<SimulaBase name="impactOn:branchingFrequency">

			<SimulaBase name="impactOn:interBranchingDistance">

		<!-- fine laterals -->

				<SimulaConstant

					name="aggregationFunction"
@@ -130,7 +130,7 @@ You should have received the GNU GENERAL PUBLIC LICENSE v3 with this file in lic 
					name_column1="localConcentration"> -1 1.5 0 1.5 100 1 2000 1

				</SimulaTable>

			</SimulaBase>

			<SimulaBase name="impactOn:branchingFrequency">

			<SimulaBase name="impactOn:interBranchingDistance">

		<!-- note that branching freq is in cm, so lower numbers, more branches!

		     also note that this will influence the branches that branch from this axis, independent from the class of that branch -->
@@ -207,7 +207,7 @@ if carbon status is good - produce more branches (this would replace the allomet 
					name_column2="impactBy:nitrate"

					name_column1="localConcentration"> 0 1 10000 1</SimulaTable>

			</SimulaBase>

			<SimulaBase name="impactOn:branchingFrequency">

			<SimulaBase name="impactOn:interBranchingDistance">

		<!-- fine laterals -->

				<SimulaConstant

					name="aggregationFunction"

OpenSimRoot/InputFiles/plantParameters/Barley/Barke/stressImpact.xml

+1 −1
Original line number Diff line number Diff line
@@ -192,7 +192,7 @@ You should have received the GNU GENERAL PUBLIC LICENSE v3 with this file in lic 
				1 1  0.2 1 0 0

			</SimulaTable>

		</SimulaBase>

		<SimulaBase name="impactOn:branchingFrequencyMultiplier">

		<SimulaBase name="impactOn:interBranchingDistanceMultiplier">

			<SimulaTable

				name_column2="impactBy:phosphorus"

				name_column1="phosphorus stress factor"> 1 0 0.5 1 0 1

OpenSimRoot/InputFiles/plantParameters/Barley/Scarlett/barley.xml

+10 −10
Original line number Diff line number Diff line
@@ -125,14 +125,14 @@ Scarlett 13.2 14.4 7 
						unit="#">

						13 <!--original value: 6-->

					</SimulaConstant>					

					<!--SimulaConstant name="branchingFrequency" unit="cm">0.0003</SimulaConstant-->

					<!--SimulaConstant name="interBranchingDistance" unit="cm">0.0003</SimulaConstant-->

					<SimulaStochastic

						name="branchingFrequency"

						name="interBranchingDistance"

						unit="cm"

						distribution="uniform"

						minimum="0.001"

						maximum="0.003" />

					<!--SimulaStochastic name="branchingFrequency" unit="cm" distribution="lognormal" mean="0.62" stdev="0.15" minimum="0.1" maximum="2.0" /-->

					<!--SimulaStochastic name="interBranchingDistance" unit="cm" distribution="lognormal" mean="0.62" stdev="0.15" minimum="0.1" maximum="2.0" /-->

					<SimulaConstant

						type="time"

						name="branchingTimeOffset"
@@ -281,13 +281,13 @@ Scarlett 13.2 14.4 7 
				note="for visualization output only">99</SimulaConstant>

			<SimulaBase name="branchList">

				<SimulaBase name="lateral">

					<!--SimulaConstant name="branchingFrequency" unit="cm">0.3</SimulaConstant -->

					<!--SimulaConstant name="interBranchingDistance" unit="cm">0.3</SimulaConstant -->

					<!-- Hecht: PT2: for Sca lateral branching frequency at seminal between 2 and 5.75 laterals per cm of root, 

					measured at root base, 10 cm distance and 20cm distance,

					overall average: 4.384 lat. per cm root

					 -->

					<SimulaStochastic

						name="branchingFrequency"

						name="interBranchingDistance"

						unit="cm"

						distribution="lognormal"

						mean="0.33"
@@ -325,9 +325,9 @@ Scarlett 13.2 14.4 7 
				note="for visualization output only">99</SimulaConstant>

			<SimulaBase name="branchList">

				<SimulaBase name="lateral">

					<!--SimulaConstant name="branchingFrequency" unit="cm">0.3</SimulaConstant -->

					<!--SimulaConstant name="interBranchingDistance" unit="cm">0.3</SimulaConstant -->

					<SimulaStochastic

						name="branchingFrequency"

						name="interBranchingDistance"

						unit="cm"

						distribution="lognormal"

						mean="0.4"
@@ -367,7 +367,7 @@ Scarlett 13.2 14.4 7 
				<!-- v.hecht: CKA2013 field experiment (coring data, 48-56 DAS) branching frequency at nodal roots ranged between 2-4 laterals per cm root

				v.hecht: CKA2013 shovelomics, branching frequency ranged between 4.4 - 7.4 laterals per cm (nodal?) root (average 6) or 0.15 - 0.27 cm (average 0.2) between laterals (75 DAS)-->

					<SimulaStochastic

						name="branchingFrequency"

						name="interBranchingDistance"

						unit="cm"

						distribution="lognormal"

						mean="0.4"
@@ -405,7 +405,7 @@ Scarlett 13.2 14.4 7 
			<SimulaBase name="branchList">

				<SimulaBase name="lateral">

					<SimulaStochastic

						name="branchingFrequency"

						name="interBranchingDistance"

						unit="cm"

						distribution="lognormal"

						mean="0.4"
@@ -440,7 +440,7 @@ Scarlett 13.2 14.4 7 
			<SimulaBase name="branchList">

				<SimulaBase name="finelateral">

					<SimulaStochastic

						name="branchingFrequency"

						name="interBranchingDistance"

						unit="cm"

						distribution="lognormal"

						mean="1."