--- trunk/src/io/Globals.cpp	2005/12/05 23:37:56	789
+++ trunk/src/io/Globals.cpp	2006/09/01 19:16:02	1032
@@ -45,10 +45,10 @@
 #include <string>
 
 #include "io/Globals.hpp"
+#include "io/ParamConstraint.hpp"
+#include "utils/MemoryUtils.hpp"
 #include "utils/simError.h"
 
-#include "io/ParamConstraint.hpp"
-
 namespace oopse {
 Globals::Globals() {
   DefineParameter(ForceField, "forceField")
@@ -57,7 +57,7 @@ Globals::Globals() {
   DefineOptionalParameter(Ensemble, "ensemble");
   DefineOptionalParameter(Dt, "dt");
   DefineOptionalParameter(RunTime, "runTime");
-  DefineOptionalParameter(InitialConfig, "initialConfig");
+  //DefineOptionalParameter(InitialConfig, "initialConfig");
   DefineOptionalParameter(FinalConfig, "finalConfig");
   DefineOptionalParameter(SampleTime, "sampleTime");
   DefineOptionalParameter(ResetTime, "resetTime");
@@ -98,7 +98,12 @@ Globals::Globals() {
   DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
   DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
   DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
-  DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
+  DefineOptionalParameter(HydroPropFile, "HydroPropFile");
+  DefineOptionalParameter(Viscosity, "viscosity");
+  DefineOptionalParameter(BeadSize, "beadSize");
+  DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
+  DefineOptionalParameter(LangevinBufferRadius, "langevinBufferRadius");
+  
   DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
   DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
   DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
@@ -113,16 +118,19 @@ Globals::Globals() {
   DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 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);
+  DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
 
 
     deprecatedKeywords_.insert("nComponents");
     deprecatedKeywords_.insert("nZconstraints");
+    deprecatedKeywords_.insert("initialConfig");
     
 }
 
 Globals::~Globals() {
-
-
+    MemoryUtils::deletePointers(components_);
+    MemoryUtils::deletePointers(zconstraints_);
 }
 
