--- branches/development/src/io/Globals.cpp	2012/05/24 14:23:40	1722
+++ branches/development/src/io/Globals.cpp	2012/06/06 02:18:54	1746
@@ -52,6 +52,11 @@ Globals::Globals() {
 
 namespace OpenMD {
 Globals::Globals() {
+  
+  flucQpars_ = new FluctuatingChargeParameters();
+  rnemdPars_ = new RNEMDParameters();
+  minimizerPars_ = new MinimizerParameters();
+
   DefineParameter(ForceField, "forceField")
  
   DefineOptionalParameter(TargetTemp, "targetTemp");
@@ -73,14 +78,6 @@ Globals::Globals() {
   DefineOptionalParameter(ZconsTol, "zconsTol");
   DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
   DefineOptionalParameter(Seed, "seed");
-  DefineOptionalParameter(Minimizer, "minimizer");
-  DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
-  DefineOptionalParameter(MinimizerWriteFreq, "minimizerWriteFreq");
-  DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
-  DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
-  DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
-  DefineOptionalParameter(MinimizerLSTol, "minimizerLSTol");
-  DefineOptionalParameter(MinimizerLSMaxIter, "minimizerLSMaxIter");
   DefineOptionalParameter(ZconsGap, "zconsGap");
   DefineOptionalParameter(ZconsFixtime, "zconsFixtime");
   DefineOptionalParameter(ZconsUsingSMD, "zconsUsingSMD");
@@ -91,6 +88,7 @@ Globals::Globals() {
   DefineOptionalParameter(DampingAlpha, "dampingAlpha");
   DefineOptionalParameter(SurfaceTension, "surfaceTension");
   DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
+  DefineOptionalParameter(PrintHeatFlux, "printHeatFlux");
   DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
   DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
   DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
@@ -128,34 +126,10 @@ Globals::Globals() {
   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_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_outputTemperature, "RNEMD_outputTemperature", false);
-  DefineOptionalParameterWithDefaultValue(RNEMD_outputVx, "RNEMD_outputVx", false);
-  DefineOptionalParameterWithDefaultValue(RNEMD_outputVy, "RNEMD_outputVy", 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");
@@ -165,6 +139,14 @@ Globals::Globals() {
   deprecatedKeywords_.insert("thermIntOmegaSpringConst");
   deprecatedKeywords_.insert("useSolidThermInt");  
   deprecatedKeywords_.insert("useLiquidThermInt");
+  deprecatedKeywords_.insert("minimizerMaxIter");
+  deprecatedKeywords_.insert("minimizerWriteFreq");
+  deprecatedKeywords_.insert("minimizerStepSize");
+  deprecatedKeywords_.insert("minimizerFTol");
+  deprecatedKeywords_.insert("minimizerGTol");
+  deprecatedKeywords_.insert("minimizerLSTol");
+  deprecatedKeywords_.insert("minimizerLSMaxIter");
+
     
 }
 
@@ -195,14 +177,6 @@ void Globals::validate() {
   CheckParameter(ZconsTime, isPositive());
   CheckParameter(ZconsTol, isPositive());
   CheckParameter(Seed, isPositive());
-  CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
-  CheckParameter(MinimizerMaxIter, isPositive());
-  CheckParameter(MinimizerWriteFreq, isPositive());
-  CheckParameter(MinimizerStepSize, isPositive());
-  CheckParameter(MinimizerFTol, isPositive());
-  CheckParameter(MinimizerGTol, isPositive());
-  CheckParameter(MinimizerLSTol, isPositive());
-  CheckParameter(MinimizerLSMaxIter, isPositive());
   CheckParameter(ZconsGap, isPositive());
   CheckParameter(ZconsFixtime, isPositive());
   CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
@@ -222,17 +196,8 @@ 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("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_)) {
@@ -258,6 +223,30 @@ 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::addMinimizerParameters(MinimizerParameters* miniPars) {
+  if (minimizerPars_ != NULL)
+    delete minimizerPars_;
+    
+  minimizerPars_ = miniPars;
+  return true;
+}
+
 bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
     std::string molStampName = molStamp->getName();
     std::map<std::string, MoleculeStamp*>::iterator i;