Manual edits after master (fb83a495) · Commits · rootmodels / OpenSimRoot

OpenSimRoot/InputFiles/templates/plantTemplate.IncludeLeafSenescence.xml

+15 −10

Original line number	Diff line number	Diff line
		@@ -29,24 +29,29 @@ note that this requires historical information on leave area, so the garbage col
		name="senescedLeafDryWeight"
		unit="g"
		function="leafSenescence" />

		<!-- these are optional and can be renamed, the code does not use them -->
		<SimulaDerivative name="leafArea_green" function="useFormula">
		<SimulaConstant name="formula" type="string"> leafArea - senescedLeafArea </SimulaConstant>
		</SimulaDerivative>
		<SimulaDerivative name="leafDryWeight_green" function="useFormula">
		<SimulaConstant name="formula" type="string"> leafDryWeight - senescedLeafDryWeight </SimulaConstant>
		<SimulaDerivative
		name="greenLeafArea"
		unit="cm2"
		function="useFormula">
		<SimulaConstant
		name="formula"
		type="string"> leafArea - senescedLeafArea
		</SimulaConstant>
		</SimulaDerivative>
		</SimulaDirective>
		<SimulaDirective path="/plants">
		<SimulaVariable name="senescedLeafArea" function="sumOverAllPlantShoots" unit="cm2" />
		</SimulaDirective>


		<SimulaDirective path="/plantTemplate">
		<SimulaDerivative name="shootDryWeight_green" function="useFormula">
		<SimulaDerivative name="greenShootDryWeight" function="useFormula">
		<SimulaConstant name="formula" type="string"> shootDryWeight - senescedLeafDryWeight </SimulaConstant>
		<SimulaBase name="variablePaths">
		<SimulaConstant name="senescedLeafDryWeight" type="string"> plantPosition/shoot/senescedLeafDryWeight </SimulaConstant>
		</SimulaBase>
		</SimulaDerivative>
		<SimulaDerivative name="plantDryWeight_green" function="useFormula">
		<SimulaDerivative name="greenPlantDryWeight" function="useFormula">
		<SimulaConstant name="formula" type="string"> plantDryWeight - senescedLeafDryWeight </SimulaConstant>
		<SimulaBase name="variablePaths">
		<SimulaConstant name="senescedLeafDryWeight" type="string"> plantPosition/shoot/senescedLeafDryWeight </SimulaConstant>

OpenSimRoot/src/engine/SimulaBase.cpp

+70 −39

Original line number	Diff line number	Diff line
		@@ -412,42 +412,21 @@ SimulaBase* SimulaBase::existingSibling(const std::string& name,const Unit& u){


		SimulaBase* SimulaBase::getPath(const std::string &name, const Time &t){
		SimulaBase *probe(getPath(name));
		if(!probe->evaluateTime(t)) msg::error("SimulaBase::getPath: path "+getPath()+'/'+name+" found but life time is not correct.");
		SimulaBase *probe(existingPath(name,t));
		if(!probe) msg::error("SimulaBase::getPath: path "+getPath()+name+" not found");
		return probe;
		}
		SimulaBase* SimulaBase::getPath(const std::string &name, const Unit &u){
		SimulaBase *probe(getPath(name));
		probe->checkUnit(u);
		SimulaBase *probe(existingPath(name,u));
		if(!probe) {
		std::string p(name[0]=='/'?"":getPath());
		msg::error("SimulaBase::getPath: path "+p+name+" not found");
		}
		return probe;
		}
		SimulaBase* SimulaBase::getPath(const std::string &name){
		//Separate path into list names
		std::list<std::string> list;
		std::string::size_type pos(0);
		//loop through the list
		SimulaBase* probe;
		Database* l;
		if(name[pos]=='/'){
		++pos;
		while (pos<name.size()) list.push_back(nextWord(name,pos,'/'));
		probe=ORIGIN;
		}else{
		while (pos<name.size()) list.push_back(nextWord(name,pos,'/'));
		probe=this;
		}
		for(std::list<std::string>::iterator it(list.begin());it!=list.end() && probe!=nullptr ;++it){
		if(*it==".."){
		probe=probe->getParent();
		}else{
		l=probe->hasChildren();
		if(l){
		probe=l->get(*it);
		}else{
		msg::error("SimulaBase::getPath: path "+getPath()+'/'+name+" not found. "+probe->getPath()+" has no children.");
		}
		}
		}
		SimulaBase *probe(existingPath(name));
		if(!probe) msg::error("SimulaBase::getPath: path "+getPath()+name+" not found");
		return probe;
		}

