[Echempp-devel] Experiment/Data Data.cpp, 1.1, 1.2 Data.hpp, 1.1, 1.2 Makefile.am, 1.11, 1.12
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[Echempp-devel] Experiment/Data Data.cpp, 1.1, 1.2 Data.hpp, 1.1, 1.2 Makefile.am, 1.11, 1.12
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From: beeblbrox <bee...@us...> - 2007-12-22 15:47:51
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Update of /cvsroot/echempp/Experiment/Data In directory sc8-pr-cvs17.sourceforge.net:/tmp/cvs-serv24265/Experiment/Data Modified Files: Data.cpp Data.hpp Makefile.am Log Message: Excluded all files except Data.{hpp,cpp} remove obsolete files later. Index: Data.cpp =================================================================== RCS file: /cvsroot/echempp/Experiment/Data/Data.cpp,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** Data.cpp 19 Dec 2007 13:24:54 -0000 1.1 --- Data.cpp 22 Dec 2007 15:47:38 -0000 1.2 *************** *** 5,9 **** --- 5,12 ---- const std::string MeasurementData::GUID = "MeasurementData"; const std::string MeasurementDataModSim::GUID = "MeasurementDataModSim"; + const std::string ModelPlotWidgetData::GUID = "ModelPlotWidgetData"; const std::string ConditionData::GUID = "ConditionData"; + const std::string MechanismConditions::GUID = "MechanismConditions"; + const std::string ModelParameterConditions::GUID = "ModelParameterConditions"; const std::string SolverConditions::GUID = "SolverConditions"; const std::string ConditionDataModSim::GUID = "ConditionDataModSim"; Index: Data.hpp =================================================================== RCS file: /cvsroot/echempp/Experiment/Data/Data.hpp,v retrieving revision 1.1 retrieving revision 1.2 diff -C2 -d -r1.1 -r1.2 *** Data.hpp 19 Dec 2007 13:24:54 -0000 1.1 --- Data.hpp 22 Dec 2007 15:47:38 -0000 1.2 *************** *** 171,174 **** --- 171,351 ---- }; + // data written by modelPlotWidget + class ModelPlotWidgetData + { + public: + BSUtilities::Serialization::AutoRegistor<ModelPlotWidgetData> reg; + static const std::string GUID; + std::vector<std::string> ids; + std::string x_unit; + std::string y_unit; + std::string z_unit; + std::vector<std::vector<double> > data; + private: + friend class boost::serialization::access; + template<class Archive> + void serialize(Archive & ar, const unsigned int version) + { + ar & BOOST_SERIALIZATION_NVP(ids) + & BOOST_SERIALIZATION_NVP(x_unit) + & BOOST_SERIALIZATION_NVP(y_unit) + & BOOST_SERIALIZATION_NVP(z_unit) + & BOOST_SERIALIZATION_NVP(data); + } + }; + + // data from mechanism dialog + class MechanismConditions + { + public: + BSUtilities::Serialization::AutoRegistor<MechanismConditions> reg; + static const std::string GUID; + bool chargeBalance; + bool stoichiometricBalance; + std::string mechanism; + std::set<int> activeBoundaries; + private: + friend class boost::serialization::access; + template<class Archive> + void serialize(Archive & ar, const unsigned int version) + { + ar & BOOST_SERIALIZATION_NVP(chargeBalance) + & BOOST_SERIALIZATION_NVP(stoichiometricBalance) + & BOOST_SERIALIZATION_NVP(mechanism) + & BOOST_SERIALIZATION_NVP(activeBoundaries); + } + }; + + // data from model parameters