 void Globals::validate() {
@@ -130,10 +138,10 @@ void Globals::validate() {
 
   CheckParameter(ForceField, isNotEmpty());
   CheckParameter(TargetTemp, isPositive());
-  CheckParameter(Ensemble, isEqualIgnoreCase(std::string("NVE")) || isEqualIgnoreCase(std::string("NVT")) || isEqualIgnoreCase(std::string("NPTi")) || isEqualIgnoreCase(std::string("NPTf")) || isEqualIgnoreCase(std::string("NPTxyz")) );
+  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"));
   CheckParameter(Dt, isPositive());
   CheckParameter(RunTime, isPositive());
-  CheckParameter(InitialConfig, isNotEmpty());
+  //CheckParameter(InitialConfig, isNotEmpty());
   CheckParameter(FinalConfig, isNotEmpty());
   CheckParameter(SampleTime, isNonNegative());
   CheckParameter(ResetTime, isNonNegative());
@@ -142,13 +150,13 @@ void Globals::validate() {
   CheckParameter(SwitchingRadius, isNonNegative());
   CheckParameter(Dielectric, isPositive());
   CheckParameter(ThermalTime,  isNonNegative());
-  CheckParameter(TargetPressure,  isPositive());
+  //  CheckParameter(TargetPressure,  isPositive());
   CheckParameter(TauThermostat, isPositive());
   CheckParameter(TauBarostat, isPositive());
   CheckParameter(ZconsTime, isPositive());
   CheckParameter(ZconsTol, isPositive());
   CheckParameter(Seed, isPositive());
-  CheckParameter(Minimizer, isEqualIgnoreCase(std::string("SD")) || isEqualIgnoreCase(std::string("CG")));
+  CheckParameter(Minimizer, isEqualIgnoreCase("SD") || isEqualIgnoreCase("CG"));
   CheckParameter(MinimizerMaxIter, isPositive());
   CheckParameter(MinimizerWriteFrq, isPositive());
   CheckParameter(MinimizerStepSize, isPositive());
@@ -158,30 +166,34 @@ void Globals::validate() {
   CheckParameter(MinimizerLSMaxIter, isPositive());
   CheckParameter(ZconsGap, isPositive());
   CheckParameter(ZconsFixtime, isPositive());
-  CheckParameter(ThermodynamicIntegrationLambda, isPositive());
+  CheckParameter(ThermodynamicIntegrationLambda, isNonNegative());
   CheckParameter(ThermodynamicIntegrationK, isPositive());
   CheckParameter(ForceFieldVariant, isNotEmpty());
   CheckParameter(ForceFieldFileName, isNotEmpty());
   CheckParameter(ThermIntDistSpringConst, isPositive());
   CheckParameter(ThermIntThetaSpringConst, isPositive());
   CheckParameter(ThermIntOmegaSpringConst, isPositive());
-  CheckParameter(SurfaceTension, isPositive());
-  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase(std::string("NONE")) || isEqualIgnoreCase(std::string("SHIFTED_POTENTIAL")) || isEqualIgnoreCase(std::string("SHIFTED_FORCE")) || isEqualIgnoreCase(std::string("REACTION_FIELD")));
-  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase(std::string("UNDAMPED")) || isEqualIgnoreCase(std::string("DAMPED"))); 
-  CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) || isEqualIgnoreCase(std::string("MAX")) || isEqualIgnoreCase(std::string("TRADITIONAL")));
-  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase(std::string("CUBIC")) || isEqualIgnoreCase(std::string("FIFTH_ORDER_POLYNOMIAL")));
+  //  CheckParameter(SurfaceTension, isNonNegative());
+  CheckParameter(ElectrostaticSummationMethod, isEqualIgnoreCase("NONE") || isEqualIgnoreCase("SHIFTED_POTENTIAL") || isEqualIgnoreCase("SHIFTED_FORCE") || isEqualIgnoreCase("REACTION_FIELD"));
+  CheckParameter(ElectrostaticScreeningMethod, isEqualIgnoreCase("UNDAMPED") || isEqualIgnoreCase("DAMPED")); 
+  CheckParameter(CutoffPolicy, isEqualIgnoreCase("MIX") || isEqualIgnoreCase("MAX") || isEqualIgnoreCase("TRADITIONAL"));
+  CheckParameter(SwitchingFunctionType, isEqualIgnoreCase("CUBIC") || isEqualIgnoreCase("FIFTH_ORDER_POLYNOMIAL"));
   //CheckParameter(StatFileFormat,);     
-  //CheckParameter(MixingRule,);
   CheckParameter(OrthoBoxTolerance, isPositive());  
   CheckParameter(ThermIntDistSpringConst, isPositive());
   CheckParameter(ThermIntThetaSpringConst, isPositive());
   CheckParameter(ThermIntOmegaSpringConst, isPositive());
   CheckParameter(DampingAlpha,isNonNegative());
   CheckParameter(SkinThickness, isPositive());
-
+  CheckParameter(Viscosity, isNonNegative());
+  CheckParameter(BeadSize, isPositive());
+  CheckParameter(FrozenBufferRadius, isPositive());
+  CheckParameter(LangevinBufferRadius, isPositive());
   for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
     if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
-        std::cout << "Globals Error: can not find molecule stamp for component" << std::endl;
+        std::ostringstream oss;
+        oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
+        throw OOPSEException(oss.str());           
     }
   }
 }
@@ -205,7 +217,9 @@ bool Globals::addMoleculeStamp(MoleculeStamp* molStamp
         moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
         ret = true;
     } else {
-        std::cout << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
+        std::ostringstream oss;
+        oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
+        throw OOPSEException(oss.str());  
     }
     return ret;
 }