--- trunk/src/io/Globals.cpp	2009/11/25 20:02:06	1390
+++ trunk/src/io/Globals.cpp	2012/03/16 21:18:27	1698
@@ -1,5 +1,5 @@
 /*
- * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
+ * Copyright (c) 2005, 2010 The University of Notre Dame. All Rights Reserved.
  *
  * The University of Notre Dame grants you ("Licensee") a
  * non-exclusive, royalty free, license to use, modify and
@@ -74,7 +74,7 @@ Globals::Globals() {
   DefineOptionalParameter(Seed, "seed");
   DefineOptionalParameter(Minimizer, "minimizer");
   DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
-  DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq");
+  DefineOptionalParameter(MinimizerWriteFreq, "minimizerWriteFreq");
   DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
   DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
   DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
@@ -99,8 +99,6 @@ 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");
@@ -108,7 +106,7 @@ Globals::Globals() {
   DefineOptionalParameter(MTM_Io, "MTM_Io");
   DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
   DefineOptionalParameter(MTM_R, "MTM_R");
-  
+  DefineOptionalParameter(Alpha, "alpha");
 
   
   DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
@@ -121,6 +119,7 @@ Globals::Globals() {
   DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
   DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
   DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
+  DefineOptionalParameterWithDefaultValue(OutputParticlePotential, "outputParticlePotential", 0);
   DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
   DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
   DefineOptionalParameterWithDefaultValue(UseSphericalBoundaryConditions, "useSphericalBoundaryConditions", false);
@@ -132,10 +131,21 @@ 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_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");
 
 
   deprecatedKeywords_.insert("nComponents");
@@ -160,7 +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());
@@ -178,7 +188,7 @@ void Globals::validate() {
   CheckParameter(Seed, isPositive());
   CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
   CheckParameter(MinimizerMaxIter, isPositive());
-  CheckParameter(MinimizerWriteFrq, isPositive());
+  CheckParameter(MinimizerWriteFreq, isPositive());
   CheckParameter(MinimizerStepSize, isPositive());
   CheckParameter(MinimizerFTol, isPositive());
   CheckParameter(MinimizerGTol, isPositive());
@@ -199,17 +209,18 @@ void Globals::validate() {
   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_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(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(RNEMD_targetFlux, isNonNegative());
+  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_)) {
         std::ostringstream oss;