--- trunk/src/io/Globals.cpp	2006/01/13 19:17:34	866
+++ trunk/src/io/Globals.cpp	2009/09/07 16:31:51	1360
@@ -57,17 +57,15 @@ 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");
@@ -89,40 +87,70 @@ 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(TaggedAtomPair, "taggedAtomPair");
+  DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
   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");
+  DefineOptionalParameter(ThermalConductivity, "thermalConductivity");
+  DefineOptionalParameter(ThermalLength, "thermalLength");
+  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");
+  
+
+  
   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(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);
 
+  DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
+  DefineOptionalParameterWithDefaultValue(RNEMD_swapTime, "RNEMD_swapTime", 100.0);
+  DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
+  DefineOptionalParameterWithDefaultValue(RNEMD_swapType, "RNEMD_swapType", "Kinetic");
+  DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
+  DefineOptionalParameterWithDefaultValue(UseRestraints, "useRestraints", false);
+  DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
+  DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
 
-    deprecatedKeywords_.insert("nComponents");
-    deprecatedKeywords_.insert("nZconstraints");
+
+  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 +158,9 @@ 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("NPAT")  || isEqualIgnoreCase("LANGEVINDYNAMICS") || isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") || isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") || isEqualIgnoreCase("NGT") || isEqualIgnoreCase("SMIPD"));
   CheckParameter(Dt, isPositive());
   CheckParameter(RunTime, isPositive());
-  CheckParameter(InitialConfig, isNotEmpty());
   CheckParameter(FinalConfig, isNotEmpty());
   CheckParameter(SampleTime, isNonNegative());
   CheckParameter(ResetTime, isNonNegative());
@@ -142,7 +169,6 @@ void Globals::validate() {
   CheckParameter(SwitchingRadius, isNonNegative());
   CheckParameter(Dielectric, isPositive());
   CheckParameter(ThermalTime,  isNonNegative());
-  CheckParameter(TargetPressure,  isPositive());
   CheckParameter(TauThermostat, isPositive());
   CheckParameter(TauBarostat, isPositive());
   CheckParameter(ZconsTime, isPositive());
@@ -158,26 +184,28 @@ 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(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(ThermalConductivity, isNonNegative());
+  CheckParameter(ThermalLength, isNonNegative());
+  CheckParameter(BeadSize, isPositive());
+  CheckParameter(FrozenBufferRadius, isPositive());
+  CheckParameter(LangevinBufferRadius, isPositive());
+  CheckParameter(NeighborListNeighbors, isPositive());
+  CheckParameter(RNEMD_swapTime, isPositive());
+  CheckParameter(RNEMD_nBins, isPositive() && isEven());
+  CheckParameter(RNEMD_swapType, isEqualIgnoreCase("Kinetic") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz"));
 
   for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
     if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
@@ -198,6 +226,11 @@ 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<std::string, MoleculeStamp*>::iterator i;