feature: add reaction template Transfer_dormant_radical_formed (b909216e) · Commits · mcPolymer / mcPolymer

include/Reaction.h

+9 −3

Original line number	Diff line number	Diff line
		@@ -216,11 +216,17 @@ private:
		class Transfer : public Reaction {
		public:
		Transfer(const double* _kmc, std::vector <uint64_t> _eductc, std::vector<uint64_t> _productc,
		polymerSpecies* _macroEduct1, polymerSpecies* _macroProduct1, bool _keepRadical);
		polymerSpecies* _macroEduct1, polymerSpecies* _macroProduct1);
		virtual double calculatePartialProbability() const override;
		virtual TerminationConditions execute() override;
		};

		class Transfer_dormant_radical_formed : public Reaction {
		public:
		Transfer_dormant_radical_formed(const double* _kmc, std::vector <uint64_t> _eductc, std::vector<uint64_t> _productc,
		polymerSpecies* _macroEduct1, polymerSpecies* _macroProduct1);
		virtual double calculatePartialProbability() const override;
		virtual TerminationConditions execute() override;
		private:
		bool keepRadical = false;
		};

		class Depropagation : public Reaction {

include/modelObjects.h

+1 −1

Original line number	Diff line number	Diff line
		@@ -56,6 +56,7 @@ enum class ReactionTemplate : uint16_t {
		ThermalInitiation2,
		ThermalInitiation3,
		Transfer,
		Transfer_dormant_radical_formed,
		TransferToMonomer,
		TransferToPolymer,
		TransferToPolymer_HYC,
		@@ -171,7 +172,6 @@ struct reactionObject {

		std::vector<int> productIdList;
		std::string optionalParameterFilename = "";
		bool keepRadical = false;
		};
		struct pluginObject {
		int id = 0;

src/Reaction.cpp

+36 −5

Original line number	Diff line number	Diff line
		@@ -595,7 +595,7 @@ TerminationConditions ThermalInitiation3::execute() {
		}

		Transfer::Transfer(const double* _kmc, std::vector <uint64_t> _eductc, std::vector<uint64_t> _productc,
		polymerSpecies* _macroEduct1, polymerSpecies* _macroProduct1, bool _keepRadical)
		polymerSpecies* _macroEduct1, polymerSpecies* _macroProduct1)
		: Reaction(_eductc.size(), _productc.size(), _kmc, 1, 1) {
		for (size_t i = 0; i < _eductc.size(); i++) {
		eductCounter[i] = _eductc[i];
		@@ -605,7 +605,6 @@ Transfer::Transfer(const double* _kmc, std::vector <uint64_t*> _eductc, std::vec
		}
		macroEduct[0] = _macroEduct1;
		macroProduct[0] = _macroProduct1;
		keepRadical = _keepRadical;
		}
		TerminationConditions Transfer::execute() {
		for (size_t i = 0; i < eductCounter.size(); i++) {
		@@ -615,9 +614,9 @@ TerminationConditions Transfer::execute() {
		++* productCounter[i];
		}
		Polymer* p1 = macroEduct[0]->popPolymer();
		if (!keepRadical) {

		p1->removeRadical();
		}

		macroProduct[0]->addPolymer(p1);
		return TerminationConditions::Undefined;
		}
		@@ -629,6 +628,38 @@ double Transfer::calculatePartialProbability() const {
		return Probability;
		}

		Transfer_dormant_radical_formed::Transfer_dormant_radical_formed(const double* _kmc, std::vector <uint64_t> _eductc, std::vector<uint64_t> _productc,
		polymerSpecies* _macroEduct1, polymerSpecies* _macroProduct1)
		: Reaction(_eductc.size(), _productc.size(), _kmc, 1, 1) {
		for (size_t i = 0; i < _eductc.size(); i++) {
		eductCounter[i] = _eductc[i];
		}
		for (size_t i = 0; i < _productc.size(); i++) {
		productCounter[i] = _productc[i];
		}
		macroEduct[0] = _macroEduct1;
		macroProduct[0] = _macroProduct1;
		}
		TerminationConditions Transfer_dormant_radical_formed::execute() {
		for (size_t i = 0; i < eductCounter.size(); i++) {
		--*eductCounter[i];
		}
		for (size_t i = 0; i < productCounter.size(); i++) {
		++*productCounter[i];
		}
		Polymer* p1 = macroEduct[0]->popPolymer();

		macroProduct[0]->addPolymer(p1);
		return TerminationConditions::Undefined;
		}
		double Transfer_dormant_radical_formed::calculatePartialProbability() const {
		double Probability = kmc *eductCounter[0];
		for (size_t i = 1; i < eductCounter.size(); i++) {
		Probability = eductCounter[i];
		}
		return Probability;
		}

		Depropagation::Depropagation(const double* _kmc, std::vector <uint64_t> _eductc, std::vector<uint64_t> _productc,
		polymerSpecies* _macroEduct1, polymerSpecies* _macroProduct1, int _monomerID)
		: Reaction(_eductc.size(), _productc.size(), _kmc, 1, 1), monomerID(_monomerID) {

src/filesJSON.cpp

+1 −3

Original line number	Diff line number	Diff line
		@@ -136,7 +136,6 @@ void importModelFromJSON(const string &_filename, kineticModel* _mcPolymerModel)
		reactionObj.id = countReactions;
		reactionObj.coefficientID = getCoefficientID(reaction["coefficient"], coefficientObjectList);
		reactionObj.rktTemplate = StringToReactionTemplate(reaction["template"]);
		reactionObj.keepRadical = reaction["keepRadical"];

		if (reaction.count("filename") > 0) {
		reactionObj.optionalParameterFilename = reaction["filename"];
		@@ -304,7 +303,6 @@ void exportModelToJSON(const string &_filename,
		reaction[productLabel] = _speciesObjects.at(elemReactants).name;
		++countProducts;
		}
		reaction["keepRadical"] = elem.keepRadical;
		reactionArrayJSON.push_back(reaction);
		}
		json pluginArrayJSON;

src/modelObjects.cpp

+5 −0

Original line number	Diff line number	Diff line
		@@ -91,6 +91,8 @@ std::string ReactionTemplateToString(ReactionTemplate _template) {
		return "ThermalInitiation3";
		case ReactionTemplate::Transfer:
		return "Transfer";
		case ReactionTemplate::Transfer_dormant_radical_formed:
		return "Transfer_dormant_radical_formed";
		case ReactionTemplate::TransferToMonomer:
		return "TransferToMonomer";
		case ReactionTemplate::TransferToPolymer:
		@@ -173,6 +175,9 @@ ReactionTemplate StringToReactionTemplate(const std::string& _str) {
		if (_str == "Transfer") {
		return ReactionTemplate::Transfer;
		}
		if (_str == "Transfer_dormant_radical_formed") {
		return ReactionTemplate::Transfer_dormant_radical_formed;
		}
		if (_str == "Depropagation") {
		return ReactionTemplate::Depropagation;
		}