--- trunk/src/io/Globals.cpp	2005/11/02 20:36:25	710
+++ trunk/src/io/Globals.cpp	2006/03/17 23:20:35	906
@@ -45,32 +45,13 @@
 #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"
-
-#define DefineParameter(NAME,KEYWORD)                              \
-  NAME.setKeyword(KEYWORD);                  \
-  parameters_.insert(std::make_pair(std::string(KEYWORD),  &NAME));
-
-#define DefineOptionalParameter(NAME,KEYWORD)                              \
-  NAME.setKeyword(KEYWORD); NAME.setOptional(true);                    \
-  parameters_.insert(std::make_pair(std::string(KEYWORD),  &NAME));
-
-#define DefineOptionalParameterWithDefaultValue(NAME,KEYWORD, DEFAULTVALUE)                              \
-  NAME.setKeyword(KEYWORD); NAME.setOptional(true); NAME.setDefaultValue(DEFAULTVALUE);                      \
-  parameters_.insert(std::make_pair(std::string(KEYWORD),  &NAME));
-
-#define CheckParameter(NAME, CONSTRAINT)                              \
-  if (!NAME.empty()) { if (!(CONSTRAINT)(NAME.getData())) { sprintf(painCave.errMsg,"Error in checking %s : should be %s\n",NAME.getKeyword().c_str(),(CONSTRAINT).getConstraintDescription().c_str()); painCave.isFatal = 1; painCave.severity = OOPSE_ERROR; simError();} }                 
-
-Globals::Globals(){
- 
+namespace oopse {
+Globals::Globals() {
   DefineParameter(ForceField, "forceField")
-  DefineParameter(NComponents, "nComponents")
  
   DefineOptionalParameter(TargetTemp, "targetTemp");
   DefineOptionalParameter(Ensemble, "ensemble");
@@ -78,12 +59,6 @@ Globals::Globals(){
   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");
@@ -96,7 +71,6 @@ Globals::Globals(){
   DefineOptionalParameter(TauThermostat, "tauThermostat");
   DefineOptionalParameter(TauBarostat, "tauBarostat");
   DefineOptionalParameter(ZconsTime, "zconsTime");
-  DefineOptionalParameter(NZconstraints, "nZconstraints");  
   DefineOptionalParameter(ZconsTol, "zconsTol");
   DefineOptionalParameter(ZconsForcePolicy, "zconsForcePolicy");
   DefineOptionalParameter(Seed, "seed");
@@ -121,10 +95,13 @@ Globals::Globals(){
   DefineOptionalParameter(SurfaceTension, "surfaceTension");
   DefineOptionalParameter(PrintPressureTensor, "printPressureTensor");
   DefineOptionalParameter(ElectrostaticSummationMethod, "electrostaticSummationMethod");
-  DefineOptionalParameter(ScreeningMethod, "screeningMethod");
+  DefineOptionalParameter(ElectrostaticScreeningMethod, "electrostaticScreeningMethod");
   DefineOptionalParameter(CutoffPolicy, "cutoffPolicy");
+  DefineOptionalParameter(SwitchingFunctionType, "switchingFunctionType");
+  DefineOptionalParameter(HydroPropFile, "HydroPropFile");
+  DefineOptionalParameter(Viscosity, "viscosity");
+  DefineOptionalParameter(BeadSize, "beadSize");
   
-  DefineOptionalParameterWithDefaultValue(MixingRule, "mixingRule", "standard");
   DefineOptionalParameterWithDefaultValue(UsePeriodicBoundaryConditions, "usePeriodicBoundaryConditions", true);
   DefineOptionalParameterWithDefaultValue(UseInitalTime, "useInitialTime", false);
   DefineOptionalParameterWithDefaultValue(UseIntialExtendedSystemState, "useInitialExtendedSystemState", false);
@@ -134,225 +111,33 @@ Globals::Globals(){
   DefineOptionalParameterWithDefaultValue(ThermIntDistSpringConst, "thermIntDistSpringConst", 6.0);
   DefineOptionalParameterWithDefaultValue(ThermIntThetaSpringConst, "thermIntThetaSpringConst", 7.5);
   DefineOptionalParameterWithDefaultValue(ThermIntOmegaSpringConst, "thermIntOmegaSpringConst", 13.5);
-  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 1.5);
+  DefineOptionalParameterWithDefaultValue(DampingAlpha, "dampingAlpha", 0.2);
   DefineOptionalParameterWithDefaultValue(CompressDumpFile, "compressDumpFile", 0);
+  DefineOptionalParameterWithDefaultValue(OutputForceVector, "outputForceVector", 0);
   DefineOptionalParameterWithDefaultValue(SkinThickness, "skinThickness", 1.0);
   DefineOptionalParameterWithDefaultValue(StatFileFormat, "statFileFormat", "TIME|TOTAL_ENERGY|POTENTIAL_ENERGY|KINETIC_ENERGY|TEMPERATURE|PRESSURE|VOLUME|CONSERVED_QUANTITY");    
 
-  
-}
 
-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 ){
-  
-
-  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");
     
-  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_);
 }
 
-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("NPAT")  || isEqualIgnoreCase("LANGEVINDYNAMICS") );
   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());
@@ -364,11 +149,9 @@ char* Globals::checkMe( void ){
   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(MinimizerStepSize, isPositive());
@@ -386,31 +169,53 @@ char* Globals::checkMe( void ){
   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(ScreeningMethod, isEqualIgnoreCase(std::string("UNDAMPED")) || isEqualIgnoreCase(std::string("DAMPED"))); 
-  CheckParameter(CutoffPolicy, isEqualIgnoreCase(std::string("MIX")) || isEqualIgnoreCase(std::string("MAX")) || isEqualIgnoreCase(std::string("TRADITIONAL")));
+  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,isPositive());
+  CheckParameter(DampingAlpha,isNonNegative());
   CheckParameter(SkinThickness, isPositive());
-  
-  //@todo memory leak
-  if( have_err )
-    return strdup( err.c_str() );
-  
-  return NULL;
+  CheckParameter(Viscosity,isNonNegative());
+  CheckParameter(BeadSize,isPositive());
+  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 OOPSEException(oss.str());           
+    }
+  }
+}
+    
+bool Globals::addComponent(Component* comp) {
+    components_.push_back(comp);
+    return true;
+}
 
+bool Globals::addZConsStamp(ZConsStamp* zcons) {
+    zconstraints_.push_back(zcons);
+    return true;
+}
 
+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 OOPSEException(oss.str());  
+    }
+    return ret;
 }
+ 
 
-int Globals::globalEnd( event* the_event ){
-  
-  the_event->err_msg = checkMe();
-  if( the_event->err_msg != NULL ) return 0;
-
-  return 1;
 }