--- trunk/src/io/Globals.cpp 2010/01/08 17:15:27 1402 +++ branches/development/src/io/Globals.cpp 2013/02/20 15:39:39 1850 @@ -35,8 +35,9 @@ * * [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). * [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). - * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). - * [4] Vardeman & Gezelter, in progress (2009). + * [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ #include @@ -50,205 +51,272 @@ namespace OpenMD { #include "utils/simError.h" namespace OpenMD { -Globals::Globals() { - DefineParameter(ForceField, "forceField") - - DefineOptionalParameter(TargetTemp, "targetTemp"); - DefineOptionalParameter(Ensemble, "ensemble"); - DefineOptionalParameter(Dt, "dt"); - DefineOptionalParameter(RunTime, "runTime"); - DefineOptionalParameter(FinalConfig, "finalConfig"); - DefineOptionalParameter(SampleTime, "sampleTime"); - DefineOptionalParameter(ResetTime, "resetTime"); - DefineOptionalParameter(StatusTime, "statusTime"); - DefineOptionalParameter(CutoffRadius, "cutoffRadius"); - DefineOptionalParameter(SwitchingRadius, "switchingRadius"); - DefineOptionalParameter(TempSet, "tempSet"); - DefineOptionalParameter(ThermalTime, "thermalTime"); - DefineOptionalParameter(TargetPressure, "targetPressure"); - DefineOptionalParameter(TauThermostat, "tauThermostat"); - DefineOptionalParameter(TauBarostat, "tauBarostat"); - DefineOptionalParameter(ZconsTime, "zconsTime"); - DefineOptionalParameter(ZconsTol, "zconsTol"); - DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy"); - DefineOptionalParameter(Seed, "seed"); - DefineOptionalParameter(Minimizer, "minimizer"); - DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter"); - DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq"); - DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize"); - DefineOptionalParameter(MinimizerFTol, "minimizerFTol"); - DefineOptionalParameter(MinimizerGTol, "minimizerGTol"); - DefineOptionalParameter(MinimizerLSTol, "minimizerLSTol"); - DefineOptionalParameter(MinimizerLSMaxIter, "minimizerLSMaxIter"); - DefineOptionalParameter(ZconsGap, "zconsGap"); - DefineOptionalParameter(ZconsFixtime, "zconsFixtime"); - DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD"); - DefineOptionalParameter(ThermodynamicIntegrationLambda, "thermodynamicIntegrationLambda"); - DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK"); - DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant"); - DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName"); - DefineOptionalParameter(DampingAlpha, "dampingAlpha"); - DefineOptionalParameter(SurfaceTension, "surfaceTension"); - DefineOptionalParameter(PrintPressureTensor, "printPressureTensor"); - DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair"); - DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance"); - DefineOptionalParameter(CutoffPolicy, "cutoffPolicy"); - DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType"); - DefineOptionalParameter(HydroPropFile, "HydroPropFile"); - DefineOptionalParameter(Viscosity, "viscosity"); - DefineOptionalParameter(BeadSize, "beadSize"); - DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius"); - DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius"); - DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors"); - DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod"); - DefineOptionalParameter(MTM_Ce, "MTM_Ce"); - DefineOptionalParameter(MTM_G, "MTM_G"); - DefineOptionalParameter(MTM_Io, "MTM_Io"); - DefineOptionalParameter(MTM_Sigma, "MTM_Sigma"); - DefineOptionalParameter(MTM_R, "MTM_R"); - DefineOptionalParameter(Alpha, "alpha"); - + Globals::Globals() { - DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true); - DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true); - DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false); - DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false); - DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6); - DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE"); - DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED"); - DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5); - DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0); - DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0); - DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0); - DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY"); - DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false); - DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false); + flucQpars_ = new FluctuatingChargeParameters(); + rnemdPars_ = new RNEMDParameters(); + minimizerPars_ = new MinimizerParameters(); - DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false); - DefineOptionalParameterWithDefaultValue(RNEMD_exchangeTime, "RNEMD_exchangeTime", 100.0); - DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16); - DefineOptionalParameterWithDefaultValue(RNEMD_logWidth, "RNEMD_logWidth", 16); - DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale"); - DefineOptionalParameterWithDefaultValue(RNEMD_targetFlux, "RNEMD_targetFlux", 0.0); - DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all"); - DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false); - DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in"); - DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false); - DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex"); + DefineParameter(ForceField, "forceField"); + + DefineOptionalParameter(TargetTemp, "targetTemp"); + DefineOptionalParameter(Ensemble, "ensemble"); + DefineOptionalParameter(Dt, "dt"); + DefineOptionalParameter(RunTime, "runTime"); + DefineOptionalParameter(FinalConfig, "finalConfig"); + DefineOptionalParameter(SampleTime, "sampleTime"); + DefineOptionalParameter(ResetTime, "resetTime"); + DefineOptionalParameter(StatusTime, "statusTime"); + DefineOptionalParameter(CutoffRadius, "cutoffRadius"); + DefineOptionalParameter(SwitchingRadius, "switchingRadius"); + DefineOptionalParameter(TempSet, "tempSet"); + DefineOptionalParameter(ThermalTime, "thermalTime"); + DefineOptionalParameter(TargetPressure, "targetPressure"); + DefineOptionalParameter(TauThermostat, "tauThermostat"); + DefineOptionalParameter(TauBarostat, "tauBarostat"); + DefineOptionalParameter(ZconsTime, "zconsTime"); + DefineOptionalParameter(ZconsTol, "zconsTol"); + DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy"); + DefineOptionalParameter(Seed, "seed"); + DefineOptionalParameter(ZconsGap, "zconsGap"); + DefineOptionalParameter(ZconsFixtime, "zconsFixtime"); + DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD"); + DefineOptionalParameter(ThermodynamicIntegrationLambda, + "thermodynamicIntegrationLambda"); + DefineOptionalParameter(ThermodynamicIntegrationK, + "thermodynamicIntegrationK"); + DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant"); + DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName"); + DefineOptionalParameter(DampingAlpha, "dampingAlpha"); + DefineOptionalParameter(SurfaceTension, "surfaceTension"); + DefineOptionalParameter(PrintPressureTensor, "printPressureTensor"); + DefineOptionalParameter(ElectricField, "electricField"); + DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair"); + DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance"); + DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType"); + DefineOptionalParameter(HydroPropFile, "HydroPropFile"); + DefineOptionalParameter(Viscosity, "viscosity"); + DefineOptionalParameter(BeadSize, "beadSize"); + DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius"); + DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius"); + DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors"); + DefineOptionalParameter(UseMultipleTemperatureMethod, + "useMultipleTemperatureMethod"); + DefineOptionalParameter(ElectrostaticSummationMethod, + "electrostaticSummationMethod"); + DefineOptionalParameter(MTM_Ce, "MTM_Ce"); + DefineOptionalParameter(MTM_G, "MTM_G"); + DefineOptionalParameter(MTM_Io, "MTM_Io"); + DefineOptionalParameter(MTM_Sigma, "MTM_Sigma"); + DefineOptionalParameter(MTM_R, "MTM_R"); + DefineOptionalParameter(Alpha, "alpha"); - deprecatedKeywords_.insert("nComponents"); - deprecatedKeywords_.insert("nZconstraints"); - deprecatedKeywords_.insert("initialConfig"); - deprecatedKeywords_.insert("thermIntDistSpringConst"); - deprecatedKeywords_.insert("thermIntThetaSpringConst"); - deprecatedKeywords_.insert("thermIntOmegaSpringConst"); - deprecatedKeywords_.insert("useSolidThermInt"); - deprecatedKeywords_.insert("useLiquidThermInt"); - -} + + DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, + "usePeriodicBoundaryConditions", + true); + DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", + true); + DefineOptionalParameterWithDefaultValue(UseLongRangeCorrections, + "useLongRangeCorrections", true); + DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", + false); + DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, + "useInitialExtendedSystemState", + false); + DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, + "orthoBoxTolerance", 1E-6); + DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod", + "SHIFTED_FORCE"); + DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, + "electrostaticScreeningMethod", + "DAMPED"); + DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0); + DefineOptionalParameterWithDefaultValue(CompressDumpFile, + "compressDumpFile", false); + DefineOptionalParameterWithDefaultValue(PrintHeatFlux, "printHeatFlux", + false); + DefineOptionalParameterWithDefaultValue(OutputForceVector, + "outputForceVector", false); + DefineOptionalParameterWithDefaultValue(OutputParticlePotential, + "outputParticlePotential", false); + DefineOptionalParameterWithDefaultValue(OutputElectricField, + "outputElectricField", false); + DefineOptionalParameterWithDefaultValue(OutputFluctuatingCharges, + "outputFluctuatingCharges", false); + DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", + 