--- trunk/src/io/Globals.cpp	2005/11/16 23:10:02	749
+++ branches/development/src/io/Globals.cpp	2012/05/22 21:55:31	1715
@@ -1,24 +1,15 @@
 /*
- * 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
  * redistribute this software in source and binary code form, provided
  * that the following conditions are met:
  *
- * 1. Acknowledgement of the program authors must be made in any
- *    publication of scientific results based in part on use of the
- *    program.  An acceptable form of acknowledgement is citation of
- *    the article in which the program was described (Matthew
- *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
- *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
- *    Parallel Simulation Engine for Molecular Dynamics,"
- *    J. Comput. Chem. 26, pp. 252-271 (2005))
- *
- * 2. Redistributions of source code must retain the above copyright
+ * 1. Redistributions of source code must retain the above copyright
  *    notice, this list of conditions and the following disclaimer.
  *
- * 3. Redistributions in binary form must reproduce the above copyright
+ * 2. Redistributions in binary form must reproduce the above copyright
  *    notice, this list of conditions and the following disclaimer in the
  *    documentation and/or other materials provided with the
  *    distribution.
@@ -37,6 +28,16 @@
  * arising out of the use of or inability to use software, even if the
  * University of Notre Dame has been advised of the possibility of
  * such damages.
+ *
+ * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
+ * research, please cite the appropriate papers when you publish your
+ * work.  Good starting points are:
+ *                                                                      
+ * [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]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
+ * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
  */
  
 #include <stdlib.h>
@@ -45,51 +46,36 @@
 #include <string>
 
 #include "io/Globals.hpp"
+#include "io/ParamConstraint.hpp"
+#include "utils/MemoryUtils.hpp"
 #include "utils/simError.h"
-#ifdef IS_MPI
-#include "io/mpiBASS.h"
-#endif // is_mpi
 
-#include "io/ParamConstraint.hpp"
-
-using namespace oopse;
-
-Globals::Globals(){
- 
+namespace OpenMD {
+Globals::Globals() {
   DefineParameter(ForceField, "forceField")
-  DefineParameter(NComponents, "nComponents")
  
   DefineOptionalParameter(TargetTemp, "targetTemp");
   DefineOptionalParameter(Ensemble, "ensemble");
   DefineOptionalParameter(Dt, "dt");
   DefineOptionalParameter(RunTime, "runTime");
-  DefineOptionalParameter(InitialConfig, "initialConfig");
   DefineOptionalParameter(FinalConfig, "finalConfig");
-  DefineOptionalParameter(NMol, "nMol");
-  DefineOptionalParameter(Density, "density");
-  DefineOptionalParameter(Box, "box");
-  DefineOptionalParameter(BoxX, "boxX");
-  DefineOptionalParameter(BoxY, "boxY");
-  DefineOptionalParameter(BoxZ, "boxZ");
   DefineOptionalParameter(SampleTime, "sampleTime");
   DefineOptionalParameter(ResetTime, "resetTime");
   DefineOptionalParameter(StatusTime, "statusTime");
   DefineOptionalParameter(CutoffRadius, "cutoffRadius");
   DefineOptionalParameter(SwitchingRadius, "switchingRadius");
-  DefineOptionalParameter(Dielectric, "dielectric");
   DefineOptionalParameter(TempSet, "tempSet");
   DefineOptionalParameter(ThermalTime, "thermalTime");
-  DefineOptionalParameter(TargetPressure, "targetPressure");
+  DefineOptionalParameter(TargetPressure, "targetPressure");  
   DefineOptionalParameter(TauThermostat, "tauThermostat");
   DefineOptionalParameter(TauBarostat, "tauBarostat");
   DefineOptionalParameter(ZconsTime, "zconsTime");
-  DefineOptionalParameter(NZconstraints, "nZconstraints");  
   DefineOptionalParameter(ZconsTol, "zconsTol");
   DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
   DefineOptionalParameter(Seed, "seed");
   DefineOptionalParameter(Minimizer, "minimizer");
   DefineOptionalParameter(MinimizerMaxIter,"minimizerMaxIter");
-  DefineOptionalParameter(MinimizerWriteFrq, "minimizerWriteFrq");
+  DefineOptionalParameter(MinimizerWriteFreq, "minimizerWriteFreq");
   DefineOptionalParameter(MinimizerStepSize, "minimizerStepSize");
   DefineOptionalParameter(MinimizerFTol, "minimizerFTol");
   DefineOptionalParameter(MinimizerGTol, "minimizerGTol");
@@ -102,261 +88,92 @@ Globals::Globals(){
   DefineOptionalParameter(ThermodynamicIntegrationK, "thermodynamicIntegrationK");
   DefineOptionalParameter(ForceFieldVariant, "forceFieldVariant");
   DefineOptionalParameter(ForceFieldFileName, "forceFieldFileName");
-  DefineOptionalParameter(ThermIntDistSpringConst, "thermIntDistSpringConst");
-  DefineOptionalParameter(ThermIntThetaSpringConst, "thermIntThetaSpringConst");
-  DefineOptionalParameter(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst");
+  DefineOptionalParameter(DampingAlpha, "dampingAlpha");
   DefineOptionalParameter(SurfaceTension, "surfaceTension");
   DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
-  DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
-  DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
-  DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
+  DefineOptionalParameter(TaggedAtomPair, "taggedAtomPair");
+  DefineOptionalParameter(PrintTaggedPairDistance, "printTaggedPairDistance");
   DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
-  DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
+  DefineOptionalParameter(HydroPropFile, "HydroPropFile");
+  DefineOptionalParameter(Viscosity, "viscosity");
+  DefineOptionalParameter(BeadSize, "beadSize");
+  DefineOptionalParameter(FrozenBufferRadius, "frozenBufferRadius");
+  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");
+  DefineOptionalParameter(MTM_Sigma, "MTM_Sigma");
+  DefineOptionalParameter(MTM_R, "MTM_R");
+  DefineOptionalParameter(Alpha, "alpha");
+
+  
   DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
+  DefineOptionalParameterWithDefaultValue(UseAtomicVirial, "useAtomicVirial", true);
   DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
   DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
   DefineOptionalParameterWithDefaultValue(OrthoBoxTolerance, "orthoBoxTolerance", 1E-6);  
-  DefineOptionalParameterWithDefaultValue(UseSolidThermInt, "useSolidThermInt", false);
-  DefineOptionalParameterWithDefaultValue(UseLiquidThermInt, "useLiquidThermInt", false);
-  DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
-  DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
-  DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
-  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
-  DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
-  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
+  DefineOptionalParameterWithDefaultValue(CutoffMethod, "cutoffMethod", "SHIFTED_FORCE");
+  DefineOptionalParameterWithDefaultValue(ElectrostaticScreeningMethod, "electrostaticScreeningMethod", "DAMPED");
+  DefineOptionalParameterWithDefaultValue(Dielectric, "dielectric", 80.0);
+  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);
+  DefineOptionalParameterWithDefaultValue(AccumulateBoxDipole, "accumulateBoxDipole", false);
 
