--- branches/development/src/io/Globals.cpp	2010/07/09 23:08:25	1465
+++ branches/development/src/io/Globals.cpp	2012/05/19 02:58:35	1711
@@ -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>
@@ -92,7 +93,6 @@ Globals::Globals() {
   DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
   DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
   DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
-  DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
   DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
   DefineOptionalParameter(HydroPropFile, "HydroPropFile");
   DefineOptionalParameter(Viscosity, "viscosity");
@@ -101,6 +101,7 @@ Globals::Globals() {
   DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
   DefineOptionalParameter(NeighborListNeighbors,"NeighborListNeighbors");
   DefineOptionalParameter(UseMultipleTemperatureMethod, "useMultipleTemperatureMethod");
+  DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
   DefineOptionalParameter(MTM_Ce, "MTM_Ce");
   DefineOptionalParameter(MTM_G, "MTM_G");
   DefineOptionalParameter(MTM_Io, "MTM_Io");
@@ -114,11 +115,12 @@ 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(CompressDumpFile, "compressDumpFile", 0);
-  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
+  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
+  DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", false);
+  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", false);
+  DefineOptionalParameterWithDefaultValue(OutputParticlePotential, "outputParticlePotential", 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 +133,15 @@ 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");
 
 
+
   deprecatedKeywords_.insert("nComponents");
   deprecatedKeywords_.insert("nZconstraints");
   deprecatedKeywords_.insert("initialConfig");
@@ -159,7 +164,7 @@ 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());
@@ -189,11 +194,11 @@ 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("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(StatFileFormat,);     
   CheckParameter(OrthoBoxTolerance, isPositive());  
   CheckParameter(DampingAlpha,isNonNegative());
   CheckParameter(SkinThickness, isPositive());
@@ -205,7 +210,6 @@ 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()); 
 
@@ -218,7 +222,7 @@ void Globals::validate() {
     }
   }
 }
-  
+
 bool Globals::addComponent(Component* comp) {
     components_.push_back(comp);
     return true;