Light optimizations

Removed the sine correction for the light sources; added (temporary) correction at soil tile sensors to perceive fraction PAR of 1 when scene is empty (to be replaced by virtual reference sensor); added accumulated PAR at plant level and corrected this for field level

SimpleSoilModule .rgg

@@ -59,7 +59,7 @@ class Soil {
 }
 
 //Module that determines if	an apex is entering unexplored soil
-abstract module ExploredSoil extends Box() {}
+abstract module ExploredSoil extends Box().(setLayer(rootBoxLayer)) {}
 
 //Phosphorous rich soil
 module RichSoil extends ExploredSoil

initiation.rgg

@@ -67,17 +67,18 @@ static void initDatasets()
 			setColumnKey(10,"nrBranches"),
 			setColumnKey(11,"leafArea(m2)"),
 			setColumnKey(12,"fpar"),
-			setColumnKey(13,"rfr"),
-			setColumnKey(14,"biom(mg)"),
-			setColumnKey(15,"yield(mg)"),
-			setColumnKey(16,"leafMass(mg)"),
-			setColumnKey(17,"stemMass(mg)"),
-			setColumnKey(18,"rootMass(mg)"),
-			setColumnKey(19,"shootRootRatio(mg)"),
-			setColumnKey(20,"aboveBiom(mg)"),
-			setColumnKey(21,"Nuptake(mg)"),
-			setColumnKey(22,"Total N uptake(mg)"),
-			setColumnKey(23,"Root length(m)")
+			setColumnKey(13,"accumulated PAR(mol)"),
+			setColumnKey(14,"rfr"),
+			setColumnKey(15,"biom(mg)"),
+			setColumnKey(16,"yield(mg)"),
+			setColumnKey(17,"leafMass(mg)"),
+			setColumnKey(18,"stemMass(mg)"),
+			setColumnKey(19,"rootMass(mg)"),
+			setColumnKey(20,"shootRootRatio(mg)"),
+			setColumnKey(21,"aboveBiom(mg)"),
+			setColumnKey(22,"Nuptake(mg)"),
+			setColumnKey(23,"Total N uptake(mg)"),
+			setColumnKey(24,"Root length(m)")
 			
 		);
 		combiLight.clear();
@@ -116,6 +117,7 @@ static void initDatasets()
 		plantNitroTotal.clear(); chart(plantNitroTotal,XY_PLOT);		
 		plantNitroRatio.clear(); chart(plantNitroRatio,XY_PLOT);
 		plantFabs.clear(); chart(plantFabs,XY_PLOT);
+		plantCPAR.clear(); chart(plantCPAR,XY_PLOT);
 		plantLeafArea.clear(); chart(plantLeafArea,XY_PLOT);
 
 		fieldFabs.clear(); chart(fieldFabs,XY_PLOT);

modules_base.rgg

@@ -13,7 +13,7 @@ module FieldBase extends Null
 	double[] lai = new double[totalSpecies];					// leaf area index
 	double[] nrShoots = new double[totalSpecies];				// shoots per m2 (branches + main stem)
 	double[] absorbedRadiation = new double[totalSpecies];		// canopy absorbed radiation (umol / m2 / s)
-	double[] accumulatedRadiation = new double[totalSpecies];	// cumulative absorbed radiation (MJ / m2) - VALUE FACTOR 100 TOO HIGH - NEEDS CHECK
+	double[] accumulatedRadiation = new double[totalSpecies];	// cumulative absorbed radiation (mol / m2)
 	double[] fabs = new double[totalSpecies];					// fraction of global radiation absorbed by the canopy
 	double totalFabs;											// fabs for all species combined
 	double[] rfr = new double[totalSpecies];					// average R:FR in the canopy
@@ -59,7 +59,7 @@ module FieldBase extends Null
 				fieldRFR.getRow(time).(set(s,rfr[s]));
 				k[s] = - Math.log(1-fabs[s]) / lai[s];
 				//println(k[s]);
-				accumulatedRadiation[s] = sum((* pb:PlantBase, (pb.species == s) *)[accumulatedRadiation]*0.22) / area[s];
+				accumulatedRadiation[s] = sum((* pb:PlantBase, (pb.species == s) *)[accumulatedRadiation]) / area[s];
 				assCO2[s] = sum((* pb:PlantBase, (pb.species == s) *)[assimilated]) / area[s];
 				fieldAssim.getRow(time).(set(s,assCO2[s]/1e6));
 			}
@@ -302,11 +302,11 @@ module PlantBase extends Null
 	void updateAbsorbedRadiation() {
 		double leafRad = sum((* l:Leaf, (l.plantNumber == plantNumber) *)[abs]);
 		double stemRad = sum((* i:Internode, (i.plantNumber == plantNumber) *)[abs]);
-		//absorbedRadiation = leafRad + stemRad  / (leafArea+stemArea);
-		absorbedRadiation = leafRad /*/ leafArea*/;
+		absorbedRadiation = leafRad;
 		fabs = absorbedRadiation / ( (leafArea) * PPFD);
 		if (fabs < 2) {plantFabs.getRow(time).set(plantNumber,fabs);}
 		accumulatedRadiation += 1e-6 * (absorbedRadiation * dayLength*60*60);
+		plantCPAR.getRow(time).set(plantNumber,accumulatedRadiation);
 	}
 	