-  
-}
-
-Globals::~Globals(){
-  int i;
-  if( components != NULL ){
-    for( i=0; i< getNComponents(); i++ ) delete components[i];
-    delete[] components;
-  }
-  
-  if( zConstraints != NULL ){
-    for( i=0; i< getNZconstraints(); i++ ) delete zConstraints[i];
-    delete[] zConstraints;
-  }
-  
-}
-
-int Globals::globalAssign( event* the_event ){
-  char errorMessage[65535]; 
-  int key;
-  interface_assign_type the_type =  the_event->evt.asmt.asmt_type;
-  char* lhs = the_event->evt.asmt.lhs;
-  std::string keyword(lhs);
-
-  bool result = false;
-
-  /**@todo fix memory leak */  
-  ParamMap::iterator i =parameters_.find(keyword);
-  if (i != parameters_.end()) {
-    if( the_type == STRING ){
-       result = i->second->setData(std::string(the_event->evt.asmt.rhs.sval));
-       if (!result ) {
-  	    sprintf(errorMessage, "Error in parsing %s: expect %s, but get a string \"%s\".\n", keyword.c_str(), i->second->getParamType().c_str(), the_event->evt.asmt.rhs.sval);
-            the_event->err_msg = strdup(errorMessage);
-       }
-    } else if( the_type == DOUBLE ){
-      result = i->second->setData(the_event->evt.asmt.rhs.dval);
-       if (!result )
-         sprintf(errorMessage, "Error in parsing %s: expect %s, but get a double %f.\n", keyword.c_str(), i->second->getParamType().c_str(), the_event->evt.asmt.rhs.dval );
-       the_event->err_msg = strdup(errorMessage);
-    }      
-    else if (the_type == INT ){
-      result = i->second->setData(the_event->evt.asmt.rhs.ival);
-       if (!result )
-         sprintf(errorMessage,  "Error in parsing %s: expect %s, but get an int %d.\n", keyword.c_str(), i->second->getParamType().c_str(), the_event->evt.asmt.rhs.ival );
-       the_event->err_msg = strdup(errorMessage);
-      
-    } else {
-        sprintf(errorMessage,  "Internal error of parser\n");
-	the_event->err_msg = strdup(errorMessage);
-    }
-  } else {
-    sprintf(errorMessage,  "%s is an unrecognized keyword\n", keyword.c_str() );
-    the_event->err_msg = strdup(errorMessage);
-  }
-
-  if (keyword == "nComponents" && getNComponents() > 0) {
-    components = new Component*[getNComponents()];
-  }else if (keyword == "nZconstraints" && getNZconstraints() > 0) {
-    zConstraints = new ZconStamp*[getNZconstraints()];
-  }
-  
-  return result;
-}
-
-int Globals::newComponent( event* the_event ){
-  
-  current_component = new Component;
-  int index = the_event->evt.blk_index;
-  char err[200];
-  
-  if( haveNComponents() && index < getNComponents() ) 
-    components[index] = current_component;
-  else{
-    if( haveNComponents()  ){
-      sprintf( err, "meta-data parsing error: %d out of nComponents range", 
-	       index );
-      the_event->err_msg = strdup( err );
-      return 0;
-    }
-    else{
-      the_event->err_msg = strdup("meta-data parsing error: nComponents not given before"
-				  " first component declaration." );
-      return 0;
-    }
-  }  
- 
-  return 1;
-}
-
-
-
-int Globals::componentAssign( event* the_event ){
-
-  switch( the_event->evt.asmt.asmt_type ){
-    
-  case STRING:
-    return current_component->assignString( the_event->evt.asmt.lhs,
-					    the_event->evt.asmt.rhs.sval,
-					    &(the_event->err_msg));
-    break;
-    
-  case DOUBLE:
-    return current_component->assignDouble( the_event->evt.asmt.lhs,
-					    the_event->evt.asmt.rhs.dval,
-					    &(the_event->err_msg));
-    break;
-    
-  case INT:
-    return current_component->assignInt( the_event->evt.asmt.lhs,
-					 the_event->evt.asmt.rhs.ival,
-					 &(the_event->err_msg));
-    break;
-    
-  default:
-    the_event->err_msg = strdup( "Globals error. Invalid component"
-				 " assignment type" );
-    return 0;
-    break;
-  }
-  return 0;
-}
-
-int Globals::componentEnd( event* the_event ){
-
-  the_event->err_msg = current_component->checkMe();
-  if( the_event->err_msg != NULL ) return 0;
-
-  return 1;
-}
-
-int Globals::newZconstraint( event* the_event ){
-  
+  DefineOptionalParameterWithDefaultValue(UseRNEMD, "useRNEMD", false);
+  DefineOptionalParameterWithDefaultValue(RNEMD_exchangeTime, "RNEMD_exchangeTime", 100.0);
+  DefineOptionalParameterWithDefaultValue(RNEMD_nBins, "RNEMD_nBins", 16);
+  DefineOptionalParameterWithDefaultValue(RNEMD_logWidth, "RNEMD_logWidth", 16);
+  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);
 