dialog + class ModelParameterConditions + { + public: + BSUtilities::Serialization::AutoRegistor<ModelParameterConditions> reg; + static const std::string GUID; + //! temperature + quantity::ThermodynamicTemperature temp; + //! electrode area + quantity::Area area; + //! map of concentrations + //! key = species index + GUI::model::ConcentrationMap dissConcs; + quantity::Concentration refDissConc; + int refConcIndex; + //! map of surface concentrations + //! key = species index + GUI::model::SurfaceConcentrationMap adsConcs; + //! map of surface concentrations + //! key = boundary index + GUI::model::SaturationConcentrationMap saturationConcs; + //! map of diffusion coefficients + //! key = species index + GUI::model::DiffusionCoefficientMap diffCoeffs; + quantity::DiffusionCoefficient refDiffCoeff; + int maxDiffCoeff; + //! map of formal potentials. + //! key = reactions index + GUI::model::ElectricPotentialMap formalPotentials; + //! map of ET coefficients (Butler Volmer law) + //! key = reaction index + std::map<GUI::model::uint_t,double> alphas; + //! map of heterogeneous rate constants. + //! key = reaction index + GUI::model::HeterogeneousRateConstantMap khs; + //! map of Langmuir equilibrium constants. + //! key = reaction index + GUI::model::LangmuirEquilibriumConstantMap langEquilConstants; + //! map of Langmuir adsorption rate constants + //! key = reaction index + GUI::model::LangmuirAdsorptionRateConstantMap langAdsRateConstants; + //! map of first order rate constants + //! key = reaction index + GUI::model::FirstOrderRateConstantMap firstOrderRateConstants; + //! key = reaction index + std::map<GUI::model::uint_t,double> homEquilibriumConstants; + std::map<GUI::model::uint_t,double> homForwardRateConstants; + std::map<GUI::model::uint_t,double> homBackwardRateConstants; + std::map<GUI::model::uint_t,double> homSurfEquilibriumConstants; + std::map<GUI::model::uint_t,double> homSurfForwardRateConstants; + std::map<GUI::model::uint_t,double> homSurfBackwardRateConstants; + std::map<GUI::model::uint_t,double> hetSurfEquilibriumConstants; + std::map<GUI::model::uint_t,double> hetSurfForwardRateConstants; + std::map<GUI::model::uint_t,double> hetSurfBackwardRateConstants; + //! indices of fixed thermodynamic paramters + std::set<GUI::model::uint_t> fixed; + unsigned int numRowsDissSpecies; + unsigned int numRowsAdsSpecies; + unsigned int numRowsSaturation; + unsigned int numRowsBvDiss; + unsigned int numRowsBvAds; + unsigned int numRowsLangmuir; + unsigned int numRowsHomPower; + unsigned int numRowsHomGen; + unsigned int numColsHomGen; + unsigned int numRowsHomSurfPower; + unsigned int numRowsHomSurfGen; + unsigned int numColsHomSurfGen; + unsigned int numRowsHetSurfPower; + unsigned int numRowsHetSurfGen; + unsigned int numColsHetSurfGen; + std::map<std::string, std::map<GUI::model::uint_t,std::vector<GUI::model::uint_t> > > genParams; + //! Key = col in homGenericTable and surfGenericTable (shifted by -1), + //! value = name of parameter + std::map<int,std::string> genColsParams; + //! Key = name of parameter, value = col in homGenericTable and surfGenericTable (shifted by -1) + std::map<std::string,int> genParamsCols; + std::map<std::string,double> genParamsValues; + private: + friend class boost::serialization::access; + template<class Archive> + void serialize(Archive & ar, const unsigned int version) + { + ar & BOOST_SERIALIZATION_NVP(temp) + & BOOST_SERIALIZATION_NVP(area) + & BOOST_SERIALIZATION_NVP(dissConcs) + & BOOST_SERIALIZATION_NVP(refDissConc) + & BOOST_SERIALIZATION_NVP(refConcIndex) + & BOOST_SERIALIZATION_NVP(adsConcs) + & BOOST_SERIALIZATION_NVP(saturationConcs) + & BOOST_SERIALIZATION_NVP(diffCoeffs) + & BOOST_SERIALIZATION_NVP(refDiffCoeff) + & BOOST_SERIALIZATION_NVP(maxDiffCoeff) + & BOOST_SERIALIZATION_NVP(formalPotentials) + & BOOST_SERIALIZATION_NVP(alphas) + & BOOST_SERIALIZATION_NVP(khs) + & BOOST_SERIALIZATION_NVP(langEquilConstants) + & BOOST_SERIALIZATION_NVP(langAdsRateConstants) + & BOOST_SERIALIZATION_NVP(firstOrderRateConstants) + & BOOST_SERIALIZATION_NVP(homEquilibriumConstants) + & BOOST_SERIALIZATION_NVP(homForwardRateConstants) + & BOOST_SERIALIZATION_NVP(homBackwardRateConstants) + & BOOST_SERIALIZATION_NVP(homSurfEquilibriumConstants) + & BOOST_SERIALIZATION_NVP(homSurfForwardRateConstants) + & BOOST_SERIALIZATION_NVP(homSurfBackwardRateConstants) + & BOOST_SERIALIZATION_NVP(hetSurfEquilibriumConstants) + & BOOST_SERIALIZATION_NVP(hetSurfForwardRateConstants) + & BOOST_SERIALIZATION_NVP(hetSurfBackwardRateConstants) + & BOOST_SERIALIZATION_NVP(fixed) + & BOOST_SERIALIZATION_NVP(numRowsDissSpecies) + & BOOST_SERIALIZATION_NVP(numRowsAdsSpecies) + & BOOST_SERIALIZATION_NVP(numRowsSaturation) + & BOOST_SERIALIZATION_NVP(numRowsBvDiss) + & BOOST_SERIALIZATION_NVP(numRowsBvAds) + & BOOST_SERIALIZATION_NVP(numRowsLangmuir) + & BOOST_SERIALIZATION_NVP(numRowsHomPower) + & BOOST_SERIALIZATION_NVP(numRowsHomGen) + & BOOST_SERIALIZATION_NVP(numColsHomGen) + & BOOST_SERIALIZATION_NVP(numRowsHomSurfPower) + & BOOST_SERIALIZATION_NVP(numRowsHomSurfGen) + & BOOST_SERIALIZATION_NVP(numColsHomSurfGen) + & BOOST_SERIALIZATION_NVP(numRowsHetSurfPower) + & BOOST_SERIALIZATION_NVP(numRowsHetSurfGen) + & BOOST_SERIALIZATION_NVP(numColsHetSurfGen) + & BOOST_SERIALIZATION_NVP(genParams) + & BOOST_SERIALIZATION_NVP(genColsParams) + & BOOST_SERIALIZATION_NVP(genParamsCols) + & BOOST_SERIALIZATION_NVP(genParamsValues); + } + }; + // data from solver dialog class SolverConditions *************** *** 283,366 **** ExcitationFunctions::itExcitationFunction itExcitation0; ExcitationFunctions::itExcitationFunction itExcitation1; ! // data from mechanism dialog ! bool chargeBalance; ! bool stoichiometricBalance; ! std::string mechanism; ! std::set<int> activeBoundaries; ! // data from model parameters dialog ! //! temperature ! quantity::ThermodynamicTemperature temp; ! //! electrode area ! quantity::Area area; ! //! map of concentrations ! //! key = species index ! GUI::model::ConcentrationMap dissConcs; ! quantity::Concentration refDissConc; ! int refConcIndex; ! //! map of surface concentrations ! //! key = species index ! GUI::model::SurfaceConcentrationMap adsConcs; ! //! map of surface concentrations ! //! key = boundary index ! GUI::model::SaturationConcentrationMap saturationConcs; ! //! map of diffusion