Commit a995b052 authored by jouke's avatar jouke
Browse files

template updates to get rid of depricated path messages 

coarser grid by default in maize and rice to speed up

disabled explicit coupling to make sure without is also part of the test

more memory in job.sh, as current version ran into mem allocation with
maize. The stricter garbage collector should reduce the maize mem use,
however.
parent 038f3809

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

+1 −1
Original line number Diff line number Diff line
@@ -71,7 +71,7 @@ 
			<!-- average density in michaelis data (dryweight/volume) is 0.037 min 0.0114379085 max 0.0826010545 mean 0.0370240644 stdev 0.0141592529 median 0.0327526685 ; Vera Hecht PT1: Sca Low: mean=0.05339 g/cm³, max=0.082, Sca High: mean=0.0284 g/cm³, max=0.032.

			There seems to be no time or genotype or treatment effect on this. -->

			<SimulaConstant

				name="density"

				name="specificWeight"

				unit="g/cm3"> 0.05 

			</SimulaConstant>

		</SimulaBase>

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

+8 −8
Original line number Diff line number Diff line
@@ -200,7 +200,7 @@ Scarlett 13.2 14.4 7 
				</SimulaBase>

 			</SimulaBase>

			<SimulaConstant

				name="density"

				name="specificWeight"

				unit="g/cm3">

			<!-- 2013 field v.hecht 10-15 cm3/g, 2014 7-12 cm3/g = 0.0666 0.0833  0.1 0.14 g/cm3  -->

				0.08 <!-- 0.08 upper limit michaelis data ; Vera Hecht PT1: Sca Low: mean=0.05339 g/cm³, max=0.082, Sca High: mean=0.0284 g/cm³, max=0.032-->
@@ -262,7 +262,7 @@ Scarlett 13.2 14.4 7 
				</SimulaBase>

			</SimulaBase>

			<SimulaConstant

				name="density"

				name="specificWeight"

				unit="g/cm3">

				<!-- average density in michaelis data (dryweight/volume) is 0.037 min 0.0114379085 max 0.0826010545 mean 0.0370240644 stdev 0.0141592529 median 0.0327526685 ; Vera Hecht PT1: Sca Low: mean=0.05339 g/cm³, max=0.082, Sca High: mean=0.0284 g/cm³, max=0.032.

					There seems to be no time or genotype or treatment effect on this. -->
@@ -308,7 +308,7 @@ Scarlett 13.2 14.4 7 
				</SimulaBase>

			</SimulaBase>

			<SimulaConstant

				name="density"

				name="specificWeight"

				unit="g/cm3"> 0.037 

			</SimulaConstant>

		</SimulaBase>
@@ -348,7 +348,7 @@ Scarlett 13.2 14.4 7 
				</SimulaBase>

			</SimulaBase>

			<SimulaConstant

				name="density"

				name="specificWeight"

				unit="g/cm3"> 0.037 

			</SimulaConstant>

		</SimulaBase>
@@ -388,7 +388,7 @@ Scarlett 13.2 14.4 7 
				</SimulaBase>

			</SimulaBase>

			<SimulaConstant

				name="density"

				name="specificWeight"

				unit="g/cm3"> 0.037 

			</SimulaConstant>

		</SimulaBase>
@@ -426,7 +426,7 @@ Scarlett 13.2 14.4 7 
				</SimulaBase>

			</SimulaBase>

			<SimulaConstant

				name="density"

				name="specificWeight"

				unit="g/cm3"> 0.037 

			</SimulaConstant>

		</SimulaBase>
@@ -461,7 +461,7 @@ Scarlett 13.2 14.4 7 
				</SimulaBase>

			</SimulaBase>

			<SimulaConstant

				name="density"

				name="specificWeight"

				unit="g/cm3"> 0.037 

			</SimulaConstant>

		</SimulaBase>
@@ -475,7 +475,7 @@ Scarlett 13.2 14.4 7 
			<SimulaBase name="branchList">

			</SimulaBase>

			<SimulaConstant

				name="density"

				name="specificWeight"

				unit="g/cm3"> 0.037 

			</SimulaConstant>

		</SimulaBase>

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

+12 −12
Original line number Diff line number Diff line
@@ -423,7 +423,7 @@ costs 3–5 kg[C] kg [N] 1 fixed (7–12 mol CO 2 mol N 2 1 ) 
				</SimulaBase-->

