--- branches/development/src/io/Globals.cpp	2012/05/19 02:58:35	1711
+++ branches/development/src/io/Globals.cpp	2012/05/30 16:08:07	1729
@@ -91,6 +91,7 @@ Globals::Globals() {
   DefineOptionalParameter(DampingAlpha, "dampingAlpha");
   DefineOptionalParameter(SurfaceTension, "surfaceTension");
   DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
+  DefineOptionalParameter(PrintHeatFlux, "printHeatFlux");
   DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
   DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
   DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
@@ -121,6 +122,8 @@ Globals::Globals() {
   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);
@@ -132,16 +135,33 @@ Globals::Globals() {
   DefineOptionalParameterWithDefaultValue(RNEMD_logWidth, "RNEMD_logWidth", 16);
   DefineOptionalParameterWithDefaultValue(RNEMD_exchangeType, "RNEMD_exchangeType", "KineticScale");
   DefineOptionalParameterWithDefaultValue(RNEMD_targetFlux, "RNEMD_targetFlux", 0.0);
+  DefineOptionalParameterWithDefaultValue(RNEMD_targetJzKE, "RNEMD_targetJzKE", 0.0);
+  DefineOptionalParameterWithDefaultValue(RNEMD_targetJzpx, "RNEMD_targetJzpx", 0.0);
+  DefineOptionalParameterWithDefaultValue(RNEMD_targetJzpy, "RNEMD_targetJzpy", 0.0);
+  DefineOptionalParameterWithDefaultValue(RNEMD_targetJzpz, "RNEMD_targetJzpz", 0.0);
   DefineOptionalParameterWithDefaultValue(RNEMD_objectSelection, "RNEMD_objectSelection", "select all");
   DefineOptionalParameterWithDefaultValue(RNEMD_binShift, "RNEMD_binShift", false);
-  DefineOptionalParameterWithDefaultValue(RNEMD_outputDimensionalTemperature, "RNEMD_outputDimensionalTemperature", false);
+  DefineOptionalParameterWithDefaultValue(RNEMD_outputTemperature, "RNEMD_outputTemperature", false);
+  DefineOptionalParameterWithDefaultValue(RNEMD_outputVx, "RNEMD_outputVx", false);
+  DefineOptionalParameterWithDefaultValue(RNEMD_outputVy, "RNEMD_outputVy", false);
+  // James put this in.
+  DefineOptionalParameterWithDefaultValue(RNEMD_outputDen, "RNEMD_outputDen", false);
+  DefineOptionalParameterWithDefaultValue(RNEMD_outputAh, "RNEMD_outputAh", false);
+  DefineOptionalParameterWithDefaultValue(RNEMD_outputVz, "RNEMD_outputVz", false);  
+  DefineOptionalParameterWithDefaultValue(RNEMD_outputXyzTemperature, "RNEMD_outputXyzTemperature", false);
+  DefineOptionalParameterWithDefaultValue(RNEMD_outputRotTemperature, "RNEMD_outputRotTemperature", 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");
   deprecatedKeywords_.insert("initialConfig");
@@ -209,10 +229,15 @@ void Globals::validate() {
   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(RNEMD_exchangeType, isEqualIgnoreCase("KineticSwap") || isEqualIgnoreCase("KineticScale") || isEqualIgnoreCase("KineticScaleVAM") || isEqualIgnoreCase("KineticScaleAM") || isEqualIgnoreCase("Px") || isEqualIgnoreCase("Py") || isEqualIgnoreCase("Pz") || isEqualIgnoreCase("PxScale") || isEqualIgnoreCase("PyScale") || isEqualIgnoreCase("PzScale") || isEqualIgnoreCase("ShiftScaleV") || isEqualIgnoreCase("ShiftScaleVAM"));
   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<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
     if (!(*i)->findMoleculeStamp(moleculeStamps_)) {