1.0); + DefineOptionalParameterWithDefaultValue(StatFileFormat, + "statFileFormat", + "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY"); + DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, + "useSphericalBoundaryConditions", + false); + DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, + "accumulateBoxDipole", false); + DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", + false); + DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", + "idealCrystal.in"); + DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, + "useThermodynamicIntegration", + false); + DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex"); -Globals::~Globals() { + deprecatedKeywords_.insert("nComponents"); + deprecatedKeywords_.insert("nZconstraints"); + deprecatedKeywords_.insert("initialConfig"); + deprecatedKeywords_.insert("thermIntDistSpringConst"); + deprecatedKeywords_.insert("thermIntThetaSpringConst"); + deprecatedKeywords_.insert("thermIntOmegaSpringConst"); + deprecatedKeywords_.insert("useSolidThermInt"); + deprecatedKeywords_.insert("useLiquidThermInt"); + deprecatedKeywords_.insert("minimizerMaxIter"); + deprecatedKeywords_.insert("minimizerWriteFreq"); + deprecatedKeywords_.insert("minimizerStepSize"); + deprecatedKeywords_.insert("minimizerFTol"); + deprecatedKeywords_.insert("minimizerGTol"); + deprecatedKeywords_.insert("minimizerLSTol"); + deprecatedKeywords_.insert("minimizerLSMaxIter"); + + + } + + Globals::~Globals() { MemoryUtils::deletePointers(components_); MemoryUtils::deletePointers(zconstraints_); MemoryUtils::deletePointers(restraints_); -} + } -void Globals::validate() { - DataHolder::validate(); + void Globals::validate() { + DataHolder::validate(); - CheckParameter(ForceField, isNotEmpty()); - CheckParameter(TargetTemp, isPositive()); - CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || isEqualIgnoreCase("NPAT") || isEqualIgnoreCase("LANGEVINDYNAMICS") || isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") || isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") || isEqualIgnoreCase("NGT") || isEqualIgnoreCase("SMIPD")); - CheckParameter(Dt, isPositive()); - CheckParameter(RunTime, isPositive()); - CheckParameter(FinalConfig, isNotEmpty()); - CheckParameter(SampleTime, isNonNegative()); - CheckParameter(ResetTime, isNonNegative()); - CheckParameter(StatusTime, isNonNegative()); - CheckParameter(CutoffRadius, isPositive()); - CheckParameter(SwitchingRadius, isNonNegative()); - CheckParameter(Dielectric, isPositive()); - CheckParameter(ThermalTime, isNonNegative()); - CheckParameter(TauThermostat, isPositive()); - CheckParameter(TauBarostat, isPositive()); - CheckParameter(ZconsTime, isPositive()); - CheckParameter(ZconsTol, isPositive()); - CheckParameter(Seed, isPositive()); - CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG")); - CheckParameter(MinimizerMaxIter, isPositive()); - CheckParameter(MinimizerWriteFrq, isPositive()); - CheckParameter(MinimizerStepSize, isPositive()); - CheckParameter(MinimizerFTol, isPositive()); - CheckParameter(MinimizerGTol, isPositive()); - CheckParameter(MinimizerLSTol, isPositive()); - CheckParameter(MinimizerLSMaxIter, isPositive()); - CheckParameter(ZconsGap, isPositive()); - CheckParameter(ZconsFixtime, isPositive()); - CheckParameter(ThermodynamicIntegrationLambda, isNonNegative()); - CheckParameter(ThermodynamicIntegrationK, isPositive()); - CheckParameter(ForceFieldVariant, isNotEmpty()); - CheckParameter(ForceFieldFileName, isNotEmpty()); - CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD")); - CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED")); - CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL")); - CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL")); - //CheckParameter(StatFileFormat,); - CheckParameter(OrthoBoxTolerance, isPositive()); - CheckParameter(DampingAlpha,isNonNegative()); - CheckParameter(SkinThickness, isPositive()); - CheckParameter(Viscosity, isNonNegative()); - CheckParameter(BeadSize, isPositive()); - CheckParameter(FrozenBufferRadius, isPositive()); - CheckParameter(LangevinBufferRadius, isPositive()); - CheckParameter(NeighborListNeighbors, isPositive()); - CheckParameter(RNEMD_exchangeTime, isPositive()); - CheckParameter(RNEMD_nBins, isPositive() && isEven()); - CheckParameter(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale")); - CheckParameter(RNEMD_targetFlux, isNonNegative()); - CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape")); - CheckParameter(Alpha, isPositive()); - + CheckParameter(ForceField, isNotEmpty()); + CheckParameter(TargetTemp, isPositive()); + CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || + isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || + isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || + isEqualIgnoreCase("NPTsz") || isEqualIgnoreCase("NPAT") || + isEqualIgnoreCase("LANGEVINDYNAMICS") || + isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") || + isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") || + isEqualIgnoreCase("NGT") || + isEqualIgnoreCase("LANGEVINHULL") || + isEqualIgnoreCase("LHULL") || isEqualIgnoreCase("SMIPD")); + CheckParameter(Dt, isPositive()); + CheckParameter(RunTime, isPositive()); + CheckParameter(FinalConfig, isNotEmpty()); + CheckParameter(SampleTime, isNonNegative()); + CheckParameter(ResetTime, isNonNegative()); + CheckParameter(StatusTime, isNonNegative()); + CheckParameter(CutoffRadius, isPositive()); + CheckParameter(SwitchingRadius, isNonNegative()); + CheckParameter(Dielectric, isPositive()); + CheckParameter(ThermalTime, isNonNegative()); + CheckParameter(TauThermostat, isPositive()); + CheckParameter(TauBarostat, isPositive()); + CheckParameter(ZconsTime, isPositive()); + CheckParameter(ZconsTol, isPositive()); + CheckParameter(Seed, isPositive()); + CheckParameter(ZconsGap, isPositive()); + CheckParameter(ZconsFixtime, isPositive()); + CheckParameter(ThermodynamicIntegrationLambda, isNonNegative()); + CheckParameter(ThermodynamicIntegrationK, isPositive()); + CheckParameter(ForceFieldVariant, isNotEmpty()); + CheckParameter(ForceFieldFileName, isNotEmpty()); + CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") || + isEqualIgnoreCase("SWITCHED") || + isEqualIgnoreCase("SHIFTED_POTENTIAL") || + isEqualIgnoreCase("SHIFTED_FORCE")); + CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || + isEqualIgnoreCase("MAX") || + isEqualIgnoreCase("TRADITIONAL")); + CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || + isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || + isEqualIgnoreCase("SHIFTED_POTENTIAL") || + isEqualIgnoreCase("SHIFTED_FORCE") || + isEqualIgnoreCase("REACTION_FIELD")); + CheckParameter(ElectrostaticScreeningMethod, + isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED")); + CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || + isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL")); + CheckParameter(OrthoBoxTolerance, isPositive()); + CheckParameter(DampingAlpha,isNonNegative()); + CheckParameter(SkinThickness, isPositive()); + CheckParameter(Viscosity, isNonNegative()); + CheckParameter(BeadSize, isPositive()); + CheckParameter(FrozenBufferRadius, isPositive()); + CheckParameter(LangevinBufferRadius, isPositive()); + CheckParameter(NeighborListNeighbors, isPositive()); + CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || + isEqualIgnoreCase("AlphaShape")); + CheckParameter(Alpha, isPositive()); - for(std::vector::iterator i = components_.begin(); i != components_.end(); ++i) { - if (!(*i)->findMoleculeStamp(moleculeStamps_)) { + for(std::vector::iterator i = components_.begin(); + i != components_.end(); ++i) { + if (!(*i)->findMoleculeStamp(moleculeStamps_)) { std::ostringstream oss; - oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl; + oss << "Globals Error: can not find molecule stamp for component " + << (*i)->getType() << std::endl; throw OpenMDException(oss.str()); + } } } -} -bool Globals::addComponent(Component* comp) { + bool Globals::addComponent(Component* comp) { components_.push_back(comp); return true; -} + } -bool Globals::addZConsStamp(ZConsStamp* zcons) { + bool Globals::addZConsStamp(ZConsStamp* zcons) { zconstraints_.push_back(zcons); return true; -} + } -bool Globals::addRestraintStamp(RestraintStamp* rest) { + bool Globals::addRestraintStamp(RestraintStamp* rest) { restraints_.push_back(rest); return true; -} + } -bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) { + bool Globals::addFluctuatingChargeParameters(FluctuatingChargeParameters* fqp) { + if (flucQpars_ != NULL) + delete flucQpars_; + + flucQpars_ = fqp; + return true; + } + + bool Globals::addRNEMDParameters(RNEMDParameters* rnemdPars) { + if (rnemdPars_ != NULL) + delete rnemdPars_; + + rnemdPars_ = rnemdPars; + return true; + } + + bool Globals::addMinimizerParameters(MinimizerParameters* miniPars) { + if (minimizerPars_ != NULL) + delete minimizerPars_; + + minimizerPars_ = miniPars; + return true; + } + + bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) { std::string molStampName = molStamp->getName(); std::map::iterator i; bool ret = false; i = moleculeStamps_.find(molStampName); if (i == moleculeStamps_.end()) { - moleculeStamps_.insert(std::map::value_type(molStampName, molStamp)); - ret = true; + moleculeStamps_.insert(std::map::value_type(molStampName, molStamp)); + ret = true; } else { - std::ostringstream oss; - oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n"; - throw OpenMDException(oss.str()); + std::ostringstream oss; + oss << "Globals Error: Molecule Stamp " << molStamp->getName() + << "appears multiple times\n"; + throw OpenMDException(oss.str()); } return ret; + } } - - -}