 	// update plant red/far-red ratio
@@ -361,18 +361,19 @@ module PlantBase extends Null
 				set(9,ageD),
 				set(10,nrBranches),
 				set(11,leafArea),
-				set(12,fabs/*absorbedRadiation*/),
-				set(13,rfr),
-				set(14,biomass),
-				set(15,yld),
-				set(16,biomLeaf),
-				set(17,biomStem),
-				set(18,biomRoots),
-				set(19,shootRoot),
-				set(20,biomassAbove),
-				set(21,Nsource),
-				set(22,NuptakeTotal),
-				set(23,rootLength)
+				set(12,fabs),
+				set(13,accumulatedRadiation),
+				set(14,rfr),
+				set(15,biomass),
+				set(16,yld),
+				set(17,biomLeaf),
+				set(18,biomStem),
+				set(19,biomRoots),
+				set(20,shootRoot),
+				set(21,biomassAbove),
+				set(22,Nsource),
+				set(23,NuptakeTotal),
+				set(24,rootLength)
 			);
 		
 	}

modules_light.rgg

@@ -47,14 +47,35 @@ module DiffuseLight
 		power = 1e6 * 0.55 * 4.55 * DailyDiffuseRadiation / (dayLength*60*60);
 	}
 }
-==> RH(random(0,360))
+==> //RH(random(0,360))
 	RL(90)
-	[ for (int i = 1; i<=12; i++) ([ RU(i*360/12) RL(-11.7) M(dist) RL(180) SingleLight(power*0.003218/Math.sin(11.7* Math.PI/180))] )]
+	
+	// original
+	[ for (int i = 1; i<=12; i++) ([ RU(i*360/12) RL(-11.7) M(dist) RL(180) SingleLight(power*0.003218)] )]
+	[ for (int i = 1; i<=12; i++) ([ RU(20) RU(i*360/12) RL(-34.2) M(dist) RL(180) SingleLight(power*0.01163)] )]
+	[ for (int i = 1; i<=12; i++) ([ RU(40) RU(i*360/12) RL(-54.9) M(dist) RL(180) SingleLight(power*0.019812)] )]
+	[ for (int i = 1; i<=12; i++) ([ RU(60) RU(i*360/12) RL(-71.1) M(dist) RL(180) SingleLight(power*0.023022)] )]
+	[ for (int i = 1; i<=12; i++) ([ RU(80) RU(i*360/12) RL(-82.8) M(dist) RL(180) SingleLight(power*0.018522)] )]
+	[ for (int i = 1; i<=12; i++) ([ RU(80) RU(i*360/12) RL(-89.1) M(dist) RL(180) SingleLight(power*0.007096)])]
+	
+	// turtle
+	/*[ for (int i = 0; i<=0; i++) ([ RU(0) RL(-90) M(dist) RL(180) SingleLight(power*1/46)])]
+	[ for (int i = 0; i<=4; i++) ([ RU(i*72) RL(-70.95) M(dist) RL(180) SingleLight(power*1/46)])]
+	[ for (int i = 0; i<=4; i++) ([ RU(i*72+36) RL(-49.44) M(dist) RL(180) SingleLight(power*1/46)])]
+	[ for (int i = 0; i<=4; i++) ([ RU(i*72) RL(-44.12) M(dist) RL(180) SingleLight(power*1/46)])]
+	[ for (int i = 0; i<=4; i++) ([ RU(i*72+24) RL(-30.99) M(dist) RL(180) SingleLight(power*1/46)])]
+	[ for (int i = 0; i<=4; i++) ([ RU(i*72+48) RL(-30.99) M(dist) RL(180) SingleLight(power*1/46)])]
+	[ for (int i = 0; i<=4; i++) ([ RU(i*72) RL(-25.07) M(dist) RL(180) SingleLight(power*1/46)])]
+	[ for (int i = 0; i<=14; i++) ([ RU(i*24+12) RL(-13.42) M(dist) RL(180) SingleLight(power*1/46)])]*/
+	
+	// original sine corrected
+	/*[ for (int i = 1; i<=12; i++) ([ RU(i*360/12) RL(-11.7) M(dist) RL(180) SingleLight(power*0.003218/Math.sin(11.7* Math.PI/180))] )]
 	[ for (int i = 1; i<=12; i++) ([ RU(20) RU(i*360/12) RL(-34.2) M(dist) RL(180) SingleLight(power*0.01163/Math.sin(34.2* Math.PI/180))] )]
 	[ for (int i = 1; i<=12; i++) ([ RU(40) RU(i*360/12) RL(-54.9) M(dist) RL(180) SingleLight(power*0.019812/Math.sin(54.9* Math.PI/180))] )]
 	[ for (int i = 1; i<=12; i++) ([ RU(60) RU(i*360/12) RL(-71.1) M(dist) RL(180) SingleLight(power*0.023022/Math.sin(71.1* Math.PI/180))] )]
 	[ for (int i = 1; i<=12; i++) ([ RU(80) RU(i*360/12) RL(-82.8) M(dist) RL(180) SingleLight(power*0.018522/Math.sin(82.8* Math.PI/180))] )]
-	[ for (int i = 1; i<=12; i++) ([ RU(80) RU(i*360/12) RL(-89.1) M(dist) RL(180) SingleLight(power*0.007096/Math.sin(89.1* Math.PI/180))])]
+	[ for (int i = 1; i<=12; i++) ([ RU(80) RU(i*360/12) RL(-89.1) M(dist) RL(180) SingleLight(power*0.007096/Math.sin(89.1* Math.PI/180))])]*/
+
 ;
 