			</SimulaBase>

			<SimulaConstant

				name="density"

				name="specificWeight"

				unit="g/cm3"> 0.094

			</SimulaConstant>

		</SimulaBase>
@@ -487,7 +487,7 @@ costs 3–5 kg[C] kg [N] 1 fixed (7–12 mol CO 2 mol N 2 1 ) 
				</SimulaBase>

			</SimulaBase>

			<SimulaConstant

				name="density"

				name="specificWeight"

				unit="g/cm3"> 0.094

			</SimulaConstant>

		</SimulaBase>
@@ -518,7 +518,7 @@ costs 3–5 kg[C] kg [N] 1 fixed (7–12 mol CO 2 mol N 2 1 ) 
				</SimulaBase>

			</SimulaBase>

			<SimulaConstant

				name="density"

				name="specificWeight"

				unit="g/cm3"> 0.094

			</SimulaConstant>

		</SimulaBase>
@@ -548,7 +548,7 @@ costs 3–5 kg[C] kg [N] 1 fixed (7–12 mol CO 2 mol N 2 1 ) 
				</SimulaBase>

			</SimulaBase>

			<SimulaConstant

				name="density"

				name="specificWeight"

				unit="g/cm3"> 0.094

			</SimulaConstant>

		</SimulaBase>
@@ -577,7 +577,7 @@ costs 3–5 kg[C] kg [N] 1 fixed (7–12 mol CO 2 mol N 2 1 ) 
				</SimulaBase>

			</SimulaBase>

			<SimulaConstant

				name="density"

				name="specificWeight"

				unit="g/cm3"> 0.094

			</SimulaConstant>

		</SimulaBase>
@@ -604,7 +604,7 @@ costs 3–5 kg[C] kg [N] 1 fixed (7–12 mol CO 2 mol N 2 1 ) 
				</SimulaBase>

			</SimulaBase>

			<SimulaConstant

				name="density"

				name="specificWeight"

				unit="g/cm3"> 0.094

			</SimulaConstant>

		</SimulaBase>
@@ -629,7 +629,7 @@ costs 3–5 kg[C] kg [N] 1 fixed (7–12 mol CO 2 mol N 2 1 ) 
				</SimulaBase>

			</SimulaBase>

			<SimulaConstant

				name="density"

				name="specificWeight"

				unit="g/cm3"> 0.094

			</SimulaConstant>

		</SimulaBase>
@@ -656,7 +656,7 @@ costs 3–5 kg[C] kg [N] 1 fixed (7–12 mol CO 2 mol N 2 1 ) 
				</SimulaBase>

			</SimulaBase>

			<SimulaConstant

				name="density"

				name="specificWeight"

				unit="g/cm3"> 0.094

			</SimulaConstant>

		</SimulaBase>
@@ -681,7 +681,7 @@ costs 3–5 kg[C] kg [N] 1 fixed (7–12 mol CO 2 mol N 2 1 ) 
				</SimulaBase>

			</SimulaBase>

			<SimulaConstant

				name="density"

				name="specificWeight"

				unit="g/cm3"> 0.094

			</SimulaConstant>

		</SimulaBase>
@@ -693,7 +693,7 @@ costs 3–5 kg[C] kg [N] 1 fixed (7–12 mol CO 2 mol N 2 1 ) 
			<SimulaBase name="branchList">

			</SimulaBase>

			<SimulaConstant

				name="density"

				name="specificWeight"

				unit="g/cm3"> 0.094

			</SimulaConstant>

		</SimulaBase>
@@ -706,7 +706,7 @@ costs 3–5 kg[C] kg [N] 1 fixed (7–12 mol CO 2 mol N 2 1 ) 
				<!--there are no branches on lateral roots-->

			</SimulaBase>

			<SimulaConstant

				name="density"

				name="specificWeight"

				unit="g/cm3"> 0.094

			</SimulaConstant>

		</SimulaBase>
@@ -719,7 +719,7 @@ costs 3–5 kg[C] kg [N] 1 fixed (7–12 mol CO 2 mol N 2 1 ) 
				<!--there are no branches on lateral roots-->

			</SimulaBase>

			<SimulaConstant

				name="density"

				name="specificWeight"

				unit="g/cm3"> 0.094

			</SimulaConstant>

		</SimulaBase>

OpenSimRoot/InputFiles/plantParameters/Cassava/default/cassava.xml

+10 −10
Original line number Diff line number Diff line
@@ -451,7 +451,7 @@ in g C per umol of light 
				</SimulaBase>

