Commit e81f2b42 authored by Marco Drache's avatar Marco Drache
Browse files

feature: exportPolymerSegments as polmers to binary file

parent d6081bbf

include/SimulationController.h

+1 −0
Original line number Diff line number Diff line
@@ -74,6 +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 exportPolymerSegments(std::string _filename, int _speciesID, double _molPolymerSegments);

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

	

protected:

include/simulation.h

+1 −0
Original line number Diff line number Diff line
@@ -44,6 +44,7 @@ public: 
	void updateMCRates();



	bool exportPolymerSpecies(int _id, const std::string& _filename, FileTypePolymerSpecies _fileType, const kineticModel* _mcPolymerModel) const;

	bool exportPolymers(int _id, const std::string& _filename, const kineticModel* _mcPolymerModel, uint64_t _numPolymerSegments);

	const MnMw exportPolymersCLD(const std::string& _filename, const kineticModel* _mcPolymerModel) const;

	const MnMw exportPolymersCLDHompolymerization(const std::string& _filename, const kineticModel* _mcPolymerModel) const;

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

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::exportPolymerSegments(std::string _filename, int _speciesID, double _molPolymerSegments) {

	uint64_t numPolymerSegments = currentState->getNumMolecules(_molPolymerSegments);

	kMC->exportPolymers(_speciesID, _filename, currentModel, numPolymerSegments);

}



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);

src/simulation.cpp

+37 −0
Original line number Diff line number Diff line
@@ -703,6 +703,43 @@ bool Simulation::exportPolymerSpecies(int _id, const std::string& _filename, Fil 
	}

	return false;

}

bool Simulation::exportPolymers(int _id, const std::string& _filename, const kineticModel* _mcPolymerModel, uint64_t _numPolymerSegments) {

	int indexMacro = 0;

	for (auto& elem : macromolSpecies) {

		if (elem->getID() == _id) {

			string filenamebin = _filename;

			ofstream binfile(filenamebin, ofstream::out | ofstream::binary);

			uint64_t numPolymerSegmentsLeft = _numPolymerSegments;

			vector<Polymer*> polymerForExport;

			do {

				Polymer* p = elem->popPolymerForTransfer(_id);

				uint64_t numMonomersAll = 0;

				if (p != nullptr) {

					for (size_t i = 0; i < solidsContentBalance.solidsContentMoleculeCounter.size(); i++) {

						uint64_t numMonomers = p->getM(int(i));

						uint64_t& currentCount = solidsContentBalance.solidsContentMoleculeCounter[i] -= numMonomers;

						numMonomersAll += numMonomers;

					}

				}

				polymerForExport.push_back(elem->popPolymerForTransfer(_id));

				if (numPolymerSegmentsLeft < numMonomersAll) {

					numPolymerSegmentsLeft = 0;

				}

				else {

					numPolymerSegmentsLeft -= numMonomersAll;

				}

			} while (numPolymerSegmentsLeft > 0);

			size_t numPolymers = polymerForExport.size();

			binfile.write((const char*)&numPolymers, sizeof(size_t));

			for (size_t i = 0; i < polymerForExport.size(); i++) {

				polymerForExport.at(i)->exportPolymer(&binfile);

			}

			return true;

		}

		++indexMacro;

	}

	return false;

}

const MnMw Simulation::exportPolymersCLDHompolymerization(const string& _filename, const kineticModel* _mcPolymerModel) const {

	const vector<speciesObject> speciesObjects = _mcPolymerModel->getSpecies();

	vector<string> monomerName;