--- trunk/src/io/Globals.cpp	2009/03/09 14:03:31	1327
+++ trunk/src/io/Globals.cpp	2009/10/19 13:35:42	1367
@@ -88,9 +88,6 @@ Globals::Globals() {
   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(TaggedAtomPair, "taggedAtomPair");
@@ -102,6 +99,8 @@ Globals::Globals() {
   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");
@@ -117,11 +116,6 @@ Globals::Globals() {
   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(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
   DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
   DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
@@ -133,20 +127,32 @@ Globals::Globals() {
   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");
-  
+  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(UseRestraints, "useRestraints", false);
+  DefineOptionalParameterWithDefaultValue(Restraint_file, "Restraint_file", "idealCrystal.in");
+  DefineOptionalParameterWithDefaultValue(UseThermodynamicIntegration, "useThermodynamicIntegration", false);
 
+
   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() {
@@ -184,28 +190,25 @@ void Globals::validate() {
   CheckParameter(ThermodynamicIntegrationK, isPositive());
   CheckParameter(ForceFieldVariant, isNotEmpty());
   CheckParameter(ForceFieldFileName, isNotEmpty());
-  CheckParameter(ThermIntDistSpringConst, isPositive());
-  CheckParameter(ThermIntThetaSpringConst, isPositive());
-  CheckParameter(ThermIntOmegaSpringConst, 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(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());
-  CheckParameter(RNEMD_swapType, isEqualIgnoreCase("Kinetic") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz"));
+  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(RNEMD_targetFlux, isNonNegative());
 
   for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
     if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
@@ -215,7 +218,7 @@ void Globals::validate() {
     }
   }
 }
-    
+  
 bool Globals::addComponent(Component* comp) {
     components_.push_back(comp);
     return true;
@@ -226,6 +229,11 @@ 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;