			</SimulaBase>

			<SimulaConstant

				name="density"

				name="specificWeight"

				unit="g/cm3"> 0.0001</SimulaConstant><!--  very low as this is the original cutting, but for simplicity we 'grow' it first -->

		</SimulaBase>

		<SimulaBase name="primaryRoot" 	objectGenerator="copyDefaults">
@@ -460,7 +460,7 @@ in g C per umol of light 
				name="copyDefaultsFrom">../defaultsMajorAxis</SimulaConstant>

			<SimulaBase name="branchList"></SimulaBase>

			<SimulaConstant

				name="density"

				name="specificWeight"

				unit="g/cm3"> 0.00001</SimulaConstant>

		</SimulaBase>

		<SimulaBase name="basalRoot"
@@ -478,7 +478,7 @@ in g C per umol of light 
				name="lengthRootTip"

				unit="cm"> 4.0</SimulaConstant>

			<SimulaConstant

				name="density"

				name="specificWeight"

				unit="g/cm3">

				0.1 <!-- primary maize root 0.94 dry weight / fresh weight 1. Ali M. Pahlavanian and Wendy Kuhn Silk, “Effect of Temperature on Spatial and Temporal Aspects of Growth in the Primary Maize Root ,” Plant Physiol. 87, no. 2 (June 1, 1988): 529-532.-->

			</SimulaConstant>
@@ -506,7 +506,7 @@ in g C per umol of light 
				</SimulaBase>

			</SimulaBase>

			<SimulaConstant

				name="density"

				name="specificWeight"

				unit="g/cm3">

				0.1 <!-- primary maize root 0.94 dry weight / fresh weight 1. Ali M. Pahlavanian and Wendy Kuhn Silk, “Effect of Temperature on Spatial and Temporal Aspects of Growth in the Primary Maize Root ,” Plant Physiol. 87, no. 2 (June 1, 1988): 529-532.-->

			</SimulaConstant>
@@ -534,7 +534,7 @@ in g C per umol of light 
				</SimulaBase>

			</SimulaBase>

			<SimulaConstant

				name="density"

				name="specificWeight"

				unit="g/cm3"> 0.1</SimulaConstant>

		</SimulaBase>

		<SimulaBase name="lateralPrimaryRoot" objectGenerator="copyDefaults">
@@ -560,7 +560,7 @@ in g C per umol of light 
				</SimulaBase>

			</SimulaBase>

			<SimulaConstant

				name="density"

				name="specificWeight"

				unit="g/cm3"> 0.1</SimulaConstant>

		</SimulaBase>

		<!--PARAMETERS FOR tetiarySquash ROOTS-->
@@ -577,12 +577,12 @@ in g C per umol of light 
				</SimulaBase>

			</SimulaBase>

			<SimulaConstant

				name="density"

				name="specificWeight"

				unit="g/cm3"> 0.1</SimulaConstant>

		</SimulaBase>

		<SimulaBase name="finelateral" objectGenerator="copyDefaults">

			<SimulaConstant

				name="density"

				name="specificWeight"

				unit="g/cm3"> 0.1</SimulaConstant>

			<SimulaBase name="branchList"></SimulaBase>

		</SimulaBase>
@@ -592,7 +592,7 @@ in g C per umol of light 
				type="string"

				name="copyDefaultsFrom">../defaultsMajorAxis</SimulaConstant>

			<SimulaConstant

				name="density"

				name="specificWeight"

				unit="g/cm3"> 0.1</SimulaConstant>

			<!--SimulaConstant

				name="branchingAngle"
@@ -610,7 +610,7 @@ in g C per umol of light 
		</SimulaBase>

		<SimulaBase name="lateralHypocotylBornRoots" objectGenerator="copyDefaults">

			<SimulaConstant

				name="density"

				name="specificWeight"

				unit="g/cm3"> 0.1</SimulaConstant>

			<SimulaBase name="branchList"></SimulaBase>

		</SimulaBase>

OpenSimRoot/InputFiles/plantParameters/Lupin/Dunbabin04/lupin.xml

+1 −1
Original line number Diff line number Diff line
@@ -119,7 +119,7 @@ mol/mol g/mol 
	<SimulaBase name="defaults">

		<SimulaBase name="branchList">

		</SimulaBase>	

		<SimulaConstant  name="density" unit="g/cm3">

		<SimulaConstant  name="specificWeight" unit="g/cm3">

			 0.057

		</SimulaConstant>

	</SimulaBase>