coefficients ! //! key = species index ! GUI::model::DiffusionCoefficientMap diffCoeffs; ! quantity::DiffusionCoefficient refDiffCoeff; ! int maxDiffCoeff; ! //! map of formal potentials. ! //! key = reactions index ! GUI::model::ElectricPotentialMap formalPotentials; ! //! map of ET coefficients (Butler Volmer law) ! //! key = reaction index ! std::map<GUI::model::uint_t,double> alphas; ! //! map of heterogeneous rate constants. ! //! key = reaction index ! GUI::model::HeterogeneousRateConstantMap khs; ! //! map of Langmuir equilibrium constants. ! //! key = reaction index ! GUI::model::LangmuirEquilibriumConstantMap langEquilConstants; ! //! map of Langmuir adsorption rate constants ! //! key = reaction index ! GUI::model::LangmuirAdsorptionRateConstantMap langAdsRateConstants; ! //! map of first order rate constants ! //! key = reaction index ! GUI::model::FirstOrderRateConstantMap firstOrderRateConstants; ! //! key = reaction index ! std::map<GUI::model::uint_t,double> homEquilibriumConstants; ! std::map<GUI::model::uint_t,double> homForwardRateConstants; ! std::map<GUI::model::uint_t,double> homBackwardRateConstants; ! std::map<GUI::model::uint_t,double> homSurfEquilibriumConstants; ! std::map<GUI::model::uint_t,double> homSurfForwardRateConstants; ! std::map<GUI::model::uint_t,double> homSurfBackwardRateConstants; ! std::map<GUI::model::uint_t,double> hetSurfEquilibriumConstants; ! std::map<GUI::model::uint_t,double> hetSurfForwardRateConstants; ! std::map<GUI::model::uint_t,double> hetSurfBackwardRateConstants; ! //! indices of fixed thermodynamic paramters ! std::set<GUI::model::uint_t> fixed; ! unsigned int numRowsDissSpecies; ! unsigned int numRowsAdsSpecies; ! unsigned int numRowsSaturation; ! unsigned int numRowsBvDiss; ! unsigned int numRowsBvAds; ! unsigned int numRowsLangmuir; ! unsigned int numRowsHomPower; ! unsigned int numRowsHomGen; ! unsigned int numColsHomGen; ! unsigned int numRowsHomSurfPower; ! unsigned int numRowsHomSurfGen; ! unsigned int numColsHomSurfGen; ! unsigned int numRowsHetSurfPower; ! unsigned int numRowsHetSurfGen; ! unsigned int numColsHetSurfGen; ! std::map<std::string, std::map<GUI::model::uint_t,std::vector<GUI::model::uint_t> > > genParams; ! //! Key = col in homGenericTable and surfGenericTable (shifted by -1), ! //! value = name of parameter ! std::map<int,std::string> genColsParams; ! //! Key = name of parameter, value = col in homGenericTable and surfGenericTable (shifted by -1) ! std::map<std::string,int> genParamsCols; ! std::map<std::string,double> genParamsValues; ! ! // data from equilibrium dialog double maxTime; --- 460,465 ---- ExcitationFunctions::itExcitationFunction itExcitation0; ExcitationFunctions::itExcitationFunction itExcitation1; ! MechanismConditions mc; ! ModelParameterConditions mpc; // data from equilibrium dialog double maxTime; *************** *** 413,465 **** & BOOST_SERIALIZATION_NVP(itExcitation0) & BOOST_SERIALIZATION_NVP(itExcitation1) ! & BOOST_SERIALIZATION_NVP(chargeBalance) ! & BOOST_SERIALIZATION_NVP(stoichiometricBalance) ! & BOOST_SERIALIZATION_NVP(mechanism) ! & BOOST_SERIALIZATION_NVP(activeBoundaries) ! & BOOST_SERIALIZATION_NVP(temp) ! & BOOST_SERIALIZATION_NVP(area) ! & BOOST_SERIALIZATION_NVP(dissConcs) ! & BOOST_SERIALIZATION_NVP(refDissConc) ! & BOOST_SERIALIZATION_NVP(refConcIndex) ! & BOOST_SERIALIZATION_NVP(adsConcs) ! & BOOST_SERIALIZATION_NVP(saturationConcs) ! & BOOST_SERIALIZATION_NVP(diffCoeffs) ! & BOOST_SERIALIZATION_NVP(refDiffCoeff) ! & BOOST_SERIALIZATION_NVP(maxDiffCoeff) ! & BOOST_SERIALIZATION_NVP(formalPotentials) ! & BOOST_SERIALIZATION_NVP(alphas) ! & BOOST_SERIALIZATION_NVP(khs) ! & BOOST_SERIALIZATION_NVP(langEquilConstants) ! & BOOST_SERIALIZATION_NVP(langAdsRateConstants) ! & BOOST_SERIALIZATION_NVP(firstOrderRateConstants) ! & BOOST_SERIALIZATION_NVP(homEquilibriumConstants) ! & BOOST_SERIALIZATION_NVP(homForwardRateConstants) ! & BOOST_SERIALIZATION_NVP(homBackwardRateConstants) ! & BOOST_SERIALIZATION_NVP(homSurfEquilibriumConstants) ! & BOOST_SERIALIZATION_NVP(homSurfForwardRateConstants) ! & BOOST_SERIALIZATION_NVP(homSurfBackwardRateConstants) ! & BOOST_SERIALIZATION_NVP(hetSurfEquilibriumConstants) ! & BOOST_SERIALIZATION_NVP(hetSurfForwardRateConstants) ! & BOOST_SERIALIZATION_NVP(hetSurfBackwardRateConstants) ! & BOOST_SERIALIZATION_NVP(fixed) ! & BOOST_SERIALIZATION_NVP(numRowsDissSpecies) ! & BOOST_SERIALIZATION_NVP(numRowsAdsSpecies) ! & BOOST_SERIALIZATION_NVP(numRowsSaturation) ! & BOOST_SERIALIZATION_NVP(numRowsBvDiss) ! & BOOST_SERIALIZATION_NVP(numRowsBvAds) ! & BOOST_SERIALIZATION_NVP(numRowsLangmuir) ! & BOOST_SERIALIZATION_NVP(numRowsHomPower) ! & BOOST_SERIALIZATION_NVP(numRowsHomGen) ! & BOOST_SERIALIZATION_NVP(numColsHomGen) ! & BOOST_SERIALIZATION_NVP(numRowsHomSurfPower) ! & BOOST_SERIALIZATION_NVP(numRowsHomSurfGen) ! & BOOST_SERIALIZATION_NVP(numColsHomSurfGen) ! & BOOST_SERIALIZATION_NVP(numRowsHetSurfPower) ! & BOOST_SERIALIZATION_NVP(numRowsHetSurfGen) ! & BOOST_SERIALIZATION_NVP(numColsHetSurfGen) ! & BOOST_SERIALIZATION_NVP(genParams) ! & BOOST_SERIALIZATION_NVP(genColsParams) ! & BOOST_SERIALIZATION_NVP(genParamsCols) ! & BOOST_SERIALIZATION_NVP(genParamsValues) & BOOST_SERIALIZATION_NVP(maxTime) & BOOST_SERIALIZATION_NVP(accuracy) --- 512,517 ---- & BOOST_SERIALIZATION_NVP(itExcitation0) & BOOST_SERIALIZATION_NVP(itExcitation1) ! & BOOST_SERIALIZATION_NVP(mc) ! & BOOST_SERIALIZATION_NVP(mpc) & BOOST_SERIALIZATION_NVP(maxTime) & BOOST_SERIALIZATION_NVP(accuracy) Index: Makefile.am =================================================================== RCS file: /cvsroot/echempp/Experiment/Data/Makefile.am,v retrieving revision 1.11 retrieving revision 1.12 diff -C2 -d -r1.11 -r1.12 *** Makefile.am 19 Dec 2007 13:24:54 -0000 1.11 --- Makefile.am 22 Dec 2007 15:47:38 -0000 1.12 *************** *** 13,27 **** -I$(BSUTILITIESSRC) ! libeppData_la_SOURCES = data.hpp \ ! data.cpp \ ! Data.hpp \ ! Data.cpp \ ! dataError.hpp\ ! generalData.hpp\ ! electrochemicalData.hpp\ ! stateData.hpp ! libeppData_la_CXXFLAGS = -Wall -Werror -pedantic-errors\ ! -DTIXML_USE_STL=YES libeppData_la_LDFLAGS = -version-info 0:0:0 --- 13,20 ---- -I$(BSUTILITIESSRC) ! libeppData_la_SOURCES = Data.hpp \ ! Data.cpp ! libeppData_la_CXXFLAGS = -Wall -Werror -pedantic-errors libeppData_la_LDFLAGS = -version-info 0:0:0 |