 // general tile sensor
@@ -79,10 +100,11 @@ module TileSensor extends Null
 				spec = flm.getAbsorbedPower3d(this);
 			} else {
 				spec = lm.getAbsorbedPower3d(this);
+				//println(lm.getHitCount(this));
 			}
-			abs = cm * spec.x;
-			red = cm * spec.y;
-			farred = cm * spec.z;
+			abs = cm * spec.x / sensorCorrection;
+			red = cm * spec.y / sensorCorrection;
+			farred = cm * spec.z / sensorCorrection;
 			if (red / farred > 0) {rfr = red / farred;}
 			absm2 = abs / area ;
 			fabs = absm2 / PPFD;

parameters.rgg

@@ -14,26 +14,26 @@ static boolean sRFR				= false;		// toggle PAR or R:FR visualisation (default va
 static boolean snapShot			= false;			// take snapshots?
 static String path				= "d:/snapshots/";	// location for the snapshots
 static String pathData			= "d:/outputdata/";	// location for the output text files
-static boolean writePlantTable	= true;		// true: write plant-level tables
+static boolean writePlantTable	= true;			// true: write plant-level tables
 static boolean writeFieldTable	= true;			// true: write field-level tables
-static boolean writeLight		= false;			// true: record tile and sensor light variable (only for plant-independent tiles)
+static boolean writeLight		= false;		// true: record tile and sensor light variable (only for plant-independent tiles)
 
 // field parameters
 static int[] speciesSequence	= {maize};		// sequence of species in adjacent strips (nr of values determines nr of strips)
 static double stripDistance		= 0;			// extra distance between adjacent strips (THIS EXTRA AREA IS NOT INCLUDED IN THE CALCULATION OF STRIP BIOMASS OR YIELD)
 	// checkerboard
 static boolean checker			= false;		// true: primary species is placed in a checkerboard design with a second species (checkerSpecies)
-static int checkerSpecies		= sunflower;	// the second species in the checkboard design
+static int checkerSpecies		= at;			// the second species in the checkboard design
 static int checkerSize			= 1;			// size of checkerboard unit (e.g.: 3 would give units of 3x3 plants arranged in a checkboard design
 	// mixtures
-static boolean mix				= false;			// true: primary species is mixed with a second species (mixSpecies) according to a proporionality (mixProp)
-static int mixSpecies			= sunflower;		// the second species in the mix
+static boolean mix				= false;		// true: primary species is mixed with a second species (mixSpecies) according to a proporionality (mixProp)
+static int mixSpecies			= at;			// the second species in the mix
 static double mixProp			= 0.5;			// the proporion of the primary species in the mix
 	// randomization
 static boolean randomArrangement = false;		// overrule plant arrangement and fully randomize plant location in strip
 