-  int index = the_event->evt.blk_index;
-  char err[200];
-  current_zConstraint = new ZconStamp( index );
-  
-  if( haveNZconstraints() && index < getNZconstraints() ) 
-    zConstraints[index] = current_zConstraint;
-  else{
-    if( haveNZconstraints() ){
-      sprintf( err, "meta-data parsing error: %d out of nZconstraints range", 
-	       index );
-      the_event->err_msg = strdup( err );
-      return 0;
-    }
-    else{
-      the_event->err_msg = strdup("meta-data parsing error: nZconstraints"
-				  " not given before"
-				  " first zConstraint declaration." );
-      return 0;
-    }
-  }  
-
-  return 1;
-}
-
-
-
-int Globals::zConstraintAssign( event* the_event ){
-
-  switch( the_event->evt.asmt.asmt_type ){
+  deprecatedKeywords_.insert("nComponents");
+  deprecatedKeywords_.insert("nZconstraints");
+  deprecatedKeywords_.insert("initialConfig");
+  deprecatedKeywords_.insert("thermIntDistSpringConst");
+  deprecatedKeywords_.insert("thermIntThetaSpringConst");
+  deprecatedKeywords_.insert("thermIntOmegaSpringConst");
+  deprecatedKeywords_.insert("useSolidThermInt");  
+  deprecatedKeywords_.insert("useLiquidThermInt");
     
-  case STRING:
-    return current_zConstraint->assignString( the_event->evt.asmt.lhs,
-					      the_event->evt.asmt.rhs.sval,
-					      &(the_event->err_msg));
-    break;
-    
-  case DOUBLE:
-    return current_zConstraint->assignDouble( the_event->evt.asmt.lhs,
-					      the_event->evt.asmt.rhs.dval,
-					      &(the_event->err_msg));
-    break;
-    
-  case INT:
-    return current_zConstraint->assignInt( the_event->evt.asmt.lhs,
-					   the_event->evt.asmt.rhs.ival,
-					   &(the_event->err_msg));
-    break;
-    
-  default:
-    the_event->err_msg = strdup( "Globals error. Invalid zConstraint"
-				 " assignment type" );
-    return 0;
-    break;
-  }
-  return 0;
 }
 
