--- trunk/src/io/Globals.cpp 2006/01/13 19:17:34 866 +++ branches/development/src/io/Globals.cpp 2012/05/30 16:08:07 1729 @@ -1,24 +1,15 @@ /* - * 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 * redistribute this software in source and binary code form, provided * that the following conditions are met: * - * 1. Acknowledgement of the program authors must be made in any - * publication of scientific results based in part on use of the - * program. An acceptable form of acknowledgement is citation of - * the article in which the program was described (Matthew - * A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher - * J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented - * Parallel Simulation Engine for Molecular Dynamics," - * J. Comput. Chem. 26, pp. 252-271 (2005)) - * - * 2. Redistributions of source code must retain the above copyright + * 1. Redistributions of source code must retain the above copyright * notice, this list of conditions and the following disclaimer. * - * 3. Redistributions in binary form must reproduce the above copyright + * 2. Redistributions in binary form must reproduce the above copyright * notice, this list of conditions and the following disclaimer in the * documentation and/or other materials provided with the * distribution. @@ -37,6 +28,16 @@ * arising out of the use of or inability to use software, even if the * University of Notre Dame has been advised of the possibility of * such damages. + * + * SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your + * research, please cite the appropriate papers when you publish your + * work. Good starting points are: + * + * [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] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). + * [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). */ #include @@ -49,7 +50,7 @@ #include "utils/MemoryUtils.hpp" #include "utils/simError.h" -namespace oopse { +namespace OpenMD { Globals::Globals() { DefineParameter(ForceField, "forceField") @@ -57,17 +58,15 @@ Globals::Globals() { DefineOptionalParameter(Ensemble, "ensemble"); DefineOptionalParameter(Dt, "dt"); DefineOptionalParameter(RunTime, "runTime"); - DefineOptionalParameter(InitialConfig, "initialConfig"); DefineOptionalParameter(FinalConfig, "finalConfig"); DefineOptionalParameter(SampleTime, "sampleTime"); DefineOptionalParameter(ResetTime, "resetTime"); DefineOptionalParameter(StatusTime, "statusTime"); DefineOptionalParameter(CutoffRadius, "cutoffRadius"); DefineOptionalParameter(SwitchingRadius, "switchingRadius"); - DefineOptionalParameter(Dielectric, "dielectric"); DefineOptionalParameter(TempSet, "tempSet"); DefineOptionalParameter(ThermalTime, "thermalTime"); - DefineOptionalParameter(TargetPressure, "targetPressure"); + DefineOptionalParameter(TargetPressure, "targetPressure"); DefineOptionalParameter(TauThermostat, "tauThermostat"); DefineOptionalParameter(TauBarostat, "tauBarostat"); DefineOptionalParameter(ZconsTime, "zconsTime"); @@ -76,7 +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"); @@ -89,40 +88,95 @@ Globals::Globals() { DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK"); DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant"); DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName"); - DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst"); - DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst"); - DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst"); + DefineOptionalParameter(DampingAlpha, "dampingAlpha"); DefineOptionalParameter(SurfaceTension, "surfaceTension"); DefineOptionalParameter(PrintPressureTensor, "printPressureTensor"); - DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod"); - DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod"); - DefineOptionalParameter(CutoffPolicy, "cutoffPolicy"); + DefineOptionalParameter(PrintHeatFlux, "printHeatFlux"); + DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair"); + DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance"); DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType"); - DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard"); + 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"); + + DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true); + DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true); DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false); DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false); DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6); - DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false); - DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false); - DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0); - DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5); - DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5); - DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2); - DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0); - DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0); + DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod", "SHIFTED_FORCE"); + DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED"); + 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); + DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false); + 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_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); - deprecatedKeywords_.insert("nComponents"); - deprecatedKeywords_.insert("nZconstraints"); + 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"); + deprecatedKeywords_.insert("thermIntDistSpringConst"); + deprecatedKeywords_.insert("thermIntThetaSpringConst"); + deprecatedKeywords_.insert("thermIntOmegaSpringConst"); + deprecatedKeywords_.insert("useSolidThermInt"); + deprecatedKeywords_.insert("useLiquidThermInt"); } Globals::~Globals() { MemoryUtils::deletePointers(components_); MemoryUtils::deletePointers(zconstraints_); + MemoryUtils::deletePointers(restraints_); } void Globals::validate() { @@ -130,10 +184,9 @@ void Globals::validate() { CheckParameter(ForceField, isNotEmpty()); CheckParameter(TargetTemp, isPositive()); - CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || isEqualIgnoreCase("NPAT") ); + 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(InitialConfig, isNotEmpty()); CheckParameter(FinalConfig, isNotEmpty()); CheckParameter(SampleTime, isNonNegative()); CheckParameter(ResetTime, isNonNegative()); @@ -142,7 +195,6 @@ void Globals::validate() { CheckParameter(SwitchingRadius, isNonNegative()); CheckParameter(Dielectric, isPositive()); CheckParameter(ThermalTime, isNonNegative()); - CheckParameter(TargetPressure, isPositive()); CheckParameter(TauThermostat, isPositive()); CheckParameter(TauBarostat, isPositive()); CheckParameter(ZconsTime, isPositive()); @@ -150,7 +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()); @@ -158,36 +210,44 @@ void Globals::validate() { CheckParameter(MinimizerLSMaxIter, isPositive()); CheckParameter(ZconsGap, isPositive()); CheckParameter(ZconsFixtime, isPositive()); - CheckParameter(ThermodynamicIntegrationLambda, isPositive()); + CheckParameter(ThermodynamicIntegrationLambda, isNonNegative()); CheckParameter(ThermodynamicIntegrationK, isPositive()); CheckParameter(ForceFieldVariant, isNotEmpty()); CheckParameter(ForceFieldFileName, isNotEmpty()); - CheckParameter(ThermIntDistSpringConst, isPositive()); - CheckParameter(ThermIntThetaSpringConst, isPositive()); - CheckParameter(ThermIntOmegaSpringConst, isPositive()); - CheckParameter(SurfaceTension, isPositive()); - 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(MixingRule,); CheckParameter(OrthoBoxTolerance, isPositive()); - CheckParameter(ThermIntDistSpringConst, isPositive()); - CheckParameter(ThermIntThetaSpringConst, isPositive()); - CheckParameter(ThermIntOmegaSpringConst, 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("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; oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl; - throw OOPSEException(oss.str()); + throw OpenMDException(oss.str()); } } } - + bool Globals::addComponent(Component* comp) { components_.push_back(comp); return true; @@ -198,6 +258,11 @@ bool Globals::addZConsStamp(ZConsStamp* zcons) { return true; } +bool Globals::addRestraintStamp(RestraintStamp* rest) { + restraints_.push_back(rest); + return true; +} + bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) { std::string molStampName = molStamp->getName(); std::map::iterator i; @@ -209,7 +274,7 @@ bool Globals::addMoleculeStamp(MoleculeStamp* molStamp } else { std::ostringstream oss; oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n"; - throw OOPSEException(oss.str()); + throw OpenMDException(oss.str()); } return ret; }