 // root and soil parameters
-static boolean rootModule		= true;			// toggle root and soil simulation. If false, roots are present only as a simple sink for assimilates	
+static boolean rootModule		= false;		// toggle root and soil simulation. If false, roots are present only as a simple sink for assimilates	
 static double soilN				= 1000;			// uMol N / L soil
 static double soilP				= 50; 			// uMol N / L soil
 static double cellSize			= 0.1;			// size of a cubical soil cell (m*m*m); should fit within field size chosen e.g. field length and width should be divisible by cellsize!
@@ -45,21 +45,22 @@ static double P_Cmin_r			= 1.2;			// Minimum P concentration required for root u
 // weed parameters
 static boolean weeds			= false;		// true: weeds grow according to parameters below
 static double weedDens			= 12;			// density of weeds (per m2)
-static int weedSpecies			= hemp;		// which species# should represent the weed
+static int weedSpecies			= at;			// which species# should represent the weed
 static int nrWeedPlants;
 
 // general plant settings
 static boolean functional		= true;			// false: structural model only (light is intercepted but not used for growth)
 static boolean plantDeath		= false;		// toggle possibilities for entire plants to taken from the scene in case of very low source/sink ratio
-static boolean leafSenescence	= true;		// toggles falling of leaves at end of life span or when light level at leaf is low
+static boolean leafSenescence	= true;			// toggles falling of leaves at end of life span or when light level at leaf is low
 static double fallPAR 			= 25;			// light level (umol/m2/s) below which leaf should drop
 static boolean FvCB				= true;			// true: use biochemical photosynthesis model; false: use light response curve
-static int timeToFlower			= 60;	// TO BE MADE A FUNCTION OF DAYLENGTH OR OTHER ENVIRONMENTAL VARIABLE
+static int timeToFlower			= 60;			// TO BE MADE A FUNCTION OF DAYLENGTH OR OTHER ENVIRONMENTAL VARIABLE
 
 // light model options
-static double rfrIncoming		= 1.2;				// red/far-red ratio of the incoming radiation
-static int depth				= 10;				// maximum number of reflections / transmissions of a ray
-static LightModel lm			= new LightModel(2000000, depth);
+static double rfrIncoming		= 1.2;			// red/far-red ratio of the incoming radiation
+static int depth				= 10;			// maximum number of reflections / transmissions of a ray
+static double sensorCorrection = 0.87;			// correction factor for horizontal flat light sensors at soil level	
+static LightModel lm			= new LightModel(5000000, depth);
 static FluxLightModel flm		= new FluxLightModel(20000000, depth);
 static boolean seeRays			= false;		// see direction of rays from light sources if true
 static boolean infinite			= true;			// clone the canopy to eliminate border effects
@@ -86,7 +87,7 @@ static int nrTiles					= 1;		// nr tiles per plant per edge (e.g. nrTiles=3 mean
  // plant-independent tiles
 static double offSetX				= 0.1;		// x location of tile 1 with respect to plant 1
 static double offSetY				= 0.25;		// y location of tile 1 with respect to plant 1
-static int nrX						= 10;		// number of tiles in x direction
+static int nrX						= 6;		// number of tiles in x direction
 static int nrY						= 10;		// number of tiles in y direction
 static int nrZ						= 1;		// number of associated sensors in z direction (height)
 static double tSizeX				= 0.1;		// width of tile
@@ -95,8 +96,8 @@ static double tSizeZ				= 0.1;		// height of sensor
 
 //view layers
 static int leafLayer			= 3;			// layer in which to show the leaves
-static int rootBoxLayer			= 14;
-static int rootLayer			= 13;
+static int rootLayer			= 14;
+static int rootBoxLayer			= 13;
 static int tileLayer			= 12;
 
 // timers
@@ -351,6 +352,7 @@ const DatasetRef apicalDominance = new DatasetRef("Apical Dominance");
 const DatasetRef plantBranches = new DatasetRef("Branch number");
 const DatasetRef plantSAS = new DatasetRef("SAScoefficient");
 const DatasetRef plantFabs = new DatasetRef("Plant fPAR");
+const DatasetRef plantCPAR = new DatasetRef("Plant Accumulated PAR (mol)");
 const DatasetRef plantRFR = new DatasetRef("Plant R:FR");
 const DatasetRef plantNitro = new DatasetRef("Plant N uptake");
 const DatasetRef plantNitroTotal = new DatasetRef("Total plant N uptake");

parameters0.rgg

@@ -4,10 +4,10 @@ import static parameters.*;
 
