Commit d6081bbf authored by Marco Drache's avatar Marco Drache
Browse files

feature: label and filter polymers during binary export

parent 08b15b39

include/SimulationController.h

+1 −1
Original line number Diff line number Diff line
@@ -74,7 +74,7 @@ public: 
	void exportConcentrationNumMolecules(double _reactionTime) const;

	void exportReactionsCount(double _reactionTime) const;

	void exportPolymers(std::string _prefixFilename, double _reactionTime, bool _binaryExport, bool _writeHeader);

	void exportLabeledPolymers(std::string _prefixFilename, int _id1, int _id2, double _reactionTime, bool _writeHeader, bool _filter);

	void exportLabeledPolymers(std::string _prefixFilename, int _id1, int _id2, uint64_t _filter, double _reactionTime, bool _writeHeader);

	

protected:

	void exportComplete(time_t _timerStart, TerminationConditions _terminationConditions) const;

include/polymerSpecies.h

+3 −0
Original line number Diff line number Diff line
@@ -40,6 +40,8 @@ public: 
	void exportCLD(const std::string& _filename, const kineticModel* _mcPolymerModel);

	void writeCLD(const std::string& _filename, const std::map<int, std::string>& _speciesNameMap, const std::map<int, int>& _speciesTypeMap, const std::map<int, double>& _molarMassMap) const;

	void exportPolymers(std::ofstream* _os) const;

	void exportPolymersSubsetNoFilter(std::ofstream* _os, uint64_t _filter);

	void exportPolymersSubsetFilter(std::ofstream* _os, uint64_t _filter);

	void getCLD(Histogram* _CLD, const std::vector<Histogram*>& _monomerHistogram);

	void getCLDHomopolymerization(Histogram* _CLD);

	std::vector<int> getChainLengthList() const;
@@ -58,6 +60,7 @@ public: 
	void addPolymers(std::vector<Polymer*> _p);

	void addPolymerFromCombination(Polymer* p1, Polymer* p2);

	std::vector<Polymer*> getAllPolymers();

	uint64_t getNumFilterPolymers(uint64_t _filter);

private:

	Polymer* getPolymer() const;

	std::vector<Polymer*> p;

include/simulation.h

+2 −0
Original line number Diff line number Diff line
@@ -48,6 +48,8 @@ public: 
	const MnMw exportPolymersCLDHompolymerization(const std::string& _filename, const kineticModel* _mcPolymerModel) const;

	bool exportPolymersBinary(const std::string& _filename, const kineticModel* _mcPolymerModel) const;

	bool exportPolymersBinary(const std::string& _filename, const kineticModel* _mcPolymerModel, const uint64_t _addID, const bool _writeHeader) const;

	bool exportPolymersBinary(const std::string& _filename, const std::string& _filenameFilter, const kineticModel* _mcPolymerModel, const int _id1, const int _id2, const uint64_t _filter, const bool _writeHeader) const;

	

	void setMolecules(int index, uint64_t count);

	void setRateCoeficient(int _id, double _value);

	void addMolecules(int _id, int64_t _plusmole);

src/SimulationController.cpp

+5 −0
Original line number Diff line number Diff line
@@ -463,6 +463,11 @@ void SimulationController::exportPolymers(std::string _prefixFilename, double _r 
		kMC->exportPolymersCLD(simulationParameter.outputdir + "/" + "Polymers." + to_string(_reactionTime), currentModel);

	}

}

void SimulationController::exportLabeledPolymers(std::string _prefixFilename, int _id1, int _id2, uint64_t _filter, double _reactionTime, bool _writeHeader) {

	string filename = simulationParameter.outputdir + "/" + _prefixFilename + "Polymers." + to_string(_reactionTime);

	string filenameFilter = simulationParameter.outputdir + "/" + _prefixFilename + "PolymersFilter." + to_string(_reactionTime);

	kMC->exportPolymersBinary(filename, filenameFilter, currentModel, _id1, _id2, _filter, _writeHeader);

}

int SimulationController::getSpeciesIDTransferSpecies(TransferSpeciesDefinition _transferObject) {

	vector<parameterObject> parameterObjects  = currentModel->getParameters();

	string speciesName = "";

src/polymerSpecies.cpp

+47 −0
Original line number Diff line number Diff line
@@ -339,6 +339,9 @@ void polymerSpecies::getCLD(Histogram* _CLD, const vector<Histogram*> &_monomerH 
			}

		}

	}

	if (transferToPolymer) {

		p.resize(0);

	}

}

void polymerSpecies::exportCLD(const string& _filename, const kineticModel* _mcPolymerModel) {
@@ -528,6 +531,34 @@ void polymerSpecies::exportPolymers(ofstream* _os) const { 
		}

	}

}

void polymerSpecies::exportPolymersSubsetNoFilter(std::ofstream* _os, uint64_t _filter) {

	if (transferToPolymer) {

		p = bintree->analyzeAllPolymers();

	}

	for (const auto& elem : p) {

		Fragment* frg = elem->getFragment(0);

		if (frg->getLength() != _filter) {

			elem->exportPolymer(_os);

		}

	}

	if (transferToPolymer) {

		p.resize(0);

	}

}

void polymerSpecies::exportPolymersSubsetFilter(std::ofstream* _os, uint64_t _filter) {

	if (transferToPolymer) {

		p = bintree->analyzeAllPolymers();

	}

	for (const auto& elem : p) {

		Fragment* frg = elem->getFragment(0);

		if (frg->getLength() == _filter) {

			elem->exportPolymer(_os);

		}

	}

	if (transferToPolymer) {

		p.resize(0);

	}

}



size_t polymerSpecies::getSize() const {

	if (transferToPolymer) {
@@ -595,5 +626,21 @@ polymerSpeciesProperties polymerSpecies::getPolymerSpeciesProperties() { 
	}

	return properties;

}

uint64_t polymerSpecies::getNumFilterPolymers(uint64_t _filter) {

	if (transferToPolymer) {

		p = bintree->analyzeAllPolymers();

	}

	uint64_t numFilterPolymers = 0;

	for (const auto& elem : p) {

		Fragment* frg = elem->getFragment(0);

		if (frg->getLength() == _filter) {

			++numFilterPolymers;

		}

	}

	if (transferToPolymer) {

		p.resize(0);

	}

	return numFilterPolymers;

}

} // namespace