--- branches/development/src/io/Globals.cpp	2010/12/17 20:11:05	1528
+++ branches/development/src/io/Globals.cpp	2012/05/22 21:55:31	1715
@@ -36,7 +36,8 @@
  * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
  * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
  * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
- * [4]  Vardeman & Gezelter, in progress (2009).                        
+ * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
  
 #include <stdlib.h>
@@ -117,8 +118,11 @@ 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(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);
@@ -131,12 +135,18 @@ Globals::Globals() {
   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");
-
-
+  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");
@@ -146,7 +156,6 @@ Globals::Globals() {
   deprecatedKeywords_.insert("thermIntOmegaSpringConst");
   deprecatedKeywords_.insert("useSolidThermInt");  
   deprecatedKeywords_.insert("useLiquidThermInt");
-  deprecatedKeywords_.insert("cutoffPolicy");
     
 }
 
@@ -161,7 +170,7 @@ 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") || isEqualIgnoreCase("SMIPD"));
+  CheckParameter(Ensemble, isEqualIgnoreCase("NVE") || isEqualIgnoreCase("NVT") || isEqualIgnoreCase("NPTi") || isEqualIgnoreCase("NPTf") || isEqualIgnoreCase("NPTxyz") || isEqualIgnoreCase("NPTsz") || isEqualIgnoreCase("NPAT")  || isEqualIgnoreCase("LANGEVINDYNAMICS") || isEqualIgnoreCase("LD") || isEqualIgnoreCase("NPRT") || isEqualIgnoreCase("NPGT") || isEqualIgnoreCase("NGammaT") || isEqualIgnoreCase("NGT") || isEqualIgnoreCase("LANGEVINHULL") || isEqualIgnoreCase("LHULL") || isEqualIgnoreCase("SMIPD"));
   CheckParameter(Dt, isPositive());
   CheckParameter(RunTime, isPositive());
   CheckParameter(FinalConfig, isNotEmpty());
@@ -192,7 +201,8 @@ void Globals::validate() {
   CheckParameter(ForceFieldVariant, isNotEmpty());
   CheckParameter(ForceFieldFileName, isNotEmpty());
   CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE"));
-  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
+  CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
+  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
   CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED")); 
   CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
   CheckParameter(OrthoBoxTolerance, isPositive());  
@@ -206,10 +216,14 @@ void Globals::validate() {
   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());
   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_)) {
@@ -219,7 +233,7 @@ void Globals::validate() {
     }
   }
 }
-  
+
 bool Globals::addComponent(Component* comp) {
     components_.push_back(comp);
     return true;