--- trunk/src/io/Globals.cpp	2006/09/21 18:25:17	1045
+++ trunk/src/io/Globals.cpp	2009/03/09 14:03:31	1327
@@ -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");
@@ -89,13 +87,14 @@ Globals::Globals() {
   DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
   DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
   DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
+  DefineOptionalParameter(DampingAlpha, "dampingAlpha");
   DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
   DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
   DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
   DefineOptionalParameter(SurfaceTension, "surfaceTension");
   DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
-  DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
-  DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
+  DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
+  DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
   DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
   DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
   DefineOptionalParameter(HydroPropFile, "HydroPropFile");
@@ -103,8 +102,18 @@ Globals::Globals() {
   DefineOptionalParameter(BeadSize, "beadSize");
   DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
   DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
+  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);  
@@ -113,7 +122,9 @@ Globals::Globals() {
   DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
   DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
   DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
-  DefineOptionalParameter(DampingAlpha, "dampingAlpha");
+  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);
@@ -121,10 +132,15 @@ Globals::Globals() {
   DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
   DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
 
+  DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
+  DefineOptionalParameterWithDefaultValue(RNEMD_swapTime, "RNEMD_swapTime", 100.0);
+  DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 15);
+  DefineOptionalParameterWithDefaultValue(RNEMD_swapType, "RNEMD_swapType", "Kinetic");
+  
 
-    deprecatedKeywords_.insert("nComponents");
-    deprecatedKeywords_.insert("nZconstraints");
-    deprecatedKeywords_.insert("initialConfig");
+  deprecatedKeywords_.insert("nComponents");
+  deprecatedKeywords_.insert("nZconstraints");
+  deprecatedKeywords_.insert("initialConfig");
     
 }
 
@@ -138,10 +154,9 @@ 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"));
+  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());
@@ -150,7 +165,6 @@ void Globals::validate() {
   CheckParameter(SwitchingRadius, isNonNegative());
   CheckParameter(Dielectric, isPositive());
   CheckParameter(ThermalTime,  isNonNegative());
-  //  CheckParameter(TargetPressure,  isPositive());
   CheckParameter(TauThermostat, isPositive());
   CheckParameter(TauBarostat, isPositive());
   CheckParameter(ZconsTime, isPositive());
@@ -173,7 +187,6 @@ void Globals::validate() {
   CheckParameter(ThermIntDistSpringConst, isPositive());
   CheckParameter(ThermIntThetaSpringConst, isPositive());
   CheckParameter(ThermIntOmegaSpringConst, isPositive());
-  //  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"));
@@ -189,6 +202,11 @@ void Globals::validate() {
   CheckParameter(BeadSize, isPositive());
   CheckParameter(FrozenBufferRadius, isPositive());
   CheckParameter(LangevinBufferRadius, isPositive());
+  CheckParameter(NeighborListNeighbors, isPositive());
+  CheckParameter(RNEMD_swapTime, isPositive());
+  CheckParameter(RNEMD_nBins, isPositive());
+  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_)) {
         std::ostringstream oss;