--- branches/development/src/io/Globals.cpp 2012/05/22 21:55:31 1715 +++ branches/development/src/io/Globals.cpp 2012/06/05 18:07:08 1744 @@ -52,6 +52,10 @@ Globals::Globals() { namespace OpenMD { Globals::Globals() { + + flucQpars_ = new FluctuatingChargeParameters(); + rnemdPars_ = new RNEMDParameters(); + DefineParameter(ForceField, "forceField") DefineOptionalParameter(TargetTemp, "targetTemp"); @@ -91,6 +95,7 @@ Globals::Globals() { DefineOptionalParameter(DampingAlpha, "dampingAlpha"); DefineOptionalParameter(SurfaceTension, "surfaceTension"); DefineOptionalParameter(PrintPressureTensor, "printPressureTensor"); + DefineOptionalParameter(PrintHeatFlux, "printHeatFlux"); DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair"); DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance"); DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType"); @@ -128,25 +133,10 @@ Globals::Globals() { 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_objectSelection, "RNEMD_objectSelection", "select all"); - DefineOptionalParameterWithDefaultValue(RNEMD_binShift, "RNEMD_binShift", false); - DefineOptionalParameterWithDefaultValue(RNEMD_outputDimensionalTemperature, "RNEMD_outputDimensionalTemperature", 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"); @@ -213,17 +203,8 @@ void Globals::validate() { 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(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_)) { @@ -249,6 +230,22 @@ bool Globals::addRestraintStamp(RestraintStamp* rest) return true; } +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::addMoleculeStamp(MoleculeStamp* molStamp) { std::string molStampName = molStamp->getName(); std::map::iterator i;