 {
 	// field parameters
-	nrRows[dicot1] = 5;                  // number of rows
+	nrRows[dicot1] = 1;                  // number of rows
 	nrPlants[dicot1] = 1;                // number of plants in a row
-	rowDistance[dicot1] = 0.2;          // distance between rows
-	plantDistance[dicot1] = 0.2;        // distance between plants in a row
+	rowDistance[dicot1] = 10;//0.2;          // distance between rows
+	plantDistance[dicot1] = 10;//0.2;        // distance between plants in a row
 	delay[dicot1] = 0;                   // germination delay after start of simulation (in days, to represent late sowing)
 	harvest[dicot1] = 77;               // duration, i.e. harvest/removal time after emergence (in days)
 	hexa[dicot1] = false;                // true: hexagonal layout, rectangular otherwise

parameters8.rgg

@@ -4,10 +4,10 @@ import static parameters.*;
 
 {
 	// field parameters
-	nrRows[sunflower] = 5;                  // number of rows
-	nrPlants[sunflower] = 5;                // number of plants in a row
-	rowDistance[sunflower] = 0.3;          // distance between rows
-	plantDistance[sunflower] = 0.3;        // distance between plants in a row
+	nrRows[sunflower] = 1;                  // number of rows
+	nrPlants[sunflower] = 1;                // number of plants in a row
+	rowDistance[sunflower] = 0.5;          // distance between rows
+	plantDistance[sunflower] = 0.5;        // distance between plants in a row
 	delay[sunflower] = 0;                   // germination delay after start of simulation (in days, to represent late sowing)
 	harvest[sunflower] = 110;               // duration, i.e. harvest/removal time after emergence (in days)
 	hexa[sunflower] = false;                // true: hexagonal layout, rectangular otherwise
@@ -74,7 +74,7 @@ import static parameters.*;
 	EL[sunflower] = 51; 					// Root elongation rate mm mm-1 day-1 
 	Dinit[sunflower] = 0.0011;				// Initial root Diameter in m 
 	RTD[sunflower]	= 200;					// Root tissue density (g/cm3) (Pages 2013 - generic)
-	MP[sunflower] = 5;						// Maximum number of root primordia 
+	MP[sunflower] = 0;						// Maximum number of root primordia 
 	ER[sunflower] = 0.056;					// Emergence rate of root primordia per day = 0.968 at 25 degrees which is 0.056 per dregreeday. 
 	IBD[sunflower] = 0.0078;				// Inter Branch Distance 
 	IBDmax[sunflower] = 0.039; 			// Inter branch distance of the highest root order 
@@ -85,7 +85,7 @@ import static parameters.*;
 	angleAVG[sunflower] = 60;				// average insertion angle of lateral roots
 	angleVAR[sunflower] = 20;				// variation in the insertion angle of lateral roots
 	MCP[sunflower]	= 5;					//random root movement based on mechanical constraints; radial degrees/m
-	MaxRootOrder[sunflower] = 0;
+	MaxRootOrder[sunflower] = 1;
 	fineRootD[sunflower] = 0.1;			// Diameter in m/m
 	fineRootDensity[sunflower]	= 32;		// m fine roots/m coarse root	
 	RLratio[sunflower]	= 1;	 			// Root/Leaf ratio

parameters9.rgg

@@ -6,8 +6,8 @@ import static parameters.*;
 	// field parameters
 	nrRows[maize] = 2;                  // number of rows
 	nrPlants[maize] = 3;                // number of plants in a row
-	rowDistance[maize] = 0.5;          // distance between rows
-	plantDistance[maize] = 0.2;        // distance between plants in a row
+	rowDistance[maize] = 0.6;          // distance between rows
+	plantDistance[maize] = 0.1;        // distance between plants in a row
 	delay[maize] = 0;                   // germination delay after start of simulation (in days, to represent late sowing)
 	harvest[maize] = 95;               // duration, i.e. harvest/removal time after emergence (in days)
 	hexa[maize] = false;                // true: hexagonal layout, rectangular otherwise
@@ -57,7 +57,7 @@ import static parameters.*;
 	nrLeavesUpper[maize] = 1;			// number of leaves per phytomer for the upper phytomers
 	rankLower[maize] = 3;				// number of lower phytomers that contain nrLeavesLower leaves	
 	phyllotaxisLower[maize] = 137;           // angle between consecutive leaves along a stem for the lower phytomers
-	phyllotaxisUpper[maize] = 180;           // angle between consecutive leaves along a stem for the upper phytomers
+	phyllotaxisUpper[maize] = 137;           // angle between consecutive leaves along a stem for the upper phytomers
 	
 	varDelay[maize] = 2;                // max variation in germination delay (in days, 0 = simultaneous germination)
 	seedMass[maize] = 100;             // seed endosperm mass in mg