Switching to interbranching distances instead of branching frequency (508eb892) · Commits · rootmodels / OpenSimRoot

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."

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

+14 −14

Original line number	Diff line number	Diff line
		@@ -129,7 +129,7 @@ You should have received the GNU GENERAL PUBLIC LICENSE v3 with this file in lic
		name_column1="nitrate stress factor"> 1 0 0.5 1 0 1
		</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
		@@ -320,7 +320,7 @@ costs 3–5 kg[C] kg [N] 1 fixed (7–12 mol CO 2 mol N 2 1 )
		<SimulaBase name="hypocotylBornRoots">
		<!--these branch of the stem in the original model. We will just attached them to the top of the primary root-->
		<SimulaConstant
		name="branchingFrequency"
		name="interBranchingDistance"
		unit="cm"> 0.4</SimulaConstant>
		<SimulaConstant
		name="branchingSpatialOffset"
		@@ -344,7 +344,7 @@ costs 3–5 kg[C] kg [N] 1 fixed (7–12 mol CO 2 mol N 2 1 )
		<SimulaBase name="basalWhorl1">
		<!--these branch of the stem in the original model. We will just attached them to the top of the primary root-->
		<SimulaConstant
		name="branchingFrequency"
		name="interBranchingDistance"
		unit="cm"> 0.01
		</SimulaConstant>
		<SimulaConstant
		@@ -381,7 +381,7 @@ costs 3–5 kg[C] kg [N] 1 fixed (7–12 mol CO 2 mol N 2 1 )
		</SimulaBase>
		<SimulaBase name="basalWhorl2">
		<SimulaConstant
		name="branchingFrequency"
		name="interBranchingDistance"
		unit="cm"> 0.5
		</SimulaConstant>
		<SimulaConstant
		@@ -405,7 +405,7 @@ costs 3–5 kg[C] kg [N] 1 fixed (7–12 mol CO 2 mol N 2 1 )
		</SimulaConstant>
		</SimulaBase>
		<!--SimulaBase name="basalWhorl3">
		<SimulaConstant name="branchingFrequency" unit="cm">
		<SimulaConstant name="interBranchingDistance" unit="cm">
		0.5
		</SimulaConstant>
		<SimulaConstant name="branchingSpatialOffset" unit="cm">
		@@ -443,7 +443,7 @@ costs 3–5 kg[C] kg [N] 1 fixed (7–12 mol CO 2 mol N 2 1 )
		1
		</SimulaConstant>
		<SimulaConstant
		name="branchingFrequency"
		name="interBranchingDistance"
		unit="cm">
		<!--original file reads (line 20): 0.5 which equals 2/cm-->
		<!-- note that the model accepts the following units: #/cm, #/day, and the inverse cm and day apart -->
		@@ -470,7 +470,7 @@ costs 3–5 kg[C] kg [N] 1 fixed (7–12 mol CO 2 mol N 2 1 )
		1
		</SimulaConstant>
		<SimulaStochastic
		name="branchingFrequency"
		name="interBranchingDistance"
		unit="cm"
		distribution="uniform"
		minimum="1"
		@@ -500,7 +500,7 @@ costs 3–5 kg[C] kg [N] 1 fixed (7–12 mol CO 2 mol N 2 1 )
		<SimulaBase name="branchList">
		<SimulaBase name="lateralBasalRoots">
		<SimulaConstant
		name="branchingFrequency"
		name="interBranchingDistance"
		unit="cm">
		<!-- original file line 44: 0.55 -->
		<!-- original file seems much to low, this was very consistent 7/cm for basal roots in 2008 three sister experiment-->
		@@ -531,7 +531,7 @@ costs 3–5 kg[C] kg [N] 1 fixed (7–12 mol CO 2 mol N 2 1 )
		<SimulaBase name="branchList">
		<SimulaBase name="lateralBasalRoots">
		<SimulaConstant
		name="branchingFrequency"
		name="interBranchingDistance"
		unit="cm">
		<!-- see whorl 1 -->
		0.15
		@@ -560,7 +560,7 @@ costs 3–5 kg[C] kg [N] 1 fixed (7–12 mol CO 2 mol N 2 1 )
		<SimulaBase name="branchList">
		<SimulaBase name="lateralBasalRoots">
		<SimulaConstant
		name="branchingFrequency"
		name="interBranchingDistance"
		unit="cm">
		<!-- see whorl 1 -->
		0.15
		@@ -589,7 +589,7 @@ costs 3–5 kg[C] kg [N] 1 fixed (7–12 mol CO 2 mol N 2 1 )
		<SimulaBase name="branchList">
		<SimulaBase name="lateralHypocotylBornRoots">
		<SimulaConstant
		name="branchingFrequency"
		name="interBranchingDistance"
		unit="cm"> 0.4
		</SimulaConstant>
		<SimulaConstant
		@@ -616,7 +616,7 @@ costs 3–5 kg[C] kg [N] 1 fixed (7–12 mol CO 2 mol N 2 1 )
		<SimulaBase name="branchList">
		<SimulaBase name="finelateral">
		<SimulaConstant
		name="branchingFrequency"
		name="interBranchingDistance"
		unit="cm"> 0.5
		</SimulaConstant>
		<SimulaConstant
		@@ -641,7 +641,7 @@ costs 3–5 kg[C] kg [N] 1 fixed (7–12 mol CO 2 mol N 2 1 )
		<SimulaBase name="branchList">
		<SimulaBase name="finelateralFastGrowing">
		<SimulaConstant
		name="branchingFrequency"
		name="interBranchingDistance"
		unit="cm"> 0.55
		</SimulaConstant>
		<SimulaConstant
		@@ -668,7 +668,7 @@ costs 3–5 kg[C] kg [N] 1 fixed (7–12 mol CO 2 mol N 2 1 )
		<SimulaBase name="branchList">
		<SimulaBase name="finelateral">
		<SimulaConstant
		name="branchingFrequency"
		name="interBranchingDistance"
		unit="cm"> 0.5
		</SimulaConstant>
		<SimulaConstant