-int Globals::zConstraintEnd( event* the_event ){
-
-  the_event->err_msg = current_zConstraint->checkMe();
-  if( the_event->err_msg != NULL ) return 0;
-
-  return 1;
+Globals::~Globals() {
+    MemoryUtils::deletePointers(components_);
+    MemoryUtils::deletePointers(zconstraints_);
+    MemoryUtils::deletePointers(restraints_);
 }
 
-char* Globals::checkMe( void ){
+void Globals::validate() {
+  DataHolder::validate();
 
-
-  std::string err("The following required keywords are missing:\n");
-  short int have_err = 0;
-
-  ParamMap::iterator i;
-  for (i = parameters_.begin(); i != parameters_.end(); ++i) {
-    if (!i->second->isOptional() && i->second->empty()) {
-        err +=  i->second->getKeyword() + "\n";
-    }
-  }
-
   CheckParameter(ForceField, isNotEmpty());
-  CheckParameter(NComponents,isPositive()); 
   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("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(InitialConfig, isNotEmpty());
   CheckParameter(FinalConfig, isNotEmpty());
-  CheckParameter(NMol, isPositive());
-  CheckParameter(Density, isPositive());
-  CheckParameter(Box, isPositive());
-  CheckParameter(BoxX, isPositive());
-  CheckParameter(BoxY, isPositive());
-  CheckParameter(BoxZ, isPositive());
   CheckParameter(SampleTime, isNonNegative());
   CheckParameter(ResetTime, isNonNegative());
   CheckParameter(StatusTime, isNonNegative());
@@ -364,18 +181,14 @@ char* Globals::checkMe( void ){
   CheckParameter(SwitchingRadius, isNonNegative());
   CheckParameter(Dielectric, isPositive());
   CheckParameter(ThermalTime,  isNonNegative());
-  CheckParameter(TargetPressure,  isPositive());
   CheckParameter(TauThermostat, isPositive());
   CheckParameter(TauBarostat, isPositive());
   CheckParameter(ZconsTime, isPositive());
-  CheckParameter(NZconstraints, isPositive());  
   CheckParameter(ZconsTol, isPositive());
-  //CheckParameter(ZconsForcePolicy,);
   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(MinimizerWriteFreq, isPositive());
   CheckParameter(MinimizerStepSize, isPositive());
   CheckParameter(MinimizerFTol, isPositive());
   CheckParameter(MinimizerGTol, isPositive());
@@ -383,50 +196,74 @@ char* Globals::checkMe( void ){
   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(StatFileFormat,);     
-  //CheckParameter(MixingRule,);
+  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(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());
+  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(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()); 
   
-  //@todo memory leak
-  if( have_err )
-    return strdup( err.c_str() );
-  
-  return NULL;
+  for(std::vector<Component*>::iterator i = components_.begin(); i != components_.end(); ++i) {
+    if (!(*i)->findMoleculeStamp(moleculeStamps_)) {
+        std::ostringstream oss;
+        oss << "Globals Error: can not find molecule stamp for component " << (*i)->getType() << std::endl;
+        throw OpenMDException(oss.str());           
+    }
+  }
+}
 
+bool Globals::addComponent(Component* comp) {
+    components_.push_back(comp);
+    return true;
+}
 
+bool Globals::addZConsStamp(ZConsStamp* zcons) {
+    zconstraints_.push_back(zcons);
+    return true;
 }
 
-int Globals::globalEnd( event* the_event ){
-  
-  the_event->err_msg = checkMe();
-  if( the_event->err_msg != NULL ) return 0;
+bool Globals::addRestraintStamp(RestraintStamp* rest) {
+    restraints_.push_back(rest);
+    return true;
+}
 
-  return 1;
+bool Globals::addMoleculeStamp(MoleculeStamp* molStamp) {
+    std::string molStampName = molStamp->getName();
+    std::map<std::string, MoleculeStamp*>::iterator i;
+    bool ret = false;
+    i = moleculeStamps_.find(molStampName);
+    if (i == moleculeStamps_.end()) {
+        moleculeStamps_.insert(std::map<std::string, MoleculeStamp*>::value_type(molStampName, molStamp));
+        ret = true;
+    } else {
+        std::ostringstream oss;
+        oss << "Globals Error: Molecule Stamp " << molStamp->getName() << "appears multiple times\n";
+        throw OpenMDException(oss.str());  
+    }
+    return ret;
 }
+ 
+
+}