--- trunk/src/io/Globals.cpp 2009/11/25 20:02:06 1390 +++ branches/development/src/io/Globals.cpp 2012/05/30 16:08:07 1729 @@ -1,5 +1,5 @@ /* - * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. + * Copyright (c) 2005, 2010 The University of Notre Dame. All Rights Reserved. * * The University of Notre Dame grants you ("Licensee") a * non-exclusive, royalty free, license to use, modify and @@ -36,7 +36,8 @@ * [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). + * [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ #include @@ -74,7 +75,7 @@ Globals::Globals() { DefineOptionalParameter(Seed, "seed"); DefineOptionalParameter(Minimizer, "minimizer"); DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter"); - DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq"); + DefineOptionalParameter(MinimizerWriteFreq, "minimizerWriteFreq"); DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize"); DefineOptionalParameter(MinimizerFTol, "minimizerFTol"); DefineOptionalParameter(MinimizerGTol, "minimizerGTol"); @@ -90,25 +91,24 @@ Globals::Globals() { DefineOptionalParameter(DampingAlpha, "dampingAlpha"); DefineOptionalParameter(SurfaceTension, "surfaceTension"); DefineOptionalParameter(PrintPressureTensor, "printPressureTensor"); + DefineOptionalParameter(PrintHeatFlux, "printHeatFlux"); 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(ThermalConductivity, "thermalConductivity"); - DefineOptionalParameter(ThermalLength, "thermalLength"); 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"); DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true); @@ -116,11 +116,14 @@ Globals::Globals() { DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false); DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false); DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6); - DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE"); + DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod", "SHIFTED_FORCE"); DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED"); - DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5); - DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0); - DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0); + DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0); + DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 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); @@ -132,12 +135,33 @@ Globals::Globals() { DefineOptionalParameterWithDefaultValue(RNEMD_logWidth, "RNEMD_logWidth", 16); DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale"); DefineOptionalParameterWithDefaultValue(RNEMD_targetFlux, "RNEMD_targetFlux", 0.0); + DefineOptionalParameterWithDefaultValue(RNEMD_targetJzKE, "RNEMD_targetJzKE", 0.0); + DefineOptionalParameterWithDefaultValue(RNEMD_targetJzpx, "RNEMD_targetJzpx", 0.0); + DefineOptionalParameterWithDefaultValue(RNEMD_targetJzpy, "RNEMD_targetJzpy", 0.0); + DefineOptionalParameterWithDefaultValue(RNEMD_targetJzpz, "RNEMD_targetJzpz", 0.0); DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all"); + DefineOptionalParameterWithDefaultValue(RNEMD_binShift, "RNEMD_binShift", false); + DefineOptionalParameterWithDefaultValue(RNEMD_outputTemperature, "RNEMD_outputTemperature", false); + DefineOptionalParameterWithDefaultValue(RNEMD_outputVx, "RNEMD_outputVx", false); + DefineOptionalParameterWithDefaultValue(RNEMD_outputVy, "RNEMD_outputVy", false); + // James put this in. + DefineOptionalParameterWithDefaultValue(RNEMD_outputDen, "RNEMD_outputDen", false); + DefineOptionalParameterWithDefaultValue(RNEMD_outputAh, "RNEMD_outputAh", false); + DefineOptionalParameterWithDefaultValue(RNEMD_outputVz, "RNEMD_outputVz", false); + DefineOptionalParameterWithDefaultValue(RNEMD_outputXyzTemperature, "RNEMD_outputXyzTemperature", false); + DefineOptionalParameterWithDefaultValue(RNEMD_outputRotTemperature, "RNEMD_outputRotTemperature", false); + DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false); DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in"); DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false); + DefineOptionalParameterWithDefaultValue(HULL_Method,"HULL_Method","Convex"); + DefineOptionalParameterWithDefaultValue(FlucQPropagator, "flucQ.propagator", "NVT"); + DefineOptionalParameterWithDefaultValue(FlucQFriction, "flucQ.friction", 1600.0); + DefineOptionalParameterWithDefaultValue(FlucQTolerance, "flucQ.tolerance", 1.0e-6); + DefineOptionalParameterWithDefaultValue(FlucQMaxIterations, "flucQ.maxIterations", 100); + DefineOptionalParameterWithDefaultValue(FlucQTargetTemp, "flucQ.targetTemp", 1.0e-6); + DefineOptionalParameterWithDefaultValue(FlucQtauThermostat, "flucQ.tauThermostat", 10.0); - deprecatedKeywords_.insert("nComponents"); deprecatedKeywords_.insert("nZconstraints"); deprecatedKeywords_.insert("initialConfig"); @@ -160,7 +184,7 @@ void Globals::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(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()); @@ -178,7 +202,7 @@ void Globals::validate() { CheckParameter(Seed, isPositive()); CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG")); CheckParameter(MinimizerMaxIter, isPositive()); - CheckParameter(MinimizerWriteFrq, isPositive()); + CheckParameter(MinimizerWriteFreq, isPositive()); CheckParameter(MinimizerStepSize, isPositive()); CheckParameter(MinimizerFTol, isPositive()); CheckParameter(MinimizerGTol, isPositive()); @@ -190,26 +214,31 @@ void Globals::validate() { 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(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(StatFileFormat,); CheckParameter(OrthoBoxTolerance, isPositive()); CheckParameter(DampingAlpha,isNonNegative()); CheckParameter(SkinThickness, isPositive()); CheckParameter(Viscosity, isNonNegative()); - CheckParameter(ThermalConductivity, isNonNegative()); - CheckParameter(ThermalLength, 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(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("KineticScaleVAM") || isEqualIgnoreCase("KineticScaleAM") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale") || isEqualIgnoreCase("ShiftScaleV") || isEqualIgnoreCase("ShiftScaleVAM")); + CheckParameter(HULL_Method, isEqualIgnoreCase("Convex") || isEqualIgnoreCase("AlphaShape")); + CheckParameter(Alpha, isPositive()); + CheckParameter(FlucQPropagator, isEqualIgnoreCase("NVT") || isEqualIgnoreCase("Langevin") || isEqualIgnoreCase("Minimizer") || isEqualIgnoreCase("Exact") ); + CheckParameter(FlucQFriction, isNonNegative()); + CheckParameter(FlucQTolerance, isPositive()); + CheckParameter(FlucQMaxIterations, isPositive()); + CheckParameter(FlucQTargetTemp, isNonNegative()); + CheckParameter(FlucQtauThermostat, isPositive()); + for(std::vector::iterator i = components_.begin(); i != components_.end(); ++i) { if (!(*i)->findMoleculeStamp(moleculeStamps_)) { std::ostringstream oss; @@ -218,7 +247,7 @@ void Globals::validate() { } } } - + bool Globals::addComponent(Component* comp) { components_.push_back(comp); return true;