--- branches/development/src/io/Globals.cpp	2011/11/22 20:38:56	1665
+++ 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");
@@ -118,30 +123,21 @@ Globals::Globals() {
   DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod", "SHIFTED_FORCE");
   DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
   DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
-  DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
-  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
-  DefineOptionalParameterWithDefaultValue(OutputParticlePotential, "outputParticlePotential", 0);
+  DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", false);
+  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", false);
+  DefineOptionalParameterWithDefaultValue(OutputParticlePotential, "outputParticlePotential", false);
+  DefineOptionalParameterWithDefaultValue(OutputElectricField, "outputElectricField", false);
+  DefineOptionalParameterWithDefaultValue(OutputFluctuatingCharges, "outputFluctuatingCharges", false);
   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_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");
 
-
-
   deprecatedKeywords_.insert("nComponents");
   deprecatedKeywords_.insert("nZconstraints");
   deprecatedKeywords_.insert("initialConfig");
@@ -207,12 +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()); 
-
   
   for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
     if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
@@ -238,6 +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<std::string, MoleculeStamp*>::iterator i;