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
Loading
Loading
Loading
Loading
+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>
+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>
+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>
+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>
+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>
Loading