		@@ -475,7 +454,9 @@ SimulaBase* SimulaBase::getOneOfThesePathsIfExisting(const std::string &name0,
		return probe;
		}

		SimulaBase* SimulaBase::existingPath(const std::string &name){


		SimulaBase* SimulaBase::existingPath(const std::string &name, const Time &t){
		//Separate path into list names
		std::list<std::string> list;
		std::string::size_type pos(0);
		@@ -496,7 +477,7 @@ SimulaBase* SimulaBase::existingPath(const std::string &name){
		}else{
		l=probe->hasChildren();
		if(l){
		probe=l->existing(*it);
		probe=l->existing(*it,t);
		}else{
		probe=nullptr;
		}
		@@ -504,14 +485,33 @@ SimulaBase* SimulaBase::existingPath(const std::string &name){
		}
		return probe;
		}

		SimulaBase* SimulaBase::existingPath(const std::string &name, const Time &t){
		SimulaBase* probe = existingPath(name);
		if(probe && ! probe->evaluateTime(t)) probe=nullptr;
		return probe;
		}
		SimulaBase* SimulaBase::existingPath(const std::string &name, const Unit &u){
		SimulaBase* probe = existingPath(name);
		//Separate path into list names
		std::list<std::string> list;
		std::string::size_type pos(0);
		//loop through the list
		SimulaBase* probe;
		Database* l;
		if(name[pos]=='/'){
		++pos;
		while (pos<name.size()) list.push_back(nextWord(name,pos,'/'));
		probe=ORIGIN;
		}else{
		while (pos<name.size()) list.push_back(nextWord(name,pos,'/'));
		probe=this;
		}
		for(std::list<std::string>::iterator it(list.begin());it!=list.end() && probe!=nullptr ;++it){
		if(*it==".."){
		probe=probe->getParent();
		}else{
		l=probe->hasChildren();
		if(l){
		probe=l->existing(*it);
		}else{
		probe=nullptr;
		}
		}
		}
		if(probe) probe->checkUnit(u);
		return probe;
		}
		@@ -628,6 +628,37 @@ void SimulaBase::stopUpdatefunction(){
		if(attributes) attributes->stopUpdatefunction();
		}

		SimulaBase* SimulaBase::existingPath(const std::string &name){
		//Separate path into list names
		std::list<std::string> list;
		std::string::size_type pos(0);
		//loop through the list
		SimulaBase* probe;
		Database* l;
		if(name[pos]=='/'){
		++pos;
		while (pos<name.size()) list.push_back(nextWord(name,pos,'/'));
		probe=ORIGIN;
		}else{
		while (pos<name.size()) list.push_back(nextWord(name,pos,'/'));
		probe=this;
		}
		for(std::list<std::string>::iterator it(list.begin());it!=list.end() && probe!=nullptr ;++it){
		if(*it==".."){
		probe=probe->getParent();
		}else{
		l=probe->hasChildren();
		if(l){
		probe=l->existing(*it);
		}else{
		probe=nullptr;
		}
		}
		}
		return probe;
		}


		///@todo getNext, getFirst and getPrevious are expensive code, which could be done more elegantly?
		SimulaBase* SimulaBase::getNextSibling(const Time &t){
		Database *a=getParent()->getChildren();

OpenSimRoot/src/modules/PlantNutrients/OptimalNutrientContent.cpp

+43 −11

Original line number	Diff line number	Diff line
		@@ -42,13 +42,26 @@ DerivativeBase * newInstantiationUseRootClassAndNutrientSpecificTable(SimulaDyna
		bool OptimalNutrientContent::issueMessage(true);

		OptimalNutrientContent::OptimalNutrientContent(SimulaDynamic* pSD) :
		TotalBaseLabeled(pSD) {
		TotalBaseLabeled(pSD),
		current(nullptr), dw(nullptr), rca(nullptr), paramConc(nullptr) {
		std::string l(pSD->getName().substr(11, 7));
		if (l[0] == 'O')
		l[0] = 'o';
		if (l[0] == 'M')
		l[0] = 'm';
		current = pSD->getSibling(l + "NutrientConcentration");
		current = pSD->existingSibling(l + "NutrientConcentration");
		if(!current){
		//use parameter section to get target concentrations
		//plant type and root type
		std::string plantType;
		PLANTTYPE(plantType,pSD);
		//get the root type
		std::string rootType;
		pSD->getParent(4)->getChild("rootType")->get(rootType);
		SimulaBase *param=GETROOTPARAMETERS(plantType,rootType);
		paramConc=param->getChild(pSD->getParent()->getName())->getChild(l + "NutrientConcentration");
		}

