--- trunk/src/io/Globals.cpp	2009/11/25 20:02:06	1390
+++ branches/development/src/io/Globals.cpp	2011/06/08 16:05:07	1576
@@ -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");
@@ -92,23 +92,21 @@ Globals::Globals() {
   DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
   DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
   DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
-  DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
   DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
   DefineOptionalParameter(HydroPropFile, "HydroPropFile");
   DefineOptionalParameter(Viscosity, "viscosity");
   DefineOptionalParameter(BeadSize, "beadSize");
   DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
   DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
-  DefineOptionalParameter(ThermalConductivity, "thermalConductivity");
-  DefineOptionalParameter(ThermalLength, "thermalLength");
   DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
   DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
+  DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
   DefineOptionalParameter(MTM_Ce, "MTM_Ce");
   DefineOptionalParameter(MTM_G, "MTM_G");
   DefineOptionalParameter(MTM_Io, "MTM_Io");
   DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
   DefineOptionalParameter(MTM_R, "MTM_R");
-  
+  DefineOptionalParameter(Alpha, "alpha");
 
   
   DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
@@ -116,9 +114,9 @@ Globals::Globals() {
   DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
   DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
   DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
-  DefineOptionalParameterWithDefaultValue(ElectrostaticSummationMethod, "electrostaticSummationMethod", "SHIFTED_FORCE");
+  DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod", "SHIFTED_FORCE");
   DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
-  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 78.5);
+  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
   DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
   DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
   DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
@@ -136,8 +134,10 @@ Globals::Globals() {
   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");
@@ -178,7 +178,7 @@ 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());
@@ -190,17 +190,15 @@ void Globals::validate() {
   CheckParameter(ThermodynamicIntegrationK, isPositive());
   CheckParameter(ForceFieldVariant, isNotEmpty());
   CheckParameter(ForceFieldFileName, isNotEmpty());
-  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
-  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED")); 
+  CheckParameter(CutoffMethod, isEqualIgnoreCase("HARD") || isEqualIgnoreCase("SWITCHED") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE"));
   CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
+  CheckParameter(ElectrostaticSummationMethod, 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(StatFileFormat,);     
   CheckParameter(OrthoBoxTolerance, isPositive());  
   CheckParameter(DampingAlpha,isNonNegative());
   CheckParameter(SkinThickness, isPositive());
   CheckParameter(Viscosity, isNonNegative());
-  CheckParameter(ThermalConductivity, isNonNegative());
-  CheckParameter(ThermalLength, isNonNegative());
   CheckParameter(BeadSize, isPositive());
   CheckParameter(FrozenBufferRadius, isPositive());
   CheckParameter(LangevinBufferRadius, isPositive());
@@ -209,7 +207,10 @@ void Globals::validate() {
   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()); 
 
+  
   for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
     if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
         std::ostringstream oss;