Commit c2b5b0c4 authored by jouke's avatar jouke
Browse files

Updated for leaf area code 

Removed time caching
Removed some warnings which were not particularly needed.
parent 252aaf14

OpenSimRoot/src/modules/ShootModule/LeafArea.cpp

+21 −33
Original line number Diff line number Diff line
@@ -297,15 +297,11 @@ DerivativeBase * newInstantiationLeafAreaIndex(SimulaDynamic* const pSD){ 
   return new LeafAreaIndex(pSD);

}



SunlitLeafAreaIndex::SunlitLeafAreaIndex(SimulaDynamic* pSD):DerivativeBase(pSD), cachedTime(-10){

SunlitLeafAreaIndex::SunlitLeafAreaIndex(SimulaDynamic* pSD):DerivativeBase(pSD){

	leafAreaIndex = pSD->getSibling("leafAreaIndex");

	solarElevationAngle = ORIGIN->getPath("/environment/atmosphere/sineSolarElevationAngle");

}

void SunlitLeafAreaIndex::calculate(const Time &t, double &sunLAI){

	if (std::abs(t - cachedTime) < TIMEERROR){

		sunLAI = cachedSunlitLAI;

		return;

	}

	double sinEl;

	solarElevationAngle->get(t, sinEl);

	if (sinEl <= 0){
@@ -314,12 +310,10 @@ void SunlitLeafAreaIndex::calculate(const Time &t, double &sunLAI){ 
	}

	double LAI;

	leafAreaIndex->get(t, LAI);

	double extinctionCoefficient = 0.5/sinEl;

	const double extinctionCoefficient = 0.5/sinEl;

	sunLAI = (1 - exp(-extinctionCoefficient*LAI))/extinctionCoefficient;

	if (sunLAI > LAI) sunLAI = LAI;

	if (sunLAI > 1) sunLAI = 1;

	cachedTime = t;

	cachedSunlitLAI = sunLAI;

}

std::string SunlitLeafAreaIndex::getName()const{

	return "sunlitLeafAreaIndex";
@@ -329,21 +323,17 @@ DerivativeBase * newInstantiationSunlitLeafAreaIndex(SimulaDynamic* const pSD){ 
   return new SunlitLeafAreaIndex(pSD);

}



ShadedLeafAreaIndex::ShadedLeafAreaIndex(SimulaDynamic* pSD):DerivativeBase(pSD), cachedTime(-10){

ShadedLeafAreaIndex::ShadedLeafAreaIndex(SimulaDynamic* pSD):DerivativeBase(pSD){

	leafAreaIndex = pSD->getSibling("leafAreaIndex");

	sunlitLeafAreaIndex = pSD->getSibling("sunlitLeafAreaIndex");

}

void ShadedLeafAreaIndex::calculate(const Time &t, double &shadedLAI){

	if (std::abs(t - cachedTime) < TIMEERROR){

		shadedLAI = cachedShadedLAI;

		return;

	}



	double LAI, sunLAI;

	leafAreaIndex->get(t, LAI);

	sunlitLeafAreaIndex->get(t, sunLAI);

	shadedLAI = LAI - sunLAI;

	cachedTime = t;

	cachedShadedLAI = shadedLAI;



}

std::string ShadedLeafAreaIndex::getName()const{

	return "shadedLeafAreaIndex";
@@ -353,7 +343,7 @@ DerivativeBase * newInstantiationShadedLeafAreaIndex(SimulaDynamic* const pSD){ 
   return new ShadedLeafAreaIndex(pSD);

}



MeanLeafAreaIndex::MeanLeafAreaIndex(SimulaDynamic* pSD):DerivativeBase(pSD), plantsPlantedAtDifferentTimes(false), splitBySunStatus(false)

MeanLeafAreaIndex::MeanLeafAreaIndex(SimulaDynamic* pSD):DerivativeBase(pSD), splitBySunStatus(false)

{

	std::string name = pSD->getName().substr(4, 6); // name = sunlit or shaded

	if (name == "Sunlit" || name == "Shaded"){
@@ -370,20 +360,20 @@ MeanLeafAreaIndex::MeanLeafAreaIndex(SimulaDynamic* pSD):DerivativeBase(pSD), pl 
		senescedLeafArea=pSD->existingSibling("senescedLeafArea","cm2");

	}

	plantArea=pSD->getSibling("plantArea","cm2");

	plantArea->get(0,pa);

	msg::warning("MeanLeafAreaIndex: Assuming all plants are planted at t = 0. If this is not the case, add 'plantsPlantedAtDifferentTimes' under 'environment'.");

	//plantArea->get(0,pa);

	//msg::warning("MeanLeafAreaIndex: Assuming all plants are planted at t = 0. If this is not the case, add 'plantsPlantedAtDifferentTimes' under 'environment'.");

	//area

	Coordinate minCorner, maxCorner;

	SimulaBase * params(ORIGIN->getChild("environment")->getChild("dimensions"));

	params->getChild("minCorner")->get(minCorner);

	params->getChild("maxCorner")->get(maxCorner);

	double x=fabs(maxCorner.x-minCorner.x);

	double z=fabs(maxCorner.z-minCorner.z);

	area=x*z;

	if(area<0.1) msg::error("MeanLeafAreaIndex: very small area calculated, check values for min and max corners");

	if(fabs(pa-area)>1.) msg::warning("MeanLeafAreaIndex: plant area and area of the box are not the same. Using plant Area");

	SimulaBase *probe = params->existingChild("plantsPlantedAtDifferentTimes");

	if (probe) probe->get(plantsPlantedAtDifferentTimes);

	//Coordinate minCorner, maxCorner;

	//SimulaBase * params(ORIGIN->getChild("environment")->getChild("dimensions"));

	//params->getChild("minCorner")->get(minCorner);

	//params->getChild("maxCorner")->get(maxCorner);

	//double x=fabs(maxCorner.x-minCorner.x);

	//double z=fabs(maxCorner.z-minCorner.z);

	//area=x*z;

	//if(area<0.1) msg::error("MeanLeafAreaIndex: very small area calculated, check values for min and max corners");

	//if(fabs(pa-area)>1.) msg::warning("MeanLeafAreaIndex: plant area and area of the box are not the same. Using plant Area");

	//SimulaBase *probe = params->existingChild("plantsPlantedAtDifferentTimes");

	//if (probe) probe->get(plantsPlantedAtDifferentTimes);

}

void MeanLeafAreaIndex::calculate(const Time &t, double &LAI){

	//calculate LAI
@@ -393,10 +383,8 @@ void MeanLeafAreaIndex::calculate(const Time &t, double &LAI){ 
		senescedLeafArea->get(t,sLA);

		LAI-=sLA;

	}

	if (plantsPlantedAtDifferentTimes){

	double pa;

	plantArea->get(t,pa);

		if(fabs(pa-area)>1.) msg::warning("MeanLeafAreaIndex: plant area and area of the box are not the same. Using plant Area");

	}

	LAI/=pa;//cm2/cm2

}

std::string MeanLeafAreaIndex::getName()const{

OpenSimRoot/src/modules/ShootModule/LeafArea.hpp

+1 −4
Original line number Diff line number Diff line
@@ -77,7 +77,6 @@ public: 
protected:

	void calculate(const Time &t, double &LAI);

	SimulaBase *leafAreaIndex, *solarElevationAngle;

	double cachedTime, cachedSunlitLAI;

};

class ShadedLeafAreaIndex:public DerivativeBase {

public:
@@ -86,7 +85,6 @@ public: 
protected:

	void calculate(const Time &t, double &LAI);

	SimulaBase *leafAreaIndex, *sunlitLeafAreaIndex;

	double cachedTime, cachedShadedLAI;

};

class MeanLeafAreaIndex:public DerivativeBase {

public:
@@ -94,9 +92,8 @@ public: 
	std::string getName()const;

protected:

	void calculate(const Time &t, double &LAI);

	double area, pa;

	SimulaBase* leafArea, *senescedLeafArea, *plantArea;

	bool plantsPlantedAtDifferentTimes, splitBySunStatus;

	bool splitBySunStatus;

};

/// Simulates the ratio between actual and potential leaf area

class LeafAreaReductionCoefficient:public DerivativeBase {