		//dryweight
		dw = pSD->getParent(2)->getChild("rootSegmentDryWeight");

		@@ -92,15 +105,23 @@ void OptimalNutrientContent::calculate(const Time &t, double &result) {
		l[0] = 'o';
		if (l[0] == 'M')
		l[0] = 'm';
		SimulaBase *next = getNext(t)->getSibling(l + "NutrientConcentration");
		SimulaBase *next = getNext(t);


		//get optimal concentrations at these datapoints
		double concD0(0);
		double concD0(0), concD1(0);
		if(current){
		current->get(t, concD0);
		double concD1(concD0);
		next=next->getSibling(l + "NutrientConcentration");
		if(next!=current && next->evaluateTime(t)){
		next->get(t, concD1);
		}
		}else{
		const double t0=pSD->getStartTime();
		const double t1=next->getStartTime();
		paramConc->get(t-t0,concD0);
		paramConc->get(t-t1,concD1);
		}

		//get dryweight
		double d;
		@@ -124,6 +145,7 @@ void OptimalNutrientContent::calculate(const Time &t, double &result) {
		scale_ = result;
		}
		bool OptimalNutrientContent::postIntegrationCorrection(SimulaVariable::Table & data) {
		//only for old input files that expect integration, rather than a simply algabreic solution.
		bool r(false);
		//iterators
		SimulaVariable::Table::iterator eit(data.end());
		@@ -148,7 +170,7 @@ DerivativeBase * newInstantiationOptimalNutrientContent(SimulaDynamic* const pSD
		}

		ShootOptimalNutrientContent::ShootOptimalNutrientContent(SimulaDynamic* pSD) :
		DerivativeBase(pSD), dws(nullptr) { //leafs or stem
		DerivativeBase(pSD), conc(nullptr), dw(nullptr), dws(nullptr), refTime(0) { //leafs or stem
		std::string s(pSD->getName());
		std::size_t n(s.size() - 22);
		std::string sp(s.substr(0, n));
		@@ -157,7 +179,17 @@ ShootOptimalNutrientContent::ShootOptimalNutrientContent(SimulaDynamic* pSD) :
		dw = pSD->getParent(2)->getChild(sp + "DryWeight", "g");
		if(sp=="leaf") dws = pSD->getParent(2)->existingChild("senescedLeafDryWeight", "g");
		//concentration
		conc = pSD->getSibling(som + "NutrientConcentration", pSD->getUnit() / "g");
		conc = pSD->existingSibling(som + "NutrientConcentration", pSD->getUnit() / "g");
		if(!conc){
		refTime=pSD->getStartTime();
		//use parameter section to get target concentrations
		//plant type and root type
		std::string plantType;
		PLANTTYPE(plantType,pSD);
		//get the root type
		SimulaBase *param=GETSHOOTPARAMETERS(plantType);
		conc = param->getChild(pSD->getParent()->getName())->getChild(som + "NutrientConcentration", pSD->getUnit() / "g");
		}
		}
		void ShootOptimalNutrientContent::calculate(const Time &t, double &result) {
		dw->get(t, result);
		@@ -167,7 +199,7 @@ void ShootOptimalNutrientContent::calculate(const Time &t, double &result) {
		result-=senescence;
		}
		double c;
		conc->get(t, c);
		conc->get(t-refTime, c);
		result *= c;
		}
		std::string ShootOptimalNutrientContent::getName() const {

OpenSimRoot/src/modules/PlantNutrients/OptimalNutrientContent.hpp

+2 −1

Original line number	Diff line number	Diff line
		@@ -39,7 +39,7 @@ public:
		std::string getName() const;
		protected:
		void calculate(const Time &t, double &var);
		SimulaBase current, dw, *rca;
		SimulaBase current, dw, rca, paramConc;
		static bool issueMessage;
		double scale_;
		};
		@@ -50,6 +50,7 @@ public:
		protected:
		void calculate(const Time &t, double &var);
		SimulaBase conc, dw, *dws;
		Time refTime;
		};
		class ActualNutrientContent: public TotalBaseLabeled {
		public: