--- trunk/src/io/Globals.cpp 2006/01/12 04:13:46 849 +++ trunk/src/io/Globals.cpp 2006/08/24 17:42:35 1023 @@ -98,7 +98,12 @@ Globals::Globals() { DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod"); DefineOptionalParameter(CutoffPolicy, "cutoffPolicy"); DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType"); - DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard"); + DefineOptionalParameter(HydroPropFile, "HydroPropFile"); + DefineOptionalParameter(Viscosity, "viscosity"); + DefineOptionalParameter(BeadSize, "beadSize"); + DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius"); + DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius"); + DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true); DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false); DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false); @@ -113,6 +118,8 @@ Globals::Globals() { 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); deprecatedKeywords_.insert("nComponents"); @@ -130,11 +137,7 @@ void Globals::validate() { CheckParameter(ForceField, isNotEmpty()); CheckParameter(TargetTemp, isPositive()); - CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) || - isEqualIgnoreCase(std::string("NVT")) || - isEqualIgnoreCase(std::string("NPTi")) || - isEqualIgnoreCase(std::string("NPTf")) || - isEqualIgnoreCase(std::string("NPTxyz")) ); + CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || isEqualIgnoreCase("NPAT") || isEqualIgnoreCase("LANGEVINDYNAMICS") || isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") || isEqualIgnoreCase("NPGT")); CheckParameter(Dt, isPositive()); CheckParameter(RunTime, isPositive()); CheckParameter(InitialConfig, isNotEmpty()); @@ -146,14 +149,13 @@ void Globals::validate() { CheckParameter(SwitchingRadius, isNonNegative()); CheckParameter(Dielectric, isPositive()); CheckParameter(ThermalTime, isNonNegative()); - CheckParameter(TargetPressure, isPositive()); + // CheckParameter(TargetPressure, isPositive()); CheckParameter(TauThermostat, isPositive()); CheckParameter(TauBarostat, isPositive()); CheckParameter(ZconsTime, isPositive()); CheckParameter(ZconsTol, isPositive()); CheckParameter(Seed, isPositive()); - CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) || - isEqualIgnoreCase(std::string("CG"))); + CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG")); CheckParameter(MinimizerMaxIter, isPositive()); CheckParameter(MinimizerWriteFrq, isPositive()); CheckParameter(MinimizerStepSize, isPositive()); @@ -163,37 +165,29 @@ 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(std::string("NONE")) || - isEqualIgnoreCase(std::string("SHIFTED_POTENTIAL")) || - isEqualIgnoreCase(std::string("SHIFTED_FORCE")) || - isEqualIgnoreCase(std::string("REACTION_FIELD"))); - CheckParameter(ElectrostaticScreeningMethod, - isEqualIgnoreCase(std::string("UNDAMPED")) || - isEqualIgnoreCase(std::string("DAMPED"))); - CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) || - isEqualIgnoreCase(std::string("MAX")) || - isEqualIgnoreCase(std::string("TRADITIONAL"))); - CheckParameter(SwitchingFunctionType, - isEqualIgnoreCase(std::string("CUBIC")) || - isEqualIgnoreCase(std::string("FIFTH_ORDER_POLYNOMIAL"))); + // CheckParameter(SurfaceTension, isNonNegative()); + 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(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()); for(std::vector::iterator i = components_.begin(); i != components_.end(); ++i) { if (!(*i)->findMoleculeStamp(moleculeStamps_)) { std::ostringstream oss;